Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008160.1 Hibiscus syriacus cultivar Beakdansim tig00110729_pilon, 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: 1466564
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 7
Found at i:1243299 original size:6 final size:6
Alignment explanation
Indices: 1243288--1243317 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
1243278 GGATTGGTTG
1243288 AGGTGA AGGTGA AGGTGA AGGTGA AGGTGA
1 AGGTGA AGGTGA AGGTGA AGGTGA AGGTGA
1243318 TGGTAATGGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.50, T:0.17
Consensus pattern (6 bp):
AGGTGA
Found at i:1245271 original size:22 final size:23
Alignment explanation
Indices: 1245227--1245310 Score: 77
Period size: 22 Copynumber: 3.7 Consensus size: 23
1245217 TTAAAGTAAT
1245227 AATATTATATT-ATAT-TTTATAA
1 AATATTATATTAATATATTT-TAA
1245249 AATATTA-ATTAATATATTTT-A
1 AATATTATATTAATATATTTTAA
* * *
1245270 AATATCTTTATTAAAATATTATTAG
1 AATAT-TATATTAATATATT-TTAA
*
1245295 ACTATTATATTAATAT
1 AATATTATATTAATAT
1245311 TAAATACATA
Statistics
Matches: 50, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
21 9 0.18
22 13 0.26
23 13 0.26
24 11 0.22
25 4 0.08
ACGTcount: A:0.45, C:0.02, G:0.01, T:0.51
Consensus pattern (23 bp):
AATATTATATTAATATATTTTAA
Found at i:1245288 original size:23 final size:24
Alignment explanation
Indices: 1245238--1245289 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 24
1245228 ATATTATATT
*
1245238 ATATTTTATAAAATATTAATTAAT
1 ATATTTTATAAAATATTAATTAAA
* * *
1245262 ATATTTTA-AATATCTTTATTAAA
1 ATATTTTATAAAATATTAATTAAA
1245285 ATATT
1 ATATT
1245290 ATTAGACTAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
23 16 0.67
24 8 0.33
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (24 bp):
ATATTTTATAAAATATTAATTAAA
Found at i:1245311 original size:11 final size:11
Alignment explanation
Indices: 1245200--1245312 Score: 53
Period size: 11 Copynumber: 10.4 Consensus size: 11
1245190 AATATTATAA
1245200 ATTATATTAATT
1 ATTATATTAA-T
1245212 ATT-TATTAA-
1 ATTATATTAAT
*
1245221 AGTA-A-TAAT
1 ATTATATTAAT
1245230 ATTATATT-AT
1 ATTATATTAAT
* *
1245240 ATTTTATAAAAT
1 ATTATAT-TAAT
1245252 ATTA-ATTAAT
1 ATTATATTAAT
*
1245262 A-TATTTTAAAT
1 ATTATATT-AAT
*
1245273 ATCTTTATTAA-
1 AT-TATATTAAT
*
1245284 AATATTATTAGACT
1 ATTA-TATTA-A-T
1245298 ATTATATTAAT
1 ATTATATTAAT
1245309 ATTA
1 ATTA
1245313 AATACATAAA
Statistics
Matches: 75, Mismatches: 12, Indels: 29
0.65 0.10 0.25
Matches are distributed among these distances:
8 3 0.04
9 8 0.11
10 16 0.21
11 24 0.32
12 12 0.16
13 9 0.12
14 3 0.04
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (11 bp):
ATTATATTAAT
Found at i:1249811 original size:36 final size:36
Alignment explanation
Indices: 1249764--1249838 Score: 123
Period size: 36 Copynumber: 2.1 Consensus size: 36
1249754 CAAATTAAAA
**
1249764 TAAAATCTATTTAAGTTTGAATGGTAAAAGAAGTTT
1 TAAAATCTATTTAAGACTGAATGGTAAAAGAAGTTT
*
1249800 TAAAATCTATTTAAGACTGAATGGTAAAAGAGGTTT
1 TAAAATCTATTTAAGACTGAATGGTAAAAGAAGTTT
1249836 TAA
1 TAA
1249839 CTTTTGAATA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.43, C:0.04, G:0.17, T:0.36
Consensus pattern (36 bp):
TAAAATCTATTTAAGACTGAATGGTAAAAGAAGTTT
Found at i:1257309 original size:18 final size:17
Alignment explanation
Indices: 1257270--1257312 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
1257260 ATTATATGGA
1257270 TATT-TTATTCATTTAT
1 TATTATTATTCATTTAT
*
1257286 TTTTATTATTCATGTTAT
1 TATTATTATTCAT-TTAT
1257304 TATTATTAT
1 TATTATTAT
1257313 ATGTATATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.26, C:0.05, G:0.02, T:0.67
Consensus pattern (17 bp):
TATTATTATTCATTTAT
Found at i:1257622 original size:21 final size:20
Alignment explanation
Indices: 1257568--1257623 Score: 58
Period size: 21 Copynumber: 2.7 Consensus size: 20
1257558 ACTTTATATA
* *
1257568 TTTATATTATTTTTTATTAT
1 TTTATATTATTATTCATTAT
* *
1257588 TTTCATTTTTTTATTCATTAT
1 TTT-ATATTATTATTCATTAT
1257609 TATTATATTATTATT
1 T-TTATATTATTATT
1257624 TAAAAAAAAA
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
20 3 0.11
21 23 0.82
22 2 0.07
ACGTcount: A:0.25, C:0.04, G:0.00, T:0.71
Consensus pattern (20 bp):
TTTATATTATTATTCATTAT
Found at i:1262186 original size:183 final size:183
Alignment explanation
Indices: 1261878--1262414 Score: 968
Period size: 183 Copynumber: 2.9 Consensus size: 183
1261868 ATTAAATCCG
* *
1261878 TAAAGCTAAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCTTGGCTTTATGA
1 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
* *
1261943 ATAGATTATGTTCAAACTCTGATACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTT
66 ATAGATTATGTTCAAACTATGAAACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTT
1262008 TTGTCAGGCCAAAGACTTTGTGATGAGATGAACCCTTCAGTGATTTGTCCCTC
131 TTGTCAGGCCAAAGACTTTGTGATGAGATGAACCCTTCAGTGATTTGTCCCTC
1262061 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
1 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
1262126 ATAGATTATGTTCAAACTATGAAACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTT
66 ATAGATTATGTTCAAACTATGAAACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTT
*
1262191 TTGTCAGGCCAAAGACTTTGTGATGAGACGAACCCTTCAGTGATTTGTCCCTC
131 TTGTCAGGCCAAAGACTTTGTGATGAGATGAACCCTTCAGTGATTTGTCCCTC
1262244 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
1 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
** * *
1262309 ATAGATTACATTCAAA-TCATGACATTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCT
66 ATAGATTATGTTCAAACT-ATGAAACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCT
*
1262373 TTTGTCAGGTCAAAGACTTTGTGATGAGATGAACCCTTCAGT
130 TTTGTCAGGCCAAAGACTTTGTGATGAGATGAACCCTTCAGT
1262415 TAAACCTGAT
Statistics
Matches: 342, Mismatches: 11, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
182 1 0.00
183 341 1.00
ACGTcount: A:0.27, C:0.21, G:0.22, T:0.31
Consensus pattern (183 bp):
TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
ATAGATTATGTTCAAACTATGAAACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTT
TTGTCAGGCCAAAGACTTTGTGATGAGATGAACCCTTCAGTGATTTGTCCCTC
Found at i:1263608 original size:36 final size:34
Alignment explanation
Indices: 1263568--1263681 Score: 86
Period size: 36 Copynumber: 3.2 Consensus size: 34
1263558 CACTCAAATT
1263568 TGTTTTTCTTAAAACATACTTTGTCTCACTTGAGAC
1 TGTTTTTCTTAAAACA-A-TTTGTCTCACTTGAGAC
* * * ** *
1263604 TGTTTTTCTCGAAAGA-AGATTTATTTCACTCAAGAT
1 TGTTTTTCT-TAAA-ACA-ATTTGTCTCACTTGAGAC
*
1263640 TGTTTTTCTTAAAACAAGATTTGTCTCGCTTGAGAC
1 TGTTTTTCTTAAAAC-A-ATTTGTCTCACTTGAGAC
*
1263676 CGTTTT
1 TGTTTT
1263682 CACTCGAAAG
Statistics
Matches: 59, Mismatches: 15, Indels: 8
0.72 0.18 0.10
Matches are distributed among these distances:
34 1 0.02
35 3 0.05
36 49 0.83
37 5 0.08
38 1 0.02
ACGTcount: A:0.25, C:0.17, G:0.14, T:0.44
Consensus pattern (34 bp):
TGTTTTTCTTAAAACAATTTGTCTCACTTGAGAC
Found at i:1263644 original size:72 final size:75
Alignment explanation
Indices: 1263552--1263712 Score: 215
Period size: 72 Copynumber: 2.2 Consensus size: 75
1263542 ATGCAGATGA
* * * *
1263552 TTATCTCACTCAAATTTGTTTTTCTTAAAACATA-CTTTGTCTCACTTGAGACTGTTTT-TCTCG
1 TTATTTCACTCAAATTTGTTTTTCTTAAAACA-AGATTTGTCTCACTTGAGACCGTTTTCACTCG
1263615 AAAGAA-G-AT
65 AAAGAAGGCAT
*
1263624 TTATTTCACTCAAGA-TTGTTTTTCTTAAAACAAGATTTGTCTCGCTTGAGACCGTTTTCACTCG
1 TTATTTCACTCAA-ATTTGTTTTTCTTAAAACAAGATTTGTCTCACTTGAGACCGTTTTCACTCG
1263688 AAAGAAGGCAT
65 AAAGAAGGCAT
1263699 TTCATTTCACTCAA
1 TT-ATTTCACTCAA
1263713 TGCTGTTTTT
Statistics
Matches: 78, Mismatches: 5, Indels: 8
0.86 0.05 0.09
Matches are distributed among these distances:
71 1 0.01
72 50 0.64
73 11 0.14
74 1 0.01
75 4 0.05
76 11 0.14
ACGTcount: A:0.28, C:0.19, G:0.12, T:0.40
Consensus pattern (75 bp):
TTATTTCACTCAAATTTGTTTTTCTTAAAACAAGATTTGTCTCACTTGAGACCGTTTTCACTCGA
AAGAAGGCAT
Found at i:1263761 original size:73 final size:72
Alignment explanation
Indices: 1263568--1263763 Score: 170
Period size: 72 Copynumber: 2.7 Consensus size: 72
1263558 CACTCAAATT
* * * * *
1263568 TGTTTTTCTTAAAACATA-CTTTGTCTCACTTGAGACTGTTTT-TCTCGAAAGAAGATTTATTTC
1 TGTTTTTCTT-AAACA-AGATTTATCTCGCTTGAGACAGTTTTCACTCGAAAGAAGATTTATTTC
*
1263631 ACTCAAGAT
64 ACTCAAGAC
* *
1263640 TGTTTTTCTTAAAACAAGATTTGTCTCGCTTGAGACCGTTTTCACTCGAAAGAAGGCATTTCATT
1 TGTTTTTCTT-AAACAAGATTTATCTCGCTTGAGACAGTTTTCACTCGAAAGAA-G-ATTT-ATT
1263705 TCACTCAATG-C
62 TCACTCAA-GAC
* * * *
1263716 TGTTTTT-TT-AAGAAGATTTTATCTTGCTTGAGATAG-TTTCCCTCGAAA
1 TGTTTTTCTTAAACAAGA-TTTATCTCGCTTGAGACAGTTTTCACTCGAAA
1263764 CAGAAAATTT
Statistics
Matches: 106, Mismatches: 11, Indels: 13
0.82 0.08 0.10
Matches are distributed among these distances:
71 1 0.01
72 37 0.35
73 27 0.25
74 16 0.15
75 6 0.06
76 18 0.17
77 1 0.01
ACGTcount: A:0.27, C:0.17, G:0.15, T:0.41
Consensus pattern (72 bp):
TGTTTTTCTTAAACAAGATTTATCTCGCTTGAGACAGTTTTCACTCGAAAGAAGATTTATTTCAC
TCAAGAC
Found at i:1263785 original size:39 final size:39
Alignment explanation
Indices: 1263742--1263894 Score: 119
Period size: 39 Copynumber: 3.6 Consensus size: 39
1263732 TTTTATCTTG
*
1263742 CTTGAGATAGTTTCCCTCGAAACAGAAAATTTTGTCTCC
1 CTTGAGACAGTTTCCCTCGAAACAGAAAATTTTGTCTCC
* * *
1263781 CTTGAGACAGTTTCTCTTGAAAACATTTCCCTTGAAATTAATTTTTTCTCTC
1 CTTGAGACAGTTTCCCTCG-AAACA--------G-AA--AATTTTGTCTC-C
*
1263833 C-TGAGATAGTTTCCCTCGAAACAGAAAATTTTGTCTCC
1 CTTGAGACAGTTTCCCTCGAAACAGAAAATTTTGTCTCC
* *
1263871 CTTGAGACAGTTTCTCTTGAAACA
1 CTTGAGACAGTTTCCCTCGAAACA
1263895 TAAACATTGA
Statistics
Matches: 89, Mismatches: 11, Indels: 28
0.70 0.09 0.22
Matches are distributed among these distances:
38 2 0.02
39 45 0.51
40 5 0.06
41 2 0.02
42 1 0.01
48 1 0.01
49 2 0.02
50 5 0.06
51 24 0.27
52 2 0.02
ACGTcount: A:0.27, C:0.22, G:0.14, T:0.37
Consensus pattern (39 bp):
CTTGAGACAGTTTCCCTCGAAACAGAAAATTTTGTCTCC
Found at i:1263957 original size:36 final size:36
Alignment explanation
Indices: 1263910--1263985 Score: 116
Period size: 36 Copynumber: 2.1 Consensus size: 36
1263900 ATTGAAAACA
* * *
1263910 TTTCCCTTGAAATGAATTTTATCTCGCTTGAGATAG
1 TTTCCCTTGAAACGAATTTTATCTCCCTTGAGACAG
*
1263946 TTTCCCTTGAAACGAATTTTGTCTCCCTTGAGACAG
1 TTTCCCTTGAAACGAATTTTATCTCCCTTGAGACAG
1263982 TTTC
1 TTTC
1263986 TCTCCAAACA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.22, C:0.21, G:0.16, T:0.41
Consensus pattern (36 bp):
TTTCCCTTGAAACGAATTTTATCTCCCTTGAGACAG
Found at i:1264010 original size:101 final size:103
Alignment explanation
Indices: 1263797--1264010 Score: 333
Period size: 104 Copynumber: 2.1 Consensus size: 103
1263787 ACAGTTTCTC
* * *
1263797 TTGAAAACATTTCCCTTGAAATTAATTTTTTCTCTCCTGAGATAGTTTCCCTCGAAACAGAAAAT
1 TTGAAAACATTTCCCTTGAAATGAATTTTATCTCGCCTGAGATAGTTTCCCTCGAAACAG-AAAT
**
1263862 TTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
65 TTTGTCTCCCTTGAGACAGTTTCTCTCCAAACATAAACA
* *
1263901 TTGAAAACATTTCCCTTGAAATGAATTTTATCTCGCTTGAGATAGTTTCCCTTGAAAC-G-AATT
1 TTGAAAACATTTCCCTTGAAATGAATTTTATCTCGCCTGAGATAGTTTCCCTCGAAACAGAAATT
*
1263964 TTGTCTCCCTTGAGACAGTTTCTCTCCAAACATAAACT
66 TTGTCTCCCTTGAGACAGTTTCTCTCCAAACATAAACA
1264002 TTGAAAACA
1 TTGAAAACA
1264011 ATTTAACGAA
Statistics
Matches: 102, Mismatches: 8, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
101 48 0.47
103 1 0.01
104 53 0.52
ACGTcount: A:0.31, C:0.21, G:0.12, T:0.36
Consensus pattern (103 bp):
TTGAAAACATTTCCCTTGAAATGAATTTTATCTCGCCTGAGATAGTTTCCCTCGAAACAGAAATT
TTGTCTCCCTTGAGACAGTTTCTCTCCAAACATAAACA
Found at i:1264383 original size:105 final size:105
Alignment explanation
Indices: 1264185--1264816 Score: 925
Period size: 105 Copynumber: 6.0 Consensus size: 105
1264175 ATATCGTGAC
* * * * *
1264185 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAAC-AACAACTTCTC
*
1264250 AATTTCAGAGCCAATTTCAACTTCACAACGAATGATATTGG
65 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
*
1264291 ACTCCATACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCA
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCA
1264356 ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * *
1264396 ACTTCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCACTGCTTGTCAACAACAACTTCCCA
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCA
*
1264461 ATCTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
*
1264501 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCA
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCA
*
1264566 ATCTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
*
1264606 ACTCCAGACAACGCAAGTTCAACTCCACGACGAAGGGACCGCTGCTTGTCAAACAA-AA-TT-TC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTC-AACAACAACTTCTC
* *
1264668 -A-TTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGG
65 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * * * * * * *
1264707 ACTCGAGACAACACATGTTCAACTTCACAACGAAAGGACGGCTGGTTGTCAACAAACAATTTC-C
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAAC-AACAACTTCTC
*** * *
1264771 CGGTTCTAGAGCCAATTTCAACTTCACGACGGAGGATATTGG
65 AATTTC-AGAGCCAATTTCAACTTCACAACGAAGGATATTGG
1264813 ACTC
1 ACTC
1264817 GGAACAATGT
Statistics
Matches: 486, Mismatches: 32, Indels: 16
0.91 0.06 0.03
Matches are distributed among these distances:
100 3 0.01
101 79 0.16
102 3 0.01
103 4 0.01
104 2 0.00
105 308 0.63
106 87 0.18
ACGTcount: A:0.34, C:0.27, G:0.18, T:0.22
Consensus pattern (105 bp):
ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCA
ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
Found at i:1265453 original size:37 final size:37
Alignment explanation
Indices: 1265360--1265455 Score: 122
Period size: 37 Copynumber: 2.6 Consensus size: 37
1265350 ATTTTCGTCA
1265360 TACTAGGATTCAAACTCCTAAAAATAAGATAAAAGTT
1 TACTAGGATTCAAACTCCTAAAAATAAGATAAAAGTT
* * *
1265397 TGCTAGGATTCAAACTCCTAAAAATAGGAT-AGAGTT
1 TACTAGGATTCAAACTCCTAAAAATAAGATAAAAGTT
* * *
1265433 CTACTAAGATTTAAATTCCTAAA
1 -TACTAGGATTCAAACTCCTAAA
1265456 GATATGATTC
Statistics
Matches: 51, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
36 5 0.10
37 46 0.90
ACGTcount: A:0.44, C:0.15, G:0.12, T:0.29
Consensus pattern (37 bp):
TACTAGGATTCAAACTCCTAAAAATAAGATAAAAGTT
Found at i:1265859 original size:18 final size:17
Alignment explanation
Indices: 1265820--1265862 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
1265810 ATTATATGGA
1265820 TATT-TTATTCATTTAT
1 TATTATTATTCATTTAT
*
1265836 TTTTATTATTCATGTTAT
1 TATTATTATTCAT-TTAT
1265854 TATTATTAT
1 TATTATTAT
1265863 ATGTATATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.26, C:0.05, G:0.02, T:0.67
Consensus pattern (17 bp):
TATTATTATTCATTTAT
Found at i:1266151 original size:21 final size:20
Alignment explanation
Indices: 1266110--1266178 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 20
1266100 ATCTTATAAC
*
1266110 TTTATATATTTATATTATTTTT
1 TTTAT-TATTT-TATTTTTTTT
*
1266132 TTTATTATTTTCATTTTTTTA
1 TTTATTATTTT-ATTTTTTTT
* *
1266153 TTCATTATTATTATATTTTTAT
1 TTTATTATT-TTAT-TTTTTTT
1266175 TTTA
1 TTTA
1266179 AAAAAAAACC
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
20 1 0.03
21 22 0.58
22 15 0.39
ACGTcount: A:0.25, C:0.03, G:0.00, T:0.72
Consensus pattern (20 bp):
TTTATTATTTTATTTTTTTT
Found at i:1266467 original size:18 final size:17
Alignment explanation
Indices: 1266445--1266497 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 17
1266435 TCTTATCTTA
*
1266445 CTTATTTATTTTATTTAT
1 CTTATTT-TTTTCTTTAT
*
1266463 TTTATTTTTTTCTTGTAT
1 CTTATTTTTTTCTT-TAT
1266481 CTTATTTGTTTTCTTTA
1 CTTATTT-TTTTCTTTA
1266498 CCTTGTTTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
17 6 0.20
18 17 0.57
19 7 0.23
ACGTcount: A:0.15, C:0.08, G:0.04, T:0.74
Consensus pattern (17 bp):
CTTATTTTTTTCTTTAT
Found at i:1267777 original size:35 final size:35
Alignment explanation
Indices: 1267723--1267803 Score: 126
Period size: 35 Copynumber: 2.3 Consensus size: 35
1267713 ATCGAATTAA
*
1267723 ACGGGGACGGGGAAAAACCGTTTATGCTAAACGGGG
1 ACGGGGAC-GGAAAAAACCGTTTATGCTAAACGGGG
* *
1267759 ATGGGGACGGAAAAAACCGTTTATGTTAAACGGGG
1 ACGGGGACGGAAAAAACCGTTTATGCTAAACGGGG
1267794 ACGGGGACGG
1 ACGGGGACGG
1267804 GGACGGGTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
35 34 0.83
36 7 0.17
ACGTcount: A:0.31, C:0.15, G:0.40, T:0.15
Consensus pattern (35 bp):
ACGGGGACGGAAAAAACCGTTTATGCTAAACGGGG
Found at i:1267924 original size:17 final size:17
Alignment explanation
Indices: 1267901--1267945 Score: 51
Period size: 15 Copynumber: 2.8 Consensus size: 17
1267891 TAAATTAAAA
1267901 ATATATATATATAATATT
1 ATATATATATATAAT-TT
1267919 -TATATAT-T-TAATTT
1 ATATATATATATAATTT
*
1267933 AAATATATATATA
1 ATATATATATATA
1267946 CCCGGTCCGA
Statistics
Matches: 23, Mismatches: 1, Indels: 7
0.74 0.03 0.23
Matches are distributed among these distances:
14 2 0.09
15 10 0.43
16 2 0.09
17 9 0.39
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
ATATATATATATAATTT
Found at i:1269074 original size:54 final size:56
Alignment explanation
Indices: 1268958--1269090 Score: 128
Period size: 54 Copynumber: 2.4 Consensus size: 56
1268948 CTCTAATTTT
* * * ** *
1268958 TTTTTTTCAATTTTATAAAATAATCCTTATTTTCTACCTTTATAATTGAGGCATTC
1 TTTTTTTCAATTTTATAAAATAATCCATACTTTCTAACTTTATAACAGAGGCACTC
* * *
1269014 TATTTTT-AATTTTATAAAATGA-CCATACTTTCTAACTTTATAACAGA-GTACTC
1 TTTTTTTCAATTTTATAAAATAATCCATACTTTCTAACTTTATAACAGAGGCACTC
*
1269067 ATTTTTTTTCCAATTCTATAAAAT
1 --TTTTTTT-CAATTTTATAAAAT
1269091 TCTCAAATTT
Statistics
Matches: 62, Mismatches: 11, Indels: 7
0.77 0.14 0.09
Matches are distributed among these distances:
53 4 0.06
54 20 0.32
55 20 0.32
56 6 0.10
57 12 0.19
ACGTcount: A:0.32, C:0.14, G:0.05, T:0.49
Consensus pattern (56 bp):
TTTTTTTCAATTTTATAAAATAATCCATACTTTCTAACTTTATAACAGAGGCACTC
Found at i:1270120 original size:22 final size:23
Alignment explanation
Indices: 1270085--1270128 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
1270075 CACAACACAT
1270085 ACTAATAAAAAATATCTTTGAAA
1 ACTAATAAAAAATATCTTTGAAA
*
1270108 ACTAAT-AAAAATATTTTTGAA
1 ACTAATAAAAAATATCTTTGAA
1270129 GGGTCAAACT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 14 0.70
23 6 0.30
ACGTcount: A:0.55, C:0.07, G:0.05, T:0.34
Consensus pattern (23 bp):
ACTAATAAAAAATATCTTTGAAA
Found at i:1272501 original size:27 final size:29
Alignment explanation
Indices: 1272467--1272525 Score: 104
Period size: 29 Copynumber: 2.1 Consensus size: 29
1272457 CCCATATTCA
1272467 TTTGC-TTTG-TAACCACGTGTATGTGGT
1 TTTGCTTTTGTTAACCACGTGTATGTGGT
1272494 TTTGCTTTTGTTAACCACGTGTATGTGGT
1 TTTGCTTTTGTTAACCACGTGTATGTGGT
1272523 TTT
1 TTT
1272526 CATTTTTTTC
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
27 5 0.17
28 4 0.13
29 21 0.70
ACGTcount: A:0.14, C:0.14, G:0.24, T:0.49
Consensus pattern (29 bp):
TTTGCTTTTGTTAACCACGTGTATGTGGT
Found at i:1272540 original size:8 final size:9
Alignment explanation
Indices: 1272522--1272557 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
1272512 GTGTATGTGG
1272522 TTTTCATTT
1 TTTTCATTT
1272531 TTTTCATTT
1 TTTTCATTT
1272540 TTTTCATTT
1 TTTTCATTT
1272549 TTTT-ATTT
1 TTTTCATTT
1272557 T
1 T
1272558 AATATTATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 5 0.19
9 22 0.81
ACGTcount: A:0.11, C:0.08, G:0.00, T:0.81
Consensus pattern (9 bp):
TTTTCATTT
Found at i:1274446 original size:7 final size:7
Alignment explanation
Indices: 1274434--1274462 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
1274424 TTCATGCATT
1274434 TTTTGCA
1 TTTTGCA
1274441 TTTTGCA
1 TTTTGCA
1274448 TTTTGCA
1 TTTTGCA
1274455 TTTTGCA
1 TTTTGCA
1274462 T
1 T
1274463 CTACATTTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.14, C:0.14, G:0.14, T:0.59
Consensus pattern (7 bp):
TTTTGCA
Found at i:1275740 original size:16 final size:16
Alignment explanation
Indices: 1275719--1275750 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1275709 AACAAAAGCA
1275719 AAAAAAGAACAAAAAG
1 AAAAAAGAACAAAAAG
*
1275735 AAAAAAGGACAAAAAG
1 AAAAAAGAACAAAAAG
1275751 CACATGCAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.78, C:0.06, G:0.16, T:0.00
Consensus pattern (16 bp):
AAAAAAGAACAAAAAG
Found at i:1276366 original size:22 final size:22
Alignment explanation
Indices: 1276338--1276380 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
1276328 AGCTACCCCA
*
1276338 TCAAACCTTTGAGCATCAAATG
1 TCAAACCATTGAGCATCAAATG
1276360 TCAAACCATTGAGCATCAAAT
1 TCAAACCATTGAGCATCAAAT
1276381 TAACAAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.40, C:0.23, G:0.12, T:0.26
Consensus pattern (22 bp):
TCAAACCATTGAGCATCAAATG
Found at i:1276851 original size:18 final size:18
Alignment explanation
Indices: 1276817--1276852 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1276807 TCAACATCAA
* *
1276817 ATATTGGGGTATTTTTGG
1 ATATTGGGGCATATTTGG
1276835 ATATTGGGGCATATTTGG
1 ATATTGGGGCATATTTGG
1276853 GGATTCAACA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.19, C:0.03, G:0.33, T:0.44
Consensus pattern (18 bp):
ATATTGGGGCATATTTGG
Found at i:1278508 original size:106 final size:106
Alignment explanation
Indices: 1277344--1278507 Score: 1644
Period size: 106 Copynumber: 11.0 Consensus size: 106
1277334 ATATCGTGCC
* *
1277344 ACTCGAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
1 ACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
1277409 AATTTCAGAGTCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* *
1277450 ACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAATAACTTCTC
1 ACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* *
1277515 AATTTCGGAGCCAATTTCAACTTCACAACGAAAGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * *
1277556 ACTTC-AGACAACGCAAGTTCAACTTCATGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCC
1 AC-TCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCC
* *
1277620 CAATTTCAGAGCCAATTTTAACTTCACAACGAAGGATATTAG
65 CAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* *
1277662 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
1277727 AATTTTAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * *
1277768 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAATAATTTCCC
1 ACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* * *
1277833 AATTTCAGAGCCAATTTCAAATTCACAGCGAACGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* *
1277874 ACTCAAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
1 ACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* *
1277939 AATTTCAGAGCAAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * * *
1277980 ACTCCAGACAACGCAAGTTCAACTTCACGACGAATGGACCGTTGGTTGTCAACAAACAACTTCTC
1 ACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* *
1278045 AATTTTAGAGCCAATTTCAACTTCACAACAAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * * *
1278086 ACTCCAGACAACGCAAGTTCAACTTCACGATGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
1 ACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* *
1278151 AATTTCAGAGCCAATTTCAACTTCGCATC-ATAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGA-AGGATATTGG
* *
1278192 ACTCAAGACAACGCAAGTTCAACTTCACGGCGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
1 ACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* * * *
1278257 AATTTCAAAGCCAATTTCAAGTTCTCAACGAAGGATCTTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
** * * * * *
1278298 A-TCCAAGACAATACAAGCTCAACTTCACGACGAAGGGGCGGCTGATTGTCAAC-AA-AA-TT-T
1 ACT-CAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCC
* * *
1278358 C-A-TTCAGAGTCAATTTCAACTTCACAGCGAATGATATTGG
65 CAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * * * * * * *
1278398 ACTCGAGACAACACAAGTTCAACTTCACAACGAAAGGACGGTTGGTTGTCAATAAACAATTTCCC
1 ACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
** * * *
1278463 GGTTCCAGAGCCAATTTCAACTTCACGACGGAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
1278504 ACTC
1 ACTC
1278508 GGAACAATGC
Statistics
Matches: 947, Mismatches: 99, Indels: 24
0.89 0.09 0.02
Matches are distributed among these distances:
100 73 0.08
101 4 0.00
102 3 0.00
103 4 0.00
104 3 0.00
105 6 0.01
106 851 0.90
107 3 0.00
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.23
Consensus pattern (106 bp):
ACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
Found at i:1280028 original size:27 final size:29
Alignment explanation
Indices: 1279994--1280052 Score: 104
Period size: 29 Copynumber: 2.1 Consensus size: 29
1279984 CCCATATTCA
1279994 TTTGC-TTTG-TAACCACGTGTATGTGGT
1 TTTGCTTTTGTTAACCACGTGTATGTGGT
1280021 TTTGCTTTTGTTAACCACGTGTATGTGGT
1 TTTGCTTTTGTTAACCACGTGTATGTGGT
1280050 TTT
1 TTT
1280053 CATTTTTTTC
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
27 5 0.17
28 4 0.13
29 21 0.70
ACGTcount: A:0.14, C:0.14, G:0.24, T:0.49
Consensus pattern (29 bp):
TTTGCTTTTGTTAACCACGTGTATGTGGT
Found at i:1280067 original size:8 final size:9
Alignment explanation
Indices: 1280049--1280084 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
1280039 GTGTATGTGG
1280049 TTTTCATTT
1 TTTTCATTT
1280058 TTTTCATTT
1 TTTTCATTT
1280067 TTTTCATTT
1 TTTTCATTT
1280076 TTTT-ATTT
1 TTTTCATTT
1280084 T
1 T
1280085 AATATTATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 5 0.19
9 22 0.81
ACGTcount: A:0.11, C:0.08, G:0.00, T:0.81
Consensus pattern (9 bp):
TTTTCATTT
Found at i:1282845 original size:31 final size:31
Alignment explanation
Indices: 1282807--1282878 Score: 108
Period size: 31 Copynumber: 2.3 Consensus size: 31
1282797 GGACTGAAAT
*
1282807 CCTACCCAAGAAAATTATCGAGGCCTCATAG
1 CCTACCCAAGAAAATTATCGAGGCCTCAGAG
* * *
1282838 CCTACCCAAGAAAGTTCTCGGGGCCTCAGAG
1 CCTACCCAAGAAAATTATCGAGGCCTCAGAG
1282869 CCTACCCAAG
1 CCTACCCAAG
1282879 GGTCGTCTTA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.31, C:0.33, G:0.19, T:0.17
Consensus pattern (31 bp):
CCTACCCAAGAAAATTATCGAGGCCTCAGAG
Found at i:1284447 original size:4 final size:4
Alignment explanation
Indices: 1284438--1284495 Score: 64
Period size: 4 Copynumber: 14.8 Consensus size: 4
1284428 TTAAAATTAA
* * * * *
1284438 AAAT AAAT AAAT AAAT ATAT ATAT ATAT ATAT ATAT -AAT AAAT AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
1284485 AAAT AAAT AAA
1 AAAT AAAT AAA
1284496 AAGGATTAAA
Statistics
Matches: 51, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
3 2 0.04
4 49 0.96
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (4 bp):
AAAT
Found at i:1285818 original size:84 final size:82
Alignment explanation
Indices: 1285619--1286045 Score: 314
Period size: 84 Copynumber: 5.2 Consensus size: 82
1285609 AATTTGGTGA
* * * * * * * *
1285619 CAGATAACCCTTCTAG-CATTGAGTTATGCTGTAAATAATGTGCCCTTGAAGGTGAGTGTAATCG
1 CAGACAACCCTTCTAGAC-TTAAGTTATACTGCAAATGATATG-CCTTG-AGCTGAGCGTAATCG
* *
1285683 AACTCGAGGGTC--T-TTGG
63 AACTCAAAGGTCTTTGTTGG
* * * * * * * * *
1285700 CAGATAGCCCTCCTCGACTTAAGCTATGCTGCAAATGATGTGCCGTTGAGCTGAGTGTAGTCGAA
1 CAGACAACCCTTCTAGACTTAAGTTATACTGCAAATGATATGCC-TTGAGCTGAGCGTAATCGAA
1285765 CTCAAAGGTCTTTTGTTGG
65 CTCAAAGGTC-TTTGTTGG
* * *
1285784 CAGACAACCGTTCTAGACTTAAGTTGTACTGCAAATGATATG-CTTGGGAGCTGAGCGTAATCAA
1 CAGACAACCCTTCTAGACTTAAGTTATACTGCAAATGATATGCCTT--GAGCTGAGCGTAATCGA
* * *
1285848 ACTCGAAGGTCTTTGGTGA
64 ACTCAAAGGTCTTTGTTGG
* * * * * *
1285867 CAGATAACCCTTCTAGCCTTGAGTTATACTGTAAATGATATGCCCTCGAGGCTGAGTGTAATCGA
1 CAGACAACCCTTCTAGACTTAAGTTATACTGCAAATGATATG-CCTTGA-GCTGAGCGTAATCGA
***
1285932 ACTCGGGGGTC--T-TTGG
64 ACTCAAAGGTCTTTGTTGG
* * * * * * *
1285948 CAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCATTGAGCTGAGCGTAGTCGAA
1 CAGACAACCCTTCTAGACTTAAGTTATACTGCAAATGATATGCC-TTGAGCTGAGCGTAATCGAA
1286013 CTCAAAGGTCTTTTGTTGG
65 CTCAAAGGTC-TTTGTTGG
1286032 CAGAC-ACTCCTTCT
1 CAGACAAC-CCTTCT
1286046 TTGAGTTGGA
Statistics
Matches: 274, Mismatches: 55, Indels: 31
0.76 0.15 0.09
Matches are distributed among these distances:
80 48 0.18
81 75 0.27
82 4 0.01
83 48 0.18
84 97 0.35
85 2 0.01
ACGTcount: A:0.25, C:0.21, G:0.25, T:0.30
Consensus pattern (82 bp):
CAGACAACCCTTCTAGACTTAAGTTATACTGCAAATGATATGCCTTGAGCTGAGCGTAATCGAAC
TCAAAGGTCTTTGTTGG
Found at i:1286411 original size:106 final size:106
Alignment explanation
Indices: 1286226--1287620 Score: 2301
Period size: 106 Copynumber: 13.2 Consensus size: 106
1286216 TATTGTTCCA
* ** * * * *
1286226 AGTCCAATATCCTCCGCCGTGAAGTTGAAATTGGCTCTGGAACTG-GAAAATTGTTTATTGACAA
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAG-AAGTTGTTTGTTGACAA
*
1286290 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
65 CCAGCGGTCCCTTCGTCGTGAAGTTGAACATGCGTTGTCTGG
*
1286332 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTAAGAAGTTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAAC
*
1286397 CAGCGGTCCCTTCGTCGTGAAGTCGAACATGCGTTGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACATGCGTTGTCTGG
*
1286438 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTATTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAAC
*
1286503 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACATGCGTTGTCTGG
* * *
1286544 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTATGAAATTGGGAAGTTGTTTATTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAAC
* * * *
1286609 CAGCGGTCCATTCATCGTGAAGTTGAACTTGCATTGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACATGCGTTGTCTGG
1286650 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAAC
1286715 CAGCGGTCCCTTCGTCGTGAAGTTGAACATGCGTTGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACATGCGTTGTCTGG
* * *
1286756 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTATGAAATTGGGAAGTTGTTTATTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAAC
* * *
1286821 TAGCGGTCCCTTAGTCATGAAGTTGAACATGCGTTGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACATGCGTTGTCTGG
* *
1286862 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTAAGAAGTTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAAC
1286927 CAGCGGTCCCTTCGTCGTGAAGTTGAACATGCGTTGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACATGCGTTGTCTGG
* * *
1286968 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAAC
* *
1287033 TAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACATGCGTTGTCTGG
*
1287074 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAAC
*
1287139 CAGCGGTTCCTTCGTCGTGAAGTTGAACATGCGTTGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACATGCGTTGTCTGG
* *
1287180 AGTCCAATATCCTTCGCTT-TGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
1 AGTCCAATATCCTTCG-TTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
* *
1287244 CCAGCGATCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
65 CCAGCGGTCCCTTCGTCGTGAAGTTGAACATGCGTTGTCTGG
*
1287286 AGTCCAATATCCTTCGTTGTGAAGTTAAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAAC
1287351 CAGCGGTCCCTTCGTCGTGAAGTTGAACATGCGTTGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACATGCGTTGTCTGG
*
1287392 AGTCCAATATCATTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAAC
1287457 CAGCGGTCCCTTCGTCGTGAAGTTGAACATGCGTTGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACATGCGTTGTCTGG
* * * * * *
1287498 AGTCCACTATCCTTCGCTGTGAAGTTGAAATTGGCTCTAGAAGTGGA-AAATTGTTTATTGACAA
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCT-GAAATTGAGAAGTTGTTTGTTGACAA
*
1287562 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
65 CCAGCGGTCCCTTCGTCGTGAAGTTGAACATGCGTTGTCTGG
* *
1287604 AGTCCAATTTTCTTCGT
1 AGTCCAATATCCTTCGT
1287621 GCTCATGGTT
Statistics
Matches: 1208, Mismatches: 77, Indels: 8
0.93 0.06 0.01
Matches are distributed among these distances:
105 2 0.00
106 1198 0.99
107 8 0.01
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.33
Consensus pattern (106 bp):
AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAAC
CAGCGGTCCCTTCGTCGTGAAGTTGAACATGCGTTGTCTGG
Found at i:1291664 original size:4 final size:4
Alignment explanation
Indices: 1291657--1291693 Score: 67
Period size: 4 Copynumber: 9.5 Consensus size: 4
1291647 ATATAATAAT
1291657 AATA AAT- AATA AATA AATA AATA AATA AATA AATA AA
1 AATA AATA AATA AATA AATA AATA AATA AATA AATA AA
1291694 AAGGATTAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 3 0.09
4 29 0.91
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AATA
Found at i:1293834 original size:12 final size:13
Alignment explanation
Indices: 1293801--1293836 Score: 56
Period size: 12 Copynumber: 2.8 Consensus size: 13
1293791 TGACTCTGTT
1293801 CGAGTTGACTCAA
1 CGAGTTGACTCAA
*
1293814 CGGGTTGACTC-A
1 CGAGTTGACTCAA
1293826 CGAGTTGACTC
1 CGAGTTGACTC
1293837 GTTTGACTCG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 11 0.52
13 10 0.48
ACGTcount: A:0.22, C:0.25, G:0.28, T:0.25
Consensus pattern (13 bp):
CGAGTTGACTCAA
Found at i:1298473 original size:71 final size:71
Alignment explanation
Indices: 1298353--1298495 Score: 250
Period size: 71 Copynumber: 2.0 Consensus size: 71
1298343 GAACAATGGA
* * *
1298353 CAAGCTTTTAGGTTAAACACAACTCATAATTTAGTTGTTTTTTCAGTGATAAACAAAGGTAAGGG
1 CAAGCTTCTAGGTTAAACACAACTCATAATTTAATTGTTTTTCCAGTGATAAACAAAGGTAAGGG
1298418 ATAGTT
66 ATAGTT
*
1298424 CAAGCTTCTAGGTTAAACACAACTCATAATTTAATTGTTTTTCCTGTGATAAACAAAGGTAAGGG
1 CAAGCTTCTAGGTTAAACACAACTCATAATTTAATTGTTTTTCCAGTGATAAACAAAGGTAAGGG
1298489 ATAGTT
66 ATAGTT
1298495 C
1 C
1298496 GAAAGACCAT
Statistics
Matches: 68, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
71 68 1.00
ACGTcount: A:0.35, C:0.13, G:0.17, T:0.34
Consensus pattern (71 bp):
CAAGCTTCTAGGTTAAACACAACTCATAATTTAATTGTTTTTCCAGTGATAAACAAAGGTAAGGG
ATAGTT
Found at i:1298662 original size:71 final size:71
Alignment explanation
Indices: 1298546--1298688 Score: 232
Period size: 71 Copynumber: 2.0 Consensus size: 71
1298536 GAACAATGGA
* * * *
1298546 CAAGCTTCTAGGTGAAACACAACTTAGAATTTAGTTATTTTTTCGGTGATAAACAGAGGTAAGGG
1 CAAGCTTCTAGGTGAAACACAACTCAGAATTTAGCTATTGTTTCGGTGATAAACAAAGGTAAGGG
1298611 ATAGTT
66 ATAGTT
* *
1298617 CAAGCTTCTAGGTTAAACACAACTCAGAATTTAGCTGTTGTTTCGGTGATAAACAAAGGTAAGGG
1 CAAGCTTCTAGGTGAAACACAACTCAGAATTTAGCTATTGTTTCGGTGATAAACAAAGGTAAGGG
1298682 ATAGTT
66 ATAGTT
1298688 C
1 C
1298689 GAGATTTCGA
Statistics
Matches: 66, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
71 66 1.00
ACGTcount: A:0.34, C:0.13, G:0.22, T:0.31
Consensus pattern (71 bp):
CAAGCTTCTAGGTGAAACACAACTCAGAATTTAGCTATTGTTTCGGTGATAAACAAAGGTAAGGG
ATAGTT
Found at i:1298668 original size:193 final size:192
Alignment explanation
Indices: 1298306--1298690 Score: 646
Period size: 193 Copynumber: 2.0 Consensus size: 192
1298296 TTATATTATT
* *
1298306 AAGACCATTAAAATGGACTTTGACATAATTTTATAGAGAACAATGGACAAGCTTTTAGGTTAAAC
1 AAGACCATTAAAATGGACTTTGACATAATTTTATAGAGAACAATGGACAAGCTTCTAGGTGAAAC
* *
1298371 ACAACTCATAATTTAGTTGTTTTTTCAGTGATAAACAAAGGTAAGGGATAGTTCAAGCTTCTAGG
66 ACAACTCAGAATTTAGTTATTTTTTCAGTGATAAACAAAGGTAAGGGATAGTTCAAGCTTCTAGG
* * *
1298436 TTAAACACAACTCATAATTTAATTGTTTTTCCTGTGATAAACAAAGGTAAGGGATAGTTCGA
131 TTAAACACAACTCAGAATTTAACTGTTTTTCCGGTGATAAACAAAGGTAAGGGATAGTTCGA
1298498 AAGACCATTAACAATGGACTTTGACATAATTTTATAGAGAACAATGGACAAGCTTCTAGGTGAAA
1 AAGACCATTAA-AATGGACTTTGACATAATTTTATAGAGAACAATGGACAAGCTTCTAGGTGAAA
* * *
1298563 CACAACTTAGAATTTAGTTATTTTTTCGGTGATAAACAGAGGTAAGGGATAGTTCAAGCTTCTAG
65 CACAACTCAGAATTTAGTTATTTTTTCAGTGATAAACAAAGGTAAGGGATAGTTCAAGCTTCTAG
*
1298628 GTTAAACACAACTCAGAATTTAGCTGTTGTTT-CGGTGATAAACAAAGGTAAGGGATAGTTCGA
130 GTTAAACACAACTCAGAATTTAACTGTT-TTTCCGGTGATAAACAAAGGTAAGGGATAGTTCGA
1298691 GATTTCGACA
Statistics
Matches: 180, Mismatches: 11, Indels: 3
0.93 0.06 0.02
Matches are distributed among these distances:
192 11 0.06
193 166 0.92
194 3 0.02
ACGTcount: A:0.37, C:0.13, G:0.19, T:0.31
Consensus pattern (192 bp):
AAGACCATTAAAATGGACTTTGACATAATTTTATAGAGAACAATGGACAAGCTTCTAGGTGAAAC
ACAACTCAGAATTTAGTTATTTTTTCAGTGATAAACAAAGGTAAGGGATAGTTCAAGCTTCTAGG
TTAAACACAACTCAGAATTTAACTGTTTTTCCGGTGATAAACAAAGGTAAGGGATAGTTCGA
Found at i:1300099 original size:58 final size:58
Alignment explanation
Indices: 1300016--1300274 Score: 294
Period size: 58 Copynumber: 4.5 Consensus size: 58
1300006 CTAACTTTGT
** * *
1300016 AAGAAAATACGTTATTGAATATATTTTCTTGAGAATCTTGAATGATTTTGTTTTGTAA
1 AAGAAAATAAATTGTTGAATTTATTTTCTTGAGAATCTTGAATGATTTTGTTTTGTAA
* * *
1300074 AA-AGAAATAAATTGTTGAATTTATTTTCTTAAGAATCTTAAATGATTTTGTTTTCTAA
1 AAGA-AAATAAATTGTTGAATTTATTTTCTTGAGAATCTTGAATGATTTTGTTTTGTAA
* *
1300132 AA-AGAAATAAATTGTTGAATTTATTTTCTTGTGAATCTT-ATATGATTTTGGTTTGTAA
1 AAGA-AAATAAATTGTTGAATTTATTTTCTTGAGAATCTTGA-ATGATTTTGTTTTGTAA
* ** * * * *
1300190 AAGAAAATAAATCGTCAAATTTATTTTCTT-AGAAATCTTGAA-CATTTTATCTTGTAG
1 AAGAAAATAAATTGTTGAATTTATTTTCTTGAG-AATCTTGAATGATTTTGTTTTGTAA
*
1300247 AAGAAAATAAGTTGTTGAATTTATTTTC
1 AAGAAAATAAATTGTTGAATTTATTTTC
1300275 GTAAAATCTT
Statistics
Matches: 172, Mismatches: 24, Indels: 11
0.83 0.12 0.05
Matches are distributed among these distances:
57 37 0.22
58 133 0.77
59 2 0.01
ACGTcount: A:0.36, C:0.06, G:0.13, T:0.45
Consensus pattern (58 bp):
AAGAAAATAAATTGTTGAATTTATTTTCTTGAGAATCTTGAATGATTTTGTTTTGTAA
Found at i:1300159 original size:31 final size:31
Alignment explanation
Indices: 1300066--1300160 Score: 85
Period size: 31 Copynumber: 3.2 Consensus size: 31
1300056 AATGATTTTG
*
1300066 TTTTGTAAAAAGAAATAAATTGTTGAATTTA
1 TTTTCTAAAAAGAAATAAATTGTTGAATTTA
* * * *
1300097 TTTTCT--TAAGAATCTTAAA----TGATTTTG
1 TTTTCTAAAAAGAA--ATAAATTGTTGAATTTA
1300124 TTTTCTAAAAAGAAATAAATTGTTGAATTTA
1 TTTTCTAAAAAGAAATAAATTGTTGAATTTA
1300155 TTTTCT
1 TTTTCT
1300161 TGTGAATCTT
Statistics
Matches: 47, Mismatches: 9, Indels: 16
0.65 0.12 0.22
Matches are distributed among these distances:
27 16 0.34
29 10 0.21
31 21 0.45
ACGTcount: A:0.38, C:0.04, G:0.11, T:0.47
Consensus pattern (31 bp):
TTTTCTAAAAAGAAATAAATTGTTGAATTTA
Found at i:1306167 original size:14 final size:14
Alignment explanation
Indices: 1306130--1306176 Score: 51
Period size: 14 Copynumber: 3.3 Consensus size: 14
1306120 TTTTTATTCA
*
1306130 TTTACTTTTCAGTAC
1 TTTACTTTTCAG-CC
*
1306145 TTTAATTTTCAGCC
1 TTTACTTTTCAGCC
1306159 TTTACTTTT-ATGCC
1 TTTACTTTTCA-GCC
1306173 TTTA
1 TTTA
1306177 TATTTTTCAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
13 1 0.04
14 16 0.57
15 11 0.39
ACGTcount: A:0.19, C:0.19, G:0.06, T:0.55
Consensus pattern (14 bp):
TTTACTTTTCAGCC
Found at i:1307848 original size:19 final size:19
Alignment explanation
Indices: 1307824--1307870 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
1307814 TTATAAACTT
1307824 TAGTGC-TTAAATAAGTTTA
1 TAGTGCATTAAAT-AGTTTA
**
1307843 TAGTGCATTCTATAGTTTA
1 TAGTGCATTAAATAGTTTA
1307862 TAGTGCATT
1 TAGTGCATT
1307871 CTATAGTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 21 0.84
20 4 0.16
ACGTcount: A:0.30, C:0.09, G:0.17, T:0.45
Consensus pattern (19 bp):
TAGTGCATTAAATAGTTTA
Found at i:1307871 original size:19 final size:19
Alignment explanation
Indices: 1307837--1307879 Score: 86
Period size: 19 Copynumber: 2.3 Consensus size: 19
1307827 TGCTTAAATA
1307837 AGTTTATAGTGCATTCTAT
1 AGTTTATAGTGCATTCTAT
1307856 AGTTTATAGTGCATTCTAT
1 AGTTTATAGTGCATTCTAT
1307875 AGTTT
1 AGTTT
1307880 TAAAATCATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.26, C:0.09, G:0.16, T:0.49
Consensus pattern (19 bp):
AGTTTATAGTGCATTCTAT
Found at i:1307889 original size:19 final size:19
Alignment explanation
Indices: 1307846--1307889 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
1307836 AAGTTTATAG
* *
1307846 TGCATTCTATAGTTTATAG
1 TGCATTCTATAGTTTAAAA
1307865 TGCATTCTATAGTTTTAAAA
1 TGCATTCTATAG-TTTAAAA
1307885 T-CATT
1 TGCATT
1307890 AGGTGCTTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 16 0.73
20 6 0.27
ACGTcount: A:0.30, C:0.11, G:0.11, T:0.48
Consensus pattern (19 bp):
TGCATTCTATAGTTTAAAA
Found at i:1309720 original size:33 final size:33
Alignment explanation
Indices: 1309656--1309720 Score: 76
Period size: 33 Copynumber: 2.0 Consensus size: 33
1309646 GCTCATATGG
** * *
1309656 CTACCATGGATCACCGCTTGGACTCATTTGAGT
1 CTACCATGGATCACCGCTTAAACGCACTTGAGT
**
1309689 CTACCATGGATCGTCGCTTAAACGCACTTGAG
1 CTACCATGGATCACCGCTTAAACGCACTTGAG
1309721 AATGACTTGA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
33 26 1.00
ACGTcount: A:0.23, C:0.28, G:0.22, T:0.28
Consensus pattern (33 bp):
CTACCATGGATCACCGCTTAAACGCACTTGAGT
Found at i:1312241 original size:18 final size:18
Alignment explanation
Indices: 1312218--1312252 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1312208 GATCCGACCC
1312218 AAAATAATATATTTATTA
1 AAAATAATATATTTATTA
* *
1312236 AAAATATTATTTTTATT
1 AAAATAATATATTTATT
1312253 CAATAAAAAT
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
AAAATAATATATTTATTA
Found at i:1312783 original size:18 final size:18
Alignment explanation
Indices: 1312752--1312788 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1312742 ATTTGACCTG
1312752 AAATAATATATTTATTAA
1 AAATAATATATTTATTAA
* *
1312770 AAATATTATTTTTATTAA
1 AAATAATATATTTATTAA
1312788 A
1 A
1312789 TAAAAATAGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
AAATAATATATTTATTAA
Found at i:1315112 original size:36 final size:37
Alignment explanation
Indices: 1315041--1315125 Score: 120
Period size: 37 Copynumber: 2.3 Consensus size: 37
1315031 ATCCCATTAT
*
1315041 CATTTTTC-AACAAACATCTACCAAACTTTGAAAAAC
1 CATTTTTCAAAGAAACATCTACCAAACTTTGAAAAAC
* *
1315077 TATTTTTCAAAGAAACATTTACCAAACTTTG-AAAAC
1 CATTTTTCAAAGAAACATCTACCAAACTTTGAAAAAC
1315113 CATTTTTTCAAAG
1 CA-TTTTTCAAAG
1315126 TTGGTTACCA
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
36 13 0.30
37 30 0.70
ACGTcount: A:0.42, C:0.20, G:0.05, T:0.33
Consensus pattern (37 bp):
CATTTTTCAAAGAAACATCTACCAAACTTTGAAAAAC
Found at i:1319689 original size:37 final size:36
Alignment explanation
Indices: 1319627--1319745 Score: 161
Period size: 35 Copynumber: 3.3 Consensus size: 36
1319617 TCCCATTATC
* * *
1319627 ATTTTTC-AACAAACATCTACAAAACTTTGAAAAACT
1 ATTTTTCAAAGAAACATTTACCAAACTTTG-AAAACT
*
1319663 ATTTTTCAAAGAAACATTTACCAAACTTTGAAAACC
1 ATTTTTCAAAGAAACATTTACCAAACTTTGAAAACT
*
1319699 A-TTTTCAAAGAAATATTTACCAAACTTTGAAAACT
1 ATTTTTCAAAGAAACATTTACCAAACTTTGAAAACT
1319734 ATTTTTTCAAAG
1 A-TTTTTCAAAG
1319746 TTGGTTACCA
Statistics
Matches: 74, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
35 33 0.45
36 13 0.18
37 28 0.38
ACGTcount: A:0.45, C:0.17, G:0.05, T:0.34
Consensus pattern (36 bp):
ATTTTTCAAAGAAACATTTACCAAACTTTGAAAACT
Found at i:1319772 original size:34 final size:36
Alignment explanation
Indices: 1319648--1319772 Score: 125
Period size: 35 Copynumber: 3.5 Consensus size: 36
1319638 AACATCTACA
* * *
1319648 AAACTTTGAAAAAC-TATTTTTCAAAGAAACATTTACC
1 AAACTTTGAAAACCAT-TTTTTCAAAG-AATAGTTACC
*
1319685 AAACTTTGAAAACCA--TTTTCAAAGAAATATTTACC
1 AAACTTTGAAAACCATTTTTTCAAAG-AATAGTTACC
* * *
1319720 AAACTTTGAAAACTATTTTTTCAAAG-TTGGTTACC
1 AAACTTTGAAAACCATTTTTTCAAAGAATAGTTACC
1319755 AAAC-TTGAAAACCATTTT
1 AAACTTTGAAAACCATTTT
1319773 AATACTTTCA
Statistics
Matches: 78, Mismatches: 7, Indels: 9
0.83 0.07 0.10
Matches are distributed among these distances:
34 13 0.17
35 43 0.55
37 22 0.28
ACGTcount: A:0.42, C:0.16, G:0.07, T:0.34
Consensus pattern (36 bp):
AAACTTTGAAAACCATTTTTTCAAAGAATAGTTACC
Found at i:1327748 original size:58 final size:58
Alignment explanation
Indices: 1327678--1328184 Score: 663
Period size: 58 Copynumber: 8.7 Consensus size: 58
1327668 TTCCCTTTTA
*
1327678 GAAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACAAAATGCCCTATATG
1 GAAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACAAAACGCCCTATATG
* *
1327736 GAAATTCATACACATAGTATGATTTCTTAACATTTTAGCGTACAAAACACCCTATATG
1 GAAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACAAAACGCCCTATATG
*
1327794 GAAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACGCCCTATATG
1 GAAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACAAAACGCCCTATATG
* * *
1327852 GAAATTCATACACTTAGTATAATTTCTTAATATTTTAGCGTACAAAACACCCTATATG
1 GAAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACAAAACGCCCTATATG
* *
1327910 GAAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACGACCTATATG
1 GAAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACAAAACGCCCTATATG
* * * ** * ** * *
1327968 GAAATTCATACAATTAATATGATTTCCTTATCATTTTAGCACACGAAGTGCCATATCTG
1 GAAATTCATACACTTAGTATGATTT-CTTAACATTTTAGCGTACAAAACGCCCTATATG
* ** *** *
1328027 GAAATTCATACACTTAGTATGATTTCCTTATCATTTTAGCACACAAAGTACCCTATCTG
1 GAAATTCATACACTTAGTATGATTT-CTTAACATTTTAGCGTACAAAACGCCCTATATG
* ** * ** *
1328086 GAAATTCATACACTTAGTATGATTTCCTTATCATTTTAGCACACGAAGTGCCCTATCTG
1 GAAATTCATACACTTAGTATGATTT-CTTAACATTTTAGCGTACAAAACGCCCTATATG
* *
1328145 GAAATTCATACACTTAGTATTATTTCCTTATCATTTTAGC
1 GAAATTCATACACTTAGTATGATTT-CTTAACATTTTAGC
1328185 ACACTTAGTG
Statistics
Matches: 415, Mismatches: 33, Indels: 1
0.92 0.07 0.00
Matches are distributed among these distances:
58 240 0.58
59 175 0.42
ACGTcount: A:0.34, C:0.19, G:0.11, T:0.36
Consensus pattern (58 bp):
GAAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACAAAACGCCCTATATG
Found at i:1339749 original size:30 final size:30
Alignment explanation
Indices: 1339450--1339732 Score: 539
Period size: 30 Copynumber: 9.4 Consensus size: 30
1339440 TCCGAATGAC
1339450 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1339480 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
1339510 CTATCCAGAGGTCATAAAGATCCTCAGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1339540 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1339570 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1339600 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1339630 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1339660 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
1339690 CTATCCAGAGGTCATAAAGATCCTTGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
1339720 CTATCCATAGGTC
1 CTATCCAGAGGTC
1339733 TCGAAGAACC
Statistics
Matches: 249, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 249 1.00
ACGTcount: A:0.33, C:0.23, G:0.19, T:0.24
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:1339980 original size:4 final size:4
Alignment explanation
Indices: 1339971--1339996 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
1339961 ATATAACCAT
1339971 TACA TACA TACA TACA TACA TACA TA
1 TACA TACA TACA TACA TACA TACA TA
1339997 AATGTCATCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.50, C:0.23, G:0.00, T:0.27
Consensus pattern (4 bp):
TACA
Found at i:1345145 original size:2 final size:2
Alignment explanation
Indices: 1345138--1345170 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1345128 CCATAAAAGC
1345138 TA 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 TA T
1345171 TATTCACCAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1346850 original size:105 final size:105
Alignment explanation
Indices: 1346734--1346938 Score: 338
Period size: 105 Copynumber: 2.0 Consensus size: 105
1346724 ATGATCCTCT
* * *
1346734 TTATTTAACTGTATTTCATTCACAATTATCTTATGTATTACAATATGCCTAGCATACCCATCTTC
1 TTATTTAACTGTATTTCATTCACAATTATCTTAAGTATTACAATATACCTAGCATACCAATCTTC
* *
1346799 CTCTATATTTTTCTTCTCCATTTATCTATTTAGTCTCTCC
66 CTCTATATTTTTCATCTCCATTTACCTATTTAGTCTCTCC
** *
1346839 TTATTTAACTGTATTTCATTCACAATTATCTTAAGTATTTTAGTATACCTAGCATACCAATCTTC
1 TTATTTAACTGTATTTCATTCACAATTATCTTAAGTATTACAATATACCTAGCATACCAATCTTC
1346904 CTCTATATTTTTCATCTCCATTTACCTATTTAGTC
66 CTCTATATTTTTCATCTCCATTTACCTATTTAGTC
1346939 CTAAACCTTT
Statistics
Matches: 92, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
105 92 1.00
ACGTcount: A:0.25, C:0.22, G:0.05, T:0.47
Consensus pattern (105 bp):
TTATTTAACTGTATTTCATTCACAATTATCTTAAGTATTACAATATACCTAGCATACCAATCTTC
CTCTATATTTTTCATCTCCATTTACCTATTTAGTCTCTCC
Found at i:1347518 original size:58 final size:59
Alignment explanation
Indices: 1347451--1347901 Score: 633
Period size: 58 Copynumber: 7.7 Consensus size: 59
1347441 TTTCCCATAC
* *
1347451 GGAAATTCATACACTTAGTATGATTT-CTTATCATTTTAGCGTACAAAATGCCCTATAT
1 GGAAATTCATACACTTAGTATGATTTCCTTATCATTTTAGCATACGAAATGCCCTATAT
* * * **
1347509 GAAAATTCATACACTTAGTATGATTT-CTTAACATTTTAGCGTACGAAACACCCTATAT
1 GGAAATTCATACACTTAGTATGATTTCCTTATCATTTTAGCATACGAAATGCCCTATAT
* * * *
1347567 GGAAATTCATACACTTAGTATGATTT-CTTAACATTTTAGCATATGAAACGCCTTATAT
1 GGAAATTCATACACTTAGTATGATTTCCTTATCATTTTAGCATACGAAATGCCCTATAT
* * *
1347625 GGAAATTCATACACTTAGTATGATTT-CTTAACATTTTAGCGTACGAAATGTCCTATAT
1 GGAAATTCATACACTTAGTATGATTTCCTTATCATTTTAGCATACGAAATGCCCTATAT
* * * * *
1347683 GGAAATTCATACAATTAATATGATTTCCTTATCATTTTAGCACACGAAGTGCCCTATCT
1 GGAAATTCATACACTTAGTATGATTTCCTTATCATTTTAGCATACGAAATGCCCTATAT
* * *
1347742 GGAAATTCATACACTTAGTATGATTTCCTTATCATTTTAGCACAC-AAAGTCCCCTATCT
1 GGAAATTCATACACTTAGTATGATTTCCTTATCATTTTAGCATACGAAA-TGCCCTATAT
* * *
1347801 GGAAATTCATACACTTAGTATGATTTCCTTATCATTTTAGCACACGAAGTGCCCTATCT
1 GGAAATTCATACACTTAGTATGATTTCCTTATCATTTTAGCATACGAAATGCCCTATAT
1347860 GGAAATTCATACACTTAGTATGATTTCCTTATCATTTTAGCA
1 GGAAATTCATACACTTAGTATGATTTCCTTATCATTTTAGCA
1347902 CACTTAGTGC
Statistics
Matches: 361, Mismatches: 29, Indels: 5
0.91 0.07 0.01
Matches are distributed among these distances:
58 185 0.51
59 174 0.48
60 2 0.01
ACGTcount: A:0.32, C:0.19, G:0.12, T:0.37
Consensus pattern (59 bp):
GGAAATTCATACACTTAGTATGATTTCCTTATCATTTTAGCATACGAAATGCCCTATAT
Found at i:1348258 original size:20 final size:22
Alignment explanation
Indices: 1348229--1348281 Score: 56
Period size: 20 Copynumber: 2.5 Consensus size: 22
1348219 AAGCTCAATA
* *
1348229 GTATCTATACCACTA-CCT-TG
1 GTATCGATACCACTATACTATG
**
1348249 GTATCGATACTTCTATACTATG
1 GTATCGATACCACTATACTATG
1348271 GTATCGATACC
1 GTATCGATACC
1348282 CCTTTTTGGT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
20 12 0.46
21 2 0.08
22 12 0.46
ACGTcount: A:0.26, C:0.25, G:0.13, T:0.36
Consensus pattern (22 bp):
GTATCGATACCACTATACTATG
Found at i:1348348 original size:21 final size:21
Alignment explanation
Indices: 1348322--1348376 Score: 78
Period size: 20 Copynumber: 2.7 Consensus size: 21
1348312 CGATGTTTCT
*
1348322 TGGTATCGATAC-CCCTTATC
1 TGGTATCGATACTACCTTATC
1348342 ATGGTATCGATACTACCTTATC
1 -TGGTATCGATACTACCTTATC
1348364 -GGTATCGATACTA
1 TGGTATCGATACTA
1348377 TTGAATTTGT
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
20 13 0.41
21 12 0.38
22 7 0.22
ACGTcount: A:0.25, C:0.24, G:0.16, T:0.35
Consensus pattern (21 bp):
TGGTATCGATACTACCTTATC
Found at i:1350543 original size:58 final size:58
Alignment explanation
Indices: 1350473--1350921 Score: 612
Period size: 58 Copynumber: 7.7 Consensus size: 58
1350463 TTTCCCGAAC
*
1350473 GGAAATTCATACACTTAGTATGATTTCTTAACATTTTAGCATACAAAACGCCCTATAT
1 GGAAATTCATACACTTAGTATGATTTCTTAACATTTTAGCATACGAAACGCCCTATAT
* *
1350531 GGAAATTCATACACTTAGTATGATTTTTTAACATTTTAGCATACGAAACACCCTATAT
1 GGAAATTCATACACTTAGTATGATTTCTTAACATTTTAGCATACGAAACGCCCTATAT
* * * *
1350589 GGAAATTTATACACTTAGTATGATTTCTTAACATTTTAGCGTATGAAACGTCCTATAT
1 GGAAATTCATACACTTAGTATGATTTCTTAACATTTTAGCATACGAAACGCCCTATAT
* *
1350647 GGAAATTCATACACTTAGTATGATTTCTTAATATTTTAGCGTACGAAACGCCCTATAT
1 GGAAATTCATACACTTAGTATGATTTCTTAACATTTTAGCATACGAAACGCCCTATAT
* * *
1350705 GAAAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACAAAACG-CCTATAT
1 GGAAATTCATACACTTAGTATGATTTCTTAACATTTTAGCATACGAAACGCCCTATAT
* * * * * * ** *
1350762 GGAAATTCATACAATTAATATGATTTCCTTATCTTTTTAGTACACGAAGTGCCCTATCT
1 GGAAATTCATACACTTAGTATGATTT-CTTAACATTTTAGCATACGAAACGCCCTATAT
* * ** *
1350821 GGAAATTCATACACTTAGTATGATTTCCTTATCATTTTAGCACACGAAGTGCCCTATCT
1 GGAAATTCATACACTTAGTATGATTT-CTTAACATTTTAGCATACGAAACGCCCTATAT
* *
1350880 GAAAATTCATACACTTAGTATGATTTCCTTATCATTTTAGCA
1 GGAAATTCATACACTTAGTATGATTT-CTTAACATTTTAGCA
1350922 CACTTAGTTT
Statistics
Matches: 356, Mismatches: 33, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
57 30 0.08
58 224 0.63
59 102 0.29
ACGTcount: A:0.33, C:0.18, G:0.12, T:0.37
Consensus pattern (58 bp):
GGAAATTCATACACTTAGTATGATTTCTTAACATTTTAGCATACGAAACGCCCTATAT
Found at i:1352876 original size:81 final size:81
Alignment explanation
Indices: 1352739--1354726 Score: 2832
Period size: 81 Copynumber: 24.7 Consensus size: 81
1352729 TGAATAATTA
* * * *
1352739 TTTGAGTAAAAGATTAATGGCCTAGTTGTGCATTTGACAGAAATGTGTCAAATATGCTAGTTAGA
1 TTTGAGTAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGA
1352804 TGAAAGGTTAAATACC
66 TGAAAGGTTAAATACC
** * * * *
1352820 TTTGAGTAAATTATTAATGGTCTAGCTGTGCATTTGACATAAATGTATCAATTATGCCAGTTAGA
1 TTTGAGTAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGA
* **
1352885 TGATAGGTTAAATATG
66 TGAAAGGTTAAATACC
* *
1352901 TTTGAGTAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCGATTATGCCAGTTATA
1 TTTGAGTAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGA
1352966 TGAAAGGTTAAATACC
66 TGAAAGGTTAAATACC
* * *
1352982 TTTGAGTAAAATATTAATGGCCTAGCTGTGCATTTGATAGAAAGGTGTCAATTATACCAGTTAGA
1 TTTGAGTAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGA
*
1353047 TGAAACGTTAAATACC
66 TGAAAGGTTAAATACC
* * * **
1353063 TTTGAGTAAAAGATTAATGGCCTAGCTGTGCGTTTGACAGAAATGTGTTAATTATGCCTTTTAGA
1 TTTGAGTAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGA
*
1353128 TGAAATGTTAAATACC
66 TGAAAGGTTAAATACC
* * ** * *
1353144 TTTGAGTAAATGATTAAGGGGTTAGCTGTGCATTTGACAAAAAGGTGTTAATTATGCCAGTTAGA
1 TTTGAGTAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGA
* *
1353209 TGAAAAGTTAAGTACC
66 TGAAAGGTTAAATACC
* *
1353225 TTTGAGTAAAATATTAATGGCCTAGCTCTGCATTTGACAGAAAGGTGTCAATTATG-CAGTTAGA
1 TTTGAGTAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGA
*
1353289 TGAAATGTTAAATACC
66 TGAAAGGTTAAATACC
* * * *
1353305 TTTGAGTAAAAGATTGATGGCCTAGTTGTGAATTTGACAGAAATGTGTCAATTATG-C---TAG-
1 TTTGAGTAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGA
* *
1353365 T--TAGCTTAAATACC
66 TGAAAGGTTAAATACC
* * * *
1353379 TTTGAGTAAAAGGTTAATGACCTAGCTGTGAATTTGACAGAAATGTGTCAATTATGCCAGTTAGA
1 TTTGAGTAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGA
*
1353444 TGTAAGGTTAAATACC
66 TGAAAGGTTAAATACC
*
1353460 TTTGAGTAAAAGATTAATGACCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGA
1 TTTGAGTAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGA
1353525 TGAAAGGTTAAATACC
66 TGAAAGGTTAAATACC
* * *
1353541 TTTGAGTAAAAGATTAATGGCCTAGCTGTGCATTTGATAGAAAGGTGTAAATTATTCCAGTTAGA
1 TTTGAGTAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGA
1353606 TGAAAGGTTAAATACC
66 TGAAAGGTTAAATACC
* * * * *
1353622 TTTGAGTAAAATATTAAAGGCCTAGCTGTGCATTTGACAGAAATGTATTAATTATGCCAGTTAGA
1 TTTGAGTAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGA
* *
1353687 TAAAAGTTTAAATACC
66 TGAAAGGTTAAATACC
* * *
1353703 TTTGAGTAAAATATTAATGGCCTAGATGTGCATTTGACAAAAAGGTGTCAATTATGCCAGTTAGA
1 TTTGAGTAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGA
*
1353768 TGAAAGGTTAAATACT
66 TGAAAGGTTAAATACC
* **
1353784 TTTGAGTAAAAGATTAATGGCCTAGCTGTGCATTTGACATAAAGGTGTCAATTATGTGAGTTAGA
1 TTTGAGTAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGA
*
1353849 GGAAAGGTTAAATACC
66 TGAAAGGTTAAATACC
* * * * * * * *
1353865 TTTGAATAAAAGATTAATGGCATAGTTGTGCATTTGACATAAATGTGTTAATTATGTCAATTAGA
1 TTTGAGTAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGA
*
1353930 TGAAAGGTTAAATAAC
66 TGAAAGGTTAAATACC
* * * *
1353946 TTTGAGTAAAATATTAATGGTCTAGCCGTGCATTTGACATAAAGGTGTCAATTATGCCAGTTAGA
1 TTTGAGTAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGA
*
1354011 TGAAAGGTTAAATACT
66 TGAAAGGTTAAATACC
* * * * * * *
1354027 TTTGAGCAAAAGATTAATGGTCTAACTGTGTATTTGATAGAAAAGTGCCAATTATGCCAGTTAGA
1 TTTGAGTAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGA
*
1354092 TTAAAGGTTAAATACC
66 TGAAAGGTTAAATACC
* *
1354108 TTTGAGTAGAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTTTCAATTATGCCAGTTAGA
1 TTTGAGTAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGA
1354173 TGAAAGGTTAAATACC
66 TGAAAGGTTAAATACC
* * * * * * *
1354189 TTTGAGTAAAAGATTAATGGTCTAGTTCTACATTTGACAGAAAGATGTCAATTATGACAGATAGA
1 TTTGAGTAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGA
1354254 TGAAAGGTTAAATACC
66 TGAAAGGTTAAATACC
* * * * * * *
1354270 TTAGAGTAAAATATTAATGGCCTAGTTGTGCATTTGACATAAATGTGTCAATTATACCAGTTACA
1 TTTGAGTAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGA
1354335 TG-AAGGTTAAATACC
66 TGAAAGGTTAAATACC
*
1354350 TTTGAGTAAAAGATTAATGGCCTAG-TAGTGCATTTGACAGAAATGTGTCAATTATGCCAGTTAG
1 TTTGAGTAAAAGATTAATGGCCTAGCT-GTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAG
1354414 ATGAAAGGTTAAATACC
65 ATGAAAGGTTAAATACC
* * *
1354431 TTTGAGTAAAAGATTAATGGTCTAGTTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTATA
1 TTTGAGTAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGA
1354496 TGAAAGGTTAAATACC
66 TGAAAGGTTAAATACC
* * * *
1354512 TTAGAGTAAAAGATTAATGGCCTAGCTATGCATTTGAAAGAAAGGTGTCAATTATACCAGTTAGA
1 TTTGAGTAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGA
1354577 TG-AAGGTTAAATACC
66 TGAAAGGTTAAATACC
* *
1354592 TTTGAGTAAAATATTAATGGCCTAGCAGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGA
1 TTTGAGTAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGA
1354657 TGAAAGGTTAAATACC
66 TGAAAGGTTAAATACC
* *
1354673 --TGAGTAAAAGATTAATGGCCTAGTTGTGCATTTGACAGAAAGGTGTTAATTATG
1 TTTGAGTAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATG
1354727 AAAGAAATGT
Statistics
Matches: 1702, Mismatches: 194, Indels: 24
0.89 0.10 0.01
Matches are distributed among these distances:
74 62 0.04
75 1 0.00
76 1 0.00
77 3 0.00
78 3 0.00
79 52 0.03
80 220 0.13
81 1359 0.80
82 1 0.00
ACGTcount: A:0.36, C:0.11, G:0.21, T:0.32
Consensus pattern (81 bp):
TTTGAGTAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGA
TGAAAGGTTAAATACC
Found at i:1355624 original size:45 final size:45
Alignment explanation
Indices: 1355548--1355639 Score: 121
Period size: 45 Copynumber: 2.0 Consensus size: 45
1355538 CATTAGCTTA
* * * * * *
1355548 AAATCTGGTAATATTTTAAGTGCAACCTAAAATGTTGATTATATT
1 AAATCTGATAACATTCTAAGAGAAACCTAAAATGTTAATTATATT
*
1355593 AAATCTGATAACATTCTAAGAGAAACTTAAAATGTTAATTATATT
1 AAATCTGATAACATTCTAAGAGAAACCTAAAATGTTAATTATATT
1355638 AA
1 AA
1355640 TAACATTGAT
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
45 40 1.00
ACGTcount: A:0.43, C:0.09, G:0.11, T:0.37
Consensus pattern (45 bp):
AAATCTGATAACATTCTAAGAGAAACCTAAAATGTTAATTATATT
Found at i:1364173 original size:77 final size:77
Alignment explanation
Indices: 1363988--1364160 Score: 274
Period size: 77 Copynumber: 2.2 Consensus size: 77
1363978 TATTAATGTC
*
1363988 CTTAGTGAACCATGACATTCTTGGATGTAACCTATTTTATTAATAAAAATAATAACATTACATAC
1 CTTAGTGAACCATGACATTCTTGGATGCAACCTATTTTATTAATAAAAATAATAACATTACATAC
1364053 CCCAACCTATTT
66 CCCAACCTATTT
* * * **
1364065 CTCAGTGAACCATGACATTCTTGGATGCAACCTATTTTATTAATAAAAATATTATCATTACATGT
1 CTTAGTGAACCATGACATTCTTGGATGCAACCTATTTTATTAATAAAAATAATAACATTACATAC
*
1364130 CGCAACCTATTT
66 CCCAACCTATTT
*
1364142 CTTAGTGAACCATGGCATT
1 CTTAGTGAACCATGACATT
1364161 TTTTGGCGCA
Statistics
Matches: 87, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
77 87 1.00
ACGTcount: A:0.35, C:0.20, G:0.10, T:0.35
Consensus pattern (77 bp):
CTTAGTGAACCATGACATTCTTGGATGCAACCTATTTTATTAATAAAAATAATAACATTACATAC
CCCAACCTATTT
Found at i:1364690 original size:78 final size:78
Alignment explanation
Indices: 1364524--1364690 Score: 192
Period size: 78 Copynumber: 2.1 Consensus size: 78
1364514 AACTTTAGGC
* * * * * * *
1364524 GCAACCCATTTTATTATTAAAAATATTAAGATTCCAGATTATAACCTACTTTCTTAGTGAACCAT
1 GCAACCTATTTTATTAATAAAAATATTAACATTACAGATCACAACATACTTTCTTAGTGAACCAT
* **
1364589 GGCATTCTTGGGT
66 GACATTCTTGGAA
* * *
1364602 GCAACCTATTTTATTAATAAAAATATTGACATTACAGATCACAACAT-CTTTCTTAGTGAATCTT
1 GCAACCTATTTTATTAATAAAAATATTAACATTACAGATCACAACATACTTTCTTAGTGAACCAT
*
1364666 GACCTTCTTGGAA
66 GACATTCTTGGAA
1364679 GCAACCTTATTT
1 GCAACC-TATTT
1364691 CTTATATATA
Statistics
Matches: 74, Mismatches: 14, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
77 30 0.41
78 44 0.59
ACGTcount: A:0.33, C:0.19, G:0.11, T:0.37
Consensus pattern (78 bp):
GCAACCTATTTTATTAATAAAAATATTAACATTACAGATCACAACATACTTTCTTAGTGAACCAT
GACATTCTTGGAA
Found at i:1364945 original size:21 final size:21
Alignment explanation
Indices: 1364920--1364960 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1364910 CTTTCTTTTA
1364920 TTCT-TTCTT-TTATTCTTTC
1 TTCTCTTCTTCTTATTCTTTC
*
1364939 TTCTCTTCTTCTTGTTCTTTC
1 TTCTCTTCTTCTTATTCTTTC
1364960 T
1 T
1364961 CCTTTATCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 4 0.21
20 5 0.26
21 10 0.53
ACGTcount: A:0.02, C:0.24, G:0.02, T:0.71
Consensus pattern (21 bp):
TTCTCTTCTTCTTATTCTTTC
Found at i:1364948 original size:12 final size:12
Alignment explanation
Indices: 1364908--1364940 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
1364898 ACAACATCTT
1364908 TTCTTTCTTTTA
1 TTCTTTCTTTTA
1364920 TTCTTTCTTTTA
1 TTCTTTCTTTTA
1364932 TTCTTTCTT
1 TTCTTTCTT
1364941 CTCTTCTTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.06, C:0.18, G:0.00, T:0.76
Consensus pattern (12 bp):
TTCTTTCTTTTA
Found at i:1365291 original size:65 final size:65
Alignment explanation
Indices: 1365187--1365322 Score: 218
Period size: 65 Copynumber: 2.1 Consensus size: 65
1365177 ATCTTTATCT
* * *
1365187 GGTTTCATCTTAAAATTTTCATAGTTATGGTTGAGAAGATCGATTTTTGTTTCCCTCACTTCACC
1 GGTTTCATCTTAAAATTTTCATAGATATGGTTAAGAAGATCAATTTTTGTTTCCCTCACTTCACC
* * *
1365252 GGTTTCATCTTATAATTTTCATAGATATGGTTAAGAAGATCAATTTTTGTTTTCCTCACTTCACT
1 GGTTTCATCTTAAAATTTTCATAGATATGGTTAAGAAGATCAATTTTTGTTTCCCTCACTTCACC
1365317 GGTTTC
1 GGTTTC
1365323 TTCATGAGTG
Statistics
Matches: 65, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
65 65 1.00
ACGTcount: A:0.24, C:0.17, G:0.15, T:0.45
Consensus pattern (65 bp):
GGTTTCATCTTAAAATTTTCATAGATATGGTTAAGAAGATCAATTTTTGTTTCCCTCACTTCACC
Found at i:1365630 original size:15 final size:16
Alignment explanation
Indices: 1365610--1365644 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
1365600 ACTCTTCCTT
1365610 TCTCTTCATCTT-TTC
1 TCTCTTCATCTTCTTC
*
1365625 TCTCTTCTTCTTCTTC
1 TCTCTTCATCTTCTTC
1365641 TCTC
1 TCTC
1365645 AAGTTTAAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 11 0.61
16 7 0.39
ACGTcount: A:0.03, C:0.37, G:0.00, T:0.60
Consensus pattern (16 bp):
TCTCTTCATCTTCTTC
Found at i:1368125 original size:20 final size:20
Alignment explanation
Indices: 1368100--1368142 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
1368090 TCATGGGTAC
* *
1368100 CGATACTGAACCTTTAGTAT
1 CGATACTAAAACTTTAGTAT
*
1368120 CGATACTAAAACTTTGGTAT
1 CGATACTAAAACTTTAGTAT
1368140 CGA
1 CGA
1368143 ACCCACATGC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.33
Consensus pattern (20 bp):
CGATACTAAAACTTTAGTAT
Found at i:1368221 original size:20 final size:20
Alignment explanation
Indices: 1368196--1368306 Score: 195
Period size: 20 Copynumber: 5.5 Consensus size: 20
1368186 GGATTAAGAC
1368196 AGTATCGATACCCTCATGTG
1 AGTATCGATACCCTCATGTG
* *
1368216 AGTATCGATACCCTTATATG
1 AGTATCGATACCCTCATGTG
1368236 AGTATCGATACCCTCATGTG
1 AGTATCGATACCCTCATGTG
*
1368256 AGTATCGATACCCTCATATG
1 AGTATCGATACCCTCATGTG
1368276 AGTATCGATACCCTCATGTG
1 AGTATCGATACCCTCATGTG
1368296 AGTATCGATAC
1 AGTATCGATAC
1368307 TAAGGTGTTG
Statistics
Matches: 85, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 85 1.00
ACGTcount: A:0.28, C:0.23, G:0.18, T:0.31
Consensus pattern (20 bp):
AGTATCGATACCCTCATGTG
Found at i:1370743 original size:22 final size:21
Alignment explanation
Indices: 1370708--1370766 Score: 75
Period size: 22 Copynumber: 2.8 Consensus size: 21
1370698 TCATTGGAAT
*
1370708 AGGAGGTTTAGAAACCAGAAATG
1 AGGA-GTTTCGAAACCAGAAA-G
1370731 AGGAGTTTCGAAACCAGAAAG
1 AGGAGTTTCGAAACCAGAAAG
*
1370752 AGG-GTTTCAAAACCA
1 AGGAGTTTCGAAACCA
1370767 TAAGTGAAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
20 11 0.32
21 4 0.12
22 15 0.44
23 4 0.12
ACGTcount: A:0.42, C:0.14, G:0.27, T:0.17
Consensus pattern (21 bp):
AGGAGTTTCGAAACCAGAAAG
Found at i:1370764 original size:20 final size:22
Alignment explanation
Indices: 1370719--1370766 Score: 73
Period size: 20 Copynumber: 2.3 Consensus size: 22
1370709 GGAGGTTTAG
*
1370719 AAACCAGAAATGAGGAGTTTCG
1 AAACCAGAAATGAGGAGTTTCA
1370741 AAACCAGAAA-GAGG-GTTTCA
1 AAACCAGAAATGAGGAGTTTCA
1370761 AAACCA
1 AAACCA
1370767 TAAGTGAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 11 0.44
21 4 0.16
22 10 0.40
ACGTcount: A:0.46, C:0.17, G:0.23, T:0.15
Consensus pattern (22 bp):
AAACCAGAAATGAGGAGTTTCA
Found at i:1374079 original size:53 final size:53
Alignment explanation
Indices: 1374021--1374129 Score: 159
Period size: 51 Copynumber: 2.1 Consensus size: 53
1374011 ATATTTACAC
* * * *
1374021 TTATATATGAATCATATCAATTTAAACTA-AA-ATAAATTTAAAAAAATATTA
1 TTATATATGAATCAAATCAATTTAAACTATAATAAAAATATAAAAAAATATAA
*
1374072 TTATATATGAATTAAATCAATTTAAACTATAATAAAAATATAAAAAAATATAA
1 TTATATATGAATCAAATCAATTTAAACTATAATAAAAATATAAAAAAATATAA
1374125 TTATA
1 TTATA
1374130 ATAAAGATAT
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
51 27 0.53
52 2 0.04
53 22 0.43
ACGTcount: A:0.57, C:0.05, G:0.02, T:0.37
Consensus pattern (53 bp):
TTATATATGAATCAAATCAATTTAAACTATAATAAAAATATAAAAAAATATAA
Found at i:1375010 original size:14 final size:14
Alignment explanation
Indices: 1374978--1375004 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1374968 TTTAAACTAT
1374978 AATAAAAATATAAA
1 AATAAAAATATAAA
1374992 AATAAAAATATAA
1 AATAAAAATATAA
1375005 TTATAATAAA
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:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (14 bp):
AATAAAAATATAAA
Found at i:1376679 original size:2 final size:2
Alignment explanation
Indices: 1376672--1376698 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1376662 CTTCCAGATT
1376672 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 T
1376699 CACACTTTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1379741 original size:150 final size:150
Alignment explanation
Indices: 1379470--1379920 Score: 839
Period size: 150 Copynumber: 3.0 Consensus size: 150
1379460 ACTTAAAACA
*
1379470 TTATAAATTACTTGATTTGATTATTAATCCGACTATAAGGTATAATGAAGCTCAGTAACACCTAC
1 TTATAAATTACTTGATTTGATTATTAATCCGACTATAAGGTATAATGAAGCTTAGTAACACCTAC
1379535 CTGAGTCCGGGCAGAGTATTGGATCCTTCAAGGAGGAAGCAAGGTTCTCCTTTGCAAAGATTTAG
66 CTGAGTCCGGGCAGAGTATTGGATCCTTCAAGGAGGAAGCAAGGTTCTCCTTTGCAAAGATTTAG
*
1379600 CTATAGCTATAGCTCACCAC
131 CCATAGCTATAGCTCACCAC
* *
1379620 TTATAAATTACTTGACTTGATTATTAATCCGACTATAAGGTATAATGAAGCTTAGTAACACCAAC
1 TTATAAATTACTTGATTTGATTATTAATCCGACTATAAGGTATAATGAAGCTTAGTAACACCTAC
1379685 CTGAGTCCGGGCAGAGTATTGGATCCTTCAAGGAGGAAGCAAGGTTCTCCTTTGCAAAGATTTAG
66 CTGAGTCCGGGCAGAGTATTGGATCCTTCAAGGAGGAAGCAAGGTTCTCCTTTGCAAAGATTTAG
1379750 CCATAGCTATAGCTCACCAC
131 CCATAGCTATAGCTCACCAC
1379770 TTATAAATTACTTGATTTGATTATTAATCCGACTATAAGGTATAATGAAGCTTAGTAACACCTAC
1 TTATAAATTACTTGATTTGATTATTAATCCGACTATAAGGTATAATGAAGCTTAGTAACACCTAC
* *
1379835 CTGAGTCTGGGAAGAGTATTGGATCCTTCAAGGAGGAAGCAAGGTTCTCCTTTGCAAAGATTTAG
66 CTGAGTCCGGGCAGAGTATTGGATCCTTCAAGGAGGAAGCAAGGTTCTCCTTTGCAAAGATTTAG
*
1379900 CCATAGCTCTAGCTCACCAC
131 CCATAGCTATAGCTCACCAC
1379920 T
1 T
1379921 CGTCCGTGAC
Statistics
Matches: 292, Mismatches: 9, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
150 292 1.00
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.30
Consensus pattern (150 bp):
TTATAAATTACTTGATTTGATTATTAATCCGACTATAAGGTATAATGAAGCTTAGTAACACCTAC
CTGAGTCCGGGCAGAGTATTGGATCCTTCAAGGAGGAAGCAAGGTTCTCCTTTGCAAAGATTTAG
CCATAGCTATAGCTCACCAC
Found at i:1386719 original size:19 final size:19
Alignment explanation
Indices: 1386695--1386740 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
1386685 AGGGGGTGTT
1386695 GTAAATTCGGTTTCATTGG
1 GTAAATTCGGTTTCATTGG
*
1386714 GTAAATTCGGTTTCATTTG
1 GTAAATTCGGTTTCATTGG
*
1386733 GTATATTC
1 GTAAATTC
1386741 AGTGAGTTTG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.22, C:0.11, G:0.22, T:0.46
Consensus pattern (19 bp):
GTAAATTCGGTTTCATTGG
Found at i:1391945 original size:18 final size:19
Alignment explanation
Indices: 1391922--1391985 Score: 66
Period size: 18 Copynumber: 3.5 Consensus size: 19
1391912 TTTATTGAAA
*
1391922 AACCGATAAA-CCGAACCG
1 AACCGAAAAACCCGAACCG
1391940 AACCGAAAAACCCGAACCG
1 AACCGAAAAACCCGAACCG
1391959 TTAA---AAAAA-CCGAACCG
1 --AACCGAAAAACCCGAACCG
1391976 AACCGAAAAA
1 AACCGAAAAA
1391986 ACCGGTTTCG
Statistics
Matches: 39, Mismatches: 1, Indels: 12
0.75 0.02 0.23
Matches are distributed among these distances:
15 2 0.05
17 8 0.21
18 19 0.49
19 8 0.21
21 2 0.05
ACGTcount: A:0.52, C:0.30, G:0.14, T:0.05
Consensus pattern (19 bp):
AACCGAAAAACCCGAACCG
Found at i:1391986 original size:19 final size:19
Alignment explanation
Indices: 1391929--1391989 Score: 74
Period size: 19 Copynumber: 3.3 Consensus size: 19
1391919 AAAAACCGAT
1391929 AAACCGAACCGAACCGAAA
1 AAACCGAACCGAACCGAAA
* *
1391948 AACCCGAACCGTTA---AAA
1 AAACCGAACCG-AACCGAAA
1391965 AAACCGAACCGAACCGAAA
1 AAACCGAACCGAACCGAAA
1391984 AAACCG
1 AAACCG
1391990 GTTTCGATTT
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
16 1 0.03
17 13 0.38
19 19 0.56
20 1 0.03
ACGTcount: A:0.51, C:0.31, G:0.15, T:0.03
Consensus pattern (19 bp):
AAACCGAACCGAACCGAAA
Found at i:1401865 original size:21 final size:21
Alignment explanation
Indices: 1401839--1401933 Score: 163
Period size: 21 Copynumber: 4.5 Consensus size: 21
1401829 GTTTCCAGAT
1401839 TCGCAACGCGAACATCGACTA
1 TCGCAACGCGAACATCGACTA
1401860 TCGCAACGCGAACATCGACTA
1 TCGCAACGCGAACATCGACTA
*
1401881 TCGCAATGCGAACATCGACTA
1 TCGCAACGCGAACATCGACTA
*
1401902 TCGCAACGCGAACTTCGACTA
1 TCGCAACGCGAACATCGACTA
*
1401923 TCGCAATGCGA
1 TCGCAACGCGA
1401934 TTTTCCAAAT
Statistics
Matches: 70, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 70 1.00
ACGTcount: A:0.32, C:0.32, G:0.20, T:0.17
Consensus pattern (21 bp):
TCGCAACGCGAACATCGACTA
Found at i:1401986 original size:42 final size:42
Alignment explanation
Indices: 1401929--1402214 Score: 400
Period size: 42 Copynumber: 6.8 Consensus size: 42
1401919 ACTATCGCAA
* *
1401929 TGCGA-TT-TTCCAAATTCGTTGCGATAGTCCAAGTTTGCGT
1 TGCGATTTATTCCAAGTTCGTTGCGATAGTCCAAGTTCGCGT
* * *
1401969 TGCGATTTATTCCAAATTCGCGTTGCGATTTATTCCAAATTCGCGT
1 TGCGATTTATTCCAAGTT--CGTTGCGA--TAGTCCAAGTTCGCGT
* *
1402015 TGCGA--TAGTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGT
1 TGCGATTTATTCCAAGTTCGTTGCGATAGTCCAAGTTCGCGT
*
1402055 TGCGATTTATTCCAAGTTCGTTACGATAGTCCAAGTTCGCGT
1 TGCGATTTATTCCAAGTTCGTTGCGATAGTCCAAGTTCGCGT
1402097 TGCGATTTATTCCAAGTTCGTTGCGATAGTCCAAGTTCGCGT
1 TGCGATTTATTCCAAGTTCGTTGCGATAGTCCAAGTTCGCGT
* **
1402139 TGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAGTTCGAAT
1 TGCGATTTATTCCAAGTTCGTTGCGATAGTCCAAGTTCGCGT
*
1402181 TGTGATTTATTCCAAGTTCGTTGCGATAGTCCAA
1 TGCGATTTATTCCAAGTTCGTTGCGATAGTCCAA
1402215 AATCGTAACG
Statistics
Matches: 221, Mismatches: 17, Indels: 14
0.88 0.07 0.06
Matches are distributed among these distances:
40 23 0.10
41 2 0.01
42 161 0.73
44 17 0.08
46 18 0.08
ACGTcount: A:0.21, C:0.20, G:0.23, T:0.36
Consensus pattern (42 bp):
TGCGATTTATTCCAAGTTCGTTGCGATAGTCCAAGTTCGCGT
Found at i:1402586 original size:21 final size:22
Alignment explanation
Indices: 1402557--1402601 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
1402547 TTGTGGTTCG
1402557 TTTAGTTTTC-ATGTAATTCTAA
1 TTTAGTTTTCAAT-TAATTCTAA
*
1402579 TTTA-TTTTCAATTAATTGTAA
1 TTTAGTTTTCAATTAATTCTAA
1402600 TT
1 TT
1402602 GCACAATAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 15 0.71
22 6 0.29
ACGTcount: A:0.29, C:0.07, G:0.07, T:0.58
Consensus pattern (22 bp):
TTTAGTTTTCAATTAATTCTAA
Found at i:1402966 original size:6 final size:6
Alignment explanation
Indices: 1402955--1403089 Score: 270
Period size: 6 Copynumber: 22.5 Consensus size: 6
1402945 CTCGTCTCGG
1402955 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1403003 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1403051 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
1403090 AATACGTGTC
Statistics
Matches: 129, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 129 1.00
ACGTcount: A:0.00, C:0.16, G:0.50, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:1404094 original size:2 final size:2
Alignment explanation
Indices: 1404087--1404112 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1404077 GTCATTAGAA
1404087 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
1404113 GCAAGTATTA
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):
AT
Found at i:1406934 original size:28 final size:31
Alignment explanation
Indices: 1406901--1406959 Score: 79
Period size: 28 Copynumber: 2.0 Consensus size: 31
1406891 ATAGTTATAA
1406901 TCAAAATACT-TA-CTTTAACA-TTTATTTT
1 TCAAAATACTATAGCTTTAACACTTTATTTT
* *
1406929 TCAAAATATTATAGCTTTAATACTTTATTTT
1 TCAAAATACTATAGCTTTAACACTTTATTTT
1406960 AGAAAAAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
28 9 0.35
29 2 0.08
30 7 0.27
31 8 0.31
ACGTcount: A:0.36, C:0.12, G:0.02, T:0.51
Consensus pattern (31 bp):
TCAAAATACTATAGCTTTAACACTTTATTTT
Found at i:1407600 original size:59 final size:60
Alignment explanation
Indices: 1407460--1407593 Score: 180
Period size: 60 Copynumber: 2.2 Consensus size: 60
1407450 GCACCATATG
* * * *
1407460 TCCCCAAATTATAACTCTCATTTTAAATTAACCCTTAAACTTCTGAATATTCCAAATTCA
1 TCCCCAAAATATGACTCTTATTTTAAACTAACCCTTAAACTTCTGAATATTCCAAATTCA
* * * *
1407520 TCTCCAAAATATGACTCTTATTTTAAACTATCCCTTAAACTT-TGAATATTTCAATTTCA
1 TCCCCAAAATATGACTCTTATTTTAAACTAACCCTTAAACTTCTGAATATTCCAAATTCA
*
1407579 TCCCCAAACTATGAC
1 TCCCCAAAATATGAC
1407594 ATTTATTCTA
Statistics
Matches: 64, Mismatches: 10, Indels: 1
0.85 0.13 0.01
Matches are distributed among these distances:
59 28 0.44
60 36 0.56
ACGTcount: A:0.35, C:0.25, G:0.03, T:0.37
Consensus pattern (60 bp):
TCCCCAAAATATGACTCTTATTTTAAACTAACCCTTAAACTTCTGAATATTCCAAATTCA
Found at i:1407621 original size:59 final size:59
Alignment explanation
Indices: 1407460--1407605 Score: 168
Period size: 59 Copynumber: 2.5 Consensus size: 59
1407450 GCACCATATG
* * * * * *
1407460 TCCCCAAATTATAACTCTCATTTTAAATTAACCCTTAAACTTCTGAATATTCCAAATTCA
1 TCCCCAAAATATGACTCTTATTCTAAACTATCCCTTAAACTT-TGAATATTCCAAATTCA
* * * *
1407520 TCTCCAAAATATGACTCTTATTTTAAACTATCCCTTAAACTTTGAATATTTCAATTTCA
1 TCCCCAAAATATGACTCTTATTCTAAACTATCCCTTAAACTTTGAATATTCCAAATTCA
*
1407579 TCCCCAAACTATGACAT-TTATTCTAAA
1 TCCCCAAAATATGAC-TCTTATTCTAAA
1407606 GTGGTCCCTA
Statistics
Matches: 74, Mismatches: 11, Indels: 3
0.84 0.12 0.03
Matches are distributed among these distances:
59 37 0.50
60 37 0.50
ACGTcount: A:0.36, C:0.23, G:0.03, T:0.38
Consensus pattern (59 bp):
TCCCCAAAATATGACTCTTATTCTAAACTATCCCTTAAACTTTGAATATTCCAAATTCA
Found at i:1411930 original size:17 final size:17
Alignment explanation
Indices: 1411910--1411942 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1411900 AAAAAATTGA
*
1411910 AAAACTTTTAAAACCCC
1 AAAACTTTGAAAACCCC
1411927 AAAACTTTGAAAACCC
1 AAAACTTTGAAAACCC
1411943 TAATTCTAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.48, C:0.27, G:0.03, T:0.21
Consensus pattern (17 bp):
AAAACTTTGAAAACCCC
Found at i:1412528 original size:10 final size:10
Alignment explanation
Indices: 1412513--1412540 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
1412503 TTGAAAAATA
1412513 AAAAATGTGT
1 AAAAATGTGT
1412523 AAAAATGTGT
1 AAAAATGTGT
1412533 AAAAATGT
1 AAAAATGT
1412541 AAAATTAAAA
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:0.54, C:0.00, G:0.18, T:0.29
Consensus pattern (10 bp):
AAAAATGTGT
Found at i:1414062 original size:42 final size:42
Alignment explanation
Indices: 1414003--1414104 Score: 150
Period size: 42 Copynumber: 2.4 Consensus size: 42
1413993 CGTGCATGTT
* **
1414003 GTTGCTGCTACTCCCTCATGCACTCGTGATTCCTTTTCTGCC
1 GTTGCTGCTACTCCCTCATGCACGCGTGATTCCTCCTCTGCC
1414045 GTTGCTGCTACTCCCTCATGCACGCGTGATTCCTCCTCTGCC
1 GTTGCTGCTACTCCCTCATGCACGCGTGATTCCTCCTCTGCC
** *
1414087 ACTGCTGCTGCTCCCTCA
1 GTTGCTGCTACTCCCTCA
1414105 CCTCATGCAT
Statistics
Matches: 54, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 54 1.00
ACGTcount: A:0.10, C:0.39, G:0.18, T:0.33
Consensus pattern (42 bp):
GTTGCTGCTACTCCCTCATGCACGCGTGATTCCTCCTCTGCC
Found at i:1414266 original size:4 final size:4
Alignment explanation
Indices: 1414257--1414319 Score: 126
Period size: 4 Copynumber: 15.8 Consensus size: 4
1414247 CATGAAACAC
1414257 AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA
1 AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA
1414305 AAGA AAGA AAGA AAG
1 AAGA AAGA AAGA AAG
1414320 GGAGAAGAGA
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 59 1.00
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (4 bp):
AAGA
Found at i:1414520 original size:58 final size:54
Alignment explanation
Indices: 1414458--1414567 Score: 148
Period size: 54 Copynumber: 2.0 Consensus size: 54
1414448 ATTTAGTTAA
*
1414458 TTAGTTTGTTAGTTTAAGTTATATATTATATTATATAAAAAAATAGTTAATTAGTTTG
1 TTAGTTTCTTAGTTTAAG-T-TATATTATA-TAT-TAAAAAAATAGTTAATTAGTTTG
* * *
1414516 TTAGTTTCTTAGTTTAAGTTATATTATATGTTAAAAAATTATTTAATTAGTT
1 TTAGTTTCTTAGTTTAAGTTATATTATATATTAAAAAAATAGTTAATTAGTT
1414568 GTTTGTTAGT
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
54 19 0.40
55 2 0.04
56 9 0.19
57 1 0.02
58 17 0.35
ACGTcount: A:0.36, C:0.01, G:0.11, T:0.52
Consensus pattern (54 bp):
TTAGTTTCTTAGTTTAAGTTATATTATATATTAAAAAAATAGTTAATTAGTTTG
Found at i:1415010 original size:17 final size:17
Alignment explanation
Indices: 1414988--1415047 Score: 84
Period size: 17 Copynumber: 3.4 Consensus size: 17
1414978 ATTTATTCCC
1414988 GTTTAAAAAAATATTTT
1 GTTTAAAAAAATATTTT
*
1415005 GTTTAAAAATATTTATTGTT
1 GTTTAAAAA-A-ATATT-TT
1415025 GTTTAAAAAAATATTTT
1 GTTTAAAAAAATATTTT
1415042 GTTTAA
1 GTTTAA
1415048 TTTATATTAG
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
17 17 0.45
18 5 0.13
19 5 0.13
20 11 0.29
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (17 bp):
GTTTAAAAAAATATTTT
Found at i:1418340 original size:11 final size:11
Alignment explanation
Indices: 1418324--1418365 Score: 59
Period size: 11 Copynumber: 3.8 Consensus size: 11
1418314 TTTAATTGAA
1418324 TTATTTATATT
1 TTATTTATATT
1418335 TTATTTATATT
1 TTATTTATATT
*
1418346 TTATCTTAT-TG
1 TTAT-TTATATT
1418357 TTATTTATA
1 TTATTTATA
1418366 AATAGTCGAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
10 4 0.14
11 20 0.71
12 4 0.14
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.69
Consensus pattern (11 bp):
TTATTTATATT
Found at i:1418361 original size:16 final size:16
Alignment explanation
Indices: 1418324--1418365 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
1418314 TTTAATTGAA
*
1418324 TTATTTATATTTTATT
1 TTATTTATATCTTATT
1418340 TATATTT-TATCTTATT
1 T-TATTTATATCTTATT
1418356 GTTATTTATA
1 -TTATTTATA
1418366 AATAGTCGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
16 14 0.64
17 8 0.36
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.69
Consensus pattern (16 bp):
TTATTTATATCTTATT
Found at i:1418781 original size:21 final size:20
Alignment explanation
Indices: 1418695--1418852 Score: 86
Period size: 21 Copynumber: 7.8 Consensus size: 20
1418685 AAATGACCAA
**
1418695 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
1418714 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
1418734 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
1418754 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
1418775 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
1418796 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
1418816 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
1418837 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
1418853 ACACATAAAT
Statistics
Matches: 104, Mismatches: 29, Indels: 11
0.72 0.20 0.08
Matches are distributed among these distances:
19 16 0.15
20 41 0.39
21 47 0.45
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:1418868 original size:40 final size:40
Alignment explanation
Indices: 1418819--1418973 Score: 186
Period size: 40 Copynumber: 3.9 Consensus size: 40
1418809 CGATTTTCCA
* ** *
1418819 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACAT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAACACAT
* * *
1418859 AAATCGCAACGCGTATCCGTAAATCGCAACGTGTATC-CGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCG-AACACAT
* ** *
1418899 ATATCGCAACGCGTATCCGTAAATCGCAACGATAATACAT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAACACAT
1418939 AAAATCGCAACGCGTATCCGTAAATCGCAACGCGA
1 -AAATCGCAACGCGTATCCGTAAATCGCAACGCGA
1418974 TATTTAAAGC
Statistics
Matches: 96, Mismatches: 16, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
39 1 0.01
40 62 0.65
41 33 0.34
ACGTcount: A:0.37, C:0.26, G:0.18, T:0.18
Consensus pattern (40 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCGAACACAT
Found at i:1418881 original size:20 final size:20
Alignment explanation
Indices: 1418819--1418972 Score: 168
Period size: 20 Copynumber: 7.7 Consensus size: 20
1418809 CGATTTTCCA
* ** *
1418819 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
1418839 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
1418859 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
1418879 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
1418899 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* * *
1418919 AAATCGCAACG-ATAATACAT
1 AAATCGCAACGCGT-ATCCGT
1418939 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTATCCGT
1418960 AAATCGCAACGCG
1 AAATCGCAACGCG
1418973 ATATTTAAAG
Statistics
Matches: 112, Mismatches: 17, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
19 2 0.02
20 92 0.82
21 17 0.15
22 1 0.01
ACGTcount: A:0.37, C:0.27, G:0.18, T:0.18
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:1419392 original size:33 final size:33
Alignment explanation
Indices: 1419353--1419423 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
1419343 TTCACTTAGA
*
1419353 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
1419386 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
1419419 TTTCA
1 TTTCA
1419424 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:1419547 original size:20 final size:19
Alignment explanation
Indices: 1419503--1419578 Score: 89
Period size: 20 Copynumber: 3.8 Consensus size: 19
1419493 TGCAGAAGAG
*
1419503 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGA-GAATG-AAA
**
1419524 TCGCAACGAGAGAATGACTG
1 TCGCAACGAGAGAATGA-AA
1419544 TCGCAACGAGAGAAATGAAA
1 TCGCAACGAGAG-AATGAAA
1419564 TCGCAACGAGAGAAT
1 TCGCAACGAGAGAAT
1419579 CGCAACGCGA
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
19 4 0.08
20 28 0.58
21 16 0.33
ACGTcount: A:0.45, C:0.17, G:0.25, T:0.13
Consensus pattern (19 bp):
TCGCAACGAGAGAATGAAA
Found at i:1419576 original size:40 final size:41
Alignment explanation
Indices: 1419502--1419578 Score: 138
Period size: 40 Copynumber: 1.9 Consensus size: 41
1419492 TTGCAGAAGA
*
1419502 GTCGCAACGAGATAAATGAAAATCGCAACGAGAGAATGACT
1 GTCGCAACGAGAGAAATGAAAATCGCAACGAGAGAATGACT
1419543 GTCGCAACGAGAGAAATG-AAATCGCAACGAGAGAAT
1 GTCGCAACGAGAGAAATGAAAATCGCAACGAGAGAAT
1419579 CGCAACGCGA
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
40 18 0.51
41 17 0.49
ACGTcount: A:0.44, C:0.17, G:0.26, T:0.13
Consensus pattern (41 bp):
GTCGCAACGAGAGAAATGAAAATCGCAACGAGAGAATGACT
Found at i:1419581 original size:14 final size:14
Alignment explanation
Indices: 1419562--1419618 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
1419552 AGAGAAATGA
1419562 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
1419576 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
*
1419595 AATCGCAACTAGAG
1 AATCGCAACGAGAG
1419609 AATCGCAACG
1 AATCGCAACG
1419619 CGAAACCAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
14 19 0.56
15 1 0.03
16 2 0.06
17 1 0.03
18 1 0.03
19 10 0.29
ACGTcount: A:0.44, C:0.23, G:0.23, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:1419602 original size:33 final size:33
Alignment explanation
Indices: 1419555--1419634 Score: 126
Period size: 33 Copynumber: 2.5 Consensus size: 33
1419545 CGCAACGAGA
1419555 GAAATG-AAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
*
1419587 GAAATGAAAATCGCAACTAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
**
1419620 GAAACCAAAATCGCA
1 GAAATGAAAATCGCA
1419635 TTGCGATTTT
Statistics
Matches: 44, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
32 6 0.14
33 38 0.86
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:1419652 original size:19 final size:19
Alignment explanation
Indices: 1419630--1419727 Score: 90
Period size: 19 Copynumber: 5.7 Consensus size: 19
1419620 GAAACCAAAA
*
1419630 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1419649 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
1419663 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1419682 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
**
1419696 TCTAGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1419715 TCGCGTTGCGATT
1 TCGCGTTGCGATT
1419728 CTCTCGTTGC
Statistics
Matches: 62, Mismatches: 7, Indels: 20
0.70 0.08 0.22
Matches are distributed among these distances:
14 19 0.31
16 6 0.10
17 6 0.10
19 31 0.50
ACGTcount: A:0.11, C:0.22, G:0.21, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1419671 original size:14 final size:14
Alignment explanation
Indices: 1419652--1419741 Score: 63
Period size: 14 Copynumber: 5.7 Consensus size: 14
1419642 TTTCATTTCG
1419652 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
1419666 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
1419685 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
* *
1419699 AGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
1419718 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
1419732 CGTTGCGATT
1 CGTTGCGATT
1419742 TTCATTTCAA
Statistics
Matches: 60, Mismatches: 6, Indels: 20
0.70 0.07 0.23
Matches are distributed among these distances:
14 29 0.48
16 6 0.10
17 6 0.10
19 19 0.32
ACGTcount: A:0.10, C:0.23, G:0.22, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:1419677 original size:33 final size:33
Alignment explanation
Indices: 1419635--1419749 Score: 221
Period size: 33 Copynumber: 3.5 Consensus size: 33
1419625 CAAAATCGCA
1419635 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
1419668 TTGCGATTTTCATTTCGCGTTGCGATTCTCTAG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1419701 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1419734 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
1419750 AACCAAAAGA
Statistics
Matches: 80, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 80 1.00
ACGTcount: A:0.10, C:0.23, G:0.20, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:1421610 original size:93 final size:93
Alignment explanation
Indices: 1421451--1422009 Score: 1081
Period size: 93 Copynumber: 6.1 Consensus size: 93
1421441 TAGATTGCTT
*
1421451 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1421516 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1421544 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1421609 TTTGTCTTTGTTTTGTC-TTTGGTTG-A
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1421635 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1421700 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1421728 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1421793 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1421821 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1421886 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1421914 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTC-TTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1421978 TTTGTCTTTGTTTTGTCTTTTGGTTG-A
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1422005 AGTAA
1 AGTAA
1422010 TGCAATCCAT
Statistics
Matches: 463, Mismatches: 1, Indels: 6
0.99 0.00 0.01
Matches are distributed among these distances:
91 89 0.19
92 61 0.13
93 313 0.68
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:1421760 original size:184 final size:185
Alignment explanation
Indices: 1421451--1422009 Score: 1086
Period size: 184 Copynumber: 3.0 Consensus size: 185
1421441 TAGATTGCTT
*
1421451 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1421516 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
1421581 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTC-TTTGGTTGA
131 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGA
1421635 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1421700 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
1421765 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTG-A
1421821 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1421886 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
1421951 GTGTATTC-TTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGA
131 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGA
1422005 AGTAA
1 AGTAA
1422010 TGCAATCCAT
Statistics
Matches: 372, Mismatches: 1, Indels: 4
0.99 0.00 0.01
Matches are distributed among these distances:
184 180 0.48
185 53 0.14
186 139 0.37
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (185 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGA
Found at i:1422097 original size:19 final size:19
Alignment explanation
Indices: 1422073--1422185 Score: 120
Period size: 19 Copynumber: 6.5 Consensus size: 19
1422063 TACGAAACTT
1422073 AAAATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAACC
**
1422092 AAAATCGCAACGCGAAATG
1 AAAATCGCAACGCGAAACC
1422111 AAAATCGCAA--CG--A-C
1 AAAATCGCAACGCGAAACC
*
1422125 AGAATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAACC
1422144 AAAATCGCAA--CG--A-C
1 AAAATCGCAACGCGAAACC
*
1422158 AAGATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAACC
1422177 AAAATCGCA
1 AAAATCGCA
1422186 TTGCGATTTT
Statistics
Matches: 77, Mismatches: 7, Indels: 20
0.74 0.07 0.19
Matches are distributed among these distances:
14 19 0.25
15 2 0.03
16 4 0.05
17 4 0.05
18 2 0.03
19 46 0.60
ACGTcount: A:0.47, C:0.28, G:0.18, T:0.07
Consensus pattern (19 bp):
AAAATCGCAACGCGAAACC
Found at i:1422136 original size:33 final size:32
Alignment explanation
Indices: 1422093--1422185 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 32
1422083 CGCGAAACCA
**
1422093 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
1422125 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
1422158 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
1422186 TTGCGATTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 2 0.04
33 55 0.96
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:1422183 original size:52 final size:51
Alignment explanation
Indices: 1422073--1422185 Score: 131
Period size: 52 Copynumber: 2.2 Consensus size: 51
1422063 TACGAAACTT
* *
1422073 AAAATCGCAACGCGAAACCAAAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAAATCGCAACGCGAAACCAAAATCGCAACGCGAAATGAAAAGCGAAAC-AC
* * *
1422125 AGAATCGCAACGCGAAACCAAAATCGCAACGAC-AAGATCGCAACGCGAAAC-C
1 AAAATCGCAACGCGAAACCAAAATCGCAACG-CGAA-AT-GAAAAGCGAAACAC
1422177 AAAATCGCA
1 AAAATCGCA
1422186 TTGCGATTTT
Statistics
Matches: 52, Mismatches: 6, Indels: 6
0.81 0.09 0.09
Matches are distributed among these distances:
52 41 0.79
53 3 0.06
54 8 0.15
ACGTcount: A:0.47, C:0.28, G:0.18, T:0.07
Consensus pattern (51 bp):
AAAATCGCAACGCGAAACCAAAATCGCAACGCGAAATGAAAAGCGAAACAC
Found at i:1422219 original size:21 final size:19
Alignment explanation
Indices: 1422181--1422299 Score: 114
Period size: 19 Copynumber: 6.8 Consensus size: 19
1422171 GAAACCAAAA
1422181 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
1422200 TCGCGTTGCGA--TTC-TT
1 TCGCATTGCGATTTTCATT
1422216 T--CATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
1422233 TCGCATTGCGA--TTC-TG
1 TCGCATTGCGATTTTCATT
1422249 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
* **
1422266 TCGCGTTGCGATTTTGGTT
1 TCGCATTGCGATTTTCATT
*
1422285 TCGCGTTGCGATTTT
1 TCGCATTGCGATTTT
1422300 AAGTTTCGTG
Statistics
Matches: 84, Mismatches: 6, Indels: 20
0.76 0.05 0.18
Matches are distributed among these distances:
14 13 0.15
16 13 0.15
17 13 0.15
19 45 0.54
ACGTcount: A:0.11, C:0.20, G:0.22, T:0.47
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:1422226 original size:33 final size:33
Alignment explanation
Indices: 1422184--1422278 Score: 163
Period size: 33 Copynumber: 2.9 Consensus size: 33
1422174 ACCAAAATCG
*
1422184 CATTGCGATTTTCATTTCGCGTTGCGATTCTTT
1 CATTGCGATTTTCATTTCGCGTTGCGATTCTGT
*
1422217 CATTGCGATTTTCATTTCGCATTGCGATTCTGT
1 CATTGCGATTTTCATTTCGCGTTGCGATTCTGT
*
1422250 CGTTGCGATTTTCATTTCGCGTTGCGATT
1 CATTGCGATTTTCATTTCGCGTTGCGATT
1422279 TTGGTTTCGC
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 58 1.00
ACGTcount: A:0.13, C:0.21, G:0.20, T:0.46
Consensus pattern (33 bp):
CATTGCGATTTTCATTTCGCGTTGCGATTCTGT
Found at i:1422307 original size:20 final size:19
Alignment explanation
Indices: 1422250--1422315 Score: 89
Period size: 19 Copynumber: 3.4 Consensus size: 19
1422240 GCGATTCTGT
1422250 CGTTGCGATTTTCA-TTTCG
1 CGTTGCGATTTT-AGTTTCG
*
1422269 CGTTGCGATTTTGGTTTCG
1 CGTTGCGATTTTAGTTTCG
1422288 CGTTGCGATTTTAAGTTTCG
1 CGTTGCGATTTT-AGTTTCG
*
1422308 TGTTGCGA
1 CGTTGCGA
1422316 AAGTAAACTA
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
19 29 0.69
20 13 0.31
ACGTcount: A:0.11, C:0.17, G:0.27, T:0.45
Consensus pattern (19 bp):
CGTTGCGATTTTAGTTTCG
Found at i:1424247 original size:14 final size:14
Alignment explanation
Indices: 1424228--1424263 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
1424218 ATTGTTTAAT
1424228 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
1424242 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
1424256 TGATTTGT
1 TGATTTGT
1424264 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:1424393 original size:19 final size:19
Alignment explanation
Indices: 1424369--1424465 Score: 132
Period size: 19 Copynumber: 5.4 Consensus size: 19
1424359 CAAATTGACT
*
1424369 ATCGCAATGCGAAATAAAA
1 ATCGCAATGCGAAATGAAA
1424388 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
1424407 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
1424421 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
1424440 ATCGCAATGCGGAATGAAA
1 ATCGCAATGCGAAATGAAA
1424459 ATCGCAA
1 ATCGCAA
1424466 CGGGAGAATC
Statistics
Matches: 69, Mismatches: 4, Indels: 10
0.83 0.05 0.12
Matches are distributed among these distances:
14 10 0.14
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 53 0.77
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:1424497 original size:52 final size:52
Alignment explanation
Indices: 1424369--1424484 Score: 205
Period size: 52 Copynumber: 2.2 Consensus size: 52
1424359 CAAATTGACT
*
1424369 ATCGCAATGCGAAATAAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
1424421 ATCGCAATGCGAAATGAAAATCGCAATGCGGAATGAAAATCGCAACGGGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1424473 ATCGCAATGCGA
1 ATCGCAATGCGA
1424485 TTTTAATTTC
Statistics
Matches: 61, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 61 1.00
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.14
Consensus pattern (52 bp):
ATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:1424502 original size:19 final size:19
Alignment explanation
Indices: 1424474--1424643 Score: 181
Period size: 19 Copynumber: 9.7 Consensus size: 19
1424464 AACGGGAGAA
* *
1424474 TCGCAATGCGATTTTAATT
1 TCGCATTGCGATTTTCATT
*
1424493 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
1424509 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1424526 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
1424545 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
1424561 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1424578 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1424597 TCCGCATTGCGATTTTCA--
1 T-CGCATTGCGATTTTCATT
*
1424615 T-G--TTGGGATTTTCATT
1 TCGCATTGCGATTTTCATT
1424631 TCGCATTGCGATT
1 TCGCATTGCGATT
1424644 CTCTCGTTGC
Statistics
Matches: 127, Mismatches: 8, Indels: 32
0.76 0.05 0.19
Matches are distributed among these distances:
14 23 0.18
16 16 0.13
17 14 0.11
18 1 0.01
19 57 0.45
20 16 0.13
ACGTcount: A:0.15, C:0.21, G:0.18, T:0.45
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Done.