Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397277.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_2.0, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 2651878
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.33
Warning! 95949 characters in sequence are not A, C, G, or T
File 3 of 6
Found at i:1044961 original size:60 final size:56
Alignment explanation
Indices: 1044859--1045057 Score: 175
Period size: 60 Copynumber: 3.4 Consensus size: 56
1044849 AAATAAAATA
* * * * * **
1044859 TTTTGTCTAAATTGAGCCAAACATGTTTTCTTGTCTAGATTAAGACAAAACATTTTT
1 TTTTGTCTAAATTAAG-AAAACATGTTTTCATGTCTAAATTAAGAAAAAACAAGTTT
* * * *
1044916 TTCTTATTTTAAATTAAGACATACATGTTTTTCCTGTCTAAATTAAGAAAAAACAAGTTT
1 TT-TT-GTCTAAATTAAGA-AAACATG-TTTTCATGTCTAAATTAAGAAAAAACAAGTTT
* * *
1044976 TTTTGTCTAAATTAAGAAAAAATGTTTTCATGTCTAAATTAAG-ATAAACATGTTT
1 TTTTGTCTAAATTAAGAAAACATGTTTTCATGTCTAAATTAAGAAAAAACAAGTTT
** *
1045031 TCATGTCTAAATAAAGACAAAACATGT
1 TTTTGTCTAAATTAAG--AAAACATGT
1045058 CTAAATTAAG
Statistics
Matches: 115, Mismatches: 21, Indels: 12
0.78 0.14 0.08
Matches are distributed among these distances:
55 23 0.20
56 18 0.16
57 15 0.13
58 13 0.11
59 17 0.15
60 29 0.25
ACGTcount: A:0.38, C:0.12, G:0.11, T:0.40
Consensus pattern (56 bp):
TTTTGTCTAAATTAAGAAAACATGTTTTCATGTCTAAATTAAGAAAAAACAAGTTT
Found at i:1045057 original size:21 final size:21
Alignment explanation
Indices: 1045032--1045072 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
1045022 AACATGTTTT
1045032 CATGTCTAAATAAAGACAAAA
1 CATGTCTAAATAAAGACAAAA
*
1045053 CATGTCTAAATTAAGACAAA
1 CATGTCTAAATAAAGACAAA
1045073 CTTGTAAAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.54, C:0.15, G:0.10, T:0.22
Consensus pattern (21 bp):
CATGTCTAAATAAAGACAAAA
Found at i:1051741 original size:2 final size:2
Alignment explanation
Indices: 1051734--1051759 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1051724 ATCTTGGTTA
1051734 TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG
1051760 GCATTTTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:1057542 original size:68 final size:68
Alignment explanation
Indices: 1057468--1057604 Score: 229
Period size: 68 Copynumber: 2.0 Consensus size: 68
1057458 TAGTTTCAAG
*
1057468 TACCTCTATACTTCAATCTATGAGATAGAGTGCTCACTTCTAAAGTAAGGAACATAGAATGTACC
1 TACCTCTATACTTCAATCTATGAAATAGAGTGCTCACTTCTAAAGTAAGGAACATAGAATGTACC
1057533 AGT
66 AGT
* * * *
1057536 TACCTCTATACTTTAATCTATGAAATAGATTGCTCGCTTCTAAAGTAAGGAACATAGAATGTACT
1 TACCTCTATACTTCAATCTATGAAATAGAGTGCTCACTTCTAAAGTAAGGAACATAGAATGTACC
1057601 AGT
66 AGT
1057604 T
1 T
1057605 TCTAAGCATC
Statistics
Matches: 64, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
68 64 1.00
ACGTcount: A:0.35, C:0.18, G:0.15, T:0.32
Consensus pattern (68 bp):
TACCTCTATACTTCAATCTATGAAATAGAGTGCTCACTTCTAAAGTAAGGAACATAGAATGTACC
AGT
Found at i:1075632 original size:20 final size:21
Alignment explanation
Indices: 1075604--1075649 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
1075594 TATTTCTATT
* *
1075604 TAAAGTTATAAT-ATTAAATA
1 TAAAATTATAATCATAAAATA
1075624 TAAAATTATAATGCATAAAATA
1 TAAAATTATAAT-CATAAAATA
1075646 TAAA
1 TAAA
1075650 TAGTTAAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 11 0.50
22 11 0.50
ACGTcount: A:0.59, C:0.02, G:0.04, T:0.35
Consensus pattern (21 bp):
TAAAATTATAATCATAAAATA
Found at i:1078019 original size:19 final size:20
Alignment explanation
Indices: 1077975--1078021 Score: 53
Period size: 19 Copynumber: 2.4 Consensus size: 20
1077965 AATTTGAGCA
*
1077975 AGAAACTAAGTGTTTGAAATG
1 AGAAACT-AGTGTTAGAAATG
*
1077996 -TAAACTAGTGTTAGAAA-G
1 AGAAACTAGTGTTAGAAATG
1078014 AGAAACTA
1 AGAAACTA
1078022 ATGAACAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 4
0.76 0.10 0.14
Matches are distributed among these distances:
18 1 0.05
19 16 0.73
20 5 0.23
ACGTcount: A:0.47, C:0.06, G:0.21, T:0.26
Consensus pattern (20 bp):
AGAAACTAGTGTTAGAAATG
Found at i:1081015 original size:35 final size:35
Alignment explanation
Indices: 1080976--1081196 Score: 142
Period size: 35 Copynumber: 6.3 Consensus size: 35
1080966 TTAATTGTTT
* * *
1080976 AATTTCATCAATTAGGTCAAACAACTTAACTAAAA
1 AATTTAATCAATTAGGCCAAACAACTTAATTAAAA
* * * *
1081011 AATTTAATTAATTAAGCCCAACAATTTAATTAAAA
1 AATTTAATCAATTAGGCCAAACAACTTAATTAAAA
* **
1081046 AATTTTAATCAATTAGGCCCAATGACTTAATTAAACA
1 AA-TTTAATCAATTAGGCCAAACAACTTAATTAAA-A
* * * * ***
1081083 AATTTCATTAATTAGGTCATACAACTTAATTATTT
1 AATTTAATCAATTAGGCCAAACAACTTAATTAAAA
* * * ** * * *
1081118 AATTTAATTAATTAAGCCCAATGATTTCATTAAAT
1 AATTTAATCAATTAGGCCAAACAACTTAATTAAAA
* *
1081153 AATTTAATTAATTAGG-C--ACATCTTAATTAAACA
1 AATTTAATCAATTAGGCCAAACAACTTAATTAAA-A
*
1081186 ATTTTAATCAA
1 AATTTAATCAA
1081197 GCGCTTGAGA
Statistics
Matches: 141, Mismatches: 42, Indels: 8
0.74 0.22 0.04
Matches are distributed among these distances:
32 9 0.06
33 9 0.06
34 1 0.01
35 69 0.49
36 50 0.35
37 3 0.02
ACGTcount: A:0.45, C:0.13, G:0.05, T:0.37
Consensus pattern (35 bp):
AATTTAATCAATTAGGCCAAACAACTTAATTAAAA
Found at i:1081054 original size:36 final size:35
Alignment explanation
Indices: 1080995--1081166 Score: 157
Period size: 35 Copynumber: 4.9 Consensus size: 35
1080985 AATTAGGTCA
*
1080995 AACAACTTAACTAAAAAATTTAATTAATTAAGCCC
1 AACAACTTAATTAAAAAATTTAATTAATTAAGCCC
* * *
1081030 AACAATTTAATTAAAAAATTTTAATCAATTAGGCCC
1 AACAACTTAATTAAAAAA-TTTAATTAATTAAGCCC
** * **
1081066 AATGACTTAATTAAACAAATTTCATTAATT-AGGTC
1 AACAACTTAATTAAA-AAATTTAATTAATTAAGCCC
***
1081101 ATACAACTTAATTATTTAATTTAATTAATTAAGCCC
1 A-ACAACTTAATTAAAAAATTTAATTAATTAAGCCC
** * * *
1081137 AATGATTTCATTAAATAATTTAATTAATTA
1 AACAACTTAATTAAAAAATTTAATTAATTA
1081167 GGCACATCTT
Statistics
Matches: 107, Mismatches: 26, Indels: 8
0.76 0.18 0.06
Matches are distributed among these distances:
35 54 0.50
36 50 0.47
37 3 0.03
ACGTcount: A:0.46, C:0.12, G:0.05, T:0.37
Consensus pattern (35 bp):
AACAACTTAATTAAAAAATTTAATTAATTAAGCCC
Found at i:1081096 original size:107 final size:103
Alignment explanation
Indices: 1080976--1081196 Score: 280
Period size: 107 Copynumber: 2.1 Consensus size: 103
1080966 TTAATTGTTT
1080976 AATTTCATCAATTAGGTCAAACAACTTAACTAAAAAATTTAATTAATTAAGCCCAACAATTTAAT
1 AATTTCATCAATTAGGTCAAACAACTTAACTAAAAAATTTAATTAATTAAGCCCAACAATTTAAT
*
1081041 TAAAAAATTTTAATCAATTAGGCCCAATGACTTAATTAAACA
66 TAAAAAA-TTTAATCAATTAGGCAC-AT--CTTAATTAAACA
* * * *** ** *
1081083 AATTTCATTAATTAGGTCATACAACTTAATTATTTAATTTAATTAATTAAGCCCAATGATTTCAT
1 AATTTCATCAATTAGGTCAAACAACTTAACTAAAAAATTTAATTAATTAAGCCCAACAATTTAAT
* *
1081148 TAAATAATTTAATTAATTAGGCACATCTTAATTAAACA
66 TAAAAAATTTAATCAATTAGGCACATCTTAATTAAACA
* *
1081186 ATTTTAATCAA
1 AATTTCATCAA
1081197 GCGCTTGAGA
Statistics
Matches: 99, Mismatches: 15, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
103 20 0.20
105 2 0.02
106 15 0.15
107 62 0.63
ACGTcount: A:0.45, C:0.13, G:0.05, T:0.37
Consensus pattern (103 bp):
AATTTCATCAATTAGGTCAAACAACTTAACTAAAAAATTTAATTAATTAAGCCCAACAATTTAAT
TAAAAAATTTAATCAATTAGGCACATCTTAATTAAACA
Found at i:1081131 original size:71 final size:69
Alignment explanation
Indices: 1080963--1081181 Score: 208
Period size: 71 Copynumber: 3.1 Consensus size: 69
1080953 AAGCCCAATT
* * * * ** * *
1080963 AACTTAATTGTTTAATTTCATCAATTAGGTCAAACAACTTAACTAAAAAATTTAATTAATTAAGC
1 AACTTAATTATTTAATTTAATCAATTAGGCCCAATGACTTAATTAAAAAATTTAATTAATT-AGG
1081028 CCAAC
65 CCAAC
* *** *
1081033 AATTTAATTAAAAAATTTTAATCAATTAGGCCCAATGACTTAATTAAACAAATTTCATTAATTAG
1 AACTTAATTATTTAA-TTTAATCAATTAGGCCCAATGACTTAATTAAA-AAATTTAATTAATTAG
*
1081098 GTCATAC
64 GCCA-AC
* * * * *
1081105 AACTTAATTATTTAATTTAATTAATTAAGCCCAATGATTTCATTAAATAATTTAATTAATTAGG-
1 AACTTAATTATTTAATTTAATCAATTAGGCCCAATGACTTAATTAAAAAATTTAATTAATTAGGC
1081169 C-AC
66 CAAC
*
1081172 ATCTTAATTA
1 AACTTAATTA
1081182 AACAATTTTA
Statistics
Matches: 121, Mismatches: 25, Indels: 9
0.78 0.16 0.06
Matches are distributed among these distances:
67 11 0.09
69 1 0.01
70 25 0.21
71 58 0.48
72 26 0.21
ACGTcount: A:0.43, C:0.13, G:0.06, T:0.38
Consensus pattern (69 bp):
AACTTAATTATTTAATTTAATCAATTAGGCCCAATGACTTAATTAAAAAATTTAATTAATTAGGC
CAAC
Found at i:1094609 original size:16 final size:16
Alignment explanation
Indices: 1094588--1094629 Score: 75
Period size: 16 Copynumber: 2.6 Consensus size: 16
1094578 TCTTTAAGCA
1094588 TTGTCAATACCCTATC
1 TTGTCAATACCCTATC
1094604 TTGTCAATACCCTATC
1 TTGTCAATACCCTATC
*
1094620 TTGACAATAC
1 TTGTCAATAC
1094630 AATGATCAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.29, C:0.29, G:0.07, T:0.36
Consensus pattern (16 bp):
TTGTCAATACCCTATC
Found at i:1096787 original size:3 final size:3
Alignment explanation
Indices: 1096779--1096813 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
1096769 CGTATCTGTC
* *
1096779 TCT TCT TCT TCT GCT TCT TCT GCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
1096814 ATCATCATCA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.00, C:0.34, G:0.06, T:0.60
Consensus pattern (3 bp):
TCT
Found at i:1102029 original size:261 final size:261
Alignment explanation
Indices: 1101565--1102341 Score: 1467
Period size: 261 Copynumber: 3.0 Consensus size: 261
1101555 AGGTGCTTGT
* *
1101565 TAAAGAACAAGTTCACTAAACATGACCTGATATGAGAACTCCATTTGGTATTTCACTGAAGTGTC
1 TAAAGAACAAGTTCACTAAACATGACCTAATATGAGAACTCCATTTGATATTTCACTGAAGTGTC
*
1101630 TATGAAAAATGTTCTCATGTGATAGTCGTGTAACTAGTCCTTAGACTTGAGACACCAGGTCATCT
66 TATAAAAAATGTTCTCATGTGATAGTCGTGTAACTAGTCCTTAGACTTGAGACACCAGGTCATCT
*
1101695 TGTATTGGAAATGACATACTTTGATTTCACCCCAATAGGTTTGGAAGCAACCAAATGCCTAAATA
131 TGTATTGGAAATGACATACTTTGATTTCACCCCTATAGGTTTGGAAGCAACCAAATGCCTAAATA
1101760 AGGTGTTTTTGGATATGCCATGAAGCATGCGAAGGTGAATGAGTGGTCAAAAGAGGATTCATCAC
196 AGGTGTTTTTGGATATGCCATGAAGCATGCGAAGGTGAATGAGTGGTCAAAAGAGGATTCATCAC
1101825 C
261 C
1101826 TAAAGAACAAGTTCACTAAACATGACCTAATATGAGAACTCCATTTGATATTTCACTGAAGTGTC
1 TAAAGAACAAGTTCACTAAACATGACCTAATATGAGAACTCCATTTGATATTTCACTGAAGTGTC
1101891 TATAAAAAATGTTCTCATGTGATAGTCGTGTAACTAGTCCTTAGACTTGAGACACCAGGTCATCT
66 TATAAAAAATGTTCTCATGTGATAGTCGTGTAACTAGTCCTTAGACTTGAGACACCAGGTCATCT
1101956 TGTATTGGAAATGACATACTTTGATTTCACCCCTATAGGTTTGGAAGCAACCAAATGCCTAAATA
131 TGTATTGGAAATGACATACTTTGATTTCACCCCTATAGGTTTGGAAGCAACCAAATGCCTAAATA
1102021 AGGTGTTTTTGGATATGCCATGAAGCATGCGAAGGTG-ATGAGTGGTC-AAAGAGGATTCATCAC
196 AGGTGTTTTTGGATATGCCATGAAGCATGCGAAGGTGAATGAGTGGTCAAAAGAGGATTCATCAC
1102084 C
261 C
1102085 TAAAGAACAAGTTCACTAAACATGACCTAATATGAGAACTCCATTTGATATTTCACTG-AGTGTC
1 TAAAGAACAAGTTCACTAAACATGACCTAATATGAGAACTCCATTTGATATTTCACTGAAGTGTC
1102149 --TAAAAAATGTTCTCATGTGATAGTCGTGTAACTAGTCCTTAGACTTGAGACACCAGGTCATCT
66 TATAAAAAATGTTCTCATGTGATAGTCGTGTAACTAGTCCTTAGACTTGAGACACCAGGTCATCT
1102212 TGTATTGGAAATGACATACTTTGATTTCA-CCCTATAGGTTTGGAAGCAACCAAATGCCTAAATA
131 TGTATTGGAAATGACATACTTTGATTTCACCCCTATAGGTTTGGAAGCAACCAAATGCCTAAATA
*
1102276 AGGTGTTTTTGGTTATGCCATGAAGCATGCGAAGGTGAATGAGTGGTCAAAAGAGGATTCATCAC
196 AGGTGTTTTTGGATATGCCATGAAGCATGCGAAGGTGAATGAGTGGTCAAAAGAGGATTCATCAC
1102341 C
261 C
1102342 CCAAGTGATA
Statistics
Matches: 509, Mismatches: 5, Indels: 8
0.98 0.01 0.02
Matches are distributed among these distances:
255 71 0.14
256 102 0.20
257 17 0.03
258 6 0.01
259 75 0.15
260 10 0.02
261 228 0.45
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.30
Consensus pattern (261 bp):
TAAAGAACAAGTTCACTAAACATGACCTAATATGAGAACTCCATTTGATATTTCACTGAAGTGTC
TATAAAAAATGTTCTCATGTGATAGTCGTGTAACTAGTCCTTAGACTTGAGACACCAGGTCATCT
TGTATTGGAAATGACATACTTTGATTTCACCCCTATAGGTTTGGAAGCAACCAAATGCCTAAATA
AGGTGTTTTTGGATATGCCATGAAGCATGCGAAGGTGAATGAGTGGTCAAAAGAGGATTCATCAC
C
Found at i:1104157 original size:75 final size:76
Alignment explanation
Indices: 1104010--1104170 Score: 229
Period size: 75 Copynumber: 2.1 Consensus size: 76
1104000 AAAACCATCT
* *
1104010 ATTTTAATTTTGAGTGATCTATAAAAATAGAAAATTGTTTCCTACTTTAAAAGCAATTTATAAAA
1 ATTTTAATTTTGAGTGATCTATAAAAATAGAAAATTGTTTCCCACTTTAAAAGAAATTTATAAAA
1104075 TTAAGGATAGA
66 TTAAGGATAGA
* * *
1104086 ATTTTAATTTTGGGTGAT-TCATATAAATAGGAAATT-TTTCCCACTTTAAAAGAAATTCT-TAA
1 ATTTTAATTTTGAGTGATCT-ATAAAAATAGAAAATTGTTTCCCACTTTAAAAGAAATT-TATAA
*
1104148 AATTAAGGATAGT
64 AATTAAGGATAGA
1104161 ATTTTAATTT
1 ATTTTAATTT
1104171 GAAAAATTAA
Statistics
Matches: 77, Mismatches: 6, Indels: 5
0.88 0.07 0.06
Matches are distributed among these distances:
75 45 0.58
76 32 0.42
ACGTcount: A:0.40, C:0.07, G:0.12, T:0.41
Consensus pattern (76 bp):
ATTTTAATTTTGAGTGATCTATAAAAATAGAAAATTGTTTCCCACTTTAAAAGAAATTTATAAAA
TTAAGGATAGA
Found at i:1104189 original size:75 final size:76
Alignment explanation
Indices: 1104034--1104190 Score: 185
Period size: 75 Copynumber: 2.1 Consensus size: 76
1104024 TGATCTATAA
* * *
1104034 AAATAGAAAATTGTTTCCTACTTTAAAAGCAATTTATAAAATTAAGGATAGAATTTTAATTTTGG
1 AAATAGAAAATTGTTTCCCACTTTAAAAGAAATTTATAAAATTAAGGATAGAATTTTAATTTTGA
*** * *
1104099 GTGATTCATAT
66 AAAATTAATAG
* *
1104110 AAATAGGAAATT-TTTCCCACTTTAAAAGAAATTCT-TAAAATTAAGGATAGTATTTTAA-TTTG
1 AAATAGAAAATTGTTTCCCACTTTAAAAGAAATT-TATAAAATTAAGGATAGAATTTTAATTTTG
1104172 AAAAATTAATAGG
65 AAAAATTAATA-G
1104185 AAATAG
1 AAATAG
1104191 TTTCCTACTT
Statistics
Matches: 69, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
74 10 0.14
75 47 0.68
76 12 0.17
ACGTcount: A:0.44, C:0.06, G:0.13, T:0.37
Consensus pattern (76 bp):
AAATAGAAAATTGTTTCCCACTTTAAAAGAAATTTATAAAATTAAGGATAGAATTTTAATTTTGA
AAAATTAATAG
Found at i:1105118 original size:2 final size:2
Alignment explanation
Indices: 1105111--1105154 Score: 79
Period size: 2 Copynumber: 21.5 Consensus size: 2
1105101 TTATTTTCAG
1105111 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TGA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA
1105154 T
1 T
1105155 GTGAAATGTG
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 39 0.95
3 2 0.05
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1109335 original size:19 final size:18
Alignment explanation
Indices: 1109313--1109375 Score: 67
Period size: 18 Copynumber: 3.4 Consensus size: 18
1109303 TTTCACTACG
1109313 TTATATTTTAATTTATAGA
1 TTAT-TTTTAATTTATAGA
* *
1109332 TTATTTTTCATTCTA-CG-
1 TTATTTTTAATT-TATAGA
1109349 TTATATTTTAATTTATAGA
1 TTAT-TTTTAATTTATAGA
1109368 TTATTTTT
1 TTATTTTT
1109376 CATATTTAAG
Statistics
Matches: 36, Mismatches: 4, Indels: 9
0.73 0.08 0.18
Matches are distributed among these distances:
17 6 0.17
18 20 0.56
19 10 0.28
ACGTcount: A:0.29, C:0.05, G:0.05, T:0.62
Consensus pattern (18 bp):
TTATTTTTAATTTATAGA
Found at i:1109348 original size:36 final size:35
Alignment explanation
Indices: 1109301--1109378 Score: 140
Period size: 36 Copynumber: 2.2 Consensus size: 35
1109291 TTATTTTATT
1109301 TTTTTCA-CTACGTTATATTTTAATTTATAGATTA
1 TTTTTCATCTACGTTATATTTTAATTTATAGATTA
1109335 TTTTTCATTCTACGTTATATTTTAATTTATAGATTA
1 TTTTTCA-TCTACGTTATATTTTAATTTATAGATTA
1109371 TTTTTCAT
1 TTTTTCAT
1109379 ATTTAAGCAT
Statistics
Matches: 42, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
34 7 0.17
35 1 0.02
36 34 0.81
ACGTcount: A:0.27, C:0.09, G:0.05, T:0.59
Consensus pattern (35 bp):
TTTTTCATCTACGTTATATTTTAATTTATAGATTA
Found at i:1119865 original size:15 final size:15
Alignment explanation
Indices: 1119847--1119899 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
1119837 TTCATTGAAA
* *
1119847 TAAAATTTTCCTTTT
1 TAAAACTTTCCATTT
1119862 TAAAACTTTCCATTT
1 TAAAACTTTCCATTT
** *
1119877 TAATTCTTTCCATAAT
1 TAAAACTTTCCAT-TT
1119893 TAAAACT
1 TAAAACT
1119900 CCTTTTAATC
Statistics
Matches: 30, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
15 24 0.80
16 6 0.20
ACGTcount: A:0.34, C:0.17, G:0.00, T:0.49
Consensus pattern (15 bp):
TAAAACTTTCCATTT
Found at i:1120264 original size:77 final size:78
Alignment explanation
Indices: 1120134--1120297 Score: 233
Period size: 77 Copynumber: 2.1 Consensus size: 78
1120124 AATTTCTCAT
* ***
1120134 ATTAAAATACTATCTTTAATTTTAAGAATTTTTTTTTAAAGTAGGAAACAATTTCCTATTCTTTA
1 ATTAAAATACTATCCTTAATTTTAAGAATTTACATTTAAAGTAGGAAACAATTTCCTATTCTTTA
*
1120199 TGAATCACTCAAA
66 TGAATCACCCAAA
* * *
1120212 ATTAAAATTCTATCCTTAATTTTAAGAA-TTACATTTAAAGTA-GAAGATAATTTCCTATTTTTT
1 ATTAAAATACTATCCTTAATTTTAAGAATTTACATTTAAAGTAGGAA-ACAATTTCCTATTCTTT
1120275 ATGAATCACCCAAA
65 ATGAATCACCCAAA
1120289 ATTAAAATA
1 ATTAAAATA
1120298 TATGGCATTT
Statistics
Matches: 76, Mismatches: 9, Indels: 3
0.86 0.10 0.03
Matches are distributed among these distances:
76 3 0.04
77 47 0.62
78 26 0.34
ACGTcount: A:0.41, C:0.12, G:0.06, T:0.41
Consensus pattern (78 bp):
ATTAAAATACTATCCTTAATTTTAAGAATTTACATTTAAAGTAGGAAACAATTTCCTATTCTTTA
TGAATCACCCAAA
Found at i:1123363 original size:145 final size:145
Alignment explanation
Indices: 1123100--1123375 Score: 380
Period size: 145 Copynumber: 1.9 Consensus size: 145
1123090 AAGTCGAATC
* * *
1123100 AAACAATTTAGAAAAGGATATACAATTGATTTTTCTATTTTTGACATTAACTGGTAGCTCTCTAA
1 AAACAATTTAGAAAAGGATATACAATTGATTTTTCTACTTTTAACATTAACTGGCAGCTCTCTAA
** *
1123165 GAGAGTTGAAACACTTTACAAACAAGGATCTTGCCTAATATCAAGTTCAAAATGCTCCAATTCAT
66 GAGAGTTGAAACACTTTACAAACAAGGATCTCACCTAATATCAAGTTCAAAATGCTACAATTCAT
1123230 ATTTTATATGCAATT
131 ATTTTATATGCAATT
* * *
1123245 AAACAATTTAGGAGAA-GATATACAATTTATTTTTCTACTTTTAATATTAACTGGCACAGCT-T-
1 AAACAATTTA-GAAAAGGATATACAATTGATTTTTCTACTTTTAACATTAACTGG--CAGCTCTC
* * *
1123307 TGAA-AGAGTTGAAATACTTTGCAAACATGGATCTCACCTAATATCAAGTTCAAAATGCTACAAT
63 T-AAGAGAGTTGAAACACTTTACAAACAAGGATCTCACCTAATATCAAGTTCAAAATGCTACAAT
1123371 TCATA
127 TCATA
1123376 ACTCATGGGC
Statistics
Matches: 115, Mismatches: 12, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
145 104 0.90
146 7 0.06
147 4 0.03
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.34
Consensus pattern (145 bp):
AAACAATTTAGAAAAGGATATACAATTGATTTTTCTACTTTTAACATTAACTGGCAGCTCTCTAA
GAGAGTTGAAACACTTTACAAACAAGGATCTCACCTAATATCAAGTTCAAAATGCTACAATTCAT
ATTTTATATGCAATT
Found at i:1139342 original size:21 final size:21
Alignment explanation
Indices: 1139318--1139357 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
1139308 AGATTGCAAC
1139318 AGGGCTTGT-ATAATTGATAAT
1 AGGGCTTGTGA-AATTGATAAT
1139339 AGGGCTTGTGAAATTGATA
1 AGGGCTTGTGAAATTGATA
1139358 TTACCCCGCT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 17 0.94
22 1 0.06
ACGTcount: A:0.33, C:0.05, G:0.28, T:0.35
Consensus pattern (21 bp):
AGGGCTTGTGAAATTGATAAT
Found at i:1165315 original size:27 final size:28
Alignment explanation
Indices: 1165177--1165360 Score: 196
Period size: 27 Copynumber: 6.5 Consensus size: 28
1165167 ATTAAGAAAA
*
1165177 AAACAT-TTTGTCTTGTCTAAATTGAGAC
1 AAACATGTTT-TCTTGTCTAAATTAAGAC
* * *
1165205 AAATAT-TCTTTCTTGTCTAGATTAAAAC
1 AAACATGT-TTTCTTGTCTAAATTAAGAC
* * *
1165233 AAAAAATATTTTTCTTGTCTTAAATTAAGTCC
1 -AAACAT-GTTTTCTTGTC-TAAATTAAG-AC
*
1165265 ACACATGTTTTCTTGTCTAAATTAAGAC
1 AAACATGTTTTCTTGTCTAAATTAAGAC
1165293 AAACATGTTTT-TTGTCTAAATTAAGAC
1 AAACATGTTTTCTTGTCTAAATTAAGAC
**
1165320 ATGCATGTTTT-TTGTCTAAATTAAGAC
1 AAACATGTTTTCTTGTCTAAATTAAGAC
1165347 AAACATGTTTTCTT
1 AAACATGTTTTCTT
1165361 ATTGATAAGA
Statistics
Matches: 132, Mismatches: 17, Indels: 14
0.81 0.10 0.09
Matches are distributed among these distances:
27 50 0.38
28 34 0.26
29 16 0.12
30 19 0.14
31 12 0.09
32 1 0.01
ACGTcount: A:0.34, C:0.14, G:0.10, T:0.42
Consensus pattern (28 bp):
AAACATGTTTTCTTGTCTAAATTAAGAC
Found at i:1166771 original size:171 final size:169
Alignment explanation
Indices: 1166454--1169825 Score: 1240
Period size: 171 Copynumber: 19.9 Consensus size: 169
1166444 NNNNNNNNNN
* * * * * *
1166454 ATTATAAAACCATTTAAAGCAAGTAATAAGGCTTTCGAAGGCAT-AGGTAACTATGAATAGACTT
1 ATTATAAAACCATTTAAAGTAAGTAATAA-GCTTTCAAAGGCTTGA-GTGACTATAAATAAACTT
* * * ** * * * * * * * * *
1166518 TTCTTTTTAACGAATGGCTTTTTATTCACG-TTTCTCAAGGTAAATATTCAAATATAGTTTGTTT
64 TTCTTATCAATG-ATGGCTTTTGCTTCACGTTTTTTGAA-GCAGACATTCAATTATAATATATTT
* * * *
1166582 TATCAAAAAACATAAAAAAATTCATCTTAAAATCAATTATGAG
127 TAACTAAAAATATAAAAAAATTCAACTTAAAATCAATTATGAG
** ** * * * * *
1166625 ATTATAAAATTATTTAAAGCGAGTAATAAGAGTCTCGAAGACTTGAGTGACTAAAAATAAACTTT
1 ATTATAAAACCATTTAAAGTAAGTAATAAG-CTTTCAAAGGCTTGAGTGACTATAAATAAACTTT
* * *
1166690 TCTTATCAATTGATGGCTTTTGCTTCACGTTTTTTGAAGCAGACATTTAATTGTAATATATTTCA
65 TCTTATCAA-TGATGGCTTTTGCTTCACGTTTTTTGAAGCAGACATTCAATTATAATATATTTTA
* * *
1166755 AATAAAAATGTAAAAAAATTTAACTTAAAATCAATTATGAG
129 ACTAAAAATATAAAAAAATTCAACTTAAAATCAATTATGAG
* * * * *
1166796 ATTATAAAACCATTTAAAGCAAATAATGAGGCTTTCAAAGGCAT-AGGTGACTATAAATGAACTT
1 ATTATAAAACCATTTAAAGTAAGTAAT-AAGCTTTCAAAGGCTTGA-GTGACTATAAATAAAC-T
* ** * * *
1166860 TTTTTTATCAATGAATGGCTTTTGCTTCACGTTTCCT-AAGATAAACACTCAATTAT-ATAATAT
63 TTTCTTATCAATG-ATGGCTTTTGCTTCACGTTTTTTGAAG-CAGACATTCAATTATAAT-ATAT
*
1166923 TTTAACTAAAAATATAAAAACAATT-AACTTAAAATCAATTATGAT
125 TTTAACTAAAAATATAAAAA-AATTCAACTTAAAATCAATTATGAG
* ** * * * ** *
1166968 ATTATAAACCCATTTAAAGGGAGTAATCACA-CTTTCGAATGCATT-AGTAACTATAAATGGATT
1 ATTATAAAACCATTTAAAGTAAGTAAT-A-AGCTTTCAAAGGC-TTGAGTGACTATAAATAAACT
* * ** * * *
1167031 TTTCTCT-TAAATAGATGGCTTCTGCTTCATATTTCTT-AAGGTAGACATTCAATTATAATCTAT
63 TTTCT-TATCAAT-GATGGCTTTTGCTTCACGTTTTTTGAA-GCAGACATTCAATTATAATATAT
* * * * * * *
1167094 TTTAACCAACAACAT-AAAATATTTAAATTAAAATAAATTATGAG
125 TTTAACTAAAAATATAAAAAAATTCAACTTAAAATCAATTATGAG
* * * * * *
1167138 ATTATAAAACTATTTGACGTAAGTAATAATGCTTTCGAAGG-TATAAGCGACTATAAATAAACTT
1 ATTATAAAACCATTTAAAGTAAGTAATAA-GCTTTCAAAGGCT-TGAGTGACTATAAATAAACTT
* * * * * * *
1167202 TTCTTA-CTAATGAATGGTTTTTTCTTCATGTTTCTCATG--GTCA-ACATTCAAATATTATCTA
64 TTCTTATC-AATG-ATGGCTTTTGCTTCACGTTT-T-TTGAAG-CAGACATTCAATTATAATATA
* * * * *
1167263 TTTTAATTAAAAATATAAAAACAAATCAGCTTAAATTCAGTTATGAG
124 TTTTAACTAAAAATATAAAAA-AATTCAACTTAAAATCAATTATGAG
* * * * * ** **
1167310 ATTGTAAAACCATTTTAAGTGAGTAATAAGGCCTCCAAAGGCTTGAGTGACTGCAAATGGACTTT
1 ATTATAAAACCATTTAAAGTAAGTAATAA-GCTTTCAAAGGCTTGAGTGACTATAAATAAACTTT
* * * ** * *
1167375 TCTTGTC-A--ATGGATTTTCCTTCACGTTTACTAAAGTAGACATTCAATTATAATATATTTTAA
65 TCTTATCAATGATGGCTTTTGCTTCACGTTTTTTGAAGCAGACATTCAATTATAATATATTTTAA
* * * *
1167437 CAAAAAATGTATAAAAATTTAACTTAAAATCAATTATGAG
130 CTAAAAATATAAAAAAATTCAACTTAAAATCAATTATGAG
** * * * *
1167477 ATTGCAAAACCATTTAAAGTAAGTAATAAGACTTTCAAAGGCTCGAATGGCTATAAATAGACTTT
1 ATTATAAAACCATTTAAAGTAAGTAATAAG-CTTTCAAAGGCTTGAGTGACTATAAATAAACTTT
** * * * * * *
1167542 TCTTGCCAATGGGTAGCTTTTGCTTCACGTTTTTAGAAGCAAACATTTAATTATAATATTTTTTA
65 TCTTATCAAT-GATGGCTTTTGCTTCACGTTTTTTGAAGCAGACATTCAATTATAATATATTTTA
* * * *
1167607 ACCAAAAATGTAAAAACGATTCAACTTATAATCAATTATGAG
129 ACTAAAAATATAAAAA-AATTCAACTTAAAATCAATTATGAG
* ** * * * * * **
1167649 ATTAAAAAATAATTTAAAAT-GGTAATAGGGCTTTCAAAGG-TGTCAGTGACTATGAATGGACTT
1 ATTATAAAACCATTTAAAGTAAGTAATA-AGCTTTCAAAGGCT-TGAGTGACTATAAATAAAC--
* * * * *** * **** * * * * *
1167712 TTTTTTTACCAATAAATGGGTTTTTAATCAGGTTTCCCAAAGCAAACATTGAAATATAATCTGTT
62 TTTTCTTATCAAT-GATGGCTTTTGCTTCACGTTTTTTGAAGCAGACATTCAATTATAATATATT
* * * * * * *
1167777 TTAACTAAATATGTAAAAACATTCAACTCAAAACCATTTA-AAG
126 TTAACTAAAAATATAAAAAAATTCAACTTAAAATCAATTATGAG
* * * * * * *** *
1167820 CA--AGTAATAA--AGGTT-ACG-AAGGCCTAAGTGA-CTATAAATAGACTTTTCTTG-CTAGTG
1 -ATTA-TAA-AACCA-TTTAAAGTAA-G--TAA-TAAGCTTTCAA-AGGC-TTGAGTGACTA-TA
* * * ** *** ** * * * * ** **
1167877 TAT-AGCTTTTGC--ATC-ACG-TTTCTCAGAGC-AAACATTCAATTAT-AA-TATATTTTCACC
55 AATAAACTTTT-CTTATCAATGATGGCT-TTTGCTTCACGTT---TTTTGAAGCAGACATTCAAT
* * *** * ** * * *
1167934 AAAAATATA-AAAAAATTCAACT-TAAAATAAATTATGAGACTATAAAATC-ATT-TAACG
115 TATAATATATTTTAACTAAAAATATAAAA-AAA-T-TCA-ACT-TAAAATCAATTATGA-G
* * * ** * * * *
1167991 -TAAGTAATAAGGC-TTTCATA-TACTTGAGTGA-CTAT-AAA----T--G-GAC-AT---T--T
1 ATTA-TAA-AA-CCATTT-AAAGTAAGT-AATAAGCTTTCAAAGGCTTGAGTGACTATAAATAAA
** * * * ** ** *
1168038 C-TTTC-TA--ATGGGTAGCTTTTACTTCATATTTCCTGAAGCAGATATTCAATTATAATATA-T
61 CTTTTCTTATCAATGATGGCTTTTGCTTCACGTTTTTTGAAGCAGACATTCAATTATAATATATT
* * * *
1168098 TTAAATAAAAAATATTAAAAAATACAACTTAAAATCAATTATAAG
126 TTAACT-AAAAATATAAAAAAATTCAACTTAAAATCAATTATGAG
* ** * * * **
1168143 ATTATAAAACCATTTGAAGCGAGTAATAAGGCTTT-AAAAGCTTAAGTGATTATAAATGGACTTT
1 ATTATAAAACCATTTAAAGTAAGTAATAA-GCTTTCAAAGGCTTGAGTGACTATAAATAAACTTT
* * * * * *
1168207 TCTTGTTAGTGGATGGCTTTTGCTT--CTTATTTTTGAAGCAAACATTCAATTATAATATTTTTT
65 TCTTATCAAT-GATGGCTTTTGCTTCACGT-TTTTTGAAGCAGACATTCAATTATAATATATTTT
* ** *
1168270 AACAAAAAATATATAAAAAATTTGACTTAAAATCAATTACGAG
128 AACTAAAAATATA-AAAAAATTCAACTTAAAATCAATTATGAG
* * ** * * * **
1168313 ATTATAAAACCATTTAAAGCAAGTATTAAGACTTTTGAAGGCATGGGTAACTATAAATGGACTTT
1 ATTATAAAACCATTTAAAGTAAGTAATAAG-CTTTCAAAGGCTTGAGTGACTATAAATAAACTTT
* * * * *
1168378 TCTTGTCAATGAATGACTTTTGCTTCACGTTTATT-AAGGTAGAGATTCAATTATAATATATTTT
65 TCTTATCAATG-ATGGCTTTTGCTTCACGTTTTTTGAA-GCAGACATTCAATTATAATATATTTT
* * *
1168442 AACTAAAAATATAAAAAAATTTAA-TCTAAAATTAGTTATGAG
128 AACTAAAAATATAAAAAAATTCAACT-TAAAATCAATTATGAG
* * ** * * * * * * * *
1168484 ATTCTAAAACCATTTATAGCGAGTAATAAGCTTTCGAAGGCATGGGTTACAACAAATGGACCTTT
1 ATTATAAAACCATTTAAAGTAAGTAATAAGCTTTCAAAGGCTTGAGTGACTATAAAT-AAACTTT
* * * * * ** *
1168549 T-TTACCAATAAATGGGTTTTGCTTTATGTTTCCT-AAGGTAGACATTCAATTATAATATATTTT
65 TCTTATCAAT-GATGGCTTTTGCTTCACGTTTTTTGAA-GCAGACATTCAATTATAATATATTTT
* * * * *
1168612 AACTAAAAATATAAAAAAATTTAACTCAAAATCTATTATAAC
128 AACTAAAAATATAAAAAAATTCAACTTAAAATCAATTATGAG
* * * ** * * **
1168654 ATTATAAAAACAGTTAAA-TCAAGTAATAATGCTTTTAATTGCATCAGTGACTATAAATGGACTT
1 ATTATAAAACCATTTAAAGT-AAGTAATAA-GCTTTCAAAGGCTTGAGTGACTATAAATAAACTT
* ** * * * * *
1168718 TTCTCT-TCAATGGATGACTTTTGCTTCACGTTTCCTGAGGTAAACATTCAATTGTAATCTATTT
64 TTCT-TATCAAT-GATGGCTTTTGCTTCACGTTTTTTGAAGCAGACATTCAATTATAATATATTT
* * * * * *
1168782 TAACCAACAATAGAAAAAACTTCAACTTAAACTTAATTATGAG
127 TAACTAAAAATATAAAAAAATTCAACTTAAAATCAATTATGAG
* ** * *
1168825 ATAATAAAACCATTTAAAGCGAGTAATAAGGCTTTCAAAAGCTTGAGTGA-TAATAAATAGACTT
1 ATTATAAAACCATTTAAAGTAAGTAATAA-GCTTTCAAAGGCTTGAGTGACT-ATAAATAAACTT
* ** * * ** * *
1168889 TCCTTGCCAATGGATGGCTTTTTCTTCTCGTTTCCTAAAGTAGACATTCAATTATAATATA-TTT
64 TTCTTATCAAT-GATGGCTTTTGCTTCACGTTTTTTGAAGCAGACATTCAATTATAATATATTTT
* * *
1168953 AA-TCAAAAATGTAAAAAACATTCAGCTTAAAATCAATTAAGAG
128 AACT-AAAAATATAAAAAA-ATTCAACTTAAAATCAATTATGAG
* * * * * * * * * * ** *
1168996 ATTAT-AAACTATTTAAAGCAAATACTAAGGCTTTCGAATGCATGGGCGAGTATAAATGTA-GTT
1 ATTATAAAACCATTTAAAGTAAGTAATAA-GCTTTCAAAGGCTTGAGTGACTATAAATAAACTTT
* * * * * * * * * * *
1169059 TCTTGTCAATGAATGG-GTTTGTTTCACATTTCTT-AAGGCAAATATTCAAATATTATGTGTTTT
65 TCTTATCAATG-ATGGCTTTTGCTTCACGTTTTTTGAA-GCAGACATTCAATTATAATATATTTT
* * * *
1169122 AAC-CAAAATGTAAAAAAATTCAGCTTAAAATCAATTATAAG
128 AACTAAAAATATAAAAAAATTCAACTTAAAATCAATTATGAG
** ** * * *
1169163 ATTATAAAATCC-TTTAAAGCGAGTAATAAGGCTTTCGTAGACCTGAGTGACTAATAAATAGACT
1 ATTATAAAA-CCATTTAAAGTAAGTAATAA-GCTTTCAAAGGCTTGAGTGACT-ATAAATAAACT
* * * ** * *
1169227 TTTCTTGTCAATGGATAGCTTTCGCTTCATATTTCTCGAAGCAGACATTCAATTATAATATA-TT
63 TTTCTTATCAAT-GATGGCTTTTGCTTCACGTTTTTTGAAGCAGACATTCAATTATAATATATTT
* *
1169291 TAAATAAAAAATATAAAAAAATTCAA-TTAAAATCAATTATGCG
127 TAACT-AAAAATATAAAAAAATTCAACTTAAAATCAATTATGAG
* * * * * * *
1169334 ATTATAAAACTATTTAAAGCAAGTAATAAGGCTTTTAAAGGCATGGGTGGCTATAAA-AGGACTT
1 ATTATAAAACCATTTAAAGTAAGTAATAA-GCTTTCAAAGGCTTGAGTGACTATAAATA-AACTT
* ** * * * * ** * * * * * *
1169398 TTCTTACCAATGAATGATTTTTTCATCATGGTTCCT-AGGGCATACGTTTAAATATAATCTATTT
64 TTCTTATCAATG-ATGGCTTTTGCTTCACGTTTTTTGA-AGCAGACATTCAATTATAATATATTT
* *
1169462 TAA-TCAAATATGTAAAAAAATT-ATACTTAAAATCAATTATGAG
127 TAACT-AAAAATATAAAAAAATTCA-ACTTAAAATCAATTATGAG
* * ** * ** *
1169505 GTTA-CAAACTGTTGAAAGCGAGTAATAAGTGTTTCAAAGGCTTGAGTGACTATAAATAAACTTT
1 ATTATAAAACCATTTAAAGTAAGTAATAAG-CTTTCAAAGGCTTGAGTGACTATAAATAAACTTT
* * * ** *
1169569 T-TTTTACAGTGGATGGCTTTTGTTTCACGTTTTTCAAAGCAGACATTTAATTATAATATATTTT
65 TCTTAT-CAAT-GATGGCTTTTGCTTCACGTTTTTTGAAGCAGACATTCAATTATAATATATTTT
* * * *
1169633 AA-TCACAAATGTAAAAAAATTTAACTTAAAATCAATTATAAG
128 AACT-AAAAATATAAAAAAATTCAACTTAAAATCAATTATGAG
** * * * ** * * **
1169675 ATTATAAAATTATTTAAAGCAAGCAATATGACTTTTTAAGGCATGGGTGACTATAAATGGACTTT
1 ATTATAAAACCATTTAAAGTAAGTAATAAG-CTTTCAAAGGCTTGAGTGACTATAAATAAACTTT
* * ** * * * * * * *
1169740 TCTTGTCAATGAATGGCTTTTTCTTCACACTTCTTGAGGCAAACATTCAAATATTATCTGTTTTA
65 TCTTATCAATG-ATGGCTTTTGCTTCACGTTTTTTGAAGCAGACATTCAATTATAATATATTTTA
* *
1169805 ACCAAAAATACAAAAAAATTC
129 ACTAAAAATATAAAAAAATTC
1169826 TATAACGACC
Statistics
Matches: 2395, Mismatches: 638, Indels: 336
0.71 0.19 0.10
Matches are distributed among these distances:
150 5 0.00
151 13 0.01
152 18 0.01
153 8 0.00
154 22 0.01
155 17 0.01
156 6 0.00
157 1 0.00
158 1 0.00
159 2 0.00
160 3 0.00
161 2 0.00
162 1 0.00
163 1 0.00
164 1 0.00
165 1 0.00
166 11 0.00
167 121 0.05
168 139 0.06
169 82 0.03
170 616 0.26
171 892 0.37
172 340 0.14
173 82 0.03
174 9 0.00
175 1 0.00
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.35
Consensus pattern (169 bp):
ATTATAAAACCATTTAAAGTAAGTAATAAGCTTTCAAAGGCTTGAGTGACTATAAATAAACTTTT
CTTATCAATGATGGCTTTTGCTTCACGTTTTTTGAAGCAGACATTCAATTATAATATATTTTAAC
TAAAAATATAAAAAAATTCAACTTAAAATCAATTATGAG
Found at i:1167370 original size:342 final size:336
Alignment explanation
Indices: 1166454--1169759 Score: 1606
Period size: 341 Copynumber: 9.8 Consensus size: 336
1166444 NNNNNNNNNN
* * *
1166454 ATTATAAAACCATTTAAAGCAAGTAATAAGGCTTTCGAAGGCATAGGTAACTATGAATAGACTTT
1 ATTATAAAACCATTTAAAGCAAGTAATAAGGCTTTCGAAGGCATAGGTGACTATAAATAAACTTT
* * * * * *
1166519 TCTTTTTAACGAATGGCTTTTTATTCACGTTTCTCAAGGTAAATATTCAAATATAGTTTGTTTT-
66 TC-TTATAATGAATGGCTTTTTCTTCACGTTTCTCAAGGTAAACATTCAAATATA-TATATTTTA
* * * * **
1166583 ATCAAAAAACATAAAAA-AATTCATCTTAAAATCAATTATGAGATTATAAAATTATTTAAAGCGA
129 AT-TAAAAATATAAAAACAAATCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGA
* * ** *
1166647 GTAATAAGAGTCTCGAAGACTTGAGTGACTAAAAATAAACTTTTCTTATCAATTGATGGCTTTTG
193 GTAATAAG-GCCTCGAAGGCTTGAGTGACTAAAAATGGACTTTTCTTATCAATAGATGGC-TTTG
* * * * * *
1166712 CTTCACGTTTTTTGAAGCAGACATTTAATTGTAATATATTTCAA-ATAAAAATGTAAAAAAATTT
256 CTTCACGTTTCTT-AAGTAGACATTCAATTATAATATATTTTAACA-AAAAA--TATAAAAATTT
1166776 AACTTAAAATCAATTATGAG
317 AACTTAAAATCAATTATGAG
* * * *
1166796 ATTATAAAACCATTTAAAGCAAATAATGAGGCTTTCAAAGGCATAGGTGACTATAAATGAACTTT
1 ATTATAAAACCATTTAAAGCAAGTAATAAGGCTTTCGAAGGCATAGGTGACTATAAATAAAC-TT
* * * * *
1166861 TTTTTATCAATGAATGGCTTTTGCTTCACGTTTC-CTAAGATAAACACTCAATTATATAATATTT
65 TTCTTAT-AATGAATGGCTTTTTCTTCACGTTTCTC-AAGGTAAACATTCAAATATAT-ATATTT
* * * * *
1166925 TAACTAAAAATATAAAAAC-AATTAACTTAAAATCAATTATGATATTATAAACCCATTTAAAGGG
127 TAATTAAAAATATAAAAACAAATCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCG
* ** * * * * * *
1166989 AGTAATCACACTTTCGAATGCATT-AGTAACTATAAATGGATTTTTCTCT-TAAATAGATGGCTT
192 AGTAATAAGGC-CTCGAAGGC-TTGAGTGACTAAAAATGGACTTTTCT-TATCAATAGATGGCTT
** * * * *
1167052 CTGCTTCATATTTCTTAAGGTAGACATTCAATTATAATCTATTTTAACCAACAACATAAAATATT
254 -TGCTTCACGTTTCTTAA-GTAGACATTCAATTATAATATATTTTAACAAAAAATATAAAA-ATT
* *
1167117 TAAATTAAAATAAATTATGAG
316 TAACTTAAAATCAATTATGAG
* * * * * * * *
1167138 ATTATAAAACTATTTGACGTAAGTAATAATGCTTTCGAAGGTATAAGCGACTATAAATAAACTTT
1 ATTATAAAACCATTTAAAGCAAGTAATAAGGCTTTCGAAGGCATAGGTGACTATAAATAAACTTT
* * * * *
1167203 TCTTACTAATGAATGGTTTTTTCTTCATGTTTCTCATGGTCAACATTCAAATATTATCTATTTTA
66 TCTTA-TAATGAATGGCTTTTTCTTCACGTTTCTCAAGGTAAACATTCAAATA-TATATATTTTA
* * * * * *
1167268 ATTAAAAATATAAAAACAAATCAGCTTAAATTCAGTTATGAGATTGTAAAACCATTTTAAGTGAG
129 ATTAAAAATATAAAAACAAATCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAG
* ** * * *
1167333 TAATAAGGCCTCCAAAGGCTTGAGTGACTGCAAATGGACTTTTCTTGTCAATGGAT---TTTCCT
194 TAATAAGGCCT-CGAAGGCTTGAGTGACTAAAAATGGACTTTTCTTATCAATAGATGGCTTTGCT
*
1167395 TCACGTTTACTAAAGTAGACATTCAATTATAATATATTTTAACAAAAAATGTATAAAAATTTAAC
258 TCACGTTT-CTTAAGTAGACATTCAATTATAATATATTTTAACAAAAAA--TATAAAAATTTAAC
1167460 TTAAAATCAATTATGAG
320 TTAAAATCAATTATGAG
** * * * * * * *
1167477 ATTGCAAAACCATTTAAAGTAAGTAATAAGACTTTCAAAGGC-TCGAATGGCTATAAATAGACTT
1 ATTATAAAACCATTTAAAGCAAGTAATAAGGCTTTCGAAGGCATAG-GTGACTATAAATAAACTT
** ** * * * * * * * *
1167541 TTCTTGCCAATGGGTAGCTTTTGCTTCACGTTT-TTAGAAGCAAACATTTAATTATAATATTTTT
65 TTCTT-ATAATGAATGGCTTTTTCTTCACGTTTCTCA-AGGTAAACATTCAAATAT-ATATATTT
** * * * * * ** **
1167605 TAACCAAAAATGTAAAAACGATTCAACTTATAATCAATTATGAGATTAAAAAATAATTTAAAATG
127 TAATTAAAAATATAAAAACAAATCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCG
* * * * ** * * * *
1167670 -GTAATAGGGCTTTCAAAGG-TGTCAGTGACTATGAATGGACTTTTTTTTTACCAATAAATGGGT
192 AGTAATAAGGC-CTCGAAGGCT-TGAGTGACTAAAAATGGAC--TTTTCTTATCAATAGATGGCT
* * ** * * * * * * *
1167733 TT-TTAATCAGGTTTCCCAAAGCAAACATTGAAATATAATCTGTTTTAAC--------TAAATAT
253 TTGCT--TCACGTTT-CTTAAGTAGACATTCAATTATAATATATTTTAACAAAAAATATAAAAAT
* *
1167789 GT-A---AAAA-C-A-T-TCA-
315 TTAACTTAAAATCAATTATGAG
* * * * * *
1167802 ACT-CAAAACCATTTAAAGCAAGTAATAAAGG-TTACGAAGGCCTAAGTGACTATAAATAGACTT
1 ATTATAAAACCATTTAAAGCAAGTAAT-AAGGCTTTCGAAGGCATAGGTGACTATAAATAAACTT
* * * * * * * *
1167865 TTCTTGCTAGTGTATAGCTTTTGCATCACGTTTCTC-AGAGCAAACATTCAATTATAATATATTT
65 TTCTT-ATAATGAATGGCTTTTTCTTCACGTTTCTCAAG-GTAAACATTCAAATAT-ATATATTT
* ** * * * * * **
1167929 TCACCAAAAATATAAAAA-AATTCAACTTAAAATAAATTATGAGACTATAAAATCATTTAACGTA
127 TAATTAAAAATATAAAAACAAATCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCG
* ** * * * * *
1167993 AGTAATAAGGCTTTC-ATATACTTGAGTGACTATAAATGGACATTTCTT-TCTAATGGGTAGCTT
192 AGTAATAAGGC-CTCGA-AGGCTTGAGTGACTAAAAATGGACTTTTCTTATC-AATAGATGGC-T
* ** * * * * *
1168056 TTACTTCATATTTCCTGAAGCAGATATTCAATTATAATATATTTAAATAAAAAATATTAAAAAAT
253 TTGCTTCACGTTT-CTTAAGTAGACATTCAATTATAATATATTTTAACAAAAAATA-T-AAAAAT
** *
1168121 ACAACTTAAAATCAATTATAAG
315 TTAACTTAAAATCAATTATGAG
* * * * * * * **
1168143 ATTATAAAACCATTTGAAGCGAGTAATAAGGCTTT-AAAAGCTTAAGTGATTATAAATGGACTTT
1 ATTATAAAACCATTTAAAGCAAGTAATAAGGCTTTCGAAGGCATAGGTGACTATAAATAAACTTT
* * * * *** * * * * *
1168207 TCTTGTTAGTGGATGGCTTTTGCTTCTTATTTTTGAA-GCAAACATTCAATTATAATATTTTTTA
66 TCTT-ATAATGAATGGCTTTTTCTTCACGTTTCTCAAGGTAAACATTCAAATAT-ATATATTTTA
** * ** * *
1168271 ACAAAAAATATATAAAA-AATTTGACTTAAAATCAATTACGAGATTATAAAACCATTTAAAGCAA
129 ATTAAAAATATA-AAAACAAATCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGA
* * * * * * * * * *
1168335 GTATTAAGACTTTTGAAGGCATGGGTAACTATAAATGGACTTTTCTTGTCAAT-GAATGACTTTT
193 GTAATAAGGC-CTCGAAGGCTTGAGTGACTAAAAATGGACTTTTCTTATCAATAG-ATGGC-TTT
* * *
1168399 GCTTCACGTTTATTAAGGTAGAGATTCAATTATAATATATTTTAACTAAAAATATAAAAAAATTT
255 GCTTCACGTTTCTTAA-GTAGACATTCAATTATAATATATTTTAAC-AAAAA-ATATAAAAATTT
* *
1168464 AA-TCTAAAATTAGTTATGAG
317 AACT-TAAAATCAATTATGAG
* * * * * * * * *
1168484 ATTCTAAAACCATTTATAGCGAGTAATAA-GCTTTCGAAGGCATGGGTTACAACAAATGGACCTT
1 ATTATAAAACCATTTAAAGCAAGTAATAAGGCTTTCGAAGGCATAGGTGACTATAAAT-AAACTT
* * * * * * * *
1168548 TT-TTACCAATAAATGGGTTTTGCTTTATGTTTC-CTAAGGTAGACATTCAATTATAATATATTT
65 TTCTTA-TAATGAATGGCTTTTTCTTCACGTTTCTC-AAGGTAAACATTCAAATAT-ATATATTT
* * * * * * * * * * *
1168611 TAACTAAAAATATAAAAA-AATTTAACTCAAAATCTATTATAACATTATAAAAACAGTTAAATCA
127 TAATTAAAAATATAAAAACAAATCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCG
* * ** * * * * * *
1168675 AGTAATAATGCTTTTAATTGCATCAGTGACTATAAATGGACTTTTCTCT-TCAATGGATGACTTT
192 AGTAATAAGGCCTCGAA-GGCTTGAGTGACTAAAAATGGACTTTTCT-TATCAATAGATGGC-TT
* * * * * * * *
1168739 TGCTTCACGTTTCCTGAGGTAAACATTCAATTGTAATCTATTTTAACCAACAATAGAAAAAACTT
254 TGCTTCACGTTT-CTTAAGTAGACATTCAATTATAATATATTTTAACAAAAAATA-TAAAAA-TT
* * *
1168804 CAACTTAAACTTAATTATGAG
316 TAACTTAAAATCAATTATGAG
* * * * * *
1168825 ATAATAAAACCATTTAAAGCGAGTAATAAGGCTTTCAAAAGC-TTGAGTGA-TAATAAATAGACT
1 ATTATAAAACCATTTAAAGCAAGTAATAAGGCTTTCGAAGGCATAG-GTGACT-ATAAATAAACT
* ** * * * * *
1168888 TTCCTTGCCAATGGATGGCTTTTTCTTCTCGTTTC-CTAAAGTAGACATTCAATTATA-ATATAT
64 TTTCTT-ATAATGAATGGCTTTTTCTTCACGTTTCTC-AAGGTAAACATTCAAATATATATAT-T
* * * * * *
1168951 TTAATCAAAAATGTAAAAA-ACATTCAGCTTAAAATCAATTAAGAGATTAT-AAACTATTTAAAG
126 TTAATTAAAAATATAAAAACA-AATCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAG
* * * * * * * * * * * * * *
1169014 CAAATACTAAGGCTTTCGAATGCATGGGCGAGTATAAATGTA-GTTTCTTGTCAAT-GAATGGGT
190 CGAGTAATAAGGC-CTCGAAGGCTTGAGTGACTAAAAATGGACTTTTCTTATCAATAG-ATGGCT
* * * * * * * * * ** *
1169077 TTGTTTCACATTTCTTAAGGCAAATATTCAAATATTATGTGTTTTAACCAAAATGTAAAAAAATT
253 TTGCTTCACGTTTCTTAA-GTAGACATTCAATTATAATATATTTTAA-CAAAAAATATAAAAATT
* * *
1169142 CAGCTTAAAATCAATTATAAG
316 TAACTTAAAATCAATTATGAG
* * * * *
1169163 ATTATAAAATCC-TTTAAAGCGAGTAATAAGGCTTTCGTAGACCT-GAGTGACTAATAAATAGAC
1 ATTATAAAA-CCATTTAAAGCAAGTAATAAGGCTTTCGAAGGCATAG-GTGACT-ATAAATAAAC
* * * ** ** * * *
1169226 TTTTCTTGTCAATGGATAGCTTTCGCTTCATATTTCTCGAA-GCAGACATTCAATTATAATATAT
63 TTTTCTTAT-AATGAATGGCTTTTTCTTCACGTTTCTC-AAGGTAAACATTCAAATAT-ATATAT
* * * * *
1169290 TTAAATAAAAAATATAAAAA-AATTCAA-TTAAAATCAATTATGCGATTATAAAACTATTTAAAG
125 TTTAATTAAAAATATAAAAACAAATCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAG
* * ** * * * * *
1169353 CAAGTAATAAGGCTTTTAAAGGCATGGGTGGCTATAAAA-GGACTTTTCTTACCAAT-GAATGAT
190 CGAGTAATAAGGC-CTCGAAGGCTTGAGTGACTA-AAAATGGACTTTTCTTATCAATAG-ATG-G
* * * * * * * * * * * * * * *
1169416 TTTTTCATCATGGTTCCTAGGGCATACGTTTAAATATAATCTATTTTAATC-AAATATGTAAAAA
251 CTTTGCTTCACGTTTCTTA-AGTAGACATTCAATTATAATATATTTTAA-CAAAAAATAT-AAAA
*
1169480 AATTATACTTAAAATCAATTATGAG
313 ATTTA-ACTTAAAATCAATTATGAG
* * ** * * * *
1169505 GTTA-CAAACTGTTGAAAGCGAGTAATAAGTG-TTTCAAAGGC-TTGAGTGACTATAAATAAACT
1 ATTATAAAACCATTTAAAGCAAGTAATAAG-GCTTTCGAAGGCATAG-GTGACTATAAATAAACT
* * * * * * * *
1169567 TTT-TTTTACAGTGGATGGCTTTTGT-TTCACGTTTTTCAAAGCAGACATTTAATTATAATATAT
64 TTTCTTATA-A-TGAATGGCTTTT-TCTTCACGTTTCTCAAGGTAAACATTCAAATAT-ATATAT
* * * * * * **
1169630 TTTAATCACAAATGTAAAAA-AATTTAACTTAAAATCAATTATAAGATTATAAAATTATTTAAAG
125 TTTAATTAAAAATATAAAAACAAATCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAG
* * * * * ** * * * *
1169694 CAAGCAATATGACTTTTTAAGGCATGGGTGACTATAAATGGACTTTTCTTGTCAAT-GAATGGCT
190 CGAGTAATAAGGC-CTCGAAGGCTTGAGTGACTAAAAATGGACTTTTCTTATCAATAG-ATGGCT
1169758 TT
253 TT
1169760 TTCTTCACAC
Statistics
Matches: 2323, Mismatches: 518, Indels: 248
0.75 0.17 0.08
Matches are distributed among these distances:
321 1 0.00
322 41 0.02
323 42 0.02
324 145 0.06
325 8 0.00
326 2 0.00
327 1 0.00
328 1 0.00
329 1 0.00
330 4 0.00
331 1 0.00
332 5 0.00
333 2 0.00
334 7 0.00
336 4 0.00
337 2 0.00
338 159 0.07
339 320 0.14
340 231 0.10
341 724 0.31
342 401 0.17
343 183 0.08
344 38 0.02
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.36
Consensus pattern (336 bp):
ATTATAAAACCATTTAAAGCAAGTAATAAGGCTTTCGAAGGCATAGGTGACTATAAATAAACTTT
TCTTATAATGAATGGCTTTTTCTTCACGTTTCTCAAGGTAAACATTCAAATATATATATTTTAAT
TAAAAATATAAAAACAAATCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTA
ATAAGGCCTCGAAGGCTTGAGTGACTAAAAATGGACTTTTCTTATCAATAGATGGCTTTGCTTCA
CGTTTCTTAAGTAGACATTCAATTATAATATATTTTAACAAAAAATATAAAAATTTAACTTAAAA
TCAATTATGAG
Found at i:1168305 original size:170 final size:169
Alignment explanation
Indices: 1167806--1169824 Score: 1504
Period size: 171 Copynumber: 11.8 Consensus size: 169
1167796 CATTCAACTC
* * * *
1167806 AAAACCATTTAAAGCAAGTAATAAAGG--TTACGAAGGCCTAAGTGACTATAAATAGACTTTTCT
1 AAAACCATTTAAAGCGAGTAAT-AAGGCTTTA--AAGGCATGAGTGACTATAAATGGACTTTTCT
* * * * * * *
1167869 TG-CTAGTGTATAGCTTTTGCATCACGTTTC-TCAGAGCAAACATTCAATTATAATATATTTTCA
63 TGTC-AATGGATGGCTTTTGCTTCACATTTCTTGA-AGCAGACATTCAATTATAATATATTTT-A
* * * *
1167932 CCAAAAATATAAAAAAATTCAACTTAAAATAAATTATGAGACTAT
125 ACAAAAATATAAAAAAATTTAACTTAAAATCAATTATGAGATTAT
* * ** * ** * *
1167977 AAAATCATTTAACGTAAGTAATAAGGCTTTCATATACTTGAGTGACTATAAATGGACATTTCTT-
1 AAAACCATTTAAAGCGAGTAATAAGGCTTT-AAAGGCATGAGTGACTATAAATGGACTTTTCTTG
* * * * * * * *
1168041 TCTAATGGGTAGCTTTTACTTCATATTTCCTGAAGCAGATATTCAATTATAATATATTTAAATAA
65 TC-AATGGATGGCTTTTGCTTCACATTTCTTGAAGCAGACATTCAATTATAATATATTTTAA-CA
* ** *
1168106 AAAATATTAAAAAATACAACTTAAAATCAATTATAAGATTAT
128 AAAATATAAAAAAATTTAACTTAAAATCAATTATGAGATTAT
* * * * *
1168148 AAAACCATTTGAAGCGAGTAATAAGGCTTTAAAAGCTTAAGTGATTATAAATGGACTTTTCTTGT
1 AAAACCATTTAAAGCGAGTAATAAGGCTTTAAAGGCATGAGTGACTATAAATGGACTTTTCTTGT
* * ** * *
1168213 TAGTGGATGGCTTTTGCTTCTTATTT-TTGAAGCAAACATTCAATTATAATATTTTTTAACAAAA
66 CAATGGATGGCTTTTGCTTCACATTTCTTGAAGCAGACATTCAATTATAATATATTTTAAC-AAA
* *
1168277 AATATATAAAAAATTTGACTTAAAATCAATTACGAGATTAT
130 AATATA-AAAAAATTTAACTTAAAATCAATTATGAGATTAT
* * * * * *
1168318 AAAACCATTTAAAGCAAGTATTAAGACTTTTGAAGGCATGGGTAACTATAAATGGACTTTTCTTG
1 AAAACCATTTAAAGCGAGTAATAAGGC-TTTAAAGGCATGAGTGACTATAAATGGACTTTTCTTG
* * * * * *
1168383 TCAATGAATGACTTTTGCTTCACGTTTATT-AAGGTAGAGATTCAATTATAATATATTTTAACTA
65 TCAATGGATGGCTTTTGCTTCACATTTCTTGAA-GCAGACATTCAATTATAATATATTTTAAC-A
* * *
1168447 AAAATATAAAAAAATTTAA-TCTAAAATTAGTTATGAGATTCT
128 AAAATATAAAAAAATTTAACT-TAAAATCAATTATGAGATTAT
* * * * * *
1168489 AAAACCATTTATAGCGAGTAATAA-GCTTTCGAAGGCATGGGTTACAACAAATGGACCTTTT-TT
1 AAAACCATTTAAAGCGAGTAATAAGGCTTT-AAAGGCATGAGTGACTATAAATGGA-CTTTTCTT
** ** * * ** * *
1168552 ACCAATAAATGGGTTTTGCTTTATGTTTCCT-AAGGTAGACATTCAATTATAATATATTTTAACT
64 GTCAATGGATGGCTTTTGCTTCACATTTCTTGAA-GCAGACATTCAATTATAATATATTTTAAC-
* * * *
1168616 AAAAATATAAAAAAATTTAACTCAAAATCTATTATAACATTAT
127 AAAAATATAAAAAAATTTAACTTAAAATCAATTATGAGATTAT
* * * * * ** *
1168659 AAAAACAGTTAAATCAAGTAATAATGCTTTTAATTGCATCAGTGACTATAAATGGACTTTTCTCT
1 AAAACCATTTAAAGCGAGTAATAAGGC-TTTAAAGGCATGAGTGACTATAAATGGACTTTTCT-T
* * * * * * * *
1168724 -TCAATGGATGACTTTTGCTTCACGTTTCCTGAGGTAAACATTCAATTGTAATCTATTTTAACCA
64 GTCAATGGATGGCTTTTGCTTCACATTTCTTGAAGCAGACATTCAATTATAATATATTTTAA-CA
* * * * * * *
1168788 ACAATAGAAAAAACTTCAACTTAAACTTAATTATGAGATAAT
128 AAAATATAAAAAAATTTAACTTAAAATCAATTATGAGATTAT
* * * *
1168830 AAAACCATTTAAAGCGAGTAATAAGGCTTTCAAAAGCTTGAGTGA-TAATAAATAGACTTTCCTT
1 AAAACCATTTAAAGCGAGTAATAAGGCTTT-AAAGGCATGAGTGACT-ATAAATGGACTTTTCTT
* * * * * * *
1168894 GCCAATGGATGGCTTTTTCTTCTCGTTTCCTAAAGTAGACATTCAATTATAATATA-TTTAATCA
64 GTCAATGGATGGCTTTTGCTTCACATTTCTTGAAGCAGACATTCAATTATAATATATTTTAA-CA
* * * *
1168958 AAAATGTAAAAAACATTCAGCTTAAAATCAATTAAGAGATTAT
128 AAAATATAAAAAA-ATTTAACTTAAAATCAATTATGAGATTAT
* * * * * * * * * * *
1169001 -AAACTATTTAAAGCAAATACTAAGGCTTTCGAATGCATGGGCGAGTATAAATGTA-GTTTCTTG
1 AAAACCATTTAAAGCGAGTAATAAGGCTTT-AAAGGCATGAGTGACTATAAATGGACTTTTCTTG
* * * * * * * * * *
1169064 TCAATGAATGG-GTTTGTTTCACATTTCTT-AAGGCAAATATTCAAATATTATGTGTTTTAACCA
65 TCAATGGATGGCTTTTGCTTCACATTTCTTGAA-GCAGACATTCAATTATAATATATTTTAACAA
* * * *
1169127 AAATGTAAAAAAATTCAGCTTAAAATCAATTATAAGATTAT
129 AAATATAAAAAAATTTAACTTAAAATCAATTATGAGATTAT
** * * *
1169168 AAAATCC-TTTAAAGCGAGTAATAAGGCTTTCGTAGACCTGAGTGACTAATAAATAGACTTTTCT
1 AAAA-CCATTTAAAGCGAGTAATAAGGCTTT-AAAGGCATGAGTGACT-ATAAATGGACTTTTCT
* * * * * *
1169232 TGTCAATGGATAGCTTTCGCTTCATATTTCTCGAAGCAGACATTCAATTATAATATATTTAAATA
63 TGTCAATGGATGGCTTTTGCTTCACATTTCTTGAAGCAGACATTCAATTATAATATATTTTAA-C
* *
1169297 AAAAATATAAAAAAATTCAA-TTAAAATCAATTATGCGATTAT
127 AAAAATATAAAAAAATTTAACTTAAAATCAATTATGAGATTAT
* * * * * *
1169339 AAAACTATTTAAAGCAAGTAATAAGGCTTTTAAAGGCATGGGTGGCTATAAAAGGACTTTTCTTA
1 AAAACCATTTAAAGCGAGTAATAAGGC-TTTAAAGGCATGAGTGACTATAAATGGACTTTTCTTG
* * * * * * * * * *
1169404 CCAATGAAT-GATTTT--TTCATCATGGTTCCT-AGGGCATACGTTTAAATATAATCTATTTTAA
65 TCAATGGATGGCTTTTGCTTCA-CAT--TTCTTGA-AGCAGACATTCAATTATAATATATTTTAA
* * *
1169465 TCAAATATGTAAAAAAA-TTATACTTAAAATCAATTATGAGGTTA-
126 -CAAAAATATAAAAAAATTTA-ACTTAAAATCAATTATGAGATTAT
* ** * * **
1169509 CAAACTGTTGAAAGCGAGTAATAAGTG-TTTCAAAGGCTTGAGTGACTATAAATAAACTTTT-TT
1 AAAACCATTTAAAGCGAGTAATAAG-GCTTT-AAAGGCATGAGTGACTATAAATGGACTTTTCTT
* * * * * *
1169572 TTACAGTGGATGGCTTTTGTTTCACGTTT-TTCAAAGCAGACATTTAATTATAATATATTTTAAT
64 GT-CAATGGATGGCTTTTGCTTCACATTTCTT-GAAGCAGACATTCAATTATAATATATTTTAA-
* * *
1169636 CACAAATGTAAAAAAATTTAACTTAAAATCAATTATAAGATTAT
126 CAAAAATATAAAAAAATTTAACTTAAAATCAATTATGAGATTAT
** * * * * * *
1169680 AAAATTATTTAAAGCAAGCAATATGACTTTTTAAGGCATGGGTGACTATAAATGGACTTTTCTTG
1 AAAACCATTTAAAGCGAGTAATAAGGC-TTTAAAGGCATGAGTGACTATAAATGGACTTTTCTTG
* * * * * * * * *
1169745 TCAATGAATGGCTTTTTCTTCACACTTCTTGAGGCAAACATTCAAATATTATCTGTTTTAACCAA
65 TCAATGGATGGCTTTTGCTTCACATTTCTTGAAGCAGACATTCAATTATAATATATTTTAA-CAA
*
1169810 AAATACAAAAAAATT
129 AAATATAAAAAAATT
1169825 CTATAACGAC
Statistics
Matches: 1462, Mismatches: 328, Indels: 116
0.77 0.17 0.06
Matches are distributed among these distances:
167 33 0.02
168 76 0.05
169 80 0.05
170 498 0.34
171 692 0.47
172 78 0.05
173 5 0.00
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.35
Consensus pattern (169 bp):
AAAACCATTTAAAGCGAGTAATAAGGCTTTAAAGGCATGAGTGACTATAAATGGACTTTTCTTGT
CAATGGATGGCTTTTGCTTCACATTTCTTGAAGCAGACATTCAATTATAATATATTTTAACAAAA
ATATAAAAAAATTTAACTTAAAATCAATTATGAGATTAT
Found at i:1168494 original size:341 final size:340
Alignment explanation
Indices: 1167806--1169824 Score: 1685
Period size: 341 Copynumber: 5.9 Consensus size: 340
1167796 CATTCAACTC
* * * * * * *
1167806 AAAACCATTTAAAGCAAGTAATAAAGG-TTACGAAGGCCTAAGTGACTATAAATAGACTTTTCTT
1 AAAACCATTTAAAGCGAGTAAT-AAGGCTTTCAAAAGCTTGAGTGACAATAAATAGACTTTTCTT
* * * * * * * * * *
1167870 GCTAGTGTATAGCTTTTGCATCACGTTTCTCAGAGCAAACATTCAATTATAATATATTTTCACCA
65 GCCAATGGATGGCTTTTGCTTCACATTT-TTAAAGCAGACATTCAATTATAATATATTTT-AACA
* * * * * *
1167935 AAAATATAAAAAAATTCAACTTAAAATAAATTATGAGACTATAAAATCATTTAACGTAAGTAATA
128 AAAATATAAAAAAATTTAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCAAGTAATA
* ** * * * ** *
1168000 AGGC-TTTCATATACTTGAGTGACTATAAATGGACATTTCTT-TCTAATGGGT-AGCTTTTACTT
193 AGGCTTTTGA-AGGCATGGGTGACTATAAATGGACTTTTCTTGTC-AATGAATGA-CTTTTGCTT
** * * * * * **
1168062 CATATTTCCTGAA-GCAGATATTCAATTATAATATA-TTTAAATAAAAAATATTAAAAAATACAA
255 CACGTTT-CTTAAGGCAAAGATTCAATTATAATATATTTTAACT-AAAAATATAAAAAAATTTAA
*
1168125 CTTAAAATCAATTATAAGATTAT
318 CTTAAAATCAATTATGAGATTAT
* * ** *
1168148 AAAACCATTTGAAGCGAGTAATAAGGCTTT-AAAAGCTTAAGTGATTATAAATGGACTTTTCTTG
1 AAAACCATTTAAAGCGAGTAATAAGGCTTTCAAAAGCTTGAGTGACAATAAATAGACTTTTCTTG
** * ** * * *
1168212 TTAGTGGATGGCTTTTGCTTCTTATTTTTGAAGCAAACATTCAATTATAATATTTTTTAACAAAA
66 CCAATGGATGGCTTTTGCTTCACATTTTTAAAGCAGACATTCAATTATAATATATTTTAAC-AAA
* * *
1168277 AATATATAAAAAATTTGACTTAAAATCAATTACGAGATTATAAAACCATTTAAAGCAAGTATTAA
130 AATATA-AAAAAATTTAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCAAGTAATAA
* *
1168342 GACTTTTGAAGGCATGGGTAACTATAAATGGACTTTTCTTGTCAATGAATGACTTTTGCTTCACG
194 GGCTTTTGAAGGCATGGGTGACTATAAATGGACTTTTCTTGTCAATGAATGACTTTTGCTTCACG
* * *
1168407 TTTATTAAGGTAGAGATTCAATTATAATATATTTTAACTAAAAATATAAAAAAATTTAA-TCTAA
259 TTTCTTAAGGCAAAGATTCAATTATAATATATTTTAACTAAAAATATAAAAAAATTTAACT-TAA
* * *
1168471 AATTAGTTATGAGATTCT
323 AATCAATTATGAGATTAT
* * * * * * * *
1168489 AAAACCATTTATAGCGAGTAATAA-GCTTTCGAAGGCATGGGTTACAACAAATGGACCTTTT-TT
1 AAAACCATTTAAAGCGAGTAATAAGGCTTTCAAAAGCTTGAGTGACAATAAATAGA-CTTTTCTT
* ** * * ** * * *
1168552 ACCAATAAATGGGTTTTGCTTTATGTTTCCTAAGGTAGACATTCAATTATAATATATTTTAACTA
65 GCCAATGGATGGCTTTTGCTTCACATTT-TTAAAGCAGACATTCAATTATAATATATTTTAAC-A
* * * * * * *
1168617 AAAATATAAAAAAATTTAACTCAAAATCTATTATAACATTATAAAAACAGTTAAATCAAGTAATA
128 AAAATATAAAAAAATTTAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCAAGTAATA
* * ** *
1168682 ATGCTTTT-AATTGCATCAGTGACTATAAATGGACTTTTCTCT-TCAATGGATGACTTTTGCTTC
193 AGGCTTTTGAA-GGCATGGGTGACTATAAATGGACTTTTCT-TGTCAATGAATGACTTTTGCTTC
* * * * * * * * * * *
1168745 ACGTTTCCTGAGGTAAACATTCAATTGTAATCTATTTTAACCAACAATAGAAAAAACTTCAACTT
256 ACGTTTCTTAAGGCAAAGATTCAATTATAATATATTTTAACTAAAAATATAAAAAAATTTAACTT
* * *
1168810 AAACTTAATTATGAGATAAT
321 AAAATCAATTATGAGATTAT
* *
1168830 AAAACCATTTAAAGCGAGTAATAAGGCTTTCAAAAGCTTGAGTGATAATAAATAGACTTTCCTTG
1 AAAACCATTTAAAGCGAGTAATAAGGCTTTCAAAAGCTTGAGTGACAATAAATAGACTTTTCTTG
* * * * *
1168895 CCAATGGATGGCTTTTTCTTCTCGTTTCCTAAAGTAGACATTCAATTATAATATA-TTTAATCAA
66 CCAATGGATGGCTTTTGCTTCACATTT-TTAAAGCAGACATTCAATTATAATATATTTTAA-CAA
* * * * * * *
1168959 AAATGTAAAAAACATTCAGCTTAAAATCAATTAAGAGATTAT-AAACTATTTAAAGCAAATACTA
129 AAATATAAAAAA-ATTTAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCAAGTAATA
* * * * * * ** *
1169023 AGGCTTTCGAATGCATGGGCGAGTATAAATGTA-GTTTCTTGTCAATGAATG-GGTTTGTTTCAC
193 AGGCTTTTGAAGGCATGGGTGACTATAAATGGACTTTTCTTGTCAATGAATGACTTTTGCTTCAC
* * * * * * * * * *
1169086 ATTTCTTAAGGCAAATATTCAAATATTATGTGTTTTAAC-CAAAATGTAAAAAAATTCAGCTTAA
258 GTTTCTTAAGGCAAAGATTCAATTATAATATATTTTAACTAAAAATATAAAAAAATTTAACTTAA
*
1169150 AATCAATTATAAGATTAT
323 AATCAATTATGAGATTAT
** *
1169168 AAAATCC-TTTAAAGCGAGTAATAAGGCTTTC-GTAGACCTGAGTGACTAATAAATAGACTTTTC
1 AAAA-CCATTTAAAGCGAGTAATAAGGCTTTCAAAAG-CTTGAGTGAC-AATAAATAGACTTTTC
* * * * ** *
1169231 TTGTCAATGGATAGCTTTCGCTTCATATTTCTCGAAGCAGACATTCAATTATAATATATTTAAAT
63 TTGCCAATGGATGGCTTTTGCTTCACATTT-TTAAAGCAGACATTCAATTATAATATATTTTAA-
* * * *
1169296 AAAAAATATAAAAAAATTCAA-TTAAAATCAATTATGCGATTATAAAACTATTTAAAGCAAGTAA
126 CAAAAATATAAAAAAATTTAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCAAGTAA
* * * ** * * *
1169360 TAAGGCTTTTAAAGGCATGGGTGGCTATAAAAGGACTTTTCTTACCAATGAATGATTTTTTCATC
191 TAAGGCTTTTGAAGGCATGGGTGACTATAAATGGACTTTTCTTGTCAATGAATGACTTTTGCTTC
* * * * * * * * * *
1169425 ATGGTTCCTAGGGCATACG-TTTAAATATAATCTATTTTAA-TCAAATATGTAAAAAAA-TTATA
256 ACGTTTCTTAAGGCA-AAGATTCAATTATAATATATTTTAACT-AAAAATATAAAAAAATTTA-A
*
1169487 CTTAAAATCAATTATGAGGTTA-
318 CTTAAAATCAATTATGAGATTAT
* ** * * * * *
1169509 CAAACTGTTGAAAGCGAGTAATAAGTG-TTTCAAAGGCTTGAGTGACTATAAATAAACTTTTTTT
1 AAAACCATTTAAAGCGAGTAATAAG-GCTTTCAAAAGCTTGAGTGACAATAAATAGACTTTTCTT
** * * * *
1169573 TACAGTGGATGGCTTTTGTTTCACGTTTTTCAAAGCAGACATTTAATTATAATATATTTTAATCA
65 GCCAATGGATGGCTTTTGCTTCACATTTTT-AAAGCAGACATTCAATTATAATATATTTTAA-CA
* * * ** *
1169638 CAAATGTAAAAAAATTTAACTTAAAATCAATTATAAGATTATAAAATTATTTAAAGCAAGCAATA
128 AAAATATAAAAAAATTTAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCAAGTAATA
* * * * *
1169703 TGACTTTTTAAGGCATGGGTGACTATAAATGGACTTTTCTTGTCAATGAATGGCTTTTTCTTCAC
193 AGGCTTTTGAAGGCATGGGTGACTATAAATGGACTTTTCTTGTCAATGAATGACTTTTGCTTCAC
** * * * * * * * *
1169768 ACTTCTTGAGGCAAACATTCAAATATTATCTGTTTTAACCAAAAATACAAAAAAATT
258 GTTTCTTAAGGCAAAGATTCAATTATAATATATTTTAACTAAAAATATAAAAAAATT
1169825 CTATAACGAC
Statistics
Matches: 1345, Mismatches: 292, Indels: 80
0.78 0.17 0.05
Matches are distributed among these distances:
337 2 0.00
338 89 0.07
339 156 0.12
340 177 0.13
341 708 0.53
342 213 0.16
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.35
Consensus pattern (340 bp):
AAAACCATTTAAAGCGAGTAATAAGGCTTTCAAAAGCTTGAGTGACAATAAATAGACTTTTCTTG
CCAATGGATGGCTTTTGCTTCACATTTTTAAAGCAGACATTCAATTATAATATATTTTAACAAAA
ATATAAAAAAATTTAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCAAGTAATAAGG
CTTTTGAAGGCATGGGTGACTATAAATGGACTTTTCTTGTCAATGAATGACTTTTGCTTCACGTT
TCTTAAGGCAAAGATTCAATTATAATATATTTTAACTAAAAATATAAAAAAATTTAACTTAAAAT
CAATTATGAGATTAT
Found at i:1174239 original size:171 final size:171
Alignment explanation
Indices: 1173903--1174651 Score: 730
Period size: 171 Copynumber: 4.4 Consensus size: 171
1173893 GAGGTGTTAC
* * ** * **
1173903 AAATTCAACTTAAAATTAATTATGAGATTATAAAACTTTTTAAAGCAGGTAATAAGGCTTTAAAA
1 AAATTTAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCAAGTAATAAGGCTTTCGAA
* * * * * * * * *
1173968 TGCATGAGTGACTATAAATAGACTTTTCTTGTCAATGAATGACTTTT-TTTGCATGTTTCCCAAG
66 GGCTTAAGTGACTATAAATAGACTTTTCTTGCCAATGGATGGCTTTTGCTT-CATGTTTCTCAAA
* * * *
1174032 GTAGACATTCAAATACAATCTGA-TTTAACT-AAAAATATAAAA
130 GCAGACATTCAATTATAATAT-ATTTTAA-TAAAAAATATAAAA
* * * * * *
1174074 AAATTTAACATAAAATTAATTACGAGATTATAAAATCATTTAAAGCGAGTAATAAGGCTTTTGAA
1 AAATTTAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCAAGTAATAAGGCTTTCGAA
* * *
1174139 GGCTTAAATGACTATAAATAGAC-TTTCGTTGCCAATGGATAGCTTTTGCATCATGTTTCTCAAA
66 GGCTTAAGTGACTATAAATAGACTTTTC-TTGCCAATGGATGGCTTTTGCTTCATGTTTCTCAAA
*
1174203 GCAGATATTCAATTATAATATATTTTAATAAAAAATATAAAA
130 GCAGACATTCAATTATAATATATTTTAATAAAAAATATAAAA
* * ** * * *
1174245 CAATTTAACTTAAAATCAATTATAAGATTATAAAATTATTTAATGTAAGTAATAAGGCTTTCGCA
1 AAATTTAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCAAGTAATAAGGCTTTCGAA
* * * * * * **
1174310 GAC-TAGAGTGACTATAAATTGATTTTTCTTGTCAATGGATGGCTTTTACTTCATATTT-TTGAA
66 GGCTTA-AGTGACTATAAATAGACTTTTCTTGCCAATGGATGGCTTTTGCTTCATGTTTCTCAAA
* **
1174373 GCAGACATTTAATTATAATATATTTTACCCAAAAAAGT-T-AAA
130 GCAGACATTCAATTATAATATATTTTA-ATAAAAAA-TATAAAA
** ** *
1174415 AAATACAA-TTGAAAATCAATTATGAGATTATAAAACCATTTAAAGTGAGTAATAAGGC-TTCAA
1 AAATTTAACTT-AAAATCAATTATGAGATTATAAAACCATTTAAAGCAAGTAATAAGGCTTTCGA
* * * * * *
1174478 AGGATTGAGTAACAATAAATGGACTTTTCTTGCCAATGGATGGCTTTTGCTTCTTGTTTC-CAAA
65 AGGCTTAAGTGACTATAAATAGACTTTTCTTGCCAATGGATGGCTTTTGCTTCATGTTTCTCAAA
* * * *
1174542 GCAAACATTCAATTATAATGTATTTT-ATCCAAAAATGTAAAA
130 GCAGACATTCAATTATAATATATTTTAAT-AAAAAATATAAAA
* * * *
1174584 AATTTTGACTTAAAATCAATTATGAGATTATAAAACCATTTAACGCAAGTAATAAGGCTATCGAA
1 AAATTTAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCAAGTAATAAGGCTTTCGAA
1174649 GGC
66 GGC
1174652 ATGGGTAACT
Statistics
Matches: 470, Mismatches: 92, Indels: 33
0.79 0.15 0.06
Matches are distributed among these distances:
167 1 0.00
168 6 0.01
169 127 0.27
170 95 0.20
171 235 0.50
172 6 0.01
ACGTcount: A:0.41, C:0.11, G:0.13, T:0.35
Consensus pattern (171 bp):
AAATTTAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCAAGTAATAAGGCTTTCGAA
GGCTTAAGTGACTATAAATAGACTTTTCTTGCCAATGGATGGCTTTTGCTTCATGTTTCTCAAAG
CAGACATTCAATTATAATATATTTTAATAAAAAATATAAAA
Found at i:1175151 original size:171 final size:170
Alignment explanation
Indices: 1174801--1178276 Score: 1744
Period size: 171 Copynumber: 20.5 Consensus size: 170
1174791 NNNNCAAAAA
* * * * * * *
1174801 CCTTATTACTCGTTTTAAATTATTTTATAATCTCATAATTGATTATAACTTGAATCTTTCTTACA
1 CCTTATTACTCGCTTTAAATGATTTTATAATCTCATAATTAATTTTAAGTTGAAT-TTTTTTATA
* * * * * *
1174866 TTTTTAGTTAAAACAGATTATACTTGAATGTCTGCT-TTAGGAAA-AGTAAAGC--AAA--A--G
65 TTTTTA-TTAAAATAGATTATAATTGAATGTCTACTCCT-GGAAACA-TGAAGCAAAAACCATCC
** * * * * *
1174923 ATTGGCAAGAAAAGTCCATTCATAGCCATTTAAGCCTTTGAAAG
127 ATTTACAAGAAAAGTCTATTTATAGTCACTTAAGCCTTCGAAAG
* ** * * *
1174967 CCTTATTACTCGCTTTAAATGATTTTATAACCTTTTAATTGATTTTAGGTTGAACTTTTTTATAT
1 CCTTATTACTCGCTTTAAATGATTTTATAATCTCATAATTAATTTTAAGTTGAATTTTTTTATAT
* * * * * * * *
1175032 ATTTGATTAAAATATAGTATAATTGAATTTCTGCTCCTGGAAGCATGAAGGAAAACCCATCCATT
66 -TTTTATTAAAATAGATTATAATTGAATGTCTACTCCTGGAAACATGAAGCAAAAACCATCCATT
* * *
1175097 TACAAGAAAAGTCCATTTATAGTCACTTAAG-CTTCCGGAGG
130 TACAAGAAAAGTCTATTTATAGTCACTTAAGCCTT-CGAAAG
* * * * * * *
1175138 CCTCATTACTCGCTTTAAATGATTTTATAATCTCATAACTGACTATAAGCTGATTTTTTTTTCAT
1 CCTTATTACTCGCTTTAAATGATTTTATAATCTCATAATTAATTTTAAGTTGA-ATTTTTTT-AT
* * * * ** *
1175203 ATTTTTAGTTAAAACAGATTATATTTGAATGTCTACT-ATGAGAAACATGAAGAAAAAATTATTC
64 ATTTTTA-TTAAAATAGATTATAATTGAATGTCTACTCCTG-GAAACATGAAGCAAAAACCATCC
* *
1175267 ATTGGTA-AA-AAAAGTCTATTTATAGTCACCTATGCCTTCGAAAG
127 ATT--TACAAGAAAAGTCTATTTATAGTCACTTAAGCCTTCGAAAG
* * * *
1175311 CCTTATTACTTC-CGTTAAATGGTTTCATAATCTTATAATTAATTTTAAGTTGAATTTTTTTATA
1 CCTTATTAC-TCGCTTTAAATGATTTTATAATCTCATAATTAATTTTAAGTTGAATTTTTTTATA
* * * * *
1175375 TTGTTCATTAAAATAGATTATAATTAAATGTCTAC-CTTAGGAAACATAAAGCAAAAGCCATCCA
65 TT-TTTATTAAAATAGATTATAATTGAATGTCTACTCCT-GGAAACATGAAGCAAAAACCATCCA
* * *
1175439 -TTAGAGAGAAAAGTCTATATATAGTCACTTATGCCTTCGAAAG
128 TTTACA-AGAAAAGTCTATTTATAGTCACTTAAGCCTTCGAAAG
** * * *
1175482 TATTATTACTAGCTTTAAATGGTTTTATAATCTCATAATTAATTTTAAGTTAAATTTTTTTATAT
1 CCTTATTACTCGCTTTAAATGATTTTATAATCTCATAATTAATTTTAAGTTGAATTTTTTTATAT
** * * * * * * * *
1175547 TTTTATTAAAATATTTTATAACTGAATGTTTGCTTCAGG-AGCTATGATGCAAAAACCATTCATT
66 TTTTATTAAAATAGATTATAATTGAATGTCTACTCCTGGAAAC-ATGAAGCAAAAACCATCCATT
** ** * * *
1175611 GGCAAGAAAAGTCTATTTATAGTCACCCATGCTTTTGAAAG
130 TACAAGAAAAGTCTATTTATAGTCACTTAAGCCTTCGAAAG
* * * ** * * *
1175652 CCGTGTTACTTGCTTTAAATGGCTTTATAATCTCATAATTGATTTTAAGTTAAATATTTTTATAT
1 CCTTATTACTCGCTTTAAATGATTTTATAATCTCATAATTAATTTTAAGTTGAATTTTTTTATAT
* * * * * * * *
1175717 TTTTAGTTAAAATAGATTACATTTGAATGTCTA-TCTTAGGAAATATGTAG-AAAAAGTCATTCG
66 TTTTA-TTAAAATAGATTATAATTGAATGTCTACTCCT-GGAAACATGAAGCAAAAA-CCATCCA
* * * * * *
1175780 TTCACAAGAAAAGACTATTTATAGACACCTATGCCTTTGAAAG
128 TTTACAAGAAAAGTCTATTTATAGTCACTTAAGCCTTCGAAAG
* ** * * * * *
1175823 CCTTATTACTAGCCATAAATGGTTTTACAATCTCATAATTGATTTTAAGTCGAATTGTTTTATAT
1 CCTTATTACTCGCTTTAAATGATTTTATAATCTCATAATTAATTTTAAGTTGAATTTTTTTATAT
* * * ** ** * ** *
1175888 TTTTAGTTAAAATATATTATAATTAAAT-ACTTGTTTTGGGAAACAAGAAGCAAAAGTCATTCAT
66 TTTTA-TTAAAATAGATTATAATTGAATGTCTACTCCT-GGAAACATGAAGCAAAAACCATCCAT
** * * * **
1175952 TGGCAAGAAAAGTCCATTTATAGTCACTCAAGCTTTTAAAAG
129 TTACAAGAAAAGTCTATTTATAGTCACTTAAGCCTTCGAAAG
* * * * *
1175994 CCATATTACTCGCTTTAAATGGTTTTCTGATCTCATAATTACATATTTAAGTTG--TATTTTT-T
1 CCTTATTACTCGCTTTAAATGATTTTATAATCTCATAATTA-AT-TTTAAGTTGAATTTTTTTAT
* * * * *
1176056 ATTTTTAGTCAAAATATATTATAATTGAATGTGTAC-CTTGGAAAACGTG-AG-AAGAAAGCCAA
64 ATTTTTA-TTAAAATAGATTATAATTGAATGTCTACTCCTGG-AAACATGAAGCAA-AAA-CC-A
* * * ** * *
1176118 T-CATTGGA-AAGAAAGGTCCATTTATAGTCACCCATGCCTTTG--AG
124 TCCATT-TACAAGAAAAGTCTATTTATAGTCACTTAAGCCTTCGAAAG
* * * * * * *
1176162 CGCTTCATTACTAGCTTTATATGGTTTTGTAATCTCAAAATTGATTTTCAGTTGAATATTTTTT-
1 C-CTT-ATTACTCGCTTTAAATGATTTTATAATCTCATAATTAATTTTAAGTTGAAT-TTTTTTA
* * * * * * * * * * ** *
1176226 TATTTTTGATTAACATATATTACAATTAAATGTCTGCT-ATAGAAAAAATAAAGAAAAAATTATT
63 TATTTTT-ATTAAAATAGATTATAATTGAATGTCTACTCCT-GGAAACATGAAGCAAAAACCATC
*** ** *
1176290 CATTGGTAAGAAAAGTCTATTTATAGTCACCCACA-CCTTCAAAAG
126 CATTTACAAGAAAAGTCTATTTATAGTCACTTA-AGCCTTCGAAAG
* * * *
1176335 CCTTATTACTCGCTTTAAATTATTTTATAATCTCATAATTGATATGAAGTTGAATTTATTTTATA
1 CCTTATTACTCGCTTTAAATGATTTTATAATCTCATAATTAATTTTAAGTTGAATTT-TTTTATA
* * * * * * **
1176400 TTTTTAGTTATAACAGATTATAATTGAATATATGC-CTTGGGAAACATGAAG-AATAGGCCATCC
65 TTTTTA-TTAAAATAGATTATAATTGAATGTCTACTCCT-GGAAACATGAAGCAA-AAACCATCC
* * ** * *
1176463 ATTGATAAGAAAAGT-TCATTTATAGTCACCCATGCCTTTGAAAG
127 ATTTACAAGAAAAGTCT-ATTTATAGTCACTTAAGCCTTCGAAAG
* * * * *
1176507 CTTTATTACCCACTTTAAATGATTTTATAATCTCATAA-TAGATTTTAAATAGAATTTTTTTATA
1 CCTTATTACTCGCTTTAAATGATTTTATAATCTCATAATTA-ATTTTAAGTTGAATTTTTTTATA
* * * * * * **
1176571 TTTTTGGTTAAAATAGATTACAATTGAATGTATAC-CTTAGGAAACATGAAGTAGAAGTCAT-CA
65 TTTTT-ATTAAAATAGATTATAATTGAATGTCTACTCCT-GGAAACATGAAGCAAAAACCATCCA
** * * *
1176634 TTTGGAGTGAAAAGT-TCATTTATAGTCACCTATGCCTTCGAAAG
128 TTTACA-AGAAAAGTCT-ATTTATAGTCACTTAAGCCTTCGAAAG
* * * * * * *
1176678 TCTCATTACTTGCTTTAAATGGTTTTATAATCTCATAATTGATTTTAAGTAGAATATTTTTATAT
1 CCTTATTACTCGCTTTAAATGATTTTATAATCTCATAATTAATTTTAAGTTGAATTTTTTTATAT
* * * *
1176743 TTTTACTTAAAATAGATTAAAATTGAATGTCTAC-CTTAGGAAACGTGAAGCAAAAGCCATCC-T
66 TTTTA-TTAAAATAGATTATAATTGAATGTCTACTCCT-GGAAACATGAAGCAAAAACCATCCAT
* * * * * *
1176806 TTAGAGAGAAAAGT-TCATTTATAATAACTGATGCATTCGAAAG
129 TTACA-AGAAAAGTCT-ATTTATAGTCACTTAAGCCTTCGAAAG
* * ** * * * * *
1176849 CATTATTACTTGAATTAGAT-AGCTTTATAATCTCATAATTGATTTTAAATTAAATTTTTTTATA
1 CCTTATTACTCGCTTTAAATGA-TTTTATAATCTCATAATTAATTTTAAGTTGAATTTTTTTATA
* * * ** * * * *
1176913 TTTTTATTTAAAGTAGATTATAATTAAATGTCT-GT-CTCAAAAAAAGTGAAGCAAAAGCTATTC
65 TTTTTA-TTAAAATAGATTATAATTGAATGTCTACTCCT-GGAAACA-TGAAGCAAAAACCATCC
* * * * **** **
1176976 ATTGATAAGAAAAGTCCATTTATAGGCACCCGTGCCTTTAAAAG
127 ATTTACAAGAAAAGTCTATTTATAGTCACTTAAGCCTTCGAAAG
* * * * * *
1177020 CCTTATTACTTGGTTT-AATGGTTTTATAGTCTCATAACTAATGTTAAGTTGAATTTTTTT-TAT
1 CCTTATTACTCGCTTTAAATGATTTTATAATCTCATAATTAATTTTAAGTTGAATTTTTTTATA-
* * * * * * * ** **
1177083 TTTTTGTTAGAATATATTATAATTGAATGTCTAC-CTCAGTAAATATAAAGCAAAAGTCATTTA-
65 TTTTTATTAAAATAGATTATAATTGAATGTCTACTC-CTGGAAACATGAAGCAAAAACCATCCAT
* * * *
1177146 TTAGGAAGAAAAGT-TCATTTATAGTCATTTATGCCGTCGAAAG
129 TTA-CAAGAAAAGTCT-ATTTATAGTCACTTAAGCCTTCGAAAG
** ** * * * *
1177189 GTTTATTACTTACTTTAAATGGTTTTATAATCTTATAATTGATTTTAAGTTG-ATTTTTTTACAT
1 CCTTATTACTCGCTTTAAATGATTTTATAATCTCATAATTAATTTTAAGTTGAATTTTTTTATAT
* * * * * * * * *
1177253 TTTTGGTTAAAACATATTATAATTGAATGTTTGCT-TTGAGAAACATAAAACAAAAGCCATCCAT
66 TTTT-ATTAAAATAGATTATAATTGAATGTCTACTCCTG-GAAACATGAAGCAAAAACCATCCAT
** * * * *
1177317 TGGCAAGAAAAGTCCATTTATAGTCACTCAATCGC-TCGAAGG
129 TTACAAGAAAAGTCTATTTATAGTCACTTAAGC-CTTCGAAAG
* * * * * * *
1177359 CCTTATTACAT-ACTTTAAATAATTTTATAATCTCATAATTGATTTCAAGTTAAATTATTTTATG
1 CCTTATTAC-TCGCTTTAAATGATTTTATAATCTCATAATTAATTTTAAGTTGAATTTTTTTATA
* * * * * *
1177423 TTTTTAGTTAAAATATATTATATTTGAATG-CT--TGCCTTAGGAAACATTAAGAAAAAACTATT
65 TTTTTA-TTAAAATAGATTATAATTGAATGTCTACT-CC-T-GGAAACATGAAGCAAAAACCATC
** * * * * *
1177485 CATCAATAAGAAAAGTCCATTTATAATCACCTATGCCTTCGAAAG
126 CATTTACAAGAAAAGTCTATTTATAGTCACTTAAGCCTTCGAAAG
* * * * * * *
1177530 CCTTATTA-TTGACGTTAAAT-AGTTTTATAATCTTATAATTGATTTTAAGTTAAATCTTTTAAT
1 CCTTATTACTCG-CTTTAAATGA-TTTTATAATCTCATAATTAATTTTAAGTTGAATTTTTTTAT
* * ** *
1177593 ATTTTTGGTT--AA-A-A-TAT-ATT--ATATCT--T-AGGGAAACATGAAG-AAAAATCTATCC
64 ATTTTT-ATTAAAATAGATTATAATTGAATGTCTACTCCTGGAAACATGAAGCAAAAA-CCATCC
* * ** * *
1177646 A-CTAGCAAGAAAAGTCTATTTATAGCCACCCATGCCTTTGAAAG
127 ATTTA-CAAGAAAAGTCTATTTATAGTCACTTAAGCCTTCGAAAG
* * * * *
1177690 CCATATTTCTCGCTTTAAATTG-TTTTATAATCTCAAAATTGATTTTAAGTTGATTTTTTTTATA
1 CCTTATTACTCGCTTTAAA-TGATTTTATAATCTCATAATTAATTTTAAGTTGAATTTTTTTATA
* * * * * * * * *
1177754 TTTTT-TGTCAAATTAGATTACAATTGAATATCTACTTCAT-GAAATATAAAGCAAAATCGATCT
65 TTTTTAT-T-AAAATAGATTATAATTGAATGTCTAC-TCCTGGAAACATGAAGCAAAAACCATCC
* * * * * * * *
1177817 A-TTAGAGAGAAAAGTCCATTTAAAATCACTGATGCATTCAAAAG
127 ATTTACA-AGAAAAGTCTATTTATAGTCACTTAAGCCTTCGAAAG
* * * * * * * *
1177861 CATTATTACTCGATTTAAACGATTTTATAATGTTATAATTGATTTGAAGCTGAATTTTTTTATAG
1 CCTTATTACTCGCTTTAAATGATTTTATAATCTCATAATTAATTTTAAGTTGAATTTTTTTATA-
* * * * * ** * * * * *
1177926 TTTTGATTAAAATATAGTATAACTGAATGTCTA-TCTTAGGAAATGTAAAGCAACAGCTATTCAT
65 TTTTTATTAAAATAGATTATAATTGAATGTCTACTCCT-GGAAACATGAAGCAAAAACCATCCAT
* *
1177990 TGACATGAAAAGTCTA--T-T--T-A--T-A-------AAAG
129 TTACAAGAAAAGTCTATTTATAGTCACTTAAGCCTTCGAAAG
* * * * * * * * *
1178016 CCTTATTGCTTGCCTTAAATGGTTTTATAATCTCATAATTGACTTTAAATTGATTTTTTTTACAT
1 CCTTATTACTCGCTTTAAATGATTTTATAATCTCATAATTAATTTTAAGTTGAATTTTTTTATAT
* * * * * * * **
1178081 TTTTGGTTAACATATATTATAATTGAATGTCTATTTCAGAAAACATGAAG-AAAAAGCCATTTAT
66 TTTT-ATTAAAATAGATTATAATTGAATGTCTACTCCTGGAAACATGAAGCAAAAA-CCATCCAT
*** * *
1178145 TGGTAAGAAAAGT-TAATTTATAGTCA-TCTATGCCTTCAAAAG
129 TTACAAGAAAAGTCT-ATTTATAGTCACT-TAAGCCTTCGAAAG
* * ** * * * * * **
1178187 CCTCATAACTCAATTTAAATGGTTCTATAATCTTATAATTGATTTTAAGTTGAAGTTTTTTACCT
1 CCTTATTACTCGCTTTAAATGATTTTATAATCTCATAATTAATTTTAAGTTGAATTTTTTTATAT
*
1178252 TTTATGATTAAAATATATTATAATT
66 TTT-T-ATTAAAATAGATTATAATT
1178277 CAATTTTTGC
Statistics
Matches: 2573, Mismatches: 585, Indels: 298
0.74 0.17 0.09
Matches are distributed among these distances:
154 8 0.00
155 102 0.04
156 1 0.00
157 1 0.00
158 2 0.00
159 8 0.00
160 104 0.04
161 4 0.00
162 1 0.00
163 4 0.00
164 4 0.00
165 45 0.02
166 59 0.02
167 3 0.00
168 25 0.01
169 113 0.04
170 460 0.18
171 1289 0.50
172 204 0.08
173 127 0.05
174 7 0.00
175 2 0.00
ACGTcount: A:0.36, C:0.12, G:0.12, T:0.40
Consensus pattern (170 bp):
CCTTATTACTCGCTTTAAATGATTTTATAATCTCATAATTAATTTTAAGTTGAATTTTTTTATAT
TTTTATTAAAATAGATTATAATTGAATGTCTACTCCTGGAAACATGAAGCAAAAACCATCCATTT
ACAAGAAAAGTCTATTTATAGTCACTTAAGCCTTCGAAAG
Found at i:1175729 original size:341 final size:337
Alignment explanation
Indices: 1174802--1178337 Score: 2389
Period size: 341 Copynumber: 10.4 Consensus size: 337
1174792 NNNCAAAAAC
* * ** * * * * *
1174802 CTTATTACTCGTTTTAAATTATTTTATAATCTCATAATTGATTATAACTTGAATCTTTCTTACAT
1 CTTATTACTAGCTTTAAATGGTTTTATAATCTCATAATTGATTTTAAGTTAAAT-TTTTTTATAT
* * * * * *
1174867 TTTTAGTTAAAACAGATTATACTTGAATGTCTGCTTTAGGAAA-AGTAAAGC--AAA--A--GAT
65 TTTTA-TTAAAATATATTATAATTGAATGTTTGC-TTA-GAAACA-TGAAGCAAAAACCATTCAT
* * * *** * * *
1174925 TGGCAAGAAAAGTCCATTCATAGCCATTTAAGCCTTTGAAAGCCTTATTACTCGCTTTAAATGAT
126 TGGCAAGAAAAGTCTATTTATAGTCACCCATGCCTTTGAAAGCCTTATTACTTGCTTTAAATGGT
* ** * * * * *
1174990 TTTATAACCTTTTAATTGATTTTAGGTTGAACTTTTTTATATATTT-GATTAAAATATAGTATAA
191 TTTATAATCTCATAATTGATTTTAAGTT-AAATTTTTTATATTTTTAG-TTAAAATAGATTATAA
* * * * * * * * *
1175054 TTGAATTTCTGCTCCT-GGAAGCATGAAGGAAAACCCATCCATTTACA-AGAAAAGTCCATTTAT
254 TTGAATGTCTAC-CTTAGGAAACATAAAGCAAAAGCCATCCA-TTAGAGAGAAAAGTCTATTTAT
* * *
1175117 AGTCACTTAAG-CTTCCGGAGG
317 AGTCACTTATGCCTT-CGAAAG
* * * * * * * **
1175138 CCTCATTACTCGCTTTAAATGATTTTATAATCTCATAACTGACTATAAGCTGATTTTTTTTTCAT
1 -CTTATTACTAGCTTTAAATGGTTTTATAATCTCATAATTGATTTTAAG-TTAAATTTTTTT-AT
* * * * * * **
1175203 ATTTTTAGTTAAAACAGATTATATTTGAATGTCTACTATGAGAAACATGAAGAAAAAATTATTCA
63 ATTTTTA-TTAAAATATATTATAATTGAATGTTTGCT-T-AGAAACATGAAGCAAAAACCATTCA
* * * * * *
1175268 TTGGTAAAAAAAGTCTATTTATAGTCACCTATGCCTTCGAAAGCCTTATTACTTCCGTTAAATGG
125 TTGGCAAGAAAAGTCTATTTATAGTCACCCATGCCTTTGAAAGCCTTATTACTTGCTTTAAATGG
* * * * *
1175333 TTTCATAATCTTATAATTAATTTTAAGTTGAATTTTTTTATATTGTTCA-TTAAAATAGATTATA
190 TTTTATAATCTCATAATTGATTTTAAGTT-AAATTTTTTATATT-TTTAGTTAAAATAGATTATA
* *
1175397 ATTAAATGTCTACCTTAGGAAACATAAAGCAAAAGCCATCCATTAGAGAGAAAAGTCTATATATA
253 ATTGAATGTCTACCTTAGGAAACATAAAGCAAAAGCCATCCATTAGAGAGAAAAGTCTATTTATA
1175462 GTCACTTATGCCTTCGAAAG
318 GTCACTTATGCCTTCGAAAG
* *
1175482 TATTATTACTAGCTTTAAATGGTTTTATAATCTCATAATTAATTTTAAGTTAAATTTTTTTATAT
1 -CTTATTACTAGCTTTAAATGGTTTTATAATCTCATAATTGATTTTAAGTTAAATTTTTTTATAT
* * * * *
1175547 TTTTATTAAAATATTTTATAACTGAATGTTTGCTTCAGGAGCTATGATGCAAAAACCATTCATTG
65 TTTTATTAAAATATATTATAATTGAATGTTTGCTT-AGAAAC-ATGAAGCAAAAACCATTCATTG
* * * *
1175612 GCAAGAAAAGTCTATTTATAGTCACCCATGCTTTTGAAAGCCGTGTTACTTGCTTTAAATGGCTT
128 GCAAGAAAAGTCTATTTATAGTCACCCATGCCTTTGAAAGCCTTATTACTTGCTTTAAATGGTTT
* *
1175677 TATAATCTCATAATTGATTTTAAGTTAAATATTTTTATATTTTTAGTTAAAATAGATTACATTTG
193 TATAATCTCATAATTGATTTTAAGTTAAAT-TTTTTATATTTTTAGTTAAAATAGATTATAATTG
* * ** * * * * * * *
1175742 AATGTCTATCTTAGGAAATATGTAGAAAAAGTCATTCGTTCACA-AGAAAAGACTATTTATAGAC
257 AATGTCTACCTTAGGAAACATAAAGCAAAAGCCATCCATT-AGAGAGAAAAGTCTATTTATAGTC
* *
1175806 ACCTATGCCTTTGAAAG
321 ACTTATGCCTTCGAAAG
** * ** *
1175823 CCTTATTACTAGCCATAAATGGTTTTACAATCTCATAATTGATTTTAAGTCGAATTGTTTTATAT
1 -CTTATTACTAGCTTTAAATGGTTTTATAATCTCATAATTGATTTTAAGTTAAATTTTTTTATAT
* ** * * * **
1175888 TTTTAGTTAAAATATATTATAATTAAATACTTGTTTTGGGAAACAAGAAGCAAAAGTCATTCATT
65 TTTTA-TTAAAATATATTATAATTGAATGTTTG-CTT-AGAAACATGAAGCAAAAACCATTCATT
* * * * * * *
1175953 GGCAAGAAAAGTCCATTTATAGTCACTCAAGCTTTTAAAAGCCATATTACTCGCTTTAAATGGTT
127 GGCAAGAAAAGTCTATTTATAGTCACCCATGCCTTTGAAAGCCTTATTACTTGCTTTAAATGGTT
* * * ** * *
1176018 TTCTGATCTCATAATTACATATTTAAGTTGTA-TTTTT-TATTTTTAGTCAAAATATATTATAAT
192 TTATAATCTCATAATT-GAT-TTTAAGTTAAATTTTTTATATTTTTAGTTAAAATAGATTATAAT
* * * * * *
1176081 TGAATGTGTACCTT-GGAAAACGTGAGAAG--AAAGCCAAT-CATTGGAAAGAAAGGTCCATTTA
255 TGAATGTCTACCTTAGG-AAACAT-A-AAGCAAAAGCC-ATCCATTAGAGAGAAAAGTCTATTTA
** * **
1176142 TAGTCACCCATGCCTTTGAGCG
316 TAGTCACTTATGCCTTCGAAAG
* * * *
1176164 CTTCATTACTAGCTTTATATGGTTTTGTAATCTCAAAATTGATTTTCAGTTGAATATTTTTTTAT
1 CTT-ATTACTAGCTTTAAATGGTTTTATAATCTCATAATTGATTTTAAGTT-AA-ATTTTTTTAT
* * * * * * * * **
1176229 -TTTTGATTAACATATATTACAATTAAATGTCTGCTATAGAAAAAATAAAGAAAAAATTATTCAT
63 ATTTTTATTAAAATATATTATAATTGAATGTTTGCT-TAG-AAACATGAAGCAAAAACCATTCAT
* ** ** * **
1176293 TGGTAAGAAAAGTCTATTTATAGTCACCCACACCTTCAAAAGCCTTATTACTCGCTTTAAATTAT
126 TGGCAAGAAAAGTCTATTTATAGTCACCCATGCCTTTGAAAGCCTTATTACTTGCTTTAAATGGT
* * * * *
1176358 TTTATAATCTCATAATTGATATGAAGTTGAATTTATTTTATATTTTTAGTTATAACAGATTATAA
191 TTTATAATCTCATAATTGATTTTAAGTT-AAATT-TTTTATATTTTTAGTTAAAATAGATTATAA
* * * * * * *
1176423 TTGAATATATGCCTTGGGAAACATGAAG-AATAGGCCATCCATT-GATAAGAAAAGT-TCATTTA
254 TTGAATGTCTACCTTAGGAAACATAAAGCAA-AAGCCATCCATTAGA-GAGAAAAGTCT-ATTTA
** *
1176485 TAGTCACCCATGCCTTTGAAAG
316 TAGTCACTTATGCCTTCGAAAG
* * * *
1176507 CTTTATTACCCA-CTTTAAATGATTTTATAATCTCATAATAGATTTTAA-ATAGAATTTTTTTAT
1 C-TTATTA-CTAGCTTTAAATGGTTTTATAATCTCATAATTGATTTTAAGTTA-AATTTTTTTAT
* * * ** * * **
1176570 ATTTTTGGTTAAAATAGATTACAATTGAATGTATACCTTAGGAAACATGAAGTAGAAGTCA-TCA
63 ATTTTT-ATTAAAATATATTATAATTGAATGT-TTGCTTA-GAAACATGAAGCAAAAACCATTCA
* * * * *
1176634 TTTGG-AGTGAAAAGT-TCATTTATAGTCACCTATGCCTTCGAAAGTCTCATTACTTGCTTTAAA
125 -TTGGCA-AGAAAAGTCT-ATTTATAGTCACCCATGCCTTTGAAAGCCTTATTACTTGCTTTAAA
*
1176697 TGGTTTTATAATCTCATAATTGATTTTAAG-TAGAATATTTTTATATTTTTACTTAAAATAGATT
187 TGGTTTTATAATCTCATAATTGATTTTAAGTTA-AAT-TTTTTATATTTTTAGTTAAAATAGATT
* * * *
1176761 AAAATTGAATGTCTACCTTAGGAAACGTGAAGCAAAAGCCATCCTTTAGAGAGAAAAGT-TCATT
250 ATAATTGAATGTCTACCTTAGGAAACATAAAGCAAAAGCCATCCATTAGAGAGAAAAGTCT-ATT
* * * *
1176825 TATAATAACTGATGCATTCGAAAG
314 TATAGTCACTTATGCCTTCGAAAG
* ** * * * *
1176849 CATTATTACTTGAATTAGATAGCTTTATAATCTCATAATTGATTTTAAATTAAATTTTTTTATAT
1 C-TTATTACTAGCTTTAAATGGTTTTATAATCTCATAATTGATTTTAAGTTAAATTTTTTTATAT
* * * * * * * * *
1176914 TTTTATTTAAAGTAGATTATAATTAAATGTCTGTCTCAAAAAAAGTGAAGCAAAAGCTATTCATT
65 TTTTA-TTAAAATATATTATAATTGAATGTTTG-CTTAGAAACA-TGAAGCAAAAACCATTCATT
** * * * * *
1176979 GATAAGAAAAGTCCATTTATAGGCACCCGTGCCTTTAAAAGCCTTATTACTTGGTTT-AATGGTT
127 GGCAAGAAAAGTCTATTTATAGTCACCCATGCCTTTGAAAGCCTTATTACTTGCTTTAAATGGTT
* * * * * * * * *
1177043 TTATAGTCTCATAACTAATGTTAAGTTGAATTTTTTTTATTTTTTGTTAGAATATATTATAATTG
192 TTATAATCTCATAATTGATTTTAAGTTAAATTTTTTATATTTTTAGTTAAAATAGATTATAATTG
* * * * **
1177108 AATGTCTACCTCAGTAAATATAAAGCAAAAGTCATTTATTAG-GAAGAAAAGT-TCATTTATAGT
257 AATGTCTACCTTAGGAAACATAAAGCAAAAGCCATCCATTAGAG-AGAAAAGTCT-ATTTATAGT
* *
1177171 CATTTATGCCGTCGAAAGG
320 CACTTATGCCTTCGAAA-G
* * * *
1177190 TTTATTACTTA-CTTTAAATGGTTTTATAATCTTATAATTGATTTTAAGTT-GATTTTTTTACAT
1 CTTATTAC-TAGCTTTAAATGGTTTTATAATCTCATAATTGATTTTAAGTTAAATTTTTTTATAT
* * * * * *
1177253 TTTTGGTTAAAACATATTATAATTGAATGTTTGCTTTGAGAAACATAAAACAAAAGCCATCCATT
65 TTTT-ATTAAAATATATTATAATTGAATGTTTGC-TT-AGAAACATGAAGCAAAAACCATTCATT
* * * * * * **
1177318 GGCAAGAAAAGTCCATTTATAGTCACTCAAT-CGC-TCGAAGGCCTTATTACATACTTTAAATAA
127 GGCAAGAAAAGTCTATTTATAGTCAC-CCATGC-CTTTGAAAGCCTTATTACTTGCTTTAAATGG
* * * *
1177381 TTTTATAATCTCATAATTGATTTCAAGTTAAATTATTTTATGTTTTTAGTTAAAATATATTATAT
190 TTTTATAATCTCATAATTGATTTTAAGTTAAATT-TTTTATATTTTTAGTTAAAATAGATTATAA
* * * * * * * * *
1177446 TTGAATG-CTTGCCTTAGGAAACATTAAGAAAAAACTATTCATCA-ATAAGAAAAGTCCATTTAT
254 TTGAATGTC-TACCTTAGGAAACATAAAGCAAAAGCCATCCATTAGA-GAGAAAAGTCTATTTAT
* *
1177509 AATCACCTATGCCTTCGAAAG
317 AGTCACTTATGCCTTCGAAAG
* * * * * *
1177530 CCTTATTA-TTGACGTTAAATAGTTTTATAATCTTATAATTGATTTTAAGTTAAATCTTTTAATA
1 -CTTATTACTAG-CTTTAAATGGTTTTATAATCTCATAATTGATTTTAAGTTAAATTTTTTTATA
* * * * *
1177594 TTTTTGGTTAAAATATATTAT-ATCT-TA-G---G----GAAACATGAAG-AAAAATCTATCCAC
64 TTTTT-ATTAAAATATATTATAAT-TGAATGTTTGCTTAGAAACATGAAGCAAAAA-CCATTCAT
* * * * * *
1177648 TAGCAAGAAAAGTCTATTTATAGCCACCCATGCCTTTGAAAGCCATATTTCTCGCTTTAAATTGT
126 TGGCAAGAAAAGTCTATTTATAGTCACCCATGCCTTTGAAAGCCTTATTACTTGCTTTAAATGGT
* ** * * * *
1177713 TTTATAATCTCAAAATTGATTTTAAGTTGATTTTTTTTATATTTTTTGTCAAATTAGATTACAAT
191 TTTATAATCTCATAATTGATTTTAAGTT-AAATTTTTTATATTTTTAGTTAAAATAGATTATAAT
* * * * * * * * *
1177778 TGAATATCTA-CTTCATGAAATATAAAGCAAAATCGATCTATTAGAGAGAAAAGTCCATTTAAAA
255 TGAATGTCTACCTT-AGGAAACATAAAGCAAAAGCCATCCATTAGAGAGAAAAGTCTATTTATAG
* * *
1177842 TCACTGATGCATTCAAAAG
319 TCACTTATGCCTTCGAAAG
* * * * * * * * *
1177861 CATTATTACTCGATTTAAACGATTTTATAATGTTATAATTGATTTGAAGCTGAATTTTTTTATAG
1 C-TTATTACTAGCTTTAAATGGTTTTATAATCTCATAATTGATTTTAAGTTAAATTTTTTTATA-
* * * * * * *
1177926 TTTTGATTAAAATATAGTATAACTGAATGTCTAT-CTTAGGAA-ATGTAAAGCAACAGCTATTCA
64 TTTTTATTAAAATATATTATAATTGAATGT-T-TGCTTAGAAACATG--AAGCAAAAACCATTCA
* * * *
1177989 TTGACATGAAAAGTCTA-TT-TA-T-----A--------AAAGCCTTATTGCTTGCCTTAAATGG
125 TTGGCAAGAAAAGTCTATTTATAGTCACCCATGCCTTTGAAAGCCTTATTACTTGCTTTAAATGG
* * ** * * * *
1178038 TTTTATAATCTCATAATTGACTTTAAATTGATTTTTTTTACATTTTTGGTTAACATATATTATAA
190 TTTTATAATCTCATAATTGATTTTAAGTT-AAATTTTTTATATTTTTAGTTAAAATAGATTATAA
* * * * ** *
1178103 TTGAATGTCTA-TTTCAGAAAACATGAAGAAAAAGCCATTTATTGGTA-AGAAAAGT-TAATTTA
254 TTGAATGTCTACCTT-AGGAAACATAAAGCAAAAGCCATCCATTAG-AGAGAAAAGTCT-ATTTA
*
1178165 TAGTCA-TCTATGCCTTCAAAAG
316 TAGTCACT-TATGCCTTCGAAAG
* * * * * * * **
1178187 CCTCATAACTCA-ATTTAAATGGTTCTATAATCTTATAATTGATTTTAAGTTGAAGTTTTTTACC
1 -CTTATTACT-AGCTTTAAATGGTTTTATAATCTCATAATTGATTTTAAGTTAAATTTTTTTATA
* * ** * * *
1178251 TTTTATGATTAAAATATATTATAATTCAATTTTTGCTTCATGAAATGTGAAGCAAAAGCTATCCA
64 TTTT-T-ATTAAAATATATTATAATTGAATGTTTGCTT-A-GAAACATGAAGCAAAAACCATTCA
** *
1178316 TTGAAAAGAAAAGTCCATTTAT
125 TTGGCAAGAAAAGTCTATTTAT
1178338 GTACCTTATA
Statistics
Matches: 2533, Mismatches: 542, Indels: 256
0.76 0.16 0.08
Matches are distributed among these distances:
325 6 0.00
326 192 0.08
327 52 0.02
328 5 0.00
329 3 0.00
330 12 0.00
331 230 0.09
332 13 0.01
333 1 0.00
334 1 0.00
337 49 0.02
338 47 0.02
339 105 0.04
340 201 0.08
341 686 0.27
342 432 0.17
343 273 0.11
344 220 0.09
345 5 0.00
ACGTcount: A:0.36, C:0.12, G:0.12, T:0.40
Consensus pattern (337 bp):
CTTATTACTAGCTTTAAATGGTTTTATAATCTCATAATTGATTTTAAGTTAAATTTTTTTATATT
TTTATTAAAATATATTATAATTGAATGTTTGCTTAGAAACATGAAGCAAAAACCATTCATTGGCA
AGAAAAGTCTATTTATAGTCACCCATGCCTTTGAAAGCCTTATTACTTGCTTTAAATGGTTTTAT
AATCTCATAATTGATTTTAAGTTAAATTTTTTATATTTTTAGTTAAAATAGATTATAATTGAATG
TCTACCTTAGGAAACATAAAGCAAAAGCCATCCATTAGAGAGAAAAGTCTATTTATAGTCACTTA
TGCCTTCGAAAG
Found at i:1175844 original size:512 final size:509
Alignment explanation
Indices: 1174801--1178237 Score: 2432
Period size: 512 Copynumber: 6.8 Consensus size: 509
1174791 NNNNCAAAAA
* ** * * * * *
1174801 CCTTATTACTCGTTTTAAATTATTTTATAATCTCATAATTGATTATAACTTGAATCTTTCTTACA
1 CCTTATTACTAGCCTTAAATGATTTTATAATCTCATAATTGATTTTAAGTTGAAT-TTTTTTATA
* * * *
1174866 TTTTTAGTTAAAACAGATTATACTTGAATGTCTGCTTTAGGAAA-AGTAAAGCAAAAG------A
65 TTTTTAGTTAAAATAGATTATAATTAAATGTCTGCCTTAGGAAACA-TAAAGCAAAAGCCATTCA
** * * *** * * * *
1174924 TTGGCAAGAAAAGTCCATTCATAGCCATTTAAGCCTTTGAAAGCCTTATTACTCGCTTTAAATGA
129 TTGATAAGAAAAGTCCATTTATAGTCACCCATGCCTTTGAAAGCATTATTACTAGCTTTAAATGG
* ** * * * * * *
1174989 TTTTATAACCTTTTAATTGATTTTAGGTTGAACTTTTTTATATATTTGATTAAAATATAGTATAA
194 TTTTATAATCTCATAATTAATTTTAAGTTAAATTTTTTTATAT-TTTTATTAAAATATATTATAA
* * * ** *
1175054 TTGAAT-TTCTGCTCCT-GGAAGCATGAAGGAAAACCCATCCATTTACAAGAAAAGTCCATTTAT
258 TTGAATGTT-TGCT--TAGGAAACATGAA-GAAAAACCATTCATTGGCAAGAAAAGTCTATTTAT
** * * * * * * *
1175117 AGTCACTTAAG-CTTCCGGAGGCCTCATTACTCGCTTTAAATGATTTTATAATCTCATAACTGAC
319 AGTCACCCATGCCTT-CGAAAGCCTCATTACTTGCTTTAAATGGTTTTATAATCTCATAATTGAT
* * ** * * * *
1175181 TATAAGCTGATTTTTTTTTCATATTTTTAGTTAAAACAGATTATATTTGAATGTCTAC-TATGAG
383 TTTAAG-TTAAATATTTTT-ATATTTTTAGTTAAAATAGATTACAATTGAATGTCTACTTA-G-G
* * * *
1175245 AAACATGAAGAAAAAATTATTCATTGGTAAAAAAAGTCTATTTATAGTCACCTATGCCTTCGAAA
444 AAACATGAAGAAAAAGTCATTCATTGGCAAGAAAAGTCTATTTATAGTCACCTATGCCTTCGAAA
1175310 G
509 G
* * * * *
1175311 CCTTATTACT-TCCGTTAAATGGTTTCATAATCTTATAATTAATTTTAAGTTGAATTTTTTTATA
1 CCTTATTACTAGCC-TTAAATGATTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTATA
* * *
1175375 TTGTTCA-TTAAAATAGATTATAATTAAATGTCTACCTTAGGAAACATAAAGCAAAAGCCATCCA
65 TT-TTTAGTTAAAATAGATTATAATTAAATGTCTGCCTTAGGAAACATAAAGCAAAAGCCATTCA
* * * ** * *
1175439 TTAGA-GAGAAAAGTCTATATATAGTCACTTATGCCTTCGAAAGTATTATTACTAGCTTTAAATG
129 TT-GATAAGAAAAGTCCATTTATAGTCACCCATGCCTTTGAAAGCATTATTACTAGCTTTAAATG
*
1175503 GTTTTATAATCTCATAATTAATTTTAAGTTAAATTTTTTTATATTTTTATTAAAATATTTTATAA
193 GTTTTATAATCTCATAATTAATTTTAAGTTAAATTTTTTTATATTTTTATTAAAATATATTATAA
* * *
1175568 CTGAATGTTTGCTTCAGG-AGCTATGATGCAAAAACCATTCATTGGCAAGAAAAGTCTATTTATA
258 TTGAATGTTTGCTT-AGGAAAC-ATGAAG-AAAAACCATTCATTGGCAAGAAAAGTCTATTTATA
* * * *
1175632 GTCACCCATGCTTTTGAAAGCCGT-GTTACTTGCTTTAAATGGCTTTATAATCTCATAATTGATT
320 GTCACCCATGCCTTCGAAAGCC-TCATTACTTGCTTTAAATGGTTTTATAATCTCATAATTGATT
* *
1175696 TTAAGTTAAATATTTTTATATTTTTAGTTAAAATAGATTACATTTGAATGTCTATCTTAGGAAAT
384 TTAAGTTAAATATTTTTATATTTTTAGTTAAAATAGATTACAATTGAATGTCTA-CTTAGGAAAC
* * ** * * *
1175761 ATGTAGAAAAAGTCATTCGTTCACAAGAAAAGACTATTTATAGACACCTATGCCTTTGAAAG
448 ATGAAGAAAAAGTCATTCATTGGCAAGAAAAGTCTATTTATAGTCACCTATGCCTTCGAAAG
* * * * *
1175823 CCTTATTACTAGCCATAAATGGTTTTACAATCTCATAATTGATTTTAAGTCGAATTGTTTTATAT
1 CCTTATTACTAGCCTTAAATGATTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTATAT
* * ** * *
1175888 TTTTAGTTAAAATATATTATAATTAAAT-ACTTGTTTTGGGAAACA-AGAAGCAAAAGTCATTCA
66 TTTTAGTTAAAATAGATTATAATTAAATGTC-TGCCTTAGGAAACATA-AAGCAAAAGCCATTCA
** * * * * *
1175951 TTGGCAAGAAAAGTCCATTTATAGTCACTCAAGCTTTTAAAAGCCA-TATTACTCGCTTTAAATG
129 TTGATAAGAAAAGTCCATTTATAGTCACCCATGCCTTTGAAAG-CATTATTACTAGCTTTAAATG
* * * * *
1176015 GTTTTCTGATCTCATAATTACATATTTAAGTT--GTATTTTT-TATTTTTAGTCAAAATATATTA
193 GTTTTATAATCTCATAATTA-AT-TTTAAGTTAAATTTTTTTATATTTTTA-TTAAAATATATTA
** * * * * *
1176077 TAATTGAATGTGTACCTT-GGAAAACGTG-AGAAGAAAGCCAATCATTGGAAAGAAAGGTCCATT
255 TAATTGAATGT-TTGCTTAGG-AAACATGAAGAA-AAA-CCATTCATTGGCAAGAAAAGTCTATT
* ** * * * * *
1176140 TATAGTCACCCATGCCTTTGAGCGCTTCATTACTAGCTTTATATGGTTTTGTAATCTCAAAATTG
316 TATAGTCACCCATGCCTTCGAAAGCCTCATTACTTGCTTTAAATGGTTTTATAATCTCATAATTG
* * * * * * * *
1176205 ATTTTCAGTTGAATATTTTTTTATTTTT-GATTAACATATATTACAATTAAATGTCTGCTATAGA
381 ATTTTAAGTTAAATATTTTTATATTTTTAG-TTAAAATAGATTACAATTGAATGTCTACT-TAGG
* * * * * * ** *
1176269 AAAAATAAAGAAAAAATTATTCATTGGTAAGAAAAGTCTATTTATAGTCACCCACACCTTCAAAA
444 AAACATGAAGAAAAAGTCATTCATTGGCAAGAAAAGTCTATTTATAGTCACCTATGCCTTCGAAA
1176334 G
509 G
* * * * *
1176335 CCTTATTACTCGCTTTAAATTATTTTATAATCTCATAATTGATATGAAGTTGAATTTATTTTATA
1 CCTTATTACTAGCCTTAAATGATTTTATAATCTCATAATTGATTTTAAGTTGAATTT-TTTTATA
* * * * * * * * *
1176400 TTTTTAGTTATAACAGATTATAATTGAATATATGCCTTGGGAAACATGAAG-AATAGGCCATCCA
65 TTTTTAGTTAAAATAGATTATAATTAAATGTCTGCCTTAGGAAACATAAAGCAA-AAGCCATTCA
* * *
1176464 TTGATAAGAAAAGTTCATTTATAGTCACCCATGCCTTTGAAAGCTTTATTACCCA-CTTTAAATG
129 TTGATAAGAAAAGTCCATTTATAGTCACCCATGCCTTTGAAAGCATTATTA-CTAGCTTTAAATG
* * * *
1176528 ATTTTATAATCTCATAA-TAGATTTTAA-ATAGAATTTTTTTATATTTTTGGTTAAAATAGATTA
193 GTTTTATAATCTCATAATTA-ATTTTAAGTTA-AATTTTTTTATATTTTT-ATTAAAATATATTA
* ** * ** *
1176591 CAATTGAATGTATACCTTAGGAAACATGAAGTAGAAGTCA-TCATTTGG-AGTGAAAAGT-TCAT
255 TAATTGAATGT-TTGCTTAGGAAACATGAAG-AAAAACCATTCA-TTGGCA-AGAAAAGTCT-AT
* *
1176653 TTATAGTCACCTATGCCTTCGAAAGTCTCATTACTTGCTTTAAATGGTTTTATAATCTCATAATT
315 TTATAGTCACCCATGCCTTCGAAAGCCTCATTACTTGCTTTAAATGGTTTTATAATCTCATAATT
* *
1176718 GATTTTAAG-TAGAATATTTTTATATTTTTACTTAAAATAGATTAAAATTGAATGTCTACCTTAG
380 GATTTTAAGTTA-AATATTTTTATATTTTTAGTTAAAATAGATTACAATTGAATGTCTA-CTTAG
* * * * * * * * *
1176782 GAAACGTGAAGCAAAAGCCATCCTTTAG-AGAGAAAAGT-TCATTTATAAT-AACTGATGCATTC
443 GAAACATGAAGAAAAAGTCATTCATTGGCA-AGAAAAGTCT-ATTTATAGTCACCT-ATGCCTTC
1176844 GAAAG
505 GAAAG
* * ** * * * *
1176849 CATTATTACTTGAATTAGAT-AGCTTTATAATCTCATAATTGATTTTAAATTAAATTTTTTTATA
1 CCTTATTACTAGCCTTAAATGA-TTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTATA
* * * * * * * *
1176913 TTTTTATTTAAAGTAGATTATAATTAAATGTCTGTCTCA-AAAAAAGTGAAGCAAAAGCTATTCA
65 TTTTTAGTTAAAATAGATTATAATTAAATGTCTGCCTTAGGAAACA-TAAAGCAAAAGCCATTCA
* * * * * *
1176977 TTGATAAGAAAAGTCCATTTATAGGCACCCGTGCCTTTAAAAGCCTTATTACTTGGTTT-AATGG
129 TTGATAAGAAAAGTCCATTTATAGTCACCCATGCCTTTGAAAGCATTATTACTAGCTTTAAATGG
* * * * * *
1177041 TTTTATAGTCTCATAACTAATGTTAAGTTGAATTTTTTT-TATTTTTTGTTAGAATATATTATAA
194 TTTTATAATCTCATAATTAATTTTAAGTTAAATTTTTTTATA-TTTTTATTAAAATATATTATAA
** * * * * ** *
1177105 TTGAATGTCTACCTCAGTAAATATAAAGCAAAAGTCATTTATTAGG-AAGAAAAGT-TCATTTAT
258 TTGAATGT-TTGCTTAGGAAACATGAAG-AAAAACCATTCATT-GGCAAGAAAAGTCT-ATTTAT
*** * ** * * *
1177168 AGTCATTTATGCCGTCGAAAGGTTTATTACTTACTTTAAATGGTTTTATAATCTTATAATTGATT
319 AGTCACCCATGCCTTCGAAAGCCTCATTACTTGCTTTAAATGGTTTTATAATCTCATAATTGATT
* * * * * * * * * *
1177233 TTAAGTT-GATTTTTTTACATTTTTGGTTAAAACATATTATAATTGAATGTTTGCTTTGAGAAAC
384 TTAAGTTAAATATTTTTATATTTTTAGTTAAAATAGATTACAATTGAATGTCTACTTAG-GAAAC
* * * * * *
1177297 AT-AAAACAAAAGCCATCCATTGGCAAGAAAAGTCCATTTATAGTCACTCAAT-CGC-TCGAAGG
448 ATGAAGA-AAAAGTCATTCATTGGCAAGAAAAGTCTATTTATAGTCAC-CTATGC-CTTCGAAAG
* * * * * *
1177359 CCTTATTACATA-CTTTAAATAATTTTATAATCTCATAATTGATTTCAAGTTAAATTATTTTATG
1 CCTTATTAC-TAGCCTTAAATGATTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTATA
* * * * * * *
1177423 TTTTTAGTTAAAATATATTATATTTGAATG-CTTGCCTTAGGAAACATTAAGAAAAAACTATTCA
65 TTTTTAGTTAAAATAGATTATAATTAAATGTC-TGCCTTAGGAAACATAAAGCAAAAGCCATTCA
** * * * * * * *
1177487 TCAATAAGAAAAGTCCATTTATAATCACCTATGCCTTCGAAAGCCTTATTA-TTGACGTTAAATA
129 TTGATAAGAAAAGTCCATTTATAGTCACCCATGCCTTTGAAAGCATTATTACTAG-CTTTAAATG
* * * * *
1177551 GTTTTATAATCTTATAATTGATTTTAAGTTAAATCTTTTAATATTTTTGGTTAAAATATA-T-T-
193 GTTTTATAATCTCATAATTAATTTTAAGTTAAATTTTTTTATATTTTT-ATTAAAATATATTATA
* * * *
1177613 A-T--A----T-CTTAGGGAAACATGAAGAAAAATCTATCCACTAGCAAGAAAAGTCTATTTATA
257 ATTGAATGTTTGCTTA-GGAAACATGAAGAAAAA-CCATTCATTGGCAAGAAAAGTCTATTTATA
* * * * * *
1177670 GCCACCCATGCCTTTGAAAGCCAT-ATTTCTCGCTTTAAATTGTTTTATAATCTCAAAATTGATT
320 GTCACCCATGCCTTCGAAAGCC-TCATTACTTGCTTTAAATGGTTTTATAATCTCATAATTGATT
* * * * * * * * *
1177734 TTAAGTTGATTTTTTTTATATTTTTTGTCAAATTAGATTACAATTGAATATCTACTTCATGAAAT
384 TTAAGTTAAATATTTTTATATTTTTAGTTAAAATAGATTACAATTGAATGTCTACTT-AGGAAAC
* * * * * * * *
1177799 ATAAAGCAAAA-TCGA-TCTATTAG-AGAGAAAAGTCCATTTAAAATCA-CTGATGCATTCAAAA
448 ATGAAGAAAAAGTC-ATTC-ATTGGCA-AGAAAAGTCTATTTATAGTCACCT-ATGCCTTCGAAA
1177860 G
509 G
* * ** * * * * * *
1177861 CATTATTACTCGATTTAAACGATTTTATAATGTTATAATTGATTTGAAGCTGAATTTTTTTATAG
1 CCTTATTACTAGCCTTAAATGATTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTATAT
* * * * ** ** * *
1177926 TTTT-GATTAAAATATAGTATAACTGAATGTCTATCTTAGGAAATGTAAAGCAACAGCTATTCAT
66 TTTTAG-TTAAAATAGATTATAATTAAATGTCTGCCTTAGGAAACATAAAGCAAAAGCCATTCAT
* * * * * * *
1177990 TGACATGAAAAGTCTA-TT-TA-T-----A--------AAAGCCTTATTGCTTGCCTTAAATGGT
130 TGATAAGAAAAGTCCATTTATAGTCACCCATGCCTTTGAAAGCATTATTACTAGCTTTAAATGGT
* * * * * * * *
1178039 TTTATAATCTCATAATTGACTTTAAATTGATTTTTTTTACATTTTTGGTTAACATATATTATAAT
195 TTTATAATCTCATAATTAATTTTAAGTTAAATTTTTTTATATTTTT-ATTAAAATATATTATAAT
* ** * * *
1178104 TGAATGTCTATTTCAGAAAACATGAAGAAAAAGCCATTTATTGGTAAGAAAAGT-TAATTTATAG
259 TGAATGTTTGCTT-AGGAAACATGAAGAAAAA-CCATTCATTGGCAAGAAAAGTCT-ATTTATAG
* * * * *** * *
1178168 TCATCTATGCCTTCAAAAGCCTCATAACTCAATTTAAATGGTTCTATAATCTTATAATTGATTTT
321 TCACCCATGCCTTCGAAAGCCTCATTACTTGCTTTAAATGGTTTTATAATCTCATAATTGATTTT
1178233 AAGTT
386 AAGTT
1178238 GAAGTTTTTT
Statistics
Matches: 2327, Mismatches: 484, Indels: 245
0.76 0.16 0.08
Matches are distributed among these distances:
486 69 0.03
487 4 0.00
488 1 0.00
489 1 0.00
490 1 0.00
492 1 0.00
494 1 0.00
496 3 0.00
497 96 0.04
498 1 0.00
499 1 0.00
500 11 0.00
501 93 0.04
502 189 0.08
503 3 0.00
506 1 0.00
508 1 0.00
509 63 0.03
510 271 0.12
511 205 0.09
512 579 0.25
513 259 0.11
514 371 0.16
515 100 0.04
516 2 0.00
ACGTcount: A:0.36, C:0.12, G:0.12, T:0.40
Consensus pattern (509 bp):
CCTTATTACTAGCCTTAAATGATTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTATAT
TTTTAGTTAAAATAGATTATAATTAAATGTCTGCCTTAGGAAACATAAAGCAAAAGCCATTCATT
GATAAGAAAAGTCCATTTATAGTCACCCATGCCTTTGAAAGCATTATTACTAGCTTTAAATGGTT
TTATAATCTCATAATTAATTTTAAGTTAAATTTTTTTATATTTTTATTAAAATATATTATAATTG
AATGTTTGCTTAGGAAACATGAAGAAAAACCATTCATTGGCAAGAAAAGTCTATTTATAGTCACC
CATGCCTTCGAAAGCCTCATTACTTGCTTTAAATGGTTTTATAATCTCATAATTGATTTTAAGTT
AAATATTTTTATATTTTTAGTTAAAATAGATTACAATTGAATGTCTACTTAGGAAACATGAAGAA
AAAGTCATTCATTGGCAAGAAAAGTCTATTTATAGTCACCTATGCCTTCGAAAG
Found at i:1177732 original size:160 final size:159
Alignment explanation
Indices: 1177458--1177758 Score: 374
Period size: 160 Copynumber: 1.9 Consensus size: 159
1177448 GAATGCTTGC
* * * * *
1177458 CTTAGGAAACATTAAGAAAAAACTATTCATCAATAAGAAAAGTCCATTTATAATCACCTATGCCT
1 CTTAGGAAACATGAAGAAAAAACTATCCATCAACAAGAAAAGTCCATTTATAACCACCCATGCCT
* * *
1177523 TCGAAAGCCTTATTATTGACGTTAAATAGTTTTATAATCTTATAATTGATTTTAAGTTAAATCTT
66 TCGAAAGCCATATTATTGACGTTAAATAGTTTTATAATCTCAAAATTGATTTTAAGTTAAATCTT
1177588 TTAATATTTTTGGTTAAAATATATTATAT
131 TTAATATTTTTGGTTAAAATATATTATAT
* * * *
1177617 CTTAGGGAAACATGAAGAAAAATCTATCCA-CTAGCAAGAAAAGTCTATTTATAGCCACCCATGC
1 CTTA-GGAAACATGAAGAAAAAACTATCCATC-AACAAGAAAAGTCCATTTATAACCACCCATGC
* * * * *
1177681 CTTTGAAAGCCATATT-TCTCG-CTTTAAATTGTTTTATAATCTCAAAATTGATTTTAAGTTGAT
64 CTTCGAAAGCCATATTAT-T-GACGTTAAATAGTTTTATAATCTCAAAATTGATTTTAAGTTAAA
* *
1177744 TTTTTTTATATTTTT
127 TCTTTTAATATTTTT
1177759 TGTCAAATTA
Statistics
Matches: 119, Mismatches: 19, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
159 6 0.05
160 112 0.94
161 1 0.01
ACGTcount: A:0.36, C:0.13, G:0.11, T:0.40
Consensus pattern (159 bp):
CTTAGGAAACATGAAGAAAAAACTATCCATCAACAAGAAAAGTCCATTTATAACCACCCATGCCT
TCGAAAGCCATATTATTGACGTTAAATAGTTTTATAATCTCAAAATTGATTTTAAGTTAAATCTT
TTAATATTTTTGGTTAAAATATATTATAT
Found at i:1178185 original size:326 final size:327
Alignment explanation
Indices: 1177686--1178337 Score: 733
Period size: 326 Copynumber: 2.0 Consensus size: 327
1177676 CATGCCTTTG
* * * * *
1177686 AAAGCCATATTTCTCGCTTTAAATTGTTTTATAATCTCAAAATTGATTTTAAGTTGATTTTTTTT
1 AAAGCCATATTGCTCGCCTTAAATGGTTTTATAATCTCAAAATTGACTTTAAATTGATTTTTTTT
* * * * * *
1177751 ATATTTTTTGTCAAATTAGATTACAATTGAATATCTACTTCATGAAATATAAAGCAAAATCGATC
66 ACATTTTTGGTCAAATTAGATTACAATTGAATATCTACTTCATGAAACATAAAGAAAAAGCCATC
* * * *
1177816 TATTAGAGAGAAAAGTCCATTTAAAATCACTGATGCATTCAAAAGCATTATTACTCGATTTAAAC
131 TATTAGAGAGAAAAGTCAATTTAAAATCACTGATGCATTCAAAAGCATCATAACTCAATTTAAAC
* * * *
1177881 GATTTTATAATGTTATAATTGATTTGAAGCTGAATTTTTTTATAGTTT-TGATTAAAATATAGTA
196 GATTCTATAATCTTATAATTGATTTGAAGCTGAAGTTTTTTACAGTTTATGATTAAAATATAGTA
* * * * * *
1177945 TAACTGAATGTCTAT-CTT-AGGAAATGTAAAGCAACAGCTATTCATTGACATGAAAAGTCTATT
261 TAACTCAAT-T-TATGCTTCAGGAAATGTAAAGCAAAAGCTATCCATTGAAAAGAAAAGTCCATT
1178008 TATA
324 TATA
* * *
1178012 AAAGCCTTATTGCTTGCCTTAAATGGTTTTATAATCTCATAATTGACTTTAAATTGATTTTTTTT
1 AAAGCCATATTGCTCGCCTTAAATGGTTTTATAATCTCAAAATTGACTTTAAATTGATTTTTTTT
* * * * * *
1178077 ACATTTTTGGTTAACA-TATATTATAATTGAATGTCTATTTCA-GAAAACATGAAGAAAAAGCCA
66 ACATTTTTGGTCAA-ATTAGATTACAATTGAATATCTACTTCATG-AAACATAAAGAAAAAGCCA
* * * * * * *
1178140 TTTATTGGTA-AGAAAAGTTAATTTATAGTCATCT-ATGCCTTCAAAAGCCTCATAACTCAATTT
129 TCTATTAG-AGAGAAAAGTCAATTTAAAATCA-CTGATGCATTCAAAAGCATCATAACTCAATTT
* * * * **
1178203 AAATGGTTCTATAATCTTATAATTGATTTTAAGTTGAAGTTTTTTACCTTTTATGATTAAAATAT
192 AAACGATTCTATAATCTTATAATTGATTTGAAGCTGAAGTTTTTTACAGTTTATGATTAAAATAT
* * * * *
1178268 ATTATAATTCAATTTTTGCTTCATGAAATGTGAAGCAAAAGCTATCCATTGAAAAGAAAAGTCCA
257 AGTATAACTCAATTTATGCTTCAGGAAATGTAAAGCAAAAGCTATCCATTGAAAAGAAAAGTCCA
1178333 TTTAT
322 TTTAT
1178338 GTACCTTATA
Statistics
Matches: 267, Mismatches: 52, Indels: 13
0.80 0.16 0.04
Matches are distributed among these distances:
325 3 0.01
326 197 0.74
327 67 0.25
ACGTcount: A:0.37, C:0.11, G:0.12, T:0.40
Consensus pattern (327 bp):
AAAGCCATATTGCTCGCCTTAAATGGTTTTATAATCTCAAAATTGACTTTAAATTGATTTTTTTT
ACATTTTTGGTCAAATTAGATTACAATTGAATATCTACTTCATGAAACATAAAGAAAAAGCCATC
TATTAGAGAGAAAAGTCAATTTAAAATCACTGATGCATTCAAAAGCATCATAACTCAATTTAAAC
GATTCTATAATCTTATAATTGATTTGAAGCTGAAGTTTTTTACAGTTTATGATTAAAATATAGTA
TAACTCAATTTATGCTTCAGGAAATGTAAAGCAAAAGCTATCCATTGAAAAGAAAAGTCCATTTA
TA
Found at i:1180801 original size:343 final size:340
Alignment explanation
Indices: 1180154--1182875 Score: 2090
Period size: 343 Copynumber: 8.0 Consensus size: 340
1180144 TTATCAAGTG
* * * *
1180154 ATAAGGCTTTCAAAGACTTGAGTGACTATAAATGGACTTTTCTTACGAATGGATGGCTTTTGC--
1 ATAAGGCTTTCAAAGGCATCAATGACTATAAATGGACTTTTCTTAC-AATGGATGGCTTTTGCTT
* * * *
1180217 CTCATGTTTCTTGAAGCAGACATTCAAGTATAATATATTTTG-AACAACAATGTAAGAAAATTCA
65 CACAT-TTTC-TGAAGCAGACATTCAAGTATAA-A-ATATTGAAACAACAATATAAAAAAATTCA
* * * * * ** *
1180281 ACTTAAAATCAATTATGAGATTTTAAAACCATTTAAAACTAGTAAAAAGGCTTTCGAAGATATAG
126 ACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCAAGTAATAAGGCTTTCAAAGGCATGG
* * * *
1180346 GTGACTATAAATGGACTTTTCTTCCCAATTAATTGCTTTTGCTTTACA-TTTCTCAAGGTAGACA
191 GTGACTATAAATGGACTTTTCTTACCAATTAATGGCTTTTGCTTCA-AGTTTTTCAAGGTAGACA
* * * * * * *
1180410 ATAAATTATAATATATTTTAATAAAACAA-ATATAAACATTTAACTTAAAATTAATTATGATGTT
255 TTCAATTATAATATATTTTAACAAAA-AATATAAAAAAATTTAACTTAAAATCAATTATGACGTT
* *
1180474 ATAAAACTATTTAAACCAAGTA
319 ATAAAACTATTTAAAGCGAGTA
* * * * *
1180496 ATAATGCTTTAAAAGGCATCAATGACTATAAGTGGACTTTTCTCTACGATGGATGGCTTTTACTT
1 ATAAGGCTTTCAAAGGCATCAATGACTATAAATGGACTTTTCT-TACAATGGATGGCTTTTGCTT
* * *
1180561 CACATTTTCT-AATGTAGACATTCAAGTATAAAACCATTGAAAGCAACAATATAAAAAAATTTAA
65 CACATTTTCTGAA-GCAGACATTCAAGTATAAAA-TATTGAAA-CAACAATATAAAAAAATTCAA
* * * *
1180625 CGTAAAATCAATTATGAGCTTATAAAACCATTGAAAGCAAGTAATAAGG-TATTCGAAGGCATGG
127 CTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCAAGTAATAAGGCT-TTCAAAGGCATGG
* * * *** *
1180689 GTGACTATAAATAGACTTTTCTTACAAATTAGTAATTTTTTCTTCAAGTTTTTCAAGGTAGACAT
191 GTGACTATAAATGGACTTTTCTTACCAATTAATGGCTTTTGCTTCAAGTTTTTCAAGGTAGACAT
* * * * * *
1180754 TCAAATATAATCTGTTTGAACAAAAAATATAAAATAATTTAACTTAAAATCAATTAT-AAGATTA
256 TCAATTATAATATATTTTAACAAAAAATATAAAAAAATTTAACTTAAAATCAATTATGACG-TTA
* ***
1180818 TAAAACCATTTAAATTTAGTA
320 TAAAACTATTTAAAGCGAGTA
* * * * * * * * * * *
1180839 AAAAGGCTTGCGAAGGCTTGAGTGACTATATATAGACTTTTCCTATCAATGGATGACTTTTACTT
1 ATAAGGCTTTCAAAGGCATCAATGACTATAAATGGACTTTTCTTA-CAATGGATGGCTTTTGCTT
* * * * * * *
1180904 --CATGTTTCATAAAGCAGACATTCAAGTATAATATATTTTAATCAAAAATGTAAAAAAATTTAA
65 CACAT-TTTC-TGAAGCAGACATTCAAGTATAAAATA-TTGAAACAACAATATAAAAAAATTCAA
* * * * ** *
1180967 CTTTAAATTAATTATGAGATTATAAAACCGTTTAAAGCAAGTAATAAAGCTTTTGAAGGCGTGGG
127 CTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCAAGTAATAAGGCTTTCAAAGGCATGGG
** * * * * *
1181032 TGACTATAAATAAACTTTTCTTGCCAATGAATGGGTTTTTCTTCACA--TTTTCTAAGGTAGAAA
192 TGACTATAAATGGACTTTTCTTACCAATTAATGGCTTTTGCTTCA-AGTTTTTC-AAGGTAGACA
* * * * * * * *
1181095 TTCAAATATGATCTGTTTTAACTAAAAATGTAAAAAAAATTCAACTTAAAATGAATTATGA-GAT
255 TTCAATTATAATATATTTTAACAAAAAATAT-AAAAAAATTTAACTTAAAATCAATTATGACG-T
* * *
1181159 TATAAAACTATTTATAGTGAGTG
318 TATAAAACTATTTAAAGCGAGTA
* *
1181182 ATAAGGCTTTCAAAGAC-TTAAGTGACTATAAATGGACTTTTCTTACTAATGGATGGCTTTTGCT
1 ATAAGGCTTTCAAAGGCATCAA-TGACTATAAATGGACTTTTCTTAC-AATGGATGGCTTTTGCT
* * * *
1181246 TCAC-GTTTCTTGAAGCAGACATTCAAGTATAATATATTTTGAATA-AA-AATGTAAGAAAATTC
64 TCACATTTTC-TGAAGCAGACATTCAAGTATAA-A-ATATTGAA-ACAACAATATAAAAAAATTC
*
1181308 AACTTAAAATCAATTATGAGATTATAAAACTATTTAACA-CTAA-TACA-AAGGCTTTCAAAGGC
125 AACTTAAAATCAATTATGAGATTATAAAACCATTTAA-AGC-AAGTA-ATAAGGCTTTCAAAGGC
* * * * *
1181370 ATGGGTGACTATAAATGGACTTTTCTTACCAATGAATGGCTTTTGCTTCATG-TGTCCTGAGGTA
187 ATGGGTGACTATAAATGGACTTTTCTTACCAATTAATGGCTTTTGCTTCAAGTTTTTC-AAGGTA
* **
1181434 AACATTCAATTATAATATATTTTAATC-AAAAATATAAAGAAAAACTAACTTAAAATCAATTATG
251 GACATTCAATTATAATATATTTTAA-CAAAAAATATAAA-AAAATTTAACTTAAAATCAATTATG
* * *
1181498 GCATTATAAACCTATTTAAAGCGAGTA
314 ACGTTATAAAACTATTTAAAGCGAGTA
* * * * * * *
1181525 ATAATGCTTTCGAAGACATTAGTGACTACAAATGGACTTTTCTCTCCAATGGATGGCTTTTGCTT
1 ATAAGGCTTTCAAAGGCATCAATGACTATAAATGGACTTTTCT-TACAATGGATGGCTTTTGCTT
* * * * * ** * * * *
1181590 CACGTTTCCTAAAGTAGACATTCAATTATAATCTATTTCAACCAACAATATTAAAAAATTTAACT
65 CACATTTTCTGAAGCAGACATTCAAGTATAAAATA-TTGAAACAACAATATAAAAAAATTCAACT
* * **
1181655 TAAAATCAATTATGAGATTATAATATCATTTAAAGTGAGTAATAAGGC-TTCAAAGGC-TAGGGT
129 TAAAATCAATTATGAGATTATAAAACCATTTAAAGCAAGTAATAAGGCTTTCAAAGGCAT-GGGT
* * * * * * * * *
1181718 GAGTATAAATGGACTTTTCTTACTAA-TAGATGACTTTTTCTTCATGTTTCTCAAGGCAAACAAT
193 GACTATAAATGGACTTTTCTTACCAATTA-ATGGCTTTTGCTTCAAGTTTTTCAAGGTAGACATT
* * * * * *
1181782 CAATTATAATCTTTTTTAACTAAAAATGTAAAAAAATTCAACTTAAAATCAATTAT-ATGCTTAT
257 CAATTATAATATATTTTAACAAAAAATATAAAAAAATTTAACTTAAAATCAATTATGACG-TTAT
*
1181846 AAAACTATTTAAAGAGAGTA
321 AAAACTATTTAAAGCGAGTA
* * * * *
1181866 ATAAGGCTTTCGAAGGCTTGAGTGA-TAATAAATGGACTTTTCTTGCCAATGGATGGCTTTTGCT
1 ATAAGGCTTTCAAAGGCATCAATGACT-ATAAATGGACTTTTCTT-ACAATGGATGGCTTTTGCT
* * * * * * * ** * *
1181930 TCACATTTCCTGAAGCATACATTGAATTGTAATATATTTAATGAA-AACCATAAACAAATTCAAC
64 TCACATTTTCTGAAGCAGACATTCAAGTATAAAATATTGAAACAACAA-TATAAAAAAATTCAAC
* * * * * * *
1181994 TTAAAATCAATTATGAGATTATAAAACCATTTTAAGCTAGCAGTAAGGCTTTCAAGGGCGTGGAT
128 TTAAAATCAATTATGAGATTATAAAACCATTTAAAGCAAGTAATAAGGCTTTCAAAGGCATGGGT
* ** * * * * * * *
1182059 GACTATAAATGAACTTTTCTTGTCAATGAATGACTTTCGCTTTACA-TTTCCTGAA-GCAGACAT
193 GACTATAAATGGACTTTTCTTACCAATTAATGGCTTTTGCTTCA-AGTTT-TTCAAGGTAGACAT
* * * * * *
1182122 TCCATTAAAATATATTTGAATAAAAACTATAAAAAAATTTAACTTAAAATCAATTATGACATTAT
256 TCAATTATAATATATTTTAACAAAAAATATAAAAAAATTTAACTTAAAATCAATTATGACGTTAT
* * **
1182187 GAAACCATTTAAATTGAGTA
321 AAAACTATTTAAAGCGAGTA
* * * * * * * * *
1182207 GTAATGCTTTCAAATGTATCAATAACTATATATGCACTTTTCTCTCCAATGGATGGATTTTGCTT
1 ATAAGGCTTTCAAAGGCATCAATGACTATAAATGGACTTTTCT-TACAATGGATGGCTTTTGCTT
** * * ** * * ** * *
1182272 CATGTTTCCTAAATTAGACATTCAATTGTAATCTAATTTAACCAACAATATAAAAAAATTCAACT
65 CACATTTTCTGAAGCAGACATTCAAGTATAAAAT-ATTGAAACAACAATATAAAAAAATTCAACT
* ** *
1182337 TAAAATCAATTATAAGATTATAAAATTATTCAAAGCAAGTAATAAGGCTTTCAAAGGCATGGGTC
129 TAAAATCAATTATGAGATTATAAAACCATTTAAAGCAAGTAATAAGGCTTTCAAAGGCATGGGT-
** ** * * * *
1182402 G-CTATAAATGGACTTTTCTTGTCAATGGATAGCTTTTGCTTCATG-TTTCCTAAAGTAGACATT
193 GACTATAAATGGACTTTTCTTACCAATTAATGGCTTTTGCTTCAAGTTTTTC-AAGGTAGACATT
* * ** * *
1182465 CAATTATAATATATTGTAAGAAAAAAGGTAAAAATATTTAACTTAAAATCAATTATGAGGTTATA
257 CAATTATAATATATTTTAACAAAAAATATAAAAAAATTTAACTTAAAATCAATTATGACGTTATA
* *
1182530 AAACCATTTAATG-GCAGTA
322 AAACTATTTAAAGCG-AGTA
* * * *
1182549 ATACGGCTTTCAAAGGCAT-AAGTGACTATAAATAGACTTTTCTTACCAATGGATGGTTTTTTCT
1 ATAAGGCTTTCAAAGGCATCAA-TGACTATAAATGGACTTTTCTTA-CAATGGATGGCTTTTGCT
* * * * * *
1182613 T--CATGTTTCTCAAGGTAGACATTCAAATATAATTAAT-TTTAACAAAAAAATATAAAAAAATT
64 TCACAT-TTTCTGAA-GCAGACATTCAAGTATAA--AATATTGAA-ACAACAATATAAAAAAATT
* ********** * * * *
1182675 TAACTTAANNNNNNNNNNGAGATTATAAAACCATTTCAAGCGAGTAATAAGGCCTTCGAAGG-AT
124 CAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCAAGTAATAAGGCTTTCAAAGGCA-
* ** * ** * * * *
1182739 TGAGTGACTATAAATAAACTTTTCTTATCAATGGATGGGTTTTGCTTCATG-TTTTCAAAAGCA-
188 TGGGTGACTATAAATGGACTTTTCTTACCAATTAATGGCTTTTGCTTCAAGTTTTTC-AAGGTAG
* * * *
1182802 ACCATTCAATTTTAATATATTTTAACCAAAAATATAAAAACATTTAA-TTAAAAATTAATTATGA
252 A-CATTCAATTATAATATATTTTAACAAAAAATATAAAAAAATTTAACTT-AAAATCAATTATGA
1182866 -GATTATAAAA
315 CG-TTATAAAA
1182876 TCATTCAAAG
Statistics
Matches: 1921, Mismatches: 380, Indels: 157
0.78 0.15 0.06
Matches are distributed among these distances:
339 2 0.00
340 64 0.03
341 354 0.18
342 603 0.31
343 868 0.45
344 27 0.01
345 3 0.00
ACGTcount: A:0.39, C:0.13, G:0.13, T:0.35
Consensus pattern (340 bp):
ATAAGGCTTTCAAAGGCATCAATGACTATAAATGGACTTTTCTTACAATGGATGGCTTTTGCTTC
ACATTTTCTGAAGCAGACATTCAAGTATAAAATATTGAAACAACAATATAAAAAAATTCAACTTA
AAATCAATTATGAGATTATAAAACCATTTAAAGCAAGTAATAAGGCTTTCAAAGGCATGGGTGAC
TATAAATGGACTTTTCTTACCAATTAATGGCTTTTGCTTCAAGTTTTTCAAGGTAGACATTCAAT
TATAATATATTTTAACAAAAAATATAAAAAAATTTAACTTAAAATCAATTATGACGTTATAAAAC
TATTTAAAGCGAGTA
Found at i:1181154 original size:514 final size:511
Alignment explanation
Indices: 1180154--1183374 Score: 2437
Period size: 514 Copynumber: 6.3 Consensus size: 511
1180144 TTATCAAGTG
* * * * * *
1180154 ATAAGGCTTTCAAAGACTTGAGTGACTATAAATGGACTTTTCTTACGAATGGATGGCTTTTGCCT
1 ATAAGG-TTTCAAAGGCATGAGTGACTATAAATGGACTTTTCTTACTAATAGATGACTTTTGCTT
* * *
1180219 CATGTTTCTTGAA-GCAGACATTCAAGTATAATATATTTTGAAC-AACAATGTAAGAAAATTCAA
65 CATGTTT-TTCAAGGCAGACATTCAAGTATAATCTATTTTGAACTAAAAATGTAA-AAAATTCAA
* * * * *
1180282 CTTAAAATCAATTATGAGATTTTAAAACCATTTAAAACTAGTAAAAAGGCTTTCGAA-GATAT-A
128 CTTAAAATCAATTATAAGATTATAAAACTATTTAAAGCTAGTAAAAAGGCTTTCGAAGGCT-TGA
* ** * ** *
1180345 GGTGACTATAAATGGACTTTTCTTCCCAATTAATTG-CTTTTGCTTTACATTT-CTCAAGGTAGA
192 -GTGACTATAAATGGACTTTTCTTACCAATGGA-TGACTTTTGCTTCATGTTTCCT-AAAGTAGA
* * * * * *
1180408 CAATAAATTATAATATATTTTAAT-AAAACAAATATAAACATTTAACTTAAAATTAATTATGATG
254 CATTCAATTATAATATATTTTAATCAAAA-ATATAAAAAAATTTAACTTAAAATCAATTATGA-G
* * * * * * *
1180472 -TTATAAAACTATTTAAACCAAGTAATAATGCTTTAAAAGGCATCAATGACTATAAGTGGACTTT
317 ATTATAAAACCATTTAAAGCAAGTAATAAGGCTTTCAAAGGCATGAGTGACTATAAATGGACTTT
* * * * * * * **
1180536 TCTCTACGATGGATGGCTTTTACTTCACATTTTCTAATGTAGACATTCAAGTATAAAACCATTGA
382 TCT-TCCAATGGATGGCTTTTGCTTCACATTTTCTAAGGTAGACATTCAAATAT-AATCTATTTT
* * * * **
1180601 AAGCAACAATAT-AAAAAAATTTAACGTAAAATCAATTATGAGCTTATAAAACCATTGAAAGCAA
445 AA-CAAAAATATAAAAAAAATTTAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGTGA
1180665 GTA
509 GTA
* * * * * * *
1180668 ATAAGGTATTCGAAGGCATGGGTGACTATAAATAGACTTTTCTTACAAATTAG-TAATTTTTTCT
1 ATAAGGT-TTCAAAGGCATGAGTGACTATAAATGGACTTTTCTTACTAA-TAGATGACTTTTGCT
* * * * * * *
1180732 TCAAGTTTTTCAAGGTAGACATTCAAATATAATCT-GTTTGAACAAAAAATATAAAATAATTTAA
64 TCATGTTTTTCAAGGCAGACATTCAAGTATAATCTATTTTGAACTAAAAATGTAAAA-AATTCAA
* ** *
1180796 CTTAAAATCAATTATAAGATTATAAAACCATTTAAATTTAGTAAAAAGGCTTGCGAAGGCTTGAG
128 CTTAAAATCAATTATAAGATTATAAAACTATTTAAAGCTAGTAAAAAGGCTTTCGAAGGCTTGAG
* * * * * * *
1180861 TGACTATATATAGACTTTTCCTATCAATGGATGACTTTTACTTCATGTTTCATAAAGCAGACATT
193 TGACTATAAATGGACTTTTCTTACCAATGGATGACTTTTGCTTCATGTTTCCTAAAGTAGACATT
* * * *
1180926 CAAGTATAATATATTTTAATCAAAAATGTAAAAAAATTTAACTTTAAATTAATTATGAGATTATA
258 CAATTATAATATATTTTAATCAAAAATATAAAAAAATTTAACTTAAAATCAATTATGAGATTATA
* * ** * * **
1180991 AAACCGTTTAAAGCAAGTAATAAAGCTTTTGAAGGCGTGGGTGACTATAAATAAACTTTTCTTGC
323 AAACCATTTAAAGCAAGTAATAAGGCTTTCAAAGGCATGAGTGACTATAAATGGACTTTTCTT-C
* * * * * *
1181056 CAATGAATGGGTTTTTCTTCACATTTTCTAAGGTAGAAATTCAAATATGATCTGTTTTAACTAAA
387 CAATGGATGGCTTTTGCTTCACATTTTCTAAGGTAGACATTCAAATATAATCTATTTTAAC-AAA
* * * * * *
1181121 AATGTAAAAAAAATTCAACTTAAAATGAATTATGAGATTATAAAACTATTTATAGTGAGTG
451 AATATAAAAAAAATTTAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGTGAGTA
* * * * *
1181182 ATAAGGCTTTCAAAGACTTAAGTGACTATAAATGGACTTTTCTTACTAATGGATGGCTTTTGCTT
1 ATAAGG-TTTCAAAGGCATGAGTGACTATAAATGGACTTTTCTTACTAATAGATGACTTTTGCTT
* * *
1181247 CACGTTTCTTGAA-GCAGACATTCAAGTATAATATATTTTGAA-TAAAAATGTAAGAAAATTCAA
65 CATGTTT-TTCAAGGCAGACATTCAAGTATAATCTATTTTGAACTAAAAATGTAA-AAAATTCAA
* * * * * *
1181310 CTTAAAATCAATTATGAGATTATAAAACTATTTAACA-CTAATACAAAGGCTTTCAAAGGCATGG
128 CTTAAAATCAATTATAAGATTATAAAACTATTTAA-AGCTAGTAAAAAGGCTTTCGAAGGCTTGA
* * * * * *
1181374 GTGACTATAAATGGACTTTTCTTACCAATGAATGGCTTTTGCTTCATGTGTCCTGAGGTAAACAT
192 GTGACTATAAATGGACTTTTCTTACCAATGGATGACTTTTGCTTCATGTTTCCTAAAGTAGACAT
**
1181439 TCAATTATAATATATTTTAATCAAAAATATAAAGAAAAACTAACTTAAAATCAATTATG-GCATT
257 TCAATTATAATATATTTTAATCAAAAATATAAA-AAAATTTAACTTAAAATCAATTATGAG-ATT
* * * * * *
1181503 AT-AAACCTATTTAAAGCGAGTAATAATGCTTTCGAAGACATTAGTGACTACAAATGGACTTTTC
320 ATAAAACC-ATTTAAAGCAAGTAATAAGGCTTTCAAAGGCATGAGTGACTATAAATGGACTTTTC
* * * * *
1181567 TCTCCAATGGATGGCTTTTGCTTCACGTTTCCTAAAGTAGACATTCAATTATAATCTATTTCAAC
384 T-TCCAATGGATGGCTTTTGCTTCACATTTTCTAAGGTAGACATTCAAATATAATCTATTTTAA-
* * * *
1181632 CAACAATAT-TAAAAAATTTAACTTAAAATCAATTATGAGATTATAATATCATTTAAAGTGAGTA
447 CAAAAATATAAAAAAAATTTAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGTGAGTA
* * * *
1181696 ATAAGGCTTCAAAGGC-TAGGGTGAGTATAAATGGACTTTTCTTACTAATAGATGACTTTTTCTT
1 ATAAGGTTTCAAAGGCAT-GAGTGACTATAAATGGACTTTTCTTACTAATAGATGACTTTTGCTT
* * * * *
1181760 CATGTTTCTCAAGGCAAACAATCAATTATAATCT-TTTTTAACTAAAAATGTAAAAAAATTCAAC
65 CATGTTTTTCAAGGCAGACATTCAAGTATAATCTATTTTGAACTAAAAATGT-AAAAAATTCAAC
* * ** *
1181824 TTAAAATCAATTATATGCTTATAAAACTATTTAAAGAGAGTAATAAGGCTTTCGAAGGCTTGAGT
129 TTAAAATCAATTATAAGATTATAAAACTATTTAAAGCTAGTAAAAAGGCTTTCGAAGGCTTGAGT
* * ** * * *
1181889 GA-TAATAAATGGACTTTTCTTGCCAATGGATGGCTTTTGCTTCACATTTCCTGAAGCATACATT
194 GACT-ATAAATGGACTTTTCTTACCAATGGATGACTTTTGCTTCATGTTTCCTAAAGTAGACATT
* * * ** * *
1181953 GAATTGTAATATA-TTTAATGAAAACCATAAACAAATTCAACTTAAAATCAATTATGAGATTATA
258 CAATTATAATATATTTTAATCAAAAATATAAAAAAATTTAACTTAAAATCAATTATGAGATTATA
* * * * * * *
1182017 AAACCATTTTAAGCTAGCAGTAAGGCTTTCAAGGGCGTG-GATGACTATAAATGAACTTTTCTTG
323 AAACCATTTAAAGCAAGTAATAAGGCTTTCAAAGGCATGAG-TGACTATAAATGGACTTTTCTT-
* * * * * * * * * * * * *
1182081 TCAATGAATGACTTTCGCTTTACATTTCCTGAA-GCAGACATTCCATTAAAATATATTTGAATAA
386 CCAATGGATGGCTTTTGCTTCACATTTTCT-AAGGTAGACATTCAAATATAATCTATTTTAACAA
* * *
1182145 AAACTAT-AAAAAAATTTAACTTAAAATCAATTATGACATTATGAAACCATTTAAATTGAGTA
450 AAA-TATAAAAAAAATTTAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGTGAGTA
* * * * * * * * * * *
1182207 GTAATGCTTTCAAATGTATCAATAACTATATATGCACTTTTCTCT-CCAATGGATGGA-TTTTGC
1 ATAA-GGTTTCAAAGGCATGAGTGACTATAAATGGACTTTTCT-TACTAATAGAT-GACTTTTGC
* *** * * * * * *
1182270 TTCATG-TTTCCTAAATTAGACATTCAATTGTAATCTAATTT-AACCAACAATATAAAAAAATTC
63 TTCATGTTTTTC-AAGGCAGACATTCAAGTATAATCTATTTTGAACTAAAAATGT-AAAAAATTC
* * * * * *
1182333 AACTTAAAATCAATTATAAGATTATAAAATTATTCAAAGCAAGTAATAAGGCTTTCAAAGGCATG
126 AACTTAAAATCAATTATAAGATTATAAAACTATTTAAAGCTAGTAAAAAGGCTTTCGAAGGCTTG
* **
1182398 GGTCG-CTATAAATGGACTTTTCTTGTCAATGGAT-AGCTTTTGCTTCATGTTTCCTAAAGTAGA
191 AGT-GACTATAAATGGACTTTTCTTACCAATGGATGA-CTTTTGCTTCATGTTTCCTAAAGTAGA
* ** ** * *
1182461 CATTCAATTATAATATATTGTAAGAAAAAAGGTAAAAATATTTAACTTAAAATCAATTATGAGGT
254 CATTCAATTATAATATATTTTAATCAAAAATATAAAAAAATTTAACTTAAAATCAATTATGAGAT
* * * *
1182526 TATAAAACCATTTAATGGC-AGTAATACGGCTTTCAAAGGCATAAGTGACTATAAATAGACTTTT
319 TATAAAACCATTTAA-AGCAAGTAATAAGGCTTTCAAAGGCATGAGTGACTATAAATGGACTTTT
* *
1182590 CTTACCAATGGATGGTTTTTTCTT--CATGTTTCTCAAGGTAGACATTCAAATATAAT-TAATTT
383 CTT-CCAATGGATGGCTTTTGCTTCACAT-TTTCT-AAGGTAGACATTCAAATATAATCT-ATTT
* ********** * *
1182652 TAACAAAAAAATATAAAAAAATTTAACTTAANNNNNNNNNNGAGATTATAAAACCATTTCAAGCG
444 TAACAAAAATATA-AAAAAAATTTAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGTG
1182717 AGTA
508 AGTA
* * ** * **
1182721 ATAAGGCCTTCGAAGG-ATTGAGTGACTATAAATAAACTTTTCTTA-TCAATGGATGGGTTTTGC
1 ATAAGG-TTTCAAAGGCA-TGAGTGACTATAAATGGACTTTTCTTACT-AATAGATGACTTTTGC
* * * * * *
1182784 TTCATG-TTTTCAAAAGCA-ACCATTCAATTTTAATATATTTT-AACCAAAAATATAAAAACATT
63 TTCATGTTTTTC-AAGGCAGA-CATTCAAGTATAATCTATTTTGAACTAAAAATGTAAAAA-ATT
* * * * ** ** *
1182846 TAA-TTAAAAATTAATTATGAGATTATAAAA-TCATTCAAAGGAAACAACAAGGCTTTCGAAGGC
125 CAACTT-AAAATCAATTATAAGATTATAAAACT-ATTTAAAGCTAGTAAAAAGGCTTTCGAAGGC
* * * * * * *
1182909 ATG-G-G--------T-GA-TTTT-TATAGCCAATGAATCACTTTT-TTTAATGTATCCTAAGGT
188 TTGAGTGACTATAAATGGACTTTTCT-TA-CCAATGGATGACTTTTGCTTCATGTTTCCTAAAGT
* * * * * * * *
1182960 AAACATTCAAATATTATCTATTTGAA-CTAAAAATGTAAAAAAATGTAACTTAAAATCAGTTATG
251 AGACATTCAATTATAATATATTTTAATC-AAAAATATAAAAAAATTTAACTTAAAATCAATTATG
* * ** ** * *
1183024 AGATTATATAACCACTTAAAGTGAGTAATAATACTTTCGAAA-GCATGTGTGACTATAAATGAAC
315 AGATTATAAAACCATTTAAAGCAAGTAATAAGGCTTTC-AAAGGCATGAGTGACTATAAATGGAC
* ** * * * * * * * * * *
1183088 TTCTCTTACCAATAAAAGACTTTT-CTTCACGTTTCCTGAGATTGACAATCAAATATTATCTGTT
379 TTTTCTT-CCAATGGATGGCTTTTGCTTCACATTTTCTAAGGTAGACATTCAAATATAATCTATT
* * **********
1183152 TTAATCAAAAATAT--AAAAAATTTCTATTTAAAATCAATTATGAGATTACT-NNNNNNNNNNAA
443 TTAA-CAAAAATATAAAAAAAATTT-AACTTAAAATCAATTATGAGATTA-TAAAACCATTTAAA
*
1183214 GCGAGTA
505 GTGAGTA
* * * * * * ** *
1183221 ATAAGGCTTTCGAAGGCTTGAGTGAGTATAAATAGACTTTTCTTACCAATGGATGGGTTTTACTT
1 ATAAGG-TTTCAAAGGCATGAGTGACTATAAATGGACTTTTCTTACTAATAGATGACTTTTGCTT
* ** * * * * * *
1183286 CATG-TTTCCTAAAACAGACATTCAATTATAATTTAATTT-AACAAAAAATGAAAAAAAATCAAC
65 CATGTTTTTC-AAGGCAGACATTCAAGTATAATCTATTTTGAACTAAAAATGTAAAAAATTCAAC
*
1183349 ATAAAATCAATTATAAGATTATAAAA
129 TTAAAATCAATTATAAGATTATAAAA
1183375 NNNNNNNNNN
Statistics
Matches: 2172, Mismatches: 456, Indels: 173
0.78 0.16 0.06
Matches are distributed among these distances:
499 35 0.02
500 124 0.06
501 30 0.01
502 148 0.07
503 19 0.01
504 2 0.00
510 6 0.00
511 178 0.08
512 247 0.11
513 391 0.18
514 838 0.39
515 152 0.07
516 2 0.00
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.34
Consensus pattern (511 bp):
ATAAGGTTTCAAAGGCATGAGTGACTATAAATGGACTTTTCTTACTAATAGATGACTTTTGCTTC
ATGTTTTTCAAGGCAGACATTCAAGTATAATCTATTTTGAACTAAAAATGTAAAAAATTCAACTT
AAAATCAATTATAAGATTATAAAACTATTTAAAGCTAGTAAAAAGGCTTTCGAAGGCTTGAGTGA
CTATAAATGGACTTTTCTTACCAATGGATGACTTTTGCTTCATGTTTCCTAAAGTAGACATTCAA
TTATAATATATTTTAATCAAAAATATAAAAAAATTTAACTTAAAATCAATTATGAGATTATAAAA
CCATTTAAAGCAAGTAATAAGGCTTTCAAAGGCATGAGTGACTATAAATGGACTTTTCTTCCAAT
GGATGGCTTTTGCTTCACATTTTCTAAGGTAGACATTCAAATATAATCTATTTTAACAAAAATAT
AAAAAAAATTTAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGTGAGTA
Found at i:1182789 original size:172 final size:172
Alignment explanation
Indices: 1180154--1182880 Score: 2029
Period size: 171 Copynumber: 15.9 Consensus size: 172
1180144 TTATCAAGTG
* * * *
1180154 ATAAGGCTTTCAAAGACTTGAGTGACTATAAATGGACTTTTCTTA-CGAATGGATGGCTTTTGCC
1 ATAAGGCTTTCAAAGGCATGAGTGACTATAAATAGACTTTTCTTATC-AATGGATGGCTTTTGCT
** * * * * * *
1180218 TCATGTTTCT-TGAAGCAGACATTCAAGTATAATATATTTTGAAC-AACAATGTAAGAAAATTCA
65 TCATGTTTCTCAAAAGTAGACATTCAATTATAATATATTTT-AACAAAAAATATAAAAAAATTTA
* * * *
1180281 ACTTAAAATCAATTATGAGATTTTAAAACCATTTAAAACTAGTA
129 ACTTAAAATCAATTATGAGATTATAAAACCATTTCAAGCGAGTA
* * ** * ** ** *
1180325 AAAAGGCTTTCGAAGATAT-AGGTGACTATAAATGGACTTTTCTTCCCAATTAATTGCTTTTGCT
1 ATAAGGCTTTCAAAGGCATGA-GTGACTATAAATAGACTTTTCTTATCAATGGATGGCTTTTGCT
* ** * * * * * *
1180389 TTACATTTCTC-AAGGTAGACAATAAATTATAATATATTTTAATAAAACAA-ATATAAACATTTA
65 TCATGTTTCTCAAAAGTAGACATTCAATTATAATATATTTTAACAAAA-AATATAAAAAAATTTA
* * * * *
1180452 ACTTAAAATTAATTATGATG-TTATAAAACTATTTAAACCAAGTA
129 ACTTAAAATCAATTATGA-GATTATAAAACCATTTCAAGCGAGTA
* * * * * * * *
1180496 ATAATGCTTTAAAAGGCATCAATGACTATAAGTGGACTTTTCTCTA-CGATGGATGGCTTTTACT
1 ATAAGGCTTTCAAAGGCATGAGTGACTATAAATAGACTTTTCT-TATCAATGGATGGCTTTTGCT
** * * * * * ** *
1180560 TCACATTT-TCTAATGTAGACATTCAAGTATAAAACCATTGAAAGC-AACAATATAAAAAAATTT
65 TCATGTTTCTCAAAAGTAGACATTCAATTATAATA-TATTTTAA-CAAAAAATATAAAAAAATTT
* * ** *
1180623 AACGTAAAATCAATTATGAGCTTATAAAACCATTGAAAGCAAGTA
128 AACTTAAAATCAATTATGAGATTATAAAACCATTTCAAGCGAGTA
* * * *** *
1180668 ATAAGG-TATTCGAAGGCATGGGTGACTATAAATAGACTTTTCTTA-CAAAT-TAGTAATTTTTT
1 ATAAGGCT-TTCAAAGGCATGAGTGACTATAAATAGACTTTTCTTATC-AATGGA-TGGCTTTTG
* * * * * * * *
1180730 CTTCAAGTTTTTC-AAGGTAGACATTCAAATATAATCTGTTTGAACAAAAAATATAAAATAATTT
63 CTTCATGTTTCTCAAAAGTAGACATTCAATTATAATATATTTTAACAAAAAATATAAAAAAATTT
* * ***
1180794 AACTTAAAATCAATTATAAGATTATAAAACCATTTAAATTTAGTA
128 AACTTAAAATCAATTATGAGATTATAAAACCATTTCAAGCGAGTA
* * * * * * * *
1180839 AAAAGGCTTGCGAAGGCTTGAGTGACTATATATAGACTTTTCCTATCAATGGATGACTTTTACTT
1 ATAAGGCTTTCAAAGGCATGAGTGACTATAAATAGACTTTTCTTATCAATGGATGGCTTTTGCTT
* * *
1180904 CATG-TT-TCATAAAGCAGACATTCAAGTATAATATATTTTAATC-AAAAATGTAAAAAAATTTA
66 CATGTTTCTCA-AAAGTAGACATTCAATTATAATATATTTTAA-CAAAAAATATAAAAAAATTTA
* * * * *
1180966 ACTTTAAATTAATTATGAGATTATAAAACCGTTTAAAGCAAGTA
129 ACTTAAAATCAATTATGAGATTATAAAACCATTTCAAGCGAGTA
* ** * * * ** * * *
1181010 ATAAAGCTTTTGAAGGCGTGGGTGACTATAAATAAACTTTTCTTGCCAATGAATGGGTTTTTCTT
1 ATAAGGCTTTCAAAGGCATGAGTGACTATAAATAGACTTTTCTTATCAATGGATGGCTTTTGCTT
** * * * * * * * * * *
1181075 CACATTT-TCTAAGGTAGAAATTCAAATATGATCTGTTTTAACTAAAAATGTAAAAAAAATTCAA
66 CATGTTTCTCAAAAGTAGACATTCAATTATAATATATTTTAACAAAAAATAT-AAAAAAATTTAA
* * * *
1181139 CTTAAAATGAATTATGAGATTATAAAACTATTT-ATAGTGAGTG
130 CTTAAAATCAATTATGAGATTATAAAACCATTTCA-AGCGAGTA
* * * *
1181182 ATAAGGCTTTCAAAGACTTAAGTGACTATAAATGGACTTTTCTTA-CTAATGGATGGCTTTTGCT
1 ATAAGGCTTTCAAAGGCATGAGTGACTATAAATAGACTTTTCTTATC-AATGGATGGCTTTTGCT
* ** * * * * * *
1181246 TCACGTTTCT-TGAAGCAGACATTCAAGTATAATATATTTTGAA-TAAAAATGTAAGAAAATTCA
65 TCATGTTTCTCAAAAGTAGACATTCAATTATAATATATTTT-AACAAAAAATATAAAAAAATTTA
* *
1181309 ACTTAAAATCAATTATGAGATTATAAAACTATTT-AA-C-ACTA
129 ACTTAAAATCAATTATGAGATTATAAAACCATTTCAAGCGAGTA
* * * *
1181350 ATACAAAGGCTTTCAAAGGCATGGGTGACTATAAATGGACTTTTCTTACCAATGAATGGCTTTTG
1 AT---AAGGCTTTCAAAGGCATGAGTGACTATAAATAGACTTTTCTTATCAATGGATGGCTTTTG
* ** * * *
1181415 CTTCATGTGTC-CTGAGGTAAACATTCAATTATAATATATTTTAATC-AAAAATATAAAGAAAAA
63 CTTCATGTTTCTCAAAAGTAGACATTCAATTATAATATATTTTAA-CAAAAAATATAAA-AAAAT
* *
1181478 CTAACTTAAAATCAATTATG-GCATTAT-AAACCTATTTAAAGCGAGTA
126 TTAACTTAAAATCAATTATGAG-ATTATAAAACC-ATTTCAAGCGAGTA
* * * * * * *
1181525 ATAATGCTTTCGAAGACATTAGTGACTACAAATGGACTTTTCTCT-CCAATGGATGGCTTTTGCT
1 ATAAGGCTTTCAAAGGCATGAGTGACTATAAATAGACTTTTCT-TATCAATGGATGGCTTTTGCT
* * * * * * *
1181589 TCACGTTTC-CTAAAGTAGACATTCAATTATAATCTATTTCAACCAACAATATTAAAAAATTTAA
65 TCATGTTTCTCAAAAGTAGACATTCAATTATAATATATTTTAACAAAAAATATAAAAAAATTTAA
* * * *
1181653 CTTAAAATCAATTATGAGATTATAATATCATTTAAAGTGAGTA
130 CTTAAAATCAATTATGAGATTATAAAACCATTTCAAGCGAGTA
* * * * * *
1181696 ATAAGGC-TTCAAAGGC-TAGGGTGAGTATAAATGGACTTTTCTTA-CTAATAGATGACTTTTTC
1 ATAAGGCTTTCAAAGGCAT-GAGTGACTATAAATAGACTTTTCTTATC-AATGGATGGCTTTTGC
* * * * * * * * *
1181758 TTCATGTTTCTC-AAGGCAAACAATCAATTATAATCTTTTTTAACTAAAAATGTAAAAAAATTCA
64 TTCATGTTTCTCAAAAGTAGACATTCAATTATAATATATTTTAACAAAAAATATAAAAAAATTTA
* * * *
1181822 ACTTAAAATCAATTAT-ATGCTTATAAAACTATTTAAAGAGAGTA
129 ACTTAAAATCAATTATGA-GATTATAAAACCATTTCAAGCGAGTA
* * * **
1181866 ATAAGGCTTTCGAAGGCTTGAGTGA-TAATAAATGGACTTTTCTTGCCAATGGATGGCTTTTGCT
1 ATAAGGCTTTCAAAGGCATGAGTGACT-ATAAATAGACTTTTCTTATCAATGGATGGCTTTTGCT
** ** * * * * ** ** * *
1181930 TCACATTTC-CTGAAGCATACATTGAATTGTAATATA-TTTAATGAAAACCATAAACAAATTCAA
65 TCATGTTTCTCAAAAGTAGACATTCAATTATAATATATTTTAACAAAAAATATAAAAAAATTTAA
* * *
1181993 CTTAAAATCAATTATGAGATTATAAAACCATTTTAAGCTAGCA
130 CTTAAAATCAATTATGAGATTATAAAACCATTTCAAGCGAGTA
* * * * * * *
1182036 GTAAGGCTTTCAAGGGCGTG-GATGACTATAAAT-GAACTTTTCTTGTCAATGAATGACTTTCGC
1 ATAAGGCTTTCAAAGGCATGAG-TGACTATAAATAG-ACTTTTCTTATCAATGGATGGCTTTTGC
* ** ** * * * * * *
1182099 TTTACATTTC-CTGAAGCAGACATTCCATTAAAATATATTTGAATAAAAACTATAAAAAAATTTA
64 TTCATGTTTCTCAAAAGTAGACATTCAATTATAATATATTTTAACAAAAAATATAAAAAAATTTA
* * * **
1182163 ACTTAAAATCAATTATGACATTATGAAACCATTTAAATTGAGTA
129 ACTTAAAATCAATTATGAGATTATAAAACCATTTCAAGCGAGTA
* * * * * * * * * *
1182207 GTAATGCTTTCAAATGTATCAATAACTATATAT-GCACTTTTCTCT-CCAATGGATGGATTTTGC
1 ATAAGGCTTTCAAAGGCATGAGTGACTATAAATAG-ACTTTTCT-TATCAATGGATGGCTTTTGC
* * * * * * * *
1182270 TTCATGTTTC-CTAAATTAGACATTCAATTGTAATCTAATTTAACCAACAATATAAAAAAATTCA
64 TTCATGTTTCTCAAAAGTAGACATTCAATTATAATATATTTTAACAAAAAATATAAAAAAATTTA
* ** *
1182334 ACTTAAAATCAATTATAAGATTATAAAATTA-TTCAAAGCAAGTA
129 ACTTAAAATCAATTATGAGATTATAAAACCATTTC-AAGCGAGTA
* * * *
1182378 ATAAGGCTTTCAAAGGCATGGGTCG-CTATAAATGGACTTTTCTTGTCAATGGATAGCTTTTGCT
1 ATAAGGCTTTCAAAGGCATGAGT-GACTATAAATAGACTTTTCTTATCAATGGATGGCTTTTGCT
* * * ** *
1182442 TCATGTTTC-CTAAAGTAGACATTCAATTATAATATATTGTAAGAAAAAAGGTAAAAATATTTAA
65 TCATGTTTCTCAAAAGTAGACATTCAATTATAATATATTTTAACAAAAAATATAAAAAAATTTAA
*
1182506 CTTAAAATCAATTATGAGGTTATAAAACCATTT-AATG-GCAGTA
130 CTTAAAATCAATTATGAGATTATAAAACCATTTCAA-GCG-AGTA
* * * * *
1182549 ATACGGCTTTCAAAGGCATAAGTGACTATAAATAGACTTTTCTTACCAATGGATGGTTTTTTCTT
1 ATAAGGCTTTCAAAGGCATGAGTGACTATAAATAGACTTTTCTTATCAATGGATGGCTTTTGCTT
* *
1182614 CATGTTTCTC-AAGGTAGACATTCAAATATAAT-TAATTTTAACAAAAAAATATAAAAAAATTTA
66 CATGTTTCTCAAAAGTAGACATTCAATTATAATAT-ATTTTAAC-AAAAAATATAAAAAAATTTA
**********
1182677 ACTTAANNNNNNNNNNGAGATTATAAAACCATTTCAAGCGAGTA
129 ACTTAAAATCAATTATGAGATTATAAAACCATTTCAAGCGAGTA
* * * *
1182721 ATAAGGCCTTCGAAGG-ATTGAGTGACTATAAATAAACTTTTCTTATCAATGGATGGGTTTTGCT
1 ATAAGGCTTTCAAAGGCA-TGAGTGACTATAAATAGACTTTTCTTATCAATGGATGGCTTTTGCT
* * * *
1182785 TCATGTTT-TCAAAAGCA-ACCATTCAATTTTAATATATTTTAACCAAAAATATAAAAACATTTA
65 TCATGTTTCTCAAAAGTAGA-CATTCAATTATAATATATTTTAACAAAAAATATAAAAAAATTTA
* *
1182848 A-TTAAAAATTAATTATGAGATTATAAAATCATT
129 ACTT-AAAATCAATTATGAGATTATAAAACCATT
1182881 CAAAGGAAAC
Statistics
Matches: 2050, Mismatches: 423, Indels: 166
0.78 0.16 0.06
Matches are distributed among these distances:
168 4 0.00
169 8 0.00
170 293 0.14
171 1188 0.58
172 539 0.26
173 12 0.01
174 1 0.00
175 5 0.00
ACGTcount: A:0.39, C:0.13, G:0.13, T:0.35
Consensus pattern (172 bp):
ATAAGGCTTTCAAAGGCATGAGTGACTATAAATAGACTTTTCTTATCAATGGATGGCTTTTGCTT
CATGTTTCTCAAAAGTAGACATTCAATTATAATATATTTTAACAAAAAATATAAAAAAATTTAAC
TTAAAATCAATTATGAGATTATAAAACCATTTCAAGCGAGTA
Found at i:1183393 original size:170 final size:161
Alignment explanation
Indices: 1183217--1183546 Score: 324
Period size: 170 Copynumber: 2.0 Consensus size: 161
1183207 NNNNNAAGCG
* * * * *
1183217 AGTAATAAGGCTTTCGAAGGCTTGAGTGAGTATAAATAGACTTTTCTTACCAATGGATGGGTTT-
1 AGTAATAAGGCTTTCGAAGGCATGAGAGAATATAAATAGACTTTTCTTACCAAAGAATGGGTTTG
* * * * ** *
1183281 TACTTCATGTTTCCTAAAACAGACATTCAATTATAATTTAATTTAA-CAAAAA-ATGAAAAAAAA
66 T-CTTCATGTTTCCCAAAACAAACAATCAAATATAAACTAACTTAACCAAAAATAT-AAAAAAAA
1183344 TCAACATAAAATCAATTATAAGATTATAAAANNNNNNNNNNCA
129 TCAACATAAAATCAATTATAAGATTATAAAA----------CA
* * * *
1183387 AGTAATAAGGCTTTTGAAGGCATGGGAGAATATATATAGACTTTTCTTAGCAAAGAATGGGTTTG
1 AGTAATAAGGCTTTCGAAGGCATGAGAGAATATAAATAGACTTTTCTTACCAAAGAATGGGTTTG
* ** * *
1183452 TCTTCATGTTTCCCAAGACAAACAATCAAATATAAACTGCCTTAACCAAAAATATTAAAAAATTC
66 TCTTCATGTTTCCCAAAACAAACAATCAAATATAAACTAACTTAACCAAAAATATAAAAAAAATC
* *
1183517 AACTTAAAATCAATTATGAGATTATAAAAC
131 AACATAAAATCAATTATAAGATTATAAAAC
1183547 NNNNNNNNNN
Statistics
Matches: 134, Mismatches: 23, Indels: 15
0.78 0.13 0.09
Matches are distributed among these distances:
161 1 0.01
170 89 0.66
171 42 0.31
172 2 0.01
ACGTcount: A:0.42, C:0.12, G:0.13, T:0.30
Consensus pattern (161 bp):
AGTAATAAGGCTTTCGAAGGCATGAGAGAATATAAATAGACTTTTCTTACCAAAGAATGGGTTTG
TCTTCATGTTTCCCAAAACAAACAATCAAATATAAACTAACTTAACCAAAAATATAAAAAAAATC
AACATAAAATCAATTATAAGATTATAAAACA
Found at i:1187688 original size:25 final size:25
Alignment explanation
Indices: 1187631--1187690 Score: 77
Period size: 25 Copynumber: 2.4 Consensus size: 25
1187621 ACGTGTATAT
*
1187631 AGATGTTCAAGAAAGATAACATTTA
1 AGATGTTCAAGAAAGATAACATTAA
* *
1187656 TGAAGTTCAAGAAAGATAAGCA-TAA
1 AGATGTTCAAGAAAGATAA-CATTAA
1187681 AGATGTTCAA
1 AGATGTTCAA
1187691 TAAGCACATA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
25 27 0.93
26 2 0.07
ACGTcount: A:0.48, C:0.08, G:0.18, T:0.25
Consensus pattern (25 bp):
AGATGTTCAAGAAAGATAACATTAA
Found at i:1200121 original size:32 final size:32
Alignment explanation
Indices: 1200085--1200148 Score: 83
Period size: 32 Copynumber: 2.0 Consensus size: 32
1200075 CAAGCAACTC
* *
1200085 CATAAAGACAACAATTAGTAAGTAGCATGCGT
1 CATAAAGACAACAATTAGCAAGCAGCATGCGT
* * *
1200117 CATAAGGATAACAATTAGCAGGCAGCATGCGT
1 CATAAAGACAACAATTAGCAAGCAGCATGCGT
1200149 AATGCTAGCT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.41, C:0.17, G:0.22, T:0.20
Consensus pattern (32 bp):
CATAAAGACAACAATTAGCAAGCAGCATGCGT
Found at i:1202844 original size:52 final size:51
Alignment explanation
Indices: 1202760--1202858 Score: 126
Period size: 52 Copynumber: 1.9 Consensus size: 51
1202750 GATTAAGTTA
* *
1202760 GACTTAATCAATTAAAAACTTATAAGCTTTTAGACTTAATCGATTAATTATG
1 GACTTAATCAATTAAAAACATATAAGCGTTTAGACTT-ATCGATTAATTATG
* * * **
1202812 GACTTAATCAATTGAGAACATATATGCGTTTAGTGTTATCGATTAAT
1 GACTTAATCAATTAAAAACATATAAGCGTTTAGACTTATCGATTAAT
1202859 GTAATCATTA
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
51 10 0.25
52 30 0.75
ACGTcount: A:0.37, C:0.11, G:0.13, T:0.38
Consensus pattern (51 bp):
GACTTAATCAATTAAAAACATATAAGCGTTTAGACTTATCGATTAATTATG
Found at i:1206504 original size:24 final size:24
Alignment explanation
Indices: 1206477--1206550 Score: 73
Period size: 24 Copynumber: 3.2 Consensus size: 24
1206467 TCAATCGTTC
1206477 AACTTCCATACATAAATCAAGGCA
1 AACTTCCATACATAAATCAAGGCA
* * * **
1206501 AACTTCC-CACTTTCAATC-ATTC-
1 AACTTCCATAC-ATAAATCAAGGCA
1206523 AACTTCCATACATAAATCAAGGCA
1 AACTTCCATACATAAATCAAGGCA
1206547 AACT
1 AACT
1206551 ATACTTACAA
Statistics
Matches: 36, Mismatches: 10, Indels: 8
0.67 0.19 0.15
Matches are distributed among these distances:
22 12 0.33
23 8 0.22
24 16 0.44
ACGTcount: A:0.41, C:0.28, G:0.05, T:0.26
Consensus pattern (24 bp):
AACTTCCATACATAAATCAAGGCA
Found at i:1206511 original size:46 final size:46
Alignment explanation
Indices: 1206459--1206550 Score: 175
Period size: 46 Copynumber: 2.0 Consensus size: 46
1206449 GAACCAAATA
*
1206459 TCCCACTTTCAATCGTTCAACTTCCATACATAAATCAAGGCAAACT
1 TCCCACTTTCAATCATTCAACTTCCATACATAAATCAAGGCAAACT
1206505 TCCCACTTTCAATCATTCAACTTCCATACATAAATCAAGGCAAACT
1 TCCCACTTTCAATCATTCAACTTCCATACATAAATCAAGGCAAACT
1206551 ATACTTACAA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.36, C:0.30, G:0.05, T:0.28
Consensus pattern (46 bp):
TCCCACTTTCAATCATTCAACTTCCATACATAAATCAAGGCAAACT
Found at i:1206540 original size:22 final size:22
Alignment explanation
Indices: 1206469--1206541 Score: 58
Period size: 22 Copynumber: 3.2 Consensus size: 22
1206459 TCCCACTTTC
*
1206469 AATCGTTCAACTTCCATACATA
1 AATCATTCAACTTCCATACATA
** * * *
1206491 AATCAAGGCAAACTTCC-CACTTTC
1 AATC-ATTC-AACTTCCATAC-ATA
1206515 AATCATTCAACTTCCATACATA
1 AATCATTCAACTTCCATACATA
1206537 AATCA
1 AATCA
1206542 AGGCAAACTA
Statistics
Matches: 36, Mismatches: 11, Indels: 8
0.65 0.20 0.15
Matches are distributed among these distances:
22 17 0.47
23 7 0.19
24 12 0.33
ACGTcount: A:0.38, C:0.29, G:0.04, T:0.29
Consensus pattern (22 bp):
AATCATTCAACTTCCATACATA
Found at i:1212072 original size:7 final size:7
Alignment explanation
Indices: 1212062--1212118 Score: 60
Period size: 7 Copynumber: 7.7 Consensus size: 7
1212052 TCCTTTCTCT
1212062 TTTCTTC
1 TTTCTTC
*
1212069 TTTCTCC
1 TTTCTTC
1212076 TTTCTTCC
1 TTTCTT-C
1212084 TTTCTTC
1 TTTCTTC
1212091 TTTCTTC
1 TTTCTTC
* *
1212098 CTTCCTC
1 TTTCTTC
1212105 TTTTCTTCC
1 -TTTCTT-C
1212114 TTTCT
1 TTTCT
1212119 CCTTCCTTCC
Statistics
Matches: 41, Mismatches: 6, Indels: 5
0.79 0.12 0.10
Matches are distributed among these distances:
7 24 0.59
8 16 0.39
9 1 0.02
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (7 bp):
TTTCTTC
Found at i:1212121 original size:22 final size:21
Alignment explanation
Indices: 1212052--1212125 Score: 94
Period size: 22 Copynumber: 3.4 Consensus size: 21
1212042 AACCAAACCT
*
1212052 TCCTTTCTCTTTTCTTCTTTC
1 TCCTTCCTCTTTTCTTCTTTC
* *
1212073 TCCTTTCTTCCTTTCTTCTTTC
1 TCC-TTCCTCTTTTCTTCTTTC
1212095 TTCCTTCCTCTTTTCTTCCTTTC
1 -TCCTTCCTCTTTTCTT-CTTTC
1212118 TCCTTCCT
1 TCCTTCCT
1212126 TCCTTCCTTT
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
21 3 0.07
22 34 0.76
23 8 0.18
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (21 bp):
TCCTTCCTCTTTTCTTCTTTC
Found at i:1212127 original size:15 final size:15
Alignment explanation
Indices: 1212050--1212130 Score: 110
Period size: 15 Copynumber: 5.5 Consensus size: 15
1212040 AAAACCAAAC
*
1212050 CTTCCTTTCTCTTTT
1 CTTCCTTTCTCCTTT
1212065 CTT-CTTTCTCCTTT
1 CTTCCTTTCTCCTTT
*
1212079 CTTCCTTTCTTCTTT
1 CTTCCTTTCTCCTTT
* *
1212094 CTTCCTTCCTCTTTT
1 CTTCCTTTCTCCTTT
*
1212109 CTTCCTTTCTCCTTC
1 CTTCCTTTCTCCTTT
1212124 CTTCCTT
1 CTTCCTT
1212131 CCTTTTTTTT
Statistics
Matches: 57, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
14 13 0.23
15 44 0.77
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (15 bp):
CTTCCTTTCTCCTTT
Found at i:1212189 original size:12 final size:10
Alignment explanation
Indices: 1212161--1212188 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
1212151 CAATTCTCTC
1212161 TTTTCTCTTT
1 TTTTCTCTTT
1212171 TTTTCTCTTT
1 TTTTCTCTTT
1212181 TTTTCTCT
1 TTTTCTCT
1212189 CAAGGTGCGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (10 bp):
TTTTCTCTTT
Found at i:1213688 original size:24 final size:24
Alignment explanation
Indices: 1213661--1213708 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
1213651 ATCTTTTAAG
*
1213661 GTATTTCTCTCAACTTCAGCTTTC
1 GTATTTCTCTCAACTTAAGCTTTC
1213685 GTATTTCTCTCAACTTAAGCTTTC
1 GTATTTCTCTCAACTTAAGCTTTC
1213709 TTAACCTATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.19, C:0.27, G:0.08, T:0.46
Consensus pattern (24 bp):
GTATTTCTCTCAACTTAAGCTTTC
Found at i:1223651 original size:68 final size:68
Alignment explanation
Indices: 1223542--1223735 Score: 239
Period size: 68 Copynumber: 2.9 Consensus size: 68
1223532 CATGCATGGT
* * * *
1223542 ATGATGAATACCATGAGATTGTGTATAAGATGTAAATTCCATATACCATATGAGATGATT-AGAT
1 ATGATGAATGCCATGAGATTATGTATATGATGTATATTCCATATACCATATGAGATGATTGAGA-
*
1223606 AGGC
65 AAGC
* * * *
1223610 ATGATGAATGCCCTGAGATTATGT-TCATGATGTGTATTCCATATACTACATGAGATGATTGAGA
1 ATGATGAATGCCATGAGATTATGTAT-ATGATGTATATTCCATATACCATATGAGATGATTGAGA
1223674 AAGC
65 AAGC
* * * *
1223678 ATGATGAATGCCATGAGTTTATGTATATGATGAATTTTCCATATACCTTATGAGATGA
1 ATGATGAATGCCATGAGATTATGTATATGATGTATATTCCATATACCATATGAGATGA
1223736 GTAAACATGT
Statistics
Matches: 106, Mismatches: 17, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
67 1 0.01
68 101 0.95
69 4 0.04
ACGTcount: A:0.35, C:0.11, G:0.21, T:0.34
Consensus pattern (68 bp):
ATGATGAATGCCATGAGATTATGTATATGATGTATATTCCATATACCATATGAGATGATTGAGAA
AGC
Found at i:1230037 original size:27 final size:27
Alignment explanation
Indices: 1229986--1230048 Score: 76
Period size: 27 Copynumber: 2.3 Consensus size: 27
1229976 AACCAAATCT
*
1229986 AAAGATGCTAAGGCATCTATCAATTTCC
1 AAAGATGTTAAGGCATCTATCAA-TTCC
*
1230014 AAA-ATGTTAAGGCATTTAAT-AATTCC
1 AAAGATGTTAAGGCATCT-ATCAATTCC
1230040 AAAGATGTT
1 AAAGATGTT
1230049 GGTGCACTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
26 7 0.23
27 19 0.61
28 5 0.16
ACGTcount: A:0.40, C:0.14, G:0.14, T:0.32
Consensus pattern (27 bp):
AAAGATGTTAAGGCATCTATCAATTCC
Found at i:1230068 original size:28 final size:28
Alignment explanation
Indices: 1229986--1230097 Score: 83
Period size: 28 Copynumber: 4.1 Consensus size: 28
1229976 AACCAAATCT
*
1229986 AAAGATGCTAAG-GCATCTATCA-ATTTCC
1 AAAGATGCT-AGTGCATCTA-AATATTTCC
* * *
1230014 AAA-ATGTTAAG-GCAT-TTAATAATTCC
1 AAAGATGCT-AGTGCATCTAAATATTTCC
* *
1230040 AAAGATGTTGGTGCA-CTTAAATATTTCC
1 AAAGATGCTAGTGCATC-TAAATATTTCC
*
1230068 AAAGCTGCTAGTGCATCTAAATATTTCC
1 AAAGATGCTAGTGCATCTAAATATTTCC
1230096 AA
1 AA
1230098 GAGTGCAGCA
Statistics
Matches: 68, Mismatches: 10, Indels: 12
0.76 0.11 0.13
Matches are distributed among these distances:
25 1 0.01
26 10 0.15
27 19 0.28
28 37 0.54
29 1 0.01
ACGTcount: A:0.37, C:0.17, G:0.14, T:0.32
Consensus pattern (28 bp):
AAAGATGCTAGTGCATCTAAATATTTCC
Found at i:1233142 original size:2 final size:2
Alignment explanation
Indices: 1233137--1233167 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1233127 GCTCTCTTAC
1233137 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1233168 TGGTTTCAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1241039 original size:189 final size:189
Alignment explanation
Indices: 1240734--1241312 Score: 648
Period size: 189 Copynumber: 3.1 Consensus size: 189
1240724 TGTAACAATC
* * **
1240734 ACATTTTTCAACATGGCATTGTAACAACTTTTATTTCAAAATAATGTGTCAAAATATTTT-TGAG
1 ACATCTTTCAACATGGCA-TGTAACAACCTTTATTTCAAAATGGTGTGTCAAAATATTTTGTGA-
* * * ** * *
1240798 CGTGGCATGTACTAATATATTTTTT-AACATGGCGTGTAAAAACAACATTTTTTCAATATGGCAT
64 CATGGCATGTACCAACAT-TTTTTTGAACATGATGT-TAACAACAACATTTTTTCAATATGGTAT
*
1240862 GGAACATCTTCTTTTCACCATGGTGTGTAGCTCAA-TTTTTTCTAACATGGTGTGTAACAGCA
127 GGAACATCTTCTTTTCACCATGGTGTGTAGCTCAAGTTTTTTCTAACATGGTATGTAACAGCA
* **
1240924 ACATCTTTCAACATGGCATGTACCAACCTTTATTTCAAAATGGCATGTCAAAATATTTTGTGACA
1 ACATCTTTCAACATGGCATGTAACAACCTTTATTTCAAAATGGTGTGTCAAAATATTTTGTGACA
* ** * * **
1240989 TAGTGTGTACCAACATTTTTTTGAACATGATGTCTAACAACAATATTTTTTCAACATGGTGCGGA
66 TGGCATGTACCAACATTTTTTTGAACATGATGT-TAACAACAACATTTTTTCAATATGGTATGGA
* * * ** * *
1241054 ACATCTTCTTTTCACCATTGCGTGTAGCTCAATTTTTTTCTAACATGGCCTGCAATAGCA
130 ACATCTTCTTTTCACCATGGTGTGTAGCTCAAGTTTTTTCTAACATGGTATGTAACAGCA
* * * **
1241114 ACATCTTTCAACATAGCATGTAACAACCTTTATTTCAAAAGGGTGTGTCAAAATAGTTTGCAACA
1 ACATCTTTCAACATGGCATGTAACAACCTTTATTTCAAAATGGTGTGTCAAAATATTTTGTGACA
* * * *
1241179 TGGCATGTACCAACA-TTTTTTGAACGTGGCATG-TAACAACTACCTTTTTT-TATCATGGTATG
66 TGGCATGTACCAACATTTTTTTGAACAT-G-ATGTTAACAACAACATTTTTTCAAT-ATGGTATG
* * * * *
1241241 GAACAACTTATTTTCACCATGGTGTGCAGCTCAAGTTTTTTTTAACATGTTATGTAACAGCA
128 GAACATCTTCTTTTCACCATGGTGTGTAGCTCAAGTTTTTTCTAACATGGTATGTAACAGCA
*
1241303 ACATTTTTCA
1 ACATCTTTCA
1241313 CCTTGTGCAT
Statistics
Matches: 323, Mismatches: 60, Indels: 13
0.82 0.15 0.03
Matches are distributed among these distances:
188 7 0.02
189 200 0.62
190 113 0.35
191 3 0.01
ACGTcount: A:0.30, C:0.18, G:0.15, T:0.37
Consensus pattern (189 bp):
ACATCTTTCAACATGGCATGTAACAACCTTTATTTCAAAATGGTGTGTCAAAATATTTTGTGACA
TGGCATGTACCAACATTTTTTTGAACATGATGTTAACAACAACATTTTTTCAATATGGTATGGAA
CATCTTCTTTTCACCATGGTGTGTAGCTCAAGTTTTTTCTAACATGGTATGTAACAGCA
Found at i:1241226 original size:27 final size:27
Alignment explanation
Indices: 1241170--1241226 Score: 62
Period size: 26 Copynumber: 2.1 Consensus size: 27
1241160 GTCAAAATAG
* **
1241170 TTTGCAACATGGCATGTACCAACATTT
1 TTTGCAACATGGCATGTAACAACACCT
*
1241197 TTTG-AACGTGGCATGTAACAACTACCT
1 TTTGCAACATGGCATGTAACAAC-ACCT
1241224 TTT
1 TTT
1241227 TTTATCATGG
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
26 16 0.64
27 9 0.36
ACGTcount: A:0.28, C:0.21, G:0.16, T:0.35
Consensus pattern (27 bp):
TTTGCAACATGGCATGTAACAACACCT
Found at i:1241808 original size:29 final size:28
Alignment explanation
Indices: 1241767--1241823 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 28
1241757 GCAATTGTTG
1241767 CTAAACACCATGCCAATATATATTGTCA
1 CTAAACACCATGCCAATATATATTGTCA
*
1241795 CTAACACACCATGCCTATATATATTGTCA
1 CTAA-ACACCATGCCAATATATATTGTCA
1241824 GTTGCACGCA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
28 4 0.15
29 23 0.85
ACGTcount: A:0.37, C:0.26, G:0.07, T:0.30
Consensus pattern (28 bp):
CTAAACACCATGCCAATATATATTGTCA
Found at i:1241935 original size:29 final size:30
Alignment explanation
Indices: 1241883--1241942 Score: 86
Period size: 29 Copynumber: 2.0 Consensus size: 30
1241873 ACATTGTTAT
* *
1241883 TACATGCAATGCTTAAAATTCCTAAGATGC
1 TACATGCAAAGCATAAAATTCCTAAGATGC
*
1241913 TACATGCAAAGCAT-AAATTCCTAAGTTGC
1 TACATGCAAAGCATAAAATTCCTAAGATGC
1241942 T
1 T
1241943 TCAAGCCAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 15 0.56
30 12 0.44
ACGTcount: A:0.37, C:0.20, G:0.13, T:0.30
Consensus pattern (30 bp):
TACATGCAAAGCATAAAATTCCTAAGATGC
Found at i:1243311 original size:2 final size:2
Alignment explanation
Indices: 1243304--1243329 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1243294 CACATAAAAT
1243304 CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA
1243330 TATATATATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:1250258 original size:18 final size:18
Alignment explanation
Indices: 1250217--1250258 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
1250207 AGACTTTATT
* *
1250217 GAAGAACTTTTAATGGAA
1 GAAGGACTTTTAATGCAA
1250235 GAAGGACTTTTAATGCAA
1 GAAGGACTTTTAATGCAA
*
1250253 GTAGGA
1 GAAGGA
1250259 GAGAAATTTC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.40, C:0.07, G:0.26, T:0.26
Consensus pattern (18 bp):
GAAGGACTTTTAATGCAA
Found at i:1251712 original size:18 final size:19
Alignment explanation
Indices: 1251689--1251728 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
1251679 CAAGTGAAGA
1251689 ATTTTA-GAATAAAATAAT
1 ATTTTATGAATAAAATAAT
* *
1251707 ATTTTATTAATAAATTAAT
1 ATTTTATGAATAAAATAAT
1251726 ATT
1 ATT
1251729 AAAACATTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 6 0.32
19 13 0.68
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (19 bp):
ATTTTATGAATAAAATAAT
Found at i:1254944 original size:73 final size:73
Alignment explanation
Indices: 1254855--1254994 Score: 172
Period size: 73 Copynumber: 1.9 Consensus size: 73
1254845 CAAGAGACTG
* * *
1254855 TGTTAGTCTATTAAGAGCTTACTACCAGATACCGGGTTCAAAGACAGAAACAACTTAATCGACTA
1 TGTTAGTCGACTAAGAGCTTACTACCAGAAACCGGGTTCAAAGACAGAAACAACTTAATCGACTA
1254920 AGAAGTTT
66 AGAAGTTT
* * * * * * * **
1254928 TGTTAGTCGACTAAGAGGTTACTGCCAGAAACTGGGTTTAGATACAGAGACAACTTGGTCGACTA
1 TGTTAGTCGACTAAGAGCTTACTACCAGAAACCGGGTTCAAAGACAGAAACAACTTAATCGACTA
1254993 AG
66 AG
1254995 TGATAATGGT
Statistics
Matches: 55, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
73 55 1.00
ACGTcount: A:0.34, C:0.17, G:0.22, T:0.26
Consensus pattern (73 bp):
TGTTAGTCGACTAAGAGCTTACTACCAGAAACCGGGTTCAAAGACAGAAACAACTTAATCGACTA
AGAAGTTT
Found at i:1255251 original size:14 final size:14
Alignment explanation
Indices: 1255232--1255258 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1255222 TACTTTCTGC
1255232 AGATTATTATTCTA
1 AGATTATTATTCTA
1255246 AGATTATTATTCT
1 AGATTATTATTCT
1255259 TATTCCAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.33, C:0.07, G:0.07, T:0.52
Consensus pattern (14 bp):
AGATTATTATTCTA
Found at i:1266874 original size:8 final size:9
Alignment explanation
Indices: 1266854--1266897 Score: 54
Period size: 9 Copynumber: 4.7 Consensus size: 9
1266844 CACCGAACAA
1266854 TTTATTCTTT
1 TTTATT-TTT
1266864 TTTATTTTT
1 TTTATTTTT
1266873 TTTATTTTT
1 TTTATTTTT
1266882 TCTT-TCTTTT
1 T-TTAT-TTTT
1266892 TTTATT
1 TTTATT
1266898 CACAATTTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
9 17 0.55
10 14 0.45
ACGTcount: A:0.09, C:0.07, G:0.00, T:0.84
Consensus pattern (9 bp):
TTTATTTTT
Found at i:1266878 original size:19 final size:20
Alignment explanation
Indices: 1266854--1266898 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
1266844 CACCGAACAA
1266854 TTTATTCTTTT-TTAT-TTTT
1 TTTATTCTTTTCTT-TCTTTT
1266873 TTTATT-TTTTCTTTCTTTT
1 TTTATTCTTTTCTTTCTTTT
1266892 TTTATTC
1 TTTATTC
1266899 ACAATTTAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
18 5 0.22
19 18 0.78
ACGTcount: A:0.09, C:0.09, G:0.00, T:0.82
Consensus pattern (20 bp):
TTTATTCTTTTCTTTCTTTT
Found at i:1284994 original size:27 final size:29
Alignment explanation
Indices: 1284946--1285011 Score: 73
Period size: 27 Copynumber: 2.3 Consensus size: 29
1284936 GTTACACATT
* * * *
1284946 ATGTTTAAAAAATATAATTATTATACGTC
1 ATGTTCAAAAAATATAACTATTACACGAC
1284975 ATGTTCAAAAAA-AT-ACTATTACACGAC
1 ATGTTCAAAAAATATAACTATTACACGAC
*
1285002 ATGTTGAAAA
1 ATGTTCAAAA
1285012 CAAAAAAGTT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
27 19 0.59
28 2 0.06
29 11 0.34
ACGTcount: A:0.47, C:0.11, G:0.09, T:0.33
Consensus pattern (29 bp):
ATGTTCAAAAAATATAACTATTACACGAC
Found at i:1290599 original size:16 final size:16
Alignment explanation
Indices: 1290578--1290608 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1290568 AAAATATTAA
*
1290578 TATTTTAATATCATTT
1 TATTTTAAAATCATTT
1290594 TATTTTAAAATCATT
1 TATTTTAAAATCATT
1290609 CACTTGACTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.06, G:0.00, T:0.58
Consensus pattern (16 bp):
TATTTTAAAATCATTT
Found at i:1291270 original size:18 final size:19
Alignment explanation
Indices: 1291247--1291284 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
1291237 GTAAGGGTTT
*
1291247 CTAAAAATGATTAA-TATG
1 CTAAAAATAATTAATTATG
1291265 CTAAAAATAATTAATTATG
1 CTAAAAATAATTAATTATG
1291284 C
1 C
1291285 CTTTACCTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 13 0.72
19 5 0.28
ACGTcount: A:0.50, C:0.08, G:0.08, T:0.34
Consensus pattern (19 bp):
CTAAAAATAATTAATTATG
Found at i:1306876 original size:31 final size:30
Alignment explanation
Indices: 1306841--1306938 Score: 85
Period size: 31 Copynumber: 3.2 Consensus size: 30
1306831 ATTTTCTTGA
1306841 TGATTATGGTTAGGGTTAGTAGAATTTTGTT
1 TGATTATGGTT-GGGTTAGTAGAATTTTGTT
* * *
1306872 TGATTGATGATT-GGTGT-GTTGAGATTCTT-CT
1 TGATT-ATGGTTGGGT-TAGTAGA-ATT-TTGTT
*
1306903 CGATTATGGTTTGGGTTAGTAGAATTTTGTT
1 TGATTATGG-TTGGGTTAGTAGAATTTTGTT
1306934 TGATT
1 TGATT
1306939 GATGATGAAT
Statistics
Matches: 51, Mismatches: 8, Indels: 16
0.68 0.11 0.21
Matches are distributed among these distances:
30 12 0.24
31 25 0.49
32 14 0.27
ACGTcount: A:0.19, C:0.03, G:0.29, T:0.49
Consensus pattern (30 bp):
TGATTATGGTTGGGTTAGTAGAATTTTGTT
Found at i:1306970 original size:62 final size:61
Alignment explanation
Indices: 1306834--1307007 Score: 197
Period size: 62 Copynumber: 2.8 Consensus size: 61
1306824 TATGTAGATT
* * * *
1306834 TTCTTGATGATTATGGTTAGGGTTAGTAGAATTTTGTTTGATTGATGATTGGTGTGTTGAGA
1 TTCTTGATGATTATGGTTTGGGTTAGTAGAATTTTGTTTGATTGATGA-TGATATGTTGAAA
*
1306896 TTCTT-CTCGATTATGGTTTGGGTTAGTAGAATTTTGTTTGATTGATGATGAATATGTTGAAA
1 TTCTTGAT-GATTATGGTTTGGGTTAGTAGAATTTTGTTTGATTGATGATG-ATATGTTGAAA
* ** * * * * *
1306958 TTCTTGATGATTAGGGCGTGCGTTAGTAGAAATTTGCTTGGTGGATGATG
1 TTCTTGATGATTATGGTTTGGGTTAGTAGAATTTTGTTTGATTGATGATG
1307008 GGTTTATGGA
Statistics
Matches: 95, Mismatches: 14, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
61 3 0.03
62 91 0.96
63 1 0.01
ACGTcount: A:0.22, C:0.05, G:0.29, T:0.44
Consensus pattern (61 bp):
TTCTTGATGATTATGGTTTGGGTTAGTAGAATTTTGTTTGATTGATGATGATATGTTGAAA
Found at i:1308323 original size:13 final size:13
Alignment explanation
Indices: 1308284--1308329 Score: 56
Period size: 14 Copynumber: 3.4 Consensus size: 13
1308274 ACCCACTACC
*
1308284 AAGAAGAAAAGAGA
1 AAGAAGAGAA-AGA
*
1308298 AAGGAGAAGAAAGA
1 AAGAAG-AGAAAGA
1308312 AAGAAGAGAAAGA
1 AAGAAGAGAAAGA
1308325 AAGAA
1 AAGAA
1308330 AGGAAGGAGA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
13 12 0.43
14 13 0.46
15 3 0.11
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (13 bp):
AAGAAGAGAAAGA
Found at i:1308351 original size:21 final size:21
Alignment explanation
Indices: 1308293--1308358 Score: 71
Period size: 21 Copynumber: 3.1 Consensus size: 21
1308283 CAAGAAGAAA
* *
1308293 AGAGAAAGGAGAAGAAAGAAAGA
1 AGAGAAAGG-G-AGAAAGGAAGG
**
1308316 AGAGAAAGAAAGAAAGGAAGG
1 AGAGAAAGGGAGAAAGGAAGG
1308337 AGAGAAAGGGAGAAAGG-AGG
1 AGAGAAAGGGAGAAAGGAAGG
1308357 AG
1 AG
1308359 GAAGAAAAAG
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
20 5 0.14
21 24 0.65
23 8 0.22
ACGTcount: A:0.59, C:0.00, G:0.41, T:0.00
Consensus pattern (21 bp):
AGAGAAAGGGAGAAAGGAAGG
Found at i:1308368 original size:24 final size:21
Alignment explanation
Indices: 1308326--1308368 Score: 50
Period size: 21 Copynumber: 1.9 Consensus size: 21
1308316 AGAGAAAGAA
*
1308326 AGAAAGGAAGGAGAGAAAGGG
1 AGAAAGGAAGGAGAAAAAGGG
1308347 AGAAAGGAGGAGGAAGAAAAAG
1 AGAAAGGA--AGG-AGAAAAAG
1308369 AAAGGGAGGG
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
21 8 0.44
23 3 0.17
24 7 0.39
ACGTcount: A:0.56, C:0.00, G:0.44, T:0.00
Consensus pattern (21 bp):
AGAAAGGAAGGAGAAAAAGGG
Found at i:1313663 original size:15 final size:16
Alignment explanation
Indices: 1313645--1313689 Score: 58
Period size: 15 Copynumber: 2.9 Consensus size: 16
1313635 TTTTATTTTC
1313645 TGTT-AATTAATTTAG
1 TGTTGAATTAATTTAG
*
1313660 TGTTTGATTTAATTTAG
1 TG-TTGAATTAATTTAG
1313677 T-TTGAATTAATTT
1 TGTTGAATTAATTT
1313690 TCTAAAAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
15 13 0.50
16 2 0.08
17 11 0.42
ACGTcount: A:0.29, C:0.00, G:0.13, T:0.58
Consensus pattern (16 bp):
TGTTGAATTAATTTAG
Found at i:1317790 original size:44 final size:43
Alignment explanation
Indices: 1317675--1317810 Score: 159
Period size: 44 Copynumber: 3.1 Consensus size: 43
1317665 ACTAGAGCTA
* *
1317675 ATCATAACACAATCATGGGAA-GTGGAGACCTTTTCAATCCAC
1 ATCACAACACAATCATGGGAATGTGGAGACCTTCTCAATCCAC
* * *
1317717 TTCACAACACAATCATGGGAATATGGAGACCATCTCAATCCAC
1 ATCACAACACAATCATGGGAATGTGGAGACCTTCTCAATCCAC
* * *
1317760 ATCACAATGC-CAATCATGGGAATGTAGAGACCTTCTTAACCCAC
1 ATCACAA--CACAATCATGGGAATGTGGAGACCTTCTCAATCCAC
1317804 ATTCACA
1 A-TCACA
1317811 GTACTCACAT
Statistics
Matches: 79, Mismatches: 11, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
42 19 0.24
43 24 0.30
44 30 0.38
45 6 0.08
ACGTcount: A:0.36, C:0.26, G:0.15, T:0.23
Consensus pattern (43 bp):
ATCACAACACAATCATGGGAATGTGGAGACCTTCTCAATCCAC
Found at i:1319005 original size:16 final size:16
Alignment explanation
Indices: 1318980--1319010 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1318970 AAAAATATCA
1318980 GAAAAAAATCAAAATC
1 GAAAAAAATCAAAATC
*
1318996 GAAAAGAATCAAAAT
1 GAAAAAAATCAAAAT
1319011 TTAAATTTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.68, C:0.10, G:0.10, T:0.13
Consensus pattern (16 bp):
GAAAAAAATCAAAATC
Found at i:1328304 original size:44 final size:43
Alignment explanation
Indices: 1328208--1328316 Score: 155
Period size: 44 Copynumber: 2.5 Consensus size: 43
1328198 TCATGATAAC
* *
1328208 TGGAGACCTTCTCAATCCACTTCACAACACAATCATGGGAATA
1 TGGAGACCTTCTCAATCCACATCACAAAACAATCATGGGAATA
*
1328251 TGGAGACCTTCTCAATCCACATCACAAAACCAATCATTGGAATA
1 TGGAGACCTTCTCAATCCACATCACAAAA-CAATCATGGGAATA
* * *
1328295 TGGAAACCTTATCAACCCACAT
1 TGGAGACCTTCTCAATCCACAT
1328317 TCAAAATACT
Statistics
Matches: 59, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
43 27 0.46
44 32 0.54
ACGTcount: A:0.37, C:0.28, G:0.12, T:0.23
Consensus pattern (43 bp):
TGGAGACCTTCTCAATCCACATCACAAAACAATCATGGGAATA
Found at i:1333904 original size:17 final size:16
Alignment explanation
Indices: 1333882--1333913 Score: 55
Period size: 16 Copynumber: 1.9 Consensus size: 16
1333872 AGTTAATTGC
1333882 TTTAGTTTTTAATTGAA
1 TTTAG-TTTTAATTGAA
1333899 TTTAGTTTTAATTGA
1 TTTAGTTTTAATTGA
1333914 TTTTCTATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.28, C:0.00, G:0.12, T:0.59
Consensus pattern (16 bp):
TTTAGTTTTAATTGAA
Found at i:1355177 original size:24 final size:24
Alignment explanation
Indices: 1355150--1355203 Score: 92
Period size: 24 Copynumber: 2.3 Consensus size: 24
1355140 ATAGTCACAC
*
1355150 TGAATATTCTAGAATGAGGCTATT
1 TGAATATTCTAGAATAAGGCTATT
1355174 TGAATATTCTAGAATAAGGCTATT
1 TGAATATTCTAGAATAAGGCTATT
1355198 T-AATAT
1 TGAATAT
1355204 AAAAAATTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
23 5 0.17
24 24 0.83
ACGTcount: A:0.37, C:0.07, G:0.17, T:0.39
Consensus pattern (24 bp):
TGAATATTCTAGAATAAGGCTATT
Found at i:1356450 original size:29 final size:29
Alignment explanation
Indices: 1356417--1356482 Score: 114
Period size: 29 Copynumber: 2.3 Consensus size: 29
1356407 ATTAGTCTAC
*
1356417 AAACCTTCTTTTCATTTCCAGAAAATATA
1 AAACCTTCTTTTCATTTCCAAAAAATATA
*
1356446 AAACCTTCTTTTCATTTCTAAAAAATATA
1 AAACCTTCTTTTCATTTCCAAAAAATATA
1356475 AAACCTTC
1 AAACCTTC
1356483 AGGTTGTTCT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.39, C:0.21, G:0.02, T:0.38
Consensus pattern (29 bp):
AAACCTTCTTTTCATTTCCAAAAAATATA
Found at i:1369365 original size:40 final size:40
Alignment explanation
Indices: 1369321--1369435 Score: 160
Period size: 40 Copynumber: 2.9 Consensus size: 40
1369311 TTTGGAATCA
** * *
1369321 CCATTAATATGGCTTAAATGCCTTAGCATATTTGTATTTT
1 CCATTAATATGGCTTACGTGCCTTAGCATATTTGGATTTG
*
1369361 CCATTAATATGGCTTACGCGCCTTAGCA-AGTTTGGATTTG
1 CCATTAATATGGCTTACGTGCCTTAGCATA-TTTGGATTTG
*
1369401 CCATTAATATGGCTTACGTGCCTTAGCATGTTTGG
1 CCATTAATATGGCTTACGTGCCTTAGCATATTTGG
1369436 TTTACATGAC
Statistics
Matches: 66, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
39 1 0.02
40 65 0.98
ACGTcount: A:0.23, C:0.18, G:0.19, T:0.39
Consensus pattern (40 bp):
CCATTAATATGGCTTACGTGCCTTAGCATATTTGGATTTG
Found at i:1378829 original size:2 final size:2
Alignment explanation
Indices: 1378822--1378847 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1378812 AACCTAATTT
1378822 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
1378848 GATGAAGAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1389259 original size:28 final size:29
Alignment explanation
Indices: 1389227--1389321 Score: 85
Period size: 29 Copynumber: 3.4 Consensus size: 29
1389217 TAAAGGCCTG
*
1389227 AAATG-ATGTGTGCATACGTTTGGCACCT
1 AAATGAATGTGTGCATATGTTTGGCACCT
* *
1389255 AAATGATAT-TGAGCATATGTTTAGCACACT
1 AAATGA-ATGTGTGCATATGTTTGGCAC-CT
*
1389285 -AATGGTATG-GTGCAT-TGTTTGGCA-CT
1 AAAT-GAATGTGTGCATATGTTTGGCACCT
1389311 AAATGAATGTG
1 AAATGAATGTG
1389322 ATATGTAAGC
Statistics
Matches: 53, Mismatches: 7, Indels: 15
0.71 0.09 0.20
Matches are distributed among these distances:
26 6 0.11
27 4 0.08
28 13 0.25
29 25 0.47
30 5 0.09
ACGTcount: A:0.29, C:0.13, G:0.24, T:0.34
Consensus pattern (29 bp):
AAATGAATGTGTGCATATGTTTGGCACCT
Found at i:1401172 original size:17 final size:17
Alignment explanation
Indices: 1401150--1401188 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
1401140 ATTTGGGGAT
*
1401150 TGCTCCCCCTGAATATG
1 TGCTCCCCCTAAATATG
*
1401167 TGCTCCCTCTAAATATG
1 TGCTCCCCCTAAATATG
1401184 TGCTC
1 TGCTC
1401189 TATTAAAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.18, C:0.33, G:0.15, T:0.33
Consensus pattern (17 bp):
TGCTCCCCCTAAATATG
Found at i:1401315 original size:24 final size:24
Alignment explanation
Indices: 1401285--1401338 Score: 83
Period size: 24 Copynumber: 2.2 Consensus size: 24
1401275 TTCCATCATA
1401285 AAAACATA-AGCTTCAACATAGCAT
1 AAAACATATA-CTTCAACATAGCAT
*
1401309 AAAACATATACTTCTACATAGCAT
1 AAAACATATACTTCAACATAGCAT
1401333 AAAACA
1 AAAACA
1401339 CATAAGGCGC
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
24 27 0.96
25 1 0.04
ACGTcount: A:0.52, C:0.20, G:0.06, T:0.22
Consensus pattern (24 bp):
AAAACATATACTTCAACATAGCAT
Found at i:1414167 original size:20 final size:20
Alignment explanation
Indices: 1414139--1414176 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1414129 CTCACTACCT
1414139 CAAAAGTATTGATACATTAA
1 CAAAAGTATTGATACATTAA
*
1414159 CAAATGTATTGATACATT
1 CAAAAGTATTGATACATT
1414177 TTTAACAGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.45, C:0.11, G:0.11, T:0.34
Consensus pattern (20 bp):
CAAAAGTATTGATACATTAA
Found at i:1422678 original size:15 final size:17
Alignment explanation
Indices: 1422650--1422684 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
1422640 AAAATTAAAT
1422650 TTTGATTCTTTTAGA-A
1 TTTGATTCTTTTAGATA
1422666 TTTGATT-TTTTAGATA
1 TTTGATTCTTTTAGATA
1422682 TTT
1 TTT
1422685 TTATTGAATC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 7 0.39
16 11 0.61
ACGTcount: A:0.23, C:0.03, G:0.11, T:0.63
Consensus pattern (17 bp):
TTTGATTCTTTTAGATA
Found at i:1424229 original size:40 final size:41
Alignment explanation
Indices: 1424174--1424278 Score: 128
Period size: 40 Copynumber: 2.6 Consensus size: 41
1424164 TTGATTATAT
* * *
1424174 GTCTAATGTGGTGATTTAGG-GTGAA-TATTATGGGATGAAC
1 GTCTAATGTGGTGATTTAGGACT-AAGTATTAAGGAATGAAC
*
1424214 GTCTAATGTGGTGATTT-GGACTAAGTATTAAGGAATGAAT
1 GTCTAATGTGGTGATTTAGGACTAAGTATTAAGGAATGAAC
*
1424254 GTATAATGTGGTGATTTA-GACTAAG
1 GTCTAATGTGGTGATTTAGGACTAAG
1424279 ACATTATTGA
Statistics
Matches: 57, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
39 4 0.07
40 53 0.93
ACGTcount: A:0.30, C:0.05, G:0.30, T:0.35
Consensus pattern (41 bp):
GTCTAATGTGGTGATTTAGGACTAAGTATTAAGGAATGAAC
Found at i:1429857 original size:20 final size:21
Alignment explanation
Indices: 1429834--1429889 Score: 57
Period size: 19 Copynumber: 2.8 Consensus size: 21
1429824 TATTAAGTTG
1429834 TTTTAATTTTATGTTTATT-T
1 TTTTAATTTTATGTTTATTAT
1429854 TTTT-ATTTTA-G-TTATTAT
1 TTTTAATTTTATGTTTATTAT
*
1429872 TTATTAGTTTTTATGTTT
1 TT-TTA-ATTTTATGTTT
1429890 TTGTAGGATT
Statistics
Matches: 29, Mismatches: 1, Indels: 9
0.74 0.03 0.23
Matches are distributed among these distances:
17 5 0.17
18 4 0.14
19 8 0.28
20 4 0.14
21 5 0.17
22 1 0.03
23 2 0.07
ACGTcount: A:0.20, C:0.00, G:0.07, T:0.73
Consensus pattern (21 bp):
TTTTAATTTTATGTTTATTAT
Found at i:1434279 original size:20 final size:21
Alignment explanation
Indices: 1434241--1434279 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1434231 TCATGCAATT
*
1434241 CATGACAAAGATTGATGCCTA
1 CATGACAAAGATAGATGCCTA
1434262 CATGACAAAGA-AGATGCC
1 CATGACAAAGATAGATGCC
1434280 ATCATTCCGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.41, C:0.21, G:0.21, T:0.18
Consensus pattern (21 bp):
CATGACAAAGATAGATGCCTA
Found at i:1439578 original size:30 final size:30
Alignment explanation
Indices: 1439542--1439611 Score: 131
Period size: 30 Copynumber: 2.3 Consensus size: 30
1439532 CTATCTCCAC
1439542 AGAAAAGGTAGTTAAGGGTTATACCTCTAT
1 AGAAAAGGTAGTTAAGGGTTATACCTCTAT
1439572 AGAAAAGGTAGTTAAGGGTTATACCTCTAT
1 AGAAAAGGTAGTTAAGGGTTATACCTCTAT
*
1439602 AGAAAGGGTA
1 AGAAAAGGTA
1439612 ATTATTATTG
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.39, C:0.09, G:0.26, T:0.27
Consensus pattern (30 bp):
AGAAAAGGTAGTTAAGGGTTATACCTCTAT
Found at i:1445477 original size:18 final size:18
Alignment explanation
Indices: 1445446--1445480 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1445436 AAATCTATGT
1445446 TCTATGTATCTTTTTCTC
1 TCTATGTATCTTTTTCTC
* *
1445464 TCTATTTATTTTTTTCT
1 TCTATGTATCTTTTTCT
1445481 TTGTCGAGCA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.11, C:0.17, G:0.03, T:0.69
Consensus pattern (18 bp):
TCTATGTATCTTTTTCTC
Found at i:1453837 original size:21 final size:22
Alignment explanation
Indices: 1453802--1453847 Score: 60
Period size: 21 Copynumber: 2.1 Consensus size: 22
1453792 GGGAATTGCA
*
1453802 ATTTTGATATATTCATATATGAC
1 ATTTTGATATATTCATA-ATAAC
1453825 ATTTTG-T-TATTCATAATAAC
1 ATTTTGATATATTCATAATAAC
1453845 ATT
1 ATT
1453848 GANNNNNNNN
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 7 0.32
21 8 0.36
22 1 0.05
23 6 0.27
ACGTcount: A:0.35, C:0.09, G:0.07, T:0.50
Consensus pattern (22 bp):
ATTTTGATATATTCATAATAAC
Found at i:1470865 original size:28 final size:27
Alignment explanation
Indices: 1470812--1470866 Score: 65
Period size: 28 Copynumber: 2.0 Consensus size: 27
1470802 GTAGTTGTGA
* * **
1470812 AAAAAAATTTAAATTTTATTTTTAAAT
1 AAAAAAATTTAAAATTAATTAATAAAT
1470839 AAAAAAATTTATAAATTAATTAATAAAT
1 AAAAAAATTTA-AAATTAATTAATAAAT
1470867 CAAATACTTG
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
27 11 0.48
28 12 0.52
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (27 bp):
AAAAAAATTTAAAATTAATTAATAAAT
Found at i:1479356 original size:23 final size:23
Alignment explanation
Indices: 1479326--1479369 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
1479316 GAAGTCACAT
1479326 TTTGTACCCTCTATCGTTGTAAC
1 TTTGTACCCTCTATCGTTGTAAC
1479349 TTTGTACCCTCTATCGTTGTA
1 TTTGTACCCTCTATCGTTGTA
1479370 TCACCATGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.16, C:0.25, G:0.14, T:0.45
Consensus pattern (23 bp):
TTTGTACCCTCTATCGTTGTAAC
Found at i:1480134 original size:20 final size:20
Alignment explanation
Indices: 1480109--1480152 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
1480099 CCCCTATAAT
*
1480109 CCCACAGGAATGTATAAATG
1 CCCACAAGAATGTATAAATG
1480129 CCCACAAGAATGTATAAATG
1 CCCACAAGAATGTATAAATG
1480149 CCCA
1 CCCA
1480153 ACTTTAAGCA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.41, C:0.25, G:0.16, T:0.18
Consensus pattern (20 bp):
CCCACAAGAATGTATAAATG
Found at i:1494512 original size:30 final size:30
Alignment explanation
Indices: 1494476--1494532 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
1494466 AGGATCGATC
*
1494476 TTGTAAAGTAGAAATTTAGGGGTAAATAAT
1 TTGTAAACTAGAAATTTAGGGGTAAATAAT
*
1494506 TTGTAAACTGGAAATTTAGGGGTAAAT
1 TTGTAAACTAGAAATTTAGGGGTAAAT
1494533 GATAGCCCTG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.40, C:0.02, G:0.25, T:0.33
Consensus pattern (30 bp):
TTGTAAACTAGAAATTTAGGGGTAAATAAT
Found at i:1510322 original size:28 final size:28
Alignment explanation
Indices: 1510290--1510346 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 28
1510280 TAAGTTAAGA
* *
1510290 AAGAGATGTAAGATTTAGATTAAGTGTG
1 AAGAGAGGTAAGATTTAGATGAAGTGTG
1510318 AAGAGAGGTAAGATTTAGATGAAGTGTG
1 AAGAGAGGTAAGATTTAGATGAAGTGTG
1510346 A
1 A
1510347 GGGATATTGT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.40, C:0.00, G:0.32, T:0.28
Consensus pattern (28 bp):
AAGAGAGGTAAGATTTAGATGAAGTGTG
Found at i:1514084 original size:15 final size:16
Alignment explanation
Indices: 1514064--1514095 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
1514054 TAATACCTTA
1514064 TAAATTTT-TAAATAT
1 TAAATTTTGTAAATAT
1514079 TAAATTTTGTAAATAT
1 TAAATTTTGTAAATAT
1514095 T
1 T
1514096 GTTAGCAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (16 bp):
TAAATTTTGTAAATAT
Found at i:1514345 original size:26 final size:26
Alignment explanation
Indices: 1514316--1514371 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
1514306 AGAATAATCA
*
1514316 ATTTTTAAGGTT-TTTAATTTTATATT
1 ATTTTTAAGATTATTTAATTTTATA-T
* *
1514342 ATTTTTAATATTATTTAATTTTTTAT
1 ATTTTTAAGATTATTTAATTTTATAT
1514368 ATTT
1 ATTT
1514372 ACCTTTAAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
26 15 0.58
27 11 0.42
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.68
Consensus pattern (26 bp):
ATTTTTAAGATTATTTAATTTTATAT
Found at i:1514348 original size:17 final size:17
Alignment explanation
Indices: 1514326--1514370 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
1514316 ATTTTTAAGG
*
1514326 TTTTTAATTTTATATT-A
1 TTTTTAATATTAT-TTAA
1514343 TTTTTAATATTATTTAA
1 TTTTTAATATTATTTAA
*
1514360 TTTTTTATATT
1 TTTTTAATATT
1514371 TACCTTTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 2 0.08
17 23 0.92
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (17 bp):
TTTTTAATATTATTTAA
Found at i:1526653 original size:134 final size:134
Alignment explanation
Indices: 1526408--1526672 Score: 422
Period size: 134 Copynumber: 2.0 Consensus size: 134
1526398 AAATCCAGCA
* *
1526408 ATGCTATCAAAAATTGCATCAGACATGCTGACTTGGCACAAGATAGCATTTCTAATCAATTTTGC
1 ATGCTATCAAAAATTGCAGCAGACATGCTGACTTGGCACAAGATAGCATATCTAATCAATTTTGC
* * *
1526473 CAAGTTCAATTCTTGAATGATTTAAACATAATCTGCACATAGCACCAACTTCATCAAATTCAAAT
66 CAAGTCCAATTCTTGAATGATTTAAACATAATCTGCACATACCACCAACTTCATCAAACTCAAAT
1526538 CCAT
131 CCAT
* * *
1526542 ATGCTATCAAAACTTGCAGCAGACATGCTGATTTGGCACTAGATAGCATATCTAATCAATTTTGC
1 ATGCTATCAAAAATTGCAGCAGACATGCTGACTTGGCACAAGATAGCATATCTAATCAATTTTGC
* * * *
1526607 CAAGTCCAATTCTTGAATGATTTACACATAATCTTCATATACCACCAACTTCCTCAAACTCAAAT
66 CAAGTCCAATTCTTGAATGATTTAAACATAATCTGCACATACCACCAACTTCATCAAACTCAAAT
1526672 C
131 C
1526673 TAACTTGGCA
Statistics
Matches: 119, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
134 119 1.00
ACGTcount: A:0.35, C:0.23, G:0.11, T:0.31
Consensus pattern (134 bp):
ATGCTATCAAAAATTGCAGCAGACATGCTGACTTGGCACAAGATAGCATATCTAATCAATTTTGC
CAAGTCCAATTCTTGAATGATTTAAACATAATCTGCACATACCACCAACTTCATCAAACTCAAAT
CCAT
Found at i:1526815 original size:24 final size:25
Alignment explanation
Indices: 1526782--1526832 Score: 77
Period size: 24 Copynumber: 2.1 Consensus size: 25
1526772 CACTGCTTTT
1526782 AGTACAATTGTACAGAAGATTCTTA
1 AGTACAATTGTACAGAAGATTCTTA
* *
1526807 AGTA-AATTGTGCAGAAGATTTTTA
1 AGTACAATTGTACAGAAGATTCTTA
1526831 AG
1 AG
1526833 GTTGAACAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
24 20 0.83
25 4 0.17
ACGTcount: A:0.39, C:0.08, G:0.20, T:0.33
Consensus pattern (25 bp):
AGTACAATTGTACAGAAGATTCTTA
Found at i:1529239 original size:38 final size:40
Alignment explanation
Indices: 1529147--1529271 Score: 114
Period size: 40 Copynumber: 3.2 Consensus size: 40
1529137 ATTAAAGCAC
** *
1529147 AACCTTTCACAAAACCTCTGCGTTTTCAAGGTT-AAACAAT
1 AACCTTTCAC-AAAGTTCTGCCTTTTCAAGGTTAAAACAAT
1529187 AACCTTTCACAAAG-TCTGCCTTTTCAAGGTTAAAAC-AT
1 AACCTTTCACAAAGTTCTGCCTTTTCAAGGTTAAAACAAT
** * * * * *
1529225 AATGTTTTATAAAGTTTTTACCTTTTCAAGGTTAAAGCAA-
1 AACCTTTCACAAAG-TTCTGCCTTTTCAAGGTTAAAACAAT
1529265 AACCTTT
1 AACCTTT
1529272 TTACCTTTTC
Statistics
Matches: 70, Mismatches: 11, Indels: 8
0.79 0.12 0.09
Matches are distributed among these distances:
38 28 0.40
39 7 0.10
40 34 0.49
41 1 0.01
ACGTcount: A:0.34, C:0.20, G:0.10, T:0.35
Consensus pattern (40 bp):
AACCTTTCACAAAGTTCTGCCTTTTCAAGGTTAAAACAAT
Found at i:1537441 original size:24 final size:25
Alignment explanation
Indices: 1537399--1537455 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 25
1537389 AAGTGAGAAG
* * *
1537399 AGAAAGGGAGTAAGAAGGAA-AGGA
1 AGAAAGGAAGAAAGAAGGAACAAGA
*
1537423 AGAAAGGAAGAAAGGAGGAACAAGA
1 AGAAAGGAAGAAAGAAGGAACAAGA
1537448 A-AAAGGAA
1 AGAAAGGAA
1537456 AGGAAGGTTC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
24 24 0.86
25 4 0.14
ACGTcount: A:0.60, C:0.02, G:0.37, T:0.02
Consensus pattern (25 bp):
AGAAAGGAAGAAAGAAGGAACAAGA
Found at i:1546702 original size:18 final size:18
Alignment explanation
Indices: 1546679--1546720 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
1546669 GAAACACCAG
*
1546679 AAGCCATATTT-GAGCCAA
1 AAGCCAT-TTTCGAGCAAA
1546697 AAGCCATTTTCGAGCAAA
1 AAGCCATTTTCGAGCAAA
1546715 AAGCCA
1 AAGCCA
1546721 AAGAACCTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 3 0.14
18 19 0.86
ACGTcount: A:0.40, C:0.24, G:0.17, T:0.19
Consensus pattern (18 bp):
AAGCCATTTTCGAGCAAA
Found at i:1551439 original size:18 final size:19
Alignment explanation
Indices: 1551416--1551451 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1551406 TTTTATTTAC
1551416 TTAG-TTAAATAATCATTG
1 TTAGTTTAAATAATCATTG
*
1551434 TTAGTTTAAGTAATCATT
1 TTAGTTTAAATAATCATT
1551452 TGAAATTAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.36, C:0.06, G:0.11, T:0.47
Consensus pattern (19 bp):
TTAGTTTAAATAATCATTG
Found at i:1561060 original size:76 final size:75
Alignment explanation
Indices: 1560934--1561108 Score: 217
Period size: 76 Copynumber: 2.3 Consensus size: 75
1560924 AAACAATTTC
* * *
1560934 TTATGAATCACCTAAATTAAAATGCTAACCATAATTTTAGGAATTCACTTTAAGTAGAAAATAAT
1 TTATGAATCACCAAAATTAAAATGCTAACCAAAATTTTAGGAATTCACTTTAAGTAGAAAACAAT
1560999 TTCCTACTCT
66 TTCCTACTCT
* * * *
1561009 TTATGAGTCACCCAAAATTAAAATGTTAACCAAAATTTTAAGG-ATTTACTTTAAGTAGGAAACA
1 TTATGAATCA-CCAAAATTAAAATGCTAACCAAAATTTT-AGGAATTCACTTTAAGTAGAAAACA
* *
1561073 ATTTCTTATTCT
64 ATTTCCTACTCT
* *
1561085 TTATGAATCAACTAAAATTGAAAT
1 TTATGAATC-ACCAAAATTAAAAT
1561109 AGATAGCATC
Statistics
Matches: 85, Mismatches: 12, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
75 9 0.11
76 72 0.85
77 4 0.05
ACGTcount: A:0.41, C:0.14, G:0.09, T:0.36
Consensus pattern (75 bp):
TTATGAATCACCAAAATTAAAATGCTAACCAAAATTTTAGGAATTCACTTTAAGTAGAAAACAAT
TTCCTACTCT
Found at i:1563327 original size:144 final size:141
Alignment explanation
Indices: 1563153--1563433 Score: 445
Period size: 144 Copynumber: 2.0 Consensus size: 141
1563143 TAATGAGGTA
*
1563153 TGTTCAGTGAACTTCTCTAACAAGCACTCACATGCCATCCTCAAGTGTCATATATACTTCAATCT
1 TGTTCAGTGAACTTCTCTAACAAGCACTCACATGCCATCCTCAAGTATCATATATACTTCAATCT
*
1563218 ATGAGATCAATTGCTTACTTATCAAGTAAGAAAGCTTAACATGTACCAGTCTTTAAGCATTGTTA
66 ATGAGATCAATTGCTTACTTATCAAGTAAGAAAGCTTAACATATACCAGTCTTTAAGCATTGTTA
1563283 ATGCCCTATCT
131 ATGCCCTATCT
* *
1563294 TGTTCAGTGAACTTGTTCTCTAACAAGCACTCACATGTCATCCTCAAGTATCTTATATACTTCAA
1 TGTTCAGTGAAC---TTCTCTAACAAGCACTCACATGCCATCCTCAAGTATCATATATACTTCAA
* * * * * *
1563359 TTTATGAGATCAATTGCTTACTTCTCAAGTAATAAGGCTTAGCATATATCAGTCTTTAAGCATTG
63 TCTATGAGATCAATTGCTTACTTATCAAGTAAGAAAGCTTAACATATACCAGTCTTTAAGCATTG
1563424 TTAATGCCCT
128 TTAATGCCCT
1563434 GTCTGGACAA
Statistics
Matches: 127, Mismatches: 10, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
141 12 0.09
144 115 0.91
ACGTcount: A:0.30, C:0.22, G:0.13, T:0.35
Consensus pattern (141 bp):
TGTTCAGTGAACTTCTCTAACAAGCACTCACATGCCATCCTCAAGTATCATATATACTTCAATCT
ATGAGATCAATTGCTTACTTATCAAGTAAGAAAGCTTAACATATACCAGTCTTTAAGCATTGTTA
ATGCCCTATCT
Found at i:1564090 original size:67 final size:67
Alignment explanation
Indices: 1563982--1564118 Score: 229
Period size: 67 Copynumber: 2.0 Consensus size: 67
1563972 ATAAAAGAAA
* *
1563982 GAAAAAAGAGAGAGTTTTAGATCCAAAAGCACGAAACTAGGGAGGCACGATGGGGCAGTCGTGCC
1 GAAAAAAGAGAGAGTTTTAGATCCAAAAGCACGAAACTAGGGAGGCACGAGGGGGCAGTCATGCC
1564047 TC
66 TC
* * *
1564049 GAAAAAAGAGAGAGTTTTAGATCTAAAAGCATGAAACTAGGGAGGCACGGGGGGGCAGTCATGCC
1 GAAAAAAGAGAGAGTTTTAGATCCAAAAGCACGAAACTAGGGAGGCACGAGGGGGCAGTCATGCC
1564114 TC
66 TC
1564116 GAA
1 GAA
1564119 GTTTGTAAAA
Statistics
Matches: 65, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
67 65 1.00
ACGTcount: A:0.36, C:0.16, G:0.32, T:0.15
Consensus pattern (67 bp):
GAAAAAAGAGAGAGTTTTAGATCCAAAAGCACGAAACTAGGGAGGCACGAGGGGGCAGTCATGCC
TC
Found at i:1566239 original size:34 final size:34
Alignment explanation
Indices: 1566201--1566274 Score: 89
Period size: 34 Copynumber: 2.2 Consensus size: 34
1566191 ATGCTAAGTT
* *
1566201 CAAAGCTTCAAT-GCCAAATGTTATACGCCA-AGAC
1 CAAAGCTTC-ATCACCAAATATTATACGCCATAG-C
*
1566235 CAAAGCTTCATCACCAGATATTATACGCCATAGC
1 CAAAGCTTCATCACCAAATATTATACGCCATAGC
1566269 CAAAGC
1 CAAAGC
1566275 AAAAGATGTT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
33 2 0.06
34 31 0.89
35 2 0.06
ACGTcount: A:0.38, C:0.28, G:0.14, T:0.20
Consensus pattern (34 bp):
CAAAGCTTCATCACCAAATATTATACGCCATAGC
Found at i:1569638 original size:19 final size:17
Alignment explanation
Indices: 1569596--1569629 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
1569586 AATTAAATTT
1569596 TTAAAATTTTTTTAAAA
1 TTAAAATTTTTTTAAAA
1569613 TTAAAATTTTTTTAAAA
1 TTAAAATTTTTTTAAAA
1569630 AAGTTAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TTAAAATTTTTTTAAAA
Found at i:1572855 original size:65 final size:65
Alignment explanation
Indices: 1572777--1572900 Score: 178
Period size: 65 Copynumber: 1.9 Consensus size: 65
1572767 ATTATTCAAA
*
1572777 ATTGAATCCATTTTCAAATGAATCAAGCCTTGATTAAATCAGAG-TGTTTTAGATTTTTTTTTTG
1 ATTGAATCCATTTTCAAATGAATCAAACCTTGATTAAATCAGAGAT-TTTTAGATTTTTTTTTTG
1572841 T
65 T
* * * *
1572842 ATTGAATCCATTTTCAGATGGATCAAACCTTGATTAAGTTAGAGAATTTTTAGATTTTT
1 ATTGAATCCATTTTCAAATGAATCAAACCTTGATTAAATCAGAG-ATTTTTAGATTTTT
1572901 GAAAATCAAA
Statistics
Matches: 52, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
65 39 0.75
66 12 0.23
67 1 0.02
ACGTcount: A:0.31, C:0.10, G:0.15, T:0.44
Consensus pattern (65 bp):
ATTGAATCCATTTTCAAATGAATCAAACCTTGATTAAATCAGAGATTTTTAGATTTTTTTTTTGT
Found at i:1594532 original size:28 final size:29
Alignment explanation
Indices: 1594501--1594567 Score: 73
Period size: 29 Copynumber: 2.3 Consensus size: 29
1594491 CATAGCATAC
* * **
1594501 TCATTTAAGTGCC-AACATATGCATTATT
1 TCATTTAAGTGCCAAACATAGGCATAACA
* *
1594529 TCATTCATGTGCCAAACATAGGCATAACA
1 TCATTTAAGTGCCAAACATAGGCATAACA
1594558 TCATTTAAGT
1 TCATTTAAGT
1594568 CTTTACATAC
Statistics
Matches: 30, Mismatches: 8, Indels: 1
0.77 0.21 0.03
Matches are distributed among these distances:
28 11 0.37
29 19 0.63
ACGTcount: A:0.34, C:0.19, G:0.12, T:0.34
Consensus pattern (29 bp):
TCATTTAAGTGCCAAACATAGGCATAACA
Found at i:1599627 original size:22 final size:23
Alignment explanation
Indices: 1599599--1599645 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
1599589 ATTTCTATGT
1599599 ATTACTAT-AAGAACTAAGCT-AA
1 ATTACTATCAA-AACTAAGCTCAA
*
1599621 ATTACTATCAAAATTAAGCTCAA
1 ATTACTATCAAAACTAAGCTCAA
1599644 AT
1 AT
1599646 AACTCTATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 16 0.73
23 6 0.27
ACGTcount: A:0.49, C:0.15, G:0.06, T:0.30
Consensus pattern (23 bp):
ATTACTATCAAAACTAAGCTCAA
Found at i:1611323 original size:30 final size:33
Alignment explanation
Indices: 1611266--1611346 Score: 91
Period size: 30 Copynumber: 2.5 Consensus size: 33
1611256 TTGTAAATTA
1611266 AAATATTAATATTTTAAATTAATTTTTTTAA-AGTT
1 AAATATTAATATTTT--ATTAATTTTTTTAATA-TT
1611301 AAATATTAATATTTT-TT-A-TTTTTTAATATT
1 AAATATTAATATTTTATTAATTTTTTTAATATT
1611331 AAA-ATTAAATATTTTA
1 AAATATT-AATATTTTA
1611347 CTGCAAAACA
Statistics
Matches: 43, Mismatches: 0, Indels: 10
0.81 0.00 0.19
Matches are distributed among these distances:
29 3 0.07
30 21 0.49
31 2 0.05
32 2 0.05
35 15 0.35
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (33 bp):
AAATATTAATATTTTATTAATTTTTTTAATATT
Found at i:1611328 original size:23 final size:22
Alignment explanation
Indices: 1611271--1611332 Score: 63
Period size: 23 Copynumber: 2.8 Consensus size: 22
1611261 AATTAAAATA
1611271 TTAATATTTTAA-ATTAATTTTT
1 TTAA-ATTTTAATATTAATTTTT
* *
1611293 TTAAAGTTAAATATTAATATTTT
1 TTAAATTTTAATATTAAT-TTTT
**
1611316 TTATTTTTTAATATTAA
1 TTAAATTTTAATATTAA
1611333 AATTAAATAT
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
21 5 0.16
22 10 0.31
23 17 0.53
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.60
Consensus pattern (22 bp):
TTAAATTTTAATATTAATTTTT
Found at i:1615492 original size:58 final size:58
Alignment explanation
Indices: 1615402--1615518 Score: 209
Period size: 58 Copynumber: 2.0 Consensus size: 58
1615392 GGTATGCCGA
*
1615402 AATTTACATTAATGAGATTATGAAGCTACATGGTA-TTCTGGTAATGATAGTGTCTAAC
1 AATTTACATTAATGAGATTATAAAGCTACATGGTACTT-TGGTAATGATAGTGTCTAAC
1615460 AATTTACATTAATGAGATTATAAAGCTACATGGTACTTTGGTAATGATAGTGTCTAAC
1 AATTTACATTAATGAGATTATAAAGCTACATGGTACTTTGGTAATGATAGTGTCTAAC
1615518 A
1 A
1615519 GAAGACTATA
Statistics
Matches: 57, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
58 55 0.96
59 2 0.04
ACGTcount: A:0.36, C:0.10, G:0.18, T:0.36
Consensus pattern (58 bp):
AATTTACATTAATGAGATTATAAAGCTACATGGTACTTTGGTAATGATAGTGTCTAAC
Found at i:1623417 original size:9 final size:9
Alignment explanation
Indices: 1623403--1623427 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
1623393 TTTTATTAAG
1623403 TTTCTTTAT
1 TTTCTTTAT
1623412 TTTCTTTAT
1 TTTCTTTAT
1623421 TTTCTTT
1 TTTCTTT
1623428 TCTTTTCCTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.08, C:0.12, G:0.00, T:0.80
Consensus pattern (9 bp):
TTTCTTTAT
Found at i:1642166 original size:28 final size:29
Alignment explanation
Indices: 1642135--1642190 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
1642125 ATCAATTGAA
*
1642135 TCCCTTTA-TTTAAAATTTATT-AATTTAG
1 TCCCTGTATTTTAAAATTT-TTAAATTTAG
1642163 TCCCTGTATTTTAAAATTTTTAAATTTA
1 TCCCTGTATTTTAAAATTTTTAAATTTA
1642191 TGATTTTAGA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
28 9 0.36
29 16 0.64
ACGTcount: A:0.32, C:0.11, G:0.04, T:0.54
Consensus pattern (29 bp):
TCCCTGTATTTTAAAATTTTTAAATTTAG
Found at i:1643476 original size:2 final size:2
Alignment explanation
Indices: 1643469--1643493 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1643459 TCAAGTAAAC
1643469 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
1643494 TTCTATCAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1646701 original size:49 final size:48
Alignment explanation
Indices: 1646648--1646819 Score: 175
Period size: 49 Copynumber: 3.5 Consensus size: 48
1646638 TATGTAATCA
* *
1646648 ACATCATAACATCATCTAAAATCATCCATAGACGGAACATACATACCTC
1 ACATCATAACATCATCCAAAATCATCCACAGACGGAACATACATA-CTC
* * **
1646697 ACATCATATCATCATCCAAAATCATCTACAGATAGAACATACATATCTC
1 ACATCATAACATCATCCAAAATCATCCACAGACGGAACATACATA-CTC
* ** * * *
1646746 ATATCATATTATCATCCAGAATCATCCACGGACGAAACATACATTA-TC
1 ACATCATAACATCATCCAAAATCATCCACAGACGGAACATACA-TACTC
* *
1646794 AACATCATAACATCGTCCAGAATCAT
1 -ACATCATAACATCATCCAAAATCAT
1646820 TTAGGGATGG
Statistics
Matches: 102, Mismatches: 19, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
48 2 0.02
49 98 0.96
50 2 0.02
ACGTcount: A:0.42, C:0.27, G:0.06, T:0.25
Consensus pattern (48 bp):
ACATCATAACATCATCCAAAATCATCCACAGACGGAACATACATACTC
Done.