Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032254.1 Gossypioides kirkii chromosome KI_12
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: 43711324
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 122 of 135
Found at i:40423708 original size:15 final size:15
Alignment explanation
Indices: 40423688--40423721 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
40423678 TTTTTAAAAA
40423688 TATTTGTTTATTTAT
1 TATTTGTTTATTTAT
*
40423703 TATTTGTTTGTTTAT
1 TATTTGTTTATTTAT
40423718 TATT
1 TATT
40423722 CATTATCATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.18, C:0.00, G:0.09, T:0.74
Consensus pattern (15 bp):
TATTTGTTTATTTAT
Found at i:40424554 original size:20 final size:22
Alignment explanation
Indices: 40424513--40424558 Score: 69
Period size: 20 Copynumber: 2.1 Consensus size: 22
40424503 GCCCCTACCT
40424513 TTTTATTATTTAAAAATTAAGTA
1 TTTTATTATTTAAAAA-TAAGTA
40424536 TTTTATTA-TTAAAAA-AAGTA
1 TTTTATTATTTAAAAATAAGTA
40424556 TTT
1 TTT
40424559 AGTACACAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 8 0.35
22 7 0.30
23 8 0.35
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.52
Consensus pattern (22 bp):
TTTTATTATTTAAAAATAAGTA
Found at i:40432221 original size:15 final size:15
Alignment explanation
Indices: 40432201--40432239 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
40432191 GCACATCAAA
*
40432201 CAAGAATTAATATAT
1 CAAGAATTAATAAAT
*
40432216 CAAGAA-TACTAAAT
1 CAAGAATTAATAAAT
40432230 CAAGAATTAA
1 CAAGAATTAA
40432240 GCACACATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
14 12 0.60
15 8 0.40
ACGTcount: A:0.56, C:0.10, G:0.08, T:0.26
Consensus pattern (15 bp):
CAAGAATTAATAAAT
Found at i:40432378 original size:11 final size:11
Alignment explanation
Indices: 40432362--40432389 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
40432352 CTAATAAATG
40432362 GAAACATCTCA
1 GAAACATCTCA
40432373 GAAACATCTCA
1 GAAACATCTCA
40432384 GAAACA
1 GAAACA
40432390 ATATAACCAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.50, C:0.25, G:0.11, T:0.14
Consensus pattern (11 bp):
GAAACATCTCA
Found at i:40432700 original size:13 final size:13
Alignment explanation
Indices: 40432679--40432711 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
40432669 ATAATATAAT
40432679 AATAATAATCCTA
1 AATAATAATCCTA
*
40432692 AATATTAATCCTA
1 AATAATAATCCTA
40432705 AA-AATAA
1 AATAATAA
40432712 AGTTTAAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
12 4 0.22
13 14 0.78
ACGTcount: A:0.58, C:0.12, G:0.00, T:0.30
Consensus pattern (13 bp):
AATAATAATCCTA
Found at i:40433653 original size:16 final size:17
Alignment explanation
Indices: 40433615--40433656 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
40433605 TTTTGTCTTT
*
40433615 TTTTTTTTTTTTCCTCAA
1 TTTTTCTTTTTT-CTCAA
40433633 -TTTTCTTTTTT-TCAA
1 TTTTTCTTTTTTCTCAA
40433648 TTTTTCTTT
1 TTTTTCTTT
40433657 CGACTTTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 4 0.18
16 8 0.36
17 10 0.45
ACGTcount: A:0.10, C:0.14, G:0.00, T:0.76
Consensus pattern (17 bp):
TTTTTCTTTTTTCTCAA
Found at i:40433802 original size:13 final size:13
Alignment explanation
Indices: 40433784--40433809 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
40433774 AAATATATGG
40433784 ATTATGGGTTAAT
1 ATTATGGGTTAAT
40433797 ATTATGGGTTAAT
1 ATTATGGGTTAAT
40433810 GAATAGAACG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.00, G:0.23, T:0.46
Consensus pattern (13 bp):
ATTATGGGTTAAT
Found at i:40435157 original size:15 final size:15
Alignment explanation
Indices: 40435137--40435175 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
40435127 GCACATCAAA
*
40435137 CAAGAATTAATATAT
1 CAAGAATTAATAAAT
*
40435152 CAAGAA-TACTAAAT
1 CAAGAATTAATAAAT
40435166 CAAGAATTAA
1 CAAGAATTAA
40435176 GCACACATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
14 12 0.60
15 8 0.40
ACGTcount: A:0.56, C:0.10, G:0.08, T:0.26
Consensus pattern (15 bp):
CAAGAATTAATAAAT
Found at i:40435608 original size:25 final size:25
Alignment explanation
Indices: 40435555--40435600 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
40435545 GTCGGATCCA
40435555 AATTAAATTCTAAAAAGATAATTTG
1 AATTAAATTCTAAAAAGATAATTTG
*
40435580 AATTAAATT-TAAACA-ATAATT
1 AATTAAATTCTAAAAAGATAATT
40435601 CTCTAATTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 5 0.25
25 9 0.45
ACGTcount: A:0.54, C:0.04, G:0.04, T:0.37
Consensus pattern (25 bp):
AATTAAATTCTAAAAAGATAATTTG
Found at i:40435698 original size:16 final size:13
Alignment explanation
Indices: 40435666--40435693 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
40435656 ACAATATAAT
40435666 AATATTAATCCTA
1 AATATTAATCCTA
40435679 AATATTAATCCTA
1 AATATTAATCCTA
40435692 AA
1 AA
40435694 AAATAAAGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.50, C:0.14, G:0.00, T:0.36
Consensus pattern (13 bp):
AATATTAATCCTA
Found at i:40437832 original size:5 final size:5
Alignment explanation
Indices: 40437818--40437872 Score: 103
Period size: 5 Copynumber: 11.2 Consensus size: 5
40437808 AATAAAGTGC
40437818 TATA- TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
40437867 TATAT T
1 TATAT T
40437873 TCCATATCTT
Statistics
Matches: 50, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
4 4 0.08
5 46 0.92
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TATAT
Found at i:40438062 original size:25 final size:23
Alignment explanation
Indices: 40438033--40438078 Score: 65
Period size: 25 Copynumber: 1.9 Consensus size: 23
40438023 ATCGGATCCA
40438033 AATTAAATTCTAAAAAGATAATTTG
1 AATTAAATT-TAAAAA-ATAATTTG
*
40438058 AATTAAATTTAAACAATAATT
1 AATTAAATTTAAAAAATAATT
40438079 CCCTAATTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 5 0.25
25 9 0.45
ACGTcount: A:0.54, C:0.04, G:0.04, T:0.37
Consensus pattern (23 bp):
AATTAAATTTAAAAAATAATTTG
Found at i:40438176 original size:16 final size:13
Alignment explanation
Indices: 40438144--40438171 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
40438134 ACAATATAAT
40438144 AATATTAATCCTA
1 AATATTAATCCTA
40438157 AATATTAATCCTA
1 AATATTAATCCTA
40438170 AA
1 AA
40438172 AAATAAAGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.50, C:0.14, G:0.00, T:0.36
Consensus pattern (13 bp):
AATATTAATCCTA
Found at i:40440313 original size:5 final size:5
Alignment explanation
Indices: 40440299--40440333 Score: 63
Period size: 5 Copynumber: 7.2 Consensus size: 5
40440289 AATAAAGTGC
40440299 TATA- TATAT TATAT TATAT TATAT TATAT TATAT T
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT T
40440334 TCCATATCTT
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
4 4 0.13
5 26 0.87
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TATAT
Found at i:40449791 original size:18 final size:17
Alignment explanation
Indices: 40449750--40449793 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
40449740 TTTTATATTA
*
40449750 AGTTTTTATTTTCTTTT
1 AGTTTTTATTTTCTTCT
40449767 A-TATTTTGATTTTCTTCT
1 AGT-TTTT-ATTTTCTTCT
40449785 AGTTTTTAT
1 AGTTTTTAT
40449794 CTGCCTTTGT
Statistics
Matches: 23, Mismatches: 1, Indels: 6
0.77 0.03 0.20
Matches are distributed among these distances:
16 1 0.04
17 7 0.30
18 14 0.61
19 1 0.04
ACGTcount: A:0.16, C:0.07, G:0.07, T:0.70
Consensus pattern (17 bp):
AGTTTTTATTTTCTTCT
Found at i:40454706 original size:12 final size:12
Alignment explanation
Indices: 40454686--40454719 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
40454676 AAAACTTTAG
*
40454686 AAAATATAATTA
1 AAAAAATAATTA
*
40454698 AAAAAATAAGTA
1 AAAAAATAATTA
40454710 AAAAAATAAT
1 AAAAAATAAT
40454720 AGGAGTGGCC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.24
Consensus pattern (12 bp):
AAAAAATAATTA
Found at i:40456630 original size:21 final size:22
Alignment explanation
Indices: 40456589--40456638 Score: 68
Period size: 21 Copynumber: 2.3 Consensus size: 22
40456579 GCATTATAAT
40456589 AGCAAAATGTCAGCAAAACAAC
1 AGCAAAATGTCAGCAAAACAAC
*
40456611 ATCAAAATGGT-AGC-AAACAAC
1 AGCAAAAT-GTCAGCAAAACAAC
40456632 AGCAAAA
1 AGCAAAA
40456639 CAGTAGTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 13 0.52
22 10 0.40
23 2 0.08
ACGTcount: A:0.56, C:0.20, G:0.14, T:0.10
Consensus pattern (22 bp):
AGCAAAATGTCAGCAAAACAAC
Found at i:40456644 original size:21 final size:21
Alignment explanation
Indices: 40456604--40456644 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
40456594 AATGTCAGCA
* **
40456604 AAACAACATCAAAATGGTAGC
1 AAACAACAGCAAAACAGTAGC
40456625 AAACAACAGCAAAACAGTAG
1 AAACAACAGCAAAACAGTAG
40456645 TAAATAGCAG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.56, C:0.20, G:0.15, T:0.10
Consensus pattern (21 bp):
AAACAACAGCAAAACAGTAGC
Found at i:40464127 original size:58 final size:58
Alignment explanation
Indices: 40464060--40464187 Score: 172
Period size: 58 Copynumber: 2.2 Consensus size: 58
40464050 TAATTCATAT
* *
40464060 TTTAATAATAATTATATTAAAA-AT-ATT-ATTAAATTACATATTATTTTATTAAACTGTA
1 TTTAATAATAATTATATTAAAATATAATTAAATAAATTA-ATA-T-TTTTATTAAACTATA
* *
40464118 TTTAATAATAATTATGTTAAAATATAATTAAATAAATTAATATTTTTATTAAATTATA
1 TTTAATAATAATTATATTAAAATATAATTAAATAAATTAATATTTTTATTAAACTATA
40464176 TTTAATAATAAT
1 TTTAATAATAAT
40464188 CATTAAAATT
Statistics
Matches: 63, Mismatches: 4, Indels: 6
0.86 0.05 0.08
Matches are distributed among these distances:
58 46 0.73
59 3 0.05
60 6 0.10
61 8 0.13
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (58 bp):
TTTAATAATAATTATATTAAAATATAATTAAATAAATTAATATTTTTATTAAACTATA
Found at i:40464379 original size:16 final size:16
Alignment explanation
Indices: 40464358--40464429 Score: 108
Period size: 16 Copynumber: 4.5 Consensus size: 16
40464348 TGAATTACTG
*
40464358 ATTACAGCTCTATTTC
1 ATTACAGCTCTATTCC
40464374 ATTACAGCTCTATTCC
1 ATTACAGCTCTATTCC
*
40464390 ATTACAGTTCTATTCC
1 ATTACAGCTCTATTCC
* *
40464406 ATTACACCTCTATTCT
1 ATTACAGCTCTATTCC
40464422 ATTACAGC
1 ATTACAGC
40464430 GAACCAAACG
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 50 1.00
ACGTcount: A:0.26, C:0.28, G:0.06, T:0.40
Consensus pattern (16 bp):
ATTACAGCTCTATTCC
Found at i:40471588 original size:31 final size:31
Alignment explanation
Indices: 40471552--40471612 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
40471542 ATGGCCTAGT
*
40471552 GACTTAAAT-ACAAACTTTCGGATAGTTCAGC
1 GACTTAAATGA-AAACTTTCGAATAGTTCAGC
*
40471583 GACTTAAATGAAACCTTTCGAATAGTTCAG
1 GACTTAAATGAAAACTTTCGAATAGTTCAG
40471613 TGACCATCTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
31 26 0.96
32 1 0.04
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.30
Consensus pattern (31 bp):
GACTTAAATGAAAACTTTCGAATAGTTCAGC
Found at i:40477256 original size:2 final size:2
Alignment explanation
Indices: 40477249--40477313 Score: 130
Period size: 2 Copynumber: 32.5 Consensus size: 2
40477239 ATAAGTCATA
40477249 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
40477291 AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT A
40477314 AAGAAAAGAA
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 63 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:40479041 original size:24 final size:24
Alignment explanation
Indices: 40479013--40479075 Score: 99
Period size: 24 Copynumber: 2.6 Consensus size: 24
40479003 ATAAATAATC
40479013 TTTCAGTTAAACTCTGTTTATTTG
1 TTTCAGTTAAACTCTGTTTATTTG
*
40479037 TTTCAATTAAACTCTGTTTATTTG
1 TTTCAGTTAAACTCTGTTTATTTG
* *
40479061 TTTGAGTCAAACTCT
1 TTTCAGTTAAACTCT
40479076 TATTAGTCTA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.24, C:0.14, G:0.11, T:0.51
Consensus pattern (24 bp):
TTTCAGTTAAACTCTGTTTATTTG
Found at i:40481010 original size:24 final size:24
Alignment explanation
Indices: 40480982--40481044 Score: 90
Period size: 24 Copynumber: 2.6 Consensus size: 24
40480972 AGAAATAATC
40480982 TTTCAGTTAAACTCTATTTATTTG
1 TTTCAGTTAAACTCTATTTATTTG
* *
40481006 TTTCAATTAAACTCTGTTTATTTG
1 TTTCAGTTAAACTCTATTTATTTG
* *
40481030 TTTGAGTCAAACTCT
1 TTTCAGTTAAACTCT
40481045 TATTAATCTA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.25, C:0.14, G:0.10, T:0.51
Consensus pattern (24 bp):
TTTCAGTTAAACTCTATTTATTTG
Found at i:40483867 original size:3 final size:3
Alignment explanation
Indices: 40483859--40483885 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
40483849 TGAATAACTT
40483859 GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA
40483886 TTAGTGAGGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:40492011 original size:18 final size:16
Alignment explanation
Indices: 40491979--40492022 Score: 56
Period size: 14 Copynumber: 2.8 Consensus size: 16
40491969 ATGGGATGAG
40491979 AATAAATTTTTAATTA
1 AATAAATTTTTAATTA
40491995 AATAAA--TTTAATTA
1 AATAAATTTTTAATTA
*
40492009 ATTAAAATTTTTAA
1 AAT-AAATTTTTAA
40492023 ACCTAAACAT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
14 10 0.42
15 3 0.12
16 6 0.25
17 5 0.21
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
AATAAATTTTTAATTA
Found at i:40493888 original size:26 final size:27
Alignment explanation
Indices: 40493836--40493888 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
40493826 GGAATCAAGG
*
40493836 ATTCAAAATGTTTGAAACTAATGTACT
1 ATTCAAAATGATTGAAACTAATGTACT
*
40493863 ATTCAAATTGATT-AAATCTAAT-TACT
1 ATTCAAAATGATTGAAA-CTAATGTACT
40493889 TGCATTAACA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
26 7 0.30
27 16 0.70
ACGTcount: A:0.42, C:0.11, G:0.08, T:0.40
Consensus pattern (27 bp):
ATTCAAAATGATTGAAACTAATGTACT
Found at i:40494216 original size:40 final size:40
Alignment explanation
Indices: 40494161--40494241 Score: 162
Period size: 40 Copynumber: 2.0 Consensus size: 40
40494151 CGATTTTAGA
40494161 TTTTGAATGCATAAGTAATAGCCTAATAGGTGTAGAATCT
1 TTTTGAATGCATAAGTAATAGCCTAATAGGTGTAGAATCT
40494201 TTTTGAATGCATAAGTAATAGCCTAATAGGTGTAGAATCT
1 TTTTGAATGCATAAGTAATAGCCTAATAGGTGTAGAATCT
40494241 T
1 T
40494242 ACATGATCAG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.35, C:0.10, G:0.20, T:0.36
Consensus pattern (40 bp):
TTTTGAATGCATAAGTAATAGCCTAATAGGTGTAGAATCT
Found at i:40498288 original size:22 final size:22
Alignment explanation
Indices: 40498263--40498304 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
40498253 TAAAAAACAT
*
40498263 TTTTATTAAAAACAATTTTTAA
1 TTTTAATAAAAACAATTTTTAA
**
40498285 TTTTAATAAAATTAATTTTT
1 TTTTAATAAAAACAATTTTT
40498305 TACTAATTAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (22 bp):
TTTTAATAAAAACAATTTTTAA
Found at i:40501305 original size:89 final size:89
Alignment explanation
Indices: 40501154--40501324 Score: 281
Period size: 89 Copynumber: 1.9 Consensus size: 89
40501144 TTTTTTAAAA
* *
40501154 AAAACAATAGTAAGGATGTTAAATATTTACGAGAAACCTAAAGTGTTAATAAAATGACCTGATAA
1 AAAACAATAATAAAGATGTTAAATATTTACGAGAAACCTAAAGTGTTAATAAAATGACCTGATAA
* *
40501219 TTAGACGACAGTTTGGATTTTTTT
66 TTAGACAACAATTTGGATTTTTTT
*
40501243 AAAACAATAATAAAGATGTTAAATATTTACGAGAAACCTAAAGTGTTAATAAAAT-ATGCTGATA
1 AAAACAATAATAAAGATGTTAAATATTTACGAGAAACCTAAAGTGTTAATAAAATGA-CCTGATA
40501307 ATTAGACAACAATTTGGA
65 ATTAGACAACAATTTGGA
40501325 AAATAAGGTA
Statistics
Matches: 76, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
88 1 0.01
89 75 0.99
ACGTcount: A:0.46, C:0.09, G:0.15, T:0.30
Consensus pattern (89 bp):
AAAACAATAATAAAGATGTTAAATATTTACGAGAAACCTAAAGTGTTAATAAAATGACCTGATAA
TTAGACAACAATTTGGATTTTTTT
Found at i:40504764 original size:12 final size:13
Alignment explanation
Indices: 40504734--40504764 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
40504724 TCTTTAGTTG
40504734 TTAAATATTAGTA
1 TTAAATATTAGTA
40504747 TTAAATATTAGT-
1 TTAAATATTAGTA
40504759 TTAAAT
1 TTAAAT
40504765 TTAATATGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 6 0.33
13 12 0.67
ACGTcount: A:0.45, C:0.00, G:0.06, T:0.48
Consensus pattern (13 bp):
TTAAATATTAGTA
Found at i:40513420 original size:19 final size:19
Alignment explanation
Indices: 40513396--40513432 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
40513386 ATCAGAGTTT
40513396 CTCACACAAGCTAACATTG
1 CTCACACAAGCTAACATTG
40513415 CTCACACAAGCTAACATT
1 CTCACACAAGCTAACATT
40513433 TACGAATTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.38, C:0.32, G:0.08, T:0.22
Consensus pattern (19 bp):
CTCACACAAGCTAACATTG
Found at i:40516693 original size:17 final size:16
Alignment explanation
Indices: 40516666--40516743 Score: 75
Period size: 17 Copynumber: 4.6 Consensus size: 16
40516656 AAACCCACTT
40516666 TTAAGATTTATTTTAAGA
1 TTAA-ATTTATTTTAA-A
*
40516684 TTAAATTTATTTTGAAT
1 TTAAATTTATTTT-AAA
*
40516701 TTAAATTTATCTTAAA
1 TTAAATTTATTTTAAA
* *
40516717 TTTAATTTAAATTTAAA
1 TTAAATTT-ATTTTAAA
40516734 TTTAAATTTA
1 -TTAAATTTA
40516744 AATTTAAGAC
Statistics
Matches: 50, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
16 9 0.18
17 28 0.56
18 13 0.26
ACGTcount: A:0.41, C:0.01, G:0.04, T:0.54
Consensus pattern (16 bp):
TTAAATTTATTTTAAA
Found at i:40516709 original size:6 final size:6
Alignment explanation
Indices: 40516684--40516750 Score: 79
Period size: 6 Copynumber: 11.7 Consensus size: 6
40516674 TATTTTAAGA
* *
40516684 TTAAAT TT-ATT TTGAAT TTAAAT TT--AT CTTAAAT TT-AAT TTAAAT
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT -TTAAAT TTAAAT TTAAAT
40516729 TTAAAT TTAAAT TTAAAT TTAA
1 TTAAAT TTAAAT TTAAAT TTAA
40516751 GACTTAATAT
Statistics
Matches: 53, Mismatches: 3, Indels: 10
0.80 0.05 0.15
Matches are distributed among these distances:
4 2 0.04
5 11 0.21
6 38 0.72
7 2 0.04
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.54
Consensus pattern (6 bp):
TTAAAT
Found at i:40516715 original size:11 final size:10
Alignment explanation
Indices: 40516699--40516743 Score: 54
Period size: 11 Copynumber: 4.1 Consensus size: 10
40516689 TTTATTTTGA
40516699 ATTTAAATTT
1 ATTTAAATTT
40516709 ATCTTAAATTT
1 AT-TTAAATTT
40516720 AATTTAAATTT
1 -ATTTAAATTT
40516731 AAATTTAAATTT
1 --ATTTAAATTT
40516743 A
1 A
40516744 AATTTAAGAC
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
10 3 0.09
11 16 0.50
12 13 0.41
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (10 bp):
ATTTAAATTT
Found at i:40516763 original size:18 final size:17
Alignment explanation
Indices: 40516712--40516770 Score: 64
Period size: 18 Copynumber: 3.3 Consensus size: 17
40516702 TAAATTTATC
*
40516712 TTAAATTTAATTTAAAT
1 TTAAACTTAATTTAAAT
*
40516729 TTAAATTTAAATTTAAAT
1 TTAAACTT-AATTTAAAT
*
40516747 TTAAGACTTAATATAAAT
1 TTAA-ACTTAATTTAAAT
40516765 ATTAAA
1 -TTAAA
40516771 GTCCATTACA
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
17 8 0.22
18 22 0.59
19 7 0.19
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.46
Consensus pattern (17 bp):
TTAAACTTAATTTAAAT
Found at i:40518624 original size:30 final size:29
Alignment explanation
Indices: 40518586--40518809 Score: 197
Period size: 30 Copynumber: 7.6 Consensus size: 29
40518576 CCCTAGAGGT
40518586 CCCT-AAACTGTCCAAAAATTACATTTTGA
1 CCCTCAAACT-TCCAAAAATTACATTTTGA
* ** * *
40518615 CACTCAAACTTTAAAAAACTACATTTTTAA
1 CCCTCAAACTTCCAAAAATTACA-TTTTGA
* *
40518645 CCCTAAAACTTCTAAAAATTACATTTT-A
1 CCCTCAAACTTCCAAAAATTACATTTTGA
40518673 CCC-CTAAACTTCCAAAAATTACATTTTGA
1 CCCTC-AAACTTCCAAAAATTACATTTTGA
* *
40518702 CCC-CTAAACTTTCAAAAATTACATTTTTAA
1 CCCTC-AAACTTCCAAAAATTACA-TTTTGA
* * *
40518732 CCCTAAAACTTCCAAAAATTCCTTTTTTAGA
1 CCCTCAAACTTCCAAAAATTAC-ATTTT-GA
* * *
40518763 CCCTTAAACTTCCAAAAATTCCATTTTTA
1 CCCTCAAACTTCCAAAAATTACATTTTGA
*
40518792 CCCTCGAAA-GTCCAAAAA
1 CCCTC-AAACTTCCAAAAA
40518810 CTCGATTTTT
Statistics
Matches: 162, Mismatches: 24, Indels: 18
0.79 0.12 0.09
Matches are distributed among these distances:
28 25 0.15
29 53 0.33
30 62 0.38
31 22 0.14
ACGTcount: A:0.40, C:0.25, G:0.03, T:0.33
Consensus pattern (29 bp):
CCCTCAAACTTCCAAAAATTACATTTTGA
Found at i:40518693 original size:87 final size:89
Alignment explanation
Indices: 40518586--40518794 Score: 289
Period size: 87 Copynumber: 2.3 Consensus size: 89
40518576 CCCTAGAGGT
*
40518586 CCCTAAACTGTCCAAAAATTACATTTTGA-CACTCAAACTTTAAAAAACTACATTTTTAACCCTA
1 CCCTAAACT-TCCAAAAATTACATTTTGACCCCT-AAACTTTAAAAAACTACATTTTTAACCCTA
*
40518650 AAACTTCTAAAAATTAC-ATTTT-AC
64 AAACTTCCAAAAATTACTATTTTAAC
* *
40518674 CCCTAAACTTCCAAAAATTACATTTTGACCCCTAAACTTTCAAAAATTACATTTTTAACCCTAAA
1 CCCTAAACTTCCAAAAATTACATTTTGACCCCTAAACTTTAAAAAACTACATTTTTAACCCTAAA
* *
40518739 ACTTCCAAAAATTCCTTTTTTAGAC
66 ACTTCCAAAAATTACTATTTTA-AC
* * *
40518764 CCTTAAACTTCCAAAAATTCCATTTTTACCC
1 CCCTAAACTTCCAAAAATTACATTTTGACCC
40518795 TCGAAAGTCC
Statistics
Matches: 108, Mismatches: 9, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
87 62 0.57
88 16 0.15
90 30 0.28
ACGTcount: A:0.39, C:0.25, G:0.02, T:0.34
Consensus pattern (89 bp):
CCCTAAACTTCCAAAAATTACATTTTGACCCCTAAACTTTAAAAAACTACATTTTTAACCCTAAA
ACTTCCAAAAATTACTATTTTAAC
Found at i:40518805 original size:29 final size:30
Alignment explanation
Indices: 40518588--40518809 Score: 208
Period size: 29 Copynumber: 7.5 Consensus size: 30
40518578 CTAGAGGTCC
* *
40518588 CTAAACTGTCCAAAAATTACATTTTGACACT
1 CTAAACT-TCCAAAAATTACATTTTTACCCT
** *
40518619 C-AAACTTTAAAAAACTACATTTTTAACCCT
1 CTAAACTTCCAAAAATTACATTTTT-ACCCT
* *
40518649 -AAAACTTCTAAAAATTACA-TTTTACCC-
1 CTAAACTTCCAAAAATTACATTTTTACCCT
*
40518676 CTAAACTTCCAAAAATTACATTTTGACCC-
1 CTAAACTTCCAAAAATTACATTTTTACCCT
*
40518705 CTAAACTTTCAAAAATTACATTTTTAACCCT
1 CTAAACTTCCAAAAATTACATTTTT-ACCCT
* * *
40518736 -AAAACTTCCAAAAATTCCTTTTTTAGACCCT
1 CTAAACTTCCAAAAATTACATTTTT--ACCCT
*
40518767 -TAAACTTCCAAAAATTCCATTTTTACCCT
1 CTAAACTTCCAAAAATTACATTTTTACCCT
* *
40518796 CGAAA-GTCCAAAAA
1 CTAAACTTCCAAAAA
40518810 CTCGATTTTT
Statistics
Matches: 161, Mismatches: 22, Indels: 18
0.80 0.11 0.09
Matches are distributed among these distances:
28 21 0.13
29 61 0.38
30 51 0.32
31 28 0.17
ACGTcount: A:0.40, C:0.24, G:0.03, T:0.33
Consensus pattern (30 bp):
CTAAACTTCCAAAAATTACATTTTTACCCT
Found at i:40525339 original size:101 final size:101
Alignment explanation
Indices: 40525167--40525605 Score: 483
Period size: 101 Copynumber: 4.4 Consensus size: 101
40525157 AAACACGTCA
* * * *
40525167 GGAAAGATCTAAGACTGCAACGGCGGATCCAGTACCGCAAAGATACAAAAGGGAAAGGTCTAAGT
1 GGAAAGATCTAAGACCGCAACGACGGATCCAGTACCGCAAAAAGACAAAAGGGAAAGGTCTAAGT
** *
40525232 CGCAACGGTAGACTGTGTACCTCAAAAGACACGAGG
66 CGCAACGACAGACTGTGTACCTCAAAAGACACGACG
* *
40525268 GGAAATATCTAAGACCGCAACGACGGATCCAGTACTGCAAAAAGACAAAAGGGAAAGGTCTAAGT
1 GGAAAGATCTAAGACCGCAACGACGGATCCAGTACCGCAAAAAGACAAAAGGGAAAGGTCTAAGT
*
40525333 CTCAACGACAGA-TCGTGTACCTCAAAA-ACCACGACG
66 CGCAACGACAGACT-GTGTACCTCAAAAGA-CACGACG
* * * * * *
40525369 GGAAAGATTTAAGACCGCAACGATGGATCTAGTATCGCAAAGATACAAAAGGGAAAGGTCTAAGT
1 GGAAAGATCTAAGACCGCAACGACGGATCCAGTACCGCAAAAAGACAAAAGGGAAAGGTCTAAGT
* * * *
40525434 GGCAACTACAGACCGTGTACCTCAGAAGACACGACG
66 CGCAACGACAGACTGTGTACCTCAAAAGACACGACG
* * * ** *
40525470 GGAAAGATCTAAGACCGCAACGACGGATCCAGTACCACAAAAAGATAGAAGGGAAATATCTAAGA
1 GGAAAGATCTAAGACCGCAACGACGGATCCAGTACCGCAAAAAGACAAAAGGGAAAGGTCTAAGT
* * ** * * * *
40525535 CAGCAATGGCAGA-TCCAGTACCAC-GAAGACATGAAG
66 C-GCAACGACAGACT-GTGTACCTCAAAAGACACGACG
* *
40525571 GGAAAGATCTAA-ACCGCGACGGCGGATCCAGTACC
1 GGAAAGATCTAAGACCGCAACGACGGATCCAGTACC
40525606 ACGAAGACAT
Statistics
Matches: 285, Mismatches: 47, Indels: 13
0.83 0.14 0.04
Matches are distributed among these distances:
100 23 0.08
101 247 0.87
102 15 0.05
ACGTcount: A:0.39, C:0.22, G:0.25, T:0.14
Consensus pattern (101 bp):
GGAAAGATCTAAGACCGCAACGACGGATCCAGTACCGCAAAAAGACAAAAGGGAAAGGTCTAAGT
CGCAACGACAGACTGTGTACCTCAAAAGACACGACG
Found at i:40525576 original size:202 final size:202
Alignment explanation
Indices: 40525167--40525798 Score: 572
Period size: 202 Copynumber: 3.2 Consensus size: 202
40525157 AAACACGTCA
* *
40525167 GGAAAGATCTAAGACTGCAACGGCGGATCCAGTACCGCAAAGATACAAAAGGGAAAGGTCTAAGT
1 GGAAAGATCTAAGACCGCAACGACGGATCCAGTACCGCAAAGATACAAAAGGGAAAGGTCTAAGT
** * * *
40525232 CGCAACGGTAGACTGTGTACCTCAAAAGACACGAGGGGAAATATCTAAGACCGCAACGACGGATC
66 CGCAACGACAGACCGTGTACCTCAAAAGACACGACGGGAAAGATCTAAGACCGCAACGACGGATC
** * * * ** *
40525297 CAGTACTGCAAAAAGACAAAAGGGAAAGGTCTAAGTCTCAACGACAGATCGTGTACCTCAAAAAC
131 CAGTACCACAAAAAGACAAAAGGGAAAGATCTAAGACGCAACGACAGATCCAGTACCACAAAAAC
*
40525362 CACGACG
196 CACGAAG
* * * *
40525369 GGAAAGATTTAAGACCGCAACGATGGATCTAGTATCGCAAAGATACAAAAGGGAAAGGTCTAAGT
1 GGAAAGATCTAAGACCGCAACGACGGATCCAGTACCGCAAAGATACAAAAGGGAAAGGTCTAAGT
* * *
40525434 GGCAACTACAGACCGTGTACCTCAGAAGACACGACGGGAAAGATCTAAGACCGCAACGACGGATC
66 CGCAACGACAGACCGTGTACCTCAAAAGACACGACGGGAAAGATCTAAGACCGCAACGACGGATC
* * * * * * *
40525499 CAGTACCACAAAAAGATAGAAGGGAAATATCTAAGACAGCAATGGCAGATCCAGTACCACGAAGA
131 CAGTACCACAAAAAGACAAAAGGGAAAGATCTAAGAC-GCAACGACAGATCCAGTACCACAAAAA
*
40525564 -CATGAAG
195 CCACGAAG
* * * * *
40525571 GGAAAGATCTAA-ACCGCGACGGCGGATCCAGTACCACGAAG--ACATAAA-GGAAAGATCTAAG
1 GGAAAGATCTAAGACCGCAACGACGGATCCAGTACCGCAAAGATACA-AAAGGGAAAGGTCTAAG
* * *** * ** * * **
40525632 CCGTAACGGTGGATCC-AGTA-C-CATTGAGACATGAAGGGAAAGATCTAAG-CCGCAACGGTGG
65 TCGCAACGACAGA-CCGTGTACCTCA-AAAGACACGACGGGAAAGATCTAAGACCGCAACGACGG
* * * * * *** *
40525693 ATCCAGTACCAC--GAAGACACGACGAGAAAGATCTAAGACCGTAACGGTGGATCCAGTACCGCA
128 ATCCAGTACCACAAAAAGACA-AAAGGGAAAGATCTAAGA-CGCAACGACAGATCCAGTACCACA
* *
40525756 AAGA-CA-TAAG
191 AAAACCACGAAG
*
40525766 GGAAAGATATAAG-CCGCAACGACGGATCCAGTA
1 GGAAAGATCTAAGACCGCAACGACGGATCCAGTA
40525799 TCACCAAGAC
Statistics
Matches: 354, Mismatches: 69, Indels: 21
0.80 0.16 0.05
Matches are distributed among these distances:
195 37 0.10
196 38 0.11
197 25 0.07
198 22 0.06
199 24 0.07
200 5 0.01
201 22 0.06
202 162 0.46
203 19 0.05
ACGTcount: A:0.39, C:0.22, G:0.25, T:0.14
Consensus pattern (202 bp):
GGAAAGATCTAAGACCGCAACGACGGATCCAGTACCGCAAAGATACAAAAGGGAAAGGTCTAAGT
CGCAACGACAGACCGTGTACCTCAAAAGACACGACGGGAAAGATCTAAGACCGCAACGACGGATC
CAGTACCACAAAAAGACAAAAGGGAAAGATCTAAGACGCAACGACAGATCCAGTACCACAAAAAC
CACGAAG
Found at i:40525609 original size:49 final size:49
Alignment explanation
Indices: 40525458--40525936 Score: 514
Period size: 49 Copynumber: 9.7 Consensus size: 49
40525448 GTGTACCTCA
* * *
40525458 GAAGACACGACGGGAAAGATCTAAGACCGCAACGACGGATCCAGTACCAC
1 GAAGACATGAAGGGAAAGATCTAAG-CCGCAACGGCGGATCCAGTACCAC
* * * * * * *
40525508 AAAAAGATAGAAGGGAAATATCTAAGACAGCAATGGCAGATCCAGTACCAC
1 GAAGACAT-GAAGGGAAAGATCTAAG-CCGCAACGGCGGATCCAGTACCAC
* *
40525559 GAAGACATGAAGGGAAAGATCTAAACCGCGACGGCGGATCCAGTACCAC
1 GAAGACATGAAGGGAAAGATCTAAGCCGCAACGGCGGATCCAGTACCAC
* * * *
40525608 GAAGACAT-AAAGGAAAGATCTAAGCCGTAACGGTGGATCCAGTACCATT
1 GAAGACATGAAGGGAAAGATCTAAGCCGCAACGGCGGATCCAGTACCA-C
*
40525657 G-AGACATGAAGGGAAAGATCTAAGCCGCAACGGTGGATCCAGTACCAC
1 GAAGACATGAAGGGAAAGATCTAAGCCGCAACGGCGGATCCAGTACCAC
* * * * * *
40525705 GAAGACACGACGAGAAAGATCTAAGACCGTAACGGTGGATCCAGTACCGC
1 GAAGACATGAAGGGAAAGATCTAAG-CCGCAACGGCGGATCCAGTACCAC
* * * *
40525755 AAAGACAT-AAGGGAAAGATATAAGCCGCAACGACGGATCCAGTATCAC
1 GAAGACATGAAGGGAAAGATCTAAGCCGCAACGGCGGATCCAGTACCAC
* * * *
40525803 CAAGACATGAAGGGAAAGATCTAAGCCGCGACTGCGGATCCAATACCAC
1 GAAGACATGAAGGGAAAGATCTAAGCCGCAACGGCGGATCCAGTACCAC
* * * * *
40525852 CAAGACATGAAAGGAAAGATCTAAGTCGCGACGGCAGATCCAGTACCAC
1 GAAGACATGAAGGGAAAGATCTAAGCCGCAACGGCGGATCCAGTACCAC
** * * * *
40525901 GAAGATTTGAAGGGAAAGGTTTAAGTCGCAATGGCG
1 GAAGACATGAAGGGAAAGATCTAAGCCGCAACGGCG
40525937 AACCTGGTAC
Statistics
Matches: 359, Mismatches: 64, Indels: 13
0.82 0.15 0.03
Matches are distributed among these distances:
48 67 0.19
49 204 0.57
50 47 0.13
51 41 0.11
ACGTcount: A:0.39, C:0.22, G:0.26, T:0.13
Consensus pattern (49 bp):
GAAGACATGAAGGGAAAGATCTAAGCCGCAACGGCGGATCCAGTACCAC
Found at i:40526912 original size:206 final size:205
Alignment explanation
Indices: 40526348--40527001 Score: 881
Period size: 205 Copynumber: 3.2 Consensus size: 205
40526338 ACAGTGAGGT
* * * * * *
40526348 GGTCATCTTCTTGATGAGATACAGAGAAGTATACCAACTC-AG---TGCTCGATGCGAGCAAATC
1 GGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAGCCATGCTCGATGTGAGCAAATC
* * *
40526409 TTCGAACTCCAGCTTCCTGATGAGATACTGA-AGAGTAGGTCGAAACAATAAAATGGTTAGCTTC
66 TTCGAACCCCAGCTTCCTGATGAGATACTGAGA-AGCAGGTCGAAGCAATAAAATGGTTAGCTTC
*
40526473 CTGATGAGATACTGAGAAGTGGA-CAGAATTAGTCTTCCTGATGAGATACAGAGAAGCGGATTGA
130 CTGATGAGATACTGAGAAGTGGACCA-AATTCGTCTTCCTGATGAGATACAGAGAAGCGGATTGA
*
40526537 AACAAGTGATGT
194 AACAAGTGATGC
* * * *
40526549 GGTCATCTTCCTGATGAGATAATGAGAAGAAGACCAAATCAAACTCACGCTCAAT-TGAGCAAAT
1 GGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAGC-CATGCTCGATGTGAGCAAAT
* * *
40526613 CTTCGAACCCTAGCTTCCTTATGAGATACTGAGAAGCATGTCGAAGCAATAAAATGGTTAGCTTC
65 CTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTC
* * *
40526678 CTAATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATATAGAGAAGCGAATTGAA
130 CTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGATTGAA
***
40526743 ACAAACAATGC
195 ACAAGTGATGC
40526754 GGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAGCCCATGCTCGATGTGAGCAAAT
1 GGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAG-CCATGCTCGATGTGAGCAAAT
* *
40526819 CTTCGAACCCCAGCTTCCTGATGAGATATTGAGAAGCAGGTCGAAGCAATAAAATAGTTAGCTTC
65 CTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTC
* *** *
40526884 CTGATGAGACACTGAGAAGCATACCAAATTCGTCTTCCTAATGAGATACAGAGAAGCGGATTGAA
130 CTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGATTGAA
40526949 ACAAGTGATGC
195 ACAAGTGATGC
** * * * * *
40526960 ACTCATCTACCGGATGAGATACTGAGGAGAAGGCCAACTCAA
1 GGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAA
40527002 TGAAACCAGA
Statistics
Matches: 393, Mismatches: 51, Indels: 13
0.86 0.11 0.03
Matches are distributed among these distances:
201 34 0.09
202 1 0.00
205 179 0.46
206 179 0.46
ACGTcount: A:0.35, C:0.19, G:0.23, T:0.23
Consensus pattern (205 bp):
GGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAGCCATGCTCGATGTGAGCAAATC
TTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCC
TGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGATTGAAA
CAAGTGATGC
Found at i:40527346 original size:17 final size:17
Alignment explanation
Indices: 40527319--40527397 Score: 79
Period size: 17 Copynumber: 4.5 Consensus size: 17
40527309 TAAACCCCTT
40527319 TTAAGATTTATTTTAAGA
1 TTAA-ATTTATTTTAAGA
*
40527337 TTAAATTTATTTTGAA-T
1 TTAAATTTATTTT-AAGA
* *
40527354 TTAAATTTATCTTAAGT
1 TTAAATTTATTTTAAGA
* *
40527371 TTAAATTTGTTTTAAAA
1 TTAAATTTATTTTAAGA
40527388 TTTAAATTTA
1 -TTAAATTTA
40527398 AATTTAAATT
Statistics
Matches: 51, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
16 2 0.04
17 35 0.69
18 14 0.27
ACGTcount: A:0.38, C:0.01, G:0.06, T:0.54
Consensus pattern (17 bp):
TTAAATTTATTTTAAGA
Found at i:40527393 original size:7 final size:6
Alignment explanation
Indices: 40527337--40527409 Score: 55
Period size: 6 Copynumber: 12.5 Consensus size: 6
40527327 TATTTTAAGA
* * * **
40527337 TTAAAT TT-ATT TTGAAT TTAAAT TT--AT CTTAAGT TTAAAT TT-GTT
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT -TTAAAT TTAAAT TTAAAT
40527382 TTAAAAT TTAAAT TTAAAT TTAAAT TTA
1 TT-AAAT TTAAAT TTAAAT TTAAAT TTA
40527410 GGACTTAATA
Statistics
Matches: 52, Mismatches: 9, Indels: 12
0.71 0.12 0.16
Matches are distributed among these distances:
4 2 0.04
5 9 0.17
6 37 0.71
7 4 0.08
ACGTcount: A:0.40, C:0.01, G:0.04, T:0.55
Consensus pattern (6 bp):
TTAAAT
Found at i:40528499 original size:22 final size:21
Alignment explanation
Indices: 40528473--40528515 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
40528463 TGGACTTTGG
40528473 TTTAATAA-AAAAGAGAAAAGGT
1 TTTAA-AACAAAAGA-AAAAGGT
40528495 TTTAAAATCAAAAGAAAAAGG
1 TTTAAAA-CAAAAGAAAAAGG
40528516 AAAAAGAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
21 2 0.11
22 11 0.58
23 6 0.32
ACGTcount: A:0.60, C:0.02, G:0.16, T:0.21
Consensus pattern (21 bp):
TTTAAAACAAAAGAAAAAGGT
Found at i:40529342 original size:29 final size:29
Alignment explanation
Indices: 40529235--40529343 Score: 128
Period size: 29 Copynumber: 3.7 Consensus size: 29
40529225 CCCTAAGCTA
* *
40529235 TCCAAAAATTACATTTTGACCCCCGAACT
1 TCCAAAAATTACATTTTTACCCCCAAACT
* *
40529264 TTCAAAAATTACATTTTTAACCCCGAAACT
1 TCCAAAAATTACATTTTT-ACCCCCAAACT
* * **
40529294 TCCAAAAATTATATTATTACCCTTAAACT
1 TCCAAAAATTACATTTTTACCCCCAAACT
*
40529323 TCCAAAAATTCCATTTTTACC
1 TCCAAAAATTACATTTTTACC
40529344 TCTGAAAGTG
Statistics
Matches: 67, Mismatches: 12, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
29 43 0.64
30 24 0.36
ACGTcount: A:0.38, C:0.26, G:0.03, T:0.34
Consensus pattern (29 bp):
TCCAAAAATTACATTTTTACCCCCAAACT
Found at i:40535313 original size:12 final size:12
Alignment explanation
Indices: 40535272--40535314 Score: 50
Period size: 12 Copynumber: 3.4 Consensus size: 12
40535262 AATTAATTTT
40535272 TAATAAAAAAATA
1 TAAT-AAAAAATA
* *
40535285 TTAATAAAAATTC
1 -TAATAAAAAATA
40535298 TAATAAAAAATA
1 TAATAAAAAATA
40535310 TAATA
1 TAATA
40535315 TAGATAGAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
12 15 0.60
13 6 0.24
14 4 0.16
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.30
Consensus pattern (12 bp):
TAATAAAAAATA
Found at i:40536686 original size:31 final size:32
Alignment explanation
Indices: 40536650--40536709 Score: 88
Period size: 31 Copynumber: 1.9 Consensus size: 32
40536640 ATGGTAACTG
*
40536650 AACTA-TTAGAAAGTTTTTATT-TAAGTCACTA
1 AACTATTTA-AAAGTTTATATTATAAGTCACTA
40536681 AACTATTTAAAAGTTTATATTATAAGTCA
1 AACTATTTAAAAGTTTATATTATAAGTCA
40536710 TTAGATTGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
31 16 0.62
32 10 0.38
ACGTcount: A:0.42, C:0.08, G:0.08, T:0.42
Consensus pattern (32 bp):
AACTATTTAAAAGTTTATATTATAAGTCACTA
Found at i:40538314 original size:23 final size:23
Alignment explanation
Indices: 40538288--40538331 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
40538278 TAAGTTTATT
40538288 TTTACTATTTTAAAT-ATAAAATA
1 TTTA-TATTTTAAATCATAAAATA
* *
40538311 TTTATTTTTTATATCATAAAA
1 TTTATATTTTAAATCATAAAA
40538332 ATATAAAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 8 0.44
23 10 0.56
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (23 bp):
TTTATATTTTAAATCATAAAATA
Found at i:40558267 original size:2 final size:2
Alignment explanation
Indices: 40558260--40558284 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
40558250 TCCACTATCA
40558260 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
40558285 ATCACAAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:40562370 original size:41 final size:40
Alignment explanation
Indices: 40562325--40562404 Score: 106
Period size: 40 Copynumber: 2.0 Consensus size: 40
40562315 CATTTTTAAT
*
40562325 GGCGTTTGGACAGAAAACGCCGTAAAAGGTAAAGCAATAGC
1 GGCGTTTCGACA-AAAACGCCGTAAAAGGTAAAGCAATAGC
* * * *
40562366 GGCGTTTCTACATAAACGTCGTAAAAGGTAGAGCAATAG
1 GGCGTTTCGACAAAAACGCCGTAAAAGGTAAAGCAATAG
40562405 TGGTGCTTAT
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
40 24 0.71
41 10 0.29
ACGTcount: A:0.38, C:0.16, G:0.28, T:0.19
Consensus pattern (40 bp):
GGCGTTTCGACAAAAACGCCGTAAAAGGTAAAGCAATAGC
Found at i:40562451 original size:41 final size:41
Alignment explanation
Indices: 40562389--40562716 Score: 406
Period size: 41 Copynumber: 8.0 Consensus size: 41
40562379 AAACGTCGTA
*
40562389 AAAGGT-AGAGCAATAGTGGTGCTTATGGGAAAGCGCCGCT
1 AAAGGTCAGAGCAATAGCGGTGCTTATGGGAAAGCGCCGCT
* ** * *
40562429 AAAGGTCAGAGCAATAACGGTGCTTATGTAAAAGTGCCGGT
1 AAAGGTCAGAGCAATAGCGGTGCTTATGGGAAAGCGCCGCT
* * * * *
40562470 AAAGGCCAGAGCAATAGCGGTACTTACGAGCAAGCGCCGCT
1 AAAGGTCAGAGCAATAGCGGTGCTTATGGGAAAGCGCCGCT
* * ** *
40562511 AAAGGTCAGAGCAATAGCGGCGCCTATGGGAAAATGCTGCT
1 AAAGGTCAGAGCAATAGCGGTGCTTATGGGAAAGCGCCGCT
**
40562552 AAAGGTCAGAGCAATAGCGACGCTTATGGGAAAGCGCCGCT
1 AAAGGTCAGAGCAATAGCGGTGCTTATGGGAAAGCGCCGCT
* * *
40562593 AAAGGTCAAAGCAATAGCGGAGCTTATGGGCAAGCGCCGCT
1 AAAGGTCAGAGCAATAGCGGTGCTTATGGGAAAGCGCCGCT
*
40562634 AAAGGTCAGAGCAATAGCGGTGCTTATGGGTAAGCGCCGCT
1 AAAGGTCAGAGCAATAGCGGTGCTTATGGGAAAGCGCCGCT
* ** * *
40562675 AAAGGTCGGAGCAATAGCGACGCTTATGGGCAAGCGTCGCT
1 AAAGGTCAGAGCAATAGCGGTGCTTATGGGAAAGCGCCGCT
40562716 A
1 A
40562717 TTGGGTGCTT
Statistics
Matches: 245, Mismatches: 42, Indels: 1
0.85 0.15 0.00
Matches are distributed among these distances:
40 6 0.02
41 239 0.98
ACGTcount: A:0.31, C:0.20, G:0.32, T:0.17
Consensus pattern (41 bp):
AAAGGTCAGAGCAATAGCGGTGCTTATGGGAAAGCGCCGCT
Found at i:40562704 original size:123 final size:123
Alignment explanation
Indices: 40562389--40562802 Score: 446
Period size: 123 Copynumber: 3.5 Consensus size: 123
40562379 AAACGTCGTA
* * **
40562389 AAAGGT-AGAGCAATAGTGGTGCTTATGGGAAAGCGCCGCTAAAGGTCAGAGCAATAACGGTGCT
1 AAAGGTCAGAGCAATAGCGGTGCTTATGGGAAAGCGCCGCTAAAGGTCAGAGCAATAGCGACGCT
** * * *
40562453 TATGTAAAAGTGCCGGTAAAGGCCAGAGCAATAGCGGTACTTACGAGCAAGCGCCGCT
66 TATGGGAAAGCGCCGCTAAAGGCCAAAGCAATAGCGGTACTTACGAGCAAGCGCCGCT
* * ** *
40562511 AAAGGTCAGAGCAATAGCGGCGCCTATGGGAAAATGCTGCTAAAGGTCAGAGCAATAGCGACGCT
1 AAAGGTCAGAGCAATAGCGGTGCTTATGGGAAAGCGCCGCTAAAGGTCAGAGCAATAGCGACGCT
* * *
40562576 TATGGGAAAGCGCCGCTAAAGGTCAAAGCAATAGCGG-AGCTTATGGGCAAGCGCCGCT
66 TATGGGAAAGCGCCGCTAAAGGCCAAAGCAATAGCGGTA-CTTACGAGCAAGCGCCGCT
* *
40562634 AAAGGTCAGAGCAATAGCGGTGCTTATGGGTAAGCGCCGCTAAAGGTCGGAGCAATAGCGACGCT
1 AAAGGTCAGAGCAATAGCGGTGCTTATGGGAAAGCGCCGCTAAAGGTCAGAGCAATAGCGACGCT
* * ** * * *
40562699 TATGGGCAAGCGTCGCTATTGG-----G---T-GC--T--TT-TGTGCAAGTGCCGCT
66 TATGGGAAAGCGCCGCTAAAGGCCAAAGCAATAGCGGTACTTACGAGCAAGCGCCGCT
* * *
40562743 AAAGGTCAGAGCAATAGCGGCGCTTATGTGAAAGCGCCGCTAAAGGTCAGAGCATTAGCG
1 AAAGGTCAGAGCAATAGCGGTGCTTATGGGAAAGCGCCGCTAAAGGTCAGAGCAATAGCG
40562803 GGGCTTATTT
Statistics
Matches: 254, Mismatches: 35, Indels: 19
0.82 0.11 0.06
Matches are distributed among these distances:
109 68 0.27
110 2 0.01
114 2 0.01
115 1 0.00
118 1 0.00
122 7 0.03
123 173 0.68
ACGTcount: A:0.29, C:0.20, G:0.32, T:0.18
Consensus pattern (123 bp):
AAAGGTCAGAGCAATAGCGGTGCTTATGGGAAAGCGCCGCTAAAGGTCAGAGCAATAGCGACGCT
TATGGGAAAGCGCCGCTAAAGGCCAAAGCAATAGCGGTACTTACGAGCAAGCGCCGCT
Found at i:40562794 original size:41 final size:41
Alignment explanation
Indices: 40562723--40562827 Score: 138
Period size: 41 Copynumber: 2.5 Consensus size: 41
40562713 GCTATTGGGT
* * *
40562723 GCTTTTGTGCAAGTGCCGCTAAAGGTCAGAGCAATAGCGGC
1 GCTTATGTGAAAGCGCCGCTAAAGGTCAGAGCAATAGCGGC
* *
40562764 GCTTATGTGAAAGCGCCGCTAAAGGTCAGAGCATTAGCGGG
1 GCTTATGTGAAAGCGCCGCTAAAGGTCAGAGCAATAGCGGC
* *
40562805 GCTTATTTGAAAAACGCCGCTAA
1 GCTTATGTG-AAAGCGCCGCTAA
40562828 TTTATTTACC
Statistics
Matches: 56, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
41 44 0.79
42 12 0.21
ACGTcount: A:0.28, C:0.21, G:0.30, T:0.22
Consensus pattern (41 bp):
GCTTATGTGAAAGCGCCGCTAAAGGTCAGAGCAATAGCGGC
Found at i:40565797 original size:43 final size:43
Alignment explanation
Indices: 40565744--40566012 Score: 272
Period size: 43 Copynumber: 6.3 Consensus size: 43
40565734 TTTGTTAATA
* ** * *
40565744 TTAGTGGCGTTTGTAGGAAAAATGCCACTAAAGACCATATTCT
1 TTAGCGGCGTTTGTAGGAAAAGCGCCGCTAAAGACCATGTTCT
* * * * * *
40565787 TTAACGGCGTTTGCAGGAAAAGTGTCGCTAAAGATCATGGTCT
1 TTAGCGGCGTTTGTAGGAAAAGCGCCGCTAAAGACCATGTTCT
* * *
40565830 TTAGCGGCGTTTATGGGAAAAGCGTCGCTAAAGACCATGTTCT
1 TTAGCGGCGTTTGTAGGAAAAGCGCCGCTAAAGACCATGTTCT
* *
40565873 TTAGCGGCGTTTGTAGGAAAAGCACCGCTAAAGATCATGTTCT
1 TTAGCGGCGTTTGTAGGAAAAGCGCCGCTAAAGACCATGTTCT
* *
40565916 TTAGCGGCGTTTGT-GGAAAGGCGTCGCTAAAGACCATGTTCT
1 TTAGCGGCGTTTGTAGGAAAAGCGCCGCTAAAGACCATGTTCT
* * * * * * *
40565958 TTAGTGGCATTTAT-GAGATAAGCGTCGCTAAAGATCATGATCT
1 TTAGCGGCGTTTGTAG-GAAAAGCGCCGCTAAAGACCATGTTCT
* *
40566001 ATAGCGGAGTTT
1 TTAGCGGCGTTT
40566013 TTCCTCATAA
Statistics
Matches: 189, Mismatches: 36, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
42 36 0.19
43 153 0.81
ACGTcount: A:0.28, C:0.17, G:0.26, T:0.29
Consensus pattern (43 bp):
TTAGCGGCGTTTGTAGGAAAAGCGCCGCTAAAGACCATGTTCT
Found at i:40565894 original size:86 final size:85
Alignment explanation
Indices: 40565771--40566012 Score: 315
Period size: 85 Copynumber: 2.8 Consensus size: 85
40565761 AAAAATGCCA
* * * * *
40565771 CTAAAGACCATATTCTTTAACGGCGTTTGCAGGAAAAGTGTCGCTAAAGATCATGGTCTTTAGCG
1 CTAAAGACCATGTTCTTTAGCGGCGTTTGTAGGAAAAGCGTCGCTAAAGATCATGATCTTTAGCG
40565836 GCGTTTATGGGAAAAGCGTCG
66 GCGTTTAT-GGAAAAGCGTCG
** *
40565857 CTAAAGACCATGTTCTTTAGCGGCGTTTGTAGGAAAAGCACCGCTAAAGATCATGTTCTTTAGCG
1 CTAAAGACCATGTTCTTTAGCGGCGTTTGTAGGAAAAGCGTCGCTAAAGATCATGATCTTTAGCG
* *
40565922 GCGTTTGTGGAAAGGCGTCG
66 GCGTTTATGGAAAAGCGTCG
* * * * *
40565942 CTAAAGACCATGTTCTTTAGTGGCATTTAT-GAGATAAGCGTCGCTAAAGATCATGATCTATAGC
1 CTAAAGACCATGTTCTTTAGCGGCGTTTGTAG-GAAAAGCGTCGCTAAAGATCATGATCTTTAGC
*
40566006 GGAGTTT
65 GGCGTTT
40566013 TTCCTCATAA
Statistics
Matches: 137, Mismatches: 18, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
84 1 0.01
85 71 0.52
86 65 0.47
ACGTcount: A:0.27, C:0.17, G:0.26, T:0.29
Consensus pattern (85 bp):
CTAAAGACCATGTTCTTTAGCGGCGTTTGTAGGAAAAGCGTCGCTAAAGATCATGATCTTTAGCG
GCGTTTATGGAAAAGCGTCG
Found at i:40571133 original size:102 final size:101
Alignment explanation
Indices: 40570957--40571289 Score: 432
Period size: 102 Copynumber: 3.3 Consensus size: 101
40570947 GTTCACTCTT
* *
40570957 GCGGTTTATCCACTAGGCACTGGGTGCCATAACCGTCAGTTTATCTGACTAGCGTTGGGCGCAAA
1 GCGGTTTATCCGCTAGGCACTGGGTGCCATAACCGTCAGTTTATCTGACTAGCGTT-AGCGCAAA
* * *
40571022 CTGTTGGTTAATCCAACCAAAGCTGGGCTCAAATATC
65 CCGTTGGTTAATCCAACCAGAGCTGGGCTCACATATC
* * * *
40571059 GCGGTTTATCCGCTAGGCACTGGGTGTCATAACCGTCAGTTTATCTAACTAGCGCTACGCACAAA
1 GCGGTTTATCCGCTAGGCACTGGGTGCCATAACCGTCAGTTTATCTGACTAGCGTTA-GCGCAAA
*
40571124 CCGTTGGTTAATCCAACCAGAGCTGGGCTCACATATT
65 CCGTTGGTTAATCCAACCAGAGCTGGGCTCACATATC
** * * *
40571161 GCTATTTATCCGCTAGGCATTGGGTGCCATAACCGTCAGTTTATCCGACTAGCATTGAGCGCAAA
1 GCGGTTTATCCGCTAGGCACTGGGTGCCATAACCGTCAGTTTATCTGACTAGCGTT-AGCGCAAA
* * * *
40571226 CCGTTGGATAATCCAACTAGAGCTAGGCTCACATACC
65 CCGTTGGTTAATCCAACCAGAGCTGGGCTCACATATC
* * * *
40571263 GTGGTATATCCGATAGGCACCGGGTGC
1 GCGGTTTATCCGCTAGGCACTGGGTGC
40571290 AATGAATTGA
Statistics
Matches: 198, Mismatches: 31, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
102 197 0.99
103 1 0.01
ACGTcount: A:0.25, C:0.26, G:0.24, T:0.26
Consensus pattern (101 bp):
GCGGTTTATCCGCTAGGCACTGGGTGCCATAACCGTCAGTTTATCTGACTAGCGTTAGCGCAAAC
CGTTGGTTAATCCAACCAGAGCTGGGCTCACATATC
Found at i:40573554 original size:8 final size:8
Alignment explanation
Indices: 40573541--40573565 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
40573531 AAAGGCTTGG
40573541 GAAGAAGA
1 GAAGAAGA
40573549 GAAGAAGA
1 GAAGAAGA
40573557 GAAGAAGA
1 GAAGAAGA
40573565 G
1 G
40573566 GAGAGAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.60, C:0.00, G:0.40, T:0.00
Consensus pattern (8 bp):
GAAGAAGA
Found at i:40575406 original size:31 final size:28
Alignment explanation
Indices: 40575368--40575433 Score: 87
Period size: 30 Copynumber: 2.2 Consensus size: 28
40575358 ATATTAGAAA
40575368 TTTTTTATTTTTTTTAAATTTCTTAAATATT
1 TTTTTTA-TTTTTTTAAATTT-TTAAA-ATT
* *
40575399 TTTTTTATTTTTTTCAATTTTTATAATT
1 TTTTTTATTTTTTTAAATTTTTAAAATT
40575427 TTTTTTA
1 TTTTTTA
40575434 AAAAAAATTA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
28 10 0.30
29 4 0.12
30 12 0.36
31 7 0.21
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.74
Consensus pattern (28 bp):
TTTTTTATTTTTTTAAATTTTTAAAATT
Found at i:40575763 original size:27 final size:27
Alignment explanation
Indices: 40575733--40575790 Score: 66
Period size: 27 Copynumber: 2.1 Consensus size: 27
40575723 CATATATAAT
40575733 CACAACCTATAA-TAAAATTAAACATTA
1 CACAACCTA-AATTAAAATTAAACATTA
* *
40575760 CAC-ACCTAAATTTAAATTTCAACATTA
1 CACAACCTAAA-TTAAAATTAAACATTA
40575787 CACA
1 CACA
40575791 CCTCTTGCAG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
25 2 0.08
26 5 0.19
27 19 0.73
ACGTcount: A:0.50, C:0.22, G:0.00, T:0.28
Consensus pattern (27 bp):
CACAACCTAAATTAAAATTAAACATTA
Found at i:40580457 original size:2 final size:2
Alignment explanation
Indices: 40580452--40580481 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
40580442 GGTTCCTAAT
40580452 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
40580482 TAAGGTAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:40588384 original size:8 final size:9
Alignment explanation
Indices: 40588362--40588386 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
40588352 AATAACCCAT
40588362 ATTTTTATA
1 ATTTTTATA
40588371 ATTTTTATA
1 ATTTTTATA
40588380 ATTTTTA
1 ATTTTTA
40588387 AAGGATTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (9 bp):
ATTTTTATA
Found at i:40592060 original size:43 final size:42
Alignment explanation
Indices: 40592011--40592100 Score: 162
Period size: 43 Copynumber: 2.1 Consensus size: 42
40592001 TCAAATAAGC
*
40592011 TTATTCAAAGTTGTTATTTTCTTAATTTTATTTTGACTAAAT
1 TTATTCAAAGTTGTTATTTTCTTAATTTTAATTTGACTAAAT
40592053 TATATTCAAAGTTGTTATTTTCTTAATTTTAATTTGACTAAAT
1 T-TATTCAAAGTTGTTATTTTCTTAATTTTAATTTGACTAAAT
40592096 TTATT
1 TTATT
40592101 TATTTTAAGT
Statistics
Matches: 46, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
42 5 0.11
43 41 0.89
ACGTcount: A:0.30, C:0.07, G:0.07, T:0.57
Consensus pattern (42 bp):
TTATTCAAAGTTGTTATTTTCTTAATTTTAATTTGACTAAAT
Found at i:40594506 original size:91 final size:91
Alignment explanation
Indices: 40594351--40594533 Score: 357
Period size: 91 Copynumber: 2.0 Consensus size: 91
40594341 TTCTAGGTCT
40594351 ACCCCAAAGACGGTACGATCCCTATGCGAACACATACAATGTAGGGTGGAAGGACCATCCGAATC
1 ACCCCAAAGACGGTACGATCCCTATGCGAACACATACAATGTAGGGTGGAAGGACCATCCGAATC
40594416 TAAGTTATGGATCCAATCCTCGATTC
66 TAAGTTATGGATCCAATCCTCGATTC
*
40594442 ACCCCAAAGACGGTACGATCCCTATGCGAACACATACAATGTAGGGTGGAAGGACCATCGGAATC
1 ACCCCAAAGACGGTACGATCCCTATGCGAACACATACAATGTAGGGTGGAAGGACCATCCGAATC
40594507 TAAGTTATGGATCCAATCCTCGATTC
66 TAAGTTATGGATCCAATCCTCGATTC
40594533 A
1 A
40594534 ATCAATTGTA
Statistics
Matches: 91, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
91 91 1.00
ACGTcount: A:0.32, C:0.26, G:0.21, T:0.21
Consensus pattern (91 bp):
ACCCCAAAGACGGTACGATCCCTATGCGAACACATACAATGTAGGGTGGAAGGACCATCCGAATC
TAAGTTATGGATCCAATCCTCGATTC
Found at i:40595500 original size:20 final size:19
Alignment explanation
Indices: 40595467--40595504 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
40595457 TGCATCAAGA
40595467 TTTATTTCACTTTATTTAT
1 TTTATTTCACTTTATTTAT
*
40595486 TTTATTTTCATTTTATTTA
1 TTTA-TTTCACTTTATTTA
40595505 AGTTTAATGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.21, C:0.08, G:0.00, T:0.71
Consensus pattern (19 bp):
TTTATTTCACTTTATTTAT
Found at i:40601173 original size:30 final size:28
Alignment explanation
Indices: 40601121--40601198 Score: 79
Period size: 30 Copynumber: 2.7 Consensus size: 28
40601111 CCAACAACTG
* * *
40601121 AAATTGAATTTTGAAATCTAAAAGTTATAT
1 AAATTAAATTTTGAAATATAAAA-TTA-AA
40601151 AAATTAAATTCTTGAAA-ATAAAATTAAA
1 AAATTAAATT-TTGAAATATAAAATTAAA
40601179 AAGATTAAATTTT-AAATATA
1 AA-ATTAAATTTTGAAATATA
40601199 CAAAGAATAC
Statistics
Matches: 42, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
27 3 0.07
28 8 0.19
29 11 0.26
30 14 0.33
31 6 0.14
ACGTcount: A:0.54, C:0.03, G:0.06, T:0.37
Consensus pattern (28 bp):
AAATTAAATTTTGAAATATAAAATTAAA
Found at i:40608134 original size:30 final size:28
Alignment explanation
Indices: 40608090--40608146 Score: 71
Period size: 30 Copynumber: 2.0 Consensus size: 28
40608080 TTATTGTTAT
*
40608090 ATAATTTATACTATTGATTTTTTTTTTTTA
1 ATAATTTATACTATT--TTTTTATTTTTTA
40608120 ATAATTTA-ATCTATTTTTTTATTTTTT
1 ATAATTTATA-CTATTTTTTTATTTTTT
40608147 CATCAACTTG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
28 11 0.44
29 1 0.04
30 13 0.52
ACGTcount: A:0.26, C:0.04, G:0.02, T:0.68
Consensus pattern (28 bp):
ATAATTTATACTATTTTTTTATTTTTTA
Found at i:40608593 original size:10 final size:11
Alignment explanation
Indices: 40608573--40608597 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
40608563 AATAACACAA
40608573 TTTTTGTTTTT
1 TTTTTGTTTTT
40608584 TTTTTGTTTTT
1 TTTTTGTTTTT
40608595 TTT
1 TTT
40608598 AAAAGTTTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.00, C:0.00, G:0.08, T:0.92
Consensus pattern (11 bp):
TTTTTGTTTTT
Found at i:40612157 original size:21 final size:23
Alignment explanation
Indices: 40612114--40612158 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
40612104 TAAATTACAT
40612114 AAAAAAGCTTAAATATCATATTA
1 AAAAAAGCTTAAATATCATATTA
40612137 AAAAAATG-TTAAAT-TCA-ATTA
1 AAAAAA-GCTTAAATATCATATTA
40612158 A
1 A
40612159 TTATACAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
21 5 0.24
22 3 0.14
23 12 0.57
24 1 0.05
ACGTcount: A:0.58, C:0.07, G:0.04, T:0.31
Consensus pattern (23 bp):
AAAAAAGCTTAAATATCATATTA
Found at i:40613943 original size:20 final size:19
Alignment explanation
Indices: 40613918--40613961 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
40613908 ACATTGATCC
*
40613918 TTAAAAATTAAAAAAACT-T
1 TTAAAAAATAAAAAAA-TAT
40613937 TTAAAAAATAAAAAAATAT
1 TTAAAAAATAAAAAAATAT
40613956 TTAAAA
1 TTAAAA
40613962 CTTCTTTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 1 0.04
19 22 0.96
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (19 bp):
TTAAAAAATAAAAAAATAT
Found at i:40614521 original size:18 final size:18
Alignment explanation
Indices: 40614486--40614521 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
40614476 TTGTTTGTAG
40614486 ATTTTAAAAATATATATT
1 ATTTTAAAAATATATATT
40614504 ATTTATAAAAATAT-TATT
1 ATTT-TAAAAATATATATT
40614522 TTAATAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
ATTTTAAAAATATATATT
Found at i:40614528 original size:17 final size:19
Alignment explanation
Indices: 40614490--40614529 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
40614480 TTGTAGATTT
*
40614490 TAAAAATATATATTATTTA
1 TAAAAATATATATTATTAA
40614509 TAAAAATAT-TATT-TTAA
1 TAAAAATATATATTATTAA
40614526 TAAA
1 TAAA
40614530 TAAATTTCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 7 0.35
18 4 0.20
19 9 0.45
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
TAAAAATATATATTATTAA
Found at i:40614534 original size:19 final size:19
Alignment explanation
Indices: 40614486--40614534 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 19
40614476 TTGTTTGTAG
*
40614486 ATTTTAA-AAATATATATT
1 ATTTTAATAAATAAATATT
40614504 A-TTT-AT-AA-AAATATT
1 ATTTTAATAAATAAATATT
40614519 ATTTTAATAAATAAAT
1 ATTTTAATAAATAAAT
40614535 TTCATTTTGA
Statistics
Matches: 25, Mismatches: 1, Indels: 9
0.71 0.03 0.26
Matches are distributed among these distances:
15 7 0.28
16 6 0.24
17 5 0.20
18 3 0.12
19 4 0.16
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
ATTTTAATAAATAAATATT
Found at i:40614694 original size:56 final size:56
Alignment explanation
Indices: 40614634--40614745 Score: 224
Period size: 56 Copynumber: 2.0 Consensus size: 56
40614624 AAATGAACGT
40614634 TTAATTATATATATATTATTTTTAAAAGTTTTTTAAATTTTAATTTTAAATTTTTA
1 TTAATTATATATATATTATTTTTAAAAGTTTTTTAAATTTTAATTTTAAATTTTTA
40614690 TTAATTATATATATATTATTTTTAAAAGTTTTTTAAATTTTAATTTTAAATTTTTA
1 TTAATTATATATATATTATTTTTAAAAGTTTTTTAAATTTTAATTTTAAATTTTTA
40614746 AGAACTAAAA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 56 1.00
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.61
Consensus pattern (56 bp):
TTAATTATATATATATTATTTTTAAAAGTTTTTTAAATTTTAATTTTAAATTTTTA
Found at i:40617245 original size:30 final size:29
Alignment explanation
Indices: 40617209--40617283 Score: 80
Period size: 30 Copynumber: 2.5 Consensus size: 29
40617199 TAGAAATATC
**
40617209 GAAAAAAATAAAAAGACTGGATTAATTTTA
1 GAAAAAAATAAAAAGAAAGGATTAA-TTTA
*
40617239 GAAAAAAA-AAGAAATAAAGGATTAATTTA
1 GAAAAAAATAA-AAAGAAAGGATTAATTTA
*
40617268 AAATAAAAATAAAAAG
1 GAA-AAAAATAAAAAG
40617284 TTTGGGATAA
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
29 8 0.22
30 27 0.73
31 2 0.05
ACGTcount: A:0.65, C:0.01, G:0.12, T:0.21
Consensus pattern (29 bp):
GAAAAAAATAAAAAGAAAGGATTAATTTA
Found at i:40617371 original size:30 final size:28
Alignment explanation
Indices: 40617318--40617491 Score: 93
Period size: 30 Copynumber: 6.0 Consensus size: 28
40617308 GGAAAAACAA
** * *
40617318 GGTCAAAAACAAAATTTTGGAAAGTTCGG
1 GGTCAAATTCAAATTTTTAGAAAGTTC-G
*
40617347 TGGTCAAATTCAAATTTTTAGAAAGCTCG
1 -GGTCAAATTCAAATTTTTAGAAAGTTCG
* ** *
40617376 AGGTTAAATTTGAATTTTT-GAAAAGTTTAG
1 -GGTCAAATTCAAATTTTTAG-AAAG-TTCG
* *
40617406 GGTCAAATTCAAATTTTTAAAAAGTTTAAG
1 GGTCAAATTCAAATTTTTAGAAAG-TT-CG
* * *
40617436 GGTCAAAAAT-AAAATTTTAGAAAGTTTAAG
1 GGTC-AAATTCAAATTTTTAGAAAG-TT-CG
* *
40617466 GGTCAAATTCGAATTTTGA-AAAGTTC
1 GGTCAAATTCAAATTTTTAGAAAGTTC
40617492 AAGAGTCAAA
Statistics
Matches: 115, Mismatches: 23, Indels: 15
0.75 0.15 0.10
Matches are distributed among these distances:
28 3 0.03
29 50 0.43
30 58 0.50
31 4 0.03
ACGTcount: A:0.40, C:0.07, G:0.18, T:0.34
Consensus pattern (28 bp):
GGTCAAATTCAAATTTTTAGAAAGTTCG
Found at i:40617481 original size:60 final size:59
Alignment explanation
Indices: 40617315--40617502 Score: 161
Period size: 59 Copynumber: 3.2 Consensus size: 59
40617305 TATGGAAAAA
* * ** * *
40617315 CAAG-GTCAAAAACAAAATTTT-GGAAAGTTCGGTGGTCAAATTCAAATTTTTAGAAAGCT
1 CAAGAGTCAAAAATAAAATTTTAGAAAAGTTTAG-GGTCAAATTCAAA-TTTTAAAAAGTT
* * * ** *
40617374 CGAG-GT-TAAATTTGAATTTTTGAAAAGTTTAGGGTCAAATTCAAATTTTTAAAAAGTT
1 CAAGAGTCAAAAATAAAATTTTAGAAAAGTTTAGGGTCAAATTCAAA-TTTTAAAAAGTT
* * * *
40617432 TAAGGGTCAAAAATAAAATTTTAG-AAAGTTTAAGGGTCAAATTCGAATTTTGAAAAGTT
1 CAAGAGTCAAAAATAAAATTTTAGAAAAGTTT-AGGGTCAAATTCAAATTTTAAAAAGTT
40617491 CAAGAGTCAAAA
1 CAAGAGTCAAAA
40617503 TATTATTTTT
Statistics
Matches: 103, Mismatches: 22, Indels: 8
0.77 0.17 0.06
Matches are distributed among these distances:
58 35 0.34
59 43 0.42
60 25 0.24
ACGTcount: A:0.42, C:0.08, G:0.18, T:0.32
Consensus pattern (59 bp):
CAAGAGTCAAAAATAAAATTTTAGAAAAGTTTAGGGTCAAATTCAAATTTTAAAAAGTT
Found at i:40617499 original size:29 final size:29
Alignment explanation
Indices: 40617329--40617501 Score: 120
Period size: 29 Copynumber: 5.9 Consensus size: 29
40617319 GTCAAAAACA
* *
40617329 AAATTTTGGAAAGTTC-GGTGGTCAAATTC
1 AAATTTTGAAAAGTTCAAG-GGTCAAATTC
* * * * *
40617358 AAATTTTTAGAAAGCTCGA-GGTTAAATTTG
1 AAATTTTGA-AAAGTTCAAGGGTCAAA-TTC
* *
40617388 AATTTTTGAAAAGTT-TAGGGTCAAATTC
1 AAATTTTGAAAAGTTCAAGGGTCAAATTC
* * * *
40617416 AAATTTTTAAAAAGTTTAAGGGTCAAAAATA
1 AAA-TTTTGAAAAGTTCAAGGGTC-AAATTC
*
40617447 AAATTTT-AGAAAGTTTAAGGGTCAAATTC
1 AAATTTTGA-AAAGTTCAAGGGTCAAATTC
* *
40617476 GAATTTTGAAAAGTTCAAGAGTCAAA
1 AAATTTTGAAAAGTTCAAGGGTCAAA
40617502 ATATTATTTT
Statistics
Matches: 113, Mismatches: 22, Indels: 18
0.74 0.14 0.12
Matches are distributed among these distances:
28 5 0.04
29 61 0.54
30 40 0.35
31 7 0.06
ACGTcount: A:0.40, C:0.07, G:0.18, T:0.34
Consensus pattern (29 bp):
AAATTTTGAAAAGTTCAAGGGTCAAATTC
Found at i:40617513 original size:59 final size:60
Alignment explanation
Indices: 40617348--40617502 Score: 165
Period size: 59 Copynumber: 2.6 Consensus size: 60
40617338 AAAGTTCGGT
* * * * ** *
40617348 GGTCAAATTCAAATTTTTAGAAAGCTCGAG-GTTAAATTTGAATTTTT-GAAAAGTTTAG
1 GGTCAAATTCAAATTTTTAAAAAGTTCAAGAGTCAAAAATAAATTTTTAGAAAAGTTTAG
* * *
40617406 GGTCAAATTCAAATTTTTAAAAAGTTTAAGGGTCAAAAATAAAATTTTAG-AAAGTTTAAG
1 GGTCAAATTCAAATTTTTAAAAAGTTCAAGAGTCAAAAATAAATTTTTAGAAAAGTTT-AG
* *
40617466 GGTCAAATTCGAA-TTTTGAAAAGTTCAAGAGTCAAAA
1 GGTCAAATTCAAATTTTTAAAAAGTTCAAGAGTCAAAA
40617503 TATTATTTTT
Statistics
Matches: 81, Mismatches: 13, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
58 26 0.32
59 40 0.49
60 15 0.19
ACGTcount: A:0.42, C:0.07, G:0.17, T:0.34
Consensus pattern (60 bp):
GGTCAAATTCAAATTTTTAAAAAGTTCAAGAGTCAAAAATAAATTTTTAGAAAAGTTTAG
Found at i:40622768 original size:58 final size:59
Alignment explanation
Indices: 40622676--40622789 Score: 169
Period size: 58 Copynumber: 1.9 Consensus size: 59
40622666 TTTGATAGTT
* * *
40622676 GTCTTCAATTTTAGGACCGTTTTCTGTTAAAGCTTTTAT-AGTGGCAAGTTTCACATCTA
1 GTCTTCAATTTCAGGACCATTTTCTGTTAAAGCTTTTATAAG-GGCAAGTATCACATCTA
*
40622735 GTCTTCAATTTCAGGATCATTTT-TGTTAAAGCTTTTATAAGGGCAAGTATCACAT
1 GTCTTCAATTTCAGGACCATTTTCTGTTAAAGCTTTTATAAGGGCAAGTATCACAT
40622790 TCTTTCAAGA
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
58 28 0.56
59 22 0.44
ACGTcount: A:0.26, C:0.16, G:0.17, T:0.41
Consensus pattern (59 bp):
GTCTTCAATTTCAGGACCATTTTCTGTTAAAGCTTTTATAAGGGCAAGTATCACATCTA
Found at i:40634847 original size:21 final size:24
Alignment explanation
Indices: 40634805--40634848 Score: 58
Period size: 25 Copynumber: 1.9 Consensus size: 24
40634795 TAAGGATAAT
40634805 TAATTATAAATATCAATATTTTACG
1 TAATTAT-AATATCAATATTTTACG
40634830 TAATTAT-ATAT-AAT-TTTTA
1 TAATTATAATATCAATATTTTA
40634849 TTGGTATAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
21 5 0.26
22 3 0.16
23 4 0.21
25 7 0.37
ACGTcount: A:0.43, C:0.05, G:0.02, T:0.50
Consensus pattern (24 bp):
TAATTATAATATCAATATTTTACG
Found at i:40651022 original size:31 final size:30
Alignment explanation
Indices: 40650978--40651042 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 30
40650968 TAGTCTATAT
*
40650978 TTTTATAATTTTTAAAAGATTAAATTAAAA
1 TTTTATAATTTTTAAAAGATTAAAATAAAA
* * *
40651008 TTTTATTATCTTTTAAAATATTAAAATATAA
1 TTTTATAAT-TTTTAAAAGATTAAAATAAAA
40651039 TTTT
1 TTTT
40651043 GCTGTTACTA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
30 8 0.27
31 22 0.73
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (30 bp):
TTTTATAATTTTTAAAAGATTAAAATAAAA
Found at i:40653975 original size:61 final size:61
Alignment explanation
Indices: 40653900--40654024 Score: 223
Period size: 61 Copynumber: 2.0 Consensus size: 61
40653890 TTTGCCTTCA
* *
40653900 AATTCACTACATTAATATGTGTTATTGAATTGAATATCTGTCTTTTTCTTCAAGCTCAAGC
1 AATTCACTACATTAATATGTGTTATTGAATTGAATATCAGTCTTTTGCTTCAAGCTCAAGC
*
40653961 AATTCACTGCATTAATATGTGTTATTGAATTGAATATCAGTCTTTTGCTTCAAGCTCAAGC
1 AATTCACTACATTAATATGTGTTATTGAATTGAATATCAGTCTTTTGCTTCAAGCTCAAGC
40654022 AAT
1 AAT
40654025 CAAACATGGA
Statistics
Matches: 61, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
61 61 1.00
ACGTcount: A:0.30, C:0.16, G:0.13, T:0.41
Consensus pattern (61 bp):
AATTCACTACATTAATATGTGTTATTGAATTGAATATCAGTCTTTTGCTTCAAGCTCAAGC
Found at i:40657831 original size:29 final size:29
Alignment explanation
Indices: 40657789--40657848 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 29
40657779 TATGGTTTAA
* *
40657789 TGTGTAATTGTATACAT-GAATTTTGACTT
1 TGTGCAATTGTATACATAAAATTTTGA-TT
*
40657818 TGTGCAATTTTATACATAAAATTTTGATT
1 TGTGCAATTGTATACATAAAATTTTGATT
40657847 TG
1 TG
40657849 ATCCAATTCT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
29 19 0.70
30 8 0.30
ACGTcount: A:0.30, C:0.07, G:0.15, T:0.48
Consensus pattern (29 bp):
TGTGCAATTGTATACATAAAATTTTGATT
Found at i:40657856 original size:30 final size:29
Alignment explanation
Indices: 40657794--40657856 Score: 74
Period size: 29 Copynumber: 2.1 Consensus size: 29
40657784 TTTAATGTGT
* *
40657794 AATTGTATACATGAATTTTGACTTTGTGC
1 AATTGTATACATAAATTTTGACTTTGTCC
*
40657823 AATTTTATACATAAAATTTTGA-TTTGATCC
1 AATTGTATACAT-AAATTTTGACTTTG-TCC
40657853 AATT
1 AATT
40657857 CTTGTAAATT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
29 15 0.52
30 14 0.48
ACGTcount: A:0.33, C:0.10, G:0.11, T:0.46
Consensus pattern (29 bp):
AATTGTATACATAAATTTTGACTTTGTCC
Found at i:40658646 original size:11 final size:10
Alignment explanation
Indices: 40658602--40658677 Score: 64
Period size: 10 Copynumber: 7.5 Consensus size: 10
40658592 TATTCTAGAA
40658602 TTTTTAAATT
1 TTTTTAAATT
*
40658612 TTTTTAACTT
1 TTTTTAAATT
* *
40658622 TCTTTATATAT
1 TTTTTAAAT-T
40658633 TTTTTAGAATT
1 TTTTTA-AATT
*
40658644 TTTTTAAAAT
1 TTTTTAAATT
*
40658654 TTTTGAAATT
1 TTTTTAAATT
* *
40658664 ATTTT-GATT
1 TTTTTAAATT
40658673 TTTTT
1 TTTTT
40658678 GTAATTTTTG
Statistics
Matches: 51, Mismatches: 13, Indels: 5
0.74 0.19 0.07
Matches are distributed among these distances:
9 7 0.14
10 29 0.57
11 13 0.25
12 2 0.04
ACGTcount: A:0.26, C:0.03, G:0.04, T:0.67
Consensus pattern (10 bp):
TTTTTAAATT
Found at i:40659811 original size:11 final size:11
Alignment explanation
Indices: 40659794--40659850 Score: 50
Period size: 10 Copynumber: 5.5 Consensus size: 11
40659784 TTGGAAATTG
40659794 TAAAAA-ATTA
1 TAAAAATATTA
* *
40659804 TAAAAAAACTA
1 TAAAAATATTA
* *
40659815 TTAAAATAGTA
1 TAAAAATATTA
40659826 -AAAAATATT-
1 TAAAAATATTA
40659835 TAAAAATA-TA
1 TAAAAATATTA
40659845 TAAAAA
1 TAAAAA
40659851 GTAAAAAATT
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
9 1 0.03
10 26 0.68
11 11 0.29
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.28
Consensus pattern (11 bp):
TAAAAATATTA
Found at i:40659829 original size:30 final size:30
Alignment explanation
Indices: 40659788--40659861 Score: 91
Period size: 29 Copynumber: 2.5 Consensus size: 30
40659778 TACTTTTTGG
*
40659788 AAATTGTAAAAAATTATAAAAAAACTAT-TA
1 AAATAGTAAAAAATTATAAAAAAA-TATATA
**
40659818 AAATAGTAAAAAA-TATTTAAAAATATATA
1 AAATAGTAAAAAATTATAAAAAAATATATA
40659847 AAA-AGTAAAAAATTA
1 AAATAGTAAAAAATTA
40659862 AAGTATTAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
28 12 0.31
29 15 0.38
30 12 0.31
ACGTcount: A:0.66, C:0.01, G:0.04, T:0.28
Consensus pattern (30 bp):
AAATAGTAAAAAATTATAAAAAAATATATA
Found at i:40659849 original size:20 final size:22
Alignment explanation
Indices: 40659796--40659850 Score: 57
Period size: 20 Copynumber: 2.7 Consensus size: 22
40659786 GGAAATTGTA
40659796 AAAAAT-TATAAAAAAACTATT
1 AAAAATATATAAAAAAACTATT
*
40659817 -AAAATA-GT-AAAAAA-TATTT
1 AAAAATATATAAAAAAACTA-TT
40659836 AAAAATATATAAAAA
1 AAAAATATATAAAAA
40659851 GTAAAAAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 9
0.71 0.05 0.24
Matches are distributed among these distances:
18 2 0.07
19 8 0.30
20 12 0.44
21 1 0.04
22 4 0.15
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.27
Consensus pattern (22 bp):
AAAAATATATAAAAAAACTATT
Found at i:40659927 original size:20 final size:19
Alignment explanation
Indices: 40659902--40660002 Score: 71
Period size: 20 Copynumber: 5.0 Consensus size: 19
40659892 GGTTAAATAT
40659902 TATTGTAAACAATTATTAAA
1 TATTGTAAA-AATTATTAAA
* *
40659922 TATTGTTAAAAATATTTTACA
1 TATTG-TAAAAAT-TATTAAA
*
40659943 -ACTGTAAAAAAGTTATTAAA
1 TATTGT-AAAAA-TTATTAAA
* *
40659963 AATTATAAAACATTATTTAAA
1 TATTGTAAAA-ATTA-TTAAA
40659984 T-TTGTTAAAAATTATTAAA
1 TATTG-TAAAAATTATTAAA
40660003 AACAGTAAAT
Statistics
Matches: 64, Mismatches: 9, Indels: 17
0.71 0.10 0.19
Matches are distributed among these distances:
19 6 0.09
20 34 0.53
21 24 0.38
ACGTcount: A:0.50, C:0.04, G:0.05, T:0.41
Consensus pattern (19 bp):
TATTGTAAAAATTATTAAA
Found at i:40659968 original size:10 final size:10
Alignment explanation
Indices: 40659949--40660004 Score: 60
Period size: 10 Copynumber: 5.5 Consensus size: 10
40659939 TACAACTGTA
40659949 AAAAAGTTATT
1 AAAAA-TTATT
40659960 AAAAATTA-T
1 AAAAATTATT
40659969 AAAACATTATT
1 AAAA-ATTATT
* * *
40659980 TAAATTTGTT
1 AAAAATTATT
40659990 AAAAATTATT
1 AAAAATTATT
40660000 AAAAA
1 AAAAA
40660005 CAGTAAATAA
Statistics
Matches: 37, Mismatches: 6, Indels: 5
0.77 0.12 0.10
Matches are distributed among these distances:
9 5 0.14
10 23 0.62
11 9 0.24
ACGTcount: A:0.57, C:0.02, G:0.04, T:0.38
Consensus pattern (10 bp):
AAAAATTATT
Found at i:40660026 original size:61 final size:62
Alignment explanation
Indices: 40659908--40660024 Score: 152
Period size: 61 Copynumber: 1.9 Consensus size: 62
40659898 ATATTATTGT
* * *
40659908 AAACAATTATTAAATATTGTTAAAAATATTTTACAACTGTAAAAAAGTTATTAAAAATTATA
1 AAACAATTATTAAATATTGTTAAAAATATTTAAAAACAGTAAAAAAGTTATTAAAAATTATA
*
40659970 AAAC-ATTATTTAAAT-TTGTTAAAAAT-TATTAAAAACAGTAAATAAG-TATTAAAAA
1 AAACAATTA-TTAAATATTGTTAAAAATAT-TTAAAAACAGTAAAAAAGTTATTAAAAA
40660025 ATAGTGAGAT
Statistics
Matches: 49, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
60 10 0.20
61 29 0.59
62 10 0.20
ACGTcount: A:0.55, C:0.04, G:0.05, T:0.36
Consensus pattern (62 bp):
AAACAATTATTAAATATTGTTAAAAATATTTAAAAACAGTAAAAAAGTTATTAAAAATTATA
Found at i:40660061 original size:11 final size:11
Alignment explanation
Indices: 40660041--40660156 Score: 74
Period size: 10 Copynumber: 11.4 Consensus size: 11
40660031 AGATTGCCGA
40660041 TTAAATAATTT
1 TTAAATAATTT
**
40660052 TTTTATAATTT
1 TTAAATAATTT
40660063 TTAAATAA-TT
1 TTAAATAATTT
* *
40660073 TT-CACAATTT
1 TTAAATAATTT
*
40660083 TT-ATTAATTT
1 TTAAATAATTT
40660093 TTAAA-AA-TT
1 TTAAATAATTT
40660102 TTAAATAATGTT
1 TTAAATAAT-TT
40660114 TT--ATAATTT
1 TTAAATAATTT
40660123 TT-AATAAATTT
1 TTAAAT-AATTT
*
40660134 TT--ACAATTT
1 TTAAATAATTT
*
40660143 TAAAAT-ATTT
1 TTAAATAATTT
40660153 TTAA
1 TTAA
40660157 CAATATTTAA
Statistics
Matches: 82, Mismatches: 14, Indels: 19
0.71 0.12 0.17
Matches are distributed among these distances:
9 20 0.24
10 34 0.41
11 24 0.29
12 4 0.05
ACGTcount: A:0.41, C:0.03, G:0.01, T:0.56
Consensus pattern (11 bp):
TTAAATAATTT
Found at i:40660074 original size:10 final size:10
Alignment explanation
Indices: 40660041--40660156 Score: 51
Period size: 11 Copynumber: 11.4 Consensus size: 10
40660031 AGATTGCCGA
40660041 TTAAATAATTT
1 TTAAATAA-TT
**
40660052 TTTTATAATTT
1 TTAAATAA-TT
40660063 TTAAATAATT
1 TTAAATAATT
* *
40660073 TT-CACAATT
1 TTAAATAATT
* *
40660082 TTTATTAATTT
1 TTAAATAA-TT
40660093 TTAAA-AATT
1 TTAAATAATT
40660102 TTAAATAATGT
1 TTAAATAAT-T
*
40660113 TT-TATAATT
1 TTAAATAATT
*
40660122 TTTAATAAATT
1 TTAAAT-AATT
* *
40660133 TT-TACAATT
1 TTAAATAATT
*
40660142 TTAAAATATTT
1 TT-AAATAATT
40660153 TTAA
1 TTAA
40660157 CAATATTTAA
Statistics
Matches: 79, Mismatches: 18, Indels: 17
0.69 0.16 0.15
Matches are distributed among these distances:
9 23 0.29
10 21 0.27
11 35 0.44
ACGTcount: A:0.41, C:0.03, G:0.01, T:0.56
Consensus pattern (10 bp):
TTAAATAATT
Found at i:40660081 original size:20 final size:19
Alignment explanation
Indices: 40660051--40660201 Score: 135
Period size: 20 Copynumber: 7.7 Consensus size: 19
40660041 TTAAATAATT
*
40660051 TTTTTATAATTTTTAAATAA
1 TTTTTACAATTTTT-AATAA
* *
40660071 TTTTCACAATTTTTATTAA
1 TTTTTACAATTTTTAATAA
* *
40660090 TTTTTAAAAATTTTAAATAA
1 TTTTT-ACAATTTTTAATAA
*
40660110 TGTTTTATAATTTTTAATAAA
1 T-TTTTACAATTTTTAAT-AA
*
40660131 TTTTTACAA-TTTTAAAATA
1 TTTTTACAATTTTTAATA-A
*
40660150 TTTTTAACAATATTTAATAA
1 TTTTT-ACAATTTTTAATAA
* *
40660170 TTATTTACAATATTTAAT-T
1 TT-TTTACAATTTTTAATAA
40660189 TTTTTACAATTTT
1 TTTTTACAATTTT
40660202 AAAATATTCT
Statistics
Matches: 109, Mismatches: 15, Indels: 16
0.78 0.11 0.11
Matches are distributed among these distances:
18 11 0.10
19 22 0.20
20 60 0.55
21 16 0.15
ACGTcount: A:0.39, C:0.04, G:0.01, T:0.56
Consensus pattern (19 bp):
TTTTTACAATTTTTAATAA
Found at i:40660091 original size:30 final size:29
Alignment explanation
Indices: 40660051--40660143 Score: 109
Period size: 30 Copynumber: 3.1 Consensus size: 29
40660041 TTAAATAATT
*
40660051 TTTTTATAATTTTTAAATAATTTTCACAA
1 TTTTTATAATTTTTAAATAATTTTAACAA
*
40660080 TTTTTATTAATTTTTAAA-AATTTTAAATAA
1 TTTTTA-TAATTTTTAAATAATTTT-AACAA
*
40660110 TGTTTTATAATTTTT-AATAAATTTTTACAA
1 T-TTTTATAATTTTTAAAT-AATTTTAACAA
40660140 TTTT
1 TTTT
40660144 AAAATATTTT
Statistics
Matches: 55, Mismatches: 4, Indels: 10
0.80 0.06 0.14
Matches are distributed among these distances:
29 17 0.31
30 27 0.49
31 11 0.20
ACGTcount: A:0.38, C:0.03, G:0.01, T:0.58
Consensus pattern (29 bp):
TTTTTATAATTTTTAAATAATTTTAACAA
Found at i:40660153 original size:60 final size:60
Alignment explanation
Indices: 40660041--40660209 Score: 179
Period size: 60 Copynumber: 2.8 Consensus size: 60
40660031 AGATTGCCGA
* * *
40660041 TTAAATAATTTTTTTATAATTTTTAA-ATAATTTTCACAATTTT-TATTAATTTTTAAAAAT-T
1 TTAAATAA--TTTTTATAATTTTTAATA-AATTTTTACAATTTTAAAAT-ATTTTTAAAAATAT
*
40660102 TTAAATAATGTTTTATAATTTTTAATAAATTTTTACAATTTTAAAATATTTTTAACAATAT
1 TTAAATAAT-TTTTATAATTTTTAATAAATTTTTACAATTTTAAAATATTTTTAAAAATAT
* * *
40660163 TT-AATAATTATTTACAATATTTAAT--TTTTTTACAATTTTAAAATATT
1 TTAAATAATT-TTTATAATTTTTAATAAATTTTTACAATTTTAAAATATT
40660210 CTTTTTACTA
Statistics
Matches: 96, Mismatches: 7, Indels: 13
0.83 0.06 0.11
Matches are distributed among these distances:
58 21 0.22
59 2 0.02
60 59 0.61
61 14 0.15
ACGTcount: A:0.41, C:0.04, G:0.01, T:0.55
Consensus pattern (60 bp):
TTAAATAATTTTTATAATTTTTAATAAATTTTTACAATTTTAAAATATTTTTAAAAATAT
Found at i:40660251 original size:58 final size:57
Alignment explanation
Indices: 40660130--40660259 Score: 140
Period size: 58 Copynumber: 2.2 Consensus size: 57
40660120 TTTTTAATAA
*
40660130 ATTTTTACAATTTTAAAATATTTTTAACAATATTTAATAATTATTTACAATATTTAAT
1 ATTTTTACAATTTTAAAATATTTTTAAC-ATATTTAATAATTATTTACAATATTAAAT
* * * * *
40660188 TTTTTTACAATTTTAAAATATTCTTTTTAC-TATTCTCA-AATTTTTTGATAAT-TTAAAT
1 ATTTTTACAATTTTAAAATA-T-TTTTAACATATT-TAATAATTATTT-ACAATATTAAAT
40660246 ATTTTTACAATTTT
1 ATTTTTACAATTTT
40660260 TAATGTTTTT
Statistics
Matches: 61, Mismatches: 7, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
58 48 0.79
59 7 0.11
60 6 0.10
ACGTcount: A:0.37, C:0.07, G:0.01, T:0.55
Consensus pattern (57 bp):
ATTTTTACAATTTTAAAATATTTTTAACATATTTAATAATTATTTACAATATTAAAT
Found at i:40660257 original size:17 final size:18
Alignment explanation
Indices: 40660130--40660258 Score: 68
Period size: 18 Copynumber: 6.7 Consensus size: 18
40660120 TTTTTAATAA
40660130 ATTTTTACAATTTTAAAAT
1 ATTTTTACAA-TTTAAAAT
40660149 ATTTTTAACAATATTTAATAAT
1 ATTTTT-AC-A-ATTTAA-AAT
* *
40660171 -TATTTACAATATT-TAAT
1 ATTTTTACAAT-TTAAAAT
*
40660188 TTTTTTACAATTTTAAAAT
1 ATTTTTACAA-TTTAAAAT
* *
40660207 ATTCTTTTTACTATTCTCAAAT
1 A---TTTTTACAATT-TAAAAT
*
40660229 -TTTTTGATAATTT-AAAT
1 ATTTTT-ACAATTTAAAAT
40660246 ATTTTTACAATTT
1 ATTTTTACAATTT
40660259 TTAATGTTTT
Statistics
Matches: 86, Mismatches: 10, Indels: 30
0.68 0.08 0.24
Matches are distributed among these distances:
17 13 0.15
18 23 0.27
19 17 0.20
20 4 0.05
21 12 0.14
22 17 0.20
ACGTcount: A:0.37, C:0.07, G:0.01, T:0.55
Consensus pattern (18 bp):
ATTTTTACAATTTAAAAT
Found at i:40664918 original size:16 final size:17
Alignment explanation
Indices: 40664899--40664931 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
40664889 AAATTTATTT
*
40664899 TTATATAAAAA-TAATA
1 TTATAAAAAAATTAATA
40664915 TTATAAAAAAATTAATA
1 TTATAAAAAAATTAATA
40664932 CCGATCGAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (17 bp):
TTATAAAAAAATTAATA
Found at i:40667751 original size:53 final size:52
Alignment explanation
Indices: 40667671--40667856 Score: 184
Period size: 51 Copynumber: 3.6 Consensus size: 52
40667661 CATTTCATTT
**
40667671 AATACTCACGATGACA-TATAGTCATCGGACCCCTTGTTTCG-AATAGAAATTCA
1 AATACTCACGATGACACT-TAGTCATCGGACCCCTTAATTCGTAA-AG-AATTCA
* * * *
40667724 AATACTCACGATGACACTGAGTTATCGGA-CCTTTAATTCGTAAAGGATTCA
1 AATACTCACGATGACACTTAGTCATCGGACCCCTTAATTCGTAAAGAATTCA
** * * *
40667775 TTTACTCACGATGACACTTAGTCATCGGA-CCTTTAA-TCTATAAAGGATTCA
1 AATACTCACGATGACACTTAGTCATCGGACCCCTTAATTC-GTAAAGAATTCA
**
40667826 TTTACTCACGATGACACTTAGTCATCGGACC
1 AATACTCACGATGACACTTAGTCATCGGACC
40667857 TTTTCGTTTA
Statistics
Matches: 118, Mismatches: 11, Indels: 9
0.86 0.08 0.07
Matches are distributed among these distances:
50 2 0.02
51 77 0.65
52 11 0.09
53 27 0.23
54 1 0.01
ACGTcount: A:0.32, C:0.23, G:0.16, T:0.30
Consensus pattern (52 bp):
AATACTCACGATGACACTTAGTCATCGGACCCCTTAATTCGTAAAGAATTCA
Found at i:40667792 original size:51 final size:51
Alignment explanation
Indices: 40667726--40667859 Score: 225
Period size: 51 Copynumber: 2.6 Consensus size: 51
40667716 GAAATTCAAA
* * *
40667726 TACTCACGATGACACTGAGTTATCGGACCTTTAAT-TCGTAAAGGATTCATT
1 TACTCACGATGACACTTAGTCATCGGACCTTTAATCT-ATAAAGGATTCATT
40667777 TACTCACGATGACACTTAGTCATCGGACCTTTAATCTATAAAGGATTCATT
1 TACTCACGATGACACTTAGTCATCGGACCTTTAATCTATAAAGGATTCATT
40667828 TACTCACGATGACACTTAGTCATCGGACCTTT
1 TACTCACGATGACACTTAGTCATCGGACCTTT
40667860 TCGTTTATAG
Statistics
Matches: 79, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
51 78 0.99
52 1 0.01
ACGTcount: A:0.29, C:0.22, G:0.16, T:0.33
Consensus pattern (51 bp):
TACTCACGATGACACTTAGTCATCGGACCTTTAATCTATAAAGGATTCATT
Found at i:40671369 original size:30 final size:28
Alignment explanation
Indices: 40671335--40671485 Score: 108
Period size: 30 Copynumber: 5.1 Consensus size: 28
40671325 CTTAGAAGGT
40671335 CCTCAAATTTCTTAAAAATTACATTTTGAC
1 CCTCAAATTTC--AAAAATTACATTTTGAC
*
40671365 CCTCAAACTTTGCAAAAATTATATTTTGAC
1 CCTCAAA-TTT-CAAAAATTACATTTTGAC
* *
40671395 CC-CAAACTTTGCAAAAATTATATTTTAAC
1 CCTCAAA-TTT-CAAAAATTACATTTTGAC
* * *
40671424 CCCCAAACTTCACAAAAATTACATTTT-AA
1 CCTCAAA-TT-TCAAAAATTACATTTTGAC
** * *
40671453 CCTTGAATTTCACAAAAATCACATTTTGGC
1 CCTCAAATTT--CAAAAATTACATTTTGAC
40671483 CCT
1 CCT
40671486 TGAACTCCTC
Statistics
Matches: 102, Mismatches: 12, Indels: 14
0.80 0.09 0.11
Matches are distributed among these distances:
28 2 0.02
29 47 0.46
30 49 0.48
31 3 0.03
32 1 0.01
ACGTcount: A:0.38, C:0.23, G:0.05, T:0.34
Consensus pattern (28 bp):
CCTCAAATTTCAAAAATTACATTTTGAC
Found at i:40671401 original size:29 final size:29
Alignment explanation
Indices: 40671348--40671450 Score: 143
Period size: 30 Copynumber: 3.5 Consensus size: 29
40671338 CAAATTTCTT
40671348 AAAAATTACATTTTGACCCTCAAACTTTGC
1 AAAAATTACATTTTGACCC-CAAACTTTGC
*
40671378 AAAAATTATATTTTGACCCCAAACTTTGC
1 AAAAATTACATTTTGACCCCAAACTTTGC
* * **
40671407 AAAAATTATATTTTAACCCCCAAACTTCAC
1 AAAAATTACATTTTGA-CCCCAAACTTTGC
40671437 AAAAATTACATTTT
1 AAAAATTACATTTT
40671451 AACCTTGAAT
Statistics
Matches: 67, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
29 25 0.37
30 42 0.63
ACGTcount: A:0.41, C:0.21, G:0.04, T:0.34
Consensus pattern (29 bp):
AAAAATTACATTTTGACCCCAAACTTTGC
Found at i:40673006 original size:11 final size:11
Alignment explanation
Indices: 40672990--40673018 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
40672980 TTTCTAGGTC
40672990 AAATAATAATA
1 AAATAATAATA
40673001 AAATAATAATA
1 AAATAATAATA
40673012 AAATAAT
1 AAATAAT
40673019 CTAGAGTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (11 bp):
AAATAATAATA
Found at i:40690425 original size:20 final size:20
Alignment explanation
Indices: 40690400--40690441 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
40690390 ATTAACTAAC
40690400 AATTTAAAA-AGAAAAAAGAA
1 AATTTAAAACAGAAAAAA-AA
*
40690420 AATTTAAAACATAAAAAAAA
1 AATTTAAAACAGAAAAAAAA
40690440 AA
1 AA
40690442 CCAGATTTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 13 0.65
21 7 0.35
ACGTcount: A:0.76, C:0.02, G:0.05, T:0.17
Consensus pattern (20 bp):
AATTTAAAACAGAAAAAAAA
Found at i:40693629 original size:163 final size:163
Alignment explanation
Indices: 40693452--40693783 Score: 574
Period size: 163 Copynumber: 2.0 Consensus size: 163
40693442 AAAAAGCTTA
* *
40693452 CCTATTAAATTAATCCTTAGTTAATCCCTTTGATCCTAACATATTTTTTGTTTGTTTTAACTCGT
1 CCTATTAAATTAATCCTTAGTTAACCCCTTTGATCCTAACACATTTTTTGTTTGTTTTAACTCGT
40693517 AATATTAACCCATGACCCATATATATGTTGTATATTTATCCTTTTTATTAACTCCCTTTTTGTCG
66 AATATTAACCCATGACCCATATATATGTTGTATATTTATCCTTTTTATTAACTCCCTTTTTGTCG
*
40693582 AGATTTGATTTAGTTAGTTGCCTAACTATGCTC
131 AGATTTGATTTAGTTAGTTACCTAACTATGCTC
* *
40693615 CCTATTAAATTAATCCTTTGTTAACCCCTTTGATCCTAACACATTTTTTTTTTGTTTTAACTCGT
1 CCTATTAAATTAATCCTTAGTTAACCCCTTTGATCCTAACACATTTTTTGTTTGTTTTAACTCGT
* * * * *
40693680 AATATTAACCCATGACCCATATATATGTTGTATGTTTATTCTTTTTATTGATTCTCTTTTTGTCG
66 AATATTAACCCATGACCCATATATATGTTGTATATTTATCCTTTTTATTAACTCCCTTTTTGTCG
40693745 AGATTTGATTTAGTTAGTTACCTAACTATGCTC
131 AGATTTGATTTAGTTAGTTACCTAACTATGCTC
40693778 CCTATT
1 CCTATT
40693784 TGAATTGCTG
Statistics
Matches: 159, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
163 159 1.00
ACGTcount: A:0.24, C:0.18, G:0.10, T:0.48
Consensus pattern (163 bp):
CCTATTAAATTAATCCTTAGTTAACCCCTTTGATCCTAACACATTTTTTGTTTGTTTTAACTCGT
AATATTAACCCATGACCCATATATATGTTGTATATTTATCCTTTTTATTAACTCCCTTTTTGTCG
AGATTTGATTTAGTTAGTTACCTAACTATGCTC
Found at i:40693837 original size:13 final size:13
Alignment explanation
Indices: 40693821--40693845 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
40693811 AAAAAATCAA
40693821 AAAAGAAAAAAAG
1 AAAAGAAAAAAAG
40693834 AAAAGAAAAAAA
1 AAAAGAAAAAAA
40693846 ACTGTTCGAG
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:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (13 bp):
AAAAGAAAAAAAG
Found at i:40697731 original size:36 final size:37
Alignment explanation
Indices: 40697656--40697736 Score: 110
Period size: 37 Copynumber: 2.2 Consensus size: 37
40697646 ATAAGCGTAT
** *
40697656 ATGTACTCTTTAATCATTTGAAGGTATTTCATTATAG
1 ATGTACTCTTTAATCATTTGAAGGTATTTCACCACAG
**
40697693 ATGTACTCTTTAATCATTTGTTGG-ATTTCACCACAG
1 ATGTACTCTTTAATCATTTGAAGGTATTTCACCACAG
40697729 ATGTACTC
1 ATGTACTC
40697737 ATCATATCAC
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
36 17 0.44
37 22 0.56
ACGTcount: A:0.27, C:0.16, G:0.14, T:0.43
Consensus pattern (37 bp):
ATGTACTCTTTAATCATTTGAAGGTATTTCACCACAG
Found at i:40710629 original size:6 final size:6
Alignment explanation
Indices: 40710609--40710696 Score: 69
Period size: 6 Copynumber: 15.0 Consensus size: 6
40710599 CTTTTAAAAG
* **
40710609 TTTAAA -TTAAT TTTAAA TTTATT TTTAAA TTT--A TCTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T-TTAAA TTTAAA
* *
40710655 TTTACTTA TTTAAA TTT-AT TTTAAA TTTAAA TTT-AA TTTAAA
1 TTTA--AA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
40710697 ATAATATTAA
Statistics
Matches: 64, Mismatches: 10, Indels: 16
0.71 0.11 0.18
Matches are distributed among these distances:
4 2 0.03
5 15 0.23
6 40 0.62
7 2 0.03
8 5 0.08
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (6 bp):
TTTAAA
Found at i:40710635 original size:31 final size:29
Alignment explanation
Indices: 40710595--40710712 Score: 112
Period size: 31 Copynumber: 4.0 Consensus size: 29
40710585 TGAGCTTTTG
* * * *
40710595 ATTTCTTTTAAAAGTTTAAATTAATTTTAA
1 ATTTATTTTTAAA-TTTATATTAAATTTAA
*
40710625 ATTTATTTTTAAATTTATCTTAAATTTAA
1 ATTTATTTTTAAATTTATATTAAATTTAA
*
40710654 ATTTACTTATTTAAATTTATTTTAAATTTAA
1 ATTTA-TT-TTTAAATTTATATTAAATTTAA
* * * *
40710685 ATTTA-ATTTAAAATAATATTAAACTTAA
1 ATTTATTTTTAAATTTATATTAAATTTAA
40710713 TAAATAAAAG
Statistics
Matches: 75, Mismatches: 11, Indels: 6
0.82 0.12 0.07
Matches are distributed among these distances:
28 18 0.24
29 18 0.24
30 13 0.17
31 26 0.35
ACGTcount: A:0.42, C:0.03, G:0.01, T:0.53
Consensus pattern (29 bp):
ATTTATTTTTAAATTTATATTAAATTTAA
Found at i:40710654 original size:17 final size:17
Alignment explanation
Indices: 40710632--40710689 Score: 86
Period size: 17 Copynumber: 3.6 Consensus size: 17
40710622 TAAATTTATT
40710632 TTTAAATTTATCTTAAA
1 TTTAAATTTATCTTAAA
40710649 TTTAAATTTA-CTT--A
1 TTTAAATTTATCTTAAA
*
40710663 TTTAAATTTATTTTAAA
1 TTTAAATTTATCTTAAA
40710680 TTTAAATTTA
1 TTTAAATTTA
40710690 ATTTAAAATA
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
14 11 0.30
15 2 0.05
16 3 0.08
17 21 0.57
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (17 bp):
TTTAAATTTATCTTAAA
Found at i:40710694 original size:17 final size:17
Alignment explanation
Indices: 40710609--40710696 Score: 78
Period size: 17 Copynumber: 5.4 Consensus size: 17
40710599 CTTTTAAAAG
*
40710609 TTTAAA-TTAATTTTAAA
1 TTTAAATTTAAATTT-AA
**
40710626 TTTATTTTTAAATTT-A
1 TTTAAATTTAAATTTAA
40710642 TCTTAAATTTAAATTT-A
1 T-TTAAATTTAAATTTAA
* *
40710659 CTT--ATTTAAATTTAT
1 TTTAAATTTAAATTTAA
40710674 TTTAAATTTAAATTTAA
1 TTTAAATTTAAATTTAA
40710691 TTTAAA
1 TTTAAA
40710697 ATAATATTAA
Statistics
Matches: 57, Mismatches: 9, Indels: 10
0.75 0.12 0.13
Matches are distributed among these distances:
14 10 0.18
15 2 0.04
16 4 0.07
17 34 0.60
18 7 0.12
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (17 bp):
TTTAAATTTAAATTTAA
Found at i:40710696 original size:11 final size:11
Alignment explanation
Indices: 40710609--40710695 Score: 60
Period size: 11 Copynumber: 8.0 Consensus size: 11
40710599 CTTTTAAAAG
40710609 TTTAAA-TTAA
1 TTTAAATTTAA
*
40710619 TTTTAAATTTATT
1 -TTTAAATTTA-A
40710632 TTTAAATTT-A
1 TTTAAATTTAA
40710642 TCTTAAATTTAAA
1 T-TTAAATTT-AA
*
40710655 TTT--ACTT-A
1 TTTAAATTTAA
*
40710663 TTTAAATTTAT
1 TTTAAATTTAA
40710674 TTTAAATTTAAA
1 TTTAAATTT-AA
40710686 TTT-AATTTAA
1 TTTAAATTTAA
40710696 AATAATATTA
Statistics
Matches: 61, Mismatches: 6, Indels: 19
0.71 0.07 0.22
Matches are distributed among these distances:
8 4 0.07
10 9 0.15
11 28 0.46
12 18 0.30
13 2 0.03
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.57
Consensus pattern (11 bp):
TTTAAATTTAA
Found at i:40711447 original size:18 final size:16
Alignment explanation
Indices: 40711424--40711466 Score: 59
Period size: 18 Copynumber: 2.6 Consensus size: 16
40711414 GGCATTAATG
40711424 ATAATATTAACAATAA
1 ATAATATTAACAATAA
*
40711440 GTATAATATTAATAATAA
1 --ATAATATTAACAATAA
40711458 ATAATATTA
1 ATAATATTA
40711467 GTATTAATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
16 9 0.38
18 15 0.62
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.37
Consensus pattern (16 bp):
ATAATATTAACAATAA
Found at i:40711769 original size:9 final size:9
Alignment explanation
Indices: 40711752--40711808 Score: 55
Period size: 9 Copynumber: 6.4 Consensus size: 9
40711742 GTTTTGTTTT
40711752 AAAAAGAAG
1 AAAAAGAAG
*
40711761 AAAATGAAG
1 AAAAAGAAG
40711770 AAAAAGAA-
1 AAAAAGAAG
*
40711778 ATAAAGAA-
1 AAAAAGAAG
* *
40711786 TAAAAGATG
1 AAAAAGAAG
40711795 AAAAAGAAAG
1 AAAAAG-AAG
40711805 AAAA
1 AAAA
40711809 GAGAGAAGAG
Statistics
Matches: 38, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
8 12 0.32
9 20 0.53
10 6 0.16
ACGTcount: A:0.75, C:0.00, G:0.18, T:0.07
Consensus pattern (9 bp):
AAAAAGAAG
Found at i:40711803 original size:25 final size:26
Alignment explanation
Indices: 40711754--40711803 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 26
40711744 TTTGTTTTAA
40711754 AAAGAAGAAAATGAAGAAAAAGAAAT
1 AAAGAAGAAAATGAAGAAAAAGAAAT
* *
40711780 AAAGAATAAAA-GATGAAAAAGAAA
1 AAAGAAGAAAATGAAGAAAAAGAAA
40711804 GAAAAGAGAG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 12 0.55
26 10 0.45
ACGTcount: A:0.74, C:0.00, G:0.18, T:0.08
Consensus pattern (26 bp):
AAAGAAGAAAATGAAGAAAAAGAAAT
Found at i:40711809 original size:26 final size:26
Alignment explanation
Indices: 40711752--40711815 Score: 76
Period size: 26 Copynumber: 2.4 Consensus size: 26
40711742 GTTTTGTTTT
40711752 AAAAAGAAGAAAATGAAGAAAAAGAA
1 AAAAAGAAGAAAATGAAGAAAAAGAA
* * *
40711778 ATAAAGAATAAAA-GATGAAAAAGAA
1 AAAAAGAAGAAAATGAAGAAAAAGAA
40711803 AGAAAAGAGAGAA
1 A-AAAAGA-AGAA
40711816 GAGACTTACC
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
25 12 0.39
26 16 0.52
27 3 0.10
ACGTcount: A:0.73, C:0.00, G:0.20, T:0.06
Consensus pattern (26 bp):
AAAAAGAAGAAAATGAAGAAAAAGAA
Found at i:40712434 original size:163 final size:162
Alignment explanation
Indices: 40712241--40712561 Score: 507
Period size: 163 Copynumber: 2.0 Consensus size: 162
40712231 TTTTAATTGG
* * *
40712241 TTTTTAATTTAGTCCTTTGACTATTTGACTGTACCAGAGGCTGCCACGTGTCACTTTTTGGTTTA
1 TTTTTAAATTAATCCTTTGACTATTTGACTGCACCAGAGGCTGCCACGTGTCACTTTTTGGTTTA
* *
40712306 TTTTTGTATCTAGTCCCTGCCATTTTTTAATTTGTTTTAATTTAATCCTTAAATCAACTTTTGCT
66 TTTATGTATCTAGTCCCTGCCA-TTTTTAATTTGTTTTAATTTAATCCTTAAATCAACTTTTACT
*
40712371 TAATTACAAAATTGACCCAGGAATCTTTTGAGT
130 TAATTACAAAATTGACCCAAGAATCTTTTGAGT
* * *
40712404 TTTTTAAATTAATCTTTTGACTGTTTGACTGCACTAGAGGCTGCCACGTGTCACTTTTTGGTTTA
1 TTTTTAAATTAATCCTTTGACTATTTGACTGCACCAGAGGCTGCCACGTGTCACTTTTTGGTTTA
* * *
40712469 TTTATGTATCTAGTCTCTGTCATTTTTAATTTGTTTTAATTTAATCCTTAAATCAACTTTTATTT
66 TTTATGTATCTAGTCCCTGCCATTTTTAATTTGTTTTAATTTAATCCTTAAATCAACTTTTACTT
* *
40712534 AATTACAAAATTGGCCCAAGAATTTTTT
131 AATTACAAAATTGACCCAAGAATCTTTT
40712562 AAGATTTACA
Statistics
Matches: 144, Mismatches: 14, Indels: 1
0.91 0.09 0.01
Matches are distributed among these distances:
162 66 0.46
163 78 0.54
ACGTcount: A:0.24, C:0.16, G:0.13, T:0.47
Consensus pattern (162 bp):
TTTTTAAATTAATCCTTTGACTATTTGACTGCACCAGAGGCTGCCACGTGTCACTTTTTGGTTTA
TTTATGTATCTAGTCCCTGCCATTTTTAATTTGTTTTAATTTAATCCTTAAATCAACTTTTACTT
AATTACAAAATTGACCCAAGAATCTTTTGAGT
Done.