Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032247.1 Gossypioides kirkii chromosome KI_05
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: 50980411
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1700 characters in sequence are not A, C, G, or T
File 86 of 171
Found at i:28264899 original size:21 final size:21
Alignment explanation
Indices: 28264873--28264912 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
28264863 ATGTTTTTAA
28264873 TATTTGTATTATAAATAATAT
1 TATTTGTATTATAAATAATAT
28264894 TATTTGTATTATAAATAAT
1 TATTTGTATTATAAATAAT
28264913 CCCAATTGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (21 bp):
TATTTGTATTATAAATAATAT
Found at i:28264921 original size:21 final size:21
Alignment explanation
Indices: 28264876--28264922 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
28264866 TTTTTAATAT
** *
28264876 TTGTATTATAAATAATATTAT
1 TTGTATTATAAATAATACCAA
*
28264897 TTGTATTATAAATAATCCCAA
1 TTGTATTATAAATAATACCAA
28264918 TTGTA
1 TTGTA
28264923 AATATAAAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.40, C:0.06, G:0.06, T:0.47
Consensus pattern (21 bp):
TTGTATTATAAATAATACCAA
Found at i:28270740 original size:27 final size:25
Alignment explanation
Indices: 28270680--28270745 Score: 69
Period size: 27 Copynumber: 2.5 Consensus size: 25
28270670 ATACTTTTGA
*
28270680 CAAAGGCATCACTAGTGCCGCCTAC
1 CAAAGGCACCACTAGTGCCGCCTAC
* *
28270705 CAAGTAGGCACCATTGGTGCCGCCTACCC
1 CAA--AGGCACCACTAGTGCCGCCTA--C
28270734 CAAAGGCACCAC
1 CAAAGGCACCAC
28270746 CCGTCAAATT
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
25 3 0.09
27 26 0.79
29 4 0.12
ACGTcount: A:0.27, C:0.38, G:0.21, T:0.14
Consensus pattern (25 bp):
CAAAGGCACCACTAGTGCCGCCTAC
Found at i:28271027 original size:2 final size:2
Alignment explanation
Indices: 28271020--28271061 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
28271010 AGGGTTAAAA
*
28271020 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
28271062 TATTTAAGTT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:28276899 original size:52 final size:52
Alignment explanation
Indices: 28276811--28277055 Score: 323
Period size: 52 Copynumber: 4.7 Consensus size: 52
28276801 ATTTCACTTC
* * * * * * * *
28276811 ATTCATTTACTCACGATGTCACATAGCCATCAGACCT-TATAACCCGCAAGGG
1 ATTCATATACTCACGATGACACTTAGTCATCGGACCTCT-TAATCCGTAAAGG
*
28276863 ATTCATATACTCACGATGACA-TAGAGTCATCGGACCTCTTAATCCGTAAAGG
1 ATTCATATACTCACGATGACACT-TAGTCATCGGACCTCTTAATCCGTAAAGG
*
28276915 ATTCATATACTCATGATGACACTTAGTCATCGGACCTCTTAATCCGTAAAGG
1 ATTCATATACTCACGATGACACTTAGTCATCGGACCTCTTAATCCGTAAAGG
* * * *
28276967 ATTCATATACTCATGATGACACTTAGTAATCGAACCTCTTAATTCGTAAAGG
1 ATTCATATACTCACGATGACACTTAGTCATCGGACCTCTTAATCCGTAAAGG
*
28277019 ATTCATATACTCACGATGACACTTAGTCATCGAACCT
1 ATTCATATACTCACGATGACACTTAGTCATCGGACCT
28277056 TTTCGTATAT
Statistics
Matches: 174, Mismatches: 16, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
52 172 0.99
53 2 0.01
ACGTcount: A:0.32, C:0.24, G:0.15, T:0.29
Consensus pattern (52 bp):
ATTCATATACTCACGATGACACTTAGTCATCGGACCTCTTAATCCGTAAAGG
Found at i:28280650 original size:4 final size:4
Alignment explanation
Indices: 28280624--28280663 Score: 55
Period size: 4 Copynumber: 10.0 Consensus size: 4
28280614 TTATATTGAC
*
28280624 ATTT AATTT ATTG ATTT -TTT ATTT ATTT ATTT ATTT ATTT
1 ATTT -ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT
28280664 TTATTTTCAT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
3 3 0.09
4 25 0.78
5 4 0.12
ACGTcount: A:0.25, C:0.00, G:0.03, T:0.72
Consensus pattern (4 bp):
ATTT
Found at i:28280656 original size:23 final size:23
Alignment explanation
Indices: 28280624--28280669 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
28280614 TTATATTGAC
28280624 ATTTAATTTATTGATTTTTTATTT
1 ATTTAATTTATTGA-TTTTTATTT
*
28280648 ATTT-ATTTATTTATTTTTATTT
1 ATTTAATTTATTGATTTTTATTT
28280670 TCATGCCTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 9 0.43
23 8 0.38
24 4 0.19
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.74
Consensus pattern (23 bp):
ATTTAATTTATTGATTTTTATTT
Found at i:28280759 original size:98 final size:96
Alignment explanation
Indices: 28280587--28280770 Score: 216
Period size: 98 Copynumber: 1.9 Consensus size: 96
28280577 TTTTTCTTTT
28280587 TTATTATTATTATTTATATTTAGTTGTTTATATTGACATTTAATTTATTGATTTTTTATTTATTT
1 TTATTATTATTATTTATATTTAGTTGTTTATATTGACATTTAATTTATTGATTTTTTATTTATTT
28280652 ATTTATTTATTTTTATTTTCATGCCTAATCCAA
66 ATTTATTTA--TTTATTTTCATGCCTAATCCAA
* * * * *
28280685 TTATTTTTATTGTTTATATTT-GTTTGTTTGT-TTTAGCATTTAATTT-TT-A-TTTTTGTTTAT
1 TTATTATTATTATTTATATTTAG-TTGTTTATATTGA-CATTTAATTTATTGATTTTTTATTTAT
*
28280745 TTATCTTGTTTTTATTTATTTTCATG
64 TTA--TT-TATTTATTTATTTTCATG
28280771 TCATTTTTTT
Statistics
Matches: 75, Mismatches: 6, Indels: 12
0.81 0.06 0.13
Matches are distributed among these distances:
95 13 0.17
96 13 0.17
97 8 0.11
98 41 0.55
ACGTcount: A:0.22, C:0.05, G:0.07, T:0.66
Consensus pattern (96 bp):
TTATTATTATTATTTATATTTAGTTGTTTATATTGACATTTAATTTATTGATTTTTTATTTATTT
ATTTATTTATTTATTTTCATGCCTAATCCAA
Found at i:28280848 original size:40 final size:41
Alignment explanation
Indices: 28280745--28280848 Score: 94
Period size: 40 Copynumber: 2.6 Consensus size: 41
28280735 TTTTGTTTAT
* *
28280745 TTATCTTG-TTTTTATTTATTT-TCATGTCATTTTTTTCTA
1 TTATCTTGTTTTTTATTTATTTATCATGTCATTTATTGCTA
* *
28280784 -TCTCTT-TTATTATTTTTTATTTTATC-TG-CATTTATTGCTA
1 TTATCTTGTT-TT-TTATTTA-TTTATCATGTCATTTATTGCTA
28280824 TTATCTTGTTTGTTTATTTATTTAT
1 TTATCTTGTTT-TTTATTTATTTAT
28280849 TTATCATTAA
Statistics
Matches: 51, Mismatches: 6, Indels: 15
0.71 0.08 0.21
Matches are distributed among these distances:
38 6 0.12
39 2 0.04
40 21 0.41
41 17 0.33
42 5 0.10
ACGTcount: A:0.16, C:0.10, G:0.06, T:0.68
Consensus pattern (41 bp):
TTATCTTGTTTTTTATTTATTTATCATGTCATTTATTGCTA
Found at i:28283797 original size:195 final size:192
Alignment explanation
Indices: 28283467--28283902 Score: 585
Period size: 195 Copynumber: 2.3 Consensus size: 192
28283457 GTGATGGTTA
* * * * * *
28283467 AGGTACCACATACGTTGCAAGTTCTCGACAGCTCGTGTGAGCAACATCGTGAGTCAAAATGAAAA
1 AGGTACCGCATATGTTGCGAGTCCTCGACAGCTCGTGTGAGCAGCATCGTAAGTCAAAATGAAAA
*
28283532 ATGAATCCAAGAATGGATTACAGGCCCTACGATGGCTAGGATTTATGCTTAAGTGCATATTCTCG
66 ATGAATCCAAGAATGGATTACAGACCCTACGATGGCTAGGATTTATGCTTAAGTGCATATTCTCG
** * *
28283597 ACAGCTTGTGTGAGCAGCATCGTTAGGGGACAATTATA-TGCACAGATATCGTATCGATAGCTG
131 ACAGCTCATGTGAGCAGCATCGTTAGGGGACAATT-TACAG-ACAGACATCGTATCGATAGCTG
* * *
28283660 AGGTACCGCATTTGTTGCGAGTCCTCGACAGCTCGTGTGAGCAGCATCGTAAGTCGGAAGA-GAG
1 AGGTACCGCATATGTTGCGAGTCCTCGACAGCTCGTGTGAGCAGCATCGTAAGTC--AAAATGAA
* * *
28283724 ATATGAAATCCTAA-AATGGATTACAGACTCTACGATGGCT-GAGATTTATGTTTGAA-TGCATA
64 AAATG-AATCC-AAGAATGGATTACAGACCCTACGATGGCTAG-GATTTATGCTT-AAGTGCATA
* *
28283786 TTCTCGACAGCTCATGTGAGCAGCATCGTTAGGGGACAGTTTACAGACAGACATCGTATCGATGG
125 TTCTCGACAGCTCATGTGAGCAGCATCGTTAGGGGACAATTTACAGACAGACATCGTATCGATAG
28283851 CTG
190 CTG
*
28283854 AGGTACCGCATATGTTGCGAGTCCTCGACAGCTCGTATGAGCAGCATCG
1 AGGTACCGCATATGTTGCGAGTCCTCGACAGCTCGTGTGAGCAGCATCG
28283903 GGTATTGGTA
Statistics
Matches: 215, Mismatches: 21, Indels: 13
0.86 0.08 0.05
Matches are distributed among these distances:
193 48 0.22
194 76 0.35
195 87 0.40
196 4 0.02
ACGTcount: A:0.28, C:0.20, G:0.26, T:0.26
Consensus pattern (192 bp):
AGGTACCGCATATGTTGCGAGTCCTCGACAGCTCGTGTGAGCAGCATCGTAAGTCAAAATGAAAA
ATGAATCCAAGAATGGATTACAGACCCTACGATGGCTAGGATTTATGCTTAAGTGCATATTCTCG
ACAGCTCATGTGAGCAGCATCGTTAGGGGACAATTTACAGACAGACATCGTATCGATAGCTG
Found at i:28286929 original size:24 final size:24
Alignment explanation
Indices: 28286902--28286949 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
28286892 CAGGCAAAAG
28286902 TTCAATTTGGAAATTAAAGAAATA
1 TTCAATTTGGAAATTAAAGAAATA
28286926 TTCAATTTGGAAATTAAAGAAATA
1 TTCAATTTGGAAATTAAAGAAATA
28286950 AGATGTCACG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.50, C:0.04, G:0.12, T:0.33
Consensus pattern (24 bp):
TTCAATTTGGAAATTAAAGAAATA
Found at i:28288828 original size:14 final size:14
Alignment explanation
Indices: 28288787--28288830 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
28288777 CAAAAGTCGA
*
28288787 AAAATACAAAAAAT
1 AAAATACAAAAATT
28288801 AAAATA-AACCAAATT
1 AAAATACAA--AAATT
28288816 AAAATACAAAAATT
1 AAAATACAAAAATT
28288830 A
1 A
28288831 TATTTATAGA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
13 2 0.08
14 12 0.46
15 10 0.38
16 2 0.08
ACGTcount: A:0.73, C:0.09, G:0.00, T:0.18
Consensus pattern (14 bp):
AAAATACAAAAATT
Found at i:28290498 original size:414 final size:414
Alignment explanation
Indices: 28289728--28290561 Score: 1294
Period size: 414 Copynumber: 2.0 Consensus size: 414
28289718 ATCTCGCATA
* *
28289728 TGTTTATTAGGGTAAGCACACGCTGCCAAGATATACCCTTCACTGTCTCTTGCAATAATCCTTGA
1 TGTTTATTAGGGTAAACACACACTGCCAAGATATACCCTTCACTGTCTCTTGCAATAATCCTTGA
*
28289793 AATTGAGTTGTTTGTATGGCTGTCATAACATGCGTCGAAATTTATTTTGATAATGTCCTCTGTCG
66 AATTGAGTTGTTTGTATGGCTATCATAACATGCGTCGAAATTTATTTTGATAATGTCCTCTGTCG
* * * * *
28289858 GCGGTTTCCATCTAGTGATTTGTCTTTCTGGCACACTGTTTGAAATAGCACTTAGGCTATCTATT
131 ACGGCTGCCATCTAGTGATTTGTCTTTCTGGCACACTATTTGAAATAGCACTTAGGCTATCTAAT
* * *
28289923 TCAGAGATGAAGGCATTTATGAACGAAATTACTCTGAATGTGTTTTGACCTACTCCAGTATGATA
196 TCAAAGATGAAGGCATTTATGAACAAAATTACTCTGAATGTGTTTTGACCTACTCCAATATGATA
* *
28289988 CACCTTGTTGTGATTATACCAAAGTGCCCAGAATGTTACTACAAATTTTCTTATTGATAATGTGT
261 CACCTTGTTGCGATTATACCAAAGTGCCCAGAATGTTACTACAAATTTTCTTATAGATAATGTGT
* * * * *
28290053 TGGTTGTTACTAGTTTTATTGCTAACCAATCTTTCCATCTTTTATCCGTACTGTTGGTCGAGTAT
326 TGGTTGTTACTAGTTCTATTGCTAACCAATCTTTCCATCTTTGATCCATACTATTGATCGAGTAT
* * *
28290118 GCTACGCGAACACTCTTCAAG-ACT
391 GCGACGCCAACACTCTGC-AGCACT
* * *
28290142 TGTTTATTAGGGTAAACACACACTGCCAAGATATACCTTTCATTTTCTCTTGCAATAATCCTTGA
1 TGTTTATTAGGGTAAACACACACTGCCAAGATATACCCTTCACTGTCTCTTGCAATAATCCTTGA
* * * *
28290207 AATTGAGTTGTTTGTATGGCTATCATAACATGTGTCGAAATTTATTTTGATAGTGTCCTTTGTTG
66 AATTGAGTTGTTTGTATGGCTATCATAACATGCGTCGAAATTTATTTTGATAATGTCCTCTGTCG
*
28290272 ACGGCTGCCATCTAGTGATTTTTCTTTCTGGCACACTATTTGAAATAGCACTTAGGCTATCTAAT
131 ACGGCTGCCATCTAGTGATTTGTCTTTCTGGCACACTATTTGAAATAGCACTTAGGCTATCTAAT
* * ** *
28290337 TCAAAGATGAAGGCATTTGTGAACAAAATTACT-TCGAATGTGTTTTGACTTGGTTCAATATGAT
196 TCAAAGATGAAGGCATTTATGAACAAAATTACTCT-GAATGTGTTTTGACCTACTCCAATATGAT
* *
28290401 ACACCTTGTTGCGATTATGCCAAAGTGCCCAGAATGTTACTACAAGTTTTCTTATAGATAATGTG
260 ACACCTTGTTGCGATTATACCAAAGTGCCCAGAATGTTACTACAAATTTTCTTATAGATAATGTG
*
28290466 TTGGTTGTTACTAGTTCTGTTGCTAACCAATCTTTCCATCTTTGATCCATACTATTGATCGAGTA
325 TTGGTTGTTACTAGTTCTATTGCTAACCAATCTTTCCATCTTTGATCCATACTATTGATCGAGTA
*
28290531 TGCGACTCCAACACTCTGCAGCACT
390 TGCGACGCCAACACTCTGCAGCACT
28290556 TGTTTA
1 TGTTTA
28290562 GAGAACGGAC
Statistics
Matches: 380, Mismatches: 38, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
413 3 0.01
414 377 0.99
ACGTcount: A:0.26, C:0.19, G:0.18, T:0.38
Consensus pattern (414 bp):
TGTTTATTAGGGTAAACACACACTGCCAAGATATACCCTTCACTGTCTCTTGCAATAATCCTTGA
AATTGAGTTGTTTGTATGGCTATCATAACATGCGTCGAAATTTATTTTGATAATGTCCTCTGTCG
ACGGCTGCCATCTAGTGATTTGTCTTTCTGGCACACTATTTGAAATAGCACTTAGGCTATCTAAT
TCAAAGATGAAGGCATTTATGAACAAAATTACTCTGAATGTGTTTTGACCTACTCCAATATGATA
CACCTTGTTGCGATTATACCAAAGTGCCCAGAATGTTACTACAAATTTTCTTATAGATAATGTGT
TGGTTGTTACTAGTTCTATTGCTAACCAATCTTTCCATCTTTGATCCATACTATTGATCGAGTAT
GCGACGCCAACACTCTGCAGCACT
Found at i:28295658 original size:30 final size:30
Alignment explanation
Indices: 28295622--28295693 Score: 83
Period size: 31 Copynumber: 2.4 Consensus size: 30
28295612 TGTATACATG
*
28295622 AACTTTAATTTGGTAT-AATTATACACGTGA
1 AACTTTAATTTGGT-TCAAATATACACGTGA
* * *
28295652 AACTTTAATTATGGTTCAAATGTATACTTGA
1 AACTTTAATT-TGGTTCAAATATACACGTGA
28295683 AACTTTAATTT
1 AACTTTAATTT
28295694 TGATTTAATC
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
30 12 0.33
31 24 0.67
ACGTcount: A:0.36, C:0.10, G:0.11, T:0.43
Consensus pattern (30 bp):
AACTTTAATTTGGTTCAAATATACACGTGA
Found at i:28295790 original size:29 final size:30
Alignment explanation
Indices: 28295709--28295790 Score: 87
Period size: 29 Copynumber: 2.8 Consensus size: 30
28295699 TAATCATGCA
*
28295709 TATTTAAATAATAAATAAATAT-ATCAATT
1 TATTTATATAATAAATAAATATAATCAATT
* * * *
28295738 TATTTTTATATTAGATAAATATAAT-TATT
1 TATTTATATAATAAATAAATATAATCAATT
* *
28295767 TATTTATGTAATATATAAATATAA
1 TATTTATATAATAAATAAATATAA
28295791 AATAATATTA
Statistics
Matches: 43, Mismatches: 9, Indels: 2
0.80 0.17 0.04
Matches are distributed among these distances:
29 41 0.95
30 2 0.05
ACGTcount: A:0.49, C:0.01, G:0.02, T:0.48
Consensus pattern (30 bp):
TATTTATATAATAAATAAATATAATCAATT
Found at i:28295849 original size:16 final size:15
Alignment explanation
Indices: 28295828--28295879 Score: 52
Period size: 16 Copynumber: 3.4 Consensus size: 15
28295818 ATAATTTGCA
28295828 AAAATTAAATCAAATC
1 AAAATTAAA-CAAATC
* *
28295844 AAAATTACACATAT-
1 AAAATTAAACAAATC
*
28295858 AAAATTATACAAAATC
1 AAAATTAAAC-AAATC
28295874 AAAATT
1 AAAATT
28295880 TATTTATATA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
14 9 0.30
15 7 0.23
16 14 0.47
ACGTcount: A:0.62, C:0.12, G:0.00, T:0.27
Consensus pattern (15 bp):
AAAATTAAACAAATC
Found at i:28301355 original size:19 final size:19
Alignment explanation
Indices: 28301331--28301370 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
28301321 TTGTACCTTC
* *
28301331 AAATAATAAAACTTATTTT
1 AAATAAAAAAACATATTTT
*
28301350 AAATAAAAAAAGATATTTT
1 AAATAAAAAAACATATTTT
28301369 AA
1 AA
28301371 TAGTTTCCTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.60, C:0.03, G:0.03, T:0.35
Consensus pattern (19 bp):
AAATAAAAAAACATATTTT
Found at i:28304782 original size:18 final size:18
Alignment explanation
Indices: 28304760--28304804 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
28304750 ATAAAATATA
*
28304760 TAAAAATATT-AAAAATT
1 TAAAAAAATTCAAAAATT
*
28304777 TAAAAAAATTCAAATATT
1 TAAAAAAATTCAAAAATT
28304795 TAAAATAAAT
1 TAAAA-AAAT
28304805 CATTCACATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 9 0.38
18 11 0.46
19 4 0.17
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (18 bp):
TAAAAAAATTCAAAAATT
Found at i:28305517 original size:3 final size:3
Alignment explanation
Indices: 28305509--28305551 Score: 77
Period size: 3 Copynumber: 14.0 Consensus size: 3
28305499 AGTAGTTACT
28305509 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTAA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA
28305552 AAAAAAATTC
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 36 0.92
4 3 0.08
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:28312774 original size:58 final size:58
Alignment explanation
Indices: 28312686--28312831 Score: 174
Period size: 58 Copynumber: 2.5 Consensus size: 58
28312676 ATATATTATA
* *
28312686 ATTTTTACT-AATTCATATTTTAATAATAATTATATTAAAA-AT-ATT-ATTAAATTACAT
1 ATTTTTATTAAATT-ATA-TTTAATAATAATTATATTAAAATATAATTAAATAAATTA-AT
* *
28312743 ATTATTTTATTAAATTGTATTTAATAATAATTATGTTAAAATATAATTAAATAAATTAAT
1 A-T-TTTTATTAAATTATATTTAATAATAATTATATTAAAATATAATTAAATAAATTAAT
*
28312803 ATTTTTATTCAATTATATTTAATAATAAT
1 ATTTTTATTAAATTATATTTAATAATAAT
28312832 CATTAAAATT
Statistics
Matches: 77, Mismatches: 6, Indels: 11
0.82 0.06 0.12
Matches are distributed among these distances:
57 1 0.01
58 47 0.61
59 11 0.14
60 10 0.13
61 8 0.10
ACGTcount: A:0.46, C:0.03, G:0.01, T:0.50
Consensus pattern (58 bp):
ATTTTTATTAAATTATATTTAATAATAATTATATTAAAATATAATTAAATAAATTAAT
Found at i:28313022 original size:16 final size:16
Alignment explanation
Indices: 28313001--28313072 Score: 90
Period size: 16 Copynumber: 4.5 Consensus size: 16
28312991 TGAATTACTG
28313001 ATTACAGCTATATTCC
1 ATTACAGCTATATTCC
28313017 ATTACAGCTATATTCC
1 ATTACAGCTATATTCC
* * *
28313033 ATTACAGTTTTATTCT
1 ATTACAGCTATATTCC
* * *
28313049 ATTACACCTCTATTCT
1 ATTACAGCTATATTCC
28313065 ATTACAGC
1 ATTACAGC
28313073 GAACCAAACG
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 49 1.00
ACGTcount: A:0.29, C:0.24, G:0.06, T:0.42
Consensus pattern (16 bp):
ATTACAGCTATATTCC
Found at i:28315805 original size:29 final size:26
Alignment explanation
Indices: 28315738--28315793 Score: 103
Period size: 26 Copynumber: 2.2 Consensus size: 26
28315728 TCGTTGGATT
28315738 TTTTTATATTTTTATTACGTGCATAA
1 TTTTTATATTTTTATTACGTGCATAA
*
28315764 TTTTTATATTTTTATTATGTGCATAA
1 TTTTTATATTTTTATTACGTGCATAA
28315790 TTTT
1 TTTT
28315794 GGTTAAGTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.25, C:0.05, G:0.07, T:0.62
Consensus pattern (26 bp):
TTTTTATATTTTTATTACGTGCATAA
Found at i:28317074 original size:12 final size:12
Alignment explanation
Indices: 28317057--28317082 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
28317047 CTCAACATTG
28317057 AGTATAAATAAT
1 AGTATAAATAAT
28317069 AGTATAAATAAT
1 AGTATAAATAAT
28317081 AG
1 AG
28317083 GATTCGTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.58, C:0.00, G:0.12, T:0.31
Consensus pattern (12 bp):
AGTATAAATAAT
Found at i:28320217 original size:20 final size:19
Alignment explanation
Indices: 28320185--28320259 Score: 80
Period size: 20 Copynumber: 3.7 Consensus size: 19
28320175 AAATTCTTGA
28320185 AATAATTCTTTTTCTAACT
1 AATAATTCTTTTTCTAACT
28320204 AATAATTCCTTTTT-TAATAGCT
1 AATAATT-CTTTTTCT-A-A-CT
* *
28320226 AATAATTCTTTTTAATAGCT
1 AATAATTCTTTTT-CTAACT
28320246 AATAATTCTTTTTC
1 AATAATTCTTTTTC
28320260 AGGAAAGAAA
Statistics
Matches: 48, Mismatches: 2, Indels: 12
0.77 0.03 0.19
Matches are distributed among these distances:
19 8 0.17
20 22 0.46
21 7 0.15
22 10 0.21
23 1 0.02
ACGTcount: A:0.32, C:0.13, G:0.03, T:0.52
Consensus pattern (19 bp):
AATAATTCTTTTTCTAACT
Found at i:28331985 original size:26 final size:26
Alignment explanation
Indices: 28331940--28331995 Score: 71
Period size: 25 Copynumber: 2.2 Consensus size: 26
28331930 AATTTATAAC
*
28331940 TTTATTTTTCTAATTTTTAA-TAAAT
1 TTTATTTTTCTAATTTTTAATTAAAA
28331965 TTTATTTTT-TATATTTGTTAATTAAAA
1 TTTATTTTTCTA-ATTT-TTAATTAAAA
28331992 TTTA
1 TTTA
28331996 ATAAATTTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
24 2 0.07
25 13 0.48
26 4 0.15
27 8 0.30
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (26 bp):
TTTATTTTTCTAATTTTTAATTAAAA
Found at i:28334634 original size:92 final size:89
Alignment explanation
Indices: 28334477--28334685 Score: 258
Period size: 92 Copynumber: 2.3 Consensus size: 89
28334467 GTAATTTTTT
*
28334477 TTAA-TGCTTTTTTTGAAAAAAATTTGAGGGTCTTTCTGATGCATTTTGAAAGTTCAAGTATCCA
1 TTAATTGCTTTTTTTG-AAAAAATTTGAGGGTCTTTCTGATGCATTTTGAAAGTTCAAGTACCCA
* *
28334541 ATTGAGTACAAAAAAAAAGATAGGGAC
65 ATTGAATACAAAAAAAAAG-CAGGG-C
* * * * *
28334568 TTAATTGCTTTTTTTTGAAAAAGTTTGAGTGTCTTTTTTATGCATTTTGATAGTTCAAGTACCCA
1 TTAATTGC-TTTTTTTGAAAAAATTTGAGGGTCTTTCTGATGCATTTTGAAAGTTCAAGTACCCA
* * *
28334633 ATTGAATGCAAAAAGAAAGCAGGGG
65 ATTGAATACAAAAAAAAAGCAGGGC
*
28334658 TTCAATAGCTTTTTTTGAAAAAATTTGA
1 TT-AATTGCTTTTTTTGAAAAAATTTGA
28334686 AGGCTTTTTA
Statistics
Matches: 102, Mismatches: 13, Indels: 7
0.84 0.11 0.06
Matches are distributed among these distances:
90 20 0.20
91 13 0.13
92 61 0.60
93 8 0.08
ACGTcount: A:0.34, C:0.10, G:0.18, T:0.38
Consensus pattern (89 bp):
TTAATTGCTTTTTTTGAAAAAATTTGAGGGTCTTTCTGATGCATTTTGAAAGTTCAAGTACCCAA
TTGAATACAAAAAAAAAGCAGGGC
Found at i:28348493 original size:29 final size:30
Alignment explanation
Indices: 28348461--28348538 Score: 88
Period size: 30 Copynumber: 2.6 Consensus size: 30
28348451 TCGGGGGGCA
*
28348461 AAAATGGAATTTTTGGACA-TTTGAGGGTC
1 AAAATGGAATTTTTGGACAGTTCGAGGGTC
* * *
28348490 AAAATGTAATTTTTAGAAAGTTCGAGGGTC
1 AAAATGGAATTTTTGGACAGTTCGAGGGTC
*
28348520 AAAATATG-ATTTTTGGACA
1 AAAAT-GGAATTTTTGGACA
28348539 ATTTAGAGAC
Statistics
Matches: 39, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
29 16 0.41
30 23 0.59
ACGTcount: A:0.36, C:0.06, G:0.23, T:0.35
Consensus pattern (30 bp):
AAAATGGAATTTTTGGACAGTTCGAGGGTC
Found at i:28349696 original size:13 final size:13
Alignment explanation
Indices: 28349678--28349729 Score: 52
Period size: 13 Copynumber: 4.1 Consensus size: 13
28349668 TTTTATTAAC
*
28349678 ATTTATTAATGTT
1 ATTTATTAATATT
*
28349691 ATTTATTACTATT
1 ATTTATTAATATT
*
28349704 ATTTATTATTATT
1 ATTTATTAATATT
* *
28349717 -GTTATTATTATT
1 ATTTATTAATATT
28349729 A
1 A
28349730 ATCGTTTTTA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
12 11 0.32
13 23 0.68
ACGTcount: A:0.31, C:0.02, G:0.04, T:0.63
Consensus pattern (13 bp):
ATTTATTAATATT
Found at i:28354995 original size:16 final size:15
Alignment explanation
Indices: 28354974--28355003 Score: 51
Period size: 15 Copynumber: 1.9 Consensus size: 15
28354964 AATTATTTAA
28354974 TTAAAAATATTAAATT
1 TTAAAAA-ATTAAATT
28354990 TTAAAAAATTAAAT
1 TTAAAAAATTAAAT
28355004 ATTCATTCCA
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:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
TTAAAAAATTAAATT
Found at i:28359290 original size:24 final size:23
Alignment explanation
Indices: 28359263--28359313 Score: 61
Period size: 22 Copynumber: 2.2 Consensus size: 23
28359253 TTTATGTGTT
*
28359263 TATTTTTA-AATTTATTAAATAATA
1 TATTTTTATAA-TT-TTAAAAAATA
28359287 TA-TTTTATAATTTTAAAAAATA
1 TATTTTTATAATTTTAAAAAATA
28359309 TATTT
1 TATTT
28359314 GACAATTAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
22 11 0.46
23 9 0.38
24 4 0.17
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (23 bp):
TATTTTTATAATTTTAAAAAATA
Found at i:28359320 original size:22 final size:22
Alignment explanation
Indices: 28359277--28359320 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
28359267 TTTAAATTTA
* * *
28359277 TTAAATAATATATTTTATAATT
1 TTAAAAAATATATTTGACAATT
28359299 TTAAAAAATATATTTGACAATT
1 TTAAAAAATATATTTGACAATT
28359321 AAATGAGAAC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (22 bp):
TTAAAAAATATATTTGACAATT
Found at i:28360831 original size:17 final size:18
Alignment explanation
Indices: 28360809--28360850 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
28360799 AATTGTTATC
28360809 ATATTTAAAAT-AAAATT
1 ATATTTAAAATAAAAATT
* *
28360826 ATATTTTTATATAAAAATT
1 ATA-TTTAAAATAAAAATT
28360845 ATATTT
1 ATATTT
28360851 TTTAAATTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
17 3 0.14
18 9 0.43
19 9 0.43
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
ATATTTAAAATAAAAATT
Found at i:28362789 original size:23 final size:22
Alignment explanation
Indices: 28362759--28362934 Score: 99
Period size: 25 Copynumber: 7.5 Consensus size: 22
28362749 ACACTAGCGC
28362759 GCTCTCTGTTTAGCACGTCTTGT
1 GCTCTCTGTTTAGCACGT-TTGT
*
28362782 GCTCTCTGTTATTAGCACTGTGTGT
1 GCTCTCTG-T-TTAGCAC-GTTTGT
* **
28362807 GCTCTCTGATTAGCAATTTGTGT
1 GCTCTCTGTTTAGCACGTT-TGT
* *
28362830 GCTCTCTGATTAGTAC-TTTGT
1 GCTCTCTGTTTAGCACGTTTGT
*
28362851 GTACTCTCTGTTATTAGCACTGTGTGT
1 G--CTCTCTG-T-TTAGCAC-GTTTGT
*
28362878 GCTCTCTGTTGCCCAGCAC-TTATGT
1 GCTCTCTGTT---TAGCACGTT-TGT
*
28362903 GCTCTCTG-TTAGTAC-TTTGGT
1 GCTCTCTGTTTAGCACGTTT-GT
*
28362924 ACTCTCTGTTT
1 GCTCTCTGTTT
28362935 GTTCCGTATA
Statistics
Matches: 122, Mismatches: 15, Indels: 33
0.72 0.09 0.19
Matches are distributed among these distances:
20 1 0.01
21 19 0.16
22 5 0.04
23 39 0.32
24 4 0.03
25 42 0.34
26 7 0.06
27 5 0.04
ACGTcount: A:0.12, C:0.22, G:0.21, T:0.44
Consensus pattern (22 bp):
GCTCTCTGTTTAGCACGTTTGT
Found at i:28362796 original size:25 final size:23
Alignment explanation
Indices: 28362759--28362886 Score: 111
Period size: 23 Copynumber: 5.4 Consensus size: 23
28362749 ACACTAGCGC
28362759 GCTCTCTGT-TTAGCACGTCTTGT
1 GCTCTCTGTATTAGCACGT-TTGT
*
28362782 GCTCTCTGTTATTAGCACTGTGTGT
1 GCTCTCTG-TATTAGCAC-GTTTGT
**
28362807 GCTCTCTG-ATTAGCAATTTGTGT
1 GCTCTCTGTATTAGCACGTT-TGT
*
28362830 GCTCTCTG-ATTAGTAC-TTTGT
1 GCTCTCTGTATTAGCACGTTTGT
*
28362851 GTACTCTCTGTTATTAGCACTGTGTGT
1 G--CTCTCTG-TATTAGCAC-GTTTGT
28362878 GCTCTCTGT
1 GCTCTCTGT
28362887 TGCCCAGCAC
Statistics
Matches: 87, Mismatches: 8, Indels: 19
0.76 0.07 0.17
Matches are distributed among these distances:
21 4 0.05
22 3 0.03
23 39 0.45
24 2 0.02
25 32 0.37
26 2 0.02
27 5 0.06
ACGTcount: A:0.12, C:0.21, G:0.22, T:0.45
Consensus pattern (23 bp):
GCTCTCTGTATTAGCACGTTTGT
Found at i:28362858 original size:71 final size:69
Alignment explanation
Indices: 28362783--28362933 Score: 216
Period size: 71 Copynumber: 2.1 Consensus size: 69
28362773 ACGTCTTGTG
* *
28362783 CTCTCTGTTATTAGCACTGTGTGTGCTCTCTGATTAG-CA-ATTTGTGTGCTCTCTGATTAGTAC
1 CTCTCTGTTATTAGCACTGTGTGTGCTCTCTG-TT-GCCACACTTATGTGCTCTCTG-TTAGTAC
28362846 TTTGTGTA
63 TTTG-GTA
28362854 CTCTCTGTTATTAGCACTGTGTGTGCTCTCTGTTGCCCAGCACTTATGTGCTCTCTGTTAGTACT
1 CTCTCTGTTATTAGCACTGTGTGTGCTCTCTGTTG-CCA-CACTTATGTGCTCTCTGTTAGTACT
28362919 TTGGTA
64 TTGGTA
28362925 CTCTCTGTT
1 CTCTCTGTT
28362934 TGTTCCGTAT
Statistics
Matches: 74, Mismatches: 2, Indels: 8
0.88 0.02 0.10
Matches are distributed among these distances:
69 1 0.01
70 2 0.03
71 46 0.62
72 11 0.15
73 14 0.19
ACGTcount: A:0.13, C:0.22, G:0.21, T:0.44
Consensus pattern (69 bp):
CTCTCTGTTATTAGCACTGTGTGTGCTCTCTGTTGCCACACTTATGTGCTCTCTGTTAGTACTTT
GGTA
Found at i:28362887 original size:25 final size:25
Alignment explanation
Indices: 28362759--28362913 Score: 146
Period size: 25 Copynumber: 6.4 Consensus size: 25
28362749 ACACTAGCGC
*
28362759 GCTCTCTG-T-TTAGCAC-GTCTTGT
1 GCTCTCTGTTATTAGCACTGT-GTGT
28362782 GCTCTCTGTTATTAGCACTGTGTGT
1 GCTCTCTGTTATTAGCACTGTGTGT
* *
28362807 GCTCTCTG--ATTAGCAATTTGTGT
1 GCTCTCTGTTATTAGCACTGTGTGT
* *
28362830 GCTCTCTG--ATTAGTACTTTGTGT
1 GCTCTCTGTTATTAGCACTGTGTGT
*
28362853 ACTCTCTGTTATTAGCACTGTGTGT
1 GCTCTCTGTTATTAGCACTGTGTGT
*** *
28362878 GCTCTCTGTTGCCCAGCACT-TATGT
1 GCTCTCTGTT-ATTAGCACTGTGTGT
28362903 GCTCTCTGTTA
1 GCTCTCTGTTA
28362914 GTACTTTGGT
Statistics
Matches: 112, Mismatches: 14, Indels: 11
0.82 0.10 0.08
Matches are distributed among these distances:
23 49 0.44
24 1 0.01
25 54 0.48
26 8 0.07
ACGTcount: A:0.13, C:0.23, G:0.21, T:0.43
Consensus pattern (25 bp):
GCTCTCTGTTATTAGCACTGTGTGT
Found at i:28364274 original size:21 final size:21
Alignment explanation
Indices: 28364250--28364291 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
28364240 TTTAAAAATA
28364250 GTTAATTAGATAAACTAGAAT
1 GTTAATTAGATAAACTAGAAT
*
28364271 GTTATTTAGATAAACTAGAAT
1 GTTAATTAGATAAACTAGAAT
28364292 ATTTGACTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.45, C:0.05, G:0.14, T:0.36
Consensus pattern (21 bp):
GTTAATTAGATAAACTAGAAT
Found at i:28365627 original size:5 final size:6
Alignment explanation
Indices: 28365610--28365637 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
28365600 ATTATTATAA
28365610 TATTTT TATTTT TATTTT TATTTT TATT
1 TATTTT TATTTT TATTTT TATTTT TATT
28365638 AATTTTTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (6 bp):
TATTTT
Found at i:28366668 original size:40 final size:41
Alignment explanation
Indices: 28366624--28366733 Score: 136
Period size: 40 Copynumber: 2.7 Consensus size: 41
28366614 AATATTTACT
*
28366624 GAACTGGCAGTGACATTGTAAACACTGCAAC-ATAT-CAATC
1 GAACTGGCAGTGACACTGTAAACACTGCAACGAT-TGCAATC
* * *
28366664 GAACTGGCAATGACACTGTAAACACTGC-GCGATTGCAATT
1 GAACTGGCAGTGACACTGTAAACACTGCAACGATTGCAATC
* *
28366704 GAATTGGCAGTGAAACTGTAAACACTGCAA
1 GAACTGGCAGTGACACTGTAAACACTGCAA
28366734 TGTGTTAGAT
Statistics
Matches: 59, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
39 2 0.03
40 57 0.97
ACGTcount: A:0.36, C:0.21, G:0.21, T:0.22
Consensus pattern (41 bp):
GAACTGGCAGTGACACTGTAAACACTGCAACGATTGCAATC
Found at i:28367659 original size:13 final size:13
Alignment explanation
Indices: 28367621--28367666 Score: 65
Period size: 13 Copynumber: 3.4 Consensus size: 13
28367611 TATATAGTGT
*
28367621 TAATATATGATACA
1 TAATATATTATA-A
28367635 TAATAGTATTATAA
1 TAATA-TATTATAA
28367649 TAATATATTATAA
1 TAATATATTATAA
28367662 TAATA
1 TAATA
28367667 AAAAATAGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
13 13 0.43
14 11 0.37
15 6 0.20
ACGTcount: A:0.52, C:0.02, G:0.04, T:0.41
Consensus pattern (13 bp):
TAATATATTATAA
Found at i:28368800 original size:17 final size:17
Alignment explanation
Indices: 28368778--28368811 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
28368768 GGTTGATATG
* *
28368778 GAAAATGTTATTGAAAT
1 GAAAATGATATTAAAAT
28368795 GAAAATGATATTAAAAT
1 GAAAATGATATTAAAAT
28368812 AACGAGTGAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.53, C:0.00, G:0.15, T:0.32
Consensus pattern (17 bp):
GAAAATGATATTAAAAT
Found at i:28374012 original size:24 final size:24
Alignment explanation
Indices: 28373951--28374013 Score: 81
Period size: 24 Copynumber: 2.6 Consensus size: 24
28373941 TAGACTAATA
* *
28373951 AGAGTTTGACTCAAACAAATAAAT
1 AGAGTTTAACTGAAACAAATAAAT
* * *
28373975 AAAGTTTAATTGAAACAAATGAAT
1 AGAGTTTAACTGAAACAAATAAAT
28373999 AGAGTTTAACTGAAA
1 AGAGTTTAACTGAAA
28374014 GATTATTTTT
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.51, C:0.08, G:0.14, T:0.27
Consensus pattern (24 bp):
AGAGTTTAACTGAAACAAATAAAT
Found at i:28376023 original size:24 final size:24
Alignment explanation
Indices: 28375928--28376026 Score: 90
Period size: 24 Copynumber: 4.1 Consensus size: 24
28375918 TAAAATAATC
* * *
28375928 TAAACTAATAAGAGTTTGACTTAAA
1 TAAA-TAAAAAGAGTTTAACTGAAA
* * *
28375953 CAAATAAAAAGAGTTTAATTAAAA
1 TAAATAAAAAGAGTTTAACTGAAA
* * *
28375977 TAAATAAACAGAGCTTAATTGAAA
1 TAAATAAAAAGAGTTTAACTGAAA
* *
28376001 TAATTAAATAGAGTTTAACTGAAA
1 TAAATAAAAAGAGTTTAACTGAAA
28376025 TA
1 TA
28376027 TTATTTTTCA
Statistics
Matches: 61, Mismatches: 13, Indels: 1
0.81 0.17 0.01
Matches are distributed among these distances:
24 58 0.95
25 3 0.05
ACGTcount: A:0.54, C:0.06, G:0.11, T:0.29
Consensus pattern (24 bp):
TAAATAAAAAGAGTTTAACTGAAA
Found at i:28376802 original size:46 final size:46
Alignment explanation
Indices: 28376728--28376829 Score: 170
Period size: 46 Copynumber: 2.2 Consensus size: 46
28376718 ACATCCTTAT
* *
28376728 TTAA-TTTTGTATTTATTTATTTTACAAATAGTTGTGTTGATTTAA
1 TTAAGTTTTTTATTTATTCATTTTACAAATAGTTGTGTTGATTTAA
*
28376773 TTAGGTTTTTTATTTATTCATTTTACAAATAGTTGTGTTGATTTAA
1 TTAAGTTTTTTATTTATTCATTTTACAAATAGTTGTGTTGATTTAA
28376819 TTAAGTTTTTT
1 TTAAGTTTTTT
28376830 TTAATTACAA
Statistics
Matches: 52, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
45 3 0.06
46 49 0.94
ACGTcount: A:0.26, C:0.03, G:0.12, T:0.59
Consensus pattern (46 bp):
TTAAGTTTTTTATTTATTCATTTTACAAATAGTTGTGTTGATTTAA
Found at i:28387263 original size:30 final size:30
Alignment explanation
Indices: 28387187--28387252 Score: 98
Period size: 30 Copynumber: 2.2 Consensus size: 30
28387177 AGTTTTTAGC
* *
28387187 ACCCCTTAAAAACTAAAAAAATAAAATTAA
1 ACCCCTTAAAAATTGAAAAAATAAAATTAA
*
28387217 ACCTCTTAAAAATTGAAAAAA-AAAATTAA
1 ACCCCTTAAAAATTGAAAAAATAAAATTAA
28387246 ACCCCTT
1 ACCCCTT
28387253 TCAACATTGA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
29 14 0.44
30 18 0.56
ACGTcount: A:0.58, C:0.18, G:0.02, T:0.23
Consensus pattern (30 bp):
ACCCCTTAAAAATTGAAAAAATAAAATTAA
Found at i:28393355 original size:23 final size:22
Alignment explanation
Indices: 28393323--28393374 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 22
28393313 TTTTTTTTAA
28393323 TTTTTAATTTCTTT-ATATATAT
1 TTTTTAATTT-TTTAATATATAT
* *
28393345 TTTTTATATTTTTTAATTTTTAT
1 TTTTTA-ATTTTTTAATATATAT
28393368 TTTTTAA
1 TTTTTAA
28393375 AAAATATAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
22 10 0.38
23 16 0.62
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (22 bp):
TTTTTAATTTTTTAATATATAT
Found at i:28393370 original size:14 final size:15
Alignment explanation
Indices: 28393346--28393374 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
28393336 TATATATATT
28393346 TTTTATATTTTTTAA
1 TTTTATATTTTTTAA
28393361 TTTT-TATTTTTTAA
1 TTTTATATTTTTTAA
28393375 AAAATATAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (15 bp):
TTTTATATTTTTTAA
Found at i:28393400 original size:18 final size:19
Alignment explanation
Indices: 28393379--28393415 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
28393369 TTTTAAAAAA
28393379 TATAAAT-TTTGGAATTTT
1 TATAAATATTTGGAATTTT
*
28393397 TATAAATATTTTGAATTTT
1 TATAAATATTTGGAATTTT
28393416 AATTTTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.35, C:0.00, G:0.08, T:0.57
Consensus pattern (19 bp):
TATAAATATTTGGAATTTT
Found at i:28399791 original size:22 final size:22
Alignment explanation
Indices: 28399765--28399812 Score: 87
Period size: 22 Copynumber: 2.2 Consensus size: 22
28399755 TCATTATATC
28399765 AAAATAATATTAATTACATTGT
1 AAAATAATATTAATTACATTGT
*
28399787 AAAATAATATTAATTGCATTGT
1 AAAATAATATTAATTACATTGT
28399809 AAAA
1 AAAA
28399813 AAAAAAACAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.52, C:0.04, G:0.06, T:0.38
Consensus pattern (22 bp):
AAAATAATATTAATTACATTGT
Found at i:28404667 original size:13 final size:13
Alignment explanation
Indices: 28404649--28404673 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
28404639 TAAAATTGCC
28404649 AATAATTTATATT
1 AATAATTTATATT
28404662 AATAATTTATAT
1 AATAATTTATAT
28404674 ATTCAACTTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
AATAATTTATATT
Found at i:28409287 original size:59 final size:59
Alignment explanation
Indices: 28409209--28409679 Score: 499
Period size: 59 Copynumber: 8.0 Consensus size: 59
28409199 ATTTTTGACT
* *
28409209 TTCGAGGGTGAAAAT-GTAATTTTTGATGAAA-CTGGGGTTAAAAATGGAATTTTGGAGAG
1 TTCGAGGGT-AAAATGGTAATTTTTGGTGAAATC-GGGGTTAAAAATGGAATTTTGGAAAG
* * * ** * *
28409268 CTT-GAGGGTAAAACGGTAATTTTTGTTGGAATTAGGGTT-AAAATAGG-GTTTTAGAAAG
1 -TTCGAGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAAT-GGAATTTTGGAAAG
** * * **
28409326 TTTAAGGGTAAAATGGTAA-TTTTGGTGAAATCGAGGTTAAAAATGGGATTTTAAAAAG
1 TTCGAGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAG
* * *
28409384 TTCGAGGGTAAAATGGTAATTTTTGGTGAAATCAGGGTTAAAAATGGGATTTTGAAAAG
1 TTCGAGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAG
* * * * * *
28409443 TTCGAGAGTAAAATGGTGATTTTGGGTGAAATCGAGGTTAAAAATGGGATTTTGAAAAG
1 TTCGAGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAG
* * * * * * *
28409502 TTCGGGGGTAAAACGGTGATTTTGGGTGACATTGGGGTCAAAAATGGAATTTTGGAAAG
1 TTCGAGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAG
* * * *
28409561 TTCGGGGGTAAAATGGTAATTTTAGGTGAAATCAGGGTTAAAAATGGAATTTTAGAAAG
1 TTCGAGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAG
* * *
28409620 TT-TAGGGGTAAAATGGTAATTTTGGGTGAAATCGGGG-TAAAAATGGAATTTTAGAAAG
1 TTCGA-GGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAG
28409678 TT
1 TT
28409680 TAAGGACTAG
Statistics
Matches: 355, Mismatches: 48, Indels: 18
0.84 0.11 0.04
Matches are distributed among these distances:
57 18 0.05
58 85 0.24
59 250 0.70
60 2 0.01
ACGTcount: A:0.35, C:0.03, G:0.30, T:0.32
Consensus pattern (59 bp):
TTCGAGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAG
Found at i:28410751 original size:3 final size:3
Alignment explanation
Indices: 28410745--28410823 Score: 77
Period size: 3 Copynumber: 24.3 Consensus size: 3
28410735 CCTTTTTTTT
* * *
28410745 TTA TTA TGTTA TTTA TTA TTA TTAA TAA CTTCA TTA TTA TTG CTA TTA
1 TTA TTA T-T-A TT-A TTA TTA TT-A TTA -TT-A TTA TTA TTA TTA TTA
28410793 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
28410824 CATAAATTAA
Statistics
Matches: 65, Mismatches: 6, Indels: 10
0.80 0.07 0.12
Matches are distributed among these distances:
3 51 0.78
4 11 0.17
5 3 0.05
ACGTcount: A:0.32, C:0.04, G:0.03, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:28418295 original size:113 final size:113
Alignment explanation
Indices: 28418092--28418431 Score: 653
Period size: 113 Copynumber: 3.0 Consensus size: 113
28418082 ACCTTCTTCC
*
28418092 ATGCCTTTGCCACTTCTCGGACCTTTTTCTTATAATCATTCCCCTTATATGAAACTCGCAATGTG
1 ATGCGTTTGCCACTTCTCGGACCTTTTTCTTATAATCATTCCCCTTATATGAAACTCGCAATGTG
*
28418157 CTATACCATGAGTTGTAGGGATAAACTGTCTTGTCTTATATTGTCTCA
66 CTTTACCATGAGTTGTAGGGATAAACTGTCTTGTCTTATATTGTCTCA
*
28418205 ATGCGTTTGCCACTTCTCGGACCTTTTTCTTATAATCATTCCCTTTATATGAAACTCGCAATGTG
1 ATGCGTTTGCCACTTCTCGGACCTTTTTCTTATAATCATTCCCCTTATATGAAACTCGCAATGTG
28418270 CTTTACCATGAGTTGTAGGGATAAACTGTCTTGTCTTATATTGTCTCA
66 CTTTACCATGAGTTGTAGGGATAAACTGTCTTGTCTTATATTGTCTCA
28418318 ATGCGTTTGCCACTTCTCGGACCTTTTTCTTATAATCATTCCCCTTATATGAAACTCGCAATGTG
1 ATGCGTTTGCCACTTCTCGGACCTTTTTCTTATAATCATTCCCCTTATATGAAACTCGCAATGTG
28418383 CTTTACCATGAGTTGTAGGGATAAACTGTCTTGTCTTATATTGTCTCA
66 CTTTACCATGAGTTGTAGGGATAAACTGTCTTGTCTTATATTGTCTCA
28418431 A
1 A
28418432 AACGAGTAGA
Statistics
Matches: 223, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
113 223 1.00
ACGTcount: A:0.23, C:0.22, G:0.16, T:0.40
Consensus pattern (113 bp):
ATGCGTTTGCCACTTCTCGGACCTTTTTCTTATAATCATTCCCCTTATATGAAACTCGCAATGTG
CTTTACCATGAGTTGTAGGGATAAACTGTCTTGTCTTATATTGTCTCA
Found at i:28421497 original size:59 final size:59
Alignment explanation
Indices: 28421373--28421899 Score: 599
Period size: 59 Copynumber: 9.0 Consensus size: 59
28421363 TTGACTTTCG
* * * * * * *
28421373 AGGGTGAAAAT-GTAATTTTTGATGAAACCGGGGTT-AAAATGGAATTTTGGAGAGTTTT
1 AGGGT-AAAATGGTAATTTTGGGTGAAATCGAGGTTAAAAATGGAATTTTGAAAAGTTTA
* * * * * **
28421431 AGGGTAAAACGGTAATTTTTGGTGGAATTGAGGTTAAGAATGGGGTTTTGAAAAGTTTA
1 AGGGTAAAATGGTAATTTTGGGTGAAATCGAGGTTAAAAATGGAATTTTGAAAAGTTTA
* * * **
28421490 AGAGTAAAATGGTAATTTT-GGTAAAATCGAGG-TAAAAATGGGATTTTGAAAAGTTCG
1 AGGGTAAAATGGTAATTTTGGGTGAAATCGAGGTTAAAAATGGAATTTTGAAAAGTTTA
* * * *
28421547 AGGGTAAAATGGTGATTTTGGGTGAAATCGGGGTTAAAAATGGGATTTTGAAAAGTTTG
1 AGGGTAAAATGGTAATTTTGGGTGAAATCGAGGTTAAAAATGGAATTTTGAAAAGTTTA
* *
28421606 AGGGTAAAATGGTGATTTTGGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTT-
1 AGGGTAAAATGGTAATTTTGGGTGAAATCGAGGTTAAAAATGGAATTTTGAAAAGTTTA
* *
28421664 AGGAGTAAAATGGTAATTTTGGGTGAAATCGGGGTTAAAAATGAAATTTT-AGAAAGTTTA
1 AGG-GTAAAATGGTAATTTTGGGTGAAATCGAGGTTAAAAATGGAATTTTGA-AAAGTTTA
* * * * *
28421724 GGGGTAAAATGGTAATTTTGGGTAAAATTGGGGTT-AAAATGGAATTTT-AGAAAGTTTG
1 AGGGTAAAATGGTAATTTTGGGTGAAATCGAGGTTAAAAATGGAATTTTGA-AAAGTTTA
* *
28421782 AGGGTAAAATGGTAATTTTGGGTGAAATC-AGGGTTAAAAATGGAATTTT-AGAATGTTTG
1 AGGGTAAAATGGTAATTTTGGGTGAAATCGA-GGTTAAAAATGGAATTTTGA-AAAGTTTA
*
28421841 AGGGTAAAATGGTAATTTTGGGTGAAATCGGGGTTAAAAATGGAATTTT-AGAAAGTTTA
1 AGGGTAAAATGGTAATTTTGGGTGAAATCGAGGTTAAAAATGGAATTTTGA-AAAGTTTA
28421900 GGGACTAGAG
Statistics
Matches: 413, Mismatches: 46, Indels: 19
0.86 0.10 0.04
Matches are distributed among these distances:
57 42 0.10
58 99 0.24
59 270 0.65
60 2 0.00
ACGTcount: A:0.35, C:0.02, G:0.30, T:0.33
Consensus pattern (59 bp):
AGGGTAAAATGGTAATTTTGGGTGAAATCGAGGTTAAAAATGGAATTTTGAAAAGTTTA
Found at i:28421594 original size:30 final size:31
Alignment explanation
Indices: 28421552--28421706 Score: 109
Period size: 29 Copynumber: 5.2 Consensus size: 31
28421542 GTTCGAGGGT
28421552 AAAATGGTGATTTTGGGTGAAATCGGGGTTA
1 AAAATGGTGATTTTGGGTGAAATCGGGGTTA
* *
28421583 AAAATGG-GATTTT--G-AAAAGTTTGAGGG-T-
1 AAAATGGTGATTTTGGGTGAAA--TCG-GGGTTA
*
28421611 AAAATGGTGATTTTGGGTGAAATCGAGGTTA
1 AAAATGGTGATTTTGGGTGAAATCGGGGTTA
* * *
28421642 AAAATGG-AATTTT--G-GAAAGTTTAGGAG-T-
1 AAAATGGTGATTTTGGGTGAAA---TCGGGGTTA
*
28421670 AAAATGGTAATTTTGGGTGAAATCGGGGTTA
1 AAAATGGTGATTTTGGGTGAAATCGGGGTTA
28421701 AAAATG
1 AAAATG
28421707 AAATTTTAGA
Statistics
Matches: 95, Mismatches: 11, Indels: 36
0.67 0.08 0.25
Matches are distributed among these distances:
27 7 0.07
28 16 0.17
29 22 0.23
30 21 0.22
31 22 0.23
32 7 0.07
ACGTcount: A:0.35, C:0.02, G:0.32, T:0.32
Consensus pattern (31 bp):
AAAATGGTGATTTTGGGTGAAATCGGGGTTA
Found at i:28421712 original size:30 final size:30
Alignment explanation
Indices: 28421620--28421713 Score: 72
Period size: 30 Copynumber: 3.2 Consensus size: 30
28421610 TAAAATGGTG
* *
28421620 ATTTTGGGTGAAATCGAGGTTAAAAATGGA
1 ATTTTGGGTGAAATCGGGGTTAAAAATGAA
* * *
28421650 ATTTT--G-GAAAGTTTAGGAG-T-AAAATGGTA
1 ATTTTGGGTGAAA---TCGGGGTTAAAAAT-GAA
28421679 ATTTTGGGTGAAATCGGGGTTAAAAATGAA
1 ATTTTGGGTGAAATCGGGGTTAAAAATGAA
28421709 ATTTT
1 ATTTT
28421714 AGAAAGTTTA
Statistics
Matches: 48, Mismatches: 7, Indels: 18
0.66 0.10 0.25
Matches are distributed among these distances:
27 4 0.08
28 6 0.12
29 12 0.25
30 16 0.33
31 6 0.12
32 4 0.08
ACGTcount: A:0.36, C:0.02, G:0.28, T:0.34
Consensus pattern (30 bp):
ATTTTGGGTGAAATCGGGGTTAAAAATGAA
Found at i:28421728 original size:30 final size:29
Alignment explanation
Indices: 28421694--28421792 Score: 82
Period size: 29 Copynumber: 3.4 Consensus size: 29
28421684 GGGTGAAATC
28421694 GGGGTTAAAAATGAAATTTTAGAAAGTTTA
1 GGGGTT-AAAATGAAATTTTAGAAAGTTTA
* * *
28421724 GGGG-TAAAATGGTAATTTTGGGTAAA-ATT-
1 GGGGTTAAAAT-GAAATTTT-AG-AAAGTTTA
*
28421753 GGGGTTAAAATGGAATTTTAGAAAGTTT-
1 GGGGTTAAAATGAAATTTTAGAAAGTTTA
28421781 GAGGG-TAAAATG
1 G-GGGTTAAAATG
28421793 GTAATTTTGG
Statistics
Matches: 57, Mismatches: 6, Indels: 14
0.74 0.08 0.18
Matches are distributed among these distances:
27 3 0.05
28 16 0.28
29 22 0.39
30 13 0.23
31 3 0.05
ACGTcount: A:0.38, C:0.00, G:0.29, T:0.32
Consensus pattern (29 bp):
GGGGTTAAAATGAAATTTTAGAAAGTTTA
Found at i:28421806 original size:176 final size:175
Alignment explanation
Indices: 28421374--28421902 Score: 685
Period size: 176 Copynumber: 3.0 Consensus size: 175
28421364 TGACTTTCGA
* * * * * *
28421374 GGGTGAAAAT-GTAATTTTTGATGAAACCGGGGTTAAAATGGAATTTTGGAGAGTTTTAGGGTAA
1 GGGT-AAAATGGTAATTTTGGGTAAAATCGGGGTTAAAATGGAATTTT-GAAAGTTTGAGGGTAA
* * * * * ** * *
28421438 AACGGTAATTTTTGGTGGAATTGAGGTTAAGAATGGGGTTTTGAAAAGTTTAAGAGTAAAATGGT
64 AATGGTAATTTTGGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTTAGGAGTAAAATGGT
* * * *
28421503 AATTTT-GGTAAAATCGAGG-TAAAAATGGGATTTT-GAAAAG-TTCG
129 AATTTTGGGTGAAATCGGGGTTAAAAATGGAATTTTAG-AAAGTTTAG
* * *
28421547 AGGGTAAAATGGTGATTTTGGGTGAAATCGGGGTTAAAAATGGGATTTTGAAAAGTTTGAGGGTA
1 -GGGTAAAATGGTAATTTTGGGTAAAATCGGGGTT-AAAATGGAATTTTG-AAAGTTTGAGGGTA
*
28421612 AAATGGTGATTTTGGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTTAGGAGTAAAATGG
63 AAATGGTAATTTTGGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTTAGGAGTAAAATGG
*
28421677 TAATTTTGGGTGAAATCGGGGTTAAAAATGAAATTTTAGAAAGTTTAG
128 TAATTTTGGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAAGTTTAG
*
28421725 GGGTAAAATGGTAATTTTGGGTAAAATTGGGGTTAAAATGGAATTTTAGAAAGTTTGAGGGTAAA
1 GGGTAAAATGGTAATTTTGGGTAAAATCGGGGTTAAAATGGAATTTT-GAAAGTTTGAGGGTAAA
* *
28421790 ATGGTAATTTTGGGTGAAATC-AGGGTTAAAAATGGAATTTTAGAATGTTTGAGG-GTAAAATGG
65 ATGGTAATTTTGGGTGAAATCGA-GGTTAAAAATGGAATTTTGGAAAGTTT-AGGAGTAAAATGG
28421853 TAATTTTGGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAAGTTTAG
128 TAATTTTGGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAAGTTTAG
28421901 GG
1 GG
28421903 ACTAGAGAGT
Statistics
Matches: 315, Mismatches: 30, Indels: 18
0.87 0.08 0.05
Matches are distributed among these distances:
173 5 0.02
174 25 0.08
175 87 0.28
176 142 0.45
177 52 0.17
178 4 0.01
ACGTcount: A:0.35, C:0.02, G:0.30, T:0.33
Consensus pattern (175 bp):
GGGTAAAATGGTAATTTTGGGTAAAATCGGGGTTAAAATGGAATTTTGAAAGTTTGAGGGTAAAA
TGGTAATTTTGGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTTAGGAGTAAAATGGTAA
TTTTGGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAAGTTTAG
Found at i:28421829 original size:117 final size:116
Alignment explanation
Indices: 28421372--28421902 Score: 642
Period size: 117 Copynumber: 4.5 Consensus size: 116
28421362 TTTGACTTTC
* * * * * *
28421372 GAGGGTGAAAAT-GTAATTTTTGATGAAACCGGGGTTAAAATGGAATTTTGGAGAGTTTTAGGGT
1 GAGGGT-AAAATGGTAATTTTGGGTAAAATCGGGGTTAAAATGGAATTTTAGAAAG-TTTAGGGT
* * * * * * **
28421436 AAAACGGTAATTTTTGGTGGAATTGAGGTTAAGAATGGGGTTTTGAAAAGTTT
64 AAAATGGTAATTTTGGGTGAAATCGGGGTTAAAAATGGAATTTTGAAAAGTTT
* * * * * *
28421489 AAGAGTAAAATGGTAATTTT-GGTAAAATCGAGGTAAAAATGGGATTTT-GAAAAGTTCGAGGGT
1 GAGGGTAAAATGGTAATTTTGGGTAAAATCGGGGTTAAAATGGAATTTTAG-AAAGTT-TAGGGT
* *
28421552 AAAATGGTGATTTTGGGTGAAATCGGGGTTAAAAATGGGATTTTGAAAAGTTT
64 AAAATGGTAATTTTGGGTGAAATCGGGGTTAAAAATGGAATTTTGAAAAGTTT
* * * *
28421605 GAGGGTAAAATGGTGATTTTGGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTTAGGAGT
1 GAGGGTAAAATGGTAATTTTGGGTAAAATCGGGGTT-AAAATGGAATTTTAGAAAGTTTAGG-GT
*
28421670 AAAATGGTAATTTTGGGTGAAATCGGGGTTAAAAATGAAATTTT-AGAAAGTTT
64 AAAATGGTAATTTTGGGTGAAATCGGGGTTAAAAATGGAATTTTGA-AAAGTTT
*
28421723 -AGGGGTAAAATGGTAATTTTGGGTAAAATTGGGGTTAAAATGGAATTTTAGAAAGTTTGAGGGT
1 GA-GGGTAAAATGGTAATTTTGGGTAAAATCGGGGTTAAAATGGAATTTTAGAAAGTTT-AGGGT
* *
28421787 AAAATGGTAATTTTGGGTGAAATCAGGGTTAAAAATGGAATTTT-AGAATGTTT
64 AAAATGGTAATTTTGGGTGAAATCGGGGTTAAAAATGGAATTTTGA-AAAGTTT
*
28421840 GAGGGTAAAATGGTAATTTTGGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAAGTTTAGGG
1 GAGGGTAAAATGGTAATTTTGGGTAAAATCGGGGTT-AAAATGGAATTTTAGAAAGTTTAGGG
28421903 ACTAGAGAGT
Statistics
Matches: 364, Mismatches: 38, Indels: 24
0.85 0.09 0.06
Matches are distributed among these distances:
115 3 0.01
116 97 0.27
117 139 0.38
118 124 0.34
119 1 0.00
ACGTcount: A:0.35, C:0.02, G:0.30, T:0.33
Consensus pattern (116 bp):
GAGGGTAAAATGGTAATTTTGGGTAAAATCGGGGTTAAAATGGAATTTTAGAAAGTTTAGGGTAA
AATGGTAATTTTGGGTGAAATCGGGGTTAAAAATGGAATTTTGAAAAGTTT
Found at i:28422965 original size:3 final size:3
Alignment explanation
Indices: 28422942--28423017 Score: 75
Period size: 3 Copynumber: 25.3 Consensus size: 3
28422932 TTTCCCTTTT
* * * * *
28422942 TTA TT- TTA TTA -TG TTA TTTA TTA TTA TTAA TAA CTA TTG CTA TTA
1 TTA TTA TTA TTA TTA TTA -TTA TTA TTA TT-A TTA TTA TTA TTA TTA
28422987 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
28423018 CATAAATTAA
Statistics
Matches: 59, Mismatches: 10, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
2 3 0.05
3 51 0.86
4 5 0.08
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:28423719 original size:11 final size:11
Alignment explanation
Indices: 28423703--28423740 Score: 58
Period size: 11 Copynumber: 3.5 Consensus size: 11
28423693 ATTTTAAATT
28423703 TAAATTTATAA
1 TAAATTTATAA
28423714 TAAATTTATAA
1 TAAATTTATAA
* *
28423725 TAAATTCAAAA
1 TAAATTTATAA
28423736 TAAAT
1 TAAAT
28423741 CTAAATTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
11 25 1.00
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (11 bp):
TAAATTTATAA
Found at i:28424022 original size:22 final size:22
Alignment explanation
Indices: 28423997--28424044 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
28423987 ACATTGGAAA
*
28423997 ATATCCAATT-TAATTTAATCTC
1 ATATCCAATTATAAATTAAT-TC
*
28424019 ATATCCATTTATAAATTAATTC
1 ATATCCAATTATAAATTAATTC
28424041 ATAT
1 ATAT
28424045 GTGACAATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 15 0.65
23 8 0.35
ACGTcount: A:0.40, C:0.15, G:0.00, T:0.46
Consensus pattern (22 bp):
ATATCCAATTATAAATTAATTC
Found at i:28437838 original size:21 final size:21
Alignment explanation
Indices: 28437812--28437856 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
28437802 TTTTACTAAA
* * *
28437812 AAAAATATTTTTATTAAAATT
1 AAAAATAATTATATTAAAAAT
28437833 AAAAATAATTATATTAAAAAT
1 AAAAATAATTATATTAAAAAT
28437854 AAA
1 AAA
28437857 GTTTAAAACA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
AAAAATAATTATATTAAAAAT
Found at i:28439408 original size:23 final size:23
Alignment explanation
Indices: 28439382--28439431 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
28439372 CGATTCTATT
*
28439382 AAATAAATTATT-AAAATTCATAA
1 AAATAAAATATTAAAAATT-ATAA
28439405 AAATAAAATATTAAAAATTATAA
1 AAATAAAATATTAAAAATTATAA
28439428 AAAT
1 AAAT
28439432 TGGTTTCATC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 19 0.76
24 6 0.24
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (23 bp):
AAATAAAATATTAAAAATTATAA
Found at i:28440367 original size:36 final size:36
Alignment explanation
Indices: 28440290--28440378 Score: 99
Period size: 36 Copynumber: 2.5 Consensus size: 36
28440280 GAATCCACTA
* * *
28440290 GATCTTTAGCCTCATCTTCATGCGCACGTTAGGGTT
1 GATCTTCAGCCTCGTCTTCATGAGCACGTTAGGGTT
* * *
28440326 AATCTTCAGCCTCGTCTTTATGAGCACG-TCGGAGTT
1 GATCTTCAGCCTCGTCTTCATGAGCACGTTAGG-GTT
*
28440362 GATCTTCGGCCTCGTCT
1 GATCTTCAGCCTCGTCT
28440379 CCTCCCTTCG
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
35 3 0.07
36 41 0.93
ACGTcount: A:0.16, C:0.27, G:0.22, T:0.35
Consensus pattern (36 bp):
GATCTTCAGCCTCGTCTTCATGAGCACGTTAGGGTT
Found at i:28442220 original size:6 final size:6
Alignment explanation
Indices: 28442211--28442240 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
28442201 TATTTTCAGC
28442211 ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT
1 ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT
28442241 TATGTCCTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (6 bp):
ATTTTT
Found at i:28442423 original size:16 final size:17
Alignment explanation
Indices: 28442384--28442425 Score: 52
Period size: 16 Copynumber: 2.5 Consensus size: 17
28442374 TTACATCTTT
*
28442384 TATTTATGTTATTAATTG
1 TATTTAT-TTATTAAGTG
28442402 TA-TTATTTATT-AGTG
1 TATTTATTTATTAAGTG
28442417 TATTTATTT
1 TATTTATTT
28442426 TATTGTACTA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 5 0.23
16 11 0.50
17 4 0.18
18 2 0.09
ACGTcount: A:0.26, C:0.00, G:0.10, T:0.64
Consensus pattern (17 bp):
TATTTATTTATTAAGTG
Found at i:28442982 original size:9 final size:9
Alignment explanation
Indices: 28442968--28443026 Score: 51
Period size: 9 Copynumber: 7.1 Consensus size: 9
28442958 GTAAATGATT
28442968 TTAAAATTA
1 TTAAAATTA
28442977 TTAAAATTA
1 TTAAAATTA
28442986 TT----TT-
1 TTAAAATTA
28442990 TTAAAA-TA
1 TTAAAATTA
28442998 -TAAAATTA
1 TTAAAATTA
28443006 TTAAAATTA
1 TTAAAATTA
28443015 TTTTAAAATTA
1 --TTAAAATTA
28443026 T
1 T
28443027 AATCATTACG
Statistics
Matches: 41, Mismatches: 0, Indels: 18
0.69 0.00 0.31
Matches are distributed among these distances:
4 2 0.05
5 2 0.05
7 6 0.15
8 2 0.05
9 20 0.49
11 9 0.22
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (9 bp):
TTAAAATTA
Found at i:28442988 original size:20 final size:20
Alignment explanation
Indices: 28442960--28443026 Score: 61
Period size: 20 Copynumber: 3.4 Consensus size: 20
28442950 TCACGTTAGT
*
28442960 AAATGATTTTAAAATTATTA
1 AAATTATTTTAAAATTATTA
28442980 AAATTATTTTTTAAAA-TA-TA
1 AAATTA--TTTTAAAATTATTA
28443000 AAATTA--TTAAAATTATTTTA
1 AAATTATTTTAAAATTA--TTA
28443020 AAATTAT
1 AAATTAT
28443027 AATCATTACG
Statistics
Matches: 39, Mismatches: 1, Indels: 13
0.74 0.02 0.25
Matches are distributed among these distances:
16 6 0.15
17 2 0.05
20 21 0.54
21 2 0.05
22 8 0.21
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (20 bp):
AAATTATTTTAAAATTATTA
Found at i:28443034 original size:29 final size:28
Alignment explanation
Indices: 28442969--28443028 Score: 95
Period size: 29 Copynumber: 2.1 Consensus size: 28
28442959 TAAATGATTT
28442969 TAAAATTATTAAAATTATTTTTTAAAATA
1 TAAAATTATTAAAATTA-TTTTTAAAATA
28442998 TAAAATTATTAAAATTA-TTTTAAAATTA
1 TAAAATTATTAAAATTATTTTTAAAA-TA
28443026 TAA
1 TAA
28443029 TCATTACGTC
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
27 8 0.27
28 5 0.17
29 17 0.57
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (28 bp):
TAAAATTATTAAAATTATTTTTAAAATA
Found at i:28443692 original size:23 final size:23
Alignment explanation
Indices: 28443666--28443720 Score: 76
Period size: 23 Copynumber: 2.3 Consensus size: 23
28443656 GACCACCCAA
28443666 AACCTAAAATC-CCTAAATTCAAC
1 AACCTAAAATCTCC-AAATTCAAC
*
28443689 AACCTAAAATCTCCAAATTCGAC
1 AACCTAAAATCTCCAAATTCAAC
28443712 AACCATAAA
1 AACC-TAAA
28443721 CAATTCATGG
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
23 23 0.79
24 6 0.21
ACGTcount: A:0.49, C:0.29, G:0.02, T:0.20
Consensus pattern (23 bp):
AACCTAAAATCTCCAAATTCAAC
Found at i:28446522 original size:22 final size:21
Alignment explanation
Indices: 28446480--28446523 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
28446470 ATGAGTTGAA
* *
28446480 ATCCAAATCTAAATTTAAATT
1 ATCCAAATATAAATTCAAATT
*
28446501 ATCCAAATAATAAATTCGAATT
1 ATCCAAAT-ATAAATTCAAATT
28446523 A
1 A
28446524 ATTCAAAATC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.50, C:0.14, G:0.02, T:0.34
Consensus pattern (21 bp):
ATCCAAATATAAATTCAAATT
Found at i:28448058 original size:30 final size:30
Alignment explanation
Indices: 28448022--28448082 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
28448012 TTTATTTCAT
28448022 TAATTGTTAGAATAGCGCTACAGAACAGAA
1 TAATTGTTAGAATAGCGCTACAGAACAGAA
28448052 TAATTGTTAGAATAGCGCTACAGAACAGAA
1 TAATTGTTAGAATAGCGCTACAGAACAGAA
28448082 T
1 T
28448083 GCAAGCATCC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.43, C:0.13, G:0.20, T:0.25
Consensus pattern (30 bp):
TAATTGTTAGAATAGCGCTACAGAACAGAA
Found at i:28461346 original size:14 final size:14
Alignment explanation
Indices: 28461323--28461357 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
28461313 AGATATTAGT
28461323 TAATAATAATAAAA
1 TAATAATAATAAAA
* *
28461337 TAATATTAATGAAA
1 TAATAATAATAAAA
28461351 TAATAAT
1 TAATAAT
28461358 TTATATTATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (14 bp):
TAATAATAATAAAA
Found at i:28465112 original size:16 final size:17
Alignment explanation
Indices: 28465091--28465130 Score: 73
Period size: 16 Copynumber: 2.4 Consensus size: 17
28465081 TTTTACTCTC
28465091 TATAATAGTTTTTCA-T
1 TATAATAGTTTTTCATT
28465107 TATAATAGTTTTTCATT
1 TATAATAGTTTTTCATT
28465124 TATAATA
1 TATAATA
28465131 ATAACTGTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 15 0.65
17 8 0.35
ACGTcount: A:0.35, C:0.05, G:0.05, T:0.55
Consensus pattern (17 bp):
TATAATAGTTTTTCATT
Found at i:28472327 original size:24 final size:24
Alignment explanation
Indices: 28472295--28472340 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
28472285 ATGTGGAACC
28472295 AGTAGAAAATGAAGATCCAACTCT
1 AGTAGAAAATGAAGATCCAACTCT
28472319 AGTAGAAAATGAAGATCCAACT
1 AGTAGAAAATGAAGATCCAACT
28472341 TCGTGTATGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.48, C:0.15, G:0.17, T:0.20
Consensus pattern (24 bp):
AGTAGAAAATGAAGATCCAACTCT
Found at i:28474697 original size:28 final size:28
Alignment explanation
Indices: 28474638--28474723 Score: 79
Period size: 28 Copynumber: 3.1 Consensus size: 28
28474628 GACATTTTTC
* * *
28474638 ATTTGAAATTAATTAAGTTTATAA-ATGA
1 ATTTGAAATTAATTATGTTTA-AATTTGT
28474666 ATTTGAAATTAATTATGTTTAAATTTGT
1 ATTTGAAATTAATTATGTTTAAATTTGT
* * **
28474694 ATTT--AATTAATAATTTTTATGTTTGT
1 ATTTGAAATTAATTATGTTTAAATTTGT
28474720 ATTT
1 ATTT
28474724 TGGTTTACGG
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
26 22 0.44
27 2 0.04
28 26 0.52
ACGTcount: A:0.37, C:0.00, G:0.09, T:0.53
Consensus pattern (28 bp):
ATTTGAAATTAATTATGTTTAAATTTGT
Found at i:28474701 original size:26 final size:26
Alignment explanation
Indices: 28474672--28474723 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
28474662 ATGAATTTGA
*
28474672 AATTAATTATGTTTAAATTTGTATTT
1 AATTAATAATGTTTAAATTTGTATTT
* **
28474698 AATTAATAATTTTTATGTTTGTATTT
1 AATTAATAATGTTTAAATTTGTATTT
28474724 TGGTTTACGG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.33, C:0.00, G:0.08, T:0.60
Consensus pattern (26 bp):
AATTAATAATGTTTAAATTTGTATTT
Found at i:28475865 original size:43 final size:43
Alignment explanation
Indices: 28475817--28476124 Score: 345
Period size: 43 Copynumber: 7.2 Consensus size: 43
28475807 GAGAAAAAAT
*
28475817 GCCGCTATAA-AACATGGTCTTTAGCGGCGCTTTTCCCACAAAC
1 GCCGCTA-AAGAACATGGTCTTTAGCGGCGCTTTCCCCACAAAC
* **
28475860 GCCGCTAAAGAACATGGTCTTTAGCGACGCTTTCCCCACAAGT
1 GCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTCCCCACAAAC
* * * *
28475903 GCCGTTAAAGAACATGGTCTTTAACGGCACTTTCCCCACAAAT
1 GCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTCCCCACAAAC
* * * *
28475946 GCTGCTAAAGAACATGGTTTTTAGCGGCGTTTTCCCCAAAAAC
1 GCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTCCCCACAAAC
* * * *
28475989 GCCGCAAAAAAACATGGTCTTTAGCGGCTCTTTCCACACAAAC
1 GCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTCCCCACAAAC
* * *
28476032 GCAGCTAAAGAACATGATCTTTAGCGGCGC-TTCCCTCCCAAAC
1 GCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTCCC-CACAAAC
* * * *
28476075 GCCACTAAAGAA-ATGATCTTTAGCGGTGC-TTCCCTCCCAAAC
1 GCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTCCC-CACAAAC
*
28476117 TCCGCTAA
1 GCCGCTAA
28476125 TCTTTAGCGG
Statistics
Matches: 226, Mismatches: 37, Indels: 5
0.84 0.14 0.02
Matches are distributed among these distances:
42 41 0.18
43 185 0.82
ACGTcount: A:0.28, C:0.30, G:0.18, T:0.24
Consensus pattern (43 bp):
GCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTCCCCACAAAC
Found at i:28476970 original size:13 final size:14
Alignment explanation
Indices: 28476943--28476971 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
28476933 ATAAATGACG
28476943 AATTAAACTATTAT
1 AATTAAACTATTAT
28476957 AATTAAAC-ATTAT
1 AATTAAACTATTAT
28476970 AA
1 AA
28476972 ATATTTAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (14 bp):
AATTAAACTATTAT
Found at i:28477427 original size:250 final size:250
Alignment explanation
Indices: 28476986--28477486 Score: 993
Period size: 250 Copynumber: 2.0 Consensus size: 250
28476976 TTAAAATAAT
28476986 TCAAATTTTATTAAGTAAATATACCATAATTTCTGCAGCTTCAGAAGTCATAAGAGATCCATCTT
1 TCAAATTTTATTAAGTAAATATACCATAATTTCTGCAGCTTCAGAAGTCATAAGAGATCCATCTT
28477051 TCTTTCTATGTGTAATGTCAAAAAGCTGAAGGCGTCTAACTTTTTTACTTAACGACTATTCTTAC
66 TCTTTCTATGTGTAATGTCAAAAAGCTGAAGGCGTCTAACTTTTTTACTTAACGACTATTCTTAC
28477116 ATTATAGTAGGAAAATATTAATTAGTAGAAAGTAATTAATATTTGACACAATTAATAAATTCAAA
131 ATTATAGTAGGAAAATATTAATTAGTAGAAAGTAATTAATATTTGACACAATTAATAAATTCAAA
*
28477181 ATACCTCATCAGCAGCTACACAAGCAAAACTTCTCGATCCAGTTATGTGCGTGAA
196 ATACCTCATCAGCAGCTACACAAGCAAAACTTCTCGATCCAGCTATGTGCGTGAA
28477236 TCAAATTTTATTAAGTAAATATACCATAATTTCTGCAGCTTCAGAAGTCATAAGAGATCCATCTT
1 TCAAATTTTATTAAGTAAATATACCATAATTTCTGCAGCTTCAGAAGTCATAAGAGATCCATCTT
28477301 TCTTTCTATGTGTAATGTCAAAAAGCTGAAGGCGTCTAACTTTTTTACTTAACGACTATTCTTAC
66 TCTTTCTATGTGTAATGTCAAAAAGCTGAAGGCGTCTAACTTTTTTACTTAACGACTATTCTTAC
28477366 ATTATAGTAGGAAAATATTAATTAGTAGAAAGTAATTAATATTTGACACAATTAATAAATTCAAA
131 ATTATAGTAGGAAAATATTAATTAGTAGAAAGTAATTAATATTTGACACAATTAATAAATTCAAA
28477431 ATACCTCATCAGCAGCTACACAAGCAAAACTTCTCGATCCAGCTATGTGCGTGAA
196 ATACCTCATCAGCAGCTACACAAGCAAAACTTCTCGATCCAGCTATGTGCGTGAA
28477486 T
1 T
28477487 TTTTGTTTTT
Statistics
Matches: 250, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
250 250 1.00
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.34
Consensus pattern (250 bp):
TCAAATTTTATTAAGTAAATATACCATAATTTCTGCAGCTTCAGAAGTCATAAGAGATCCATCTT
TCTTTCTATGTGTAATGTCAAAAAGCTGAAGGCGTCTAACTTTTTTACTTAACGACTATTCTTAC
ATTATAGTAGGAAAATATTAATTAGTAGAAAGTAATTAATATTTGACACAATTAATAAATTCAAA
ATACCTCATCAGCAGCTACACAAGCAAAACTTCTCGATCCAGCTATGTGCGTGAA
Found at i:28482616 original size:70 final size:69
Alignment explanation
Indices: 28482527--28482722 Score: 304
Period size: 70 Copynumber: 2.8 Consensus size: 69
28482517 AAATATTTTG
*
28482527 AATTAAATATTTGGATTTAGGGTTTAATAAATAACTT-ATTAAATAATTAAATATTTTGGTTGTT
1 AATTAAATATTTGG-TTTAGGGTTTAATAAATAA-TTAATTAAATAATTAAATATTTGGGTTGTT
28482591 TTTAAT
64 TTTAAT
* *
28482597 AATTAAATAGTTTAGTTTAGGGTTTAATAAATAATTAATTAAATAAGTAAATATTTGGGTTGTTT
1 AATTAAATA-TTTGGTTTAGGGTTTAATAAATAATTAATTAAATAATTAAATATTTGGGTTGTTT
28482662 TTAAT
65 TTAAT
* *
28482667 AATTAAATAATTCGGTTTAGGGTTTAATAAATAATTAATTAAATAATTAATTATTT
1 AATTAAAT-ATTTGGTTTAGGGTTTAATAAATAATTAATTAAATAATTAAATATTT
28482723 CAATATTTGT
Statistics
Matches: 116, Mismatches: 7, Indels: 6
0.90 0.05 0.05
Matches are distributed among these distances:
69 2 0.02
70 109 0.94
71 5 0.04
ACGTcount: A:0.41, C:0.01, G:0.12, T:0.46
Consensus pattern (69 bp):
AATTAAATATTTGGTTTAGGGTTTAATAAATAATTAATTAAATAATTAAATATTTGGGTTGTTTT
TAAT
Found at i:28482711 original size:12 final size:12
Alignment explanation
Indices: 28482690--28482719 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
28482680 GGTTTAGGGT
28482690 TTAA-TAAATAA
1 TTAATTAAATAA
28482701 TTAATTAAATAA
1 TTAATTAAATAA
28482713 TTAATTA
1 TTAATTA
28482720 TTTCAATATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 4 0.22
12 14 0.78
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (12 bp):
TTAATTAAATAA
Found at i:28482813 original size:122 final size:112
Alignment explanation
Indices: 28482667--28482956 Score: 373
Period size: 113 Copynumber: 2.5 Consensus size: 112
28482657 TGTTTTTAAT
* * *
28482667 AATTAAATAATTCGGTTTAGGGTTTAATAAATAATTAATTAAATAATTAATTATTTCAATATTTG
1 AATTAAAT-ATTTGATTTAGGGTTTAATAAATAACTAATTAAATAATTAATTATTTCAATATTTG
* * **
28482732 TTATGTTTTTTATTGTTTAATATTTATTTAAATATAATTAAATAATTTAATATTTTG
65 TTAT-ATTTTTAATAATTAA-A-TT-TTT--ATATAA-T--ATAATTTAATATTTTG
*
28482789 AATTAAATATTTTGATTTAGGGTTTAATAAATAACTAATTAAATAATTAATTATTTTAATATTTG
1 AATTAAATA-TTTGATTTAGGGTTTAATAAATAACTAATTAAATAATTAATTATTTCAATATTTG
* * *
28482854 TTCTATTTTTAATAATTGAATTTTTATTTAATATAATTTAATATTTTG
65 TTATATTTTTAATAATTAAATTTTTATATAATATAATTTAATATTTTG
28482902 AATTAAATATTTGAGTTTAGGGTTTAATAAATAACTAATTAAATAATTAATTATT
1 AATTAAATATTTGA-TTTAGGGTTTAATAAATAACTAATTAAATAATTAATTATT
28482957 GGTATTTTGA
Statistics
Matches: 155, Mismatches: 11, Indels: 13
0.87 0.06 0.07
Matches are distributed among these distances:
112 5 0.03
113 65 0.42
115 1 0.01
116 5 0.03
118 3 0.02
119 2 0.01
120 1 0.01
121 11 0.07
122 62 0.40
ACGTcount: A:0.40, C:0.02, G:0.07, T:0.51
Consensus pattern (112 bp):
AATTAAATATTTGATTTAGGGTTTAATAAATAACTAATTAAATAATTAATTATTTCAATATTTGT
TATATTTTTAATAATTAAATTTTTATATAATATAATTTAATATTTTG
Found at i:28484789 original size:20 final size:20
Alignment explanation
Indices: 28484764--28484803 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
28484754 GGTGTAGATT
*
28484764 GGAGTGGAGAATGAAATGGA
1 GGAGTGGAGAACGAAATGGA
28484784 GGAGTGGAGAACGAAATGGA
1 GGAGTGGAGAACGAAATGGA
28484804 TAGGAGAATG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.40, C:0.03, G:0.45, T:0.12
Consensus pattern (20 bp):
GGAGTGGAGAACGAAATGGA
Found at i:28485088 original size:41 final size:41
Alignment explanation
Indices: 28484989--28485120 Score: 158
Period size: 41 Copynumber: 3.2 Consensus size: 41
28484979 TTATTACAAT
* * *
28484989 ACCTTTAGCGGCGTTTATGA-GATAAATGCCGCTAATGCTTTGG
1 ACCTTTAGCGGCGTTT-TTACCATAAATGCCGCTATTGC-TT-G
*
28485032 ACCTTTTGCGGCGTTTTTACCATAAATGCCGCTATTGCTTG
1 ACCTTTAGCGGCGTTTTTACCATAAATGCCGCTATTGCTTG
* * **
28485073 ACCTTTAGCGGCGTTTTTACCACAAACGCTACTATTGCTTG
1 ACCTTTAGCGGCGTTTTTACCATAAATGCCGCTATTGCTTG
28485114 ACCTTTA
1 ACCTTTA
28485121 ATTTTTTTTA
Statistics
Matches: 79, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
41 44 0.56
42 4 0.05
43 31 0.39
ACGTcount: A:0.21, C:0.23, G:0.20, T:0.36
Consensus pattern (41 bp):
ACCTTTAGCGGCGTTTTTACCATAAATGCCGCTATTGCTTG
Found at i:28486579 original size:41 final size:41
Alignment explanation
Indices: 28486522--28486882 Score: 323
Period size: 41 Copynumber: 8.8 Consensus size: 41
28486512 CAACACTTTC
* * * ** *
28486522 CCAAAAACGCCACTAATGTTCTGACCTTTAACAACGTTTCT
1 CCAAAAACGCCGCTAATGCTCTGACCTTTAGCGGCGCTTCT
* * * *
28486563 CCAAAAATGCCGCTAATGCTATGACTTTTAGCGGTGCCTTC-
1 CCAAAAACGCCGCTAATGCTCTGACCTTTAGCGGCG-CTTCT
* * * *
28486604 CCAAAAACGTCTCTAATGCTCTGATCTTTAGCGGTGCTTC-
1 CCAAAAACGCCGCTAATGCTCTGACCTTTAGCGGCGCTTCT
*** * * * *
28486644 CCAAAAACATTGCTAATGCTCTAACATTTAGTGACGCTTCT
1 CCAAAAACGCCGCTAATGCTCTGACCTTTAGCGGCGCTTCT
* * *
28486685 ACAAAAACACCGCTAATGCTCTGACCTTTAGCAGCGCTTCT
1 CCAAAAACGCCGCTAATGCTCTGACCTTTAGCGGCGCTTCT
* * * **
28486726 CAAAAAATGCCGTTAATGCTCTGACCTTTAATGGCGCTTCT
1 CCAAAAACGCCGCTAATGCTCTGACCTTTAGCGGCGCTTCT
* * *
28486767 CCAAAAACGCCGCTAGTGCTTTGACCTTTAGCGACGCTTCT
1 CCAAAAACGCCGCTAATGCTCTGACCTTTAGCGGCGCTTCT
* * * *
28486808 TCAAAAACGCCGCTAATGCTCTGACCTTTAGCGCCGTTTTT
1 CCAAAAACGCCGCTAATGCTCTGACCTTTAGCGGCGCTTCT
* * * *
28486849 CCGACAAACGCCGCTATTGCT-TTACCTTTTGCGG
1 CC-AAAAACGCCGCTAATGCTCTGACCTTTAGCGG
28486883 TGTTTATGAA
Statistics
Matches: 256, Mismatches: 61, Indels: 6
0.79 0.19 0.02
Matches are distributed among these distances:
40 35 0.14
41 202 0.79
42 19 0.07
ACGTcount: A:0.25, C:0.29, G:0.16, T:0.30
Consensus pattern (41 bp):
CCAAAAACGCCGCTAATGCTCTGACCTTTAGCGGCGCTTCT
Found at i:28486896 original size:82 final size:81
Alignment explanation
Indices: 28486655--28486967 Score: 234
Period size: 82 Copynumber: 3.8 Consensus size: 81
28486645 CAAAAACATT
* * * * * * * * * * * *
28486655 GCTAATGCTCTAACATTTAGTGACGCTTCTACAAAAACACCGCTAATGCTCTGACCTTTAGCAGC
1 GCTAATGCTCTGACCTTTAGTGGCGTTTATCCGAAAACGCCGCTATTGCT-TTACCTTTTGCGGC
* * * *
28486720 GCTTCTCAAAAAATGCC
65 GTTTATGAAAAAACGCC
* * * * * * * *
28486737 GTTAATGCTCTGACCTTTAATGGCGCTTCTCCAAAAACGCCGCTAGTGCTTTGACCTTTAGCGAC
1 GCTAATGCTCTGACCTTTAGTGGCGTTTATCCGAAAACGCCGCTATTGCTTT-ACCTTTTGCGGC
* * **
28486802 GCTTCTTCAAAAACGCC
65 GTTTATGAAAAAACGCC
* * * *
28486819 GCTAATGCTCTGACCTTTAGCGCCGTTTTTCCGACAAACGCCGCTATTGCTTTACCTTTTGCGGT
1 GCTAATGCTCTGACCTTTAGTGGCGTTTATCCGA-AAACGCCGCTATTGCTTTACCTTTTGCGGC
*
28486884 GTTTATGAAAAAACGTC
65 GTTTATGAAAAAACGCC
* * * * *
28486901 GCTATTGCT-TTACCTTTTGTGGCGTTTAT-GGAAAAGCGCCGCTATTGTTTTACCTTTTGCGGC
1 GCTAATGCTCTGACCTTTAGTGGCGTTTATCCGAAAA-CGCCGCTATTGCTTTACCTTTTGCGGC
28486964 GTTT
65 GTTT
28486968 TCTGTCCAAA
Statistics
Matches: 189, Mismatches: 39, Indels: 8
0.80 0.17 0.03
Matches are distributed among these distances:
79 3 0.02
80 31 0.16
81 16 0.08
82 122 0.65
83 17 0.09
ACGTcount: A:0.22, C:0.26, G:0.19, T:0.33
Consensus pattern (81 bp):
GCTAATGCTCTGACCTTTAGTGGCGTTTATCCGAAAACGCCGCTATTGCTTTACCTTTTGCGGCG
TTTATGAAAAAACGCC
Found at i:28486905 original size:40 final size:40
Alignment explanation
Indices: 28486769--28486967 Score: 184
Period size: 40 Copynumber: 4.9 Consensus size: 40
28486759 GCGCTTCTCC
* * * * * **
28486769 AAAAACGCCGCTAGTGCTTTGACCTTTAGCGACGCTTCTTC
1 AAAAACGCCGCTATTGCTTT-ACCTTTTGCGGCGTTTATGA
* * * * *
28486810 AAAAACGCCGCTAATGCTCTGACCTTTAGCGCCGTTTTTCCG-
1 AAAAACGCCGCTATTGCT-TTACCTTTTGCGGCGTTTAT--GA
* *
28486852 ACAAACGCCGCTATTGCTTTACCTTTTGCGGTGTTTATGA
1 AAAAACGCCGCTATTGCTTTACCTTTTGCGGCGTTTATGA
* * *
28486892 AAAAACGTCGCTATTGCTTTACCTTTTGTGGCGTTTATGG
1 AAAAACGCCGCTATTGCTTTACCTTTTGCGGCGTTTATGA
* *
28486932 AAAAGCGCCGCTATTGTTTTACCTTTTGCGGCGTTT
1 AAAAACGCCGCTATTGCTTTACCTTTTGCGGCGTTT
28486968 TCTGTCCAAA
Statistics
Matches: 132, Mismatches: 22, Indels: 9
0.81 0.13 0.06
Matches are distributed among these distances:
39 1 0.01
40 67 0.51
41 47 0.36
42 17 0.13
ACGTcount: A:0.20, C:0.25, G:0.21, T:0.35
Consensus pattern (40 bp):
AAAAACGCCGCTATTGCTTTACCTTTTGCGGCGTTTATGA
Found at i:28488519 original size:36 final size:36
Alignment explanation
Indices: 28488471--28488570 Score: 157
Period size: 36 Copynumber: 2.8 Consensus size: 36
28488461 CGATATTCGA
* *
28488471 TTTACTCTCTGTTGACACAAAGGTCATGATGCTCCT
1 TTTACTCCCTGTTGACACAAAGGTCATGATGCTCAT
*
28488507 TTTACTCCCTGTTGACCCAAAGGTCATGATGCTCAT
1 TTTACTCCCTGTTGACACAAAGGTCATGATGCTCAT
28488543 TTTACTCCCTGTTGA-ACCAAAGGTCATG
1 TTTACTCCCTGTTGACA-CAAAGGTCATG
28488571 CCTGTTACCA
Statistics
Matches: 59, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
36 59 1.00
ACGTcount: A:0.23, C:0.26, G:0.17, T:0.34
Consensus pattern (36 bp):
TTTACTCCCTGTTGACACAAAGGTCATGATGCTCAT
Found at i:28491369 original size:5 final size:5
Alignment explanation
Indices: 28491359--28491403 Score: 54
Period size: 5 Copynumber: 8.8 Consensus size: 5
28491349 ACTTACTAAC
* * *
28491359 AAAAT AAAAT AAAAT AAAAT AAAATT AAATT AAATT AAATT AAAA
1 AAAAT AAAAT AAAAT AAAAT AAAA-T AAAAT AAAAT AAAAT AAAA
28491404 ATAACCAAAC
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
5 33 0.89
6 4 0.11
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (5 bp):
AAAAT
Found at i:28491761 original size:4 final size:4
Alignment explanation
Indices: 28491752--28491776 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
28491742 TCTCTCATTC
28491752 TTCT TTCT TTCT TTCT TTCT TTCT T
1 TTCT TTCT TTCT TTCT TTCT TTCT T
28491777 CTCTCTTCTC
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:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (4 bp):
TTCT
Found at i:28491766 original size:23 final size:23
Alignment explanation
Indices: 28491740--28491783 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
28491730 TAAATTTACT
*
28491740 TTTCTCTCATTCTTCTTTCTTTC
1 TTTCTCTCATTCTTCTCTCTTTC
* *
28491763 TTTCTTTCTTTCTTCTCTCTT
1 TTTCTCTCATTCTTCTCTCTT
28491784 CTCTCTCCCG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.02, C:0.30, G:0.00, T:0.68
Consensus pattern (23 bp):
TTTCTCTCATTCTTCTCTCTTTC
Found at i:28493060 original size:1 final size:1
Alignment explanation
Indices: 28493056--28493086 Score: 53
Period size: 1 Copynumber: 31.0 Consensus size: 1
28493046 TTGGCAACCT
*
28493056 GGGGGTGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
28493087 CGTCCACACA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.97, T:0.03
Consensus pattern (1 bp):
G
Found at i:28498942 original size:19 final size:19
Alignment explanation
Indices: 28498918--28498955 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
28498908 CAAGTTTGTC
28498918 TTTGGATTTGGGTGACATA
1 TTTGGATTTGGGTGACATA
28498937 TTTGGATTTGGGTGACATA
1 TTTGGATTTGGGTGACATA
28498956 AAAGTTGGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.05, G:0.32, T:0.42
Consensus pattern (19 bp):
TTTGGATTTGGGTGACATA
Found at i:28500695 original size:23 final size:23
Alignment explanation
Indices: 28500652--28500697 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
28500642 TTTTGAGAGT
*
28500652 TTTAAAGAAAAATTTATGTGAAA
1 TTTAAAGAAAAATTTAAGTGAAA
*
28500675 TTTAGAGAGAAAA-TTAAGTGAAA
1 TTTAAAGA-AAAATTTAAGTGAAA
28500698 AAGGGTTTGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 16 0.80
24 4 0.20
ACGTcount: A:0.52, C:0.00, G:0.17, T:0.30
Consensus pattern (23 bp):
TTTAAAGAAAAATTTAAGTGAAA
Found at i:28508902 original size:23 final size:22
Alignment explanation
Indices: 28508876--28509041 Score: 116
Period size: 23 Copynumber: 7.2 Consensus size: 22
28508866 ACATTAGCGC
*
28508876 GCTTACTGTTCAGCATTGTGTGT
1 GCTTACTGTTC-GCACTGTGTGT
* * *
28508899 GCTTACTAATTCGCACTATATGT
1 GCTTACT-GTTCGCACTGTGTGT
*
28508922 GCTTACTGATTTGCACTGTGTGT
1 GCTTACTG-TTCGCACTGTGTGT
* ** **
28508945 GCTTACTATTTTTCACTGCATGT
1 GCTTACT-GTTCGCACTGTGTGT
* *
28508968 GCCTACTGATTTGCACTGTGTGT
1 GCTTACTG-TTCGCACTGTGTGT
* *
28508991 GCTTACTATTTTGCACTGTGTGT
1 GCTTACT-GTTCGCACTGTGTGT
* * *
28509014 GCCTACTAATTTGCACTGTGTGT
1 GCTTACT-GTTCGCACTGTGTGT
28509037 GCTTA
1 GCTTA
28509042 TTATTTCCCG
Statistics
Matches: 116, Mismatches: 22, Indels: 10
0.78 0.15 0.07
Matches are distributed among these distances:
23 113 0.97
24 3 0.03
ACGTcount: A:0.16, C:0.20, G:0.21, T:0.43
Consensus pattern (22 bp):
GCTTACTGTTCGCACTGTGTGT
Found at i:28508943 original size:46 final size:46
Alignment explanation
Indices: 28508892--28509047 Score: 231
Period size: 46 Copynumber: 3.4 Consensus size: 46
28508882 TGTTCAGCAT
* * * *
28508892 TGTGTGTGCTTACTAATTCGCACTATATGTGCTTACTGATTTGCAC
1 TGTGTGTGCTTACTATTTTGCACTGTATGTGCCTACTGATTTGCAC
* *
28508938 TGTGTGTGCTTACTATTTTTCACTGCATGTGCCTACTGATTTGCAC
1 TGTGTGTGCTTACTATTTTGCACTGTATGTGCCTACTGATTTGCAC
* *
28508984 TGTGTGTGCTTACTATTTTGCACTGTGTGTGCCTACTAATTTGCAC
1 TGTGTGTGCTTACTATTTTGCACTGTATGTGCCTACTGATTTGCAC
*
28509030 TGTGTGTGCTTATTATTT
1 TGTGTGTGCTTACTATTT
28509048 CCCGAGCACT
Statistics
Matches: 99, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
46 99 1.00
ACGTcount: A:0.16, C:0.19, G:0.21, T:0.45
Consensus pattern (46 bp):
TGTGTGTGCTTACTATTTTGCACTGTATGTGCCTACTGATTTGCAC
Found at i:28509038 original size:69 final size:69
Alignment explanation
Indices: 28508892--28509038 Score: 188
Period size: 69 Copynumber: 2.1 Consensus size: 69
28508882 TGTTCAGCAT
* * *
28508892 TGTGTGTGCTTACTAATTCGCACTATATGTGCTTACTGATTTGCACTGTGTGTGCTTACTATTTT
1 TGTGTGTGCCTACTAATTCGCACTATATGTGCTTACTGATTTGCACTGTGTGTGCCTACTAATTT
*
28508957 TCAC
66 GCAC
** * * * *
28508961 TGCATGTGCCTACTGATTTGCACTGTGTGTGCTTACT-ATTTTGCACTGTGTGTGCCTACTAATT
1 TGTGTGTGCCTACTAATTCGCACTATATGTGCTTACTGA-TTTGCACTGTGTGTGCCTACTAATT
28509025 TGCAC
65 TGCAC
28509030 TGTGTGTGC
1 TGTGTGTGC
28509039 TTATTATTTC
Statistics
Matches: 65, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
68 1 0.02
69 64 0.98
ACGTcount: A:0.16, C:0.20, G:0.22, T:0.43
Consensus pattern (69 bp):
TGTGTGTGCCTACTAATTCGCACTATATGTGCTTACTGATTTGCACTGTGTGTGCCTACTAATTT
GCAC
Found at i:28510943 original size:51 final size:51
Alignment explanation
Indices: 28510863--28511048 Score: 241
Period size: 51 Copynumber: 3.6 Consensus size: 51
28510853 TTTCATTTAA
* * * * *
28510863 TACTCACGATGATATATTA-TCAT-AGGACCTTTAATTCGTCATGGATTCATT
1 TACTCACGATGACA-CTTAGTCATCA-GACCTTTAATCCGTAAAGGATTCATT
28510914 TACTCACGATGACACTTAGTCATCAGACCTTTAATCCGTAAAGGATTCATT
1 TACTCACGATGACACTTAGTCATCAGACCTTTAATCCGTAAAGGATTCATT
* * *
28510965 TACTCATGATGACACTTAGTCATCGGACTTTTAATCCGTAAAGGATTCATT
1 TACTCACGATGACACTTAGTCATCAGACCTTTAATCCGTAAAGGATTCATT
* *
28511016 TACTCACGATGACATTTAGTCATCGGACTCTTT
1 TACTCACGATGACACTTAGTCATCAGAC-CTTT
28511049 CGTTTATAGC
Statistics
Matches: 121, Mismatches: 11, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
50 3 0.02
51 114 0.94
52 4 0.03
ACGTcount: A:0.29, C:0.21, G:0.15, T:0.35
Consensus pattern (51 bp):
TACTCACGATGACACTTAGTCATCAGACCTTTAATCCGTAAAGGATTCATT
Found at i:28517217 original size:51 final size:51
Alignment explanation
Indices: 28517136--28517360 Score: 287
Period size: 51 Copynumber: 4.5 Consensus size: 51
28517126 TTTCATTTAA
* * * * * * *
28517136 TACTCACGATTACA-TATTGTCATAGAACCTTTAATTCGTCATGGATTCATT
1 TACTCACGATGACACT-TAGTCATCGGACCTTTAATCCGTAAAGGATTCATT
* *
28517187 TACTCACGATAACACTTAATCATCGGACCTTTAATCCGTAAAGGATTCATT
1 TACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAAAGGATTCATT
* * *
28517238 TATTCACGATGACACTTAGTCATCGGACCTTTAAT---TTACGGATTCATT
1 TACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAAAGGATTCATT
*
28517286 TACTCACGATGACACTTAGTCATTGGACCTTTAATCCGTAAAGGATTCATT
1 TACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAAAGGATTCATT
*
28517337 TACTCACGATGACATTTAGTCATC
1 TACTCACGATGACACTTAGTCATC
28517361 AAACTCTTTT
Statistics
Matches: 151, Mismatches: 19, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
48 44 0.29
51 106 0.70
52 1 0.01
ACGTcount: A:0.30, C:0.22, G:0.13, T:0.35
Consensus pattern (51 bp):
TACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAAAGGATTCATT
Found at i:28517314 original size:99 final size:99
Alignment explanation
Indices: 28517178--28517360 Score: 321
Period size: 99 Copynumber: 1.8 Consensus size: 99
28517168 AATTCGTCAT
*
28517178 GGATTCATTTACTCACGATAACACTTAATCATCGGACCTTTAATCCGTAAAGGATTCATTTATTC
1 GGATTCATTTACTCACGATAACACTTAATCATCGGACCTTTAATCCGTAAAGGATTCATTTACTC
28517243 ACGATGACACTTAGTCATCGGACCTTTAATTTAC
66 ACGATGACACTTAGTCATCGGACCTTTAATTTAC
* * *
28517277 GGATTCATTTACTCACGATGACACTTAGTCATTGGACCTTTAATCCGTAAAGGATTCATTTACTC
1 GGATTCATTTACTCACGATAACACTTAATCATCGGACCTTTAATCCGTAAAGGATTCATTTACTC
*
28517342 ACGATGACATTTAGTCATC
66 ACGATGACACTTAGTCATC
28517361 AAACTCTTTT
Statistics
Matches: 79, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
99 79 1.00
ACGTcount: A:0.30, C:0.22, G:0.14, T:0.34
Consensus pattern (99 bp):
GGATTCATTTACTCACGATAACACTTAATCATCGGACCTTTAATCCGTAAAGGATTCATTTACTC
ACGATGACACTTAGTCATCGGACCTTTAATTTAC
Found at i:28536537 original size:16 final size:17
Alignment explanation
Indices: 28536518--28536552 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
28536508 ATATTTAATA
28536518 ATTTAAT-AAATTTTTT
1 ATTTAATAAAATTTTTT
*
28536534 ATTTATTAAAATTTTTT
1 ATTTAATAAAATTTTTT
28536551 AT
1 AT
28536553 ATAGTCATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 6 0.35
17 11 0.65
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (17 bp):
ATTTAATAAAATTTTTT
Found at i:28536949 original size:24 final size:26
Alignment explanation
Indices: 28536906--28536956 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
28536896 TGTCTCAAGT
28536906 TTAAAATTTTATATTCAAAAAAAAAA
1 TTAAAATTTTATATTCAAAAAAAAAA
*
28536932 TTAAAATTTTAT-TT-AAAAATAAAA
1 TTAAAATTTTATATTCAAAAAAAAAA
28536956 T
1 T
28536957 ACTTTCATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 10 0.42
25 2 0.08
26 12 0.50
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (26 bp):
TTAAAATTTTATATTCAAAAAAAAAA
Found at i:28542818 original size:3 final size:3
Alignment explanation
Indices: 28542810--28542840 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
28542800 ATGACCTTTT
28542810 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC A
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC A
28542841 ACCAAGTAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.35, C:0.32, G:0.00, T:0.32
Consensus pattern (3 bp):
ATC
Found at i:28552051 original size:14 final size:14
Alignment explanation
Indices: 28552032--28552059 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
28552022 TATACAAAAA
28552032 CGACGAATTCCAGT
1 CGACGAATTCCAGT
28552046 CGACGAATTCCAGT
1 CGACGAATTCCAGT
28552060 TGATATACAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.21
Consensus pattern (14 bp):
CGACGAATTCCAGT
Found at i:28559193 original size:15 final size:16
Alignment explanation
Indices: 28559163--28559201 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 16
28559153 TAGTAAAAAT
28559163 ATAATTTTATTATTTTA
1 ATAA-TTTATTATTTTA
*
28559180 ATAATTTA-TATTTTT
1 ATAATTTATTATTTTA
28559195 ATAATTT
1 ATAATTT
28559202 TTAAAAGATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 13 0.62
16 4 0.19
17 4 0.19
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
ATAATTTATTATTTTA
Found at i:28563798 original size:11 final size:11
Alignment explanation
Indices: 28563782--28563811 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
28563772 GATTCAGGTG
28563782 AGATCCAATGT
1 AGATCCAATGT
28563793 AGATCCAATGT
1 AGATCCAATGT
28563804 AGATCCAA
1 AGATCCAA
28563812 CTTTCTATTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.40, C:0.20, G:0.17, T:0.23
Consensus pattern (11 bp):
AGATCCAATGT
Found at i:28571214 original size:10 final size:10
Alignment explanation
Indices: 28571199--28571228 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
28571189 GAATCTTATA
28571199 ATTTAATATT
1 ATTTAATATT
28571209 ATTTAATATT
1 ATTTAATATT
28571219 A-TTAATATT
1 ATTTAATATT
28571228 A
1 A
28571229 CTTATTCAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 9 0.45
10 11 0.55
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (10 bp):
ATTTAATATT
Found at i:28579715 original size:18 final size:16
Alignment explanation
Indices: 28579683--28579716 Score: 50
Period size: 18 Copynumber: 2.0 Consensus size: 16
28579673 ATCATCTCCC
28579683 GAATAAAATAAAGAAA
1 GAATAAAATAAAGAAA
28579699 GAATAAGAATCAAAGAAA
1 GAATAA-AAT-AAAGAAA
28579717 AGGCAACGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.38
17 3 0.19
18 7 0.44
ACGTcount: A:0.71, C:0.03, G:0.15, T:0.12
Consensus pattern (16 bp):
GAATAAAATAAAGAAA
Found at i:28582220 original size:15 final size:15
Alignment explanation
Indices: 28582202--28582232 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
28582192 GGCAAAAAAC
*
28582202 ATAAAATAAAAAGGA
1 ATAAAAAAAAAAGGA
28582217 ATAAAAAAAAAAGGA
1 ATAAAAAAAAAAGGA
28582232 A
1 A
28582233 ATGAAATCAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.77, C:0.00, G:0.13, T:0.10
Consensus pattern (15 bp):
ATAAAAAAAAAAGGA
Found at i:28584407 original size:20 final size:20
Alignment explanation
Indices: 28584384--28584421 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
28584374 GTCTATATTA
*
28584384 AGATTATATTAAATATATAT
1 AGATTATATTAAAAATATAT
*
28584404 AGATTCTATTAAAAATAT
1 AGATTATATTAAAAATAT
28584422 GGACAATCAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.50, C:0.03, G:0.05, T:0.42
Consensus pattern (20 bp):
AGATTATATTAAAAATATAT
Found at i:28587912 original size:17 final size:17
Alignment explanation
Indices: 28587874--28587912 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
28587864 AGGTGGAGAA
* *
28587874 CTTGTTCGTTGAGAGTT
1 CTTGTTCGTAGAGAATT
28587891 CTTGTTCGTAGAGAATT
1 CTTGTTCGTAGAGAATT
*
28587908 TTTGT
1 CTTGT
28587913 CAAGGTGGAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.15, C:0.10, G:0.26, T:0.49
Consensus pattern (17 bp):
CTTGTTCGTAGAGAATT
Found at i:28592085 original size:19 final size:21
Alignment explanation
Indices: 28592044--28592086 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
28592034 CTGCAACTTT
*
28592044 TACCGATACTAGTGATCAAAC
1 TACCGATACTAATGATCAAAC
28592065 TACCGATACTAAT-AT-AAAC
1 TACCGATACTAATGATCAAAC
28592084 TAC
1 TAC
28592087 TGACACTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 7 0.33
20 2 0.10
21 12 0.57
ACGTcount: A:0.42, C:0.23, G:0.09, T:0.26
Consensus pattern (21 bp):
TACCGATACTAATGATCAAAC
Found at i:28592711 original size:26 final size:27
Alignment explanation
Indices: 28592676--28592795 Score: 113
Period size: 26 Copynumber: 4.6 Consensus size: 27
28592666 CAAGTCATTC
28592676 CAGAAGTTTAGCTCATACAG-GCCTAGA
1 CAGAA-TTTAGCTCATACAGAGCCTAGA
* * *
28592703 TAGAATTTAGATCTTAC-GAGCCTAGA
1 CAGAATTTAGCTCATACAGAGCCTAGA
* * *
28592729 TAGATTTTAGCTCTTACA-AGCCTAGA
1 CAGAATTTAGCTCATACAGAGCCTAGA
* ** *
28592755 CAGAGTTTAGCTCAT-GTGAGCCCAGA
1 CAGAATTTAGCTCATACAGAGCCTAGA
28592781 CAGAATTTAGCTCAT
1 CAGAATTTAGCTCAT
28592796 GCGAGCCCAA
Statistics
Matches: 78, Mismatches: 12, Indels: 7
0.80 0.12 0.07
Matches are distributed among these distances:
25 1 0.01
26 73 0.94
27 4 0.05
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.28
Consensus pattern (27 bp):
CAGAATTTAGCTCATACAGAGCCTAGA
Found at i:28592776 original size:52 final size:52
Alignment explanation
Indices: 28592676--28592795 Score: 132
Period size: 52 Copynumber: 2.3 Consensus size: 52
28592666 CAAGTCATTC
* * * *
28592676 CAGAAGTTTAGCTCATACAGGCCTAGATAGAATTTAGATCTTACGAGCCTAGA
1 CAGAA-TTTAGCTCATACAAGCCTAGACAGAATTTAGATCATACGAGCCCAGA
* * * * * **
28592729 TAGATTTTAGCTCTTACAAGCCTAGACAGAGTTTAGCTCATGTGAGCCCAGA
1 CAGAATTTAGCTCATACAAGCCTAGACAGAATTTAGATCATACGAGCCCAGA
28592781 CAGAATTTAGCTCAT
1 CAGAATTTAGCTCAT
28592796 GCGAGCCCAA
Statistics
Matches: 53, Mismatches: 14, Indels: 1
0.78 0.21 0.01
Matches are distributed among these distances:
52 50 0.94
53 3 0.06
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.28
Consensus pattern (52 bp):
CAGAATTTAGCTCATACAAGCCTAGACAGAATTTAGATCATACGAGCCCAGA
Found at i:28594575 original size:17 final size:17
Alignment explanation
Indices: 28594553--28594587 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
28594543 TGCCCCAAAC
28594553 CTTTTTCTTTCTTTTTT
1 CTTTTTCTTTCTTTTTT
28594570 CTTTTTCTTTCTTTTTT
1 CTTTTTCTTTCTTTTTT
28594587 C
1 C
28594588 CTTGCCTTAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (17 bp):
CTTTTTCTTTCTTTTTT
Found at i:28594894 original size:3 final size:3
Alignment explanation
Indices: 28594888--28594919 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
28594878 TGTGTAGGGG
28594888 GTT GTT GTT GTT GTT GTT GTT GTT G-T GTT GTT
1 GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT
28594920 AGTGTGAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 26 0.93
ACGTcount: A:0.00, C:0.00, G:0.34, T:0.66
Consensus pattern (3 bp):
GTT
Found at i:28595111 original size:15 final size:16
Alignment explanation
Indices: 28595091--28595121 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
28595081 AACCCACATT
28595091 CATTT-AAACCAAACC
1 CATTTAAAACCAAACC
28595106 CATTTAAAACCAAACC
1 CATTTAAAACCAAACC
28595122 AAACCCATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.48, C:0.32, G:0.00, T:0.19
Consensus pattern (16 bp):
CATTTAAAACCAAACC
Found at i:28595120 original size:21 final size:21
Alignment explanation
Indices: 28595096--28595164 Score: 113
Period size: 21 Copynumber: 3.3 Consensus size: 21
28595086 ACATTCATTT
28595096 AAACCAAACCCATTTAAAACC
1 AAACCAAACCCATTTAAAACC
28595117 AAACCAAACCCATTTAAAACC
1 AAACCAAACCCATTTAAAACC
* *
28595138 TAACCAAACCCATTT-GAACC
1 AAACCAAACCCATTTAAAACC
28595158 AAACCAA
1 AAACCAA
28595165 TTGAACCAAG
Statistics
Matches: 45, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
20 10 0.22
21 35 0.78
ACGTcount: A:0.51, C:0.33, G:0.01, T:0.14
Consensus pattern (21 bp):
AAACCAAACCCATTTAAAACC
Done.