Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032250.1 Gossypioides kirkii chromosome KI_08
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: 39602670
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 500 characters in sequence are not A, C, G, or T
File 121 of 125
Found at i:38126886 original size:15 final size:17
Alignment explanation
Indices: 38126839--38126889 Score: 63
Period size: 16 Copynumber: 3.2 Consensus size: 17
38126829 AAAAAATCAG
*
38126839 AATATAAAATA-TAAAA
1 AATATAAATTATTAAAA
*
38126855 CATATAAATTATTAAAA
1 AATATAAATTATTAAAA
38126872 AATAT-AATT-TTAAAA
1 AATATAAATTATTAAAA
38126887 AAT
1 AAT
38126890 TAAGTGATGA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
15 9 0.29
16 13 0.42
17 9 0.29
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (17 bp):
AATATAAATTATTAAAA
Found at i:38132324 original size:13 final size:13
Alignment explanation
Indices: 38132287--38132330 Score: 54
Period size: 13 Copynumber: 3.4 Consensus size: 13
38132277 TAAATGAACC
* *
38132287 AAATTAAATAAAA
1 AAATTAAATATAT
38132300 AAATTAAAATATAT
1 AAATT-AAATATAT
38132314 AAATTAAATAT-T
1 AAATTAAATATAT
38132326 AAATT
1 AAATT
38132331 TCAAGATACT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
12 6 0.21
13 11 0.39
14 11 0.39
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (13 bp):
AAATTAAATATAT
Found at i:38133731 original size:69 final size:69
Alignment explanation
Indices: 38133649--38133789 Score: 282
Period size: 69 Copynumber: 2.0 Consensus size: 69
38133639 AATATCAGGT
38133649 TCCATCATTAGTTTCCTCCGGTTCCAAAATCCTTAACTCAAAAACACCTCTTTCGCTCTCTATCA
1 TCCATCATTAGTTTCCTCCGGTTCCAAAATCCTTAACTCAAAAACACCTCTTTCGCTCTCTATCA
38133714 TTTC
66 TTTC
38133718 TCCATCATTAGTTTCCTCCGGTTCCAAAATCCTTAACTCAAAAACACCTCTTTCGCTCTCTATCA
1 TCCATCATTAGTTTCCTCCGGTTCCAAAATCCTTAACTCAAAAACACCTCTTTCGCTCTCTATCA
38133783 TTTC
66 TTTC
38133787 TCC
1 TCC
38133790 CTATTGGCCG
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
69 72 1.00
ACGTcount: A:0.24, C:0.34, G:0.06, T:0.36
Consensus pattern (69 bp):
TCCATCATTAGTTTCCTCCGGTTCCAAAATCCTTAACTCAAAAACACCTCTTTCGCTCTCTATCA
TTTC
Found at i:38146796 original size:25 final size:25
Alignment explanation
Indices: 38146766--38146847 Score: 155
Period size: 25 Copynumber: 3.2 Consensus size: 25
38146756 ATATATATAT
38146766 AAATATTATAGGAAAACAGGGTAAA
1 AAATATTATAGGAAAACAGGGTAAA
38146791 AAATATTATAGGAAAACAGGGTAAAA
1 AAATATTATAGGAAAACAGGGT-AAA
38146817 AAATATTATAGGAAAACAGGGTAAA
1 AAATATTATAGGAAAACAGGGTAAA
38146842 AAATAT
1 AAATAT
38146848 AAATAAAATT
Statistics
Matches: 56, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
25 31 0.55
26 25 0.45
ACGTcount: A:0.57, C:0.04, G:0.18, T:0.21
Consensus pattern (25 bp):
AAATATTATAGGAAAACAGGGTAAA
Found at i:38146824 original size:26 final size:26
Alignment explanation
Indices: 38146766--38146844 Score: 151
Period size: 26 Copynumber: 3.1 Consensus size: 26
38146756 ATATATATAT
38146766 AAATATTATAGGAAAACAGGGT-AAA
1 AAATATTATAGGAAAACAGGGTAAAA
38146791 AAATATTATAGGAAAACAGGGTAAAA
1 AAATATTATAGGAAAACAGGGTAAAA
38146817 AAATATTATAGGAAAACAGGGTAAAA
1 AAATATTATAGGAAAACAGGGTAAAA
38146843 AA
1 AA
38146845 TATAAATAAA
Statistics
Matches: 53, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
25 22 0.42
26 31 0.58
ACGTcount: A:0.58, C:0.04, G:0.19, T:0.19
Consensus pattern (26 bp):
AAATATTATAGGAAAACAGGGTAAAA
Found at i:38153348 original size:17 final size:17
Alignment explanation
Indices: 38153326--38153360 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
38153316 ATGGAAACAA
38153326 ATATATGGTAAAATATT
1 ATATATGGTAAAATATT
*
38153343 ATATATGGTAATATATT
1 ATATATGGTAAAATATT
38153360 A
1 A
38153361 GAATATATAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.46, C:0.00, G:0.11, T:0.43
Consensus pattern (17 bp):
ATATATGGTAAAATATT
Found at i:38161862 original size:16 final size:15
Alignment explanation
Indices: 38161843--38161890 Score: 53
Period size: 16 Copynumber: 3.1 Consensus size: 15
38161833 AAAATATTAT
38161843 AAAAACTAAATAAAAC
1 AAAAA-TAAATAAAAC
38161859 AAAAATAAAATTAAAA-
1 AAAAAT-AAA-TAAAAC
*
38161875 ACAAATAAATAAAAC
1 AAAAATAAATAAAAC
38161890 A
1 A
38161891 TATGGCTAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
14 5 0.18
15 5 0.18
16 13 0.46
17 5 0.18
ACGTcount: A:0.77, C:0.08, G:0.00, T:0.15
Consensus pattern (15 bp):
AAAAATAAATAAAAC
Found at i:38177870 original size:14 final size:16
Alignment explanation
Indices: 38177848--38177886 Score: 64
Period size: 14 Copynumber: 2.6 Consensus size: 16
38177838 TGTTGATTTT
38177848 TACTAATTTGTTGAA-
1 TACTAATTTGTTGAAC
38177863 TA-TAATTTGTTGAAC
1 TACTAATTTGTTGAAC
38177878 TACTAATTT
1 TACTAATTT
38177887 TTTTTGTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 12 0.55
15 4 0.18
16 6 0.27
ACGTcount: A:0.33, C:0.08, G:0.10, T:0.49
Consensus pattern (16 bp):
TACTAATTTGTTGAAC
Found at i:38182520 original size:39 final size:36
Alignment explanation
Indices: 38182439--38182523 Score: 98
Period size: 39 Copynumber: 2.3 Consensus size: 36
38182429 TTTTGATGCC
*
38182439 TGTGATAACTCGAAGCAAAAGAAATCAGAAGATTCA
1 TGTGATAACTCGAAGCAAAAAAAATCAGAAGATTCA
* * * *
38182475 TCTGATATCTCAGAAGCAAAGCAAAAATTAGAAGATTCT
1 TGTGATAACTC-GAAGCAAA--AAAAATCAGAAGATTCA
38182514 TGTGATAACT
1 TGTGATAACT
38182524 TAGGGTCACA
Statistics
Matches: 39, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
36 9 0.23
37 8 0.21
39 22 0.56
ACGTcount: A:0.44, C:0.14, G:0.18, T:0.25
Consensus pattern (36 bp):
TGTGATAACTCGAAGCAAAAAAAATCAGAAGATTCA
Found at i:38182578 original size:39 final size:39
Alignment explanation
Indices: 38182535--38182629 Score: 113
Period size: 39 Copynumber: 2.4 Consensus size: 39
38182525 AGGGTCACAT
*
38182535 AGAAAATCTGAAGATTCCTGTAATGTTT-T-AGGGCCAAAG
1 AGAAAATCGGAAGATTCCTGT-A-GTTTCTCAGGGCCAAAG
* * * *
38182574 AGAAAATGGGACGGTTCCTGTAGTTTCTCAGGGCTAAAG
1 AGAAAATCGGAAGATTCCTGTAGTTTCTCAGGGCCAAAG
38182613 AGAAAATCGGAAGATTC
1 AGAAAATCGGAAGATTC
38182630 AAGAAAATCA
Statistics
Matches: 46, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
37 4 0.09
38 2 0.04
39 40 0.87
ACGTcount: A:0.35, C:0.14, G:0.26, T:0.25
Consensus pattern (39 bp):
AGAAAATCGGAAGATTCCTGTAGTTTCTCAGGGCCAAAG
Found at i:38185997 original size:15 final size:16
Alignment explanation
Indices: 38185967--38186007 Score: 66
Period size: 15 Copynumber: 2.6 Consensus size: 16
38185957 CAGTTTCGAA
38185967 GAAAAAGAAATATGTG
1 GAAAAAGAAATATGTG
38185983 GAAAAAGAAAT-TGTG
1 GAAAAAGAAATATGTG
*
38185998 CAAAAAGAAA
1 GAAAAAGAAA
38186008 AAGCATAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 13 0.54
16 11 0.46
ACGTcount: A:0.61, C:0.02, G:0.22, T:0.15
Consensus pattern (16 bp):
GAAAAAGAAATATGTG
Found at i:38186444 original size:20 final size:19
Alignment explanation
Indices: 38186419--38186461 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
38186409 GGCTAAACCT
38186419 TTTTATATATATTGATGGGG
1 TTTTATATATATTGAT-GGG
* *
38186439 TTTTATTTTTATTGATGGG
1 TTTTATATATATTGATGGG
38186458 TTTT
1 TTTT
38186462 GTTTTTTTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.19, C:0.00, G:0.21, T:0.60
Consensus pattern (19 bp):
TTTTATATATATTGATGGG
Found at i:38186468 original size:20 final size:20
Alignment explanation
Indices: 38186428--38186467 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
38186418 TTTTTATATA
38186428 TATTGATGGGGTTTTATTTT
1 TATTGATGGGGTTTTATTTT
*
38186448 TATTGAT-GGGTTTTGTTTT
1 TATTGATGGGGTTTTATTTT
38186467 T
1 T
38186468 TTATCAAGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 12 0.63
20 7 0.37
ACGTcount: A:0.12, C:0.00, G:0.25, T:0.62
Consensus pattern (20 bp):
TATTGATGGGGTTTTATTTT
Found at i:38187219 original size:2 final size:2
Alignment explanation
Indices: 38187212--38187239 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
38187202 TTCTGATTGG
38187212 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
38187240 TGTAACAGGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:38192593 original size:15 final size:15
Alignment explanation
Indices: 38192569--38192599 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
38192559 CATTTTAAAT
38192569 TTATAATATTTTATA
1 TTATAATATTTTATA
*
38192584 TTATATTATTTTATA
1 TTATAATATTTTATA
38192599 T
1 T
38192600 ATTATACAAT
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:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (15 bp):
TTATAATATTTTATA
Found at i:38193018 original size:25 final size:25
Alignment explanation
Indices: 38192972--38193021 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
38192962 TCTTCACAAA
* *
38192972 TTAAAAATTTAGTATTTATACTTTT
1 TTAAAAATTTAATATCTATACTTTT
* *
38192997 TTAAAAATTTAATCTCTCTACTTTT
1 TTAAAAATTTAATATCTATACTTTT
38193022 CAGATTTCAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.34, C:0.10, G:0.02, T:0.54
Consensus pattern (25 bp):
TTAAAAATTTAATATCTATACTTTT
Found at i:38194620 original size:173 final size:173
Alignment explanation
Indices: 38194331--38194677 Score: 694
Period size: 173 Copynumber: 2.0 Consensus size: 173
38194321 ACTTTTCTAG
38194331 AATATATATTTAAGAGAGTTATATTCTTTGCAGTTTTCCAAATTGAACTAGTTTTGCATTTTTTG
1 AATATATATTTAAGAGAGTTATATTCTTTGCAGTTTTCCAAATTGAACTAGTTTTGCATTTTTTG
38194396 AACTTTAAAATTTATATTTTGTTTATTTAAAAATATTTTCTTTAACATTATTGCAATATGTTTAG
66 AACTTTAAAATTTATATTTTGTTTATTTAAAAATATTTTCTTTAACATTATTGCAATATGTTTAG
38194461 AGTTTATAGCCCACAAAAAATTACGAAAAAACTTAACGATGAA
131 AGTTTATAGCCCACAAAAAATTACGAAAAAACTTAACGATGAA
38194504 AATATATATTTAAGAGAGTTATATTCTTTGCAGTTTTCCAAATTGAACTAGTTTTGCATTTTTTG
1 AATATATATTTAAGAGAGTTATATTCTTTGCAGTTTTCCAAATTGAACTAGTTTTGCATTTTTTG
38194569 AACTTTAAAATTTATATTTTGTTTATTTAAAAATATTTTCTTTAACATTATTGCAATATGTTTAG
66 AACTTTAAAATTTATATTTTGTTTATTTAAAAATATTTTCTTTAACATTATTGCAATATGTTTAG
38194634 AGTTTATAGCCCACAAAAAATTACGAAAAAACTTAACGATGAA
131 AGTTTATAGCCCACAAAAAATTACGAAAAAACTTAACGATGAA
38194677 A
1 A
38194678 TATCAGAGCC
Statistics
Matches: 174, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
173 174 1.00
ACGTcount: A:0.37, C:0.10, G:0.10, T:0.43
Consensus pattern (173 bp):
AATATATATTTAAGAGAGTTATATTCTTTGCAGTTTTCCAAATTGAACTAGTTTTGCATTTTTTG
AACTTTAAAATTTATATTTTGTTTATTTAAAAATATTTTCTTTAACATTATTGCAATATGTTTAG
AGTTTATAGCCCACAAAAAATTACGAAAAAACTTAACGATGAA
Found at i:38212038 original size:22 final size:22
Alignment explanation
Indices: 38212010--38212053 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
38212000 AATGAGACCA
* *
38212010 TTTTTTAATAATTATGTTTTAT
1 TTTTTTAATAATCATATTTTAT
*
38212032 TTTTTTATTAATCATATTTTAT
1 TTTTTTAATAATCATATTTTAT
38212054 ATTATGAGAT
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:0.27, C:0.02, G:0.02, T:0.68
Consensus pattern (22 bp):
TTTTTTAATAATCATATTTTAT
Found at i:38221187 original size:18 final size:17
Alignment explanation
Indices: 38221164--38221197 Score: 59
Period size: 17 Copynumber: 1.9 Consensus size: 17
38221154 TATGGGAAGG
38221164 TAAAAATTATTAAAAAAA
1 TAAAAA-TATTAAAAAAA
38221182 TAAAAATATTAAAAAA
1 TAAAAATATTAAAAAA
38221198 TTAATTAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (17 bp):
TAAAAATATTAAAAAAA
Found at i:38222931 original size:21 final size:21
Alignment explanation
Indices: 38222907--38222951 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
38222897 TATTACCATT
* *
38222907 TAAAACATATTTATATAAATA
1 TAAAACATATTGAAATAAATA
**
38222928 TAAAATTTATTGAAATAAATA
1 TAAAACATATTGAAATAAATA
38222949 TAA
1 TAA
38222952 TATAACAAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (21 bp):
TAAAACATATTGAAATAAATA
Found at i:38242687 original size:16 final size:16
Alignment explanation
Indices: 38242666--38242696 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
38242656 TACAAAAAAA
38242666 TTCCATGAAGACAAAG
1 TTCCATGAAGACAAAG
*
38242682 TTCCATGCAGACAAA
1 TTCCATGAAGACAAA
38242697 AGTAATTTTT
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:0.42, C:0.23, G:0.16, T:0.19
Consensus pattern (16 bp):
TTCCATGAAGACAAAG
Found at i:38254853 original size:67 final size:67
Alignment explanation
Indices: 38254763--38254898 Score: 263
Period size: 67 Copynumber: 2.0 Consensus size: 67
38254753 AAAATCCATC
38254763 TACTTTTAGAGTTAGAGGGGAATAAAAATAAATAAATAAGAGAGTTTATGAAAAAAATTACCCTT
1 TACTTTTAGAGTTAGAGGGGAATAAAAATAAATAAATAAGAGAGTTTATGAAAAAAATTACCCTT
38254828 TT
66 TT
*
38254830 TACTTTTAGTGTTAGAGGGGAATAAAAATAAATAAATAAGAGAGTTTATGAAAAAAATTACCCTT
1 TACTTTTAGAGTTAGAGGGGAATAAAAATAAATAAATAAGAGAGTTTATGAAAAAAATTACCCTT
38254895 TT
66 TT
38254897 TA
1 TA
38254899 ATAAATAAGA
Statistics
Matches: 68, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
67 68 1.00
ACGTcount: A:0.46, C:0.06, G:0.16, T:0.32
Consensus pattern (67 bp):
TACTTTTAGAGTTAGAGGGGAATAAAAATAAATAAATAAGAGAGTTTATGAAAAAAATTACCCTT
TT
Found at i:38254930 original size:39 final size:38
Alignment explanation
Indices: 38254860--38254938 Score: 122
Period size: 39 Copynumber: 2.1 Consensus size: 38
38254850 AATAAAAATA
38254860 AATAAATAAGAGAGTTTATGAAAAAAATTACCCTTTTT
1 AATAAATAAGAGAGTTTATGAAAAAAATTACCCTTTTT
** *
38254898 AATAAATAAGAGGAGTTTATGAAGGAATTTACCCTTTTT
1 AATAAATAAGA-GAGTTTATGAAAAAAATTACCCTTTTT
38254937 AA
1 AA
38254939 CATCATTAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
38 11 0.30
39 26 0.70
ACGTcount: A:0.44, C:0.08, G:0.14, T:0.34
Consensus pattern (38 bp):
AATAAATAAGAGAGTTTATGAAAAAAATTACCCTTTTT
Found at i:38258642 original size:28 final size:30
Alignment explanation
Indices: 38258597--38258654 Score: 84
Period size: 28 Copynumber: 2.0 Consensus size: 30
38258587 GGAAATACAA
38258597 GAAACACACATAATACATACACACACACAC
1 GAAACACACATAATACATACACACACACAC
* *
38258627 GAAA-ACACA-AATACATACATACATACAC
1 GAAACACACATAATACATACACACACACAC
38258655 ATACATACAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
28 17 0.65
29 5 0.19
30 4 0.15
ACGTcount: A:0.55, C:0.29, G:0.03, T:0.12
Consensus pattern (30 bp):
GAAACACACATAATACATACACACACACAC
Found at i:38258644 original size:4 final size:4
Alignment explanation
Indices: 38258637--38258681 Score: 58
Period size: 4 Copynumber: 11.8 Consensus size: 4
38258627 GAAAACACAA
* *
38258637 ATAC ATAC ATAC ATAC --AC ATAC ATAC ATAC ATGC ATAT ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
38258682 GGAACATACA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
2 2 0.06
4 33 0.94
ACGTcount: A:0.49, C:0.22, G:0.02, T:0.27
Consensus pattern (4 bp):
ATAC
Found at i:38258658 original size:14 final size:14
Alignment explanation
Indices: 38258639--38258681 Score: 59
Period size: 14 Copynumber: 2.9 Consensus size: 14
38258629 AAACACAAAT
38258639 ACATACATACATAC
1 ACATACATACATAC
38258653 ACATACATACATAC
1 ACATACATACATAC
*
38258667 ATGCATATATACATA
1 A--CATACATACATA
38258682 GGAACATACA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
14 15 0.58
16 11 0.42
ACGTcount: A:0.49, C:0.23, G:0.02, T:0.26
Consensus pattern (14 bp):
ACATACATACATAC
Found at i:38265831 original size:31 final size:31
Alignment explanation
Indices: 38265795--38265863 Score: 88
Period size: 31 Copynumber: 2.2 Consensus size: 31
38265785 CTTTGCAGTC
*
38265795 TAATGATTTAAAT-AGAAACTTT-TAAATTGTT
1 TAATGATTTAAATGA-AAACTTTCT-AATAGTT
*
38265826 TAATGACTTAAATGAAAACTTTCTAATAGTT
1 TAATGATTTAAATGAAAACTTTCTAATAGTT
38265857 TAATGAT
1 TAATGAT
38265864 CATTTTTTAA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
31 31 0.94
32 2 0.06
ACGTcount: A:0.42, C:0.06, G:0.10, T:0.42
Consensus pattern (31 bp):
TAATGATTTAAATGAAAACTTTCTAATAGTT
Found at i:38281218 original size:24 final size:24
Alignment explanation
Indices: 38281191--38281237 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
38281181 ACTTAATTGA
38281191 ATAATTAACTCAACAACTAACTAT
1 ATAATTAACTCAACAACTAACTAT
*
38281215 ATAATTATCTCAACAACTAACTA
1 ATAATTAACTCAACAACTAACTA
38281238 AACTAGAACT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.49, C:0.21, G:0.00, T:0.30
Consensus pattern (24 bp):
ATAATTAACTCAACAACTAACTAT
Found at i:38282492 original size:51 final size:50
Alignment explanation
Indices: 38282409--38282548 Score: 122
Period size: 51 Copynumber: 2.8 Consensus size: 50
38282399 ATTGCTATGA
* * * * * *
38282409 TAACAAATTTAGCCCT-CAAAGTTTATATATTTTGTCAAATTAGTAT-TGATT
1 TAACAAATTTAG-CATGCAAAATTTACACATTTTATC-AATTAG-ATCTAATT
*
38282460 TAACAAATTTAGCATGCAAAATTTACACATTTTATCAATTTGATCCTAATT
1 TAACAAATTTAGCATGCAAAATTTACACATTTTATCAATTAGAT-CTAATT
* * * * *
38282511 TAACAAATTTAGCTTGTAATATTTGCACATTATATCAA
1 TAACAAATTTAGCATGCAAAATTTACACATTTTATCAA
38282549 CTTTTACATA
Statistics
Matches: 74, Mismatches: 12, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
49 2 0.03
50 7 0.09
51 65 0.88
ACGTcount: A:0.38, C:0.14, G:0.08, T:0.41
Consensus pattern (50 bp):
TAACAAATTTAGCATGCAAAATTTACACATTTTATCAATTAGATCTAATT
Found at i:38282933 original size:2 final size:2
Alignment explanation
Indices: 38282926--38282953 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
38282916 TTCCACCTGA
38282926 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
38282954 GTAAAGCATG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:38284200 original size:23 final size:22
Alignment explanation
Indices: 38284170--38284217 Score: 53
Period size: 23 Copynumber: 2.1 Consensus size: 22
38284160 TCATTTATTT
*
38284170 TTATATAATAA-AAAATTAAAAA
1 TTATATAA-AATAAAATAAAAAA
*
38284192 TTATCATAAAATTAAATAAAAAA
1 TTAT-ATAAAATAAAATAAAAAA
38284215 TTA
1 TTA
38284218 AAATTCGATT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
22 6 0.27
23 16 0.73
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (22 bp):
TTATATAAAATAAAATAAAAAA
Found at i:38287062 original size:20 final size:20
Alignment explanation
Indices: 38287015--38287062 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 20
38287005 TACGTTTAAT
38287015 TTATTTTT-ATCTCATATTA
1 TTATTTTTAATCTCATATTA
* * * *
38287034 TAATATTTAATTTTATATTA
1 TTATTTTTAATCTCATATTA
38287054 TTATTTTTA
1 TTATTTTTA
38287063 TATTAAACAC
Statistics
Matches: 22, Mismatches: 6, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
19 6 0.27
20 16 0.73
ACGTcount: A:0.31, C:0.04, G:0.00, T:0.65
Consensus pattern (20 bp):
TTATTTTTAATCTCATATTA
Found at i:38296724 original size:2 final size:2
Alignment explanation
Indices: 38296717--38296744 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
38296707 ATATGTTTAA
38296717 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
38296745 TTGTTTTTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:38298987 original size:42 final size:41
Alignment explanation
Indices: 38298925--38299015 Score: 146
Period size: 42 Copynumber: 2.2 Consensus size: 41
38298915 TGTCCACTTT
* *
38298925 TCAGCCCAATTGACCACAGTTCATGGCTTACAGTTATAATC
1 TCAGCCCAAGTGACCACAGTTCATGGCTTACAGATATAATC
*
38298966 TCAGCCCAAGTGAACCACAGTTCATGGCTTAGAGATATAATC
1 TCAGCCCAAGTG-ACCACAGTTCATGGCTTACAGATATAATC
38299008 TCAGCCCA
1 TCAGCCCA
38299016 TCTCACTAAG
Statistics
Matches: 46, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
41 11 0.24
42 35 0.76
ACGTcount: A:0.31, C:0.27, G:0.16, T:0.25
Consensus pattern (41 bp):
TCAGCCCAAGTGACCACAGTTCATGGCTTACAGATATAATC
Found at i:38303245 original size:4 final size:4
Alignment explanation
Indices: 38303236--38303346 Score: 132
Period size: 4 Copynumber: 27.8 Consensus size: 4
38303226 AAATCCTCAC
* * * * * * *
38303236 TATG TATG TACG TACG TACG TACG TACG TATG TATG TATG TACG TACG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
* **
38303284 TACG TACA TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
38303332 TATG TATG TATG TAT
1 TATG TATG TATG TAT
38303347 TGTTTGGTTG
Statistics
Matches: 101, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 101 1.00
ACGTcount: A:0.26, C:0.08, G:0.23, T:0.42
Consensus pattern (4 bp):
TATG
Found at i:38305085 original size:18 final size:19
Alignment explanation
Indices: 38305062--38305104 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
38305052 TATATATATT
*
38305062 AATAAATTA-AAAGAATAA
1 AATAAAATATAAAGAATAA
*
38305080 AATAAAATATAAATAATAA
1 AATAAAATATAAAGAATAA
38305099 ATATAA
1 A-ATAA
38305105 TTCGAATTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 8 0.38
19 9 0.43
20 4 0.19
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (19 bp):
AATAAAATATAAAGAATAA
Found at i:38307270 original size:19 final size:20
Alignment explanation
Indices: 38307246--38307285 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
38307236 AGTCTGAGAG
38307246 AGTGAAACAG-ATCCAAGAA
1 AGTGAAACAGAATCCAAGAA
*
38307265 AGTGAATCAGAATCCAAGAA
1 AGTGAAACAGAATCCAAGAA
38307285 A
1 A
38307286 ATAGAGAGGG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.53, C:0.15, G:0.20, T:0.12
Consensus pattern (20 bp):
AGTGAAACAGAATCCAAGAA
Found at i:38324554 original size:40 final size:40
Alignment explanation
Indices: 38324491--38324568 Score: 93
Period size: 40 Copynumber: 1.9 Consensus size: 40
38324481 AAATGTGATT
** * *
38324491 TTGAACTAATAATTTTTGTTAATTTATTGCATATAAATTA
1 TTGAACTAATAATTTTTACTAATTCATTACATATAAATTA
* * *
38324531 TTGAACTATTGATTTTTACTAATTCCTTACATATAAAT
1 TTGAACTAATAATTTTTACTAATTCATTACATATAAAT
38324569 CTATGATTCA
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
40 31 1.00
ACGTcount: A:0.36, C:0.09, G:0.06, T:0.49
Consensus pattern (40 bp):
TTGAACTAATAATTTTTACTAATTCATTACATATAAATTA
Found at i:38326363 original size:24 final size:24
Alignment explanation
Indices: 38326307--38326364 Score: 68
Period size: 24 Copynumber: 2.5 Consensus size: 24
38326297 GCACGTTTCA
*
38326307 TGCCCTCTG-TTCAGCACTGTGTG
1 TGCCCTCTGTTTCAGCACTGTATG
38326330 TG-CCTACTGTTTCCAGCACT-TATG
1 TGCCCT-CTGTTT-CAGCACTGTATG
38326354 TGCCCTCTGTT
1 TGCCCTCTGTT
38326365 AAGTACTTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
22 3 0.10
23 5 0.17
24 12 0.40
25 10 0.33
ACGTcount: A:0.10, C:0.31, G:0.21, T:0.38
Consensus pattern (24 bp):
TGCCCTCTGTTTCAGCACTGTATG
Found at i:38336206 original size:20 final size:20
Alignment explanation
Indices: 38336181--38336219 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
38336171 GAAATTTAAT
* *
38336181 TTAAATATTTAAATTATATC
1 TTAAATATTAAAAATATATC
38336201 TTAAATATTAAAAATATAT
1 TTAAATATTAAAAATATAT
38336220 AATAAGAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (20 bp):
TTAAATATTAAAAATATATC
Found at i:38336236 original size:19 final size:19
Alignment explanation
Indices: 38336212--38336263 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
38336202 TAAATATTAA
38336212 AAATATATAATAAGAATAT
1 AAATATATAATAAGAATAT
* *
38336231 AAATATA-ATTTTAGAATAT
1 AAATATATA-ATAAGAATAT
38336250 AAATAATATAATAA
1 AAAT-ATATAATAA
38336264 AATGAGCCAC
Statistics
Matches: 26, Mismatches: 4, Indels: 5
0.74 0.11 0.14
Matches are distributed among these distances:
18 1 0.04
19 19 0.73
20 5 0.19
21 1 0.04
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.35
Consensus pattern (19 bp):
AAATATATAATAAGAATAT
Found at i:38336300 original size:26 final size:26
Alignment explanation
Indices: 38336264--38336327 Score: 128
Period size: 26 Copynumber: 2.5 Consensus size: 26
38336254 AATATAATAA
38336264 AATGAGCCACTCACAAGGAGCCTCCT
1 AATGAGCCACTCACAAGGAGCCTCCT
38336290 AATGAGCCACTCACAAGGAGCCTCCT
1 AATGAGCCACTCACAAGGAGCCTCCT
38336316 AATGAGCCACTC
1 AATGAGCCACTC
38336328 TTGTTCTACT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 38 1.00
ACGTcount: A:0.31, C:0.34, G:0.19, T:0.16
Consensus pattern (26 bp):
AATGAGCCACTCACAAGGAGCCTCCT
Found at i:38336815 original size:25 final size:25
Alignment explanation
Indices: 38336769--38336816 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
38336759 TAGGTCCACA
* ***
38336769 TTGATCCCTAAATTTTTTATTCACT
1 TTGATCCCTAAACTTAAAATTCACT
38336794 TTGATCCCTAAACTTAAAATTCA
1 TTGATCCCTAAACTTAAAATTCA
38336817 TTATTCATTT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.31, C:0.21, G:0.04, T:0.44
Consensus pattern (25 bp):
TTGATCCCTAAACTTAAAATTCACT
Found at i:38338179 original size:13 final size:13
Alignment explanation
Indices: 38338161--38338185 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
38338151 CGACATTTTG
38338161 AACAAGATAATTC
1 AACAAGATAATTC
38338174 AACAAGATAATT
1 AACAAGATAATT
38338186 TGTGGTTTAA
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:0.56, C:0.12, G:0.08, T:0.24
Consensus pattern (13 bp):
AACAAGATAATTC
Found at i:38342145 original size:12 final size:10
Alignment explanation
Indices: 38342123--38342156 Score: 50
Period size: 10 Copynumber: 3.2 Consensus size: 10
38342113 CTAATATGGA
38342123 TAAAAAAAAT
1 TAAAAAAAAT
38342133 TAAAGATAAAAT
1 TAAA-A-AAAAT
38342145 TAAAAAAAAT
1 TAAAAAAAAT
38342155 TA
1 TA
38342157 TCAAATTCAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
10 11 0.50
11 2 0.09
12 9 0.41
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.24
Consensus pattern (10 bp):
TAAAAAAAAT
Found at i:38347147 original size:23 final size:21
Alignment explanation
Indices: 38347121--38347178 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 21
38347111 AAATAATGTT
38347121 ATAATAAATTTAAATTTAACAAA
1 ATAA-AAATTTAAATTTAA-AAA
38347144 ATAAATAA-TTAAATTTAAAAA
1 ATAAA-AATTTAAATTTAAAAA
*
38347165 TTAAAAATATTAAA
1 ATAAAAAT-TTAAA
38347179 ATTTTAAAGT
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
20 2 0.06
21 7 0.23
22 16 0.52
23 6 0.19
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (21 bp):
ATAAAAATTTAAATTTAAAAA
Found at i:38349726 original size:18 final size:19
Alignment explanation
Indices: 38349696--38349731 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
38349686 AGTGATCATT
38349696 AATCGAGTTAATTCAATTC
1 AATCGAGTTAATTCAATTC
*
38349715 AATCGA-TTAATTTAATT
1 AATCGAGTTAATTCAATT
38349732 TTAACCAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.39, C:0.11, G:0.08, T:0.42
Consensus pattern (19 bp):
AATCGAGTTAATTCAATTC
Found at i:38350041 original size:21 final size:21
Alignment explanation
Indices: 38350017--38350057 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
38350007 AAATTACCAC
*
38350017 TACTAAGAAATTGAAAAAAAT
1 TACTAAGAAATTAAAAAAAAT
38350038 TACTAAGAAATTAAAAAAAA
1 TACTAAGAAATTAAAAAAAA
38350058 AATATTGCCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.66, C:0.05, G:0.07, T:0.22
Consensus pattern (21 bp):
TACTAAGAAATTAAAAAAAAT
Found at i:38362226 original size:29 final size:31
Alignment explanation
Indices: 38362179--38362238 Score: 81
Period size: 29 Copynumber: 2.0 Consensus size: 31
38362169 TATAAAATTT
38362179 GAAATTTAGTATATATACTTTT-AT-TTTCA
1 GAAATTTAGTATATATACTTTTCATATTTCA
*
38362208 GAAATTTAGT-TATTCTACTTTTCATATTTCA
1 GAAATTTAGTATA-TATACTTTTCATATTTCA
38362239 AAAGTCAGGT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
28 2 0.07
29 18 0.67
30 2 0.07
31 5 0.19
ACGTcount: A:0.32, C:0.10, G:0.07, T:0.52
Consensus pattern (31 bp):
GAAATTTAGTATATATACTTTTCATATTTCA
Found at i:38363794 original size:31 final size:31
Alignment explanation
Indices: 38363759--38363827 Score: 75
Period size: 31 Copynumber: 2.2 Consensus size: 31
38363749 AATATTTTTG
38363759 TTTAAGTCATTAAACTATTAGAAAGTTTCCA
1 TTTAAGTCATTAAACTATTAGAAAGTTTCCA
* * * * * **
38363790 TTTAAATCATTGAATTATTTGAACGTTTTTA
1 TTTAAGTCATTAAACTATTAGAAAGTTTCCA
38363821 TTTAAGT
1 TTTAAGT
38363828 TACTGGGCTG
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.35, C:0.09, G:0.10, T:0.46
Consensus pattern (31 bp):
TTTAAGTCATTAAACTATTAGAAAGTTTCCA
Found at i:38370876 original size:4 final size:4
Alignment explanation
Indices: 38370860--38370891 Score: 55
Period size: 4 Copynumber: 8.0 Consensus size: 4
38370850 TCTTATTTCA
*
38370860 CATG CATG GATG CATG CATG CATG CATG CATG
1 CATG CATG CATG CATG CATG CATG CATG CATG
38370892 TATGTATGTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (4 bp):
CATG
Found at i:38370896 original size:4 final size:4
Alignment explanation
Indices: 38370889--38370914 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
38370879 GCATGCATGC
38370889 ATGT ATGT ATGT ATGT ATGT ATGT AT
1 ATGT ATGT ATGT ATGT ATGT ATGT AT
38370915 TTGACAGTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.27, C:0.00, G:0.23, T:0.50
Consensus pattern (4 bp):
ATGT
Found at i:38373478 original size:16 final size:16
Alignment explanation
Indices: 38373457--38373500 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
38373447 AAAATCAAGG
*
38373457 AAAAA-TAAGAAATCGA
1 AAAAATTAA-AAATAGA
38373473 AAAAATTAAAAATAGA
1 AAAAATTAAAAATAGA
*
38373489 AAAAAATAAAAA
1 AAAAATTAAAAA
38373501 ATTTATAAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 22 0.88
17 3 0.12
ACGTcount: A:0.77, C:0.02, G:0.07, T:0.14
Consensus pattern (16 bp):
AAAAATTAAAAATAGA
Found at i:38383928 original size:55 final size:55
Alignment explanation
Indices: 38383855--38383963 Score: 193
Period size: 55 Copynumber: 2.0 Consensus size: 55
38383845 ATCAAATTGA
*
38383855 TCCAACAAAAATTAAATAAATAATTAAAAATTTAAAAAA-TCATAAAATTGTTTTG
1 TCCAACAAAAATTAAATAAATAATT-AAAAGTTAAAAAAGTCATAAAATTGTTTTG
38383910 TCCAACAAAAATTAAATAAATAATTAAAAGTTAAAAAAGTCATAAAATTGTTTT
1 TCCAACAAAAATTAAATAAATAATTAAAAGTTAAAAAAGTCATAAAATTGTTTT
38383964 ACCCTCCATT
Statistics
Matches: 52, Mismatches: 1, Indels: 2
0.95 0.02 0.04
Matches are distributed among these distances:
54 12 0.23
55 40 0.77
ACGTcount: A:0.56, C:0.07, G:0.05, T:0.32
Consensus pattern (55 bp):
TCCAACAAAAATTAAATAAATAATTAAAAGTTAAAAAAGTCATAAAATTGTTTTG
Found at i:38389296 original size:6 final size:6
Alignment explanation
Indices: 38389285--38389320 Score: 72
Period size: 6 Copynumber: 6.0 Consensus size: 6
38389275 TAATTTATGT
38389285 CACTCA CACTCA CACTCA CACTCA CACTCA CACTCA
1 CACTCA CACTCA CACTCA CACTCA CACTCA CACTCA
38389321 GGTGTGTGCG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.33, C:0.50, G:0.00, T:0.17
Consensus pattern (6 bp):
CACTCA
Found at i:38408847 original size:12 final size:12
Alignment explanation
Indices: 38408794--38408874 Score: 51
Period size: 12 Copynumber: 6.3 Consensus size: 12
38408784 CAGCAAATGA
38408794 TTTTAAAATTA-
1 TTTTAAAATTAT
38408805 --TTAAAATTATT
1 TTTTAAAATTA-T
38408816 TTTTAAAAAATATAAT
1 TTTT--AAAAT-T-AT
*
38408832 TTTTTAAATTAT
1 TTTTAAAATTAT
38408844 TTTTAAAATATAAAT
1 TTTTAAAAT-T--AT
*
38408859 TATTAAAATTAT
1 TTTTAAAATTAT
38408871 TTTT
1 TTTT
38408875 TTGAAATAAT
Statistics
Matches: 55, Mismatches: 4, Indels: 21
0.69 0.05 0.26
Matches are distributed among these distances:
9 9 0.16
12 15 0.27
13 4 0.07
14 5 0.09
15 15 0.27
16 6 0.11
17 1 0.02
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (12 bp):
TTTTAAAATTAT
Found at i:38408859 original size:27 final size:27
Alignment explanation
Indices: 38408799--38408874 Score: 107
Period size: 27 Copynumber: 2.7 Consensus size: 27
38408789 AATGATTTTA
38408799 AAATTATTAAAATTATTTTTTAAAAAAT
1 AAATTATTAAAATTA-TTTTTAAAAAAT
* * *
38408827 ATAATTTTTTAAATTATTTTTAAAATAT
1 A-AATTATTAAAATTATTTTTAAAAAAT
38408855 AAATTATTAAAATTATTTTT
1 AAATTATTAAAATTATTTTT
38408875 TTGAAATAAT
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
27 17 0.40
28 13 0.31
29 12 0.29
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (27 bp):
AAATTATTAAAATTATTTTTAAAAAAT
Found at i:38408903 original size:30 final size:29
Alignment explanation
Indices: 38408838--38408903 Score: 71
Period size: 30 Copynumber: 2.2 Consensus size: 29
38408828 TAATTTTTTA
*
38408838 AATTATTTTTAAAATATAAATTATTAAAAT
1 AATT-TTTTTAAAATATAAATTACTAAAAT
* *
38408868 TATTTTTTTGAAATAATAAAATTACT-AAAT
1 AATTTTTTTAAAAT-AT-AAATTACTAAAAT
38408898 AATTTT
1 AATTTT
38408904 AATTTCCAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
29 9 0.30
30 14 0.47
31 7 0.23
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (29 bp):
AATTTTTTTAAAATATAAATTACTAAAAT
Found at i:38408904 original size:56 final size:56
Alignment explanation
Indices: 38408799--38408905 Score: 137
Period size: 56 Copynumber: 1.9 Consensus size: 56
38408789 AATGATTTTA
* ** *
38408799 AAATTATTAAAATTATTTTTTAAAAAATATAATTTTTTAAATTATTTTTAAAATAT
1 AAATTATTAAAATTATTTTTTAAAAAATATAAATTACTAAATTAATTTTAAAATAT
*
38408855 AAATTATTAAAATTATTTTTTTGAAATAATA-AAATTACTAAA-TAATTTTAA
1 AAATTATTAAAATTA-TTTTTT-AAAAAATATAAATTACTAAATTAATTTTAA
38408906 TTTCCAATTT
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
56 23 0.52
57 14 0.32
58 7 0.16
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.49
Consensus pattern (56 bp):
AAATTATTAAAATTATTTTTTAAAAAATATAAATTACTAAATTAATTTTAAAATAT
Found at i:38410817 original size:23 final size:23
Alignment explanation
Indices: 38410779--38410997 Score: 257
Period size: 23 Copynumber: 9.4 Consensus size: 23
38410769 AGCACCTCTC
38410779 GTGCTCTCTGTTATTAGCACTGTGT
1 GTGCTCTCTG--ATTAGCACTGTGT
*
38410804 GTGCTCTCTGATTAGCACTTTGT
1 GTGCTCTCTGATTAGCACTGTGT
*
38410827 GTGCTCTCTGATTAGTACT-T-T
1 GTGCTCTCTGATTAGCACTGTGT
*
38410848 GTG-TACTCTGTTTAGCACTGTGT
1 GTGCT-CTCTGATTAGCACTGTGT
* *
38410871 GTGCTCTCTGTTTAGCAC-GTCT
1 GTGCTCTCTGATTAGCACTGTGT
38410893 CGTGCTCTCTGTTATTAGCACTGTGT
1 -GTGCTCTCTG--ATTAGCACTGTGT
* *
38410919 GTGCTCTCTGATTAGTACTTTGT
1 GTGCTCTCTGATTAGCACTGTGT
* *
38410942 GTGCTCTCTGATTAGTACTTTGT
1 GTGCTCTCTGATTAGCACTGTGT
* *
38410965 GTACTCTCTGTTTAGCACTGTGT
1 GTGCTCTCTGATTAGCACTGTGT
38410988 GTGCTCTCTG
1 GTGCTCTCTG
38410998 TTGCCCAACA
Statistics
Matches: 172, Mismatches: 14, Indels: 18
0.84 0.07 0.09
Matches are distributed among these distances:
20 1 0.01
21 16 0.09
22 5 0.03
23 119 0.69
24 1 0.01
25 27 0.16
26 3 0.02
ACGTcount: A:0.12, C:0.21, G:0.23, T:0.44
Consensus pattern (23 bp):
GTGCTCTCTGATTAGCACTGTGT
Found at i:38410960 original size:115 final size:116
Alignment explanation
Indices: 38410758--38410999 Score: 441
Period size: 115 Copynumber: 2.1 Consensus size: 116
38410748 ATACTAGCGC
*
38410758 GCTCTCTATTTAGCACCTCTCGTGCTCTCTGTTATTAGCACTGTGTGTGCTCTCTGATTAGCACT
1 GCTCTCTGTTTAGCACCTCTCGTGCTCTCTGTTATTAGCACTGTGTGTGCTCTCTGATTAGCACT
38410823 TTGTGTGCTCTCTGATTAGTACTTTGTGTA-CTCTGTTTAGCACTGTGTGT
66 TTGTGTGCTCTCTGATTAGTACTTTGTGTACCTCTGTTTAGCACTGTGTGT
* *
38410873 GCTCTCTGTTTAGCACGTCTCGTGCTCTCTGTTATTAGCACTGTGTGTGCTCTCTGATTAGTACT
1 GCTCTCTGTTTAGCACCTCTCGTGCTCTCTGTTATTAGCACTGTGTGTGCTCTCTGATTAGCACT
38410938 TTGTGTGCTCTCTGATTAGTACTTTGTGTACTCTCTGTTTAGCACTGTGTGT
66 TTGTGTGCTCTCTGATTAGTACTTTGTGTAC-CTCTGTTTAGCACTGTGTGT
38410990 GCTCTCTGTT
1 GCTCTCTGTT
38411000 GCCCAACACT
Statistics
Matches: 122, Mismatches: 3, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
115 92 0.75
117 30 0.25
ACGTcount: A:0.12, C:0.22, G:0.21, T:0.44
Consensus pattern (116 bp):
GCTCTCTGTTTAGCACCTCTCGTGCTCTCTGTTATTAGCACTGTGTGTGCTCTCTGATTAGCACT
TTGTGTGCTCTCTGATTAGTACTTTGTGTACCTCTGTTTAGCACTGTGTGT
Found at i:38411251 original size:24 final size:24
Alignment explanation
Indices: 38411224--38411274 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
38411214 GTACTATGTG
38411224 TGTATGTGTAATTAAGTGAACTAA
1 TGTATGTGTAATTAAGTGAACTAA
38411248 TGTATGTGTAATTAAGTGAACTAA
1 TGTATGTGTAATTAAGTGAACTAA
38411272 TGT
1 TGT
38411275 GGTTGAAATG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.35, C:0.04, G:0.22, T:0.39
Consensus pattern (24 bp):
TGTATGTGTAATTAAGTGAACTAA
Found at i:38416891 original size:15 final size:16
Alignment explanation
Indices: 38416861--38416891 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
38416851 ATAACAGCAT
*
38416861 CAAAATAGTAAAAAAA
1 CAAAACAGTAAAAAAA
38416877 CAAAACAGTAAAAAA
1 CAAAACAGTAAAAAA
38416892 TAATACCAAA
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:0.74, C:0.10, G:0.06, T:0.10
Consensus pattern (16 bp):
CAAAACAGTAAAAAAA
Found at i:38416926 original size:12 final size:10
Alignment explanation
Indices: 38416899--38416933 Score: 52
Period size: 10 Copynumber: 3.3 Consensus size: 10
38416889 AAATAATACC
38416899 AAAACAGCAA
1 AAAACAGCAA
38416909 AAAACAGCAA
1 AAAACAGCAA
38416919 TTAAAACAGCAA
1 --AAAACAGCAA
38416931 AAA
1 AAA
38416934 CAACAATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
10 13 0.57
12 10 0.43
ACGTcount: A:0.69, C:0.17, G:0.09, T:0.06
Consensus pattern (10 bp):
AAAACAGCAA
Found at i:38416932 original size:21 final size:22
Alignment explanation
Indices: 38416899--38416940 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
38416889 AAATAATACC
*
38416899 AAAACAGCAAAAAACAGCAATT
1 AAAACAGCAAAAAACAACAATT
38416921 AAAACAGC-AAAAACAACAAT
1 AAAACAGCAAAAAACAACAAT
38416941 ATAATTTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.67, C:0.19, G:0.07, T:0.07
Consensus pattern (22 bp):
AAAACAGCAAAAAACAACAATT
Found at i:38417678 original size:27 final size:25
Alignment explanation
Indices: 38417628--38417689 Score: 65
Period size: 27 Copynumber: 2.5 Consensus size: 25
38417618 TTTATAATAC
38417628 ATAAA-ATTTAAAATTAAGTATATT
1 ATAAATATTTAAAATTAAGTATATT
* *
38417652 ATAAATATATTAAATATTAATTTTATT
1 ATAAATAT-TTAAA-ATTAAGTATATT
*
38417679 TTAAAT-TTTAA
1 ATAAATATTTAA
38417690 TAAAACCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
24 5 0.16
25 6 0.19
26 6 0.19
27 15 0.47
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (25 bp):
ATAAATATTTAAAATTAAGTATATT
Found at i:38428520 original size:22 final size:23
Alignment explanation
Indices: 38428477--38428520 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 23
38428467 AGCAACAATA
*
38428477 ATAAAATAAATAATTAAAATATC
1 ATAAAATAAATAAATAAAATATC
* *
38428500 ATAAAA-ATATAAATAACATAT
1 ATAAAATAAATAAATAAAATAT
38428521 TTATTAAACC
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.66, C:0.05, G:0.00, T:0.30
Consensus pattern (23 bp):
ATAAAATAAATAAATAAAATATC
Found at i:38429749 original size:19 final size:17
Alignment explanation
Indices: 38429722--38429767 Score: 56
Period size: 19 Copynumber: 2.5 Consensus size: 17
38429712 AATTTAAATT
*
38429722 ATATATTTATTATTTTAA
1 ATATTTTTATT-TTTTAA
38429740 ATAATTTTTAATTTTTTAA
1 AT-ATTTTT-ATTTTTTAA
38429759 ATATTTTTA
1 ATATTTTTA
38429768 AGAATTTTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
17 1 0.04
18 8 0.32
19 13 0.52
20 3 0.12
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (17 bp):
ATATTTTTATTTTTTAA
Found at i:38429775 original size:19 final size:19
Alignment explanation
Indices: 38429733--38429779 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
38429723 TATATTTATT
*
38429733 ATTTTAAATAATTTTTAAT
1 ATTTTAAATAATTTTTAAA
*
38429752 TTTTTAAAT-ATTTTTAAGA
1 ATTTTAAATAATTTTTAA-A
38429771 ATTTTAAAT
1 ATTTTAAAT
38429780 TTTAAAAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 8 0.33
19 16 0.67
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (19 bp):
ATTTTAAATAATTTTTAAA
Found at i:38430430 original size:33 final size:33
Alignment explanation
Indices: 38430393--38430510 Score: 107
Period size: 33 Copynumber: 3.6 Consensus size: 33
38430383 CTGTAGGACT
* *
38430393 TGGTGGTGGTGGTGGTGGTTGTAATTGCCAACA
1 TGGTGGTAGTCGTGGTGGTTGTAATTGCCAACA
* ** * *
38430426 TGGTGGTAGTCGTGGTGGTGGT-GGTG-AAATA
1 TGGTGGTAGTCGTGGTGGTTGTAATTGCCAACA
* *
38430457 GTTGGTGGT-GATGGTGGTGGTTGTAATGGCCAACA
1 --TGGTGGTAG-TCGTGGTGGTTGTAATTGCCAACA
38430492 TGGTGGTAGTCGTGGTGGT
1 TGGTGGTAGTCGTGGTGGT
38430511 GGTGGGTAGA
Statistics
Matches: 64, Mismatches: 15, Indels: 12
0.70 0.16 0.13
Matches are distributed among these distances:
31 3 0.05
32 3 0.05
33 53 0.83
34 2 0.03
35 3 0.05
ACGTcount: A:0.14, C:0.07, G:0.46, T:0.33
Consensus pattern (33 bp):
TGGTGGTAGTCGTGGTGGTTGTAATTGCCAACA
Found at i:38430462 original size:66 final size:66
Alignment explanation
Indices: 38430392--38430515 Score: 230
Period size: 66 Copynumber: 1.9 Consensus size: 66
38430382 CCTGTAGGAC
* *
38430392 TTGGTGGTGGTGGTGGTGGTTGTAATTGCCAACATGGTGGTAGTCGTGGTGGTGGTGGTGAAATA
1 TTGGTGGTGATGGTGGTGGTTGTAATGGCCAACATGGTGGTAGTCGTGGTGGTGGTGGTGAAATA
38430457 G
66 G
38430458 TTGGTGGTGATGGTGGTGGTTGTAATGGCCAACATGGTGGTAGTCGTGGTGGTGGTGG
1 TTGGTGGTGATGGTGGTGGTTGTAATGGCCAACATGGTGGTAGTCGTGGTGGTGGTGG
38430516 GTAGAGTGGA
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 56 1.00
ACGTcount: A:0.14, C:0.06, G:0.47, T:0.33
Consensus pattern (66 bp):
TTGGTGGTGATGGTGGTGGTTGTAATGGCCAACATGGTGGTAGTCGTGGTGGTGGTGGTGAAATA
G
Found at i:38434217 original size:20 final size:20
Alignment explanation
Indices: 38434169--38434209 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
38434159 ATTGCTTCTC
*
38434169 AAAAGTACTTTTGAAATAAA
1 AAAATTACTTTTGAAATAAA
*
38434189 AAAATTACTTTTGAGATAAA
1 AAAATTACTTTTGAAATAAA
38434209 A
1 A
38434210 GTATTACTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.54, C:0.05, G:0.10, T:0.32
Consensus pattern (20 bp):
AAAATTACTTTTGAAATAAA
Found at i:38447625 original size:58 final size:58
Alignment explanation
Indices: 38447535--38447651 Score: 234
Period size: 58 Copynumber: 2.0 Consensus size: 58
38447525 AGCGAGTGTG
38447535 CCTCCTGCCTTTGACTACACTCGAAGTTGTTAATATTGGTTGTTTATAATGTGTGTAT
1 CCTCCTGCCTTTGACTACACTCGAAGTTGTTAATATTGGTTGTTTATAATGTGTGTAT
38447593 CCTCCTGCCTTTGACTACACTCGAAGTTGTTAATATTGGTTGTTTATAATGTGTGTAT
1 CCTCCTGCCTTTGACTACACTCGAAGTTGTTAATATTGGTTGTTTATAATGTGTGTAT
38447651 C
1 C
38447652 TTTTTTAATG
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
58 59 1.00
ACGTcount: A:0.21, C:0.18, G:0.19, T:0.43
Consensus pattern (58 bp):
CCTCCTGCCTTTGACTACACTCGAAGTTGTTAATATTGGTTGTTTATAATGTGTGTAT
Found at i:38456711 original size:15 final size:14
Alignment explanation
Indices: 38456684--38456726 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 14
38456674 TATTATAAAA
38456684 ATAAAAGATTAAATT
1 ATAAAA-ATTAAATT
* *
38456699 ATAGTAAATTAAAGT
1 ATA-AAAATTAAATT
38456714 ATAAAAATTAAAT
1 ATAAAAATTAAAT
38456727 CTCAAATTGA
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
14 8 0.35
15 13 0.57
16 2 0.09
ACGTcount: A:0.60, C:0.00, G:0.07, T:0.33
Consensus pattern (14 bp):
ATAAAAATTAAATT
Found at i:38457503 original size:24 final size:25
Alignment explanation
Indices: 38457470--38457529 Score: 86
Period size: 24 Copynumber: 2.4 Consensus size: 25
38457460 CTCACTGAAA
*
38457470 AAACACTTCATTTTGGCAT-TTTTC
1 AAACACTTCATTTAGGCATATTTTC
*
38457494 CAACACTTCATTTAGGCATATTTTC
1 AAACACTTCATTTAGGCATATTTTC
*
38457519 AAACAATTCAT
1 AAACACTTCAT
38457530 ATGCAACAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
24 17 0.55
25 14 0.45
ACGTcount: A:0.32, C:0.22, G:0.07, T:0.40
Consensus pattern (25 bp):
AAACACTTCATTTAGGCATATTTTC
Found at i:38461074 original size:72 final size:72
Alignment explanation
Indices: 38460986--38461395 Score: 570
Period size: 72 Copynumber: 5.7 Consensus size: 72
38460976 AGTGACTGTA
* * * * *
38460986 CCTCCAATAGTAAAACCA-CCAGTTACAGTCCCACCGGTGACTGTTCCTCCTGTGAAGCCACCAG
1 CCTCCAATTGCAAAACCACCCA-TCACAGTCCCACCAGTGACTGTTCCTCCTGTAAAGCCACCAG
*
38461050 TTGAACTC
65 TTGACCTC
* * * * *
38461058 CCTCCGATTGCAAAACCACCTATTACAATCCCACCAGTGACTGTTCCTCCTGTAAAGCCACCTGT
1 CCTCCAATTGCAAAACCACCCATCACAGTCCCACCAGTGACTGTTCCTCCTGTAAAGCCACCAGT
*
38461123 TGATCTC
66 TGACCTC
* * * * * *
38461130 CCTCCAATTGCAAAGCCACCTATTACAGTTCCACCTGTGACTGTTCCTCCTGTGAAGCCACCAGT
1 CCTCCAATTGCAAAACCACCCATCACAGTCCCACCAGTGACTGTTCCTCCTGTAAAGCCACCAGT
38461195 TGACCTC
66 TGACCTC
* * *
38461202 CCCCCAATTGCAAAACCACCCATCACAGTCCCTCCAGTTACTGTTCCTCCTGTAAAGCCACCAGT
1 CCTCCAATTGCAAAACCACCCATCACAGTCCCACCAGTGACTGTTCCTCCTGTAAAGCCACCAGT
38461267 TGACCTC
66 TGACCTC
* *
38461274 CCTCCAATTGTAAAACCACCCATCACAGTCCCACCAGTGATTGTTCCTCCTGTAAAGCCACCAGT
1 CCTCCAATTGCAAAACCACCCATCACAGTCCCACCAGTGACTGTTCCTCCTGTAAAGCCACCAGT
*
38461339 TGATCTC
66 TGACCTC
* *
38461346 CCCCCAATTGCAAAACCACCCATCACAGTCCCACCAGTGACTGTCCCTCC
1 CCTCCAATTGCAAAACCACCCATCACAGTCCCACCAGTGACTGTTCCTCC
38461396 GGTGACTGTT
Statistics
Matches: 301, Mismatches: 36, Indels: 2
0.89 0.11 0.01
Matches are distributed among these distances:
72 299 0.99
73 2 0.01
ACGTcount: A:0.25, C:0.38, G:0.13, T:0.23
Consensus pattern (72 bp):
CCTCCAATTGCAAAACCACCCATCACAGTCCCACCAGTGACTGTTCCTCCTGTAAAGCCACCAGT
TGACCTC
Found at i:38461184 original size:144 final size:144
Alignment explanation
Indices: 38460986--38461790 Score: 847
Period size: 144 Copynumber: 5.3 Consensus size: 144
38460976 AGTGACTGTA
* * * *
38460986 CCTCCAATAGTAAAACCA-CCAGTTACAGTCCCACCGGTGACTGTTCCTCCTGTGAAGCCACCAG
1 CCTCCAATTGCAAAACCACCCA-TCACAGTCCCACCAGTGACTGTTCCTCCTGTGAAGCCACCAG
* * * * * *
38461050 TTGAACTCCCTCCGATTGCAAAACCACCTATTACAATCCCACCAGTGACTGTTCCTCCTGTAAAG
65 TTGATCTCCCCCCAATTGCAAAACCACCCATCACAATCCCTCCAGTGACTGTTCCTCCTGTAAAG
* *
38461115 CCACCTGTTGATCTC
130 CCACCAGTTGACCTC
* * * * *
38461130 CCTCCAATTGCAAAGCCACCTATTACAGTTCCACCTGTGACTGTTCCTCCTGTGAAGCCACCAGT
1 CCTCCAATTGCAAAACCACCCATCACAGTCCCACCAGTGACTGTTCCTCCTGTGAAGCCACCAGT
* * *
38461195 TGACCTCCCCCCAATTGCAAAACCACCCATCACAGTCCCTCCAGTTACTGTTCCTCCTGTAAAGC
66 TGATCTCCCCCCAATTGCAAAACCACCCATCACAATCCCTCCAGTGACTGTTCCTCCTGTAAAGC
38461260 CACCAGTTGACCTC
131 CACCAGTTGACCTC
* * *
38461274 CCTCCAATTGTAAAACCACCCATCACAGTCCCACCAGTGATTGTTCCTCCTGTAAAGCCACCAGT
1 CCTCCAATTGCAAAACCACCCATCACAGTCCCACCAGTGACTGTTCCTCCTGTGAAGCCACCAGT
*
38461339 TGATCTCCCCCCAATTGCAAAACCACCCATCACAGTCCCACCAGTGACTGTCCCTCCGGTGACTG
66 TGATCTCCCCCCAATTGCAAAACCA--C--C-CA-T--CA-CA---A---TCCCTCCAGTGACTG
38461404 TTCCTCCTGTAAAGCCACCAGTTGACCTC
116 TTCCTCCTGTAAAGCCACCAGTTGACCTC
* * *
38461433 CCTCCAATTGCAAAACCACCCATCACAGTCCCACCAGTAACTGTTCCTCCTGTAAAGCCACCAAT
1 CCTCCAATTGCAAAACCACCCATCACAGTCCCACCAGTGACTGTTCCTCCTGTGAAGCCACCAGT
* * * * *
38461498 TGATCTCCCTCCAATTGCAAAACCACCCATCACAGTCCCTCCAATTACTGTACCTCCTGTAAAGC
66 TGATCTCCCCCCAATTGCAAAACCACCCATCACAATCCCTCCAGTGACTGTTCCTCCTGTAAAGC
* *
38461563 CACCAATTGACCTT
131 CACCAGTTGACCTC
38461577 CCTCCAATTGCAAAACCACCCATCACAGTCCCACCAGTGACCGTCCCTCCGGTGACTGTTCCTCC
1 CCTCCAATTGCAAAACCACCCATCACAGTCCCACC----A-----------GTGACTGTTCCTCC
* * *
38461642 TGTAAAGCCACCAGTTGACCTCCCTCCAATTGCAAAACCACCCATCACAGTCCCTCCAGTTACTA
51 TGTGAAGCCACCAGTTGATCTCCCCCCAATTGCAAAACCACCCAT--CA-------C----A--A
*
38461707 TCCCACCAGTGACTGTTCCTCCTGTAAAGCCACCAGTTGACCTC
101 TCCCTCCAGTGACTGTTCCTCCTGTAAAGCCACCAGTTGACCTC
38461751 CCTCCAATTGCAAAACCACCCATCACAGTCCCACCAGTGA
1 CCTCCAATTGCAAAACCACCCATCACAGTCCCACCAGTGA
38461791 TCGTCCCAGT
Statistics
Matches: 565, Mismatches: 50, Indels: 77
0.82 0.07 0.11
Matches are distributed among these distances:
144 279 0.49
145 2 0.00
146 1 0.00
148 2 0.00
149 2 0.00
150 3 0.01
151 2 0.00
152 2 0.00
153 3 0.01
154 2 0.00
155 1 0.00
157 1 0.00
159 187 0.33
161 2 0.00
168 1 0.00
170 1 0.00
172 1 0.00
174 73 0.13
ACGTcount: A:0.26, C:0.39, G:0.13, T:0.23
Consensus pattern (144 bp):
CCTCCAATTGCAAAACCACCCATCACAGTCCCACCAGTGACTGTTCCTCCTGTGAAGCCACCAGT
TGATCTCCCCCCAATTGCAAAACCACCCATCACAATCCCTCCAGTGACTGTTCCTCCTGTAAAGC
CACCAGTTGACCTC
Found at i:38461435 original size:159 final size:158
Alignment explanation
Indices: 38461229--38461791 Score: 749
Period size: 159 Copynumber: 3.5 Consensus size: 158
38461219 ACCCATCACA
* *
38461229 GTCCCTCCAGTTACTGTTCCTCCTGTAAAGCCACCAGTTGACCTCCCTCCAATTGTAAAACCACC
1 GTCCCTCCAGTGACTGTTCCTCCTGTAAAGCCACCAGTTGACCTCCCTCCAATTGCAAAACCACC
*
38461294 CATCACAGTCCCACCAGTGATTGTTCCTCCTGTAAAGCCACCAGTTGATCTCCCCCCAATTGCAA
66 CATCACAGTCCCACCAGTGATTGTTCCTCCTGTAAAGCCACCAGTTGATCTCCCTCCAATTGCAA
*
38461359 AACCACCCATCACAGTCCCACCAGTGACT
131 AACCACCCATCACAGTCCCTCCAGT-ACT
*
38461388 GTCCCTCCGGTGACTGTTCCTCCTGTAAAGCCACCAGTTGACCTCCCTCCAATTGCAAAACCACC
1 GTCCCTCCAGTGACTGTTCCTCCTGTAAAGCCACCAGTTGACCTCCCTCCAATTGCAAAACCACC
* * *
38461453 CATCACAGTCCCACCAGTAACTGTTCCTCCTGTAAAGCCACCAATTGATCTCCCTCCAATTGCAA
66 CATCACAGTCCCACCAGTGATTGTTCCTCCTGTAAAGCCACCAGTTGATCTCCCTCCAATTGCAA
38461518 AACCACCCATCACAGTCCCTCCA--A--
131 AACCACCCATCACAGTCCCTCCAGTACT
* * *
38461542 -----T----T-ACTGTACCTCCTGTAAAGCCACCAATTGACCTTCCTCCAATTGCAAAACCACC
1 GTCCCTCCAGTGACTGTTCCTCCTGTAAAGCCACCAGTTGACCTCCCTCCAATTGCAAAACCACC
*
38461597 CATCACAGTCCCACCAGTGACCGTCCCTCCGGTGACTGTTCCTCCTGTAAAGCCACCAGTTGACC
66 CATCACAGTCCCACCAGTGA------------T---TGTTCCTCCTGTAAAGCCACCAGTTGATC
38461662 TCCCTCCAATTGCAAAACCACCCATCACAGTCCCTCCAGTTACT
116 TCCCTCCAATTGCAAAACCACCCATCACAGTCCCTCCAG-TACT
* *
38461706 ATCCCACCAGTGACTGTTCCTCCTGTAAAGCCACCAGTTGACCTCCCTCCAATTGCAAAACCACC
1 GTCCCTCCAGTGACTGTTCCTCCTGTAAAGCCACCAGTTGACCTCCCTCCAATTGCAAAACCACC
38461771 CATCACAGTCCCACCAGTGAT
66 CATCACAGTCCCACCAGTGAT
38461792 CGTCCCAGTC
Statistics
Matches: 355, Mismatches: 19, Indels: 57
0.82 0.04 0.13
Matches are distributed among these distances:
144 69 0.19
145 1 0.00
149 1 0.00
156 1 0.00
159 210 0.59
162 2 0.01
173 1 0.00
174 70 0.20
ACGTcount: A:0.26, C:0.40, G:0.12, T:0.23
Consensus pattern (158 bp):
GTCCCTCCAGTGACTGTTCCTCCTGTAAAGCCACCAGTTGACCTCCCTCCAATTGCAAAACCACC
CATCACAGTCCCACCAGTGATTGTTCCTCCTGTAAAGCCACCAGTTGATCTCCCTCCAATTGCAA
AACCACCCATCACAGTCCCTCCAGTACT
Found at i:38461440 original size:87 final size:87
Alignment explanation
Indices: 38461301--38461482 Score: 301
Period size: 87 Copynumber: 2.1 Consensus size: 87
38461291 ACCCATCACA
* * *
38461301 GTCCCACCAGTGATTGTTCCTCCTGTAAAGCCACCAGTTGATCTCCCCCCAATTGCAAAACCACC
1 GTCCCTCCAGTGACTGTTCCTCCTGTAAAGCCACCAGTTGACCTCCCCCCAATTGCAAAACCACC
*
38461366 CATCACAGTCCCACCAGTGACT
66 CATCACAGTCCCACCAGTAACT
* *
38461388 GTCCCTCCGGTGACTGTTCCTCCTGTAAAGCCACCAGTTGACCTCCCTCCAATTGCAAAACCACC
1 GTCCCTCCAGTGACTGTTCCTCCTGTAAAGCCACCAGTTGACCTCCCCCCAATTGCAAAACCACC
38461453 CATCACAGTCCCACCAGTAACT
66 CATCACAGTCCCACCAGTAACT
*
38461475 GTTCCTCC
1 GTCCCTCC
38461483 TGTAAAGCCA
Statistics
Matches: 88, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
87 88 1.00
ACGTcount: A:0.24, C:0.40, G:0.14, T:0.23
Consensus pattern (87 bp):
GTCCCTCCAGTGACTGTTCCTCCTGTAAAGCCACCAGTTGACCTCCCCCCAATTGCAAAACCACC
CATCACAGTCCCACCAGTAACT
Found at i:38461459 original size:231 final size:231
Alignment explanation
Indices: 38461166--38461791 Score: 964
Period size: 231 Copynumber: 2.6 Consensus size: 231
38461156 AGTTCCACCT
* *
38461166 GTGACTGTTCCTCCTGTGAAGCCACCAGTTGACCTCCCCCCAATTGCAAAACCACCCATCACAGT
1 GTGACTGTTCCTCCTGTAAAGCCACCAGTTGACCTCCCTCCAATTGCAAAACCACCCATCACAGT
*
38461231 CCCTCCAGTTACTGTTCCTCCTGTAAAGCCACCAGTTGACCTCCCTCCAATTGTAAAACCACCCA
66 CCCTCCAGTTACTGTTCCTCCTGTAAAGCCACCAGTTGACCTCCCTCCAATTGCAAAACCACCCA
* * *
38461296 TCACAGTCCCACCAGTGATTGTTCCTCCTGTAAAGCCACCAGTTGATCTCCCCCCAATTGCAAAA
131 TCACAGTCCCACCAGTGATTGTACCTCCTGTAAAGCCACCAATTGACCTCCCCCCAATTGCAAAA
*
38461361 CCACCCATCACAGTCCCACCAGTGACTGTCCCTCCG
196 CCACCCATCACAGTCCCACCAGTGACCGTCCCTCCG
38461397 GTGACTGTTCCTCCTGTAAAGCCACCAGTTGACCTCCCTCCAATTGCAAAACCACCCATCACAGT
1 GTGACTGTTCCTCCTGTAAAGCCACCAGTTGACCTCCCTCCAATTGCAAAACCACCCATCACAGT
* * * *
38461462 CCCACCAGTAACTGTTCCTCCTGTAAAGCCACCAATTGATCTCCCTCCAATTGCAAAACCACCCA
66 CCCTCCAGTTACTGTTCCTCCTGTAAAGCCACCAGTTGACCTCCCTCCAATTGCAAAACCACCCA
* * * * * *
38461527 TCACAGTCCCTCCAATTACTGTACCTCCTGTAAAGCCACCAATTGACCTTCCTCCAATTGCAAAA
131 TCACAGTCCCACCAGTGATTGTACCTCCTGTAAAGCCACCAATTGACCTCCCCCCAATTGCAAAA
38461592 CCACCCATCACAGTCCCACCAGTGACCGTCCCTCCG
196 CCACCCATCACAGTCCCACCAGTGACCGTCCCTCCG
38461628 GTGACTGTTCCTCCTGTAAAGCCACCAGTTGACCTCCCTCCAATTGCAAAACCACCCATCACAGT
1 GTGACTGTTCCTCCTGTAAAGCCACCAGTTGACCTCCCTCCAATTGCAAAACCACCCATCACAGT
38461693 CCCTCCAGTTACTATCCCACCAGTGACTGTTCCTCCTGTAAAGCCACCAGTTGACCTCCCTCCAA
66 CCCTCCAG------T--------T-ACTGTTCCTCCTGTAAAGCCACCAGTTGACCTCCCTCCAA
38461758 TTGCAAAACCACCCATCACAGTCCCACCAGTGAT
116 TTGCAAAACCACCCATCACAGTCCCACCAGTGAT
38461792 CGTCCCAGTC
Statistics
Matches: 355, Mismatches: 25, Indels: 15
0.90 0.06 0.04
Matches are distributed among these distances:
231 286 0.81
237 1 0.00
246 68 0.19
ACGTcount: A:0.26, C:0.40, G:0.12, T:0.22
Consensus pattern (231 bp):
GTGACTGTTCCTCCTGTAAAGCCACCAGTTGACCTCCCTCCAATTGCAAAACCACCCATCACAGT
CCCTCCAGTTACTGTTCCTCCTGTAAAGCCACCAGTTGACCTCCCTCCAATTGCAAAACCACCCA
TCACAGTCCCACCAGTGATTGTACCTCCTGTAAAGCCACCAATTGACCTCCCCCCAATTGCAAAA
CCACCCATCACAGTCCCACCAGTGACCGTCCCTCCG
Found at i:38461626 original size:72 final size:72
Alignment explanation
Indices: 38461388--38461626 Score: 370
Period size: 72 Copynumber: 3.3 Consensus size: 72
38461378 ACCAGTGACT
* * *
38461388 GTCCCTCCGGTGACTGTTCCTCCTGTAAAGCCACCAGTTGACCTCCCTCCAATTGCAAAACCACC
1 GTCCCACCAGTGACTGTTCCTCCTGTAAAGCCACCAATTGACCTCCCTCCAATTGCAAAACCACC
38461453 CATCACA
66 CATCACA
* *
38461460 GTCCCACCAGTAACTGTTCCTCCTGTAAAGCCACCAATTGATCTCCCTCCAATTGCAAAACCACC
1 GTCCCACCAGTGACTGTTCCTCCTGTAAAGCCACCAATTGACCTCCCTCCAATTGCAAAACCACC
38461525 CATCACA
66 CATCACA
* * * * *
38461532 GTCCCTCCAATTACTGTACCTCCTGTAAAGCCACCAATTGACCTTCCTCCAATTGCAAAACCACC
1 GTCCCACCAGTGACTGTTCCTCCTGTAAAGCCACCAATTGACCTCCCTCCAATTGCAAAACCACC
38461597 CATCACA
66 CATCACA
* *
38461604 GTCCCACCAGTGACCGTCCCTCC
1 GTCCCACCAGTGACTGTTCCTCC
38461627 GGTGACTGTT
Statistics
Matches: 151, Mismatches: 16, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
72 151 1.00
ACGTcount: A:0.26, C:0.41, G:0.11, T:0.22
Consensus pattern (72 bp):
GTCCCACCAGTGACTGTTCCTCCTGTAAAGCCACCAATTGACCTCCCTCCAATTGCAAAACCACC
CATCACA
Found at i:38461643 original size:87 final size:87
Alignment explanation
Indices: 38461544--38461798 Score: 420
Period size: 87 Copynumber: 2.9 Consensus size: 87
38461534 CCCTCCAATT
* * *
38461544 ACTGTACCTCCTGTAAAGCCACCAATTGACCTTCCTCCAATTGCAAAACCACCCATCACAGTCCC
1 ACTGTTCCTCCTGTAAAGCCACCAGTTGACCTCCCTCCAATTGCAAAACCACCCATCACAGTCCC
* *
38461609 ACCAGTGACCGTCCCTCCGGTG
66 ACCAGTGACCGTCCCACCAGTG
38461631 ACTGTTCCTCCTGTAAAGCCACCAGTTGACCTCCCTCCAATTGCAAAACCACCCATCACAGTCCC
1 ACTGTTCCTCCTGTAAAGCCACCAGTTGACCTCCCTCCAATTGCAAAACCACCCATCACAGTCCC
* * **
38461696 TCCAGTTACTATCCCACCAGTG
66 ACCAGTGACCGTCCCACCAGTG
38461718 ACTGTTCCTCCTGTAAAGCCACCAGTTGACCTCCCTCCAATTGCAAAACCACCCATCACAGTCCC
1 ACTGTTCCTCCTGTAAAGCCACCAGTTGACCTCCCTCCAATTGCAAAACCACCCATCACAGTCCC
*
38461783 ACCAGTGATCGTCCCA
66 ACCAGTGACCGTCCCA
38461799 GTCCCACCAG
Statistics
Matches: 154, Mismatches: 14, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
87 154 1.00
ACGTcount: A:0.25, C:0.40, G:0.13, T:0.22
Consensus pattern (87 bp):
ACTGTTCCTCCTGTAAAGCCACCAGTTGACCTCCCTCCAATTGCAAAACCACCCATCACAGTCCC
ACCAGTGACCGTCCCACCAGTG
Found at i:38461818 original size:21 final size:21
Alignment explanation
Indices: 38461771--38461811 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
38461761 CAAAACCACC
*
38461771 CATCACAGTCCCACCAGTGAT
1 CATCCCAGTCCCACCAGTGAT
*
38461792 CGTCCCAGTCCCACCAGTGA
1 CATCCCAGTCCCACCAGTGA
38461812 CTATCCCTCC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.24, C:0.41, G:0.17, T:0.17
Consensus pattern (21 bp):
CATCCCAGTCCCACCAGTGAT
Found at i:38466147 original size:21 final size:22
Alignment explanation
Indices: 38466126--38466168 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
38466116 GAAGATATTT
38466126 AAATGAATTTT-TTTTAATTTTA
1 AAAT-AATTTTCTTTTAATTTTA
*
38466148 AAATATTTTTCTTTTAATTTT
1 AAATAATTTTCTTTTAATTTT
38466169 TATCCAGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (22 bp):
AAATAATTTTCTTTTAATTTTA
Found at i:38467384 original size:3 final size:3
Alignment explanation
Indices: 38467376--38467414 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
38467366 TAATAGTTGC
38467376 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
38467415 TAGGAAAAAG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:38473120 original size:21 final size:23
Alignment explanation
Indices: 38473075--38473121 Score: 62
Period size: 21 Copynumber: 2.1 Consensus size: 23
38473065 CAATACCGGC
*
38473075 TTTTATTAATAAAAATAAATGAA
1 TTTTATTAATAAAAATAAATCAA
*
38473098 TTTTTTTAA-AAAAAT-AATCAA
1 TTTTATTAATAAAAATAAATCAA
38473119 TTT
1 TTT
38473122 ACTCTTTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 8 0.36
22 6 0.27
23 8 0.36
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (23 bp):
TTTTATTAATAAAAATAAATCAA
Found at i:38474130 original size:2 final size:2
Alignment explanation
Indices: 38474123--38474150 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
38474113 ATCATGTATG
38474123 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
38474151 GAAAAATCTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:38488938 original size:12 final size:12
Alignment explanation
Indices: 38488921--38488945 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
38488911 TTGTAAATTA
38488921 ACACACATACAT
1 ACACACATACAT
38488933 ACACACATACAT
1 ACACACATACAT
38488945 A
1 A
38488946 TACCTAAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.32, G:0.00, T:0.16
Consensus pattern (12 bp):
ACACACATACAT
Found at i:38489317 original size:20 final size:20
Alignment explanation
Indices: 38489292--38489334 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
38489282 TAACATTCAT
38489292 GATAATTTTTCAAATCAATA
1 GATAATTTTTCAAATCAATA
*
38489312 GATAATTTTTCAAATTAATA
1 GATAATTTTTCAAATCAATA
38489332 GAT
1 GAT
38489335 TAAATAGGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.44, C:0.07, G:0.07, T:0.42
Consensus pattern (20 bp):
GATAATTTTTCAAATCAATA
Found at i:38489371 original size:39 final size:39
Alignment explanation
Indices: 38489319--38489398 Score: 160
Period size: 39 Copynumber: 2.1 Consensus size: 39
38489309 ATAGATAATT
38489319 TTTCAAATTAATAGATTAAATAGGTTCTTAAAATTGAAA
1 TTTCAAATTAATAGATTAAATAGGTTCTTAAAATTGAAA
38489358 TTTCAAATTAATAGATTAAATAGGTTCTTAAAATTGAAA
1 TTTCAAATTAATAGATTAAATAGGTTCTTAAAATTGAAA
38489397 TT
1 TT
38489399 ATTAAAATAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.45, C:0.05, G:0.10, T:0.40
Consensus pattern (39 bp):
TTTCAAATTAATAGATTAAATAGGTTCTTAAAATTGAAA
Found at i:38491536 original size:21 final size:20
Alignment explanation
Indices: 38491503--38491565 Score: 71
Period size: 18 Copynumber: 3.2 Consensus size: 20
38491493 ATTTATAAAA
*
38491503 ATTTTAATAAATTATTTAGTT
1 ATTTAAATAAATTATTTA-TT
38491524 A-TTAAATTAAATTATTT-TT
1 ATTTAAA-TAAATTATTTATT
38491543 ATTTAAA-AAATTATTTA-T
1 ATTTAAATAAATTATTTATT
38491561 ATTTA
1 ATTTA
38491566 TTTGGTTAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
18 15 0.39
19 3 0.08
20 9 0.24
21 11 0.29
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.56
Consensus pattern (20 bp):
ATTTAAATAAATTATTTATT
Found at i:38495093 original size:6 final size:6
Alignment explanation
Indices: 38495082--38495108 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
38495072 TTCGTTGCTT
38495082 TGATTA TGATTA TGATTA TGATTA TGA
1 TGATTA TGATTA TGATTA TGATTA TGA
38495109 AAACAATTAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.19, T:0.48
Consensus pattern (6 bp):
TGATTA
Found at i:38495631 original size:21 final size:20
Alignment explanation
Indices: 38495607--38495649 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
38495597 AATTTAAATA
38495607 TTTAT-GTTTTAATATTATTTT
1 TTTATCGTTTT-ATATT-TTTT
38495628 TTTATCGTTTTATATTTTTT
1 TTTATCGTTTTATATTTTTT
38495648 TT
1 TT
38495650 CGTATTATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 6 0.29
21 10 0.48
22 5 0.24
ACGTcount: A:0.19, C:0.02, G:0.05, T:0.74
Consensus pattern (20 bp):
TTTATCGTTTTATATTTTTT
Found at i:38495645 original size:18 final size:17
Alignment explanation
Indices: 38495622--38495661 Score: 62
Period size: 17 Copynumber: 2.3 Consensus size: 17
38495612 GTTTTAATAT
*
38495622 TATTTTTTTATCGTTTTA
1 TATTTTTTT-TCGTATTA
38495640 TATTTTTTTTCGTATTA
1 TATTTTTTTTCGTATTA
38495657 TATTT
1 TATTT
38495662 ATATATATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 12 0.57
18 9 0.43
ACGTcount: A:0.17, C:0.05, G:0.05, T:0.72
Consensus pattern (17 bp):
TATTTTTTTTCGTATTA
Found at i:38496916 original size:43 final size:43
Alignment explanation
Indices: 38496855--38496949 Score: 156
Period size: 43 Copynumber: 2.2 Consensus size: 43
38496845 GTCGCCCCCC
*
38496855 ACTTGGCCATTAAGATGATGCCACGTTAGCAACACCACAACCA
1 ACTTGGCCATTAAGATGATGCCACGTCAGCAACACCACAACCA
* *
38496898 ACTTGGCCATTAAGATGATGGCACGTCAGCAACACCACCACCA
1 ACTTGGCCATTAAGATGATGCCACGTCAGCAACACCACAACCA
38496941 ACTT-GCCAT
1 ACTTGGCCAT
38496950 CGTCATTGCC
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
42 5 0.10
43 44 0.90
ACGTcount: A:0.33, C:0.32, G:0.17, T:0.19
Consensus pattern (43 bp):
ACTTGGCCATTAAGATGATGCCACGTCAGCAACACCACAACCA
Found at i:38497542 original size:21 final size:21
Alignment explanation
Indices: 38497516--38497566 Score: 93
Period size: 21 Copynumber: 2.4 Consensus size: 21
38497506 AAAAAATAAG
38497516 GCTCGATCTTGCTAGATCGGA
1 GCTCGATCTTGCTAGATCGGA
38497537 GCTCGATCTTGCTAGATCGGA
1 GCTCGATCTTGCTAGATCGGA
*
38497558 GCCCGATCT
1 GCTCGATCT
38497567 ATGTTTTAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.18, C:0.27, G:0.27, T:0.27
Consensus pattern (21 bp):
GCTCGATCTTGCTAGATCGGA
Found at i:38498296 original size:30 final size:30
Alignment explanation
Indices: 38498220--38498607 Score: 192
Period size: 29 Copynumber: 13.4 Consensus size: 30
38498210 CCCCTATTTT
* * *
38498220 CTTTCC-AAAATCTCA-TTTTAACCGTAAA
1 CTTTCCTAAAATCACATTTTTACCCCTAAA
* * * *
38498248 CTTTTC-AAAATTATATTTTTACCCCCAAA
1 CTTTCCTAAAATCACATTTTTACCCCTAAA
*
38498277 CTTTCCTAAAATCACATTTTGACCCCTAAA
1 CTTTCCTAAAATCACATTTTTACCCCTAAA
*
38498307 CTTT-CTCAAAATCACATTTTGACCCC-AAA
1 CTTTCCT-AAAATCACATTTTTACCCCTAAA
* * * * * *
38498336 ATTTTCTAAAAAATGCA-A-TTTTGCTCTTGAA
1 CTTTCCT--AAAAT-CACATTTTTACCCCTAAA
* * *
38498367 C-TTCCAAAAATCACATTTTTACTCAT-AA
1 CTTTCCTAAAATCACATTTTTACCCCTAAA
*
38498395 C-TTCCAAAAATCACATTTTTACCACC-AAA
1 CTTTCCTAAAATCACATTTTTACC-CCTAAA
* * *
38498424 C-ATCTCAAAAATTACATTTTT--CCCTAAA
1 CTTTC-CTAAAATCACATTTTTACCCCTAAA
* * *
38498452 C-TT-CTAAAAATTACATTTTTGCCCCCAAA
1 CTTTCCT-AAAATCACATTTTTACCCCTAAA
*
38498481 CTTTCAT-AAATCACATTTTTACCCCTAAA
1 CTTTCCTAAAATCACATTTTTACCCCTAAA
* * * * *
38498510 C-TTCTTAAAAATTACATTTTT-GCCTTGAA
1 CTTTCCT-AAAATCACATTTTTACCCCTAAA
* * * *
38498539 C-TTCTCAAAAATCATATTTTTATCCC-GAA
1 CTTTC-CTAAAATCACATTTTTACCCCTAAA
* * *
38498568 CTTTCCCAAAATTATA-TTTTACCCCTAAA
1 CTTTCCTAAAATCACATTTTTACCCCTAAA
38498597 CTTTCC-AAAAT
1 CTTTCCTAAAAT
38498608 TATGTTTTAA
Statistics
Matches: 286, Mismatches: 50, Indels: 48
0.74 0.13 0.12
Matches are distributed among these distances:
26 1 0.00
27 18 0.06
28 64 0.22
29 106 0.37
30 86 0.30
31 9 0.03
32 2 0.01
ACGTcount: A:0.36, C:0.25, G:0.03, T:0.37
Consensus pattern (30 bp):
CTTTCCTAAAATCACATTTTTACCCCTAAA
Found at i:38498357 original size:31 final size:30
Alignment explanation
Indices: 38498245--38498529 Score: 150
Period size: 30 Copynumber: 9.8 Consensus size: 30
38498235 TTTTAACCGT
* * * * *
38498245 AAACTTT-TCAAAATTATATTTTTACCCCC
1 AAACTTTCTAAAAATCACATTTTGACCCCA
*
38498274 AAACTTTCCT-AAAATCACATTTTGACCCCT
1 AAACTTT-CTAAAAATCACATTTTGACCCCA
*
38498304 AAACTTTCTCAAAATCACATTTTGACCCCA
1 AAACTTTCTAAAAATCACATTTTGACCCCA
* * **
38498334 AAATTTTCTAAAAAATGCA-ATTTTG-CTCTT
1 AAACTTTCT-AAAAAT-CACATTTTGACCCCA
* * * *
38498364 GAAC-TTCCAAAAATCACATTTTTA-CTCA
1 AAACTTTCTAAAAATCACATTTTGACCCCA
* * *
38498392 TAAC-TTCCAAAAATCACATTTTTACCACC-
1 AAACTTTCTAAAAATCACATTTTGACC-CCA
* * * *
38498421 AAAC-ATCTCAAAAATTACATTTT--TCCCT
1 AAACTTTCT-AAAAATCACATTTTGACCCCA
* *
38498449 AAAC-TTCTAAAAATTACATTTTTG-CCCCC
1 AAACTTTCTAAAAATCACA-TTTTGACCCCA
* * *
38498478 AAACTTTC-ATAAATCACATTTTTACCCCT
1 AAACTTTCTAAAAATCACATTTTGACCCCA
*
38498507 AAAC-TTCTTAAAAATTACATTTT
1 AAACTTTC-TAAAAATCACATTTT
38498530 TGCCTTGAAC
Statistics
Matches: 205, Mismatches: 34, Indels: 33
0.75 0.12 0.12
Matches are distributed among these distances:
27 14 0.07
28 53 0.26
29 41 0.20
30 83 0.40
31 12 0.06
32 2 0.01
ACGTcount: A:0.37, C:0.25, G:0.02, T:0.36
Consensus pattern (30 bp):
AAACTTTCTAAAAATCACATTTTGACCCCA
Found at i:38498483 original size:86 final size:88
Alignment explanation
Indices: 38498284--38498559 Score: 248
Period size: 86 Copynumber: 3.2 Consensus size: 88
38498274 AAACTTTCCT
* * *
38498284 AAAATCACA-TTTTGACCCCTAAACTTTCTC-AAAATCACATTTTGACCCC-AAA-ATTTTCTAA
1 AAAATCACATTTTTG-CCCCCAAAC-TTC-CAAAAATCACATTTTTACCCCTAAACA-TCTC-AA
* * * * *
38498345 AAAATGCAATTTTGCTCTTGAACTTC-CA
61 AAATTACATTTTTGC-CCTAAACTTCTCA
* *
38498373 AAAATCACATTTTT--ACTCATAACTTCCAAAAATCACATTTTTACCACC-AAACATCTCAAAAA
1 AAAATCACATTTTTGCCCCCA-AACTTCCAAAAATCACATTTTTACC-CCTAAACATCTCAAAAA
38498435 TTACATTTTT-CCCTAAACTTCT-A
64 TTACATTTTTGCCCTAAACTTCTCA
* * * * *
38498458 AAAATTACATTTTTGCCCCCAAACTTTCATAAATCACATTTTTACCCCTAAACTTCTTAAAAATT
1 AAAATCACATTTTTGCCCCCAAACTTCCAAAAATCACATTTTTACCCCTAAACATCTCAAAAATT
* *
38498523 ACATTTTTGCCTTGAACTTCTCA
66 ACATTTTTGCCCTAAACTTCTCA
*
38498546 AAAATCATATTTTT
1 AAAATCACATTTTT
38498560 ATCCCGAACT
Statistics
Matches: 155, Mismatches: 21, Indels: 23
0.78 0.11 0.12
Matches are distributed among these distances:
85 24 0.15
86 47 0.30
87 46 0.30
88 24 0.15
89 10 0.06
90 4 0.03
ACGTcount: A:0.37, C:0.24, G:0.03, T:0.36
Consensus pattern (88 bp):
AAAATCACATTTTTGCCCCCAAACTTCCAAAAATCACATTTTTACCCCTAAACATCTCAAAAATT
ACATTTTTGCCCTAAACTTCTCA
Found at i:38498528 original size:59 final size:58
Alignment explanation
Indices: 38498245--38498560 Score: 232
Period size: 59 Copynumber: 5.4 Consensus size: 58
38498235 TTTTAACCGT
* * * * *
38498245 AAACTTTTC-AAAATTATATTTTTACCCCCAAACTTTCCT-AAAATCACA-TTTTGACCCCT
1 AAAC-TTTCAAAAATCACATTTTTACCCCTAAAC-TT-CTAAAAATTACATTTTTG-CCCCC
* * * * * * * * **
38498304 AAACTTTCTCAAAATCACATTTTGACCCCAAAATTTTCTAAAAAATGCAATTTTGCTCTT
1 AAACTTTC-AAAAATCACATTTTTACCCCTAAA-CTTCTAAAAATTACATTTTTGCCCCC
* * * * * * * *
38498364 GAACTTCCAAAAATCACATTTTTACTCAT-AACTTCCAAAAATCACATTTTTACCACC
1 AAACTTTCAAAAATCACATTTTTACCCCTAAACTTCTAAAAATTACATTTTTGCCCCC
* *
38498421 AAACATCTCAAAAATTACATTTTT--CCCTAAACTTCTAAAAATTACATTTTTGCCCCC
1 AAAC-TTTCAAAAATCACATTTTTACCCCTAAACTTCTAAAAATTACATTTTTGCCCCC
* **
38498478 AAACTTTCATAAATCACATTTTTACCCCTAAACTTCTTAAAAATTACATTTTTG-CCTT
1 AAACTTTCAAAAATCACATTTTTACCCCTAAACTTC-TAAAAATTACATTTTTGCCCCC
* *
38498536 GAACTTCTCAAAAATCATATTTTTA
1 AAACTT-TCAAAAATCACATTTTTA
38498561 TCCCGAACTT
Statistics
Matches: 200, Mismatches: 46, Indels: 22
0.75 0.17 0.08
Matches are distributed among these distances:
56 18 0.09
57 46 0.23
58 40 0.20
59 55 0.28
60 36 0.18
61 5 0.03
ACGTcount: A:0.36, C:0.24, G:0.03, T:0.37
Consensus pattern (58 bp):
AAACTTTCAAAAATCACATTTTTACCCCTAAACTTCTAAAAATTACATTTTTGCCCCC
Found at i:38498589 original size:87 final size:86
Alignment explanation
Indices: 38498284--38498599 Score: 295
Period size: 87 Copynumber: 3.6 Consensus size: 86
38498274 AAACTTTCCT
* * * * * *
38498284 AAAATCACATTTTGACCCCTAAACTTTCTCAAAATCACATTTTGACCCCAAAATTTTCTAAAAAA
1 AAAATCACATTTTTA-CCC-AAACTTTCCCAAAATCACATTTTTACCCCAAACTTCT-TAAAAAT
* *
38498349 TGCAATTTTGCTCTTGAACTTC-CA
63 TACATTTTTGC-CTTGAACTTCTCA
* * * *
38498373 AAAATCACATTTTTACTCATAAC-TTCCAAAAATCACATTTTTACCACCAAACATCTCAAAAATT
1 AAAATCACATTTTTACCCA-AACTTTCCCAAAATCACATTTTTACC-CCAAACTTCTTAAAAATT
* *
38498437 ACATTTTT-CCCTAAACTTCT-A
64 ACATTTTTGCCTTGAACTTCTCA
* *
38498458 AAAATTACATTTTTGCCCCCAAACTTT--CATAAATCACATTTTTACCCCTAAACTTCTTAAAAA
1 AAAATCACATTTTT--ACCCAAACTTTCCCA-AAATCACATTTTTACCCC-AAACTTCTTAAAAA
38498521 TTACATTTTTGCCTTGAACTTCTCA
62 TTACATTTTTGCCTTGAACTTCTCA
* * * *
38498546 AAAATCATATTTTTATCCCGAACTTTCCCAAAATTATA-TTTTACCCCTAAACTT
1 AAAATCACATTTTTA-CCCAAACTTTCCCAAAATCACATTTTTACCCC-AAACTT
38498600 TCCAAAATTA
Statistics
Matches: 186, Mismatches: 28, Indels: 28
0.77 0.12 0.12
Matches are distributed among these distances:
85 25 0.13
86 42 0.23
87 72 0.39
88 31 0.17
89 16 0.09
ACGTcount: A:0.36, C:0.25, G:0.03, T:0.36
Consensus pattern (86 bp):
AAAATCACATTTTTACCCAAACTTTCCCAAAATCACATTTTTACCCCAAACTTCTTAAAAATTAC
ATTTTTGCCTTGAACTTCTCA
Found at i:38498626 original size:28 final size:29
Alignment explanation
Indices: 38498546--38498626 Score: 85
Period size: 28 Copynumber: 2.8 Consensus size: 29
38498536 GAACTTCTCA
* *
38498546 AAAATCATATTTTTATCCC-GAACTTTCCC
1 AAAATTATA-TTTTAACCCTGAACTTTCCC
* *
38498575 AAAATTATATTTTACCCCTAAACTTT-CC
1 AAAATTATATTTTAACCCTGAACTTTCCC
* *
38498603 AAAATTATGTTTTAACTCTGAACT
1 AAAATTATATTTTAACCCTGAACT
38498627 CTCCGAAACT
Statistics
Matches: 44, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
28 30 0.68
29 14 0.32
ACGTcount: A:0.35, C:0.22, G:0.04, T:0.40
Consensus pattern (29 bp):
AAAATTATATTTTAACCCTGAACTTTCCC
Found at i:38499076 original size:21 final size:21
Alignment explanation
Indices: 38499052--38499102 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 21
38499042 AAAGAAAGCT
38499052 CGTTAT-TTTCGAATCTCGAAA
1 CGTTATGTTT-GAATCTCGAAA
*
38499073 CGTTATGTTTGGATCTCGAAA
1 CGTTATGTTTGAATCTCGAAA
*
38499094 TGTTATGTT
1 CGTTATGTT
38499103 CTAACTCACT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
21 24 0.89
22 3 0.11
ACGTcount: A:0.24, C:0.14, G:0.20, T:0.43
Consensus pattern (21 bp):
CGTTATGTTTGAATCTCGAAA
Found at i:38502604 original size:12 final size:12
Alignment explanation
Indices: 38502587--38502611 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
38502577 TTGTAAATTA
38502587 ACACACATACAT
1 ACACACATACAT
38502599 ACACACATACAT
1 ACACACATACAT
38502611 A
1 A
38502612 TACCTAAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.32, G:0.00, T:0.16
Consensus pattern (12 bp):
ACACACATACAT
Found at i:38502981 original size:20 final size:20
Alignment explanation
Indices: 38502956--38502998 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
38502946 TAACATTCAT
38502956 GATAATTTTTCAAATCAATA
1 GATAATTTTTCAAATCAATA
38502976 GATAATTTTTCAAATCAATA
1 GATAATTTTTCAAATCAATA
38502996 GAT
1 GAT
38502999 TAAATAGGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.44, C:0.09, G:0.07, T:0.40
Consensus pattern (20 bp):
GATAATTTTTCAAATCAATA
Found at i:38505163 original size:21 final size:20
Alignment explanation
Indices: 38505130--38505192 Score: 71
Period size: 18 Copynumber: 3.2 Consensus size: 20
38505120 ATTTATAAAA
*
38505130 ATTTTAATAAATTATTTAGTT
1 ATTTAAATAAATTATTTA-TT
38505151 A-TTAAATTAAATTATTT-TT
1 ATTTAAA-TAAATTATTTATT
38505170 ATTTAAA-AAATTATTTA-T
1 ATTTAAATAAATTATTTATT
38505188 ATTTA
1 ATTTA
38505193 TTTGGTTAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
18 15 0.39
19 3 0.08
20 9 0.24
21 11 0.29
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.56
Consensus pattern (20 bp):
ATTTAAATAAATTATTTATT
Found at i:38508702 original size:6 final size:6
Alignment explanation
Indices: 38508691--38508717 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
38508681 TTCGTTGCTT
38508691 TGATTA TGATTA TGATTA TGATTA TGA
1 TGATTA TGATTA TGATTA TGATTA TGA
38508718 AAACAATTAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.19, T:0.48
Consensus pattern (6 bp):
TGATTA
Found at i:38509240 original size:21 final size:20
Alignment explanation
Indices: 38509216--38509258 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
38509206 AATTTAAATA
38509216 TTTAT-GTTTTAATATTATTTT
1 TTTATCGTTTT-ATATT-TTTT
38509237 TTTATCGTTTTATATTTTTT
1 TTTATCGTTTTATATTTTTT
38509257 TT
1 TT
38509259 CGTATTATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 6 0.29
21 10 0.48
22 5 0.24
ACGTcount: A:0.19, C:0.02, G:0.05, T:0.74
Consensus pattern (20 bp):
TTTATCGTTTTATATTTTTT
Found at i:38509254 original size:18 final size:17
Alignment explanation
Indices: 38509231--38509270 Score: 62
Period size: 17 Copynumber: 2.3 Consensus size: 17
38509221 GTTTTAATAT
*
38509231 TATTTTTTTATCGTTTTA
1 TATTTTTTT-TCGTATTA
38509249 TATTTTTTTTCGTATTA
1 TATTTTTTTTCGTATTA
38509266 TATTT
1 TATTT
38509271 ATATATATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 12 0.57
18 9 0.43
ACGTcount: A:0.17, C:0.05, G:0.05, T:0.72
Consensus pattern (17 bp):
TATTTTTTTTCGTATTA
Found at i:38512402 original size:63 final size:63
Alignment explanation
Indices: 38512298--38512428 Score: 244
Period size: 63 Copynumber: 2.1 Consensus size: 63
38512288 GGTACCTAGT
*
38512298 AATATCAATTACTAAACCACAAAGGGAAGAATAATTGTTACCAATACATGAGGTGTAGGAAGC
1 AATATCAATTACTAAACCACAAAGGGAAGAATAATTCTTACCAATACATGAGGTGTAGGAAGC
*
38512361 AATATCAATTACTAAACCACAAAGGGAAGAATAATTCTTACCAATGCATGAGGTGTAGGAAGC
1 AATATCAATTACTAAACCACAAAGGGAAGAATAATTCTTACCAATACATGAGGTGTAGGAAGC
38512424 AATAT
1 AATAT
38512429 GGGACAACAT
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
63 66 1.00
ACGTcount: A:0.44, C:0.15, G:0.18, T:0.23
Consensus pattern (63 bp):
AATATCAATTACTAAACCACAAAGGGAAGAATAATTCTTACCAATACATGAGGTGTAGGAAGC
Found at i:38525453 original size:13 final size:13
Alignment explanation
Indices: 38525413--38525454 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
38525403 TTTACTAGAA
38525413 ATTATTTTATG-T
1 ATTATTTTATGAT
*
38525425 ATTATTTTTATTAT
1 ATTA-TTTTATGAT
*
38525439 ATTATTTAATGAT
1 ATTATTTTATGAT
38525452 ATT
1 ATT
38525455 TCGATAATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
12 4 0.16
13 16 0.64
14 5 0.20
ACGTcount: A:0.31, C:0.00, G:0.05, T:0.64
Consensus pattern (13 bp):
ATTATTTTATGAT
Found at i:38526456 original size:36 final size:38
Alignment explanation
Indices: 38526415--38526491 Score: 93
Period size: 41 Copynumber: 2.0 Consensus size: 38
38526405 TCTTTTCTAT
* * *
38526415 AAAAAA-ATTGAGTAAATTATTTATTGTATATTATATC
1 AAAAAATATGGAGCAAATTATTCATTGTATATTATATC
38526452 AAAAAATAAACTGGAGCAAATTATTCATTGTATATTATAT
1 AAAAAAT--A-TGGAGCAAATTATTCATTGTATATTATAT
38526492 TATTAGCAGC
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
37 6 0.18
40 1 0.03
41 26 0.79
ACGTcount: A:0.47, C:0.05, G:0.09, T:0.39
Consensus pattern (38 bp):
AAAAAATATGGAGCAAATTATTCATTGTATATTATATC
Found at i:38530691 original size:12 final size:12
Alignment explanation
Indices: 38530670--38530705 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
38530660 AAATTAAACA
*
38530670 AATTTTTTTAAT
1 AATTTATTTAAT
38530682 AATTTATTTAAT
1 AATTTATTTAAT
38530694 AATTTATTTAAT
1 AATTTATTTAAT
38530706 TAAATCGAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (12 bp):
AATTTATTTAAT
Found at i:38537109 original size:91 final size:91
Alignment explanation
Indices: 38536954--38537134 Score: 353
Period size: 91 Copynumber: 2.0 Consensus size: 91
38536944 GATGAGAGAG
38536954 CATCATCCAAGCAGAAATGAGAATCAGATGCATATATATAAAGTGTATCTTAAGATCAGCTTCCA
1 CATCATCCAAGCAGAAATGAGAATCAGATGCATATATATAAAGTGTATCTTAAGATCAGCTTCCA
38537019 AGTTTCAACTTGACAAAACTTATCAT
66 AGTTTCAACTTGACAAAACTTATCAT
*
38537045 CATCATCCAAGCAGAAATGAGAATCAGATGCATATATATAAAGTGTATCTTAAGATCGGCTTCCA
1 CATCATCCAAGCAGAAATGAGAATCAGATGCATATATATAAAGTGTATCTTAAGATCAGCTTCCA
38537110 AGTTTCAACTTGACAAAACTTATCA
66 AGTTTCAACTTGACAAAACTTATCA
38537135 ACCCGATATG
Statistics
Matches: 89, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
91 89 1.00
ACGTcount: A:0.39, C:0.19, G:0.14, T:0.28
Consensus pattern (91 bp):
CATCATCCAAGCAGAAATGAGAATCAGATGCATATATATAAAGTGTATCTTAAGATCAGCTTCCA
AGTTTCAACTTGACAAAACTTATCAT
Found at i:38540303 original size:21 final size:20
Alignment explanation
Indices: 38540270--38540312 Score: 59
Period size: 21 Copynumber: 2.1 Consensus size: 20
38540260 ATTGTCATTC
38540270 TATTTTTATTTTTTGGAATT
1 TATTTTTATTTTTTGGAATT
* *
38540290 TATTTTTTTGTTTTTTGAATT
1 TATTTTTAT-TTTTTGGAATT
38540311 TA
1 TA
38540313 AAAACTACAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 8 0.40
21 12 0.60
ACGTcount: A:0.19, C:0.00, G:0.09, T:0.72
Consensus pattern (20 bp):
TATTTTTATTTTTTGGAATT
Found at i:38540303 original size:22 final size:21
Alignment explanation
Indices: 38540272--38540312 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
38540262 TGTCATTCTA
38540272 TTTTTATTTTTTGGAATTTATT
1 TTTTTATTTTTT-GAATTTATT
*
38540294 TTTTTGTTTTTTGAATTTA
1 TTTTTATTTTTTGAATTTA
38540313 AAAACTACAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.17, C:0.00, G:0.10, T:0.73
Consensus pattern (21 bp):
TTTTTATTTTTTGAATTTATT
Found at i:38564609 original size:92 final size:92
Alignment explanation
Indices: 38564450--38564617 Score: 250
Period size: 92 Copynumber: 1.8 Consensus size: 92
38564440 TTTTTTTTTT
* * * *
38564450 AATTTTCATTTCGATATCTTAGTTAAGCTTATCGTAGCAATTGATTTTCATTTCTTTATAGGCCG
1 AATTTTCACTTCGATAACTTAGTTAAGCTTATCGTAGCAATTGACTTTCATTTCTTTACAGGCCG
38564515 GATCTTCAATTATTTGTTTATTTTTGA
66 GATCTTCAATTATTTGTTTATTTTTGA
* *
38564542 AATTTTCACTTCGA-ACACTTAGTTAAGCTTATCGTAGCATTTGGCTTTCATTTCTTTACATGG-
1 AATTTTCACTTCGATA-ACTTAGTTAAGCTTATCGTAGCAATTGACTTTCATTTCTTTACA-GGC
38564605 CGGATCTTCAATT
64 CGGATCTTCAATT
38564618 TTTTTATTTC
Statistics
Matches: 68, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
91 1 0.01
92 65 0.96
93 2 0.03
ACGTcount: A:0.24, C:0.16, G:0.14, T:0.46
Consensus pattern (92 bp):
AATTTTCACTTCGATAACTTAGTTAAGCTTATCGTAGCAATTGACTTTCATTTCTTTACAGGCCG
GATCTTCAATTATTTGTTTATTTTTGA
Found at i:38564719 original size:103 final size:102
Alignment explanation
Indices: 38564535--38564728 Score: 289
Period size: 103 Copynumber: 1.9 Consensus size: 102
38564525 TATTTGTTTA
* * *
38564535 TTTTTGAAATTTTCACTTCGAACACTTAGTTAAGCTTATCGTAGCATTTGGCTTTCATTTCTTTA
1 TTTTTAAAAATTTCACTTCGAACACTTAGTTAAGCTTATCGTAGCATTTGACTTTCATTTCTTTA
*
38564600 CATGGCGGATCTTCAATTTTTTTATTTCTTTGCTTTCT
66 CATGGCGGATCATCAA-TTTTTTATTTCTTTGCTTTCT
* * * * *
38564638 TTTTTAAAAATTTCATTTCGAACTCTTAGTTAAGCTTATCGTAGCATTTTATTTTCATTTTTTTA
1 TTTTTAAAAATTTCACTTCGAACACTTAGTTAAGCTTATCGTAGCATTTGACTTTCATTTCTTTA
*
38564703 TATGGCGGATCATCAATTTTTTATTT
66 CATGGCGGATCATCAATTTTTTATTT
38564729 TAATTTTCAT
Statistics
Matches: 81, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
102 10 0.12
103 71 0.88
ACGTcount: A:0.22, C:0.15, G:0.11, T:0.52
Consensus pattern (102 bp):
TTTTTAAAAATTTCACTTCGAACACTTAGTTAAGCTTATCGTAGCATTTGACTTTCATTTCTTTA
CATGGCGGATCATCAATTTTTTATTTCTTTGCTTTCT
Found at i:38564787 original size:84 final size:86
Alignment explanation
Indices: 38564648--38564813 Score: 266
Period size: 84 Copynumber: 2.0 Consensus size: 86
38564638 TTTTTAAAAA
* *
38564648 TTTCATTTCGAACTCTTAGTTAAGCTTATCGTAGCATTTTATTTTCATTTTTTTATATGGCGGAT
1 TTTCATTTCGAACTCTTAGTTAAGCTTATCGTAGCATTTTATTTTCATTTCTTTATATGCCGGAT
38564713 CATCAA-TTTTTTATTTTAAT
66 CATCAATTTTTTTATTTTAAT
*
38564733 TTTCATTTCGAACTCTTAGTTAAGC-TATCGTCGC-TTTTGATTTTCATTTCTTTATATGCCGGA
1 TTTCATTTCGAACTCTTAGTTAAGCTTATCGTAGCATTTT-ATTTTCATTTCTTTATATGCCGGA
*
38564796 TCTTCAATTTTTTTATTT
65 TCATCAATTTTTTTATTT
38564814 CTCTCTTTTC
Statistics
Matches: 75, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
83 4 0.05
84 36 0.48
85 35 0.47
ACGTcount: A:0.21, C:0.15, G:0.11, T:0.53
Consensus pattern (86 bp):
TTTCATTTCGAACTCTTAGTTAAGCTTATCGTAGCATTTTATTTTCATTTCTTTATATGCCGGAT
CATCAATTTTTTTATTTTAAT
Found at i:38564883 original size:186 final size:190
Alignment explanation
Indices: 38564467--38565118 Score: 613
Period size: 186 Copynumber: 3.4 Consensus size: 190
38564457 ATTTCGATAT
*
38564467 CTTAGTTAAGCTTATCGTAGCAATTGATTTTCATTTCTTTATA-GGCCGGATCTTCAATTATTTG
1 CTTAGTTAAGCTTATCGTAGCATTTGATTTTCATTTCTTTATATGG-CGGATCTTC-A--ATTT-
*
38564531 TTTATTTTTGAAATTTTCACTTCGAACACTTAGTTAAGCTTATCGTAGCATTTGGCTTTCATTTC
61 TTTATTTTT-AAATTTTCACTTCGAACACTTAGTTAAGCTTATCGTAGCATTTGACTTTCATTTC
* * *
38564596 TTTACATGGCGGATCTTCAATTTTTTTATTTCTTTGCTTTCTTTTTTAAAAATTTCATTTCGAAC
125 TTTACATGCCGGATCTTCAATTTTTTTATTTCTCTGCTTTCTTTTTTAAAAATTTCACTTCGAAC
*
38564661 T
190 A
* * *
38564662 CTTAGTTAAGCTTATCGTAGCATTTTATTTTCATTTTTTTATATGGCGGATCATCAATTTTTTA-
1 CTTAGTTAAGCTTATCGTAGCATTTGATTTTCATTTCTTTATATGGCGGATCTTCAATTTTTTAT
* * * * * *
38564726 TTTT-AATTTTCATTTCGAACTCTTAGTTAAGC-TATCGTCGCTTTTGATTTTCATTTCTTTATA
66 TTTTAAATTTTCACTTCGAACACTTAGTTAAGCTTATCGTAGCATTTGACTTTCATTTCTTTACA
*
38564789 TGCCGGATCTTCAATTTTTTTATTTCTCT-CTTT-TCTTTTTGAAAATTTCACTTCGAACA
131 TGCCGGATCTTCAATTTTTTTATTTCTCTGCTTTCT-TTTTTAAAAATTTCACTTCGAACA
* *
38564848 CTTACTTAAGCTTATCGTAGCATTTGATTTTCATTTCTTAATATGGCGGATCTTCAAATTTTTGT
1 CTTAGTTAAGCTTATCGTAGCATTTGATTTTCATTTCTTTATATGGCGGATCTTC-AA-------
* * * * * * * * *
38564913 TTCTCTGTTTTTTTTTTCATTTTTCATTTTGAACTCTCAGTTAAAGCTTATCATAGCAGTTGA-T
58 ---T-T-TTTTATTTTTAAATTTTCACTTCGAACACTTAGTT-AAGCTTATCGTAGCATTTGACT
* ** * * ***
38564977 TTCATTTCTTTACATGGCACATCTTCAA-ATTTTTATTTCTCTGCTGTTATTTTTT-TCCATTTC
117 TTCATTTCTTTACATGCCGGATCTTCAATTTTTTTATTTCTCTGCT-TTCTTTTTTAAAAATTTC
* *
38565040 GAAGTTCGAACT
181 --ACTTCGAACA
* * * * * * *
38565052 CTCT-GTTAACCTTATCGTAGCATTTGATTTTCATTTCCTCATATGCCGGCTCTTCAAATTTTCA
1 CT-TAGTTAAGCTTATCGTAGCATTTGATTTTCATTTCTTTATATGGCGGATCTTCAATTTTTTA
38565116 TTT
65 TTT
38565119 CTTTGTTTTT
Statistics
Matches: 384, Mismatches: 48, Indels: 54
0.79 0.10 0.11
Matches are distributed among these distances:
185 1 0.00
186 75 0.20
187 55 0.14
188 26 0.07
190 4 0.01
191 10 0.03
192 5 0.01
194 1 0.00
195 48 0.12
196 2 0.01
197 1 0.00
198 1 0.00
199 4 0.01
200 4 0.01
201 34 0.09
202 36 0.09
203 20 0.05
204 56 0.15
205 1 0.00
ACGTcount: A:0.21, C:0.17, G:0.11, T:0.50
Consensus pattern (190 bp):
CTTAGTTAAGCTTATCGTAGCATTTGATTTTCATTTCTTTATATGGCGGATCTTCAATTTTTTAT
TTTTAAATTTTCACTTCGAACACTTAGTTAAGCTTATCGTAGCATTTGACTTTCATTTCTTTACA
TGCCGGATCTTCAATTTTTTTATTTCTCTGCTTTCTTTTTTAAAAATTTCACTTCGAACA
Done.