Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008138.1 Hibiscus syriacus cultivar Beakdansim tig00110694_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: 3838456
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 18
Found at i:1086055 original size:12 final size:12
Alignment explanation
Indices: 1086034--1086082 Score: 57
Period size: 12 Copynumber: 4.2 Consensus size: 12
1086024 AATTACGAAC
1086034 TTAT-AACAAAT
1 TTATAAACAAAT
*
1086045 TGATAAACAAAT
1 TTATAAACAAAT
1086057 TTATAAA-AAAT
1 TTATAAACAAAT
*
1086068 ATTATAAATAAAT
1 -TTATAAACAAAT
1086081 TT
1 TT
1086083 GTTTGTGAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
11 7 0.21
12 22 0.67
13 4 0.12
ACGTcount: A:0.57, C:0.04, G:0.02, T:0.37
Consensus pattern (12 bp):
TTATAAACAAAT
Found at i:1086060 original size:23 final size:24
Alignment explanation
Indices: 1086034--1086082 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
1086024 AATTACGAAC
*
1086034 TTATAACAAAT-TGATAAACAAAT
1 TTATAAAAAATATGATAAACAAAT
* *
1086057 TTATAAAAAATATTATAAATAAAT
1 TTATAAAAAATATGATAAACAAAT
1086081 TT
1 TT
1086083 GTTTGTGAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 10 0.45
24 12 0.55
ACGTcount: A:0.57, C:0.04, G:0.02, T:0.37
Consensus pattern (24 bp):
TTATAAAAAATATGATAAACAAAT
Found at i:1093397 original size:28 final size:28
Alignment explanation
Indices: 1093365--1093421 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
1093355 TCGATTATAT
* *
1093365 GTTTGTTTATGTTCATTCATTTATGTTC
1 GTTTGGTTATGTTCATTCATTTACGTTC
* *
1093393 GTTTGGTTATGTTCGTTCTTTTACGTTC
1 GTTTGGTTATGTTCATTCATTTACGTTC
1093421 G
1 G
1093422 AATAGATGGC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.11, C:0.12, G:0.19, T:0.58
Consensus pattern (28 bp):
GTTTGGTTATGTTCATTCATTTACGTTC
Found at i:1093986 original size:101 final size:103
Alignment explanation
Indices: 1093767--1093991 Score: 400
Period size: 101 Copynumber: 2.2 Consensus size: 103
1093757 CGTTTATCAT
*
1093767 TTAAATGAATGAACATGAACAAGCTATATTCCTTAATGGACGAACATGAACAAAAAAAATTTTGT
1 TTAAATGAACGAACATGAACAAGCTATATTCCTTAATGGACGAACATGAACAAAAAAAATTTTGT
1093832 TCGTTTATATTCATGTTCATTTATTTGTTCGGTTAAAG
66 TCGTTTATATTCATGTTCATTTATTTGTTCGGTTAAAG
*
1093870 TTAAATGAACAAACATGAACAAGCTATATTCCTTAATGGACGAACATGAAC-AAAAAAA-TTTGT
1 TTAAATGAACGAACATGAACAAGCTATATTCCTTAATGGACGAACATGAACAAAAAAAATTTTGT
* *
1093933 TCGTTTATGTTCGTGTTCATTTATTTGTTCGGTTAAAG
66 TCGTTTATATTCATGTTCATTTATTTGTTCGGTTAAAG
1093971 TTAAATGAACGAACATGAACA
1 TTAAATGAACGAACATGAACA
1093992 TACCTTTGTT
Statistics
Matches: 117, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
101 61 0.52
102 7 0.06
103 49 0.42
ACGTcount: A:0.38, C:0.12, G:0.15, T:0.35
Consensus pattern (103 bp):
TTAAATGAACGAACATGAACAAGCTATATTCCTTAATGGACGAACATGAACAAAAAAAATTTTGT
TCGTTTATATTCATGTTCATTTATTTGTTCGGTTAAAG
Found at i:1101670 original size:42 final size:42
Alignment explanation
Indices: 1101624--1101704 Score: 162
Period size: 42 Copynumber: 1.9 Consensus size: 42
1101614 AAGCAACGTC
1101624 TTCATGAGAATTTATTCTCTGTGTCAGGCCTAGCAAGTATAT
1 TTCATGAGAATTTATTCTCTGTGTCAGGCCTAGCAAGTATAT
1101666 TTCATGAGAATTTATTCTCTGTGTCAGGCCTAGCAAGTA
1 TTCATGAGAATTTATTCTCTGTGTCAGGCCTAGCAAGTA
1101705 GAATTTATTC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.26, C:0.17, G:0.20, T:0.37
Consensus pattern (42 bp):
TTCATGAGAATTTATTCTCTGTGTCAGGCCTAGCAAGTATAT
Found at i:1105634 original size:69 final size:68
Alignment explanation
Indices: 1105463--1105645 Score: 215
Period size: 69 Copynumber: 2.7 Consensus size: 68
1105453 ATTTCATTTA
* * * *
1105463 AAAACTTTATCACACTTGAGATATTTTCTCTTAAAATACAAATTTTGAAATTGTTTAACTCGAAA
1 AAAATTTTATCTCACTTGAGATATTTTCTCTTGAAATA-AAATTTCGAAATTGTTTAACTCGAAA
1105528 CAAG
65 CAAG
* * * * **
1105532 AAAATTTTATCTTACTTGAGACACTTTCTCTTGAAATATAAATTTCGAAATTGTTTCACTTTAAA
1 AAAATTTTATCTCACTTGAGATATTTTCTCTTGAAATA-AAATTTCGAAATTGTTTAACTCGAAA
1105597 CAAG
65 CAAG
* * *
1105601 AAATTTTTATCTCACTTGAGGTTATTTTC-CTTGAAACAAAATTTC
1 AAAATTTTATCTCACTTGA-GATATTTTCTCTTGAAATAAAATTTC
1105646 ATCTCACTTA
Statistics
Matches: 96, Mismatches: 17, Indels: 3
0.83 0.15 0.03
Matches are distributed among these distances:
68 7 0.07
69 83 0.86
70 6 0.06
ACGTcount: A:0.37, C:0.15, G:0.09, T:0.40
Consensus pattern (68 bp):
AAAATTTTATCTCACTTGAGATATTTTCTCTTGAAATAAAATTTCGAAATTGTTTAACTCGAAAC
AAG
Found at i:1106238 original size:18 final size:19
Alignment explanation
Indices: 1106192--1106239 Score: 59
Period size: 18 Copynumber: 2.7 Consensus size: 19
1106182 AATGAAAGAG
1106192 TTCATAAT-AAAAAAATTAA
1 TTCATAATGAAAAAAA-TAA
1106211 TTCA-AA-GAAAAAAA-AA
1 TTCATAATGAAAAAAATAA
1106227 TTCATAATGAAAA
1 TTCATAATGAAAA
1106240 GAACATGTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
16 6 0.23
17 2 0.08
18 14 0.54
19 4 0.15
ACGTcount: A:0.65, C:0.06, G:0.04, T:0.25
Consensus pattern (19 bp):
TTCATAATGAAAAAAATAA
Found at i:1106871 original size:11 final size:11
Alignment explanation
Indices: 1106855--1106889 Score: 61
Period size: 11 Copynumber: 3.2 Consensus size: 11
1106845 AAGAAGGAAC
1106855 GAAAAATAAAA
1 GAAAAATAAAA
1106866 GAAAAATAAAA
1 GAAAAATAAAA
*
1106877 GAAAAATAGAA
1 GAAAAATAAAA
1106888 GA
1 GA
1106890 GAAAGGAAGG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.77, C:0.00, G:0.14, T:0.09
Consensus pattern (11 bp):
GAAAAATAAAA
Found at i:1107470 original size:25 final size:25
Alignment explanation
Indices: 1107433--1107481 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
1107423 CATGTTTAGC
*
1107433 CTGTCTTTCTATTCGGTTAGAGCTT
1 CTGTCTTTATATTCGGTTAGAGCTT
1107458 CTGTCTTTATATTCGGTTAGAGCT
1 CTGTCTTTATATTCGGTTAGAGCT
1107482 GACGGTTGTG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.14, C:0.18, G:0.20, T:0.47
Consensus pattern (25 bp):
CTGTCTTTATATTCGGTTAGAGCTT
Found at i:1110686 original size:17 final size:17
Alignment explanation
Indices: 1110653--1110721 Score: 75
Period size: 17 Copynumber: 3.9 Consensus size: 17
1110643 AGTATGTTGT
*
1110653 TTCATTCAATAAAACTAG
1 TTCATT-AATTAAACTAG
*
1110671 TTCACTAATTAAACTAG
1 TTCATTAATTAAACTAG
* * *
1110688 TTCGTTCATTTAAACTGG
1 TTCATT-AATTAAACTAG
1110706 TTCATTAATTAAACTA
1 TTCATTAATTAAACTA
1110722 TCTCTTTAAA
Statistics
Matches: 41, Mismatches: 9, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
17 22 0.54
18 19 0.46
ACGTcount: A:0.38, C:0.16, G:0.07, T:0.39
Consensus pattern (17 bp):
TTCATTAATTAAACTAG
Found at i:1111667 original size:20 final size:19
Alignment explanation
Indices: 1111642--1111681 Score: 71
Period size: 20 Copynumber: 2.1 Consensus size: 19
1111632 CCATCCATCA
1111642 TCAATCCTACAACATCGATT
1 TCAATCCTACAACATC-ATT
1111662 TCAATCCTACAACATCATT
1 TCAATCCTACAACATCATT
1111681 T
1 T
1111682 TATTTCAATC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 4 0.20
20 16 0.80
ACGTcount: A:0.35, C:0.30, G:0.03, T:0.33
Consensus pattern (19 bp):
TCAATCCTACAACATCATT
Found at i:1111691 original size:24 final size:25
Alignment explanation
Indices: 1111659--1111708 Score: 75
Period size: 24 Copynumber: 2.0 Consensus size: 25
1111649 TACAACATCG
*
1111659 ATTTCAATCCTACAACATCA-TTTT
1 ATTTCAATCATACAACATCACTTTT
*
1111683 ATTTCAATCATACTACATCACTTTT
1 ATTTCAATCATACAACATCACTTTT
1111708 A
1 A
1111709 ATTCTATCTC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 18 0.78
25 5 0.22
ACGTcount: A:0.34, C:0.24, G:0.00, T:0.42
Consensus pattern (25 bp):
ATTTCAATCATACAACATCACTTTT
Found at i:1116062 original size:3 final size:3
Alignment explanation
Indices: 1116049--1116154 Score: 101
Period size: 3 Copynumber: 34.3 Consensus size: 3
1116039 AAATGCAAAT
* *
1116049 ATA AT- ATA ATA ATA TATT ATA TATA ATAA ATA TGTA AT- ATA ATA ATA
1 ATA ATA ATA ATA ATA -ATA ATA -ATA AT-A ATA -ATA ATA ATA ATA ATA
*
1116096 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA GTA AT- ATA ATTA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A-TA ATA
*
1116141 ATA GTA ATA TATA A
1 ATA ATA ATA -ATA A
1116155 AAAACAGACA
Statistics
Matches: 86, Mismatches: 8, Indels: 18
0.77 0.07 0.16
Matches are distributed among these distances:
2 6 0.07
3 64 0.74
4 16 0.19
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (3 bp):
ATA
Found at i:1117166 original size:22 final size:22
Alignment explanation
Indices: 1117141--1117189 Score: 89
Period size: 22 Copynumber: 2.2 Consensus size: 22
1117131 GATAAAGCTT
1117141 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
*
1117163 TCATCTTTGAAGAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
1117185 TCATC
1 TCATC
1117190 CTTGCATAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.33
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:1117961 original size:42 final size:42
Alignment explanation
Indices: 1117900--1118004 Score: 133
Period size: 40 Copynumber: 2.5 Consensus size: 42
1117890 TTTGTGTCTG
* *
1117900 AAATGGGCTTTCAAAATGCCCCACATAAATTGTTTCTGACTA
1 AAATGGGCTTTCAACATGCCCCACATAAATTATTTCTGACTA
* * * * *
1117942 AAATGGGCCTTCAGCATG--CCTCATAGATTATTTCTGACTG
1 AAATGGGCTTTCAACATGCCCCACATAAATTATTTCTGACTA
1117982 AAATGGGCTTTCAACATGCCCCA
1 AAATGGGCTTTCAACATGCCCCA
1118005 ACATTCCAGG
Statistics
Matches: 51, Mismatches: 10, Indels: 4
0.78 0.15 0.06
Matches are distributed among these distances:
40 34 0.67
42 17 0.33
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.30
Consensus pattern (42 bp):
AAATGGGCTTTCAACATGCCCCACATAAATTATTTCTGACTA
Found at i:1132719 original size:85 final size:85
Alignment explanation
Indices: 1132567--1132723 Score: 219
Period size: 85 Copynumber: 1.8 Consensus size: 85
1132557 TTCAACAAAC
* * * *
1132567 GCCGTAATAGAGTTGTAATTTAGCGGCGTTTATAGCTCAAACGCCGGAATATAGTTGTTTATAGT
1 GCCGTAATAGAGTTGTAATTTAGCGGCATTTATA-CTCAAACACCGCAATAGAGTTGTTTATAGT
1132632 GGCGTTTTTACAAAAAAAAAT
65 GGCGTTTTTACAAAAAAAAAT
* *
1132653 GCCGTAATAGA-TTAGTAATTTAGCTGCATTTTTA-TACAAACACCGCAATAGAGTTGTTTATAG
1 GCCGTAATAGAGTT-GTAATTTAGCGGCATTTATACT-CAAACACCGCAATAGAGTTGTTTATAG
1132716 TGGCGTTT
64 TGGCGTTT
1132724 GTGCTAAAAA
Statistics
Matches: 63, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
84 1 0.02
85 34 0.54
86 28 0.44
ACGTcount: A:0.31, C:0.13, G:0.21, T:0.34
Consensus pattern (85 bp):
GCCGTAATAGAGTTGTAATTTAGCGGCATTTATACTCAAACACCGCAATAGAGTTGTTTATAGTG
GCGTTTTTACAAAAAAAAAT
Found at i:1133262 original size:26 final size:23
Alignment explanation
Indices: 1133207--1133251 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
1133197 CTTTCGTGGA
*
1133207 GAAAAATAATAGCTTTCGAATAG
1 GAAAAATAATAGCTTTCGAAAAG
*
1133230 GAAAAATAATAGCTTTTGAAAA
1 GAAAAATAATAGCTTTCGAAAA
1133252 CGTGAACAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.51, C:0.07, G:0.16, T:0.27
Consensus pattern (23 bp):
GAAAAATAATAGCTTTCGAAAAG
Found at i:1134605 original size:42 final size:42
Alignment explanation
Indices: 1134260--1134594 Score: 472
Period size: 42 Copynumber: 8.0 Consensus size: 42
1134250 TGTAAAAAAT
* * * **
1134260 GCCGCAATAGAGTAGTAATATAGCAGTGTTTATAACAAAAAC
1 GCCGCAATAGAGTAGTAATATAGCGGCGTTTATAGCTCAAAC
* *
1134302 GTCGCAATAGAGTAGTAATATAACGGCGTTTATAGCTCAAAC
1 GCCGCAATAGAGTAGTAATATAGCGGCGTTTATAGCTCAAAC
* * * *
1134344 GCCGTAATAGAGTCGTAATATAGCGGCATTTATATCTCAAAC
1 GCCGCAATAGAGTAGTAATATAGCGGCGTTTATAGCTCAAAC
* *
1134386 GCCGCAATAGAGTAGTAATATAGCAGCGTTTATAGCTCAAAT
1 GCCGCAATAGAGTAGTAATATAGCGGCGTTTATAGCTCAAAC
*
1134428 GCCGCAATAGAGTAGTAATATAGTGGCGTTTATAGCTCAAAC
1 GCCGCAATAGAGTAGTAATATAGCGGCGTTTATAGCTCAAAC
* * * *
1134470 TCTGCAATAGAGTCGTAATATAGCGGCGTTTATAGCTCAAAT
1 GCCGCAATAGAGTAGTAATATAGCGGCGTTTATAGCTCAAAC
* *
1134512 GCCGCAATATAATAGTAATATAGCGGCGTTTATAGCTCAAAC
1 GCCGCAATAGAGTAGTAATATAGCGGCGTTTATAGCTCAAAC
* *
1134554 GCCGTAATAGAGTAGTAATATAGCGGCGTTTATAGTTCAAA
1 GCCGCAATAGAGTAGTAATATAGCGGCGTTTATAGCTCAAA
1134595 TGTTGTAATA
Statistics
Matches: 256, Mismatches: 37, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 256 1.00
ACGTcount: A:0.35, C:0.16, G:0.21, T:0.27
Consensus pattern (42 bp):
GCCGCAATAGAGTAGTAATATAGCGGCGTTTATAGCTCAAAC
Found at i:1136734 original size:26 final size:24
Alignment explanation
Indices: 1136699--1136754 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 24
1136689 ATGAATTTTC
* *
1136699 TTTAGTAAAATTGTTTTTACATTT
1 TTTAGTAAAATTCTGTTTACATTT
*
1136723 TTATAGTCAAAATTCTGTTTATATTT
1 TT-TAGT-AAAATTCTGTTTACATTT
1136749 TTTAGT
1 TTTAGT
1136755 TTGATTTCCT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
24 2 0.07
25 8 0.30
26 17 0.63
ACGTcount: A:0.29, C:0.05, G:0.09, T:0.57
Consensus pattern (24 bp):
TTTAGTAAAATTCTGTTTACATTT
Found at i:1143630 original size:21 final size:21
Alignment explanation
Indices: 1143592--1143698 Score: 133
Period size: 21 Copynumber: 5.1 Consensus size: 21
1143582 AGCAGAGACC
**
1143592 AGCAGCGAAAGCACAGAGAGA
1 AGCAGCGGCAGCACAGAGAGA
* *
1143613 AGCAGCGGCATCATAGAGAGA
1 AGCAGCGGCAGCACAGAGAGA
* *
1143634 AACAGCGGCATCACAGAGAGA
1 AGCAGCGGCAGCACAGAGAGA
*
1143655 AGCAGCGGTAGCACAGAGAGA
1 AGCAGCGGCAGCACAGAGAGA
* *
1143676 AGCAGCGACAGCATAGAGAGA
1 AGCAGCGGCAGCACAGAGAGA
1143697 AG
1 AG
1143699 AAACATATCA
Statistics
Matches: 74, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 74 1.00
ACGTcount: A:0.42, C:0.20, G:0.34, T:0.05
Consensus pattern (21 bp):
AGCAGCGGCAGCACAGAGAGA
Found at i:1143714 original size:63 final size:64
Alignment explanation
Indices: 1143582--1143715 Score: 157
Period size: 63 Copynumber: 2.1 Consensus size: 64
1143572 AAGTAAGGGA
* * * * *
1143582 AGCAGAGACCAGCAGCGAAAGCACAGAGAGAAGCAGCGGCATCATAGAGAGAAACAGCGGCATC
1 AGCAGAGACAAGCAGCGAAAGCACAGAGAGAAGCAGCGACAGCATAGAGAGAAACAACGACATC
* ** *
1143646 A-CAGAGAGAAGCAGCGGTAGCACAGAGAGAAGCAGCGACAGCATAGAGAGAAGA-AAC-ATATC
1 AGCAGAGACAAGCAGCGAAAGCACAGAGAGAAGCAGCGACAGCATAGAGAGAA-ACAACGACATC
1143708 AGCAGAGA
1 AGCAGAGA
1143716 TGTGAAGAAT
Statistics
Matches: 59, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
62 4 0.07
63 53 0.90
64 2 0.03
ACGTcount: A:0.43, C:0.20, G:0.31, T:0.05
Consensus pattern (64 bp):
AGCAGAGACAAGCAGCGAAAGCACAGAGAGAAGCAGCGACAGCATAGAGAGAAACAACGACATC
Found at i:1144335 original size:43 final size:43
Alignment explanation
Indices: 1144121--1144335 Score: 198
Period size: 43 Copynumber: 5.0 Consensus size: 43
1144111 CGAAAGCTCA
* * * * * * *
1144121 AACACCTATTGCGGCGTTTGTGAGAAAAATGCAGCTAAATCTC
1 AACAACTATTACGGCGTTTGTAATAAAAACGCCGCTAAATATC
* * *
1144164 AA-AACTTATTACGGCGTTTGCAATAAAAATGCCGCTAAATCTC
1 AACAAC-TATTACGGCGTTTGTAATAAAAACGCCGCTAAATATC
*** *
1144207 AACAACTATTACGGCGTTTGTGGGAAAAACGCCGCTAAACATC
1 AACAACTATTACGGCGTTTGTAATAAAAACGCCGCTAAATATC
* * * * * * *
1144250 ACCACCTATTGCGGTGTTTTTATTACAAACGCCGCTAAATATC
1 AACAACTATTACGGCGTTTGTAATAAAAACGCCGCTAAATATC
* * *
1144293 AACATCTATTACGGCGTTTGTAATATAAACGCCGCTATATATC
1 AACAACTATTACGGCGTTTGTAATAAAAACGCCGCTAAATATC
1144336 GTAACCTATT
Statistics
Matches: 139, Mismatches: 31, Indels: 4
0.80 0.18 0.02
Matches are distributed among these distances:
42 2 0.01
43 134 0.96
44 3 0.02
ACGTcount: A:0.33, C:0.22, G:0.17, T:0.28
Consensus pattern (43 bp):
AACAACTATTACGGCGTTTGTAATAAAAACGCCGCTAAATATC
Found at i:1144343 original size:86 final size:87
Alignment explanation
Indices: 1144194--1144372 Score: 209
Period size: 86 Copynumber: 2.1 Consensus size: 87
1144184 CAATAAAAAT
* ** *
1144194 GCCGCTAAATCTCAACAACTATTACGGCGTTTGTGGGAAAAACGCCGCTAAACATCACCACCTAT
1 GCCGCTAAATATCAACAACTATTACGGCGTTTGTAAGAAAAACGCCGCTAAACATCACAACCTAT
*
1144259 TGCGG-TGTTTTTATT-ACAAAC
66 TACGGAT-TTTTTATTCACAAAC
* * * * * **
1144280 GCCGCTAAATATCAACATCTATTACGGCGTTTGTAATATAAACGCCGCTATATATCGTAACCTAT
1 GCCGCTAAATATCAACAACTATTACGGCGTTTGTAAGAAAAACGCCGCTAAACATCACAACCTAT
*
1144345 TACGGCATTTTTTTTTCACAAAC
66 TACGG-ATTTTTTATTCACAAAC
1144368 GCCGC
1 GCCGC
1144373 AAACTTTAGC
Statistics
Matches: 77, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
86 58 0.75
87 7 0.09
88 12 0.16
ACGTcount: A:0.30, C:0.25, G:0.16, T:0.30
Consensus pattern (87 bp):
GCCGCTAAATATCAACAACTATTACGGCGTTTGTAAGAAAAACGCCGCTAAACATCACAACCTAT
TACGGATTTTTTATTCACAAAC
Found at i:1148621 original size:18 final size:18
Alignment explanation
Indices: 1148598--1148638 Score: 82
Period size: 18 Copynumber: 2.3 Consensus size: 18
1148588 GTCCTAATGG
1148598 AACTTGATGCTAGGCTTT
1 AACTTGATGCTAGGCTTT
1148616 AACTTGATGCTAGGCTTT
1 AACTTGATGCTAGGCTTT
1148634 AACTT
1 AACTT
1148639 TATGACAAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.39
Consensus pattern (18 bp):
AACTTGATGCTAGGCTTT
Found at i:1151932 original size:14 final size:14
Alignment explanation
Indices: 1151913--1151941 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
1151903 ATTGCCAAAT
1151913 ATGGATCGTAATCC
1 ATGGATCGTAATCC
1151927 ATGGATCGTAATCC
1 ATGGATCGTAATCC
1151941 A
1 A
1151942 AACCCTGACA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.28
Consensus pattern (14 bp):
ATGGATCGTAATCC
Found at i:1155116 original size:60 final size:60
Alignment explanation
Indices: 1155036--1155194 Score: 148
Period size: 59 Copynumber: 2.7 Consensus size: 60
1155026 ATGAATTTAG
* *
1155036 GGATGAAATTA-AAAGATTCAAAAGCTTAGGGATCAATTTAGAAAGATGA-TCATAAATTATA
1 GGATGAAATTAGAATG-TTCAAAAGTTTAGGGATCAATTTAGAAAGA-GATTCATAAATTA-A
* * ***
1155097 -GATGAAATTAGAATGTTC-AAAGTTTAAGGGCT-AATTTAGAATGAGATTCATTGTTTAA
1 GGATGAAATTAGAATGTTCAAAAGTTT-AGGGATCAATTTAGAAAGAGATTCATAAATTAA
* * * *
1155155 GGATAAAATTGGAATATTCAAAAGTTTAAGGATCAATTTA
1 GGATGAAATTAGAATGTTCAAAAGTTTAGGGATCAATTTA
1155195 AAATAAGGAT
Statistics
Matches: 80, Mismatches: 12, Indels: 13
0.76 0.11 0.12
Matches are distributed among these distances:
58 3 0.04
59 43 0.54
60 31 0.39
61 3 0.04
ACGTcount: A:0.43, C:0.06, G:0.19, T:0.32
Consensus pattern (60 bp):
GGATGAAATTAGAATGTTCAAAAGTTTAGGGATCAATTTAGAAAGAGATTCATAAATTAA
Found at i:1167710 original size:16 final size:17
Alignment explanation
Indices: 1167689--1167721 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
1167679 TTTGGGGTTT
1167689 TTAAGG-TTTAAAAAAA
1 TTAAGGTTTTAAAAAAA
1167705 TTAAGGTTTTAAAAAAA
1 TTAAGGTTTTAAAAAAA
1167722 ATAATTTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.55, C:0.00, G:0.12, T:0.33
Consensus pattern (17 bp):
TTAAGGTTTTAAAAAAA
Found at i:1167729 original size:15 final size:16
Alignment explanation
Indices: 1167690--1167731 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
1167680 TTGGGGTTTT
* *
1167690 TAAGGTTTAAAAAAAT
1 TAAGTTTTAAAAAAAA
1167706 TAAGGTTTTAAAAAAAA
1 TAA-GTTTTAAAAAAAA
1167723 TAA-TTTTAA
1 TAAGTTTTAA
1167732 GCTTTTTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
15 6 0.26
16 3 0.13
17 14 0.61
ACGTcount: A:0.55, C:0.00, G:0.10, T:0.36
Consensus pattern (16 bp):
TAAGTTTTAAAAAAAA
Found at i:1167949 original size:18 final size:19
Alignment explanation
Indices: 1167926--1167971 Score: 85
Period size: 19 Copynumber: 2.5 Consensus size: 19
1167916 CCAAAATGGT
1167926 CATTTTAGC-TTTTTTTAG
1 CATTTTAGCTTTTTTTTAG
1167944 CATTTTAGCTTTTTTTTAG
1 CATTTTAGCTTTTTTTTAG
1167963 CATTTTAGC
1 CATTTTAGC
1167972 CCCCTTGTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 9 0.33
19 18 0.67
ACGTcount: A:0.17, C:0.13, G:0.11, T:0.59
Consensus pattern (19 bp):
CATTTTAGCTTTTTTTTAG
Found at i:1177501 original size:11 final size:11
Alignment explanation
Indices: 1177481--1177567 Score: 52
Period size: 11 Copynumber: 7.9 Consensus size: 11
1177471 AATTGAATAT
*
1177481 ATAAATGAACG
1 ATAAACGAACG
*
1177492 ATAAACGAACA
1 ATAAACGAACG
*
1177503 ATAAACAAAC-
1 ATAAACGAACG
* *
1177513 ACTAAATGAATG
1 A-TAAACGAACG
*
1177525 CTAAACGAACG
1 ATAAACGAACG
* *
1177536 CTAAACGAA-T
1 ATAAACGAACG
1177546 ACTAAACGAACG
1 A-TAAACGAACG
* *
1177558 CTAAATGAAC
1 ATAAACGAAC
1177568 ATATTCGTGA
Statistics
Matches: 58, Mismatches: 14, Indels: 8
0.73 0.17 0.10
Matches are distributed among these distances:
10 1 0.02
11 57 0.98
ACGTcount: A:0.54, C:0.18, G:0.13, T:0.15
Consensus pattern (11 bp):
ATAAACGAACG
Found at i:1177518 original size:22 final size:22
Alignment explanation
Indices: 1177482--1177568 Score: 84
Period size: 22 Copynumber: 4.0 Consensus size: 22
1177472 ATTGAATATA
* * *
1177482 TAAATGAACGATAAACGAACAA
1 TAAACGAACGCTAAACGAACAC
* * * **
1177504 TAAACAAACACTAAATGAATGC
1 TAAACGAACGCTAAACGAACAC
*
1177526 TAAACGAACGCTAAACGAATAC
1 TAAACGAACGCTAAACGAACAC
*
1177548 TAAACGAACGCTAAATGAACA
1 TAAACGAACGCTAAACGAACA
1177569 TATTCGTGAA
Statistics
Matches: 51, Mismatches: 14, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
22 51 1.00
ACGTcount: A:0.54, C:0.18, G:0.13, T:0.15
Consensus pattern (22 bp):
TAAACGAACGCTAAACGAACAC
Found at i:1177519 original size:33 final size:33
Alignment explanation
Indices: 1177482--1177568 Score: 102
Period size: 33 Copynumber: 2.6 Consensus size: 33
1177472 ATTGAATATA
*
1177482 TAAATGAACGATAAACGAACAATAAACAAACAC
1 TAAATGAACGCTAAACGAACAATAAACAAACAC
* ** * *
1177515 TAAATGAATGCTAAACGAACGCTAAACGAATAC
1 TAAATGAACGCTAAACGAACAATAAACAAACAC
* *
1177548 TAAACGAACGCTAAATGAACA
1 TAAATGAACGCTAAACGAACA
1177569 TATTCGTGAA
Statistics
Matches: 44, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
33 44 1.00
ACGTcount: A:0.54, C:0.18, G:0.13, T:0.15
Consensus pattern (33 bp):
TAAATGAACGCTAAACGAACAATAAACAAACAC
Found at i:1177641 original size:30 final size:30
Alignment explanation
Indices: 1177605--1177662 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
1177595 TCGCACAATA
* *
1177605 AATAAACGAACATGAACACCTTTAAAAATT
1 AATAAACGAACACGAACACCTTAAAAAATT
1177635 AATAAACGAACACGAACACCTTAAAAAA
1 AATAAACGAACACGAACACCTTAAAAAA
1177663 AACAAGGTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.57, C:0.19, G:0.07, T:0.17
Consensus pattern (30 bp):
AATAAACGAACACGAACACCTTAAAAAATT
Found at i:1178350 original size:16 final size:15
Alignment explanation
Indices: 1178317--1178346 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1178307 TTGTAAAAAC
1178317 AAATAAATAAAAATT
1 AAATAAATAAAAATT
1178332 AAATAAATAAAAATT
1 AAATAAATAAAAATT
1178347 TAAAAAAAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (15 bp):
AAATAAATAAAAATT
Found at i:1179665 original size:22 final size:22
Alignment explanation
Indices: 1179640--1179689 Score: 73
Period size: 22 Copynumber: 2.3 Consensus size: 22
1179630 ATTATGTAAC
1179640 ATATATTATATTTTCAAAAACT
1 ATATATTATATTTTCAAAAACT
* * *
1179662 ATATAATATGTTTTCAAAAATT
1 ATATATTATATTTTCAAAAACT
1179684 ATATAT
1 ATATAT
1179690 ATTATATATA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.46, C:0.06, G:0.02, T:0.46
Consensus pattern (22 bp):
ATATATTATATTTTCAAAAACT
Found at i:1185833 original size:20 final size:21
Alignment explanation
Indices: 1185808--1185847 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
1185798 CTATGTATAG
*
1185808 TAGTATTGATACCAT-AGGCA
1 TAGTATCGATACCATCAGGCA
1185828 TAGTATCGATACCATCAGGC
1 TAGTATCGATACCATCAGGC
1185848 CCCAACGGCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.28
Consensus pattern (21 bp):
TAGTATCGATACCATCAGGCA
Found at i:1192541 original size:24 final size:24
Alignment explanation
Indices: 1192509--1192607 Score: 164
Period size: 24 Copynumber: 4.1 Consensus size: 24
1192499 GGTTAGTTAT
1192509 TGAAGCTTGTGCTTTTGCAGTCGA
1 TGAAGCTTGTGCTTTTGCAGTCGA
1192533 TGAAGCTTGTGCTTTTGCAGTCGA
1 TGAAGCTTGTGCTTTTGCAGTCGA
*
1192557 TGAAGCTTATGCTTTTGCAG-CAGA
1 TGAAGCTTGTGCTTTTGCAGTC-GA
*
1192581 TGAAGCTTGTGCTTTTGCAGTAGA
1 TGAAGCTTGTGCTTTTGCAGTCGA
1192605 TGA
1 TGA
1192608 GTCTCCTTGA
Statistics
Matches: 70, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
23 1 0.01
24 69 0.99
ACGTcount: A:0.20, C:0.15, G:0.28, T:0.36
Consensus pattern (24 bp):
TGAAGCTTGTGCTTTTGCAGTCGA
Found at i:1194951 original size:21 final size:20
Alignment explanation
Indices: 1194920--1194974 Score: 76
Period size: 21 Copynumber: 2.8 Consensus size: 20
1194910 AATGTGTATC
1194920 GATAC-TGCTACAGTGTACA
1 GATACATGCTACAGTGTACA
*
1194939 GATACATTGCTACAATGTACA
1 GATACA-TGCTACAGTGTACA
*
1194960 TATACATGCTACAGT
1 GATACATGCTACAGT
1194975 AATTTCCGCC
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.16
20 8 0.26
21 18 0.58
ACGTcount: A:0.35, C:0.20, G:0.16, T:0.29
Consensus pattern (20 bp):
GATACATGCTACAGTGTACA
Found at i:1198859 original size:29 final size:29
Alignment explanation
Indices: 1198800--1198852 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
1198790 AATACGTACT
1198800 ATATATT-TA-TTT-AAAAATTATATAAC
1 ATATATTATATTTTCAAAAATTATATAAC
1198826 ATATATTATATTTTCAAAAATTATATA
1 ATATATTATATTTTCAAAAATTATATA
1198853 TAGTATACAT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
26 7 0.29
27 2 0.08
28 3 0.12
29 12 0.50
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (29 bp):
ATATATTATATTTTCAAAAATTATATAAC
Found at i:1201617 original size:2 final size:2
Alignment explanation
Indices: 1201610--1201644 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1201600 CATTGTACAT
1201610 TA 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 TA T
1201645 GCCTATAATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1205818 original size:3 final size:3
Alignment explanation
Indices: 1205812--1205878 Score: 70
Period size: 3 Copynumber: 22.7 Consensus size: 3
1205802 TTCATTTAAA
*
1205812 TAT TAT T-T ATAT TAT TAT TA- TAT TAT TAT TAT TAA TAT TAT TATT
1 TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T
1205857 TAT TAT TAAT T-T TAT TA- TAT TA
1 TAT TAT T-AT TAT TAT TAT TAT TA
1205879 CAGGCCCAAT
Statistics
Matches: 55, Mismatches: 2, Indels: 14
0.77 0.03 0.20
Matches are distributed among these distances:
2 7 0.13
3 41 0.75
4 7 0.13
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:1205849 original size:26 final size:25
Alignment explanation
Indices: 1205812--1205864 Score: 88
Period size: 26 Copynumber: 2.1 Consensus size: 25
1205802 TTCATTTAAA
*
1205812 TATTATTTATATTATTATTATATTAT
1 TATTATTAATATTATTATT-TATTAT
1205838 TATTATTAATATTATTATTTATTAT
1 TATTATTAATATTATTATTTATTAT
1205863 TA
1 TA
1205865 ATTTTATTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
25 8 0.31
26 18 0.69
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (25 bp):
TATTATTAATATTATTATTTATTAT
Found at i:1207201 original size:14 final size:14
Alignment explanation
Indices: 1207175--1207208 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
1207165 ATTTATATGT
1207175 TTACTTT-TTATTA
1 TTACTTTATTATTA
1207188 TTACTTTATTATTA
1 TTACTTTATTATTA
1207202 TTA-TTTA
1 TTACTTTA
1207209 ACCATTAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 11 0.55
14 9 0.45
ACGTcount: A:0.26, C:0.06, G:0.00, T:0.68
Consensus pattern (14 bp):
TTACTTTATTATTA
Found at i:1207402 original size:20 final size:19
Alignment explanation
Indices: 1207379--1207420 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
1207369 CTTATTTATA
1207379 AATTATATATTAATTGTTTT
1 AATTATATATTAATT-TTTT
* *
1207399 AATTATTTATTTATTTTTT
1 AATTATATATTAATTTTTT
1207418 AAT
1 AAT
1207421 ATCAAAGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (19 bp):
AATTATATATTAATTTTTT
Found at i:1208437 original size:16 final size:16
Alignment explanation
Indices: 1208416--1208455 Score: 80
Period size: 16 Copynumber: 2.5 Consensus size: 16
1208406 CTTAGATCTG
1208416 AAACCCTACATATAAT
1 AAACCCTACATATAAT
1208432 AAACCCTACATATAAT
1 AAACCCTACATATAAT
1208448 AAACCCTA
1 AAACCCTA
1208456 GAAACTCTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.50, C:0.28, G:0.00, T:0.23
Consensus pattern (16 bp):
AAACCCTACATATAAT
Found at i:1217247 original size:114 final size:113
Alignment explanation
Indices: 1217042--1217260 Score: 348
Period size: 114 Copynumber: 1.9 Consensus size: 113
1217032 CACGTTCTCG
*
1217042 TAGTAAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTG
1 TAGTAAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTCG
* * * *
1217107 GTATAAACCCCAAAACCAATTATTAGATTTGAAAGATGAATTTGCTCA
66 GTAGAAACCACAAAACCAATCATTAGAATTGAAAGATGAATTTGCTCA
*
1217155 TAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTC
1 TAGTA-AAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTC
* * *
1217220 GGTAGGAGCCACAGAACCAATCATTAGAATTGAAAGATGAA
65 GGTAGAAACCACAAAACCAATCATTAGAATTGAAAGATGAA
1217261 CTGCATAATT
Statistics
Matches: 96, Mismatches: 9, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
113 5 0.05
114 91 0.95
ACGTcount: A:0.34, C:0.15, G:0.21, T:0.30
Consensus pattern (113 bp):
TAGTAAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTCG
GTAGAAACCACAAAACCAATCATTAGAATTGAAAGATGAATTTGCTCA
Found at i:1218314 original size:113 final size:112
Alignment explanation
Indices: 1217999--1218646 Score: 675
Period size: 113 Copynumber: 5.7 Consensus size: 112
1217989 TGACAGTTCG
*
1217999 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAA-GAAAAAGAAGTTCATAATGAGAAGAATTTGTTC
* * * * * * *
1218064 AACCTTTTGTTTGAATTCATCATTTGATGGATCAACATTGCCAG-GTAG
65 AACCTTTTGCTTAAATTCATCACTTGATGGATCAGCTTTTCCAGAG-AA
*
1218112 AGTTCATAATGAGAAGAACTCGTCATCTGAAGAATAAAGAAGAAGTTCATAATGAGAAGAATTTG
1 AGTTCATAATGAGAAGAA--C-TCATCTGAAGAAGAAA-AAGAAGTTCATAATGAGAAGAATTTG
* * * *
1218177 TTCAACCTTTTACTCAAATCCATCACTTGATGGATTAGCTTTTCCAGAGAA
62 TTCAACCTTTTGCTTAAATTCATCACTTGATGGATCAGCTTTTCCAGAGAA
1218228 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAAAAGAAGTTCATAATGAGAAGAATTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAA-GAAAAAGAAGTTCATAATGAGAAGAATTTGTTC
** * * * * * *
1218293 AACCTTTTATTTGAATTCATCATTTGATGGATCAACATTGCCAG-GTAG
65 AACCTTTTGCTTAAATTCATCACTTGATGGATCAGCTTTTCCAGAG-AA
* *
1218341 AGTTTATAATGAGAAGAACTTGTCATCTGAAGAAG---AAGAAATTCATAATGAGAAGAATTTGT
1 AGTTCATAATGAGAAGAAC---TCATCTGAAGAAGAAAAAGAAGTTCATAATGAGAAGAATTTGT
* * *
1218403 TCAACCTTTTGCTCAAATCCATCACTTGATGGATCAGTTTTTCCAGAGAA
63 TCAACCTTTTGCTTAAATTCATCACTTGATGGATCAGCTTTTCCAGAGAA
* **
1218453 AGTTCATAATGAGAAGAACTCATCTGAAGAAG---AAGAAGTTCAAAATGAGAAGAGCTTGTTCA
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAAAGAAGTTCATAATGAGAAGAATTTGTTCA
* * * * *
1218515 ACCTTTTGCAT-AATTCTATCACAGAAGGAGATAGATTAGCATCAACCTTTCCAGAGAA
66 ACCTTTTGCTTAAATTC-ATCAC---------TTGA-T-GGATCAGCTTTTCCAGAGAA
* ** *
1218573 AGTTCATAATGAGAAGAACTCATCTGAAGAATAAAGAAGAAGTTCATAATGAGAAGAGCTTATTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGAAA-AAGAAGTTCATAATGAGAAGAATTTGTTC
1218638 AACCTTTTG
65 AACCTTTTG
1218647 AATGACTCTA
Statistics
Matches: 455, Mismatches: 53, Indels: 43
0.83 0.10 0.08
Matches are distributed among these distances:
108 4 0.01
109 53 0.12
112 82 0.18
113 114 0.25
114 4 0.01
115 4 0.01
116 106 0.23
117 1 0.00
118 3 0.01
119 1 0.00
120 47 0.10
124 36 0.08
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.29
Consensus pattern (112 bp):
AGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAAAGAAGTTCATAATGAGAAGAATTTGTTCA
ACCTTTTGCTTAAATTCATCACTTGATGGATCAGCTTTTCCAGAGAA
Found at i:1218368 original size:229 final size:224
Alignment explanation
Indices: 1217999--1218521 Score: 881
Period size: 229 Copynumber: 2.3 Consensus size: 224
1217989 TGACAGTTCG
1217999 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA-AAGAAGTTCATAATGAGAAGAATTTGTTC
*
1218064 AACCTTTTGTTTGAATTCATCATTTGATGGATCAACATTGCCAGGTAGAGTTCATAATGAGAAGA
65 AACCTTTTATTTGAATTCATCATTTGATGGATCAACATTGCCAGGTAGAGTTCATAATGAGAAGA
*
1218129 ACTCGTCATCTGAAGAATAAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACTCAA
130 ACTCGTCATCTGAAG----AAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTACTCAA
*
1218194 ATCCATCACTTGATGGATTAGCTTTTCCAGAGAA
191 ATCCATCACTTGATGGATCAGCTTTTCCAGAGAA
1218228 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAAAAGAAGTTCATAATGAGAAGAATTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGG-AAAAGAAGTTCATAATGAGAAGAATTTGTTC
*
1218293 AACCTTTTATTTGAATTCATCATTTGATGGATCAACATTGCCAGGTAGAGTTTATAATGAGAAGA
65 AACCTTTTATTTGAATTCATCATTTGATGGATCAACATTGCCAGGTAGAGTTCATAATGAGAAGA
* *
1218358 ACTTGTCATCTGAAGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCC
130 ACTCGTCATCTGAAGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTACTCAAATCC
*
1218423 ATCACTTGATGGATCAGTTTTTCCAGAGAA
195 ATCACTTGATGGATCAGCTTTTCCAGAGAA
* **
1218453 AGTTCATAATGAGAAGAACTCATCTGAAGAA-G--AAGAAGTTCAAAATGAGAAGAGCTTGTTCA
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAAAGAAGTTCATAATGAGAAGAATTTGTTCA
1218515 ACCTTTT
66 ACCTTTT
1218522 GCATAATTCT
Statistics
Matches: 283, Mismatches: 10, Indels: 10
0.93 0.03 0.03
Matches are distributed among these distances:
221 34 0.12
224 1 0.00
225 107 0.38
229 139 0.49
230 2 0.01
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.30
Consensus pattern (224 bp):
AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAAAGAAGTTCATAATGAGAAGAATTTGTTCA
ACCTTTTATTTGAATTCATCATTTGATGGATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAA
CTCGTCATCTGAAGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTACTCAAATCCA
TCACTTGATGGATCAGCTTTTCCAGAGAA
Found at i:1218658 original size:124 final size:122
Alignment explanation
Indices: 1218442--1218769 Score: 437
Period size: 124 Copynumber: 2.7 Consensus size: 122
1218432 TGGATCAGTT
*
1218442 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG--AAGAAGAAGTTCAAAATGAGAAG
1 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAAAGAAGAAGTTCATAATGAGAAG
* * * * *
1218505 AGCTTGTTCAACCTTTTGCATAATTCTATCACAGAAGGAGATAGATTAGCATCAACC
66 AGCTTGTTCAACCTTTTGAATAACTCTATCACAGAAGGAAATAGATCAACATCAACC
1218562 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAATAAAGAAGAAGTTCATAATGAGA
1 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG-A-AAAGAAGAAGTTCATAATGAGA
* * * *
1218627 AGAGCTTATTCAACCTTTTGAATGACTCTATCACAGAAGGAAATAGGTCAACATCAACT
64 AGAGCTTGTTCAACCTTTTGAATAACTCTATCACAGAAGGAAATAGATCAACATCAACC
* * * * * *
1218686 TTTCCAGGGAAAGTTCATAATAAGAAGAACTCATCTGAATAAGGAAGAA-AATTTTATAATAAGA
1 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAA--AAGAAGAAGTTCATAATGAGA
*
1218750 AGAACTTGTTCAACCCTTTT
64 AGAGCTTGTTCAA-CCTTTT
1218770 CCAAATTACA
Statistics
Matches: 183, Mismatches: 18, Indels: 10
0.87 0.09 0.05
Matches are distributed among these distances:
120 40 0.22
122 1 0.01
123 24 0.13
124 118 0.64
ACGTcount: A:0.41, C:0.15, G:0.18, T:0.26
Consensus pattern (122 bp):
TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAAAGAAGAAGTTCATAATGAGAAG
AGCTTGTTCAACCTTTTGAATAACTCTATCACAGAAGGAAATAGATCAACATCAACC
Found at i:1218999 original size:3 final size:3
Alignment explanation
Indices: 1218993--1219063 Score: 94
Period size: 3 Copynumber: 23.7 Consensus size: 3
1218983 TTCATTTAAA
1218993 TAT TAT T-T ATAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1219038 TATT TAT TAT TAAT T-T TAT TA- TAT TA
1 TA-T TAT TAT T-AT TAT TAT TAT TAT TA
1219064 CAGGCCCAAT
Statistics
Matches: 62, Mismatches: 0, Indels: 12
0.84 0.00 0.16
Matches are distributed among these distances:
2 5 0.08
3 50 0.81
4 7 0.11
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:1221504 original size:80 final size:80
Alignment explanation
Indices: 1221371--1221541 Score: 333
Period size: 80 Copynumber: 2.1 Consensus size: 80
1221361 ATTATTGCCA
1221371 AATTTGAGTAGGATGATTCAAAATTTCATATTGTAAAATCTATAAGTGATAATGTAATATTAATT
1 AATTTGAGTAGGATGATTCAAAATTTCATATTGTAAAATCTATAAGTGATAATGTAATATTAATT
1221436 TCTTTAAAAATTTTG
66 TCTTTAAAAATTTTG
1221451 AATTTGAGTAGGATGATTCAAAATTTCATATTGTAAAATCTATAAGTGATAATGTAATATTAATT
1 AATTTGAGTAGGATGATTCAAAATTTCATATTGTAAAATCTATAAGTGATAATGTAATATTAATT
1221516 TCTTTAAAAATTTTG
66 TCTTTAAAAATTTTG
*
1221531 AATTTAAGTAG
1 AATTTGAGTAG
1221542 TTGTGTTTGT
Statistics
Matches: 90, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
80 90 1.00
ACGTcount: A:0.40, C:0.05, G:0.13, T:0.42
Consensus pattern (80 bp):
AATTTGAGTAGGATGATTCAAAATTTCATATTGTAAAATCTATAAGTGATAATGTAATATTAATT
TCTTTAAAAATTTTG
Found at i:1221932 original size:22 final size:22
Alignment explanation
Indices: 1221907--1221960 Score: 58
Period size: 22 Copynumber: 2.4 Consensus size: 22
1221897 TTAATCATAT
1221907 TTTATCATA-TTCATAAATATAA
1 TTTATCATACTTCATAAATA-AA
*
1221929 TTTA-CAAACTTCATAAATAAA
1 TTTATCATACTTCATAAATAAA
1221950 TCTTATACATA
1 T-TTAT-CATA
1221961 ATTAGAATGA
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
21 6 0.23
22 17 0.65
24 3 0.12
ACGTcount: A:0.46, C:0.13, G:0.00, T:0.41
Consensus pattern (22 bp):
TTTATCATACTTCATAAATAAA
Found at i:1222344 original size:21 final size:22
Alignment explanation
Indices: 1222319--1222365 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
1222309 AAATTGTGCA
1222319 TTTAGTACC-AAAATTATC-ATT
1 TTTAGTACCTAAAATT-TCAATT
*
1222340 TTTAGTACCTAAACTTTCAATT
1 TTTAGTACCTAAAATTTCAATT
1222362 TTTA
1 TTTA
1222366 AAACCATACC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
21 11 0.48
22 12 0.52
ACGTcount: A:0.34, C:0.15, G:0.04, T:0.47
Consensus pattern (22 bp):
TTTAGTACCTAAAATTTCAATT
Found at i:1222667 original size:38 final size:37
Alignment explanation
Indices: 1222587--1222669 Score: 96
Period size: 38 Copynumber: 2.2 Consensus size: 37
1222577 TTAAAACAGA
* *
1222587 CTAAAACTGATAGTTTAAATACTAAATATAATTTATC
1 CTAAAAATAATAGTTTAAATACTAAATATAATTTATC
* * *
1222624 TTAAAAATAATAG-TTAAGTACTAAACATATAATTTTTC
1 CTAAAAATAATAGTTTAAATACT-AA-ATATAATTTATC
1222662 CTAAAAAT
1 CTAAAAAT
1222670 TAATTGACAA
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
36 8 0.21
37 12 0.32
38 18 0.47
ACGTcount: A:0.48, C:0.10, G:0.05, T:0.37
Consensus pattern (37 bp):
CTAAAAATAATAGTTTAAATACTAAATATAATTTATC
Found at i:1223255 original size:3 final size:3
Alignment explanation
Indices: 1223247--1223284 Score: 58
Period size: 3 Copynumber: 12.7 Consensus size: 3
1223237 CAAAACAAAG
* *
1223247 AGA AGA AGA AGA AGA AGA TGA TGA AGA AGA AGA AGA AG
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AG
1223285 CTCGTTCAAC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.61, C:0.00, G:0.34, T:0.05
Consensus pattern (3 bp):
AGA
Found at i:1224907 original size:91 final size:91
Alignment explanation
Indices: 1224739--1224911 Score: 249
Period size: 91 Copynumber: 1.9 Consensus size: 91
1224729 AAATCATCAA
* **
1224739 AGGTAAAATTATAAATTTGATCATATTCATATTAATATGATAATCAAAGATTGTTTTAGATATTG
1 AGGTAAAATTATAAATTTGATCAAATTCATATTAATATGATAATCAAAGACAGTTTTAGATATTG
* ** *
1224804 GAATTCTGAATATTTCAAAAGGTGTC
66 AAACCCTAAATATTTCAAAAGGTGTC
* *
1224830 AGGTAAAATTATAAATTTGATCAAACTT-ATTTTAATATGATAATCGAAGACAGTTTTAGATATT
1 AGGTAAAATTATAAATTTGATCAAA-TTCATATTAATATGATAATCAAAGACAGTTTTAGATATT
1224894 GAAACCCTAAATATTTCA
65 GAAACCCTAAATATTTCA
1224912 GAAGTCAACA
Statistics
Matches: 72, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
91 70 0.97
92 2 0.03
ACGTcount: A:0.41, C:0.08, G:0.13, T:0.38
Consensus pattern (91 bp):
AGGTAAAATTATAAATTTGATCAAATTCATATTAATATGATAATCAAAGACAGTTTTAGATATTG
AAACCCTAAATATTTCAAAAGGTGTC
Found at i:1225564 original size:4 final size:4
Alignment explanation
Indices: 1225555--1225579 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
1225545 CCATTATTAT
1225555 TTTA TTTA TTTA TTTA TTTA TTTA T
1 TTTA TTTA TTTA TTTA TTTA TTTA T
1225580 CACAATCCTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:1226801 original size:21 final size:23
Alignment explanation
Indices: 1226758--1226801 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
1226748 AACGGCGAGC
*
1226758 CGATGGGTCTTGAGCACATTCAA
1 CGATGGATCTTGAGCACATTCAA
1226781 CGATGGAT-TTGAGCA-ATTCAA
1 CGATGGATCTTGAGCACATTCAA
1226802 TAATATGTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 6 0.30
22 7 0.35
23 7 0.35
ACGTcount: A:0.30, C:0.18, G:0.25, T:0.27
Consensus pattern (23 bp):
CGATGGATCTTGAGCACATTCAA
Found at i:1228847 original size:21 final size:22
Alignment explanation
Indices: 1228814--1228856 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
1228804 ATTTAAAAAT
1228814 ATTAAAGGAAGTA-TCGATACTC
1 ATTAAAGGAAGTACT-GATACTC
1228836 ATTAAA-GAAGTACTGATACTC
1 ATTAAAGGAAGTACTGATACTC
1228857 CATGTTCTGG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.42, C:0.14, G:0.16, T:0.28
Consensus pattern (22 bp):
ATTAAAGGAAGTACTGATACTC
Found at i:1228911 original size:20 final size:20
Alignment explanation
Indices: 1228886--1228931 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
1228876 TTTTGCAGAG
1228886 AAATATCCCCAACGACTCCA
1 AAATATCCCCAACGACTCCA
* * *
1228906 AAATATTCTCAACGGCTCCA
1 AAATATCCCCAACGACTCCA
1228926 AAATAT
1 AAATAT
1228932 TCTCAACGGA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.41, C:0.30, G:0.07, T:0.22
Consensus pattern (20 bp):
AAATATCCCCAACGACTCCA
Found at i:1228932 original size:20 final size:20
Alignment explanation
Indices: 1228895--1228940 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
1228885 GAAATATCCC
*
1228895 CAACGACTCCAAAATATTCT
1 CAACGGCTCCAAAATATTCT
1228915 CAACGGCTCCAAAATATTCT
1 CAACGGCTCCAAAATATTCT
1228935 CAACGG
1 CAACGG
1228941 AAAAAAACGG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.37, C:0.30, G:0.11, T:0.22
Consensus pattern (20 bp):
CAACGGCTCCAAAATATTCT
Found at i:1230719 original size:30 final size:30
Alignment explanation
Indices: 1230685--1230744 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
1230675 CTTGAAAGTA
*
1230685 AAATTGGATTTTGAAAAGAAAAATGAAATT
1 AAATTAGATTTTGAAAAGAAAAATGAAATT
1230715 AAATTAGATTTTGAAAAGAAAAATGAAATT
1 AAATTAGATTTTGAAAAGAAAAATGAAATT
1230745 TTGAAAAATG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.55, C:0.00, G:0.15, T:0.30
Consensus pattern (30 bp):
AAATTAGATTTTGAAAAGAAAAATGAAATT
Found at i:1231358 original size:24 final size:24
Alignment explanation
Indices: 1231326--1231373 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
1231316 ATATCTCTCT
*
1231326 AACAATTTATAGCAATTTTTCAAA
1 AACAATTTATAGCAAATTTTCAAA
*
1231350 AACAATTTATATCAAATTTTCAAA
1 AACAATTTATAGCAAATTTTCAAA
1231374 TTCTTTGCTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.48, C:0.12, G:0.02, T:0.38
Consensus pattern (24 bp):
AACAATTTATAGCAAATTTTCAAA
Found at i:1232370 original size:22 final size:21
Alignment explanation
Indices: 1232342--1232382 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
1232332 ATTTAAAAAT
1232342 ATTAAAGGAAGTACCGATACTC
1 ATTAAAGG-AGTACCGATACTC
*
1232364 ATTAAAGGAGTACTGATAC
1 ATTAAAGGAGTACCGATAC
1232383 ACCCTGTCCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.41, C:0.15, G:0.20, T:0.24
Consensus pattern (21 bp):
ATTAAAGGAGTACCGATACTC
Found at i:1233086 original size:21 final size:21
Alignment explanation
Indices: 1233051--1233100 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
1233041 TCGTGAAAGA
1233051 AAAGTAAACAAGAAAGGAGA-AG
1 AAAG-AAACAAGAAAGGA-ACAG
* *
1233073 AAAGAAACATGAAATGAACAG
1 AAAGAAACAAGAAAGGAACAG
1233094 AAAGAAA
1 AAAGAAA
1233101 AATACATGCA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 1 0.04
21 20 0.80
22 4 0.16
ACGTcount: A:0.66, C:0.06, G:0.22, T:0.06
Consensus pattern (21 bp):
AAAGAAACAAGAAAGGAACAG
Found at i:1237956 original size:21 final size:19
Alignment explanation
Indices: 1237905--1237948 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
1237895 TTAGGATAAA
*
1237905 ATTTTTATTTCTTTTTCAT
1 ATTTTTATTTCTCTTTCAT
1237924 ATTTTTAATTTCTCTTTC-T
1 ATTTTT-ATTTCTCTTTCAT
1237943 ATTTTT
1 ATTTTT
1237949 TTCATTTCAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 13 0.57
20 10 0.43
ACGTcount: A:0.16, C:0.11, G:0.00, T:0.73
Consensus pattern (19 bp):
ATTTTTATTTCTCTTTCAT
Found at i:1239753 original size:38 final size:37
Alignment explanation
Indices: 1239602--1239757 Score: 144
Period size: 39 Copynumber: 4.1 Consensus size: 37
1239592 ATTTATATAT
* *
1239602 ATATATATTATATAG--TTTGAAATCATTTTGAAAAC
1 ATATATAATATATAGTTTTTGAAAACATTTTGAAAAC
*
1239637 -TATATAATATAT-GTTTTTTTAAAAAAAAACATTTTG-AAA-
1 ATATATAATATATAG--TTTTT----GAAAACATTTTGAAAAC
1239676 ATATATAATATATAGTTTTTGAAAAACATTTTTGAAAAC
1 ATATATAATATATAGTTTTTG-AAAACA-TTTTGAAAAC
* *
1239715 ATATATATTATATAGTTTTTGAAATCATTTTTGAAAAC
1 ATATATAATATATAGTTTTTGAAAACA-TTTTGAAAAC
1239753 ATATA
1 ATATA
1239758 ACATATAATT
Statistics
Matches: 101, Mismatches: 6, Indels: 25
0.77 0.05 0.19
Matches are distributed among these distances:
33 1 0.01
34 11 0.11
36 6 0.06
37 8 0.08
38 24 0.24
39 25 0.25
40 15 0.15
41 11 0.11
ACGTcount: A:0.45, C:0.04, G:0.07, T:0.44
Consensus pattern (37 bp):
ATATATAATATATAGTTTTTGAAAACATTTTGAAAAC
Found at i:1239939 original size:15 final size:14
Alignment explanation
Indices: 1239878--1239946 Score: 57
Period size: 15 Copynumber: 4.6 Consensus size: 14
1239868 TGAAAAATAT
*
1239878 TTTTTATTATTATAA
1 TTTTTATTATT-TTA
* * *
1239893 TTGTCATTTTTTTA
1 TTTTTATTATTTTA
1239907 TTTTAGTATTATTATTA
1 TTTT--TATTATT-TTA
1239924 TTTTTATTAATTTTA
1 TTTTTATT-ATTTTA
1239939 TTTTTATT
1 TTTTTATT
1239947 GTTCATGTCC
Statistics
Matches: 43, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
14 5 0.12
15 23 0.53
16 8 0.19
17 7 0.16
ACGTcount: A:0.25, C:0.01, G:0.03, T:0.71
Consensus pattern (14 bp):
TTTTTATTATTTTA
Found at i:1241314 original size:2 final size:2
Alignment explanation
Indices: 1241307--1241333 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1241297 TTATTTTTAT
1241307 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
1241334 TTTTGACTTT
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:1241492 original size:12 final size:13
Alignment explanation
Indices: 1241475--1241504 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
1241465 TCGAATCGAG
1241475 TAATTTAAA-TTT
1 TAATTTAAATTTT
1241487 TAATTTAAATTTT
1 TAATTTAAATTTT
1241500 TAATT
1 TAATT
1241505 ATTCGCAATC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 9 0.53
13 8 0.47
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
TAATTTAAATTTT
Found at i:1243130 original size:18 final size:19
Alignment explanation
Indices: 1243109--1243153 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
1243099 ATTTAGACAT
*
1243109 TTTGCATTTT-TTATTTTC
1 TTTGCATTTTGTTATTTTA
1243127 TTTGCATTTTGTTATTTTA
1 TTTGCATTTTGTTATTTTA
1243146 TTTGCATT
1 TTTGCATT
1243154 CACATTAACT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
18 10 0.40
19 15 0.60
ACGTcount: A:0.13, C:0.09, G:0.09, T:0.69
Consensus pattern (19 bp):
TTTGCATTTTGTTATTTTA
Found at i:1246369 original size:84 final size:81
Alignment explanation
Indices: 1246114--1246939 Score: 909
Period size: 84 Copynumber: 10.0 Consensus size: 81
1246104 TAAACAAACT
* * * * * *
1246114 ATTTGCAGTACAACTTAAGTCTAGAAGGGTTGTCTGCCAACAAAAGACCTTTGAGTTCGACTACG
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTG-C-ACCAAAGACCTTCGAGTTCGACTACG
1246179 CTCAGCTCAACGGCACATC
64 CTCAGCTCAA-GGCACATC
* * * * * * *
1246198 ATTTGCAGCATAGCTTAAGTCGAAAAGGGCTATCTG--CCAAAGACC-CCAAGTTCGATTACACT
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCACCAAAGACCTTCGAGTTCGACTACGCT
*
1246260 CAGCTTCGAGGGCACATC
66 CAGC-TC-AAGGCACATC
* * *
1246278 ATTTGCAGCATAACTTAAGTCGAGAAGAGTTATCTGCCAACCAAAGACCTTTGAGTTCGACGACG
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTG-C-ACCAAAGACCTTCGAGTTCGACTACG
* *
1246343 TTCAGCTCAACAGCACATC
64 CTCAGCTCAA-GGCACATC
* * * * * * *
1246362 ATTTGCAGCATAGCTTAAGTCGAAAAGGGATATCTG--CCAAAGACC-CCAAGTTCGATTACACT
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCACCAAAGACCTTCGAGTTCGACTACGCT
*
1246424 CAGCTTCGAGGGCACATC
66 CAGC-TC-AAGGCACATC
* *
1246442 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTTGAGTTCGACGACG
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTG-C-ACCAAAGACCTTCGAGTTCGACTACG
* *
1246507 TTCAGCTCCAAGGCATATC
64 CTCAGCT-CAAGGCACATC
* * * *
1246526 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG--CCAAAGA-CTCTCGAGTTCGATTACAC
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCACCAAAGACCT-TCGAGTTCGACTACGC
* *
1246588 TCAGCTTCGAGGGCATATC
65 TCAGC-TC-AAGGCACATC
* * * * * *
1246607 ATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACCTTCGGGTTCGACTACG
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTG-CACC-AAAGACCTTCGAGTTCGACTACG
1246672 CTCAGCTCCAAGGCACATC
64 CTCAGCT-CAAGGCACATC
* * *
1246691 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG--CCAAAGACCTTCGAGTTCGACTACACT
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCACCAAAGACCTTCGAGTTCGACTACGCT
*
1246754 CAGCTCCAAGACACATC
66 CAGCT-CAAGGCACATC
*
1246771 ATTTGCAGCATAACTTAAGTCGAGAAGAGTTATCTGTCACCAAAGACCTTCGAGTTCGACTACGC
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTG-CACCAAAGACCTTCGAGTTCGACTACGC
*
1246836 TCAGCTCCAAGGCATATC
65 TCAGCT-CAAGGCACATC
1246854 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACG
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTG-C-ACCAAAGACCTTCGAGTTCGACTACG
1246919 CTCAGCTCCAAGGCACATC
64 CTCAGCT-CAAGGCACATC
1246938 AT
1 AT
1246940 ATTTACAGAA
Statistics
Matches: 624, Mismatches: 89, Indels: 58
0.81 0.12 0.08
Matches are distributed among these distances:
79 32 0.05
80 197 0.32
81 44 0.07
83 78 0.12
84 218 0.35
85 53 0.08
86 2 0.00
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.24
Consensus pattern (81 bp):
ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCACCAAAGACCTTCGAGTTCGACTACGCT
CAGCTCAAGGCACATC
Found at i:1246385 original size:164 final size:164
Alignment explanation
Indices: 1246114--1246893 Score: 1138
Period size: 164 Copynumber: 4.8 Consensus size: 164
1246104 TAAACAAACT
* * * * *
1246114 ATTTGCAGTACAACTTAAGTCTAGAAGGGTTGTCTGCCAACAAAAGACCTTTGAGTTCGACTACG
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTTGAGTTCGACTACG
*
1246179 CTCAGCT-CAACGGCACATCATTTGCAGCATAGCTTAAGTCGAAAAGGGCTATCTGCCAAAGACC
66 CTCAGCTCCAA-GGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACC
1246243 CCAAGTTCGATTACACTCAGCTTCGAGGGCACATC
130 CCAAGTTCGATTACACTCAGCTTCGAGGGCACATC
* *
1246278 ATTTGCAGCATAACTTAAGTCGAGAAGAGTTATCTGCCAACCAAAGACCTTTGAGTTCGACGACG
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTTGAGTTCGACTACG
* * * *
1246343 TTCAGCT-CAACAGCACATCATTTGCAGCATAGCTTAAGTCGAAAAGGGATATCTGCCAAAGACC
66 CTCAGCTCCAA-GGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACC
1246407 CCAAGTTCGATTACACTCAGCTTCGAGGGCACATC
130 CCAAGTTCGATTACACTCAGCTTCGAGGGCACATC
*
1246442 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTTGAGTTCGACGACG
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTTGAGTTCGACTACG
* *
1246507 TTCAGCTCCAAGGCATATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACTC
66 CTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGAC-C
* * *
1246572 TCGAGTTCGATTACACTCAGCTTCGAGGGCATATC
130 CCAAGTTCGATTACACTCAGCTTCGAGGGCACATC
* * * * ** * *
1246607 ATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTG-TGACCAAAAGACCTTCGGGTTCGACTAC
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACC-AAAGACCTTTGAGTTCGACTAC
1246671 GCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACC
65 GCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACC
* * * * * *
1246736 TTCGAGTTCGACTACACTCAGC-TCCAAGACACATC
130 -CCAAGTTCGATTACACTCAGCTTCGAGGGCACATC
* * *
1246771 ATTTGCAGCATAACTTAAGTCGAGAAGAGTTATCTGTC-ACCAAAGACCTTCGAGTTCGACTACG
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTTGAGTTCGACTACG
* * *
1246835 CTCAGCTCCAAGGCATATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAA
66 CTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAA
1246894 CCAAAGACCT
Statistics
Matches: 567, Mismatches: 44, Indels: 11
0.91 0.07 0.02
Matches are distributed among these distances:
163 78 0.14
164 320 0.56
165 169 0.30
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.24
Consensus pattern (164 bp):
ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTTGAGTTCGACTACG
CTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCC
CAAGTTCGATTACACTCAGCTTCGAGGGCACATC
Found at i:1247646 original size:39 final size:37
Alignment explanation
Indices: 1247530--1247684 Score: 151
Period size: 39 Copynumber: 4.1 Consensus size: 37
1247520 TTATATATAT
* *
1247530 ATATATATTATATAG--TTTGAAATCATTTTGAAAAC
1 ATATATAATATATAGTTTTTGAAAACATTTTGAAAAC
*
1247565 -TATATAATATAT-GTTTTTTAAAAAAAAACATTTTG-AAA-
1 ATATATAATATATAG-TTTTT----GAAAACATTTTGAAAAC
1247603 ATATATAATATATAGTTTTTGAAAAACATTTTTGAAAAC
1 ATATATAATATATAGTTTTTG-AAAACA-TTTTGAAAAC
* *
1247642 ATATATATTATATAGTTTTTGAAATCATTTTTGAAAAC
1 ATATATAATATATAGTTTTTGAAAACA-TTTTGAAAAC
1247680 ATATA
1 ATATA
1247685 ACATATAATT
Statistics
Matches: 101, Mismatches: 6, Indels: 23
0.78 0.05 0.18
Matches are distributed among these distances:
33 1 0.01
34 11 0.11
36 9 0.09
37 5 0.05
38 24 0.24
39 40 0.40
40 11 0.11
ACGTcount: A:0.45, C:0.05, G:0.07, T:0.43
Consensus pattern (37 bp):
ATATATAATATATAGTTTTTGAAAACATTTTGAAAAC
Found at i:1247866 original size:15 final size:14
Alignment explanation
Indices: 1247805--1247873 Score: 57
Period size: 15 Copynumber: 4.6 Consensus size: 14
1247795 TGAAAAATAT
*
1247805 TTTTTATTATTATAA
1 TTTTTATTATT-TTA
* * *
1247820 TTGTCATTTTTTTA
1 TTTTTATTATTTTA
1247834 TTTTAGTATTATTATTA
1 TTTT--TATTATT-TTA
1247851 TTTTTATTAATTTTA
1 TTTTTATT-ATTTTA
1247866 TTTTTATT
1 TTTTTATT
1247874 GTTCATGTCC
Statistics
Matches: 43, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
14 5 0.12
15 23 0.53
16 8 0.19
17 7 0.16
ACGTcount: A:0.25, C:0.01, G:0.03, T:0.71
Consensus pattern (14 bp):
TTTTTATTATTTTA
Found at i:1249408 original size:12 final size:13
Alignment explanation
Indices: 1249391--1249420 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
1249381 TCGAATCGAG
1249391 TAATTTAAA-TTT
1 TAATTTAAATTTT
1249403 TAATTTAAATTTT
1 TAATTTAAATTTT
1249416 TAATT
1 TAATT
1249421 CTTCGCAATC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 9 0.53
13 8 0.47
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
TAATTTAAATTTT
Found at i:1251047 original size:18 final size:19
Alignment explanation
Indices: 1251026--1251070 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
1251016 ATTTAGACAT
*
1251026 TTTGCATTTT-TTATTTTC
1 TTTGCATTTTGTTATTTTA
1251044 TTTGCATTTTGTTATTTTA
1 TTTGCATTTTGTTATTTTA
1251063 TTTGCATT
1 TTTGCATT
1251071 CACATTAACT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
18 10 0.40
19 15 0.60
ACGTcount: A:0.13, C:0.09, G:0.09, T:0.69
Consensus pattern (19 bp):
TTTGCATTTTGTTATTTTA
Found at i:1254283 original size:84 final size:81
Alignment explanation
Indices: 1254028--1254853 Score: 900
Period size: 84 Copynumber: 10.0 Consensus size: 81
1254018 TAAACAAACT
* * * * * *
1254028 ATTTGCAGTACAACTTAAGTCTAGAAGGGTTGTCTGCCAACAAAAGACCTTTGAGTTCGACTACG
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTG-C-ACCAAAGACCTTCGAGTTCGACTACG
1254093 CTCAGCTCAACGGCACATC
64 CTCAGCTCAA-GGCACATC
* * * * * * *
1254112 ATTTGCAGCATAGCTTAAGTCGAAAAGGGCTATCTG--CCAAAGACC-CCAAGTTCGATTACACT
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCACCAAAGACCTTCGAGTTCGACTACGCT
*
1254174 CAGCTTCGAGGGCACATC
66 CAGC-TC-AAGGCACATC
* * *
1254192 ATTTGCAGCATAACTTAAGTCGAGAAGAGTTATCTGCCAACCAAAGACCTTTGAGTTCGACGACG
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTG-C-ACCAAAGACCTTCGAGTTCGACTACG
* *
1254257 TTCAGCTCAACAGCACATC
64 CTCAGCTCAA-GGCACATC
* * * * * * *
1254276 ATTTGCAGCATAGCTTAAGTCGAAAAGGGCTATCTG--CCAAAGACC-CCAAGTTCGATTACACT
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCACCAAAGACCTTCGAGTTCGACTACGCT
*
1254338 CAGCTTCGAGGGCACATC
66 CAGC-TC-AAGGCACATC
* *
1254356 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTTGAGTTCGACGACG
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTG-C-ACCAAAGACCTTCGAGTTCGACTACG
* *
1254421 TTCAGCTCCAAGGCATATC
64 CTCAGCT-CAAGGCACATC
* * * *
1254440 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG--CCAAAGA-CTCTCGAGTTCGATTACAC
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCACCAAAGACCT-TCGAGTTCGACTACGC
* *
1254502 TCAGCTTCGAGGGCATATC
65 TCAGC-TC-AAGGCACATC
* * * * * *
1254521 ATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACCTTCGGGTTCGACTACG
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTG-CACC-AAAGACCTTCGAGTTCGACTACG
1254586 CTCAGCTCCAAGGCACATC
64 CTCAGCT-CAAGGCACATC
* * *
1254605 ATTTGCAGCATATCTTAAGTCGAGAAGGGCTATCTG--CCAAAGACCTTCGAGTTCGACTACACT
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCACCAAAGACCTTCGAGTTCGACTACGCT
*
1254668 CAGCTCCAAGACACATC
66 CAGCT-CAAGGCACATC
*
1254685 ATTTGCAGCATAACTTAAGTCGAGAAGAGTTATCTGTCACCAAAGACCTTCGAGTTCGACTACGC
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTG-CACCAAAGACCTTCGAGTTCGACTACGC
*
1254750 TCAGCTCCAAGGCATATC
65 TCAGCT-CAAGGCACATC
*
1254768 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTTGAGTTCGACTACG
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTG-C-ACCAAAGACCTTCGAGTTCGACTACG
1254833 CTCAGCTCCAAGGCACATC
64 CTCAGCT-CAAGGCACATC
1254852 AT
1 AT
1254854 ATTTACAGAA
Statistics
Matches: 623, Mismatches: 90, Indels: 58
0.81 0.12 0.08
Matches are distributed among these distances:
79 32 0.05
80 197 0.32
81 44 0.07
83 78 0.13
84 217 0.35
85 53 0.09
86 2 0.00
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.24
Consensus pattern (81 bp):
ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCACCAAAGACCTTCGAGTTCGACTACGCT
CAGCTCAAGGCACATC
Found at i:1254299 original size:164 final size:164
Alignment explanation
Indices: 1254028--1254807 Score: 1138
Period size: 164 Copynumber: 4.8 Consensus size: 164
1254018 TAAACAAACT
* * * * *
1254028 ATTTGCAGTACAACTTAAGTCTAGAAGGGTTGTCTGCCAACAAAAGACCTTTGAGTTCGACTACG
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTTGAGTTCGACTACG
*
1254093 CTCAGCT-CAACGGCACATCATTTGCAGCATAGCTTAAGTCGAAAAGGGCTATCTGCCAAAGACC
66 CTCAGCTCCAA-GGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACC
1254157 CCAAGTTCGATTACACTCAGCTTCGAGGGCACATC
130 CCAAGTTCGATTACACTCAGCTTCGAGGGCACATC
* *
1254192 ATTTGCAGCATAACTTAAGTCGAGAAGAGTTATCTGCCAACCAAAGACCTTTGAGTTCGACGACG
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTTGAGTTCGACTACG
* * *
1254257 TTCAGCT-CAACAGCACATCATTTGCAGCATAGCTTAAGTCGAAAAGGGCTATCTGCCAAAGACC
66 CTCAGCTCCAA-GGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACC
1254321 CCAAGTTCGATTACACTCAGCTTCGAGGGCACATC
130 CCAAGTTCGATTACACTCAGCTTCGAGGGCACATC
*
1254356 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTTGAGTTCGACGACG
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTTGAGTTCGACTACG
* *
1254421 TTCAGCTCCAAGGCATATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACTC
66 CTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGAC-C
* * *
1254486 TCGAGTTCGATTACACTCAGCTTCGAGGGCATATC
130 CCAAGTTCGATTACACTCAGCTTCGAGGGCACATC
* * * * ** * *
1254521 ATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTG-TGACCAAAAGACCTTCGGGTTCGACTAC
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACC-AAAGACCTTTGAGTTCGACTAC
*
1254585 GCTCAGCTCCAAGGCACATCATTTGCAGCATATCTTAAGTCGAGAAGGGCTATCTGCCAAAGACC
65 GCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACC
* * * * * *
1254650 TTCGAGTTCGACTACACTCAGC-TCCAAGACACATC
130 -CCAAGTTCGATTACACTCAGCTTCGAGGGCACATC
* * *
1254685 ATTTGCAGCATAACTTAAGTCGAGAAGAGTTATCTGTC-ACCAAAGACCTTCGAGTTCGACTACG
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTTGAGTTCGACTACG
* * *
1254749 CTCAGCTCCAAGGCATATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAA
66 CTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAA
1254808 CCAAAGACCT
Statistics
Matches: 568, Mismatches: 43, Indels: 11
0.91 0.07 0.02
Matches are distributed among these distances:
163 78 0.14
164 322 0.57
165 168 0.30
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.24
Consensus pattern (164 bp):
ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTTGAGTTCGACTACG
CTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCC
CAAGTTCGATTACACTCAGCTTCGAGGGCACATC
Found at i:1255582 original size:38 final size:39
Alignment explanation
Indices: 1255509--1255586 Score: 131
Period size: 38 Copynumber: 2.0 Consensus size: 39
1255499 ATTTTGAAAA
1255509 ATATAATATAGTTTTTGAAAAACATTTTTGAAAACATAT
1 ATATAATATAGTTTTTGAAAAACATTTTTGAAAACATAT
* *
1255548 ATATTATATAGTTTTTG-AAATCATTTTTGAAAACATAT
1 ATATAATATAGTTTTTGAAAAACATTTTTGAAAACATAT
1255586 A
1 A
1255587 ACATATAATT
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
38 21 0.57
39 16 0.43
ACGTcount: A:0.44, C:0.05, G:0.08, T:0.44
Consensus pattern (39 bp):
ATATAATATAGTTTTTGAAAAACATTTTTGAAAACATAT
Found at i:1255739 original size:15 final size:14
Alignment explanation
Indices: 1255718--1255757 Score: 53
Period size: 15 Copynumber: 2.8 Consensus size: 14
1255708 TAATTGTCAT
1255718 TTTTTATTTTAGTA
1 TTTTTATTTTAGTA
*
1255732 TTTATTATTTTATTA
1 TTT-TTATTTTAGTA
*
1255747 ATTTTATTTTA
1 TTTTTATTTTA
1255758 TTGTTCATGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
14 11 0.48
15 12 0.52
ACGTcount: A:0.25, C:0.00, G:0.03, T:0.72
Consensus pattern (14 bp):
TTTTTATTTTAGTA
Found at i:1255755 original size:14 final size:14
Alignment explanation
Indices: 1255719--1255759 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
1255709 AATTGTCATT
* *
1255719 TTTTATTTTAGTAT
1 TTTTATTTTATTAA
1255733 TTATTATTTTATTAA
1 TT-TTATTTTATTAA
1255748 TTTTATTTTATT
1 TTTTATTTTATT
1255760 GTTCATGTCC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 12 0.50
15 12 0.50
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.73
Consensus pattern (14 bp):
TTTTATTTTATTAA
Found at i:1257167 original size:22 final size:22
Alignment explanation
Indices: 1257124--1257167 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
1257114 TTTATTTAAC
* * *
1257124 ATTTATTTATTATTATTGTTTT
1 ATTTATTTATTACTAATATTTT
*
1257146 ATTTATTTTTTACTAATATTTT
1 ATTTATTTATTACTAATATTTT
1257168 TGACTTTGTA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.25, C:0.02, G:0.02, T:0.70
Consensus pattern (22 bp):
ATTTATTTATTACTAATATTTT
Found at i:1257237 original size:12 final size:13
Alignment explanation
Indices: 1257220--1257249 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
1257210 TCGAATCGGG
1257220 TAATTTAAA-TTT
1 TAATTTAAATTTT
1257232 TAATTTAAATTTT
1 TAATTTAAATTTT
1257245 TAATT
1 TAATT
1257250 CTTCGCAATC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 9 0.53
13 8 0.47
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
TAATTTAAATTTT
Found at i:1257931 original size:181 final size:183
Alignment explanation
Indices: 1257627--1258010 Score: 618
Period size: 182 Copynumber: 2.1 Consensus size: 183
1257617 TTTTCTAATT
* *
1257627 TATATAA-A-ATTAAATATTTTTTAATTCAAAAAAAGTTTATAATTAATTGAAATAATAAATAAT
1 TATATAATATATTTAATA-TTTTTAATTCAAAAAAAGTTTACAATTAATTGAAATAATAAATAAT
*
1257690 TATAAAATAAAAATTTTAGATAAATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTATT
65 TATAAAATAAAAAATTTAGATAAATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTATT
*
1257755 GGATCTTAAATTATTAATT-GGTTTTAAATGGTTTGGGCTT-AGCCCATATGTTA
130 GGATCTTAAATTATTAATTGGGTTTTAAATGATTTGGG-TTGAGCCCATATGTTA
* * *
1257808 TATATAATATATTTAATATTTTTAATT-AAAAAATAGTTTACAATTAATTTAATTAATATATAAT
1 TATATAATATATTTAATATTTTTAATTCAAAAAA-AGTTTACAATTAATTGAAATAATAAATAAT
*
1257872 TATAAAATAAAAAATTTATAT-AATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTATT
65 TATAAAATAAAAAATTTAGATAAATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTATT
*
1257936 GGATCTTAAATTATTAATTGGGTTTTTAATGATTTGGGTTGAGCCCATATGTTA
130 GGATCTTAAATTATTAATTGGGTTTTAAATGATTTGGGTTGAGCCCATATGTTA
1257990 TATATAATATATTTAATATTT
1 TATATAATATATTTAATATTT
1258011 AAAATTTAAT
Statistics
Matches: 189, Mismatches: 9, Indels: 9
0.91 0.04 0.04
Matches are distributed among these distances:
181 77 0.41
182 105 0.56
183 7 0.04
ACGTcount: A:0.42, C:0.03, G:0.09, T:0.46
Consensus pattern (183 bp):
TATATAATATATTTAATATTTTTAATTCAAAAAAAGTTTACAATTAATTGAAATAATAAATAATT
ATAAAATAAAAAATTTAGATAAATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTATTG
GATCTTAAATTATTAATTGGGTTTTAAATGATTTGGGTTGAGCCCATATGTTA
Found at i:1271699 original size:15 final size:15
Alignment explanation
Indices: 1271679--1271715 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
1271669 ATATTTAGTT
*
1271679 GGGCGGGCGGATGTG
1 GGGCGGGCGGATGCG
1271694 GGGCGGGCGGATGCG
1 GGGCGGGCGGATGCG
1271709 GGGCGGG
1 GGGCGGG
1271716 TAAGGTCTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.05, C:0.16, G:0.70, T:0.08
Consensus pattern (15 bp):
GGGCGGGCGGATGCG
Found at i:1271920 original size:3 final size:3
Alignment explanation
Indices: 1271904--1271966 Score: 65
Period size: 3 Copynumber: 20.7 Consensus size: 3
1271894 TCTACCAAAA
* * * *
1271904 TAT TAT TAA T-T TAT TAT TAC TAT TAT AAT TAT TCT TAT TAAGT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-A-T TAT
1271950 TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TA
1271967 ATACAATATT
Statistics
Matches: 49, Mismatches: 8, Indels: 6
0.78 0.13 0.10
Matches are distributed among these distances:
2 1 0.02
3 44 0.90
4 2 0.04
5 2 0.04
ACGTcount: A:0.35, C:0.03, G:0.02, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:1271942 original size:32 final size:32
Alignment explanation
Indices: 1271906--1271966 Score: 95
Period size: 32 Copynumber: 1.9 Consensus size: 32
1271896 TACCAAAATA
*
1271906 TTATTAATTTATTATTACTATTATAATTATTC
1 TTATTAAGTTATTATTACTATTATAATTATTC
* *
1271938 TTATTAAGTTATTATTATTATTATTATTA
1 TTATTAAGTTATTATTACTATTATAATTA
1271967 ATACAATATT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.34, C:0.03, G:0.02, T:0.61
Consensus pattern (32 bp):
TTATTAAGTTATTATTACTATTATAATTATTC
Found at i:1271950 original size:23 final size:23
Alignment explanation
Indices: 1271924--1271967 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
1271914 TTATTATTAC
*
1271924 TATTATAATTATTCTTATTAAGT
1 TATTATAATTATTATTATTAAGT
*
1271947 TATTATTATTATTATTATTAA
1 TATTATAATTATTATTATTAA
1271968 TACAATATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.59
Consensus pattern (23 bp):
TATTATAATTATTATTATTAAGT
Found at i:1271954 original size:20 final size:20
Alignment explanation
Indices: 1271914--1271963 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 20
1271904 TATTATTAAT
*
1271914 TTATTATTACT-A-TTATAA
1 TTATTATTATTAAGTTATAA
* *
1271932 TTATTCTTATTAAGTTATTA
1 TTATTATTATTAAGTTATAA
1271952 TTATTATTATTA
1 TTATTATTATTA
1271964 TTAATACAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
18 9 0.35
19 1 0.04
20 16 0.62
ACGTcount: A:0.34, C:0.04, G:0.02, T:0.60
Consensus pattern (20 bp):
TTATTATTATTAAGTTATAA
Found at i:1273364 original size:29 final size:29
Alignment explanation
Indices: 1273301--1273365 Score: 98
Period size: 29 Copynumber: 2.3 Consensus size: 29
1273291 TGCTATATTA
*
1273301 TTTATTG--TATTGACCACTAACTTTTAT
1 TTTATTGCATATTAACCACTAACTTTTAT
*
1273328 TTTATTGCATATTAACCACTGACTTTTAT
1 TTTATTGCATATTAACCACTAACTTTTAT
1273357 TTTATTGCA
1 TTTATTGCA
1273366 CTCTAACCAT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
27 7 0.21
29 27 0.79
ACGTcount: A:0.26, C:0.15, G:0.08, T:0.51
Consensus pattern (29 bp):
TTTATTGCATATTAACCACTAACTTTTAT
Found at i:1273372 original size:29 final size:29
Alignment explanation
Indices: 1273313--1273374 Score: 90
Period size: 29 Copynumber: 2.1 Consensus size: 29
1273303 TATTGTATTG
*
1273313 ACCACTAACTTTTATTTTATTGCATATTA
1 ACCACTAACTTTTATTTTATTGCATACTA
*
1273342 ACCACTGACTTTTATTTTATTGCACT-CTA
1 ACCACTAACTTTTATTTTATTGCA-TACTA
1273371 ACCA
1 ACCA
1273375 TTGTTTATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 29 0.97
30 1 0.03
ACGTcount: A:0.29, C:0.23, G:0.05, T:0.44
Consensus pattern (29 bp):
ACCACTAACTTTTATTTTATTGCATACTA
Found at i:1273495 original size:126 final size:125
Alignment explanation
Indices: 1273340--1273722 Score: 518
Period size: 126 Copynumber: 3.0 Consensus size: 125
1273330 TATTGCATAT
*
1273340 TAACCACTGACTTTTATTTTATTGCACTCTAACCATTGTTTATTTATTTATTGTTTCTATTATTC
1 TAACCACTGACTTTTATTTTATTGCACTCTAACCATTGTTTATTTATTTATTGTTTATATTATTC
* * * *
1273405 GATTCGACATT-TGGTGACAAGATCCGGGGTATGATCCACATTATTATAGTTCGGACTCTGC
66 GATTCGAC-TTGTGGTGAC-CGATCCGGGGTATGATCCGCATTATTATGGTTCAGACTCTGC
*
1273466 TAACCACTGACTTTTATTTTATTGCACTCTAACCTTTGTTTATTTATTTATTGTTTATATTATTC
1 TAACCACTGACTTTTATTTTATTGCACTCTAACCATTGTTTATTTATTTATTGTTTATATTATTC
* * *
1273531 GATTCGACCTTGTGGTGACCCGATCTGGGGTATGTTTCGCATTATTATGGTTCAGACTCTGC
66 GATTCGA-CTTGTGGTGA-CCGATCCGGGGTATGATCCGCATTATTATGGTTCAGACTCTGC
* * * * * * * * *
1273593 TAACTACTAACTTTTATTTTATTGCATTTTAACTATTGTTTATTTATTTATTATTTTTAATATTT
1 TAACCACTGACTTTTATTTTATTGCACTCTAACCATTGTTTATTTATTTATTGTTTATATTATTC
* *
1273658 GATTCGGACTTGAGGTGACCGATCTC-GGGTTTGATCCGCATTATTATGGTTCAGACTCTGC
66 GATTC-GACTTGTGGTGACCGATC-CGGGGTATGATCCGCATTATTATGGTTCAGACTCTGC
1273719 TAAC
1 TAAC
1273723 TGCTAATTTT
Statistics
Matches: 228, Mismatches: 24, Indels: 10
0.87 0.09 0.04
Matches are distributed among these distances:
126 114 0.50
127 111 0.49
128 3 0.01
ACGTcount: A:0.22, C:0.17, G:0.15, T:0.45
Consensus pattern (125 bp):
TAACCACTGACTTTTATTTTATTGCACTCTAACCATTGTTTATTTATTTATTGTTTATATTATTC
GATTCGACTTGTGGTGACCGATCCGGGGTATGATCCGCATTATTATGGTTCAGACTCTGC
Found at i:1273760 original size:16 final size:16
Alignment explanation
Indices: 1273718--1273760 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
1273708 TCAGACTCTG
* *
1273718 CTAACTGCTAATTTTT
1 CTAACAGCTAACTTTT
*
1273734 CTAACAACTAACTTTT
1 CTAACAGCTAACTTTT
*
1273750 CTAACCGCTAA
1 CTAACAGCTAA
1273761 TTACTAATTG
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.33, C:0.26, G:0.05, T:0.37
Consensus pattern (16 bp):
CTAACAGCTAACTTTT
Found at i:1283766 original size:14 final size:14
Alignment explanation
Indices: 1283727--1283768 Score: 50
Period size: 15 Copynumber: 3.0 Consensus size: 14
1283717 TTAAACTTGA
1283727 ATGT-TTTGGATTT
1 ATGTGTTTGGATTT
*
1283740 GTGTGTCTTGGATTT
1 ATGTGT-TTGGATTT
*
1283755 ATTTGTTTGGATTT
1 ATGTGTTTGGATTT
1283769 TGTATATTTG
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
13 3 0.12
14 9 0.38
15 12 0.50
ACGTcount: A:0.12, C:0.02, G:0.26, T:0.60
Consensus pattern (14 bp):
ATGTGTTTGGATTT
Found at i:1287845 original size:39 final size:39
Alignment explanation
Indices: 1287791--1287910 Score: 231
Period size: 39 Copynumber: 3.1 Consensus size: 39
1287781 CACTATCAAC
*
1287791 TAACAACGAGCAACACAAACTAACAAAAAAAATATAGTT
1 TAACAACGAGCAACACAAACTAACATAAAAAATATAGTT
1287830 TAACAACGAGCAACACAAACTAACATAAAAAATATAGTT
1 TAACAACGAGCAACACAAACTAACATAAAAAATATAGTT
1287869 TAACAACGAGCAACACAAACTAACATAAAAAATATAGTT
1 TAACAACGAGCAACACAAACTAACATAAAAAATATAGTT
1287908 TAA
1 TAA
1287911 ATAGAAGAAA
Statistics
Matches: 80, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
39 80 1.00
ACGTcount: A:0.57, C:0.17, G:0.07, T:0.17
Consensus pattern (39 bp):
TAACAACGAGCAACACAAACTAACATAAAAAATATAGTT
Found at i:1288515 original size:66 final size:66
Alignment explanation
Indices: 1288409--1288584 Score: 309
Period size: 66 Copynumber: 2.7 Consensus size: 66
1288399 GTATATAATA
*
1288409 GTATGACCGTCAATTTTAAACAACAATTAAATCCAGATTATTAATTTTAATAAAGTTACGTTGTT
1 GTATGACCGTCAATTTTAAATAACAATTAAATCCAGATTATTAATTTTAATAAAGTTACGTTGTT
1288474 G
66 G
*
1288475 GTATGACCATCAATTTTAAATAACAATTAAATCCAGATTATTAATTTTAATAAAGTTACGTTGTT
1 GTATGACCGTCAATTTTAAATAACAATTAAATCCAGATTATTAATTTTAATAAAGTTACGTTGTT
1288540 G
66 G
*
1288541 GTATGACCGTCAATTTTAAATAACAATTTAATCCA-ATTTATTAA
1 GTATGACCGTCAATTTTAAATAACAATTAAATCCAGA-TTATTAA
1288585 AGTTGAATTT
Statistics
Matches: 105, Mismatches: 4, Indels: 2
0.95 0.04 0.02
Matches are distributed among these distances:
65 1 0.01
66 104 0.99
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39
Consensus pattern (66 bp):
GTATGACCGTCAATTTTAAATAACAATTAAATCCAGATTATTAATTTTAATAAAGTTACGTTGTT
G
Found at i:1289329 original size:19 final size:20
Alignment explanation
Indices: 1289287--1289329 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 20
1289277 AGTTCTCTTT
*
1289287 TTTTTCTTCTATTGTGTCAT
1 TTTTTCTTCTATTGTGTCAA
* *
1289307 TTTTTCTT-TATTTTTTCAA
1 TTTTTCTTCTATTGTGTCAA
1289326 TTTT
1 TTTT
1289330 GAATAAGAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 12 0.60
20 8 0.40
ACGTcount: A:0.12, C:0.12, G:0.05, T:0.72
Consensus pattern (20 bp):
TTTTTCTTCTATTGTGTCAA
Found at i:1291008 original size:14 final size:14
Alignment explanation
Indices: 1290956--1291017 Score: 52
Period size: 15 Copynumber: 4.1 Consensus size: 14
1290946 TCCCCGCATA
*
1290956 TTTAATTTCTTATAT
1 TTTAATTTATTA-AT
* *
1290971 TTTAATTCAAATAATT
1 TTTAATT-TATTAA-T
*
1290987 TTTTATTTATTAAT
1 TTTAATTTATTAAT
1291001 TTTAATTTATTTAAT
1 TTTAATTTA-TTAAT
1291016 TT
1 TT
1291018 GTTTTTATTT
Statistics
Matches: 37, Mismatches: 7, Indels: 6
0.74 0.14 0.12
Matches are distributed among these distances:
14 9 0.24
15 19 0.51
16 9 0.24
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (14 bp):
TTTAATTTATTAAT
Found at i:1291027 original size:15 final size:16
Alignment explanation
Indices: 1291006--1291035 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1290996 TTAATTTTAA
1291006 TTTATTT-AATTTGTT
1 TTTATTTGAATTTGTT
1291021 TTTATTTGAATTTGT
1 TTTATTTGAATTTGT
1291036 ATGACTAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.20, C:0.00, G:0.10, T:0.70
Consensus pattern (16 bp):
TTTATTTGAATTTGTT
Found at i:1293098 original size:49 final size:50
Alignment explanation
Indices: 1293002--1293098 Score: 160
Period size: 49 Copynumber: 2.0 Consensus size: 50
1292992 ATGTCCGTAA
* *
1293002 TTAGCATTTATTATTCTTCGAATTTTTTTGAATTAATTTAACTTTACTTT
1 TTAGCATTCATTATTCTTCGAATTTCTTTGAATTAATTTAACTTTACTTT
*
1293052 TTAGCATTCATTATTCTTTGAA-TTCTTTGAATTAATTTAACTTTACT
1 TTAGCATTCATTATTCTTCGAATTTCTTTGAATTAATTTAACTTTACT
1293099 AACTTATCTC
Statistics
Matches: 44, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
49 24 0.55
50 20 0.45
ACGTcount: A:0.27, C:0.11, G:0.06, T:0.56
Consensus pattern (50 bp):
TTAGCATTCATTATTCTTCGAATTTCTTTGAATTAATTTAACTTTACTTT
Found at i:1296982 original size:21 final size:21
Alignment explanation
Indices: 1296953--1296999 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
1296943 AAGACGTCGT
*
1296953 ACTCTCCTATAAGTTGACTCC
1 ACTCCCCTATAAGTTGACTCC
1296974 ACTCCCCTATAAGTTGACTCC
1 ACTCCCCTATAAGTTGACTCC
1296995 ACTCC
1 ACTCC
1297000 AACCACCTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.23, C:0.38, G:0.09, T:0.30
Consensus pattern (21 bp):
ACTCCCCTATAAGTTGACTCC
Found at i:1301646 original size:55 final size:55
Alignment explanation
Indices: 1301560--1301670 Score: 168
Period size: 55 Copynumber: 2.0 Consensus size: 55
1301550 ATGATATCTT
* * *
1301560 ACAATATATGAGATACTAAACATATCATCCATGTACATCTGAAATTGACAAGAAA
1 ACAATATATGAGATACCAAACATATCATCCATGTACACCTGAAATTGAAAAGAAA
* * *
1301615 ACAATATATGATATACCAAACATATCCTCCATGTGCACCTGAAATTGAAAAGAAA
1 ACAATATATGAGATACCAAACATATCATCCATGTACACCTGAAATTGAAAAGAAA
1301670 A
1 A
1301671 TAATCAGAAA
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
55 50 1.00
ACGTcount: A:0.47, C:0.18, G:0.11, T:0.24
Consensus pattern (55 bp):
ACAATATATGAGATACCAAACATATCATCCATGTACACCTGAAATTGAAAAGAAA
Found at i:1302892 original size:22 final size:22
Alignment explanation
Indices: 1302867--1302916 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 22
1302857 AAAGTGAAAT
1302867 AAAAAAT-GAAAAGA-AGAAAGA
1 AAAAAATAGAAAAGAGA-AAAGA
1302888 AAAAAATAGAAAAGAGAAAAGA
1 AAAAAATAGAAAAGAGAAAAGA
1302910 AAGAAAA
1 AA-AAAA
1302917 AATAAAATGT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
21 7 0.27
22 14 0.54
23 5 0.19
ACGTcount: A:0.78, C:0.00, G:0.18, T:0.04
Consensus pattern (22 bp):
AAAAAATAGAAAAGAGAAAAGA
Found at i:1302905 original size:17 final size:16
Alignment explanation
Indices: 1302875--1302916 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
1302865 ATAAAAAATG
1302875 AAAAGAAGAA-AGAAAA
1 AAAAGAA-AAGAGAAAA
1302891 AAATAGAAAAGAGAAAA
1 AAA-AGAAAAGAGAAAA
*
1302908 GAAAGAAAA
1 AAAAGAAAA
1302917 AATAAAATGT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
16 11 0.48
17 12 0.52
ACGTcount: A:0.79, C:0.00, G:0.19, T:0.02
Consensus pattern (16 bp):
AAAAGAAAAGAGAAAA
Found at i:1302937 original size:30 final size:28
Alignment explanation
Indices: 1302863--1302938 Score: 82
Period size: 30 Copynumber: 2.6 Consensus size: 28
1302853 GATGAAAGTG
*
1302863 AAATAAAAAATGAAAAGAAGAAAGAAAA
1 AAATAGAAAATGAAAAGAAGAAAGAAAA
*
1302891 AAATAGAAAAGAGAAAAGAAAGAAA-AAATA
1 AAATAGAAAA-TGAAAAG-AAGAAAGAAA-A
*
1302921 AAATGTGAAAATGAAAAG
1 AAAT-AGAAAATGAAAAG
1302939 GAGGGTTCAA
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
28 9 0.22
29 9 0.22
30 17 0.43
31 5 0.12
ACGTcount: A:0.74, C:0.00, G:0.17, T:0.09
Consensus pattern (28 bp):
AAATAGAAAATGAAAAGAAGAAAGAAAA
Found at i:1303123 original size:30 final size:30
Alignment explanation
Indices: 1303065--1303119 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
1303055 ATTATTAAAG
1303065 CTATGTTAAATATTATTACTATGTTATTAT
1 CTATGTTAAATATTATTACTATGTTATTAT
*
1303095 CTATGTTAAGTATTATTA-TAT-TTAT
1 CTATGTTAAATATTATTACTATGTTAT
1303120 ATTAGTATCA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 4 0.17
29 3 0.12
30 17 0.71
ACGTcount: A:0.33, C:0.05, G:0.07, T:0.55
Consensus pattern (30 bp):
CTATGTTAAATATTATTACTATGTTATTAT
Found at i:1303177 original size:3 final size:3
Alignment explanation
Indices: 1303169--1303276 Score: 55
Period size: 3 Copynumber: 36.3 Consensus size: 3
1303159 ATAATTTGTA
* * * *
1303169 ATT ATT ATT ATCCT ATA ATT A-T ATT ACT CTT ACTT -TT ATC ATT ATT
1 ATT ATT ATT AT--T ATT ATT ATT ATT ATT ATT A-TT ATT ATT ATT ATT
* * * * * *
1303215 AATT AAT ATC AAT ATT -TT ATT TTT ATT TTT ATT ATT A-T ATT ATA
1 -ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1303259 ATT A-T ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT A
1303277 AACAAAATAA
Statistics
Matches: 76, Mismatches: 20, Indels: 18
0.67 0.18 0.16
Matches are distributed among these distances:
2 10 0.13
3 58 0.76
4 5 0.07
5 3 0.04
ACGTcount: A:0.34, C:0.06, G:0.00, T:0.59
Consensus pattern (3 bp):
ATT
Found at i:1303262 original size:11 final size:11
Alignment explanation
Indices: 1303204--1303274 Score: 56
Period size: 11 Copynumber: 6.4 Consensus size: 11
1303194 ACTCTTACTT
1303204 TTATCATTATTAA
1 TTAT-ATTATT-A
* *
1303217 TTAATATCAATA
1 TT-ATATTATTA
* *
1303229 TTTTATTTTTA
1 TTATATTATTA
1303240 TT-T-TTATTA
1 TTATATTATTA
*
1303249 TTATATTATAA
1 TTATATTATTA
1303260 TTATATTATTA
1 TTATATTATTA
1303271 TTAT
1 TTAT
1303275 TAAACAAAAT
Statistics
Matches: 46, Mismatches: 9, Indels: 8
0.73 0.14 0.13
Matches are distributed among these distances:
9 7 0.15
10 2 0.04
11 26 0.57
12 3 0.07
13 6 0.13
14 2 0.04
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (11 bp):
TTATATTATTA
Found at i:1304625 original size:4 final size:4
Alignment explanation
Indices: 1304616--1304649 Score: 68
Period size: 4 Copynumber: 8.5 Consensus size: 4
1304606 TGCTAACTTG
1304616 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT
1304650 TATGTTCGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTAT
Found at i:1311105 original size:35 final size:35
Alignment explanation
Indices: 1311059--1311129 Score: 133
Period size: 35 Copynumber: 2.0 Consensus size: 35
1311049 CCCCGAGTTT
1311059 AGGGGTTAATACAAAAGTTGATAAACAATAAGGAG
1 AGGGGTTAATACAAAAGTTGATAAACAATAAGGAG
*
1311094 AGGGGTTAATACAAAAGTTGATGAACAATAAGGAG
1 AGGGGTTAATACAAAAGTTGATAAACAATAAGGAG
1311129 A
1 A
1311130 TAGAATATTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.48, C:0.06, G:0.27, T:0.20
Consensus pattern (35 bp):
AGGGGTTAATACAAAAGTTGATAAACAATAAGGAG
Found at i:1311561 original size:12 final size:12
Alignment explanation
Indices: 1311544--1311568 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1311534 GTGACACCCC
1311544 AAAATATATTTA
1 AAAATATATTTA
1311556 AAAATATATTTA
1 AAAATATATTTA
1311568 A
1 A
1311569 TGATTAGCCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (12 bp):
AAAATATATTTA
Found at i:1321074 original size:118 final size:118
Alignment explanation
Indices: 1320913--1321138 Score: 285
Period size: 118 Copynumber: 1.9 Consensus size: 118
1320903 CCAGTAATAC
* * * * * * *
1320913 GTTCGATTCTATCAGAGAATGAGGTGGATCAACATTTCAAATGGA-AGGGTCTATAATGAGAAGA
1 GTTCGAGTCCATCACAGAAGGAGGTGGATCAACATTTCAAATGGACAAGATCTATAACGAGAAGA
**
1320977 ACTCATCCGATAAGGGAGAAAAAGTTCATAATGAGAAGAACTTGTTCAACATTG
66 ACTCATAAGATAAGGGAG-AAAAGTTCATAATGAGAAGAACTTGTTCAACATTG
* * *
1321031 GTTCGAGTCCATCACAGAAGGAGGTGGATCAACATTTGC-AATGGATCAATATTTGTAACGAGAA
1 GTTCGAGTCCATCACAGAAGGAGGTGGATCAACATTT-CAAATGGA-CAAGATCTATAACGAGAA
* *
1321095 GAACTCATAAGATGAGGGTGAAAAGTTCATAATGAGAAGAACTT
64 GAACTCATAAGATAAGGGAGAAAAGTTCATAATGAGAAGAACTT
1321139 ATTTAACCTT
Statistics
Matches: 91, Mismatches: 14, Indels: 5
0.83 0.13 0.05
Matches are distributed among these distances:
118 39 0.43
119 25 0.27
120 27 0.30
ACGTcount: A:0.38, C:0.13, G:0.24, T:0.25
Consensus pattern (118 bp):
GTTCGAGTCCATCACAGAAGGAGGTGGATCAACATTTCAAATGGACAAGATCTATAACGAGAAGA
ACTCATAAGATAAGGGAGAAAAGTTCATAATGAGAAGAACTTGTTCAACATTG
Found at i:1325273 original size:28 final size:28
Alignment explanation
Indices: 1325233--1325309 Score: 136
Period size: 28 Copynumber: 2.7 Consensus size: 28
1325223 AAAATGTTAC
*
1325233 ATGAACCATGTGATATATGTTATGAGAT
1 ATGACCCATGTGATATATGTTATGAGAT
1325261 ATGACCCATGTGATATATGTTATGAGAT
1 ATGACCCATGTGATATATGTTATGAGAT
1325289 ATGACCCATGTGACTATATGT
1 ATGACCCATGTGA-TATATGT
1325310 GAAATGATAT
Statistics
Matches: 47, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
28 40 0.85
29 7 0.15
ACGTcount: A:0.32, C:0.12, G:0.21, T:0.35
Consensus pattern (28 bp):
ATGACCCATGTGATATATGTTATGAGAT
Found at i:1325484 original size:23 final size:23
Alignment explanation
Indices: 1325457--1325507 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
1325447 TCAAGACAAT
1325457 TATGTAGAACTTCAGTGCAAACC
1 TATGTAGAACTTCAGTGCAAACC
* * *
1325480 TATGTGGCACTTCGGTGCAAACC
1 TATGTAGAACTTCAGTGCAAACC
1325503 TATGT
1 TATGT
1325508 GGTCCTTCAG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.29
Consensus pattern (23 bp):
TATGTAGAACTTCAGTGCAAACC
Found at i:1325508 original size:23 final size:23
Alignment explanation
Indices: 1325465--1325544 Score: 103
Period size: 23 Copynumber: 3.6 Consensus size: 23
1325455 ATTATGTAGA
1325465 ACTTCAGTGCAAACCTATGTGGC
1 ACTTCAGTGCAAACCTATGTGGC
*
1325488 ACTTCGGTGCAAACCTATGTGGTC
1 ACTTCAGTGCAAACCTATGTGG-C
*
1325512 -CTTCAGT--AAAACTATGTGGC
1 ACTTCAGTGCAAACCTATGTGGC
*
1325532 ACTTCGGTGCAAA
1 ACTTCAGTGCAAA
1325545 TTATGAGCTG
Statistics
Matches: 49, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
20 1 0.02
21 17 0.35
23 30 0.61
24 1 0.02
ACGTcount: A:0.26, C:0.24, G:0.23, T:0.28
Consensus pattern (23 bp):
ACTTCAGTGCAAACCTATGTGGC
Found at i:1328054 original size:35 final size:35
Alignment explanation
Indices: 1328002--1328112 Score: 125
Period size: 35 Copynumber: 3.1 Consensus size: 35
1327992 ATGAAGTCTC
* *
1328002 TATAGGTTTAGCTCGATCAAATTGGTAATTCCTTA
1 TATAGGTTCAGCTCGATCAAACTGGTAATTCCTTA
* *
1328037 TATAGGTTCAGAC-CGATCGAACTGGTAAATCCTTA
1 TATAGGTTCAG-CTCGATCAAACTGGTAATTCCTTA
*** *
1328072 GGGCAGGTTCAGCTTGATCAAACTGGTAATTCCTTA
1 -TATAGGTTCAGCTCGATCAAACTGGTAATTCCTTA
1328108 TATAG
1 TATAG
1328113 TGTTTAACTA
Statistics
Matches: 60, Mismatches: 13, Indels: 6
0.76 0.16 0.08
Matches are distributed among these distances:
35 32 0.53
36 28 0.47
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.33
Consensus pattern (35 bp):
TATAGGTTCAGCTCGATCAAACTGGTAATTCCTTA
Found at i:1330391 original size:19 final size:19
Alignment explanation
Indices: 1330367--1330403 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
1330357 TGAAAATTAT
*
1330367 TTGATTTTGAAAGTCAAAG
1 TTGATTTTGAAAATCAAAG
1330386 TTGATTTTGAAAATCAAA
1 TTGATTTTGAAAATCAAA
1330404 ATGAAATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.41, C:0.05, G:0.16, T:0.38
Consensus pattern (19 bp):
TTGATTTTGAAAATCAAAG
Found at i:1335354 original size:21 final size:22
Alignment explanation
Indices: 1335325--1335367 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
1335315 AGAGTTTTAG
* *
1335325 CGGCTTTTTTTAGT-CCTATAA
1 CGGCGTTTTTAAGTGCCTATAA
1335346 CGGCGTTTTTAAGTGCCTATAA
1 CGGCGTTTTTAAGTGCCTATAA
1335368 AAGCACTTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.21, C:0.19, G:0.19, T:0.42
Consensus pattern (22 bp):
CGGCGTTTTTAAGTGCCTATAA
Found at i:1335518 original size:43 final size:43
Alignment explanation
Indices: 1335458--1335844 Score: 422
Period size: 43 Copynumber: 9.0 Consensus size: 43
1335448 AAAAAATGTT
* * * *
1335458 GCAATAGGTCAAGATCTATAACGGCGTTTTTAGAACAAACGCC
1 GCAAAAGGTCGAGATCTATAGCGGCGTTTTTGGAACAAACGCC
* * * *
1335501 GCAAAAGGTCGATATCTATAACGGCGCTTTTGGAACAAACGCT
1 GCAAAAGGTCGAGATCTATAGCGGCGTTTTTGGAACAAACGCC
* * * * *
1335544 ACAAAAGGTCGATATCTATAACGGC-ATTTTGGAACAAACACC
1 GCAAAAGGTCGAGATCTATAGCGGCGTTTTTGGAACAAACGCC
* * ** *
1335586 ACAAATGGTCGAGATCTATAGTAGCGTTTTTGGAACAAACGTC
1 GCAAAAGGTCGAGATCTATAGCGGCGTTTTTGGAACAAACGCC
* * *
1335629 GCAAAAGGTCGAGATCTATAGCGGCATTTTTGGAACAATCACC
1 GCAAAAGGTCGAGATCTATAGCGGCGTTTTTGGAACAAACGCC
*
1335672 GTAAAAGGTC-AGATCTATAGCGGCGTTTTTTGGAACAAACGCC
1 GCAAAAGGTCGAGATCTATAGCGGCG-TTTTTGGAACAAACGCC
* * * *
1335715 GCAAAAGGTCGAGATCTATAGCAGCATTTTTAGAACAAACGCT
1 GCAAAAGGTCGAGATCTATAGCGGCGTTTTTGGAACAAACGCC
* * **
1335758 GCAAAAGGTC-AGATCTATAGCGGCGTTCTTGAAACAAACAAC
1 GCAAAAGGTCGAGATCTATAGCGGCGTTTTTGGAACAAACGCC
* * * *
1335800 GTAAAAGGTC-AGATTTATAGCGGCGTTTTTTGATACAAAAGCC
1 GCAAAAGGTCGAGATCTATAGCGGCGTTTTTGGA-ACAAACGCC
1335843 GC
1 GC
1335845 TAATTTCCTT
Statistics
Matches: 288, Mismatches: 52, Indels: 8
0.83 0.15 0.02
Matches are distributed among these distances:
42 100 0.35
43 175 0.61
44 13 0.05
ACGTcount: A:0.34, C:0.19, G:0.22, T:0.24
Consensus pattern (43 bp):
GCAAAAGGTCGAGATCTATAGCGGCGTTTTTGGAACAAACGCC
Done.