Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 ID=Chr09-JGI_221_v2.0
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: 70713020
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1142373 characters in sequence are not A, C, G, or T
File 45 of 226
Found at i:18982060 original size:25 final size:24
Alignment explanation
Indices: 18982019--18982067 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 24
18982009 AAAATATTGT
18982019 AAAATTCAAAATAAATAAATACAA
1 AAAATTCAAAATAAATAAATACAA
* *
18982043 AAAATTTAAAACTTAATAAATACAA
1 AAAATTCAAAA-TAAATAAATACAA
18982068 TATTGCCGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 10 0.45
25 12 0.55
ACGTcount: A:0.67, C:0.08, G:0.00, T:0.24
Consensus pattern (24 bp):
AAAATTCAAAATAAATAAATACAA
Found at i:18985249 original size:2 final size:2
Alignment explanation
Indices: 18985242--18985267 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
18985232 AAAGTTAAGA
18985242 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
18985268 TGATCGGTAT
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:18994584 original size:12 final size:12
Alignment explanation
Indices: 18994567--18994596 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
18994557 GTAAAGGAAA
18994567 TGCATGCGCATG
1 TGCATGCGCATG
18994579 TGCATGCGCATG
1 TGCATGCGCATG
*
18994591 CGCATG
1 TGCATG
18994597 TACTTGCTGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.17, C:0.27, G:0.33, T:0.23
Consensus pattern (12 bp):
TGCATGCGCATG
Found at i:19000244 original size:12 final size:12
Alignment explanation
Indices: 19000229--19000265 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
19000219 AAGAGAAGAA
19000229 GGGGAAGGGGAG
1 GGGGAAGGGGAG
*
19000241 GGGGAGGGGGAG
1 GGGGAAGGGGAG
*
19000253 GGGGAAGAGGAG
1 GGGGAAGGGGAG
19000265 G
1 G
19000266 AAACACTTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.24, C:0.00, G:0.76, T:0.00
Consensus pattern (12 bp):
GGGGAAGGGGAG
Found at i:19005630 original size:20 final size:20
Alignment explanation
Indices: 19005605--19005648 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
19005595 TTTCTTCTTT
19005605 ATGCTTAACTTAGCTTATAC
1 ATGCTTAACTTAGCTTATAC
19005625 ATGCTTAACTTAGCTTATAC
1 ATGCTTAACTTAGCTTATAC
19005645 ATGC
1 ATGC
19005649 CATTATACCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.30, C:0.20, G:0.11, T:0.39
Consensus pattern (20 bp):
ATGCTTAACTTAGCTTATAC
Found at i:19006386 original size:25 final size:26
Alignment explanation
Indices: 19006358--19006407 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
19006348 AAGTTCAAGT
19006358 GAGCC-ATATCAGGAAACTCATAAAA
1 GAGCCTATATCAGGAAACTCATAAAA
* **
19006383 GAGCCTATATCGGGATGCTCATAAA
1 GAGCCTATATCAGGAAACTCATAAA
19006408 GAGTTGTGGT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 5 0.24
26 16 0.76
ACGTcount: A:0.40, C:0.20, G:0.20, T:0.20
Consensus pattern (26 bp):
GAGCCTATATCAGGAAACTCATAAAA
Found at i:19007570 original size:16 final size:16
Alignment explanation
Indices: 19007551--19007581 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
19007541 GTATAAAATA
*
19007551 ATATAAATTTTATAAT
1 ATATAAATTTAATAAT
19007567 ATATAAATTTAATAA
1 ATATAAATTTAATAA
19007582 AAATTTAAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
ATATAAATTTAATAAT
Found at i:19008049 original size:20 final size:20
Alignment explanation
Indices: 19008012--19008050 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
19008002 ATAAAATAAC
*
19008012 TTTTTAAAATTGAGTTTAAT
1 TTTTTAAAATGGAGTTTAAT
19008032 TTTTTAAAATAGGA-TTTAA
1 TTTTTAAAAT-GGAGTTTAA
19008051 GTGTAATTAC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 15 0.88
21 2 0.12
ACGTcount: A:0.38, C:0.00, G:0.10, T:0.51
Consensus pattern (20 bp):
TTTTTAAAATGGAGTTTAAT
Found at i:19008714 original size:125 final size:125
Alignment explanation
Indices: 19008482--19008858 Score: 454
Period size: 125 Copynumber: 3.0 Consensus size: 125
19008472 TTAGGGTTTT
* * * * * * **
19008482 TAGGTCCTGGAAGAAATAATTTAGAGTTGACGTTTCTGTGTAAATAGTATAACATCGCTTTTACC
1 TAGGTACTGGAAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCAACC
* * * *
19008547 AGGATGCTTTATGAGAAGAATTTGTTAAATCGCGCCCACGTGGACGCGCTTTTGCTACAG
66 AGGATGCTATATAAGAAGAATTTGTGAAATCGTGCCCACGTGGACGCGCTTTTGCTACAG
* * *
19008607 TAGGTCCT-GAAAAAATTATTTTGAGTTGACGTTTCTGAGCAAATAGTATAAAAAAT-GCTTCAA
1 TAGGTACTGGAAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTAT--AAAATCGCTTCAA
* * * * * *
19008670 GCTGTATGCTATCTAAGAAGAATTTCTGAAATCGTGCCCTCGTGGACGCGCTTTTGCTACAG
64 CCAGGATGCTATATAAGAAGAATTTGTGAAATCGTGCCCACGTGGACGCGCTTTTGCTACAG
* * *
19008732 TTGGTACTGGAAGAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTACC
1 TAGGTACTGGAAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCAACC
* * * *
19008797 AGGATGCTTTATGAGAAGAATTTGTGAAATC-TCGCCCACGTGGACGCACTTTTGCTATAG
66 AGGATGCTATATAAGAAGAATTTGTGAAATCGT-GCCCACGTGGACGCGCTTTTGCTACAG
19008857 TA
1 TA
19008859 ACATGTTTGG
Statistics
Matches: 212, Mismatches: 35, Indels: 10
0.82 0.14 0.04
Matches are distributed among these distances:
124 42 0.20
125 128 0.60
126 42 0.20
ACGTcount: A:0.29, C:0.17, G:0.22, T:0.32
Consensus pattern (125 bp):
TAGGTACTGGAAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCAACC
AGGATGCTATATAAGAAGAATTTGTGAAATCGTGCCCACGTGGACGCGCTTTTGCTACAG
Found at i:19012143 original size:11 final size:11
Alignment explanation
Indices: 19012129--19012205 Score: 63
Period size: 11 Copynumber: 6.9 Consensus size: 11
19012119 TTAAATATGG
19012129 ATTTGAGAGAA
1 ATTTGAGAGAA
*
19012140 ATTTG-GAAGGA
1 ATTTGAG-AGAA
19012151 ATTTGAGAGCAA
1 ATTTGAGAG-AA
19012163 A-TTGAGAGGAA
1 ATTTGAGA-GAA
*
19012174 ATTT-AGAGGGA
1 ATTTGAGA-GAA
19012185 A-TTGAGAAGAA
1 ATTTGAG-AGAA
19012196 ATTTGAGAGA
1 ATTTGAGAGA
19012206 GGATTAGTTT
Statistics
Matches: 54, Mismatches: 4, Indels: 16
0.73 0.05 0.22
Matches are distributed among these distances:
10 3 0.06
11 39 0.72
12 12 0.22
ACGTcount: A:0.43, C:0.01, G:0.31, T:0.25
Consensus pattern (11 bp):
ATTTGAGAGAA
Found at i:19012172 original size:22 final size:22
Alignment explanation
Indices: 19012129--19012205 Score: 79
Period size: 22 Copynumber: 3.5 Consensus size: 22
19012119 TTAAATATGG
19012129 ATTTGAGAGAAATTTG-GAAGGA
1 ATTTGAGAGAAA-TTGAGAAGGA
19012151 ATTTGAGAGCAAATTGAG-AGGAA
1 ATTTGAGAG-AAATTGAGAAGG-A
* *
19012174 ATTT-AGAGGGAATTGAGAAGAA
1 ATTTGAGA-GAAATTGAGAAGGA
19012196 ATTTGAGAGA
1 ATTTGAGAGA
19012206 GGATTAGTTT
Statistics
Matches: 46, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
22 31 0.67
23 15 0.33
ACGTcount: A:0.43, C:0.01, G:0.31, T:0.25
Consensus pattern (22 bp):
ATTTGAGAGAAATTGAGAAGGA
Found at i:19012177 original size:34 final size:34
Alignment explanation
Indices: 19012129--19012204 Score: 95
Period size: 34 Copynumber: 2.3 Consensus size: 34
19012119 TTAAATATGG
*
19012129 ATTTGAGA-GAAATTTGGAAGGAATTTGAG-AGCAA
1 ATTTGAGAGGAAATTTAGAAGGAA-TTGAGAAG-AA
*
19012163 A-TTGAGAGGAAATTTAGAGGGAATTGAGAAGAA
1 ATTTGAGAGGAAATTTAGAAGGAATTGAGAAGAA
19012196 ATTTGAGAG
1 ATTTGAGAG
19012205 AGGATTAGTT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
33 14 0.38
34 23 0.62
ACGTcount: A:0.42, C:0.01, G:0.32, T:0.25
Consensus pattern (34 bp):
ATTTGAGAGGAAATTTAGAAGGAATTGAGAAGAA
Found at i:19018807 original size:25 final size:25
Alignment explanation
Indices: 19018779--19018838 Score: 97
Period size: 23 Copynumber: 2.5 Consensus size: 25
19018769 ATTATATATT
19018779 AAATATATATTTTTTATTTTTAATA
1 AAATATATATTTTTTATTTTTAATA
*
19018804 AAATATATA--TTTTATTTTTAATC
1 AAATATATATTTTTTATTTTTAATA
19018827 AAATATATATTT
1 AAATATATATTT
19018839 AAAATGGGCC
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
23 22 0.69
25 10 0.31
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.57
Consensus pattern (25 bp):
AAATATATATTTTTTATTTTTAATA
Found at i:19023987 original size:82 final size:82
Alignment explanation
Indices: 19023850--19024018 Score: 302
Period size: 82 Copynumber: 2.1 Consensus size: 82
19023840 CGTTCGTTTG
* *
19023850 CTAACTTCTTTTTCCTCTTTAATTTGGAAAGGGGCAACCCGATTTTCCTGTTACAATTTCTGGGT
1 CTAACTTCTTTTTCCTCTTTAATTCGGAAACGGGCAACCCGATTTTCCTGTTACAATTTCTGGGT
19023915 TTAGTATATAAAATTTA
66 TTAGTATATAAAATTTA
* *
19023932 CTAACTTCTTTTTCTTCTTTAATTCGGAAACGGGCAACCCGATTTTCTTGTTACAATTTCTGGGT
1 CTAACTTCTTTTTCCTCTTTAATTCGGAAACGGGCAACCCGATTTTCCTGTTACAATTTCTGGGT
19023997 TTAGTATATAAAATTTA
66 TTAGTATATAAAATTTA
19024014 CTAAC
1 CTAAC
19024019 CCGCACTAGA
Statistics
Matches: 83, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
82 83 1.00
ACGTcount: A:0.26, C:0.18, G:0.14, T:0.43
Consensus pattern (82 bp):
CTAACTTCTTTTTCCTCTTTAATTCGGAAACGGGCAACCCGATTTTCCTGTTACAATTTCTGGGT
TTAGTATATAAAATTTA
Found at i:19025385 original size:141 final size:141
Alignment explanation
Indices: 19025131--19025395 Score: 476
Period size: 141 Copynumber: 1.9 Consensus size: 141
19025121 TTCAGGTTAC
*
19025131 ATTTTAGTCACTTATGTTTAAAATATTAAGTTTTAGTCACTTGCGTTATCGTGTTGTAACATTTT
1 ATTTTAGTCACTTATGTTTAAAATATTAAGTTTTAGTCACTTGCGTTATCATGTTGTAACATTTT
*
19025196 AGTCACTGAGTCGTTAATTGCCGTTAACAGTGTAACAGTAAGTTGACGTGGCACGTTAAATCATC
66 AGTCACTGAGTCGTTAATTGCCGTTAACAGTGTAACAGTAAGCTGACGTGGCACGTTAAATCATC
19025261 ATTTCAAACAA
131 ATTTCAAACAA
* * *
19025272 ATTTTAGTCACTTATGTTTGAAATGTTATGTTTTAGTCACTTGCGTTATCATGTTGTAACATTTT
1 ATTTTAGTCACTTATGTTTAAAATATTAAGTTTTAGTCACTTGCGTTATCATGTTGTAACATTTT
*
19025337 AGTCACTGAGTCGTTAATTGTCGTTAACAGTGTAACAGTAAGCTGACGTGGCACGTTAA
66 AGTCACTGAGTCGTTAATTGCCGTTAACAGTGTAACAGTAAGCTGACGTGGCACGTTAA
19025396 CAAATTTTAG
Statistics
Matches: 118, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
141 118 1.00
ACGTcount: A:0.28, C:0.14, G:0.18, T:0.39
Consensus pattern (141 bp):
ATTTTAGTCACTTATGTTTAAAATATTAAGTTTTAGTCACTTGCGTTATCATGTTGTAACATTTT
AGTCACTGAGTCGTTAATTGCCGTTAACAGTGTAACAGTAAGCTGACGTGGCACGTTAAATCATC
ATTTCAAACAA
Found at i:19029541 original size:20 final size:20
Alignment explanation
Indices: 19029516--19029555 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
19029506 AATATTTTCC
*
19029516 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
19029536 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
19029556 TCATTTTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:19029561 original size:34 final size:35
Alignment explanation
Indices: 19029504--19029570 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
19029494 CAAACACCGG
*
19029504 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
*
19029539 AAAACATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
19029571 TATTTTACTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.46, C:0.13, G:0.09, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:19038868 original size:29 final size:28
Alignment explanation
Indices: 19038827--19038881 Score: 83
Period size: 29 Copynumber: 1.9 Consensus size: 28
19038817 CGGAAGTTTG
*
19038827 CTGGTATTCTGTTGGTTTTGTTTTGAGT
1 CTGGTATTCTGTTGGTTTTATTTTGAGT
*
19038855 CTGGTTTTGCTGTTGGTTTTATTTTGA
1 CTGGTATT-CTGTTGGTTTTATTTTGA
19038882 TGATCTGTCT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 7 0.29
29 17 0.71
ACGTcount: A:0.07, C:0.07, G:0.27, T:0.58
Consensus pattern (28 bp):
CTGGTATTCTGTTGGTTTTATTTTGAGT
Found at i:19049709 original size:3 final size:3
Alignment explanation
Indices: 19049701--19049778 Score: 81
Period size: 3 Copynumber: 26.0 Consensus size: 3
19049691 TTCAGTAATT
19049701 TTA TTA TTA TTA TTA TTA TTA TT- TCTA TTA TTA TTA TTTA TTA -TA
1 TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA -TTA TTA TTA
* * *
19049746 TTA TTG TTA CTTA TCA -TA TTA TTA TTA TCA TTA
1 TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA
19049779 CATAATAGCT
Statistics
Matches: 63, Mismatches: 6, Indels: 12
0.78 0.07 0.15
Matches are distributed among these distances:
2 4 0.06
3 52 0.83
4 7 0.11
ACGTcount: A:0.31, C:0.05, G:0.01, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:19054671 original size:29 final size:26
Alignment explanation
Indices: 19054600--19054676 Score: 73
Period size: 27 Copynumber: 2.8 Consensus size: 26
19054590 AGAAAAAATC
*
19054600 AAAATCAAAATAAAAAACAAAAAGAAA
1 AAAATCAAAGT-AAAAACAAAAAGAAA
*
19054627 AAAATCAAAGGTAAAAGCAAAAAGAGAA
1 AAAATCAAA-GTAAAAACAAAAAGA-AA
* * *
19054655 ATCAATCAAAGTCAAAATAAAA
1 A-AAATCAAAGTAAAAACAAAA
19054677 TATGAAAAGC
Statistics
Matches: 41, Mismatches: 6, Indels: 5
0.79 0.12 0.10
Matches are distributed among these distances:
27 21 0.51
28 13 0.32
29 7 0.17
ACGTcount: A:0.71, C:0.09, G:0.09, T:0.10
Consensus pattern (26 bp):
AAAATCAAAGTAAAAACAAAAAGAAA
Found at i:19055100 original size:20 final size:20
Alignment explanation
Indices: 19055061--19055101 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
19055051 AAAGAAAAAG
* **
19055061 ATGAAGAATGAAAATGGAAA
1 ATGAAAAATGAAAAAAGAAA
19055081 ATGAAAAATGAAAAAAGAAA
1 ATGAAAAATGAAAAAAGAAA
19055101 A
1 A
19055102 GAGTAAAAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.68, C:0.00, G:0.20, T:0.12
Consensus pattern (20 bp):
ATGAAAAATGAAAAAAGAAA
Found at i:19056490 original size:87 final size:87
Alignment explanation
Indices: 19056341--19057448 Score: 1788
Period size: 87 Copynumber: 12.7 Consensus size: 87
19056331 GTGAAGATAA
* * * *
19056341 AAAACAAAGCATTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAATATAGCAAATCTTACCTTCCT
1 AAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGCCTTCCT
*
19056406 GCGTTAACAGTGAAGCAGATCG
66 GCGTTAACAGCGAAGCAGATCG
*
19056428 AAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGCCTTCTT
1 AAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGCCTTCCT
19056493 GCGTTAACAGCGAAGCAGATCG
66 GCGTTAACAGCGAAGCAGATCG
* * *
19056515 AAAACAAAGCCTTGCTTCCATCGGTTACAGTGGAGCTGGTTAAAGATAACAGATCTTGCCTTCCT
1 AAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGCCTTCCT
*
19056580 ACGTTAACAGCGAAGCAGATCG
66 GCGTTAACAGCGAAGCAGATCG
* **
19056602 AAAACAAAGCCTTACCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAATAGATCTTGCCTTCCT
1 AAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGCCTTCCT
* *
19056667 GCATTAACAGCAAAGCAGATCG
66 GCGTTAACAGCGAAGCAGATCG
* *
19056689 AAAACAAAGCCTTGCCTTCATCGGTTGCAGTGGAGCTGGTTAAAGATAACAGATCTTGCCTTCCT
1 AAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGCCTTCCT
* * * *
19056754 ACGTTAACAGCGAAGTAGACCA
66 GCGTTAACAGCGAAGCAGATCG
19056776 AAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGCCTTCCT
1 AAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGCCTTCCT
19056841 GCGTTAACAGCGAAGCAGATCG
66 GCGTTAACAGCGAAGCAGATCG
* *
19056863 AAAATAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGCCTTCTT
1 AAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGCCTTCCT
**
19056928 GTTTTAACAGCGAAGCAGATCG
66 GCGTTAACAGCGAAGCAGATCG
* * *
19056950 AAAACAAAGCATTGCCTCCATCGGTTGCAGTGGAGATGGTTAAAGATA--ATGATCTTGCCTTCA
1 AAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCA-GATCTTGCCTTCC
** * *
19057013 TGCGTTAACAGTAAAGCAAATCA
65 TGCGTTAACAGCGAAGCAGATCG
* * * * *
19057036 AAAACAAAGCATTGCCTCCATTGGTTGCAGTAGAGCTGGTTAAAGATAACAAATCTTGCCTTCCT
1 AAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGCCTTCCT
*
19057101 GCGTTAACAGCAAAGCAGATCG
66 GCGTTAACAGCGAAGCAGATCG
19057123 AAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGCCTTCCT
1 AAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGCCTTCCT
* *
19057188 GCGTTAACAACAAAGCAGATCG
66 GCGTTAACAGCGAAGCAGATCG
* *
19057210 AAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAACAGATCTTGCATTCCT
1 AAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGCCTTCCT
* *
19057275 GCGTTAACAGCAAAGCAAATCG
66 GCGTTAACAGCGAAGCAGATCG
19057297 AAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGCCTTCCT
1 AAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGCCTTCCT
19057362 GCGTTAACAGCGAAGCAGATCG
66 GCGTTAACAGCGAAGCAGATCG
*
19057384 AAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGTCTTCCT
1 AAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGCCTTCCT
19057449 AAGTACTAGC
Statistics
Matches: 948, Mismatches: 70, Indels: 6
0.93 0.07 0.01
Matches are distributed among these distances:
85 1 0.00
86 74 0.08
87 872 0.92
88 1 0.00
ACGTcount: A:0.30, C:0.23, G:0.23, T:0.24
Consensus pattern (87 bp):
AAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGCCTTCCT
GCGTTAACAGCGAAGCAGATCG
Found at i:19057051 original size:43 final size:42
Alignment explanation
Indices: 19057003--19057139 Score: 107
Period size: 43 Copynumber: 3.2 Consensus size: 42
19056993 AGATAATGAT
*
19057003 CTTGCCTTCATGCGTTAACAGTAAAGCAAATCAAAAACAAAG
1 CTTGCCTTCATGCGTTAACAGTAAAGCAGATCAAAAACAAAG
* * * * * * *
19057045 CATTGCCTCCATTG-GTT-GCAGTAGAGCTGGTTAAAGATAACAAAT
1 C-TTGCCTTCA-TGCGTTAACAGTAAAGC-AGATCAA-A-AACAAAG
* * *
19057090 CTTGCCTTCCTGCGTTAACAGCAAAGCAGATCGAAAACAAAG
1 CTTGCCTTCATGCGTTAACAGTAAAGCAGATCAAAAACAAAG
19057132 CCTTGCCT
1 -CTTGCCT
19057140 CCATCGGTTG
Statistics
Matches: 69, Mismatches: 18, Indels: 15
0.68 0.18 0.15
Matches are distributed among these distances:
42 15 0.22
43 24 0.35
44 16 0.23
45 14 0.20
ACGTcount: A:0.34, C:0.23, G:0.18, T:0.24
Consensus pattern (42 bp):
CTTGCCTTCATGCGTTAACAGTAAAGCAGATCAAAAACAAAG
Found at i:19059181 original size:12 final size:12
Alignment explanation
Indices: 19059164--19059197 Score: 68
Period size: 12 Copynumber: 2.8 Consensus size: 12
19059154 TAAGATCTGA
19059164 AGCGAGAGCTCC
1 AGCGAGAGCTCC
19059176 AGCGAGAGCTCC
1 AGCGAGAGCTCC
19059188 AGCGAGAGCT
1 AGCGAGAGCT
19059198 TATGCCATCC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.26, C:0.29, G:0.35, T:0.09
Consensus pattern (12 bp):
AGCGAGAGCTCC
Found at i:19063952 original size:23 final size:23
Alignment explanation
Indices: 19063926--19063976 Score: 84
Period size: 23 Copynumber: 2.2 Consensus size: 23
19063916 TGTTATTGAT
*
19063926 CAGTGGTAGCTTCGGCTACATAA
1 CAGTGGTAGCTTCAGCTACATAA
*
19063949 CAGTGGTAGCTTCAGCTACATAT
1 CAGTGGTAGCTTCAGCTACATAA
19063972 CAGTG
1 CAGTG
19063977 TTGCACTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.25, C:0.22, G:0.25, T:0.27
Consensus pattern (23 bp):
CAGTGGTAGCTTCAGCTACATAA
Found at i:19080239 original size:29 final size:30
Alignment explanation
Indices: 19080197--19080253 Score: 89
Period size: 29 Copynumber: 1.9 Consensus size: 30
19080187 AACTATACGA
19080197 AAGTTTTCATTTAAGTCACCG-ATTATTTG
1 AAGTTTTCATTTAAGTCACCGAATTATTTG
* *
19080226 AAGTTTTTATTTAAGTCACTGAATTATT
1 AAGTTTTCATTTAAGTCACCGAATTATT
19080254 AGTTTTTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 19 0.76
30 6 0.24
ACGTcount: A:0.30, C:0.11, G:0.12, T:0.47
Consensus pattern (30 bp):
AAGTTTTCATTTAAGTCACCGAATTATTTG
Found at i:19085216 original size:25 final size:25
Alignment explanation
Indices: 19085139--19085223 Score: 80
Period size: 25 Copynumber: 3.2 Consensus size: 25
19085129 AAAAAGGCTT
*
19085139 ATTTTATATCAATCAGGTCTTTTCC
1 ATTTTATATCAATCAGGTTTTTTCC
* * * **
19085164 ATGTATGTCTCAAAAAAGTAGTTTTTTCC
1 AT-TTTATATC-AATCAG--GTTTTTTCC
19085193 ATTTTATATCAATCAGGTTTTTTCC
1 ATTTTATATCAATCAGGTTTTTTCC
19085218 ATTTTA
1 ATTTTA
19085224 CTTCAGCAAG
Statistics
Matches: 45, Mismatches: 11, Indels: 8
0.70 0.17 0.12
Matches are distributed among these distances:
25 17 0.38
26 5 0.11
27 8 0.18
28 5 0.11
29 10 0.22
ACGTcount: A:0.27, C:0.15, G:0.09, T:0.48
Consensus pattern (25 bp):
ATTTTATATCAATCAGGTTTTTTCC
Found at i:19089310 original size:26 final size:26
Alignment explanation
Indices: 19089247--19089310 Score: 85
Period size: 26 Copynumber: 2.5 Consensus size: 26
19089237 CCTATTACAT
*
19089247 TGCTTTTGAAAAGTGTTTTTGAGAAG
1 TGCTTTTGAAAAGTGCTTTTGAGAAG
*
19089273 TGC-TGTGAAAAAGTGCTTTTGAGAAG
1 TGCTTTTG-AAAAGTGCTTTTGAGAAG
*
19089299 TTCTTTTGAAAA
1 TGCTTTTGAAAA
19089311 ATTTGAGTAT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
25 3 0.09
26 26 0.81
27 3 0.09
ACGTcount: A:0.30, C:0.06, G:0.25, T:0.39
Consensus pattern (26 bp):
TGCTTTTGAAAAGTGCTTTTGAGAAG
Found at i:19092101 original size:3 final size:3
Alignment explanation
Indices: 19092088--19092164 Score: 118
Period size: 3 Copynumber: 25.7 Consensus size: 3
19092078 TAATATTAAT
*
19092088 TTA TCA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * *
19092136 TTA TTA CTA TTA TTA TTA GTA GTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
19092165 TTCTTTTCTT
Statistics
Matches: 68, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 68 1.00
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:19098019 original size:29 final size:30
Alignment explanation
Indices: 19097982--19098038 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
19097972 TCCGAGCCTT
*
19097982 GGGGAAAAA-TGTAATTATGTAAAAGTTTA
1 GGGGAAAAATTGTAATTATGAAAAAGTTTA
* *
19098011 GGGGCAAAATTGTAATTTTGAAAAAGTT
1 GGGGAAAAATTGTAATTATGAAAAAGTT
19098039 AGAGTCGAGG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 8 0.33
30 16 0.67
ACGTcount: A:0.42, C:0.02, G:0.25, T:0.32
Consensus pattern (30 bp):
GGGGAAAAATTGTAATTATGAAAAAGTTTA
Found at i:19098549 original size:50 final size:50
Alignment explanation
Indices: 19098429--19098625 Score: 241
Period size: 50 Copynumber: 3.9 Consensus size: 50
19098419 CCTTAAGATC
* * * *
19098429 ATGAGAGGTCCCATGTAAGAACCAAGTATGGGACCTGGCGTTGGCACCGAG
1 ATGAGAGGTCCCATGTAAG-ACCATGTCTGGGACATGGCATTGGCACCGAG
* *
19098480 ATGAGAGTTCCCATGTAAGACCATGTCTGGGTCATGGCATTGGCACCGAG
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAG
* * * * * *
19098530 ATGAGAGGTCCCCTATAAGACCATGTCTGGGACATGGCATGGGTACCAAC
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAG
** *
19098580 ATGAGAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 ATGAG-AGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
19098626 TGTTATTATC
Statistics
Matches: 124, Mismatches: 21, Indels: 2
0.84 0.14 0.01
Matches are distributed among these distances:
50 73 0.59
51 51 0.41
ACGTcount: A:0.27, C:0.22, G:0.29, T:0.21
Consensus pattern (50 bp):
ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAG
Found at i:19107962 original size:5 final size:5
Alignment explanation
Indices: 19107952--19107981 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
19107942 ATTTAAATTT
19107952 AACCC AACCC AACCC AACCC AACCC AACCC
1 AACCC AACCC AACCC AACCC AACCC AACCC
19107982 TTAACACCTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.40, C:0.60, G:0.00, T:0.00
Consensus pattern (5 bp):
AACCC
Found at i:19109780 original size:24 final size:24
Alignment explanation
Indices: 19109717--19109768 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 24
19109707 TTTCTAGAAG
* *
19109717 ATTTAGCATTTATGAGTATAATAT
1 ATTTAGCATTTATTAGCATAATAT
19109741 ATTTAGCATTTATTAGCATAATAT
1 ATTTAGCATTTATTAGCATAATAT
19109765 ATTT
1 ATTT
19109769 GACTTTGATT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.37, C:0.06, G:0.10, T:0.48
Consensus pattern (24 bp):
ATTTAGCATTTATTAGCATAATAT
Found at i:19114197 original size:24 final size:24
Alignment explanation
Indices: 19114135--19114185 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
19114125 TTCTAGAAGG
* * *
19114135 TTTAGTATTTATGAGTATAATATA
1 TTTAGCATTTATTAGCATAATATA
19114159 TTTAGCATTTATTAGCATAATATA
1 TTTAGCATTTATTAGCATAATATA
19114183 TTT
1 TTT
19114186 GACTTTGATT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.35, C:0.04, G:0.10, T:0.51
Consensus pattern (24 bp):
TTTAGCATTTATTAGCATAATATA
Found at i:19115942 original size:22 final size:22
Alignment explanation
Indices: 19115880--19115951 Score: 117
Period size: 22 Copynumber: 3.3 Consensus size: 22
19115870 CCTGTTCAAA
* **
19115880 CATGAGAGCTTAGTACGTGAAA
1 CATGAGAGCTTAGTACGTTAGC
19115902 CATGAGAGCTTAGTACGTTAGC
1 CATGAGAGCTTAGTACGTTAGC
19115924 CATGAGAGCTTAGTACGTTAGC
1 CATGAGAGCTTAGTACGTTAGC
19115946 CATGAG
1 CATGAG
19115952 GGTTTACCAT
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 47 1.00
ACGTcount: A:0.31, C:0.17, G:0.28, T:0.25
Consensus pattern (22 bp):
CATGAGAGCTTAGTACGTTAGC
Found at i:19122499 original size:16 final size:16
Alignment explanation
Indices: 19122478--19122546 Score: 129
Period size: 16 Copynumber: 4.2 Consensus size: 16
19122468 GATTAGCTAT
19122478 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
19122494 TACACCTCTAATCCCAA
1 TACACCTCTAAT-CCAA
19122511 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
19122527 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
19122543 TACA
1 TACA
19122547 GCGAACCAAA
Statistics
Matches: 52, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
16 36 0.69
17 16 0.31
ACGTcount: A:0.38, C:0.38, G:0.00, T:0.25
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:19122520 original size:33 final size:32
Alignment explanation
Indices: 19122478--19122546 Score: 129
Period size: 33 Copynumber: 2.1 Consensus size: 32
19122468 GATTAGCTAT
19122478 TACACCTCTAATCCAATACACCTCTAATCCCAA
1 TACACCTCTAATCCAATACACCTCTAAT-CCAA
19122511 TACACCTCTAATCCAATACACCTCTAATCCAA
1 TACACCTCTAATCCAATACACCTCTAATCCAA
19122543 TACA
1 TACA
19122547 GCGAACCAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 8 0.22
33 28 0.78
ACGTcount: A:0.38, C:0.38, G:0.00, T:0.25
Consensus pattern (32 bp):
TACACCTCTAATCCAATACACCTCTAATCCAA
Found at i:19126829 original size:63 final size:62
Alignment explanation
Indices: 19126721--19126926 Score: 209
Period size: 63 Copynumber: 3.3 Consensus size: 62
19126711 TGTGAGGTCG
* * * * * * * *
19126721 TGTAACTCACTATTTTGGCTTTAGGGTCACACAGGCCAGGGACACAGGCGTGTGTCTAAGCCT
1 TGTAACTCATTGTTTT-GCTTTAGAGTCACACGGGCTAAGGACACAGACGTGTGTCTAAGCCA
* * * *
19126784 TGTAACTTATTGTTTTAGCTTTAGAGTCAAACGGGCTAAGGACACAAGTC-TGTGTCTAGGCCA
1 TGTAACTCATTGTTTT-GCTTTAGAGTCACACGGGCTAAGGACAC-AGACGTGTGTCTAAGCCA
* * * *
19126847 TGTAACTCACTATTTTGCCTTTAGAGTCACACGGGCT-AGAGACACAGACGTGTGTCCAAGCCG
1 TGTAACTCATTGTTTTG-CTTTAGAGTCACACGGGCTAAG-GACACAGACGTGTGTCTAAGCCA
19126910 TGTAACTCATTGTTTTG
1 TGTAACTCATTGTTTTG
19126927 GAGTTTGAGT
Statistics
Matches: 117, Mismatches: 22, Indels: 8
0.80 0.15 0.05
Matches are distributed among these distances:
62 6 0.05
63 108 0.92
64 3 0.03
ACGTcount: A:0.24, C:0.21, G:0.24, T:0.30
Consensus pattern (62 bp):
TGTAACTCATTGTTTTGCTTTAGAGTCACACGGGCTAAGGACACAGACGTGTGTCTAAGCCA
Found at i:19127682 original size:34 final size:34
Alignment explanation
Indices: 19127635--19127699 Score: 103
Period size: 34 Copynumber: 1.9 Consensus size: 34
19127625 CATTTGTATC
*
19127635 TGAATCTGAAACTGTATCTAATATGTTCTGTTTT
1 TGAATCTGAAACTGTATATAATATGTTCTGTTTT
* *
19127669 TGAATCTGTAACTGTATATGATATGTTCTGT
1 TGAATCTGAAACTGTATATAATATGTTCTGT
19127700 ATCTATTTCT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
34 28 1.00
ACGTcount: A:0.26, C:0.11, G:0.17, T:0.46
Consensus pattern (34 bp):
TGAATCTGAAACTGTATATAATATGTTCTGTTTT
Found at i:19132199 original size:17 final size:17
Alignment explanation
Indices: 19132179--19132213 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
19132169 ATAGAAATAA
*
19132179 ATAATATTGTTAAAATT
1 ATAATAATGTTAAAATT
*
19132196 ATAATAATGTTAATATT
1 ATAATAATGTTAAAATT
19132213 A
1 A
19132214 ATATATACAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.49, C:0.00, G:0.06, T:0.46
Consensus pattern (17 bp):
ATAATAATGTTAAAATT
Found at i:19132211 original size:43 final size:43
Alignment explanation
Indices: 19132175--19132262 Score: 133
Period size: 43 Copynumber: 2.0 Consensus size: 43
19132165 ATATATAGAA
*
19132175 ATAAAT-AATATTGTTAAAATTATAATAATGTTAATATTAATAT
1 ATAAATAAATATT-TTAAAATTATAATAATGTAAATATTAATAT
* *
19132218 ATACATAAATATTTTTAAATTATAATAATGTAAATATTAATAT
1 ATAAATAAATATTTTAAAATTATAATAATGTAAATATTAATAT
19132261 AT
1 AT
19132263 TCTCATTTAG
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
43 35 0.85
44 6 0.15
ACGTcount: A:0.51, C:0.01, G:0.03, T:0.44
Consensus pattern (43 bp):
ATAAATAAATATTTTAAAATTATAATAATGTAAATATTAATAT
Found at i:19134880 original size:2 final size:2
Alignment explanation
Indices: 19134873--19134906 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
19134863 ATTTTTATTT
19134873 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
19134907 CATAAATTTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:19148927 original size:44 final size:44
Alignment explanation
Indices: 19148859--19148948 Score: 171
Period size: 44 Copynumber: 2.0 Consensus size: 44
19148849 GGGTTTTGAT
19148859 AAGTGATTCTATTGGTTAACAAACTATCGGGATTAAAAAAATAA
1 AAGTGATTCTATTGGTTAACAAACTATCGGGATTAAAAAAATAA
*
19148903 AAGTGATTCTATTGGTTAATAAACTATCGGGATTAAAAAAATAA
1 AAGTGATTCTATTGGTTAACAAACTATCGGGATTAAAAAAATAA
19148947 AA
1 AA
19148949 CTGGATTATA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.47, C:0.08, G:0.16, T:0.30
Consensus pattern (44 bp):
AAGTGATTCTATTGGTTAACAAACTATCGGGATTAAAAAAATAA
Found at i:19151705 original size:2 final size:2
Alignment explanation
Indices: 19151698--19151731 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
19151688 AATTATCAGA
19151698 AT AT AT AT 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 AT AT AT AT
19151732 CAGAGACTTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:19158479 original size:22 final size:23
Alignment explanation
Indices: 19158448--19158490 Score: 63
Period size: 22 Copynumber: 1.9 Consensus size: 23
19158438 GTAAATTGAT
19158448 TTTTTAAAATTT-TATATATTTTG
1 TTTTTAAAATTTATA-ATATTTTG
19158471 TTTTT-AAATTTATAATATTT
1 TTTTTAAAATTTATAATATTT
19158491 ATAATATTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (23 bp):
TTTTTAAAATTTATAATATTTTG
Found at i:19158542 original size:16 final size:15
Alignment explanation
Indices: 19158503--19158542 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 15
19158493 AATATTTAGA
19158503 TTTTTTTTAAATATT
1 TTTTTTTTAAATATT
*
19158518 TATGTTTTTAAATATT
1 T-TTTTTTTAAATATT
19158534 TTTTATTTT
1 TTTT-TTTT
19158543 TTATAATTAG
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
15 3 0.14
16 18 0.86
ACGTcount: A:0.25, C:0.00, G:0.03, T:0.72
Consensus pattern (15 bp):
TTTTTTTTAAATATT
Found at i:19162684 original size:3 final size:3
Alignment explanation
Indices: 19162676--19162708 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
19162666 CTTCTCAATG
19162676 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
19162709 AACTTAGCCC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:19171386 original size:28 final size:27
Alignment explanation
Indices: 19171354--19171412 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 27
19171344 GATGTATCTT
* * *
19171354 TTTTATTTTTTATATATATTTTTAGATA
1 TTTTATTTATTATAT-GATTTTTACATA
*
19171382 TTTTATTTATTCTATGATTTTTACATA
1 TTTTATTTATTATATGATTTTTACATA
19171409 TTTT
1 TTTT
19171413 TAATAATTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
27 14 0.52
28 13 0.48
ACGTcount: A:0.25, C:0.03, G:0.03, T:0.68
Consensus pattern (27 bp):
TTTTATTTATTATATGATTTTTACATA
Found at i:19171430 original size:19 final size:20
Alignment explanation
Indices: 19171398--19171435 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
19171388 TTATTCTATG
*
19171398 ATTTTTACATATTTTTAATA
1 ATTTTTACATATTTGTAATA
*
19171418 ATTTTTATA-ATTTGTAAT
1 ATTTTTACATATTTGTAAT
19171436 TTTATATTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 8 0.50
20 8 0.50
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.61
Consensus pattern (20 bp):
ATTTTTACATATTTGTAATA
Found at i:19171452 original size:33 final size:32
Alignment explanation
Indices: 19171406--19171476 Score: 83
Period size: 33 Copynumber: 2.2 Consensus size: 32
19171396 TGATTTTTAC
**
19171406 ATATTTTTAATAATTTTTATAATTTGTA-ATTTT
1 ATATTTTTAATAATTTAAAT-ATTT-TATATTTT
19171439 ATATTTTCT-ATAATTTAAATATTTTATATTTT
1 ATATTTT-TAATAATTTAAATATTTTATATTTT
19171471 ATATTT
1 ATATTT
19171477 ACTTTTTTCA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
31 2 0.06
32 15 0.44
33 16 0.47
34 1 0.03
ACGTcount: A:0.34, C:0.01, G:0.01, T:0.63
Consensus pattern (32 bp):
ATATTTTTAATAATTTAAATATTTTATATTTT
Found at i:19172008 original size:16 final size:17
Alignment explanation
Indices: 19171987--19172020 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
19171977 ATTTGAACGT
*
19171987 TAATTTTAAT-ATATTA
1 TAATTTAAATAATATTA
19172003 TAATTTAAATAATATTA
1 TAATTTAAATAATATTA
19172020 T
1 T
19172021 TATTAATTTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TAATTTAAATAATATTA
Found at i:19172600 original size:22 final size:22
Alignment explanation
Indices: 19172559--19172605 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
19172549 TGGCCCGATT
* *
19172559 TTGTTGTTTTGCAGCTATTTTG
1 TTGTTGTTTTGCAGCCATTTCG
*
19172581 TTGTTGTTTTGCTGCCATTTCG
1 TTGTTGTTTTGCAGCCATTTCG
19172603 TTG
1 TTG
19172606 CTATTTTGGT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.06, C:0.13, G:0.23, T:0.57
Consensus pattern (22 bp):
TTGTTGTTTTGCAGCCATTTCG
Found at i:19189136 original size:25 final size:25
Alignment explanation
Indices: 19189108--19189171 Score: 60
Period size: 25 Copynumber: 2.5 Consensus size: 25
19189098 GACAACCATA
*
19189108 AAAATAAAAATATAGTTCAA-AAGAT
1 AAAATAAAAATA-AGTTCAAGAAAAT
*
19189133 AAAA-ACAAAATAAGTTTAAGAAAAT
1 AAAATA-AAAATAAGTTCAAGAAAAT
*
19189158 AACAATAAACATAA
1 AA-AATAAAAATAA
19189172 AAATAAAAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
24 7 0.22
25 16 0.50
26 8 0.25
27 1 0.03
ACGTcount: A:0.67, C:0.06, G:0.06, T:0.20
Consensus pattern (25 bp):
AAAATAAAAATAAGTTCAAGAAAAT
Found at i:19189176 original size:12 final size:11
Alignment explanation
Indices: 19189153--19189206 Score: 74
Period size: 12 Copynumber: 4.8 Consensus size: 11
19189143 TAAGTTTAAG
*
19189153 AAAATAACAAT
1 AAAATAAAAAT
19189164 AAACATAAAAAT
1 AAA-ATAAAAAT
19189176 AAAAATAAAAAT
1 -AAAATAAAAAT
19189188 AAAAT-AAAAT
1 AAAATAAAAAT
19189198 AAAATAAAA
1 AAAATAAAA
19189207 CAAATGGACT
Statistics
Matches: 39, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
10 10 0.26
11 11 0.28
12 15 0.38
13 3 0.08
ACGTcount: A:0.80, C:0.04, G:0.00, T:0.17
Consensus pattern (11 bp):
AAAATAAAAAT
Found at i:19189185 original size:5 final size:5
Alignment explanation
Indices: 19189153--19189206 Score: 63
Period size: 5 Copynumber: 9.8 Consensus size: 5
19189143 TAAGTTTAAG
19189153 AAAAT AACAAT AAACAT AAAAAT AAAAAT AAAAAT AAAAT AAAAT AAAAT
1 AAAAT AA-AAT AAA-AT -AAAAT -AAAAT -AAAAT AAAAT AAAAT AAAAT
19189203 AAAA
1 AAAA
19189207 CAAATGGACT
Statistics
Matches: 46, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
5 22 0.48
6 21 0.46
7 3 0.07
ACGTcount: A:0.80, C:0.04, G:0.00, T:0.17
Consensus pattern (5 bp):
AAAAT
Found at i:19196377 original size:58 final size:58
Alignment explanation
Indices: 19196303--19196413 Score: 213
Period size: 58 Copynumber: 1.9 Consensus size: 58
19196293 CATTTATCAC
*
19196303 TTGTCACTGATTAGATAAGTGTAGCTAAAGCTACCACTTATCACTTGTCACTTTTCAT
1 TTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTGTCACTTTTCAT
19196361 TTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTGTCACTT
1 TTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTGTCACTT
19196414 GTCACTGATC
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
58 52 1.00
ACGTcount: A:0.28, C:0.22, G:0.14, T:0.36
Consensus pattern (58 bp):
TTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTGTCACTTTTCAT
Found at i:19196449 original size:28 final size:28
Alignment explanation
Indices: 19196409--19196464 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
19196399 TATCACTTGT
19196409 CACTTGTCACTGATCAAATAAGTGTAGC
1 CACTTGTCACTGATCAAATAAGTGTAGC
*
19196437 CACTTGTCACTGATCAGATAAGTGTAGC
1 CACTTGTCACTGATCAAATAAGTGTAGC
19196465 TAAAGTTACC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.30, C:0.21, G:0.20, T:0.29
Consensus pattern (28 bp):
CACTTGTCACTGATCAAATAAGTGTAGC
Found at i:19196492 original size:79 final size:79
Alignment explanation
Indices: 19196361--19196515 Score: 292
Period size: 79 Copynumber: 2.0 Consensus size: 79
19196351 CACTTTTCAT
19196361 TTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTGTCACTTGTCACTGATCAA
1 TTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTGTCACTTGTCACTGATCAA
19196426 ATAAGTGTAGCCAC
66 ATAAGTGTAGCCAC
* *
19196440 TTGTCACTGATCAGATAAGTGTAGCTAAAGTTACCACTTATCACTTGTCACTTGTCACTGATCAG
1 TTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTGTCACTTGTCACTGATCAA
19196505 ATAAGTGTAGC
66 ATAAGTGTAGC
19196516 TAAAGCTACC
Statistics
Matches: 74, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
79 74 1.00
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.32
Consensus pattern (79 bp):
TTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTGTCACTTGTCACTGATCAA
ATAAGTGTAGCCAC
Found at i:19196513 original size:51 final size:51
Alignment explanation
Indices: 19196437--19196540 Score: 199
Period size: 51 Copynumber: 2.0 Consensus size: 51
19196427 TAAGTGTAGC
*
19196437 CACTTGTCACTGATCAGATAAGTGTAGCTAAAGTTACCACTTATCACTTGT
1 CACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTGT
19196488 CACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTGT
1 CACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTGT
19196539 CA
1 CA
19196541 TTGATTAGAA
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 52 1.00
ACGTcount: A:0.30, C:0.23, G:0.15, T:0.32
Consensus pattern (51 bp):
CACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTGT
Found at i:19200734 original size:14 final size:15
Alignment explanation
Indices: 19200704--19200733 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
19200694 GGCTAATAAG
19200704 ATTTTAAGAAAAAAA
1 ATTTTAAGAAAAAAA
19200719 ATTTTAAGAAAAAAA
1 ATTTTAAGAAAAAAA
19200734 TGAATATTGT
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:0.67, C:0.00, G:0.07, T:0.27
Consensus pattern (15 bp):
ATTTTAAGAAAAAAA
Found at i:19211982 original size:22 final size:22
Alignment explanation
Indices: 19211924--19211984 Score: 95
Period size: 22 Copynumber: 2.8 Consensus size: 22
19211914 AACGTCAAAC
**
19211924 ACTAAGCTCTCATGGCTAACGT
1 ACTAAGCTCTCATGTTTAACGT
*
19211946 ACTAAGCTCTCATGTTTCACGT
1 ACTAAGCTCTCATGTTTAACGT
19211968 ACTAAGCTCTCATGTTT
1 ACTAAGCTCTCATGTTT
19211985 GAACAATAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.25, C:0.26, G:0.15, T:0.34
Consensus pattern (22 bp):
ACTAAGCTCTCATGTTTAACGT
Found at i:19214656 original size:24 final size:24
Alignment explanation
Indices: 19214626--19214875 Score: 166
Period size: 24 Copynumber: 10.7 Consensus size: 24
19214616 GTATATTGTA
*
19214626 TATTATTATTTTAGATTTATCATG
1 TATTATTATTTTAAATTTATCATG
* *
19214650 TTTTATTATTTGT-AATTTATCA-A
1 TATTATTATTT-TAAATTTATCATG
19214673 TATTATTATTTTAAATTTAT--TG
1 TATTATTATTTTAAATTTATCATG
**
19214695 TTAACATTATTTTAAATTTATCATG
1 -TATTATTATTTTAAATTTATCATG
*
19214720 TA-TATCTATTTCAAATTTATCAT-
1 TATTAT-TATTTTAAATTTATCATG
* * *
19214743 TAATA-T-TTTTAAATTTATTATA
1 TATTATTATTTTAAATTTATCATG
* * *
19214765 TACTATTATTTTAGATTTATCACG
1 TATTATTATTTTAAATTTATCATG
* *
19214789 TATGATTATTCTAGAA-TTATCAT-
1 TATTATTATTTTA-AATTTATCATG
* * *
19214812 CA-AAAT-TTTTAAATTTTAT-ATG
1 TATTATTATTTTAAA-TTTATCATG
* * *
19214834 TATTATTATTTCAAATTTATTATA
1 TATTATTATTTTAAATTTATCATG
*
19214858 TATTATTTATTGTAAATT
1 TATTA-TTATTTTAAATT
19214876 ATCCAATTCA
Statistics
Matches: 175, Mismatches: 32, Indels: 37
0.72 0.13 0.15
Matches are distributed among these distances:
20 2 0.01
21 19 0.11
22 13 0.07
23 48 0.27
24 79 0.45
25 14 0.08
ACGTcount: A:0.34, C:0.06, G:0.04, T:0.56
Consensus pattern (24 bp):
TATTATTATTTTAAATTTATCATG
Found at i:19214676 original size:47 final size:46
Alignment explanation
Indices: 19214625--19214786 Score: 145
Period size: 47 Copynumber: 3.5 Consensus size: 46
19214615 AGTATATTGT
* *
19214625 ATATTATTATTTTAGATTTATCATGTTTTATTATTTGTAATTTATCA
1 ATATTATTATTTTAAATTTATCATGTTATATTATTT-TAATTTATCA
*
19214672 ATATTATTATTTTAAATTTAT--TGTTAACATTATTTTAAATTTATC-
1 ATATTATTATTTTAAATTTATCATGTT-ATATTATTTT-AATTTATCA
* * * * *
19214717 ATGTATATCTATTTCAAATTTATCAT-TAATATT-TTTAAATTTATTA
1 ATAT-TAT-TATTTTAAATTTATCATGTTATATTATTTTAATTTATCA
* *
19214763 TATACTATTATTTTAGATTTATCA
1 -ATATTATTATTTTAAATTTATCA
19214787 CGTATGATTA
Statistics
Matches: 94, Mismatches: 13, Indels: 18
0.75 0.10 0.14
Matches are distributed among these distances:
45 29 0.31
46 24 0.26
47 39 0.41
48 1 0.01
49 1 0.01
ACGTcount: A:0.34, C:0.06, G:0.04, T:0.57
Consensus pattern (46 bp):
ATATTATTATTTTAAATTTATCATGTTATATTATTTTAATTTATCA
Found at i:19214708 original size:70 final size:69
Alignment explanation
Indices: 19214619--19214791 Score: 199
Period size: 70 Copynumber: 2.5 Consensus size: 69
19214609 TATCTAAGTA
* * * ** *
19214619 TATTGTATATTATTATTTTAGATTTATCATGTTTTAT-TATTTGTAATTTATCAATATTATTATT
1 TATTATATACTATTATTTTAGATTTATCATG-TATATCTATTTCAAATTTATCAATAATA-T-TT
19214683 TTAAATT
63 TTAAATT
* * *
19214690 TATTGT-TAAC-ATTATTTTAAATTTATCATGTATATCTATTTCAAATTTATCATTAATATTTTT
1 TATTATAT-ACTATTATTTTAGATTTATCATGTATATCTATTTCAAATTTATCAATAATATTTTT
19214753 AAATT
65 AAATT
*
19214758 TATTATATACTATTATTTTAGATTTATCACGTAT
1 TATTATATACTATTATTTTAGATTTATCATGTAT
19214792 GATTATTCTA
Statistics
Matches: 88, Mismatches: 10, Indels: 10
0.81 0.09 0.09
Matches are distributed among these distances:
68 16 0.18
69 27 0.31
70 38 0.43
71 7 0.08
ACGTcount: A:0.33, C:0.06, G:0.05, T:0.57
Consensus pattern (69 bp):
TATTATATACTATTATTTTAGATTTATCATGTATATCTATTTCAAATTTATCAATAATATTTTTA
AATT
Found at i:19214715 original size:11 final size:11
Alignment explanation
Indices: 19214678--19214715 Score: 51
Period size: 11 Copynumber: 3.4 Consensus size: 11
19214668 ATCAATATTA
19214678 TTATTTTAAAT
1 TTATTTTAAAT
19214689 TTATTGTTAACA-
1 TTATT-TTAA-AT
19214701 TTATTTTAAAT
1 TTATTTTAAAT
19214712 TTAT
1 TTAT
19214716 CATGTATATC
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
10 1 0.04
11 13 0.54
12 9 0.38
13 1 0.04
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.61
Consensus pattern (11 bp):
TTATTTTAAAT
Found at i:19214809 original size:69 final size:68
Alignment explanation
Indices: 19214585--19214866 Score: 215
Period size: 69 Copynumber: 4.1 Consensus size: 68
19214575 TTATACTTAT
* * * * * * * *
19214585 TATTA-TTA-AATTAATCATTAAAATTATCTAAGTATATTGTATATTATTATTTTAGATTTATCA
1 TATTATTTAGAATTTATCATTAATATT-TTTAAATTTATTATATACTATTATTTTAAATTTATCA
*
19214648 TGTTT
65 TG-TA
* * *
19214653 TATTATTT-GTAATTTATCAATATTATTATTTTAAATTTATTGT-TAAC-ATTATTTTAAATTTA
1 TATTATTTAG-AATTTATCATTAATA-T-TTTTAAATTTATTATAT-ACTATTATTTTAAATTTA
19214715 TCATGTA
62 TCATGTA
*
19214722 TATCTATTTCA-AATTTATCATTAATATTTTTAAATTTATTATATACTATTATTTTAGATTTATC
1 TAT-TATTT-AGAATTTATCATTAATATTTTTAAATTTATTATATACTATTATTTTAAATTTATC
*
19214786 ACGTA
64 ATGTA
* * * * *
19214791 TGATTATTCTAGAA-TTATCATCAAAATTTTTAAATTT-TATATGTATTATTATTTCAAATTTAT
1 T-ATTATT-TAGAATTTATCATTAATATTTTTAAATTTAT-TATATACTATTATTTTAAATTTAT
*
19214854 --TATA
63 CATGTA
19214858 TATTATTTA
1 TATTATTTA
19214867 TTGTAAATTA
Statistics
Matches: 176, Mismatches: 23, Indels: 33
0.76 0.10 0.14
Matches are distributed among these distances:
65 2 0.01
66 6 0.03
67 3 0.02
68 22 0.12
69 75 0.43
70 54 0.31
71 13 0.07
72 1 0.01
ACGTcount: A:0.36, C:0.06, G:0.04, T:0.54
Consensus pattern (68 bp):
TATTATTTAGAATTTATCATTAATATTTTTAAATTTATTATATACTATTATTTTAAATTTATCAT
GTA
Found at i:19214954 original size:23 final size:23
Alignment explanation
Indices: 19214924--19214968 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
19214914 ATTTGTACAT
*
19214924 TCATATATATTATTTGTTTTAAC
1 TCATATATATTATTTATTTTAAC
*
19214947 TCATATATATTGTTTATTTTAA
1 TCATATATATTATTTATTTTAA
19214969 AATTTTGAAC
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:0.31, C:0.07, G:0.04, T:0.58
Consensus pattern (23 bp):
TCATATATATTATTTATTTTAAC
Found at i:19219318 original size:3 final size:3
Alignment explanation
Indices: 19219301--19219363 Score: 76
Period size: 3 Copynumber: 21.3 Consensus size: 3
19219291 ATTAAATTGT
* **
19219301 TTA TTA CTA -TA TTA TTA TTA GCA TTTA TTA TTA TTA TTA -TA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA
19219345 TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA T
19219364 ACATATATTA
Statistics
Matches: 52, Mismatches: 5, Indels: 6
0.83 0.08 0.10
Matches are distributed among these distances:
2 4 0.08
3 47 0.90
4 1 0.02
ACGTcount: A:0.33, C:0.03, G:0.02, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:19219320 original size:14 final size:14
Alignment explanation
Indices: 19219301--19219374 Score: 78
Period size: 14 Copynumber: 5.1 Consensus size: 14
19219291 ATTAAATTGT
19219301 TTATTACTATATTA
1 TTATTACTATATTA
*
19219315 TTATTAGCATTTATTA
1 TTATTA-C-TATATTA
*
19219331 TTATTATTATATTA
1 TTATTACTATATTA
*
19219345 TTATTATTATTATTA
1 TTATTACTA-TATTA
19219360 TTA-TACATATATTA
1 TTATTAC-TATATTA
19219374 T
1 T
19219375 ATGCGCATTA
Statistics
Matches: 52, Mismatches: 4, Indels: 8
0.81 0.06 0.12
Matches are distributed among these distances:
14 29 0.56
15 11 0.21
16 12 0.23
ACGTcount: A:0.35, C:0.04, G:0.01, T:0.59
Consensus pattern (14 bp):
TTATTACTATATTA
Found at i:19219372 original size:23 final size:23
Alignment explanation
Indices: 19219325--19219374 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
19219315 TTATTAGCAT
*
19219325 TTATTATTATTATTATATTATTA
1 TTATTATTATTATTATAATATTA
19219348 TTATTATTATTATTATACATA-TA
1 TTATTATTATTATTATA-ATATTA
19219371 TTAT
1 TTAT
19219375 ATGCGCATTA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 23 0.92
24 2 0.08
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (23 bp):
TTATTATTATTATTATAATATTA
Found at i:19220662 original size:18 final size:19
Alignment explanation
Indices: 19220616--19220662 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 19
19220606 ACAAGTTAGA
*
19220616 AAAATAAATTTATCTTTTT
1 AAAATTAATTTATCTTTTT
* *
19220635 -AATTTCATTTAT-TTTTT
1 AAAATTAATTTATCTTTTT
19220652 AAAATTAATTT
1 AAAATTAATTT
19220663 TAGTTCTTTT
Statistics
Matches: 22, Mismatches: 5, Indels: 3
0.73 0.17 0.10
Matches are distributed among these distances:
17 5 0.23
18 17 0.77
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.57
Consensus pattern (19 bp):
AAAATTAATTTATCTTTTT
Found at i:19226471 original size:43 final size:42
Alignment explanation
Indices: 19226424--19226560 Score: 114
Period size: 43 Copynumber: 3.2 Consensus size: 42
19226414 TCAGGGTCTT
** * *
19226424 TAGCGGCGTTTTTTTCTCAAACGCCGGAATAGACCCTGATCTA
1 TAGCGGCG-TTTTCACTCAAACGCCGCAATAGAACCTGATCTA
* * * * *
19226467 TAGCGGCGCTTTGACTACAAACGCCACTAA-AGAACCTAATCTT
1 TAGCGGCGTTTTCACT-CAAACGCCGC-AATAGAACCTGATCTA
* * * *
19226510 TAGCGGCGCTTTCCCCTAAAACGCCGCAATAGATCCTGATCTA
1 TAGCGGCG-TTTTCACTCAAACGCCGCAATAGAACCTGATCTA
19226553 TAGCGGCG
1 TAGCGGCG
19226561 CTTCGACCAC
Statistics
Matches: 73, Mismatches: 17, Indels: 8
0.74 0.17 0.08
Matches are distributed among these distances:
42 7 0.10
43 60 0.82
44 6 0.08
ACGTcount: A:0.26, C:0.28, G:0.20, T:0.25
Consensus pattern (42 bp):
TAGCGGCGTTTTCACTCAAACGCCGCAATAGAACCTGATCTA
Found at i:19226561 original size:43 final size:42
Alignment explanation
Indices: 19226458--19226694 Score: 237
Period size: 43 Copynumber: 5.5 Consensus size: 42
19226448 CGGAATAGAC
* ** * *
19226458 CCTGATCTATAGCGGCGCTTTGACTACAAACGCCACTAAAGAA
1 CCTGATCTTTAGCGGCGCTTTCCCCA-AAACGCCGCTAAAGAA
* *
19226501 CCTAATCTTTAGCGGCGCTTTCCCCTAAAACGCCGC-AATAGAT
1 CCTGATCTTTAGCGGCGCTTTCCCC-AAAACGCCGCTAA-AGAA
* *
19226544 CCTGATCTATAGCGGCGC-TTCGACCACAAAACGCCACTAAAGAA
1 CCTGATCTTTAGCGGCGCTTTC--CC-CAAAACGCCGCTAAAGAA
*
19226588 CCTAATCTTTAGCGGCGCTTTCCCCAAAAACGCCGCTAAAG-A
1 CCTGATCTTTAGCGGCGCTTTCCCC-AAAACGCCGCTAAAGAA
* ** *
19226630 CCATGATCTTTAGTGGCGCTTTTTCCACAAACGCCGCTAAAGAC
1 CC-TGATCTTTAGCGGCGCTTTCCCCA-AAACGCCGCTAAAGAA
*
19226674 CCTTATCTTTAGCGGCGCTTT
1 CCTGATCTTTAGCGGCGCTTT
19226695 GACCNNNNNN
Statistics
Matches: 162, Mismatches: 21, Indels: 22
0.79 0.10 0.11
Matches are distributed among these distances:
42 10 0.06
43 113 0.70
44 33 0.20
45 6 0.04
ACGTcount: A:0.27, C:0.31, G:0.18, T:0.24
Consensus pattern (42 bp):
CCTGATCTTTAGCGGCGCTTTCCCCAAAACGCCGCTAAAGAA
Found at i:19226610 original size:87 final size:85
Alignment explanation
Indices: 19226442--19226694 Score: 355
Period size: 86 Copynumber: 2.9 Consensus size: 85
19226432 TTTTTTTCTC
* *
19226442 AAACGCCGGAATAGACCCTGATCTATAGCGGCGCTTTGACTACAAACGCCACTAAAGAACCTAAT
1 AAACGCCGCAATAGA-CCTGATCTATAGCGGCGCTTTGACCACAAACGCCACTAAAGAACCTAAT
*
19226507 CTTTAGCGGCGCTTTCCCCTA
65 CTTTAGCGGCGCTTTCCCCAA
*
19226528 AAACGCCGCAATAGATCCTGATCTATAGCGGCGCTTCGACCACAAAACGCCACTAAAGAACCTAA
1 AAACGCCGCAATAGA-CCTGATCTATAGCGGCGCTTTGACCAC-AAACGCCACTAAAGAACCTAA
19226593 TCTTTAGCGGCGCTTTCCCCAA
64 TCTTTAGCGGCGCTTTCCCCAA
* * ** * * *
19226615 AAACGCCGCTAA-AGACCATGATCTTTAGTGGCGCTTTTTCCACAAACGCCGCTAAAGACCCTTA
1 AAACGCCGC-AATAGACC-TGATCTATAGCGGCGCTTTGACCACAAACGCCACTAAAGAACCTAA
19226679 TCTTTAGCGGCGCTTT
64 TCTTTAGCGGCGCTTT
19226695 GACCNNNNNN
Statistics
Matches: 151, Mismatches: 13, Indels: 6
0.89 0.08 0.04
Matches are distributed among these distances:
86 75 0.50
87 74 0.49
88 2 0.01
ACGTcount: A:0.28, C:0.30, G:0.18, T:0.23
Consensus pattern (85 bp):
AAACGCCGCAATAGACCTGATCTATAGCGGCGCTTTGACCACAAACGCCACTAAAGAACCTAATC
TTTAGCGGCGCTTTCCCCAA
Found at i:19226619 original size:130 final size:130
Alignment explanation
Indices: 19226462--19226698 Score: 300
Period size: 130 Copynumber: 1.8 Consensus size: 130
19226452 ATAGACCCTG
* * *
19226462 ATCTATAGCGGCGCTTTGACTACAAACGCCACTAAAGAACC-TAATCTTTAGCGGCGCTTTCCCC
1 ATCTATAGCGGCGCTTTCACCAAAAACGCCACTAAAG-ACCATAATCTTTAGCGGCGCTTTCCCC
*
19226526 TA-AAACGCCGC-AATAGATCCTGATCTATAGCGGCGCTTCGACCACAAAACGCCACTAAAGAAC
65 -ACAAACGCCGCTAA-AGACCCTGATCTATAGCGGCGCTTCGACCACAAAACGCCACTAAAGAAC
19226589 CTA
128 CTA
* * * * * **
19226592 ATCTTTAGCGGCGCTTTCCCCAAAAACGCCGCTAAAGACCATGATCTTTAGTGGCGCTTTTTCCA
1 ATCTATAGCGGCGCTTTCACCAAAAACGCCACTAAAGACCATAATCTTTAGCGGCGCTTTCCCCA
* * *
19226657 CAAACGCCGCTAAAGACCCTTATCTTTAGCGGCGCTTTGACC
66 CAAACGCCGCTAAAGACCCTGATCTATAGCGGCGCTTCGACC
19226699 NNNNNNNNNN
Statistics
Matches: 90, Mismatches: 14, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
129 4 0.04
130 84 0.93
131 2 0.02
ACGTcount: A:0.28, C:0.31, G:0.18, T:0.24
Consensus pattern (130 bp):
ATCTATAGCGGCGCTTTCACCAAAAACGCCACTAAAGACCATAATCTTTAGCGGCGCTTTCCCCA
CAAACGCCGCTAAAGACCCTGATCTATAGCGGCGCTTCGACCACAAAACGCCACTAAAGAACCTA
Found at i:19227049 original size:21 final size:21
Alignment explanation
Indices: 19227023--19227086 Score: 101
Period size: 21 Copynumber: 3.0 Consensus size: 21
19227013 TTTGACGCTG
19227023 CTCTGCTTCCCTCGCTGCAGC
1 CTCTGCTTCCCTCGCTGCAGC
**
19227044 CTCTGCTTCCCTCGCTTTAGC
1 CTCTGCTTCCCTCGCTGCAGC
*
19227065 CTCTGCTTCCTTCGCTGCAGC
1 CTCTGCTTCCCTCGCTGCAGC
19227086 C
1 C
19227087 AGTACTTCTC
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.05, C:0.45, G:0.17, T:0.33
Consensus pattern (21 bp):
CTCTGCTTCCCTCGCTGCAGC
Found at i:19227102 original size:21 final size:21
Alignment explanation
Indices: 19227078--19227118 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
19227068 TGCTTCCTTC
*
19227078 GCTGCAGCCAGTACTTCTCTA
1 GCTGCAGCCACTACTTCTCTA
* *
19227099 GCTGCCGCCTCTACTTCTCT
1 GCTGCAGCCACTACTTCTCT
19227119 TACTGCCGCA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.12, C:0.39, G:0.17, T:0.32
Consensus pattern (21 bp):
GCTGCAGCCACTACTTCTCTA
Found at i:19227252 original size:66 final size:65
Alignment explanation
Indices: 19227112--19227276 Score: 215
Period size: 66 Copynumber: 2.5 Consensus size: 65
19227102 GCCGCCTCTA
** * *
19227112 CTTCTCTTACTGCCGCATCTGCTTTAAGCTGCTGCTGGAGTTCTTCATACTTTCGTTGAACCTCA
1 CTTCTCTCGCTGCTGCATCTGCTTTAAGTTG-TGCTGGAGTTCTTCATACTTTCGTTGAACCTCA
19227177 G
65 G
* *
19227178 CTTCTCTCGCTGCTGCATCTGCTTTCAGTTGTAGCTGGAGTTCTTCATATCTTT-TTTGAACCTC
1 CTTCTCTCGCTGCTGCATCTGCTTTAAGTTGT-GCTGGAGTTCTTCATA-CTTTCGTTGAACCTC
19227242 AG
64 AG
* * *
19227244 CTTCTCTCGATGTTGCCTCTGCTTTAAGTTGTG
1 CTTCTCTCGCTGCTGCATCTGCTTTAAGTTGTG
19227277 TAATTTGCTC
Statistics
Matches: 87, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
65 2 0.02
66 81 0.93
67 4 0.05
ACGTcount: A:0.13, C:0.27, G:0.19, T:0.41
Consensus pattern (65 bp):
CTTCTCTCGCTGCTGCATCTGCTTTAAGTTGTGCTGGAGTTCTTCATACTTTCGTTGAACCTCAG
Found at i:19232821 original size:9 final size:9
Alignment explanation
Indices: 19232807--19232926 Score: 112
Period size: 9 Copynumber: 14.2 Consensus size: 9
19232797 TAAGGGATAT
19232807 TTATGTAAG
1 TTATGTAAG
19232816 TTATGTAAG
1 TTATGTAAG
19232825 TTATGT-A-
1 TTATGTAAG
* *
19232832 TTAAGTAAA
1 TTATGTAAG
19232841 TTATGTAAG
1 TTATGTAAG
19232850 TTATGT-A-
1 TTATGTAAG
*
19232857 TTATCTAAG
1 TTATGTAAG
19232866 TTATGTAAG
1 TTATGTAAG
19232875 TTATGT-A-
1 TTATGTAAG
* * *
19232882 CTAAGTAGG
1 TTATGTAAG
*
19232891 TTATGTAAT
1 TTATGTAAG
*
19232900 TTATGT--C
1 TTATGTAAG
19232907 TTATGTAAG
1 TTATGTAAG
19232916 TTATGTAAG
1 TTATGTAAG
19232925 TT
1 TT
19232927 TTTGATTTTG
Statistics
Matches: 89, Mismatches: 14, Indels: 16
0.75 0.12 0.13
Matches are distributed among these distances:
7 20 0.22
8 5 0.06
9 64 0.72
ACGTcount: A:0.33, C:0.03, G:0.18, T:0.47
Consensus pattern (9 bp):
TTATGTAAG
Found at i:19232839 original size:25 final size:25
Alignment explanation
Indices: 19232811--19232926 Score: 160
Period size: 25 Copynumber: 4.6 Consensus size: 25
19232801 GGATATTTAT
19232811 GTAAGTTATGTAAGTTATGTATTAA
1 GTAAGTTATGTAAGTTATGTATTAA
* *
19232836 GTAAATTATGTAAGTTATGTATTAT
1 GTAAGTTATGTAAGTTATGTATTAA
* *
19232861 CTAAGTTATGTAAGTTATGTACTAA
1 GTAAGTTATGTAAGTTATGTATTAA
* * * *
19232886 GTAGGTTATGTAATTTATGTCTTAT
1 GTAAGTTATGTAAGTTATGTATTAA
19232911 GTAAGTTATGTAAGTT
1 GTAAGTTATGTAAGTT
19232927 TTTGATTTTG
Statistics
Matches: 77, Mismatches: 14, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 77 1.00
ACGTcount: A:0.33, C:0.03, G:0.19, T:0.46
Consensus pattern (25 bp):
GTAAGTTATGTAAGTTATGTATTAA
Found at i:19232879 original size:34 final size:34
Alignment explanation
Indices: 19232807--19232881 Score: 91
Period size: 34 Copynumber: 2.2 Consensus size: 34
19232797 TAAGGGATAT
*
19232807 TTATGTAAGTTATGTAAGTTATGTATTAAGTAAA
1 TTATGTAAGTTATGTAAGTTATCTATTAAGTAAA
* *
19232841 TTATGTAAGTTATGT-A-TTATCTAAGTTATGTAAG
1 TTATGTAAGTTATGTAAGTTATCT-A-TTAAGTAAA
19232875 TTATGTA
1 TTATGTA
19232882 CTAAGTAGGT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
32 5 0.14
33 2 0.06
34 29 0.81
ACGTcount: A:0.35, C:0.01, G:0.17, T:0.47
Consensus pattern (34 bp):
TTATGTAAGTTATGTAAGTTATCTATTAAGTAAA
Found at i:19232887 original size:50 final size:50
Alignment explanation
Indices: 19232807--19232926 Score: 186
Period size: 50 Copynumber: 2.4 Consensus size: 50
19232797 TAAGGGATAT
*
19232807 TTATGTAAGTTATGTAAGTTATGTATTAAGTAAATTATGTAAGTTATGTA
1 TTATGTAAGTTATGTAAGTTATGTACTAAGTAAATTATGTAAGTTATGTA
* ** * *
19232857 TTATCTAAGTTATGTAAGTTATGTACTAAGTAGGTTATGTAATTTATGTC
1 TTATGTAAGTTATGTAAGTTATGTACTAAGTAAATTATGTAAGTTATGTA
19232907 TTATGTAAGTTATGTAAGTT
1 TTATGTAAGTTATGTAAGTT
19232927 TTTGATTTTG
Statistics
Matches: 63, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
50 63 1.00
ACGTcount: A:0.33, C:0.03, G:0.18, T:0.47
Consensus pattern (50 bp):
TTATGTAAGTTATGTAAGTTATGTACTAAGTAAATTATGTAAGTTATGTA
Found at i:19232945 original size:50 final size:49
Alignment explanation
Indices: 19232807--19232953 Score: 161
Period size: 50 Copynumber: 2.9 Consensus size: 49
19232797 TAAGGGATAT
* *
19232807 TTATGTAAGTTATGTAAGTTATGTATTAAGTAAATTATGTAAGTTATGTA
1 TTATGTAAGTTATGTAAGTTATGTATTAAGT-GATTATGTAACTTATGTA
* * * * *
19232857 TTATCTAAGTTATGTAAGTTATGTACTAAGTAGGTTATGTAATTTATGTC
1 TTATGTAAGTTATGTAAGTTATGTATTAAGT-GATTATGTAACTTATGTA
* **
19232907 TTATGTAAGTTATGTAAGTT-TTTGATTTTGTGTATTATGTAACTTAT
1 TTATGTAAGTTATGTAAGTTATGT-ATTAAGTG-ATTATGTAACTTAT
19232954 TTAATTTGAT
Statistics
Matches: 82, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
49 3 0.04
50 79 0.96
ACGTcount: A:0.31, C:0.03, G:0.18, T:0.49
Consensus pattern (49 bp):
TTATGTAAGTTATGTAAGTTATGTATTAAGTGATTATGTAACTTATGTA
Found at i:19237954 original size:23 final size:23
Alignment explanation
Indices: 19237928--19237973 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
19237918 AACCTTAAAT
* *
19237928 CCCTAGCTCTTAACCCCTAAACC
1 CCCTAACTCCTAACCCCTAAACC
19237951 CCCTAACTCCTAACCCCTAAACC
1 CCCTAACTCCTAACCCCTAAACC
19237974 TTAAACCATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.28, C:0.50, G:0.02, T:0.20
Consensus pattern (23 bp):
CCCTAACTCCTAACCCCTAAACC
Found at i:19238299 original size:21 final size:21
Alignment explanation
Indices: 19238257--19238329 Score: 64
Period size: 21 Copynumber: 3.6 Consensus size: 21
19238247 TTAACCCTTA
**
19238257 AACCCCTAAACCTCT-AGCCCT
1 AACCCCTAAACCT-TAAATCCT
19238278 AACCCCTAAACCTTAAATCCT
1 AACCCCTAAACCTTAAATCCT
*
19238299 AA-CCC--GACCTTAAATCCCT
1 AACCCCTAAACCTTAAAT-CCT
*
19238318 AATCCCTAAACC
1 AACCCCTAAACC
19238330 CCAACCCAAT
Statistics
Matches: 43, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
18 9 0.21
19 5 0.12
20 7 0.16
21 19 0.44
22 3 0.07
ACGTcount: A:0.34, C:0.42, G:0.03, T:0.21
Consensus pattern (21 bp):
AACCCCTAAACCTTAAATCCT
Found at i:19238446 original size:15 final size:16
Alignment explanation
Indices: 19238420--19238453 Score: 61
Period size: 15 Copynumber: 2.2 Consensus size: 16
19238410 CTATACTTTT
19238420 AACCCTTAAATCCATA
1 AACCCTTAAATCCATA
19238436 AACCC-TAAATCCATA
1 AACCCTTAAATCCATA
19238451 AAC
1 AAC
19238454 ACCATATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 13 0.72
16 5 0.28
ACGTcount: A:0.47, C:0.32, G:0.00, T:0.21
Consensus pattern (16 bp):
AACCCTTAAATCCATA
Found at i:19238800 original size:41 final size:41
Alignment explanation
Indices: 19238741--19238976 Score: 221
Period size: 41 Copynumber: 5.8 Consensus size: 41
19238731 TAAAAAATAT
* **
19238741 ATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGATCTTAGC
1 ATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGATCAGAGC
* * *
19238782 ATTAGCGGCGCTTCTTCAAAAATGCCGCTAAAGGTCAGAAC
1 ATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGATCAGAGC
* *
19238823 ATTACCGGCGCTTCTTCAAAAACGTCGCTAAAGGAT-AGAGC
1 ATTAGCGGCGCTTCTTCAAAAACGCCGCTAAA-GATCAGAGC
* * * * * *
19238864 ATTAGCGGCG-TTTTTTAAGAAGCGCCGCTAATGCTCTG-GCC
1 ATTAGCGGCGCTTCTTCAA-AAACGCCGCTAAAGATCAGAG-C
* *
19238905 TTTAGCGGCGCTTAC-TCAAAAACGCCGCTAAAG-GCTAGAGC
1 ATTAGCGGCGCTT-CTTCAAAAACGCCGCTAAAGATC-AGAGC
* * *
19238946 ATTAGCGACGCTTCCTAAAAAACGCCGCTAA
1 ATTAGCGGCGCTTCTTCAAAAACGCCGCTAA
19238977 GGGCCCCAAA
Statistics
Matches: 157, Mismatches: 29, Indels: 18
0.77 0.14 0.09
Matches are distributed among these distances:
40 11 0.07
41 138 0.88
42 8 0.05
ACGTcount: A:0.29, C:0.25, G:0.22, T:0.23
Consensus pattern (41 bp):
ATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGATCAGAGC
Found at i:19238891 original size:82 final size:82
Alignment explanation
Indices: 19238741--19238976 Score: 253
Period size: 82 Copynumber: 2.9 Consensus size: 82
19238731 TAAAAAATAT
* ** *
19238741 ATTAGCGGCGCTTTTTCAAAAACGCCGCTAAA-GATCTTAGCATTAGCGGCGCTTCTTCAAAAAT
1 ATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGAT-AGAGCATTAGCGGCGCTTCTTCAAAAAC
*
19238805 GCCGCTAAAGGTCAGAAC
65 GCCGCTAAAGCTCAGAAC
* * * * *
19238823 ATTACCGGCGCTTCTTCAAAAACGTCGCTAAAGGATAGAGCATTAGCGGCG-TTTTTTAAGAAGC
1 ATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGATAGAGCATTAGCGGCGCTTCTTCAA-AAAC
* * **
19238887 GCCGCTAATGCTCTGGCC
65 GCCGCTAAAGCTCAGAAC
* * * * *
19238905 TTTAGCGGCGCTTAC-TCAAAAACGCCGCTAAAGGCTAGAGCATTAGCGACGCTTCCTAAAAAAC
1 ATTAGCGGCGCTT-CTTCAAAAACGCCGCTAAAGGATAGAGCATTAGCGGCGCTTCTTCAAAAAC
19238969 GCCGCTAA
65 GCCGCTAA
19238977 GGGCCCCAAA
Statistics
Matches: 127, Mismatches: 23, Indels: 8
0.80 0.15 0.05
Matches are distributed among these distances:
81 6 0.05
82 112 0.88
83 9 0.07
ACGTcount: A:0.29, C:0.25, G:0.22, T:0.23
Consensus pattern (82 bp):
ATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGATAGAGCATTAGCGGCGCTTCTTCAAAAACG
CCGCTAAAGCTCAGAAC
Found at i:19239142 original size:40 final size:40
Alignment explanation
Indices: 19239018--19239152 Score: 116
Period size: 40 Copynumber: 3.4 Consensus size: 40
19239008 TGGCTTAGGC
* *
19239018 TTTTT-GCGGCGATTTTCAGAAAA-CGCCGCTAATGCT-AA
1 TTTTTAGCGGCG-TTTTTATAAAAGCGCCGCTAATGCTCAA
* * * *
19239056 TTTTTAGCAGCGTTTTCTGT-AAAGCGCCACTAATGCTCTA
1 TTTTTAGCGGCGTTTT-TATAAAAGCGCCGCTAATGCTCAA
** * * *
19239096 CCTTTAGCGGTGTTTTTATAAAAGCGCCGTTAATGCTCGA
1 TTTTTAGCGGCGTTTTTATAAAAGCGCCGCTAATGCTCAA
*
19239136 TTTTTAGTGGCGTTTTT
1 TTTTTAGCGGCGTTTTT
19239153 TGTCCAAACA
Statistics
Matches: 74, Mismatches: 18, Indels: 8
0.74 0.18 0.08
Matches are distributed among these distances:
38 12 0.16
39 19 0.26
40 43 0.58
ACGTcount: A:0.21, C:0.19, G:0.21, T:0.39
Consensus pattern (40 bp):
TTTTTAGCGGCGTTTTTATAAAAGCGCCGCTAATGCTCAA
Found at i:19241129 original size:17 final size:19
Alignment explanation
Indices: 19241093--19241129 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
19241083 GGAATTATGG
*
19241093 ATATTTTTTATAATAATTA
1 ATATTTATTATAATAATTA
19241112 ATATTTATTA-AA-AATTA
1 ATATTTATTATAATAATTA
19241129 A
1 A
19241130 AAATATATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
17 6 0.35
18 2 0.12
19 9 0.53
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
ATATTTATTATAATAATTA
Found at i:19242168 original size:34 final size:34
Alignment explanation
Indices: 19242107--19242196 Score: 108
Period size: 34 Copynumber: 2.6 Consensus size: 34
19242097 TGCACATGGG
*
19242107 TATATATTTACAAAATAGAAAAAAAATGTATAAGTA
1 TATATATTTACAACAT--AAAAAAAATGTATAAGTA
* *
19242143 TATATATTTACAACATAAAAGAAATGTATATGTA
1 TATATATTTACAACATAAAAAAAATGTATAAGTA
* * *
19242177 TATATCTATAAAACATAAAA
1 TATATATTTACAACATAAAA
19242197 TATATAAAAG
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
34 33 0.69
36 15 0.31
ACGTcount: A:0.56, C:0.06, G:0.07, T:0.32
Consensus pattern (34 bp):
TATATATTTACAACATAAAAAAAATGTATAAGTA
Found at i:19243939 original size:132 final size:133
Alignment explanation
Indices: 19243802--19244104 Score: 409
Period size: 132 Copynumber: 2.3 Consensus size: 133
19243792 GCAACTTCAA
*
19243802 GGAGATAGGAA-TACTGGCTTCAATGTACTCCACTGTAACT-TCAGGGAGGTAAAA-TCTGCCAT
1 GGAGATA-GAATTACTGGCTTCAATGTACTCCACTGTAACTCTCAGGGAGGTAAAATTC-ACCAT
* * * * *
19243864 CTTCGATCTACTCCACTATTGCCTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCTG
64 CTTCGATATACTCCACTACTGCCTAGGGAGACAAGATCCGAAATCTTCAATCTATTCCACTGCTG
19243929 CCCAG
129 CCCAG
* * *
19243934 TGAGATAAAATTAGTGGCTTCAATGTACTCCACTGTAA-TCTCAGGGAGGTAAAATTCACCATCT
1 GGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACTCTCAGGGAGGTAAAATTCACCATCT
* * * * * *
19243998 TTGATATGCTCTACTACTGCTTGGGGAGACAATATCCGAAATCTTCAATCTATTCCACTGCTGCC
66 TCGATATACTCCACTACTGCCTAGGGAGACAAGATCCGAAATCTTCAATCTATTCCACTGCTGCC
19244063 CAG
131 CAG
19244066 GGA-AGTAGAATTACTGGCTTCAATGTACTCCACTGTAAC
1 GGAGA-TAGAATTACTGGCTTCAATGTACTCCACTGTAAC
19244105 CACAGTAGTT
Statistics
Matches: 148, Mismatches: 18, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
131 4 0.03
132 142 0.96
133 2 0.01
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.29
Consensus pattern (133 bp):
GGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACTCTCAGGGAGGTAAAATTCACCATCT
TCGATATACTCCACTACTGCCTAGGGAGACAAGATCCGAAATCTTCAATCTATTCCACTGCTGCC
CAG
Found at i:19248343 original size:5 final size:5
Alignment explanation
Indices: 19248333--19248359 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
19248323 TAACACTGAA
19248333 TTCTT TTCTT TTCTT TTCTT TTCTT TT
1 TTCTT TTCTT TTCTT TTCTT TTCTT TT
19248360 TCTAATCAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (5 bp):
TTCTT
Found at i:19248785 original size:23 final size:27
Alignment explanation
Indices: 19248732--19248785 Score: 62
Period size: 24 Copynumber: 2.1 Consensus size: 27
19248722 TTATTTATAA
* *
19248732 AATATTTAAATAAAACAATTAAAAGTC
1 AATATTTAAATAAAACAATCAAAACTC
19248759 AATATTT-AA-AAAA-AATCAAAACT-
1 AATATTTAAATAAAACAATCAAAACTC
19248782 AATA
1 AATA
19248786 AGGATTTGTA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
23 4 0.16
24 8 0.32
25 4 0.16
26 2 0.08
27 7 0.28
ACGTcount: A:0.63, C:0.07, G:0.02, T:0.28
Consensus pattern (27 bp):
AATATTTAAATAAAACAATCAAAACTC
Found at i:19255724 original size:43 final size:42
Alignment explanation
Indices: 19255622--19255780 Score: 176
Period size: 43 Copynumber: 3.8 Consensus size: 42
19255612 TGTTGGTCTA
* * *
19255622 TAGCGGCGCTTCTAGCACAAACGCCGCTGAAGA-CTAATCTT
1 TAGCGGCGCTTTTACCACAAACGCCGCTAAAGACCTAATCTT
* ** * *
19255663 TAGCAGCGCTTTCCCCACAAACACCGCTAAAGACCATGATCTT
1 TAGCGGCGCTTTTACCACAAACGCCGCTAAAGACC-TAATCTT
* * *
19255706 TAGGGGCGCTTTTTCCACAAACGCCGCTAAAGAACCTTATCTT
1 TAGCGGCGCTTTTACCACAAACGCCGCTAAAG-ACCTAATCTT
* *
19255749 TAGCGGCGCTTTTACCAAAAACGCCACTAAAG
1 TAGCGGCGCTTTTACCACAAACGCCGCTAAAG
19255781 GCCAACACCT
Statistics
Matches: 97, Mismatches: 18, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
41 26 0.27
42 1 0.01
43 67 0.69
44 3 0.03
ACGTcount: A:0.29, C:0.30, G:0.18, T:0.23
Consensus pattern (42 bp):
TAGCGGCGCTTTTACCACAAACGCCGCTAAAGACCTAATCTT
Found at i:19255793 original size:86 final size:84
Alignment explanation
Indices: 19255637--19255805 Score: 194
Period size: 86 Copynumber: 2.0 Consensus size: 84
19255627 GCGCTTCTAG
* * * * **
19255637 CACAAACGCCGCTGAAGACTAATCTTTAGCAGCGCTTTCCCCACAAACACCGCTAAAGACCATGA
1 CACAAACGCCGCTAAAGACTAATCTTTAGCAGCGCTTTCACCAAAAACACCACTAAAGACCAACA
*
19255702 TCTTTAGGGGCGCTTTTTC
66 CCTTTAGGGGCGCTTTTTC
* * * * *
19255721 CACAAACGCCGCTAAAGAACCTTATCTTTAGCGGCGCTTTTACCAAAAACGCCACTAAAGGCCAA
1 CACAAACGCCGCTAAAG-A-CTAATCTTTAGCAGCGCTTTCACCAAAAACACCACTAAAGACCAA
* *
19255786 CACCTTTAGTGGCGTTTTTT
64 CACCTTTAGGGGCGCTTTTT
19255806 TTTTGAAAAA
Statistics
Matches: 69, Mismatches: 14, Indels: 2
0.81 0.16 0.02
Matches are distributed among these distances:
84 16 0.23
85 1 0.01
86 52 0.75
ACGTcount: A:0.28, C:0.30, G:0.17, T:0.25
Consensus pattern (84 bp):
CACAAACGCCGCTAAAGACTAATCTTTAGCAGCGCTTTCACCAAAAACACCACTAAAGACCAACA
CCTTTAGGGGCGCTTTTTC
Found at i:19257604 original size:34 final size:34
Alignment explanation
Indices: 19257566--19257695 Score: 206
Period size: 34 Copynumber: 3.7 Consensus size: 34
19257556 TATAATATTA
*
19257566 ATGTAAGTTATGTATAATATTAATTAATTAAGTT
1 ATGTAATTTATGTATAATATTAATTAATTAAGTT
19257600 ATGTAATTTATGTATAATACTAATTAATTAATTAAGTT
1 ATGTAATTTATGTAT-A-A-T-ATTAATTAATTAAGTT
*
19257638 ATGTAATTTATGTATAATATTAATTCATTAAGTT
1 ATGTAATTTATGTATAATATTAATTAATTAAGTT
19257672 ATGTAATTTATGTATAATATTAAT
1 ATGTAATTTATGTATAATATTAAT
19257696 GTAAGTTATG
Statistics
Matches: 90, Mismatches: 2, Indels: 8
0.90 0.02 0.08
Matches are distributed among these distances:
34 53 0.59
35 2 0.02
36 2 0.02
37 2 0.02
38 31 0.34
ACGTcount: A:0.41, C:0.02, G:0.09, T:0.48
Consensus pattern (34 bp):
ATGTAATTTATGTATAATATTAATTAATTAAGTT
Found at i:19257650 original size:9 final size:9
Alignment explanation
Indices: 19257636--19257738 Score: 50
Period size: 9 Copynumber: 10.8 Consensus size: 9
19257626 ATTAATTAAG
19257636 TTATGTAAT
1 TTATGTAAT
19257645 TTATGT-AT
1 TTATGTAAT
*
19257653 AATAT-TAAT
1 -TTATGTAAT
* *
19257662 TCAT-TAAG
1 TTATGTAAT
19257670 TTATGTAAT
1 TTATGTAAT
19257679 TTATGTATAAT
1 TTATG--TAAT
*
19257690 ATTAATGTAAG
1 -TT-ATGTAAT
19257701 TTATGTATAAT
1 TTATG--TAAT
*
19257712 ATTAATGTAAG
1 -TT-ATGTAAT
19257723 TTATGTAAT
1 TTATGTAAT
*
19257732 CTATGTA
1 TTATGTA
19257739 TATTAATTAA
Statistics
Matches: 72, Mismatches: 11, Indels: 22
0.69 0.10 0.21
Matches are distributed among these distances:
8 11 0.15
9 34 0.47
10 4 0.06
11 13 0.18
12 4 0.06
13 6 0.08
ACGTcount: A:0.38, C:0.02, G:0.12, T:0.49
Consensus pattern (9 bp):
TTATGTAAT
Found at i:19257697 original size:22 final size:22
Alignment explanation
Indices: 19257672--19257729 Score: 107
Period size: 22 Copynumber: 2.6 Consensus size: 22
19257662 TCATTAAGTT
*
19257672 ATGTAATTTATGTATAATATTA
1 ATGTAAGTTATGTATAATATTA
19257694 ATGTAAGTTATGTATAATATTA
1 ATGTAAGTTATGTATAATATTA
19257716 ATGTAAGTTATGTA
1 ATGTAAGTTATGTA
19257730 ATCTATGTAT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.40, C:0.00, G:0.14, T:0.47
Consensus pattern (22 bp):
ATGTAAGTTATGTATAATATTA
Found at i:19259245 original size:27 final size:27
Alignment explanation
Indices: 19259213--19259264 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
19259203 TCTTACTTTT
* *
19259213 AAATAATTAATTACCAATTTATTTAAC
1 AAATAAATAATTACCAACTTATTTAAC
*
19259240 AAATAAATAATTACTAACTTATTTA
1 AAATAAATAATTACCAACTTATTTA
19259265 TTTGTTTATT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.50, C:0.10, G:0.00, T:0.40
Consensus pattern (27 bp):
AAATAAATAATTACCAACTTATTTAAC
Found at i:19259351 original size:8 final size:10
Alignment explanation
Indices: 19259328--19259364 Score: 65
Period size: 10 Copynumber: 3.7 Consensus size: 10
19259318 TAATAACTAT
19259328 ATATATATCC
1 ATATATATCC
*
19259338 ATATATATTC
1 ATATATATCC
19259348 ATATATATCC
1 ATATATATCC
19259358 ATATATA
1 ATATATA
19259365 AGTAAAAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
10 25 1.00
ACGTcount: A:0.43, C:0.14, G:0.00, T:0.43
Consensus pattern (10 bp):
ATATATATCC
Found at i:19260082 original size:8 final size:10
Alignment explanation
Indices: 19260059--19260095 Score: 65
Period size: 10 Copynumber: 3.7 Consensus size: 10
19260049 NNNTAACTAT
19260059 ATATATATCC
1 ATATATATCC
*
19260069 ATATATATTC
1 ATATATATCC
19260079 ATATATATCC
1 ATATATATCC
19260089 ATATATA
1 ATATATA
19260096 AGTAAAAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
10 25 1.00
ACGTcount: A:0.43, C:0.14, G:0.00, T:0.43
Consensus pattern (10 bp):
ATATATATCC
Found at i:19262678 original size:81 final size:80
Alignment explanation
Indices: 19262559--19262818 Score: 339
Period size: 81 Copynumber: 3.2 Consensus size: 80
19262549 GCTTACCTAT
* * *
19262559 AAAACGCCGCTAAAAGCCAGAGCATTAGTGGCGCTCAGATAAAAACGCCACTAAAGATACTAACA
1 AAAAAGCCGCTAAAGGCCAGAGAATTAGTGGCGCTCAGATAAAAACGCCACTAAAGATAC-AACA
19262624 TTAGCGGCGCTTAGAA
65 TTAGCGGCGCTTAGAA
**
19262640 AAAAAGCCGCTAAAGGCCAGAGAATTAGTGGCATTCAGAT-AAAACGCCACTAAAGATACAAGCA
1 AAAAAGCCGCTAAAGGCCAGAGAATTAGTGGCGCTCAGATAAAAACGCCACTAAAGATACAA-CA
19262704 TTAGCGGCGCTTAGAGA
65 TTAGCGGCGCTTAGA-A
* * *
19262721 AAAACGCCGCTAAAGGCCAGA-ACATTAGTGGCGCTCAGATAAAAACGCCGCTAAAGAT-CGGAC
1 AAAAAGCCGCTAAAGGCCAGAGA-ATTAGTGGCGCTCAGATAAAAACGCCACTAAAGATAC--AA
*
19262784 CATTAGCGGCGC-TAAAA
63 CATTAGCGGCGCTTAGAA
19262801 TAAAAACGCCGCTAAAGG
1 -AAAAA-GCCGCTAAAGG
19262819 TTTAAAAATC
Statistics
Matches: 159, Mismatches: 12, Indels: 15
0.85 0.06 0.08
Matches are distributed among these distances:
79 2 0.01
80 38 0.24
81 79 0.50
82 39 0.25
83 1 0.01
ACGTcount: A:0.40, C:0.23, G:0.23, T:0.15
Consensus pattern (80 bp):
AAAAAGCCGCTAAAGGCCAGAGAATTAGTGGCGCTCAGATAAAAACGCCACTAAAGATACAACAT
TAGCGGCGCTTAGAA
Found at i:19262713 original size:121 final size:122
Alignment explanation
Indices: 19262557--19262776 Score: 284
Period size: 121 Copynumber: 1.8 Consensus size: 122
19262547 ACGCTTACCT
* * * * * *
19262557 ATAAAACGCCGCTAAAAGCCAGAGCATTAGTGGCGCTCAGATAAAAACGCCACTAAA-GATACTA
1 ATAAAACGCCACTAAAAGACAGAGCATTAGCGGCGCTCAGAGAAAAACGCCACTAAAGGACA-GA
*
19262621 ACATTAGCGGCGCTTAGA-AAAAAAGCCGCTAAAGGCCAGAGAATTAGTGGCATTCAG
65 ACATTAGCGGCGCTCAGATAAAAAAGCCGCTAAAGGCCAGAGAATTAGTGGCATTCAG
* * * *
19262678 ATAAAACGCCACTAAAGATACA-AGCATTAGCGGCGCTTAGAGAAAAACGCCGCTAAAGGCCAGA
1 ATAAAACGCCACTAAA-AGACAGAGCATTAGCGGCGCTCAGAGAAAAACGCCACTAAAGGACAGA
* *
19262742 ACATTAGTGGCGCTCAGATAAAAACGCCGCTAAAG
65 ACATTAGCGGCGCTCAGATAAAAAAGCCGCTAAAG
19262777 ATCGGACCAT
Statistics
Matches: 83, Mismatches: 13, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
121 63 0.76
122 20 0.24
ACGTcount: A:0.40, C:0.22, G:0.22, T:0.15
Consensus pattern (122 bp):
ATAAAACGCCACTAAAAGACAGAGCATTAGCGGCGCTCAGAGAAAAACGCCACTAAAGGACAGAA
CATTAGCGGCGCTCAGATAAAAAAGCCGCTAAAGGCCAGAGAATTAGTGGCATTCAG
Found at i:19262817 original size:41 final size:41
Alignment explanation
Indices: 19262559--19262817 Score: 242
Period size: 41 Copynumber: 6.4 Consensus size: 41
19262549 GCTTACCTAT
*
19262559 AAAACGCCGCTAAA-AGCCAGAGCATTAGTGGCGCTCAGATA
1 AAAACGCCGCTAAAGA-CCAGAGCATTAGCGGCGCTCAGATA
* * *
19262600 AAAACGCCACTAAAGATACTA-A-CATTAGCGGCGCTTAGA-A
1 AAAACGCCGCTAAAG--ACCAGAGCATTAGCGGCGCTCAGATA
* * * * **
19262640 AAAAAGCCGCTAAAGGCCAGAGAATTAGTGGCATTCAGAT-
1 AAAACGCCGCTAAAGACCAGAGCATTAGCGGCGCTCAGATA
* * * *
19262680 AAAACGCCACTAAAGATACA-AGCATTAGCGGCGCTTAGAGA
1 AAAACGCCGCTAAAGA-CCAGAGCATTAGCGGCGCTCAGATA
* * *
19262721 AAAACGCCGCTAAAGGCCAGAACATTAGTGGCGCTCAGATA
1 AAAACGCCGCTAAAGACCAGAGCATTAGCGGCGCTCAGATA
* * * * *
19262762 AAAACGCCGCTAAAGATCGGACCATTAGCGGCGCTAAAATA
1 AAAACGCCGCTAAAGACCAGAGCATTAGCGGCGCTCAGATA
19262803 AAAACGCCGCTAAAG
1 AAAACGCCGCTAAAG
19262818 GTTTAAAAAT
Statistics
Matches: 172, Mismatches: 37, Indels: 18
0.76 0.16 0.08
Matches are distributed among these distances:
38 2 0.01
39 1 0.01
40 55 0.32
41 110 0.64
42 1 0.01
43 2 0.01
44 1 0.01
ACGTcount: A:0.40, C:0.23, G:0.22, T:0.15
Consensus pattern (41 bp):
AAAACGCCGCTAAAGACCAGAGCATTAGCGGCGCTCAGATA
Found at i:19266797 original size:24 final size:24
Alignment explanation
Indices: 19266747--19266801 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 24
19266737 GACTGCGCAA
*
19266747 GAAGGAGCTGGTGAGAGCGTTAGT
1 GAAGGAGCTGGTGAGAGCGTGAGT
*
19266771 GAAGGTGCTGGTGAGAGCGCTGA-T
1 GAAGGAGCTGGTGAGAGCG-TGAGT
19266795 GAAGGAG
1 GAAGGAG
19266802 AGAGGAGAGT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
24 25 0.93
25 2 0.07
ACGTcount: A:0.25, C:0.09, G:0.47, T:0.18
Consensus pattern (24 bp):
GAAGGAGCTGGTGAGAGCGTGAGT
Found at i:19275385 original size:13 final size:11
Alignment explanation
Indices: 19275354--19275395 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 11
19275344 GTATAAATTT
19275354 AATTTTTTATGA
1 AATTTTTTAT-A
19275366 AATTTTTTATA
1 AATTTTTTATA
19275377 AATTCTTTT-TA
1 AATT-TTTTATA
19275388 TAATTTTT
1 -AATTTTT
19275396 AAAATTGTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
11 10 0.36
12 18 0.64
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.64
Consensus pattern (11 bp):
AATTTTTTATA
Found at i:19277566 original size:20 final size:21
Alignment explanation
Indices: 19277530--19277569 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
19277520 TTTGCCCGGG
*
19277530 CCCAAAACTAAATAAATAAAA
1 CCCAAAACTAAAAAAATAAAA
19277551 CCCAAAA-TAAAAAAATAAA
1 CCCAAAACTAAAAAAATAAA
19277570 CAGTCCATAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.70, C:0.17, G:0.00, T:0.12
Consensus pattern (21 bp):
CCCAAAACTAAAAAAATAAAA
Found at i:19288062 original size:16 final size:17
Alignment explanation
Indices: 19288038--19288075 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
19288028 CTCCTTTTTA
*
19288038 TATTTTTCCTTTTCTCT
1 TATTTTCCCTTTTCTCT
*
19288055 TATTTTCCCTTTTCTTT
1 TATTTTCCCTTTTCTCT
19288072 TATT
1 TATT
19288076 AAACTTTACA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.08, C:0.21, G:0.00, T:0.71
Consensus pattern (17 bp):
TATTTTCCCTTTTCTCT
Found at i:19288734 original size:27 final size:28
Alignment explanation
Indices: 19288679--19288756 Score: 113
Period size: 27 Copynumber: 2.8 Consensus size: 28
19288669 GTGTGTCTCC
*
19288679 TATTTTTTAGATTTTATGGTTTTACCCT
1 TATTTTTTAGATTTTACGGTTTTACCCT
* *
19288707 TATTTTTTAGATTCTACAGTTTTA-CCT
1 TATTTTTTAGATTTTACGGTTTTACCCT
*
19288734 TGTTTTTTAGATTTTACGGTTTT
1 TATTTTTTAGATTTTACGGTTTT
19288757 GTCTCTTGCT
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
27 23 0.52
28 21 0.48
ACGTcount: A:0.18, C:0.10, G:0.12, T:0.60
Consensus pattern (28 bp):
TATTTTTTAGATTTTACGGTTTTACCCT
Found at i:19290396 original size:17 final size:16
Alignment explanation
Indices: 19290362--19290417 Score: 55
Period size: 16 Copynumber: 3.6 Consensus size: 16
19290352 AGTATTGAAT
19290362 TATTAATATCTTAATA
1 TATTAATATCTTAATA
19290378 TATTAA-ATCTTTAA-A
1 TATTAATATC-TTAATA
*
19290393 TA-TAATATTTTAAATA
1 TATTAATATCTT-AATA
*
19290409 TTTTAATAT
1 TATTAATAT
19290418 AAAAATTAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
14 5 0.15
15 10 0.30
16 12 0.36
17 6 0.18
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.52
Consensus pattern (16 bp):
TATTAATATCTTAATA
Found at i:19290405 original size:22 final size:22
Alignment explanation
Indices: 19290373--19290427 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
19290363 ATTAATATCT
*
19290373 TAATATATTAAATCTTTAAATA
1 TAATATATTAAATATTTAAATA
* *
19290395 TAATATTTTAAATATTTTAATA
1 TAATATATTAAATATTTAAATA
*
19290417 TAA-AAATTAAA
1 TAATATATTAAA
19290428 AATATTTTAA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
21 6 0.21
22 22 0.79
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (22 bp):
TAATATATTAAATATTTAAATA
Found at i:19290637 original size:16 final size:16
Alignment explanation
Indices: 19290592--19290629 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
19290582 TTGATTATTG
* *
19290592 ATTACAACTTTATTCT
1 ATTATAACTATATTCT
19290608 ATTATAACTATATTCT
1 ATTATAACTATATTCT
19290624 ATTATA
1 ATTATA
19290630 TTAATATTAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.37, C:0.13, G:0.00, T:0.50
Consensus pattern (16 bp):
ATTATAACTATATTCT
Found at i:19295344 original size:23 final size:22
Alignment explanation
Indices: 19295305--19295352 Score: 53
Period size: 22 Copynumber: 2.1 Consensus size: 22
19295295 CAGGCTATAA
*
19295305 TTTTTCAATGTTCTA-TTAATGT
1 TTTTTCAAGGTTCTATTTAAT-T
*
19295327 TTTTTTAAGGTTCTTATTTAATT
1 TTTTTCAAGGTTC-TATTTAATT
19295350 TTT
1 TTT
19295353 AATTGTTGGT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
22 11 0.50
23 6 0.27
24 5 0.23
ACGTcount: A:0.21, C:0.06, G:0.08, T:0.65
Consensus pattern (22 bp):
TTTTTCAAGGTTCTATTTAATT
Found at i:19295388 original size:23 final size:25
Alignment explanation
Indices: 19295362--19295425 Score: 62
Period size: 23 Copynumber: 2.6 Consensus size: 25
19295352 TAATTGTTGG
19295362 TTTTATTTTTATTTATT-TTC-AAT
1 TTTTATTTTTATTTATTCTTCTAAT
* *
19295385 TTTT-TCTTTTATCTCTTCTTCTAAT
1 TTTTAT-TTTTATTTATTCTTCTAAT
19295410 TTTTAATTATTTATTT
1 TTTT-ATT-TTTATTT
19295426 CAAGTTTTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
22 1 0.03
23 13 0.41
24 3 0.09
25 7 0.22
26 1 0.03
27 7 0.22
ACGTcount: A:0.19, C:0.09, G:0.00, T:0.72
Consensus pattern (25 bp):
TTTTATTTTTATTTATTCTTCTAAT
Found at i:19297721 original size:21 final size:19
Alignment explanation
Indices: 19297679--19297722 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 19
19297669 AGTTAGATCA
* *
19297679 TGAATCAATACAAACTGAT
1 TGAATCAATAAAAAATGAT
19297698 TGAATCAACTAAAAAATCGAT
1 TGAATCAA-TAAAAAAT-GAT
19297719 TGAA
1 TGAA
19297723 CTAGATCTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 8 0.38
20 6 0.29
21 7 0.33
ACGTcount: A:0.50, C:0.14, G:0.11, T:0.25
Consensus pattern (19 bp):
TGAATCAATAAAAAATGAT
Found at i:19298294 original size:23 final size:23
Alignment explanation
Indices: 19298242--19298355 Score: 95
Period size: 23 Copynumber: 5.0 Consensus size: 23
19298232 TCTTTGAAGG
* * * *
19298242 CATCATAGAATACACCATAAAGG
1 CATCACAGAATACGCCACAAAGA
* * *
19298265 CAGCACAGAATATGCCATAAAGA
1 CATCACAGAATACGCCACAAAGA
* *
19298288 CATCACA-AGATACGCAACAAATA
1 CATCACAGA-ATACGCCACAAAGA
*
19298311 CATCACAGAATACGCCACAAAGG
1 CATCACAGAATACGCCACAAAGA
* **
19298334 CATCACAAAATACATCACAAAG
1 CATCACAGAATACGCCACAAAG
19298356 GTTTTCAAAA
Statistics
Matches: 73, Mismatches: 16, Indels: 4
0.78 0.17 0.04
Matches are distributed among these distances:
22 1 0.01
23 71 0.97
24 1 0.01
ACGTcount: A:0.49, C:0.25, G:0.12, T:0.13
Consensus pattern (23 bp):
CATCACAGAATACGCCACAAAGA
Found at i:19305778 original size:31 final size:27
Alignment explanation
Indices: 19305740--19305794 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
19305730 TATAATTTCT
*
19305740 ATCAATCAACCATTTCAAACACATACC
1 ATCAATCAATCATTTCAAACACATACC
19305767 ATCAATCAATCATTTCAAACACATACC
1 ATCAATCAATCATTTCAAACACATACC
19305794 A
1 A
19305795 AACATATCCA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.45, C:0.31, G:0.00, T:0.24
Consensus pattern (27 bp):
ATCAATCAATCATTTCAAACACATACC
Found at i:19306686 original size:26 final size:26
Alignment explanation
Indices: 19306657--19306780 Score: 88
Period size: 24 Copynumber: 5.0 Consensus size: 26
19306647 TCCTCTCTCA
19306657 AGCCATATAATAGGAAGCTCACAAAG
1 AGCCATATAATAGGAAGCTCACAAAG
*
19306683 AGCCAT-TAATCGAGAAGCTCACAAAG
1 AGCCATATAATAG-GAAGCTCACAAAG
* *
19306709 AG-C-T-T-ATCAGGAAGCTTATC--TG
1 AGCCATATAAT-AGGAAGCTCA-CAAAG
* *
19306731 -GCTATATAATAGGAAGCTCATAAA-
1 AGCCATATAATAGGAAGCTCACAAAG
* *
19306755 AGCCATA-ATTAGGAAGTTCACAAAG
1 AGCCATATAATAGGAAGCTCACAAAG
19306780 A
1 A
19306781 ACTTTTAATC
Statistics
Matches: 75, Mismatches: 12, Indels: 23
0.68 0.11 0.21
Matches are distributed among these distances:
21 1 0.01
22 1 0.01
23 10 0.13
24 28 0.37
25 14 0.19
26 21 0.28
ACGTcount: A:0.42, C:0.18, G:0.19, T:0.21
Consensus pattern (26 bp):
AGCCATATAATAGGAAGCTCACAAAG
Found at i:19311934 original size:21 final size:22
Alignment explanation
Indices: 19311900--19311945 Score: 76
Period size: 21 Copynumber: 2.1 Consensus size: 22
19311890 CCAGTATTTC
*
19311900 TCTATATTGTCATCCCTATATT
1 TCTATATTGCCATCCCTATATT
19311922 TCTA-ATTGCCATCCCTATATT
1 TCTATATTGCCATCCCTATATT
19311943 TCT
1 TCT
19311946 CTTGTAACTC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 19 0.83
22 4 0.17
ACGTcount: A:0.22, C:0.26, G:0.04, T:0.48
Consensus pattern (22 bp):
TCTATATTGCCATCCCTATATT
Done.