Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr07 ID=Chr07-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 60982465
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 868082 characters in sequence are not A, C, G, or T
File 176 of 204
Found at i:52483566 original size:2 final size:2
Alignment explanation
Indices: 52483559--52483587 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
52483549 TTTCTGCTAA
52483559 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
52483588 TTTTTACAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:52488113 original size:31 final size:32
Alignment explanation
Indices: 52488078--52488147 Score: 97
Period size: 32 Copynumber: 2.2 Consensus size: 32
52488068 AATTTTTTAA
* *
52488078 TTAAATTTAGCTCTTAA-TCTTTTAAAAAGAG
1 TTAAATTTAACTATTAATTCTTTTAAAAAGAG
* *
52488109 TTAAATTTAATTATTAATTTTTTTAAAAAGAG
1 TTAAATTTAACTATTAATTCTTTTAAAAAGAG
52488141 TTAAATT
1 TTAAATT
52488148 AAATTTTTTA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 14 0.41
32 20 0.59
ACGTcount: A:0.41, C:0.04, G:0.07, T:0.47
Consensus pattern (32 bp):
TTAAATTTAACTATTAATTCTTTTAAAAAGAG
Found at i:52499335 original size:20 final size:21
Alignment explanation
Indices: 52499295--52499347 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
52499285 AAATACAAAT
*
52499295 ATAATCATAATATATATTCAA
1 ATAATCATAATATATAATCAA
*
52499316 ATAATTATAA-ATATAATCAA
1 ATAATCATAATATATAATCAA
52499336 ATCAAT-ATAATA
1 AT-AATCATAATA
52499348 CACAATTAGA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 15 0.54
21 13 0.46
ACGTcount: A:0.57, C:0.08, G:0.00, T:0.36
Consensus pattern (21 bp):
ATAATCATAATATATAATCAA
Found at i:52499779 original size:59 final size:59
Alignment explanation
Indices: 52499650--52499792 Score: 155
Period size: 59 Copynumber: 2.4 Consensus size: 59
52499640 AAGAAATATC
* * *
52499650 AAGGATTAACTTGGATAAAAAAAAGTTCAGGCATCAAAGTGGATACAATTGTCAAGCTT
1 AAGGACTAACTTGGACAAAAAAAAGTTCAGGCATCAAAGTGGAAACAATTGTCAAGCTT
* * * * *
52499709 AAGGACCAACTTGGACAAATAAAAGTTCAGGC-CCTAATGTGGAAACAATTGTTAAG-TT
1 AAGGACTAACTTGGACAAAAAAAAGTTCAGGCATC-AAAGTGGAAACAATTGTCAAGCTT
* *
52499767 CAGAGACTAACTTGAAACAAAAAAAA
1 AAG-GACTAACTTG-GACAAAAAAAA
52499793 AATTTTAAAC
Statistics
Matches: 69, Mismatches: 12, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
58 5 0.07
59 55 0.80
60 9 0.13
ACGTcount: A:0.45, C:0.14, G:0.19, T:0.22
Consensus pattern (59 bp):
AAGGACTAACTTGGACAAAAAAAAGTTCAGGCATCAAAGTGGAAACAATTGTCAAGCTT
Found at i:52534645 original size:14 final size:14
Alignment explanation
Indices: 52534626--52534654 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
52534616 ATCATTTCAC
52534626 TATTATGTTGTTAT
1 TATTATGTTGTTAT
52534640 TATTATGTTGTTAT
1 TATTATGTTGTTAT
52534654 T
1 T
52534655 GTATAACTCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.21, C:0.00, G:0.14, T:0.66
Consensus pattern (14 bp):
TATTATGTTGTTAT
Found at i:52535809 original size:27 final size:28
Alignment explanation
Indices: 52535772--52535828 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 28
52535762 TTGACTGGAT
* *
52535772 TTTAATAATTTTTATTTTTAATATTTCA
1 TTTAATAATTTTTAGTATTAATATTTCA
*
52535800 TTTAAT-ATTTTTGGTATTAATATTTCA
1 TTTAATAATTTTTAGTATTAATATTTCA
52535827 TT
1 TT
52535829 AAAGTTATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
27 20 0.77
28 6 0.23
ACGTcount: A:0.30, C:0.04, G:0.04, T:0.63
Consensus pattern (28 bp):
TTTAATAATTTTTAGTATTAATATTTCA
Found at i:52536136 original size:11 final size:11
Alignment explanation
Indices: 52536120--52536153 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
52536110 TTTTCCCAAT
52536120 TTTTACTATTA
1 TTTTACTATTA
*
52536131 TTTTACTACTA
1 TTTTACTATTA
*
52536142 TTTTACCATTA
1 TTTTACTATTA
52536153 T
1 T
52536154 GCTGTTATTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.26, C:0.15, G:0.00, T:0.59
Consensus pattern (11 bp):
TTTTACTATTA
Found at i:52536379 original size:17 final size:16
Alignment explanation
Indices: 52536359--52536390 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
52536349 TATATATATT
52536359 TAAAAATTATAAAAAAA
1 TAAAAATTA-AAAAAAA
52536376 TAAAAATTAAAAAAA
1 TAAAAATTAAAAAAA
52536391 TTAATACGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (16 bp):
TAAAAATTAAAAAAAA
Found at i:52536781 original size:29 final size:28
Alignment explanation
Indices: 52536706--52536777 Score: 92
Period size: 31 Copynumber: 2.5 Consensus size: 28
52536696 AGATAAATCT
*
52536706 TAAAATTATACATGAATTTTAATTTAATG
1 TAAAATTATACATGAATTTTAATTT-AGG
*
52536735 TATAATTATATACATGAATTTTAATTT-GG
1 TA-AAAT-TATACATGAATTTTAATTTAGG
52536764 TAAAATTATACATG
1 TAAAATTATACATG
52536778 TGAAACTCTA
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
27 8 0.21
28 3 0.08
29 5 0.13
30 3 0.08
31 19 0.50
ACGTcount: A:0.43, C:0.04, G:0.08, T:0.44
Consensus pattern (28 bp):
TAAAATTATACATGAATTTTAATTTAGG
Found at i:52537863 original size:125 final size:125
Alignment explanation
Indices: 52537652--52538174 Score: 755
Period size: 125 Copynumber: 4.2 Consensus size: 125
52537642 TTTGCAGTCA
* *
52537652 CGCCCACGTGTACGCGCTTTTGCTACAGTCGGTCCTGGAA-AAATAATTTCGAGTTGACGTTTCT
1 CGCCCACGTGGACGCGCTTTTGCTACAGTTGGTCCTGGAAGAAATAATTTCGAGTTGACGTTTCT
*
52537716 GAGCAAATAGTATAAAAACGCTTCAAGCAGGATGCTATATGCGAAGAATTTGTGAAATCG
66 GAGCAAATAGTATAAAAACGCTTCAAGCAGGATGCTATATGAGAAGAATTTGTGAAATCG
* * * *
52537776 CGCCCTCCTAGACGCGCTTTTGCTACAGTTGGTCCTGGAAGAAATAATTTTGAGTTGACGTTTCT
1 CGCCCACGTGGACGCGCTTTTGCTACAGTTGGTCCTGGAAGAAATAATTTCGAGTTGACGTTTCT
* * * * *
52537841 GAGCAAATAGTATAAAATCGCTTCTACCAAGATGCTTTATGAGAAGAATTTGTGAAATCG
66 GAGCAAATAGTATAAAAACGCTTCAAGCAGGATGCTATATGAGAAGAATTTGTGAAATCG
* * * * *
52537901 CGCCCACGTGGACGCGCTTTTGCTACAGTAGGT-CT-GAAAAAATTATTTCAAGTTGACGTTTAT
1 CGCCCACGTGGACGCGCTTTTGCTACAGTTGGTCCTGGAAGAAATAATTTCGAGTTGACGTTTCT
* * * *
52537964 GAGCAAATAGTATAAAAAACGCTTCAAGTAGGATGTTATTTGAGAAGAATTTCTGAAATCG
66 GAGCAAATAGTAT-AAAAACGCTTCAAGCAGGATGCTATATGAGAAGAATTTGTGAAATCG
* * * *
52538025 CGCCCTCGTGGACGCACTTTTGCTACAGTTGGTCCTGGTAGAATTAATTTCGAGTTGACGTTTCT
1 CGCCCACGTGGACGCGCTTTTGCTACAGTTGGTCCTGGAAGAAATAATTTCGAGTTGACGTTTCT
* * * *
52538090 GAGCAAATAGTATAAAATCGCTTCTAGCAGGATGCTTTATGAGAAGAATTTATGAAATCG
66 GAGCAAATAGTATAAAAACGCTTCAAGCAGGATGCTATATGAGAAGAATTTGTGAAATCG
52538150 CGCCCACGTGGACGCGCTTTTGCTA
1 CGCCCACGTGGACGCGCTTTTGCTA
52538175 TAGTAGCATG
Statistics
Matches: 347, Mismatches: 48, Indels: 7
0.86 0.12 0.02
Matches are distributed among these distances:
123 36 0.10
124 105 0.30
125 171 0.49
126 35 0.10
ACGTcount: A:0.29, C:0.19, G:0.23, T:0.30
Consensus pattern (125 bp):
CGCCCACGTGGACGCGCTTTTGCTACAGTTGGTCCTGGAAGAAATAATTTCGAGTTGACGTTTCT
GAGCAAATAGTATAAAAACGCTTCAAGCAGGATGCTATATGAGAAGAATTTGTGAAATCG
Found at i:52538090 original size:249 final size:249
Alignment explanation
Indices: 52537652--52538180 Score: 853
Period size: 249 Copynumber: 2.1 Consensus size: 249
52537642 TTTGCAGTCA
* * * * *
52537652 CGCCCACGTGTACGCGCTTTTGCTACAGTCGGTCCTGGAAAAATAATTTCGAGTTGACGTTTCTG
1 CGCCCACGTGGACGCGCTTTTGCTACAGTAGGTCCTGAAAAAATAATTTCAAGTTGACGTTTATG
* *
52537717 AGCAAATAGTATAAAAACGCTTCAAGCAGGATGCTATATGCGAAGAATTTGTGAAATCGCGCCCT
66 AGCAAATAGTATAAAAACGCTTCAAGCAGGATGCTATATGAGAAGAATTTCTGAAATCGCGCCCT
* *
52537782 CCTAGACGCGCTTTTGCTACAGTTGGTCCTGGAAGAAATAATTTTGAGTTGACGTTTCTGAGCAA
131 CCTAGACGCACTTTTGCTACAGTTGGTCCTGGAAGAAATAATTTCGAGTTGACGTTTCTGAGCAA
*
52537847 ATAGTATAAAATCGCTTCTACCAAGATGCTTTATGAGAAGAATTTGTGAAATCG
196 ATAGTATAAAATCGCTTCTACCAAGATGCTTTATGAGAAGAATTTATGAAATCG
*
52537901 CGCCCACGTGGACGCGCTTTTGCTACAGTAGGT-CTGAAAAAATTATTTCAAGTTGACGTTTATG
1 CGCCCACGTGGACGCGCTTTTGCTACAGTAGGTCCTGAAAAAATAATTTCAAGTTGACGTTTATG
* * *
52537965 AGCAAATAGTATAAAAAACGCTTCAAGTAGGATGTTATTTGAGAAGAATTTCTGAAATCGCGCCC
66 AGCAAATAGTAT-AAAAACGCTTCAAGCAGGATGCTATATGAGAAGAATTTCTGAAATCGCGCCC
* * * *
52538030 TCGTGGACGCACTTTTGCTACAGTTGGTCCTGGTAGAATTAATTTCGAGTTGACGTTTCTGAGCA
130 TCCTAGACGCACTTTTGCTACAGTTGGTCCTGGAAGAAATAATTTCGAGTTGACGTTTCTGAGCA
* *
52538095 AATAGTATAAAATCGCTTCTAGCAGGATGCTTTATGAGAAGAATTTATGAAATCG
195 AATAGTATAAAATCGCTTCTACCAAGATGCTTTATGAGAAGAATTTATGAAATCG
*
52538150 CGCCCACGTGGACGCGCTTTTGCTATAGTAG
1 CGCCCACGTGGACGCGCTTTTGCTACAGTAG
52538181 CATGTATGGG
Statistics
Matches: 258, Mismatches: 21, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
248 39 0.15
249 219 0.85
ACGTcount: A:0.29, C:0.18, G:0.23, T:0.30
Consensus pattern (249 bp):
CGCCCACGTGGACGCGCTTTTGCTACAGTAGGTCCTGAAAAAATAATTTCAAGTTGACGTTTATG
AGCAAATAGTATAAAAACGCTTCAAGCAGGATGCTATATGAGAAGAATTTCTGAAATCGCGCCCT
CCTAGACGCACTTTTGCTACAGTTGGTCCTGGAAGAAATAATTTCGAGTTGACGTTTCTGAGCAA
ATAGTATAAAATCGCTTCTACCAAGATGCTTTATGAGAAGAATTTATGAAATCG
Found at i:52540383 original size:29 final size:29
Alignment explanation
Indices: 52540334--52540389 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
52540324 TAATGGTTAA
* *
52540334 TTTAGGTTTTACGATTTAGGGTTTAGGTT
1 TTTAGGTTTTAAGATTAAGGGTTTAGGTT
52540363 TTTAGGTTTTAA-AGTTAAGGGTTTAGG
1 TTTAGGTTTTAAGA-TTAAGGGTTTAGG
52540390 ATATAGGGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 1 0.04
29 23 0.96
ACGTcount: A:0.21, C:0.02, G:0.29, T:0.48
Consensus pattern (29 bp):
TTTAGGTTTTAAGATTAAGGGTTTAGGTT
Found at i:52540397 original size:43 final size:42
Alignment explanation
Indices: 52540334--52540500 Score: 144
Period size: 43 Copynumber: 3.9 Consensus size: 42
52540324 TAATGGTTAA
* * *
52540334 TTTAGGTTTTACGATTTAGGGTTTAGGTTTTTAGGTTTTAAAG
1 TTTAGGGTTTAAGATATAGGGTTTAGGTTTTTAGG-TTTAAAG
* * * *
52540377 TTAAGGGTTTAGGATATAGGG-TTAGAGGTTTTAGGTTAAAAG
1 TTTAGGGTTTAAGATATAGGGTTTAG-GTTTTTAGGTTTAAAG
* * *
52540419 TTTAGGGTTTTAAG-TAAAAGGTTTAAGGTTTTTAGGTTTAGAG
1 TTTAGGG-TTTAAGATATAGGGTTT-AGGTTTTTAGGTTTAAAG
* *
52540462 TTTAGGGTTTTAAGTTA-AAGGTTATA-GTTTTTAGGTTTA
1 TTTAGGG-TTTAAGATATAGGGTT-TAGGTTTTTAGGTTTA
52540501 GGGTTAATGG
Statistics
Matches: 105, Mismatches: 13, Indels: 13
0.80 0.10 0.10
Matches are distributed among these distances:
42 34 0.32
43 66 0.63
44 5 0.05
ACGTcount: A:0.26, C:0.01, G:0.28, T:0.46
Consensus pattern (42 bp):
TTTAGGGTTTAAGATATAGGGTTTAGGTTTTTAGGTTTAAAG
Found at i:52540427 original size:21 final size:21
Alignment explanation
Indices: 52540354--52540498 Score: 98
Period size: 21 Copynumber: 6.8 Consensus size: 21
52540344 ACGATTTAGG
* *
52540354 GTTTAGGTTTTTAGGTTTTAAA
1 GTTTAGGGTTTTAGG-TTAAAA
* * * *
52540376 GTTAAGGG-TTTAGGATATAG
1 GTTTAGGGTTTTAGGTTAAAA
*
52540396 GGTTAGAGGTTTTAGGTTAAAA
1 GTTTAG-GGTTTTAGGTTAAAA
*
52540418 GTTTAGGGTTTTAAG-TAAAA
1 GTTTAGGGTTTTAGGTTAAAA
* * *
52540438 GGTTTAAGGTTTTTAGGTTTAGA
1 -GTTT-AGGGTTTTAGGTTAAAA
* *
52540461 GTTTAGGGTTTTAAGTTAAAG
1 GTTTAGGGTTTTAGGTTAAAA
*
52540482 GTTATA-GTTTTTAGGTT
1 GTT-TAGGGTTTTAGGTT
52540499 TAGGGTTAAT
Statistics
Matches: 93, Mismatches: 24, Indels: 13
0.72 0.18 0.10
Matches are distributed among these distances:
20 11 0.12
21 44 0.47
22 35 0.38
23 3 0.03
ACGTcount: A:0.27, C:0.00, G:0.28, T:0.45
Consensus pattern (21 bp):
GTTTAGGGTTTTAGGTTAAAA
Found at i:52540446 original size:7 final size:7
Alignment explanation
Indices: 52540436--52540736 Score: 91
Period size: 7 Copynumber: 42.0 Consensus size: 7
52540426 TTTTAAGTAA
52540436 AAGGTTT
1 AAGGTTT
52540443 AAGGTTTT
1 AAGG-TTT
*
52540451 TAGGTTT
1 AAGGTTT
52540458 -AGAGTTT
1 AAG-GTTT
*
52540465 AGGGTTTT
1 AAGG-TTT
*
52540473 AA-GTTA
1 AAGGTTT
52540479 AAGG-TT
1 AAGGTTT
*
52540485 ATAGTTTT
1 A-AGGTTT
*
52540493 TAGGTTT
1 AAGGTTT
*
52540500 -AGGGTT
1 AAGGTTT
52540506 AATGGTTTTT
1 AA-GG--TTT
*
52540516 AA-TTTT
1 AAGGTTT
*
52540522 AAAGTTT
1 AAGGTTT
52540529 AAGGTTTT
1 AAGG-TTT
52540537 AAGGTTTT
1 AAGG-TTT
*
52540545 AAAGTTTT
1 -AAGGTTT
*
52540553 TAGGTTT
1 AAGGTTT
52540560 -AGAGTTT
1 AAG-GTTT
52540567 -AGTGTTT
1 AAG-GTTT
52540574 -AGAGTTT
1 AAG-GTTT
52540581 -AGAGTTT
1 AAG-GTTT
52540588 AAGGTTTTT
1 AAGG--TTT
52540597 AA-G-TT
1 AAGGTTT
*
52540602 AATAG-TT
1 AA-GGTTT
*
52540609 ATGGTTT
1 AAGGTTT
52540616 -AGAGTTT
1 AAG-GTTT
52540623 AGAGGTTTT
1 A-AGG-TTT
52540632 AA-G-TT
1 AAGGTTT
52540637 AAGGTTT
1 AAGGTTT
*
52540644 AGGGTTT
1 AAGGTTT
52540651 -AGTGTTT
1 AAG-GTTT
52540658 AAGGTTT
1 AAGGTTT
*
52540665 AGGGTTT
1 AAGGTTT
52540672 AAGGTTTTT
1 AAGG--TTT
52540681 AA-GTTT
1 AAGGTTT
52540687 AAAGGTTT
1 -AAGGTTT
*
52540695 -AGAATTT
1 AAG-GTTT
*
52540702 AGGGTTT
1 AAGGTTT
52540709 AAGGTTT
1 AAGGTTT
52540716 -AGAGTTT
1 AAG-GTTT
52540723 AAGGTTT
1 AAGGTTT
52540730 AAGGTTT
1 AAGGTTT
52540737 TTAAGTTAAG
Statistics
Matches: 228, Mismatches: 29, Indels: 74
0.69 0.09 0.22
Matches are distributed among these distances:
5 8 0.04
6 31 0.14
7 122 0.54
8 44 0.19
9 19 0.08
10 4 0.02
ACGTcount: A:0.26, C:0.00, G:0.26, T:0.48
Consensus pattern (7 bp):
AAGGTTT
Found at i:52540494 original size:64 final size:64
Alignment explanation
Indices: 52540398--52540539 Score: 144
Period size: 64 Copynumber: 2.2 Consensus size: 64
52540388 GGATATAGGG
* * * *
52540398 TTAGAGGTTTTAGGTTAAAAGTTTAGGGTTTTAAGTAAAAGGTTTAA-GGTTTTTAGGTTTAGAG
1 TTAG-GGTTTTAAGTTAAAAGTTTAGGGTTTTAAGT-AAAGGGTTAATGGTTTTTAAGTTTAAAG
52540462 T
64 T
* * * ** *
52540463 TTAGGGTTTTAAGTTAAAGGTTATA-GTTTTTAGGTTTAGGGTTAATGGTTTTTAATTTTAAAGT
1 TTAGGGTTTTAAGTTAAAAGTT-TAGGGTTTTAAGTAAAGGGTTAATGGTTTTTAAGTTTAAAGT
*
52540527 TTAAGGTTTTAAG
1 TTAGGGTTTTAAG
52540540 GTTTTAAAGT
Statistics
Matches: 64, Mismatches: 11, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
63 7 0.11
64 51 0.80
65 6 0.09
ACGTcount: A:0.28, C:0.00, G:0.25, T:0.46
Consensus pattern (64 bp):
TTAGGGTTTTAAGTTAAAAGTTTAGGGTTTTAAGTAAAGGGTTAATGGTTTTTAAGTTTAAAGT
Found at i:52540513 original size:42 final size:43
Alignment explanation
Indices: 52540353--52540543 Score: 153
Period size: 43 Copynumber: 4.5 Consensus size: 43
52540343 TACGATTTAG
* * *
52540353 GGTTT-AGGTTTTTAGGTTTTAAAGTTAAGGG-TTT-AGGATATA
1 GGTTTAAGGTTTTTAGG-TTTAGAGTTAAGGGTTTTAAGTA-AAA
* * * *
52540395 GGGTTAGAGG-TTTTAGGTTAAAAGTTTAGGGTTTTAAGTAAAA
1 GGTTTA-AGGTTTTTAGGTTTAGAGTTAAGGGTTTTAAGTAAAA
* *
52540438 GGTTTAAGGTTTTTAGGTTTAGAGTTTAGGGTTTTAAGTTAAA
1 GGTTTAAGGTTTTTAGGTTTAGAGTTAAGGGTTTTAAGTAAAA
* * * *
52540481 GG-TTATA-GTTTTTAGGTTTAGGGTTAATGGTTTTTAATTTTAAA
1 GGTTTA-AGGTTTTTAGGTTTAGAGTTAA-GGGTTTTAA-GTAAAA
*
52540525 -GTTTAAGGTTTTAAGGTTT
1 GGTTTAAGGTTTTTAGGTTT
52540544 TAAAGTTTTT
Statistics
Matches: 125, Mismatches: 14, Indels: 18
0.80 0.09 0.11
Matches are distributed among these distances:
42 40 0.32
43 60 0.48
44 25 0.20
ACGTcount: A:0.27, C:0.00, G:0.27, T:0.46
Consensus pattern (43 bp):
GGTTTAAGGTTTTTAGGTTTAGAGTTAAGGGTTTTAAGTAAAA
Found at i:52540530 original size:23 final size:22
Alignment explanation
Indices: 52540402--52540551 Score: 82
Period size: 21 Copynumber: 7.0 Consensus size: 22
52540392 ATAGGGTTAG
* *
52540402 AGGTTTT-AGGTTAAAAGTTTA
1 AGGTTTTAAGTTTTAAAGTTTA
* *
52540423 GGGTTTTAAG--TAAAAGGTTTA
1 AGGTTTTAAGTTTTAAA-GTTTA
* * *
52540444 AGGTTTTTAGGTTTAGAGTTTA
1 AGGTTTTAAGTTTTAAAGTTTA
* *
52540466 GGGTTTTAAG--TTAAAGGTTA
1 AGGTTTTAAGTTTTAAAGTTTA
* * * *
52540486 TA-GTTTTTAGGTTT-AGGGTTA
1 -AGGTTTTAAGTTTTAAAGTTTA
52540507 ATGGTTTTTAA-TTTTAAAGTTTA
1 A-GG-TTTTAAGTTTTAAAGTTTA
52540530 AGGTTTTAAGGTTTTAAAGTTT
1 AGGTTTTAA-GTTTTAAAGTTT
52540552 TTAGGTTTAG
Statistics
Matches: 100, Mismatches: 16, Indels: 24
0.71 0.11 0.17
Matches are distributed among these distances:
20 21 0.21
21 31 0.31
22 23 0.23
23 25 0.25
ACGTcount: A:0.28, C:0.00, G:0.25, T:0.47
Consensus pattern (22 bp):
AGGTTTTAAGTTTTAAAGTTTA
Found at i:52540539 original size:8 final size:8
Alignment explanation
Indices: 52540526--52540559 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
52540516 AATTTTAAAG
52540526 TTTAAGGT
1 TTTAAGGT
52540534 TTTAAGGT
1 TTTAAGGT
*
52540542 TTTAAAGT
1 TTTAAGGT
*
52540550 TTTTAGGT
1 TTTAAGGT
52540558 TT
1 TT
52540560 AGAGTTTAGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.24, C:0.00, G:0.21, T:0.56
Consensus pattern (8 bp):
TTTAAGGT
Found at i:52540551 original size:16 final size:16
Alignment explanation
Indices: 52540504--52540559 Score: 53
Period size: 16 Copynumber: 3.6 Consensus size: 16
52540494 AGGTTTAGGG
*
52540504 TTAATGGTTTTTAA-TT
1 TTAA-GGTTTTAAAGTT
* *
52540520 TTAAAG-TTTAAGGTT
1 TTAAGGTTTTAAAGTT
52540535 TTAAGGTTTTAAAGTT
1 TTAAGGTTTTAAAGTT
*
52540551 TTTAGGTTT
1 TTAAGGTTT
52540560 AGAGTTTAGT
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
14 4 0.12
15 8 0.25
16 20 0.62
ACGTcount: A:0.27, C:0.00, G:0.18, T:0.55
Consensus pattern (16 bp):
TTAAGGTTTTAAAGTT
Found at i:52540747 original size:21 final size:21
Alignment explanation
Indices: 52540619--52540736 Score: 109
Period size: 21 Copynumber: 5.5 Consensus size: 21
52540609 ATGGTTTAGA
52540619 GTTTAGAGGTTTTA-AG-TTAAG
1 GTTTA-AGG-TTTAGAGTTTAAG
* *
52540640 GTTTAGGGTTTAGTGTTTAAG
1 GTTTAAGGTTTAGAGTTTAAG
*
52540661 GTTTAGGGTTTA-AGGTTTTTAA-
1 GTTTAAGGTTTAGA-G--TTTAAG
* *
52540683 GTTTAAAGGTTTAGAATTTAGG
1 GTTT-AAGGTTTAGAGTTTAAG
52540705 GTTTAAGGTTTAGAGTTTAAG
1 GTTTAAGGTTTAGAGTTTAAG
52540726 GTTTAAGGTTT
1 GTTTAAGGTTT
52540737 TTAAGTTAAG
Statistics
Matches: 81, Mismatches: 8, Indels: 16
0.77 0.08 0.15
Matches are distributed among these distances:
19 4 0.05
20 3 0.04
21 53 0.65
22 8 0.10
23 12 0.15
24 1 0.01
ACGTcount: A:0.25, C:0.00, G:0.29, T:0.46
Consensus pattern (21 bp):
GTTTAAGGTTTAGAGTTTAAG
Found at i:52540772 original size:33 final size:34
Alignment explanation
Indices: 52540707--52540817 Score: 127
Period size: 33 Copynumber: 3.3 Consensus size: 34
52540697 AATTTAGGGT
* * * *
52540707 TTAAGGTTTAGAGTTTAAGGTTTAAGGTTTTTAAG
1 TTAAGGGTTAG-GATTAAGGATTAGGGTTTTTAAG
52540742 TTAAGGGTTAGGATTAAGG-TTAGGGTTTTTAAG
1 TTAAGGGTTAGGATTAAGGATTAGGGTTTTTAAG
* * **
52540775 TTAATGGTTAAGATT-AGGATTAGATTTTTTAAG
1 TTAAGGGTTAGGATTAAGGATTAGGGTTTTTAAG
52540808 TTAAGGGTTA
1 TTAAGGGTTA
52540818 TGGTTTTTTG
Statistics
Matches: 67, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
32 3 0.04
33 47 0.70
34 7 0.10
35 10 0.15
ACGTcount: A:0.30, C:0.00, G:0.27, T:0.43
Consensus pattern (34 bp):
TTAAGGGTTAGGATTAAGGATTAGGGTTTTTAAG
Found at i:52540861 original size:23 final size:23
Alignment explanation
Indices: 52540799--52540862 Score: 78
Period size: 22 Copynumber: 2.9 Consensus size: 23
52540789 TAGGATTAGA
*
52540799 TTTTTTAAGTTAAGGG-TTATGG
1 TTTTTTAAGTTTAGGGTTTATGG
* *
52540821 TTTTTT-GGTTTAGAGTTTATGG
1 TTTTTTAAGTTTAGGGTTTATGG
*
52540843 TTTTTTAATTTTAGGGTTTA
1 TTTTTTAAGTTTAGGGTTTA
52540863 GTGTTTAGTG
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
21 6 0.18
22 18 0.53
23 10 0.29
ACGTcount: A:0.19, C:0.00, G:0.23, T:0.58
Consensus pattern (23 bp):
TTTTTTAAGTTTAGGGTTTATGG
Found at i:52540891 original size:22 final size:24
Alignment explanation
Indices: 52540859--52540905 Score: 71
Period size: 22 Copynumber: 2.0 Consensus size: 24
52540849 AATTTTAGGG
*
52540859 TTTAGTGTTTAGTGTTTA-GATTT
1 TTTAGTGTTTAGGGTTTATGATTT
52540882 TTTAG-GTTTAGGGTTTATGATTT
1 TTTAGTGTTTAGGGTTTATGATTT
52540905 T
1 T
52540906 AAAATTTAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 11 0.50
23 11 0.50
ACGTcount: A:0.17, C:0.00, G:0.23, T:0.60
Consensus pattern (24 bp):
TTTAGTGTTTAGGGTTTATGATTT
Found at i:52540892 original size:36 final size:37
Alignment explanation
Indices: 52540828--52540898 Score: 99
Period size: 36 Copynumber: 1.9 Consensus size: 37
52540818 TGGTTTTTTG
* *
52540828 GTTTAGAGTTTATGGTTTTTTAATTTTAGGGTTTAGT
1 GTTTAGAGTTTATGATTTTTTAAGTTTAGGGTTTAGT
* *
52540865 GTTTAGTGTTTA-GATTTTTTAGGTTTAGGGTTTA
1 GTTTAGAGTTTATGATTTTTTAAGTTTAGGGTTTA
52540899 TGATTTTAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
36 19 0.63
37 11 0.37
ACGTcount: A:0.18, C:0.00, G:0.25, T:0.56
Consensus pattern (37 bp):
GTTTAGAGTTTATGATTTTTTAAGTTTAGGGTTTAGT
Found at i:52540935 original size:14 final size:15
Alignment explanation
Indices: 52540903--52540936 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
52540893 GGTTTATGAT
52540903 TTTAAAATTTAAGGG
1 TTTAAAATTTAAGGG
52540918 TTTAAAATTTAA-GG
1 TTTAAAATTTAAGGG
52540932 TTTAA
1 TTTAA
52540937 GGTTAGGGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 7 0.37
15 12 0.63
ACGTcount: A:0.41, C:0.00, G:0.15, T:0.44
Consensus pattern (15 bp):
TTTAAAATTTAAGGG
Found at i:52541035 original size:22 final size:21
Alignment explanation
Indices: 52541005--52541088 Score: 91
Period size: 22 Copynumber: 3.8 Consensus size: 21
52540995 GGGTTATGGT
52541005 TTTTAGGTTTAGGGTTTTTAA
1 TTTTAGGTTTAGGGTTTTTAA
52541026 TTTTATGGTTTAGGGTTTTTAA
1 TTTTA-GGTTTAGGGTTTTTAA
*
52541048 TGTTTAGTGTTTAAGG--TTTAA
1 T-TTTAG-GTTTAGGGTTTTTAA
52541069 GGTTTTTAGGTTTAGGGTTT
1 ---TTTTAGGTTTAGGGTTT
52541089 AGTGTTTAGG
Statistics
Matches: 53, Mismatches: 2, Indels: 13
0.78 0.03 0.19
Matches are distributed among these distances:
21 10 0.19
22 25 0.47
23 16 0.30
24 2 0.04
ACGTcount: A:0.18, C:0.00, G:0.26, T:0.56
Consensus pattern (21 bp):
TTTTAGGTTTAGGGTTTTTAA
Found at i:52541044 original size:15 final size:15
Alignment explanation
Indices: 52541026--52541088 Score: 51
Period size: 15 Copynumber: 4.2 Consensus size: 15
52541016 GGGTTTTTAA
52541026 TTTTATGGTTTAGGG
1 TTTTATGGTTTAGGG
*
52541041 TTTTTAAT-GTTTAGTG
1 -TTTT-ATGGTTTAGGG
* *
52541057 -TTTAAGGTTTAAGG
1 TTTTATGGTTTAGGG
52541071 TTTT-TAGGTTTAGGG
1 TTTTAT-GGTTTAGGG
52541086 TTT
1 TTT
52541089 AGTGTTTAGG
Statistics
Matches: 37, Mismatches: 6, Indels: 9
0.71 0.12 0.17
Matches are distributed among these distances:
13 1 0.03
14 9 0.24
15 14 0.38
16 11 0.30
17 2 0.05
ACGTcount: A:0.17, C:0.00, G:0.27, T:0.56
Consensus pattern (15 bp):
TTTTATGGTTTAGGG
Found at i:52541066 original size:14 final size:14
Alignment explanation
Indices: 52541027--52541172 Score: 82
Period size: 14 Copynumber: 10.3 Consensus size: 14
52541017 GGTTTTTAAT
*
52541027 TTTATGGTTTAGGG
1 TTTAAGGTTTAGGG
* *
52541041 TTTTTAATGTTTAGTG
1 --TTTAAGGTTTAGGG
*
52541057 TTTAAGGTTTAAGGT
1 TTTAAGGTTT-AGGG
*
52541072 TTTTAGGTTTAGGG
1 TTTAAGGTTTAGGG
52541086 TTT-AGTGTTTAGGG
1 TTTAAG-GTTTAGGG
* * *
52541100 CTTAAAGTTTAGTGT
1 TTTAAGGTTTAG-GG
*
52541115 TTTAA-GTTAAGGG
1 TTTAAGGTTTAGGG
**
52541128 -TTATTGTTTAGGG
1 TTTAAGGTTTAGGG
* **
52541141 TTTAGGGTTTAGTA
1 TTTAAGGTTTAGGG
* *
52541155 TTTAGGGTTTAGAG
1 TTTAAGGTTTAGGG
52541169 TTTA
1 TTTA
52541173 TGTATTTTAA
Statistics
Matches: 102, Mismatches: 22, Indels: 14
0.74 0.16 0.10
Matches are distributed among these distances:
12 3 0.03
13 10 0.10
14 61 0.60
15 17 0.17
16 11 0.11
ACGTcount: A:0.21, C:0.01, G:0.29, T:0.50
Consensus pattern (14 bp):
TTTAAGGTTTAGGG
Found at i:52541090 original size:7 final size:7
Alignment explanation
Indices: 52541049--52541172 Score: 65
Period size: 7 Copynumber: 17.7 Consensus size: 7
52541039 GGTTTTTAAT
*
52541049 GTTTAGT
1 GTTTAGG
*
52541056 GTTTAAG
1 GTTTAGG
52541063 GTTTAAGG
1 GTTT-AGG
*
52541071 TTTTTA-G
1 -GTTTAGG
52541078 GTTTAGG
1 GTTTAGG
*
52541085 GTTTAGT
1 GTTTAGG
52541092 GTTTAGG
1 GTTTAGG
* **
52541099 GCTTAAA
1 GTTTAGG
52541106 GTTTAGTG
1 GTTTAG-G
* *
52541114 TTTTA-A
1 GTTTAGG
*
52541120 GTTAAGG
1 GTTTAGG
**
52541127 G-TTATT
1 GTTTAGG
52541133 GTTTAGG
1 GTTTAGG
52541140 GTTTAGG
1 GTTTAGG
*
52541147 GTTTAGT
1 GTTTAGG
*
52541154 ATTTAGG
1 GTTTAGG
*
52541161 GTTTAGA
1 GTTTAGG
52541168 GTTTA
1 GTTTA
52541173 TGTATTTTAA
Statistics
Matches: 83, Mismatches: 28, Indels: 12
0.67 0.23 0.10
Matches are distributed among these distances:
6 10 0.12
7 63 0.76
8 7 0.08
9 3 0.04
ACGTcount: A:0.21, C:0.01, G:0.30, T:0.48
Consensus pattern (7 bp):
GTTTAGG
Found at i:52541096 original size:29 final size:30
Alignment explanation
Indices: 52541027--52541089 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
52541017 GGTTTTTAAT
* * * *
52541027 TTTATGGTTTAGGGTTTTTAATGTTTAGTG
1 TTTAAGGTTTAAGGTTTTTAAGGTTTAGGG
52541057 TTTAAGGTTTAAGGTTTTT-AGGTTTAGGG
1 TTTAAGGTTTAAGGTTTTTAAGGTTTAGGG
52541086 TTTA
1 TTTA
52541090 GTGTTTAGGG
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
29 12 0.41
30 17 0.59
ACGTcount: A:0.19, C:0.00, G:0.27, T:0.54
Consensus pattern (30 bp):
TTTAAGGTTTAAGGTTTTTAAGGTTTAGGG
Found at i:52541160 original size:21 final size:21
Alignment explanation
Indices: 52541006--52541179 Score: 88
Period size: 21 Copynumber: 8.1 Consensus size: 21
52540996 GGTTATGGTT
*
52541006 TTTA-GGTTTAGGGTTT-TTAA
1 TTTAGGGTTTAGGGTTTAGT-A
* * *
52541026 TTTTATGGTTTAGGGTTTTTAATG
1 -TTTAGGGTTTAGGG--TTTAGTA
* * *
52541050 TTTAGTGTTTAAGGTTTAAGGTT
1 TTTAGGGTTTAGGGTTT-A-GTA
*
52541073 TTTA-GGTTTAGGGTTTAGTG
1 TTTAGGGTTTAGGGTTTAGTA
* ** *
52541093 TTTAGGGCTTAAAGTTTAGTGT
1 TTTAGGGTTTAGGGTTTAGT-A
* * * *
52541115 TTTA-AGTTAAGGG-TTATTG
1 TTTAGGGTTTAGGGTTTAGTA
52541134 TTTAGGGTTTAGGGTTTAGTA
1 TTTAGGGTTTAGGGTTTAGTA
*
52541155 TTTAGGGTTTAGAGTTTATGTA
1 TTTAGGGTTTAGGGTTTA-GTA
52541177 TTT
1 TTT
52541180 TAAGTTAGGG
Statistics
Matches: 116, Mismatches: 26, Indels: 21
0.71 0.16 0.13
Matches are distributed among these distances:
19 4 0.03
20 17 0.15
21 45 0.39
22 30 0.26
23 16 0.14
24 3 0.03
25 1 0.01
ACGTcount: A:0.20, C:0.01, G:0.28, T:0.52
Consensus pattern (21 bp):
TTTAGGGTTTAGGGTTTAGTA
Found at i:52541282 original size:15 final size:14
Alignment explanation
Indices: 52541246--52541294 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
52541236 AAAGTTTAAA
*
52541246 GGTTTATGATTTAG
1 GGTTTAAGATTTAG
52541260 GGTTTAAGATTTATG
1 GGTTTAAGATTTA-G
* *
52541275 GTTTTAAGGTTTAG
1 GGTTTAAGATTTAG
*
52541289 AGTTTA
1 GGTTTA
52541295 GAGGTTAAAG
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
14 17 0.59
15 12 0.41
ACGTcount: A:0.24, C:0.00, G:0.27, T:0.49
Consensus pattern (14 bp):
GGTTTAAGATTTAG
Found at i:52541294 original size:22 final size:21
Alignment explanation
Indices: 52541190--52541294 Score: 72
Period size: 22 Copynumber: 4.9 Consensus size: 21
52541180 TAAGTTAGGG
52541190 TTTAAGGTTTAAAAGTTATAT-T
1 TTTAAGGTTT-AAAGTT-TATGT
* * *
52541212 TTT-AGGTTTAGAGTTCAGGGT
1 TTTAAGGTTTAAAGTTTA-TGT
* *
52541233 TTTAAAGTTTAAAGGTTTATGA
1 TTTAAGGTTTAAA-GTTTATGT
*
52541255 TTTAGGGTTT-AAGATTTATGGT
1 TTTAAGGTTTAAAG-TTTAT-GT
*
52541277 TTTAAGGTTTAGAGTTTA
1 TTTAAGGTTTAAAGTTTA
52541295 GAGGTTAAAG
Statistics
Matches: 63, Mismatches: 13, Indels: 14
0.70 0.14 0.16
Matches are distributed among these distances:
19 1 0.02
20 6 0.10
21 17 0.27
22 33 0.52
23 6 0.10
ACGTcount: A:0.29, C:0.01, G:0.23, T:0.48
Consensus pattern (21 bp):
TTTAAGGTTTAAAGTTTATGT
Found at i:52541295 original size:36 final size:37
Alignment explanation
Indices: 52541239--52541319 Score: 96
Period size: 36 Copynumber: 2.2 Consensus size: 37
52541229 GGGTTTTAAA
* *
52541239 GTTTAAAGGTTTATGATTTAG-GGTTTAAGATTTA-TG
1 GTTTTAAGGTTTATGATTTAGAGGTTAAAG-TTTAGTG
52541275 GTTTTAAGGTTTA-GAGTTTAGAGGTTAAAGTTTAGTG
1 GTTTTAAGGTTTATGA-TTTAGAGGTTAAAGTTTAGTG
*
52541312 TTTTTAAG
1 GTTTTAAG
52541320 TTAAAGGTTA
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
35 2 0.05
36 21 0.54
37 16 0.41
ACGTcount: A:0.27, C:0.00, G:0.26, T:0.47
Consensus pattern (37 bp):
GTTTTAAGGTTTATGATTTAGAGGTTAAAGTTTAGTG
Found at i:52541455 original size:22 final size:22
Alignment explanation
Indices: 52541436--52541519 Score: 98
Period size: 22 Copynumber: 3.8 Consensus size: 22
52541426 ATAGTTTAGG
* *
52541436 GTTTATGTTTTTTAGGTTTAAA
1 GTTTATGGTTTTTAAGTTTAAA
52541458 GTTTATGGTTTTTAAGTTTAAA
1 GTTTATGGTTTTTAAGTTTAAA
* * *
52541480 GTTTA-GGGTTTTATGGTTTATA
1 GTTTATGGTTTTTA-AGTTTAAA
*
52541502 GTTTAAGGTTTTTAAGTT
1 GTTTATGGTTTTTAAGTT
52541520 AAGGGTTAGG
Statistics
Matches: 53, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
21 7 0.13
22 39 0.74
23 7 0.13
ACGTcount: A:0.23, C:0.00, G:0.21, T:0.56
Consensus pattern (22 bp):
GTTTATGGTTTTTAAGTTTAAA
Found at i:52541505 original size:15 final size:14
Alignment explanation
Indices: 52541417--52541512 Score: 59
Period size: 15 Copynumber: 6.6 Consensus size: 14
52541407 AAGTTATGAG
*
52541417 TTATGATTTATAGT
1 TTATGGTTTATAGT
*
52541431 TTAGGGTTTAT-GTT
1 TTATGGTTTATAG-T
* *
52541445 TTTTAGGTTTAAAGT
1 TTAT-GGTTTATAGT
*
52541460 TTATGGTTTTTAAGT
1 TTATGGTTTAT-AGT
** **
52541475 TTAAAGTTTAGGGTT
1 TTATGGTTTATAG-T
52541490 TTATGGTTTATAGT
1 TTATGGTTTATAGT
*
52541504 TTAAGGTTT
1 TTATGGTTT
52541513 TTAAGTTAAG
Statistics
Matches: 59, Mismatches: 18, Indels: 10
0.68 0.21 0.11
Matches are distributed among these distances:
13 1 0.02
14 27 0.46
15 30 0.51
16 1 0.02
ACGTcount: A:0.23, C:0.00, G:0.22, T:0.55
Consensus pattern (14 bp):
TTATGGTTTATAGT
Found at i:52541552 original size:33 final size:33
Alignment explanation
Indices: 52541510--52541740 Score: 117
Period size: 33 Copynumber: 6.5 Consensus size: 33
52541500 TAGTTTAAGG
52541510 TTTTTAAGTTAAGGGTTAGGATTAGGGTTTGGA
1 TTTTTAAGTTAAGGGTTAGGATTAGGGTTTGGA
* *
52541543 TTTTTAAGTTAAGGGTTAGAATTAGGGTTTAG-
1 TTTTTAAGTTAAGGGTTAGGATTAGGGTTTGGA
* * * * *
52541575 TGTTTAGGGTTTAGGGTTTTAGGTTTAGTGTTTAAGG-
1 TTTTTA-AGTTAAGGG--TTAGGATTAGGGTTT--GGA
* * *
52541612 TTTTAAAGTTCAAGGATTTAGGGTTTTAAAGTTTAAGGTTTAGGA
1 TTTTTAAGTT-AAGG-GTTA-GG------A--TTAGGGTTT-GGA
* * * *
52541657 TTTGTAAGTTAAGGGTTAGGATTAAGGTTAGGG
1 TTTTTAAGTTAAGGGTTAGGATTAGGGTTTGGA
* * *
52541690 TTTTTAAGTTAATGGTTAGGATTA-GGATTAGA
1 TTTTTAAGTTAAGGGTTAGGATTAGGGTTTGGA
*
52541722 GTTTTTAAGTTTAGGGTTA
1 -TTTTTAAGTTAAGGGTTA
52541741 TGGTTTTTTG
Statistics
Matches: 150, Mismatches: 30, Indels: 36
0.69 0.14 0.17
Matches are distributed among these distances:
32 9 0.06
33 77 0.51
34 8 0.05
35 12 0.08
36 7 0.05
37 10 0.07
42 2 0.01
43 3 0.02
44 7 0.05
45 15 0.10
ACGTcount: A:0.26, C:0.00, G:0.30, T:0.44
Consensus pattern (33 bp):
TTTTTAAGTTAAGGGTTAGGATTAGGGTTTGGA
Found at i:52541574 original size:7 final size:7
Alignment explanation
Indices: 52541564--52541614 Score: 59
Period size: 7 Copynumber: 7.3 Consensus size: 7
52541554 AGGGTTAGAA
52541564 TTAGGGT
1 TTAGGGT
*
52541571 TTAGTGT
1 TTAGGGT
52541578 TTAGGGT
1 TTAGGGT
52541585 TTAGGGTT
1 TTAGGG-T
52541593 TTA-GGT
1 TTAGGGT
*
52541599 TTAGTGT
1 TTAGGGT
*
52541606 TTAAGGT
1 TTAGGGT
52541613 TT
1 TT
52541615 TAAAGTTCAA
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
6 4 0.11
7 29 0.78
8 4 0.11
ACGTcount: A:0.16, C:0.00, G:0.33, T:0.51
Consensus pattern (7 bp):
TTAGGGT
Found at i:52541583 original size:14 final size:14
Alignment explanation
Indices: 52541564--52541614 Score: 68
Period size: 14 Copynumber: 3.6 Consensus size: 14
52541554 AGGGTTAGAA
52541564 TTAGGGTTTAGTGT
1 TTAGGGTTTAGTGT
*
52541578 TTAGGGTTTAGGGTT
1 TTAGGGTTTAGTG-T
52541593 TTA-GGTTTAGTGT
1 TTAGGGTTTAGTGT
*
52541606 TTAAGGTTT
1 TTAGGGTTT
52541615 TAAAGTTCAA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
13 4 0.12
14 25 0.76
15 4 0.12
ACGTcount: A:0.16, C:0.00, G:0.33, T:0.51
Consensus pattern (14 bp):
TTAGGGTTTAGTGT
Found at i:52541588 original size:21 final size:20
Alignment explanation
Indices: 52541564--52541614 Score: 66
Period size: 21 Copynumber: 2.5 Consensus size: 20
52541554 AGGGTTAGAA
52541564 TTAGGGTTTAGTGTTTAGGGT
1 TTAGGGTTTAG-GTTTAGGGT
*
52541585 TTAGGGTTTTAGGTTTAGTGT
1 TTAGGG-TTTAGGTTTAGGGT
*
52541606 TTAAGGTTT
1 TTAGGGTTT
52541615 TAAAGTTCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
20 3 0.11
21 19 0.70
22 5 0.19
ACGTcount: A:0.16, C:0.00, G:0.33, T:0.51
Consensus pattern (20 bp):
TTAGGGTTTAGGTTTAGGGT
Found at i:52541615 original size:21 final size:22
Alignment explanation
Indices: 52541570--52541616 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 22
52541560 AGAATTAGGG
*
52541570 TTTAGTGTTTAGGGTTTAGGGT
1 TTTAGTGTTTAGGGTTTAAGGT
*
52541592 TTTAG-GTTTAGTGTTTAAGGT
1 TTTAGTGTTTAGGGTTTAAGGT
52541613 TTTA
1 TTTA
52541617 AAGTTCAAGG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 18 0.78
22 5 0.22
ACGTcount: A:0.17, C:0.00, G:0.30, T:0.53
Consensus pattern (22 bp):
TTTAGTGTTTAGGGTTTAAGGT
Found at i:52541636 original size:23 final size:22
Alignment explanation
Indices: 52541582--52541676 Score: 81
Period size: 23 Copynumber: 4.4 Consensus size: 22
52541572 TAGTGTTTAG
* *
52541582 GGTTTAGGGTTTT-AGGTT-TA
1 GGTTTAGGGTTTTAAAGTTCAA
*
52541602 GTGTTTAAGGTTTTAAAGTTCAA
1 G-GTTTAGGGTTTTAAAGTTCAA
*
52541625 GGATTTAGGGTTTTAAAGTTTAA
1 GG-TTTAGGGTTTTAAAGTTCAA
*
52541648 GGTTTAGGATTTGT-AAGTT-AA
1 GGTTTAGGGTTT-TAAAGTTCAA
*
52541669 GGGTTAGG
1 GGTTTAGG
52541677 ATTAAGGTTA
Statistics
Matches: 63, Mismatches: 7, Indels: 9
0.80 0.09 0.11
Matches are distributed among these distances:
20 1 0.02
21 20 0.32
22 19 0.30
23 23 0.37
ACGTcount: A:0.25, C:0.01, G:0.31, T:0.43
Consensus pattern (22 bp):
GGTTTAGGGTTTTAAAGTTCAA
Found at i:52541652 original size:7 final size:7
Alignment explanation
Indices: 52541576--52541653 Score: 50
Period size: 7 Copynumber: 10.7 Consensus size: 7
52541566 AGGGTTTAGT
*
52541576 GTTTAGG
1 GTTTAAG
*
52541583 GTTTAGG
1 GTTTAAG
*
52541590 GTTTTAG
1 GTTTAAG
52541597 GTTT-AG
1 GTTTAAG
52541603 TGTTTAAG
1 -GTTTAAG
*
52541611 GTTTTAAA
1 G-TTTAAG
*
52541619 GTTCAAG
1 GTTTAAG
*
52541626 GATTTAGG
1 G-TTTAAG
*
52541634 GTTTTAAA
1 G-TTTAAG
52541642 GTTTAAG
1 GTTTAAG
52541649 GTTTA
1 GTTTA
52541654 GGATTTGTAA
Statistics
Matches: 56, Mismatches: 11, Indels: 8
0.75 0.15 0.11
Matches are distributed among these distances:
6 2 0.04
7 36 0.64
8 18 0.32
ACGTcount: A:0.24, C:0.01, G:0.28, T:0.46
Consensus pattern (7 bp):
GTTTAAG
Found at i:52541665 original size:22 final size:22
Alignment explanation
Indices: 52541576--52541679 Score: 83
Period size: 21 Copynumber: 4.8 Consensus size: 22
52541566 AGGGTTTAGT
* * *
52541576 GTTTAGGGTTTAGGGTTTT-AG
1 GTTTAAGGTTTAGGATTTTAAA
52541597 GTTT-AGTGTTTAAGG-TTTTAAA
1 GTTTAAG-GTTT-AGGATTTTAAA
* *
52541619 GTTCAAGGATTTAGGGTTTTAAA
1 GTTTAAGG-TTTAGGATTTTAAA
52541642 GTTTAAGGTTTAGGATTTGT-AA
1 GTTTAAGGTTTAGGATTT-TAAA
*
52541664 G-TTAAGGGTTAGGATT
1 GTTTAAGGTTTAGGATT
52541680 AAGGTTAGGG
Statistics
Matches: 70, Mismatches: 6, Indels: 14
0.78 0.07 0.16
Matches are distributed among these distances:
20 1 0.01
21 26 0.37
22 23 0.33
23 20 0.29
ACGTcount: A:0.25, C:0.01, G:0.30, T:0.44
Consensus pattern (22 bp):
GTTTAAGGTTTAGGATTTTAAA
Found at i:52541670 original size:21 final size:22
Alignment explanation
Indices: 52541604--52541679 Score: 77
Period size: 22 Copynumber: 3.5 Consensus size: 22
52541594 TAGGTTTAGT
52541604 GTTTAAGG-TTTTAAAGTTCAAG
1 GTTT-AGGATTTTAAAGTTCAAG
* *
52541626 GATTTAGGGTTTTAAAGTTTAAG
1 G-TTTAGGATTTTAAAGTTCAAG
52541649 GTTTAGGATTTGT-AAGTT-AAG
1 GTTTAGGATTT-TAAAGTTCAAG
*
52541670 GGTTAGGATT
1 GTTTAGGATT
52541680 AAGGTTAGGG
Statistics
Matches: 48, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
21 12 0.25
22 18 0.38
23 18 0.38
ACGTcount: A:0.29, C:0.01, G:0.28, T:0.42
Consensus pattern (22 bp):
GTTTAGGATTTTAAAGTTCAAG
Found at i:52541671 original size:147 final size:147
Alignment explanation
Indices: 52541429--52541715 Score: 382
Period size: 147 Copynumber: 2.0 Consensus size: 147
52541419 ATGATTTATA
** * * * *
52541429 GTTTAGGGTTTATGTTTTTTAGGTTTAAAGTTTATGGTTTTTAAGTTTAAAGTTTAGGGTTTTAT
1 GTTTAGGGTTTATGGGTTTTAGGTTTAAAGTTTAAGGTTTTAAAGTTCAAAGTTTAGGGTTTTAA
* * * *
52541494 GGTTTATAGTTTAAGGTTTTTAAGTTAAGGGTTAGGATTAGGGTTTGGATTTTTAAGTTAAGGGT
66 AGTTTATAGTTTAAGGTTTGTAAGTTAAGGGTTAGGATTAAGGTTAGGATTTTTAAGTTAAGGGT
52541559 TAGAATTAGGGTTTAGT
131 TAGAATTAGGGTTTAGT
** *
52541576 GTTTAGGGTTTA-GGGTTTTAGGTTTAGTGTTTAAGGTTTTAAAGTTCAAGGATTTAGGGTTTTA
1 GTTTAGGGTTTATGGGTTTTAGGTTTAAAGTTTAAGGTTTTAAAGTTCAAAG-TTTAGGGTTTTA
* *
52541640 AAGTTTA-AGGTTT-AGGATTTGTAAGTTAAGGGTTAGGATTAAGGTTAGGGTTTTTAAGTTAAT
65 AAGTTTATA-GTTTAAGG-TTTGTAAGTTAAGGGTTAGGATTAAGGTTAGGATTTTTAAGTTAAG
*
52541703 GGTTAGGATTAGG
128 GGTTAGAATTAGG
52541716 ATTAGAGTTT
Statistics
Matches: 121, Mismatches: 16, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
146 35 0.29
147 86 0.71
ACGTcount: A:0.25, C:0.00, G:0.29, T:0.46
Consensus pattern (147 bp):
GTTTAGGGTTTATGGGTTTTAGGTTTAAAGTTTAAGGTTTTAAAGTTCAAAGTTTAGGGTTTTAA
AGTTTATAGTTTAAGGTTTGTAAGTTAAGGGTTAGGATTAAGGTTAGGATTTTTAAGTTAAGGGT
TAGAATTAGGGTTTAGT
Found at i:52541734 original size:147 final size:146
Alignment explanation
Indices: 52541445--52541761 Score: 372
Period size: 147 Copynumber: 2.2 Consensus size: 146
52541435 GGTTTATGTT
* * * * **
52541445 TTTTAGGTTTAAAGTTTATGGTTTTTAAGTTTAAAGTTTAGGGTTTTATGGTTTATAGTTTAAGG
1 TTTTAGGTTTAATGTTTAAGGTTTTAAAGTTCAAAGTTTAGGGTTTTAAAGTTTATAGTTTAAGG
* * * * *
52541510 TTTTTAAGTTAAGGGTTAGGATTAGGGTTTGGATTTTTAAGTTAAGGGTTAGAATTAGGGTTTAG
66 TTTGTAAGTTAAGGGTTAGGATTAAGGTTAGGATTTTTAAGTTAAGGGTTAGAATTAGGATTGAG
*
52541575 TGTTTAGGGTTTAGGG
131 TGTTTAGAGTTTAGGG
* *
52541591 TTTTAGGTTTAGTGTTTAAGGTTTTAAAGTTCAAGGATTTAGGGTTTTAAAGTTTA-AGGTTT-A
1 TTTTAGGTTTAATGTTTAAGGTTTTAAAGTTCAAAG-TTTAGGGTTTTAAAGTTTATA-GTTTAA
* * *
52541654 GGATTTGTAAGTTAAGGGTTAGGATTAAGGTTAGGGTTTTTAAGTTAATGGTTAGGATTAGGATT
64 GG-TTTGTAAGTTAAGGGTTAGGATTAAGGTTAGGATTTTTAAGTTAAGGGTTAGAATTAGGATT
*
52541719 AGAGTTTTTA-AGTTTAGGG
128 -GAGTGTTTAGAGTTTAGGG
* **
52541738 TTAT-GGTTTTTTGGTTTAAGGTTT
1 TTTTAGGTTTAAT-GTTTAAGGTTT
52541762 AGAGTTTTTT
Statistics
Matches: 145, Mismatches: 21, Indels: 9
0.83 0.12 0.05
Matches are distributed among these distances:
146 40 0.28
147 98 0.68
148 7 0.05
ACGTcount: A:0.25, C:0.00, G:0.28, T:0.47
Consensus pattern (146 bp):
TTTTAGGTTTAATGTTTAAGGTTTTAAAGTTCAAAGTTTAGGGTTTTAAAGTTTATAGTTTAAGG
TTTGTAAGTTAAGGGTTAGGATTAAGGTTAGGATTTTTAAGTTAAGGGTTAGAATTAGGATTGAG
TGTTTAGAGTTTAGGG
Found at i:52541768 original size:22 final size:21
Alignment explanation
Indices: 52541711--52541772 Score: 63
Period size: 21 Copynumber: 2.9 Consensus size: 21
52541701 ATGGTTAGGA
* *
52541711 TTAGGATTAGAGTTTTTAAGT
1 TTAGGGTTAGAGTTTTTTAGT
*
52541732 TTAGGGTTATG-GTTTTTTGGT
1 TTAGGGTTA-GAGTTTTTTAGT
*
52541753 TTAAGGTTTAGAGTTTTTTA
1 TT-AGGGTTAGAGTTTTTTA
52541773 ATTATAAAGT
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
21 19 0.58
22 14 0.42
ACGTcount: A:0.21, C:0.00, G:0.26, T:0.53
Consensus pattern (21 bp):
TTAGGGTTAGAGTTTTTTAGT
Found at i:52541918 original size:33 final size:33
Alignment explanation
Indices: 52541871--52542018 Score: 206
Period size: 33 Copynumber: 4.4 Consensus size: 33
52541861 GTTTTAAGGT
* ** *
52541871 TTAGTGTTTTTAAGTTAAATGTTAGGATTAGGG
1 TTAGGGTTTTTAAGTTAAGGGTTAGGATTAGGA
*
52541904 TTAGAGTTTTTAAGTTAAGGGTTAGGATTAGGA
1 TTAGGGTTTTTAAGTTAAGGGTTAGGATTAGGA
52541937 TTAGGGTTTTTAAGTTAAGGGTTAGGATTAGGA
1 TTAGGGTTTTTAAGTTAAGGGTTAGGATTAGGA
* *
52541970 TTAGGGTTTTTAAGTTAAGGGTTATGGTTTTTAGGT
1 TTAGGGTTTTTAAGTTAAGGGTTA-GG--ATTAGGA
52542006 TTAGGGTTTTTAA
1 TTAGGGTTTTTAA
52542019 TTTTATGGTT
Statistics
Matches: 105, Mismatches: 7, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
33 85 0.81
34 2 0.02
36 18 0.17
ACGTcount: A:0.26, C:0.00, G:0.30, T:0.45
Consensus pattern (33 bp):
TTAGGGTTTTTAAGTTAAGGGTTAGGATTAGGA
Found at i:52542000 original size:21 final size:21
Alignment explanation
Indices: 52541974--52542013 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
52541964 TTAGGATTAG
52541974 GGTTTTTAAGTTAAGGGTTAT
1 GGTTTTTAAGTTAAGGGTTAT
* *
52541995 GGTTTTTAGGTTTAGGGTT
1 GGTTTTTAAGTTAAGGGTT
52542014 TTTAATTTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.17, C:0.00, G:0.33, T:0.50
Consensus pattern (21 bp):
GGTTTTTAAGTTAAGGGTTAT
Found at i:52542022 original size:22 final size:22
Alignment explanation
Indices: 52541997--52542081 Score: 86
Period size: 22 Copynumber: 3.8 Consensus size: 22
52541987 AGGGTTATGG
52541997 TTTTTAGGTTTAGGGTTTTTAA
1 TTTTTAGGTTTAGGGTTTTTAA
*
52542019 -TTTTATGGTTTAGAGTTTTTAA
1 TTTTTA-GGTTTAGGGTTTTTAA
* *
52542041 TGTTTAGTGTTTAAGG--TTTAA
1 TTTTTAG-GTTTAGGGTTTTTAA
52542062 GGTTTTTAGGTTTAGGGTTT
1 --TTTTTAGGTTTAGGGTTT
52542082 AGGGTTTAGG
Statistics
Matches: 50, Mismatches: 6, Indels: 12
0.74 0.09 0.18
Matches are distributed among these distances:
21 10 0.20
22 23 0.46
23 16 0.32
24 1 0.02
ACGTcount: A:0.19, C:0.00, G:0.25, T:0.56
Consensus pattern (22 bp):
TTTTTAGGTTTAGGGTTTTTAA
Found at i:52542046 original size:7 final size:7
Alignment explanation
Indices: 52542036--52542244 Score: 83
Period size: 7 Copynumber: 29.4 Consensus size: 7
52542026 GTTTAGAGTT
*
52542036 TTTAATG
1 TTTAAGG
52542043 TTT-AGTG
1 TTTAAG-G
52542050 TTTAAGG
1 TTTAAGG
52542057 TTTAAGG
1 TTTAAGG
*
52542064 TTTTTAGG
1 -TTTAAGG
*
52542072 TTTAGGG
1 TTTAAGG
*
52542079 TTTAGGG
1 TTTAAGG
*
52542086 TTTAGGG
1 TTTAAGG
52542093 TTTAAGG
1 TTTAAGG
*
52542100 TTTATGG
1 TTTAAGG
52542107 -TTAATGG
1 TTTAA-GG
52542114 TTTTTAA-G
1 --TTTAAGG
*
52542122 -TTAGGG
1 TTTAAGG
52542128 TTTAAGG
1 TTTAAGG
*
52542135 TTTAA-A
1 TTTAAGG
* *
52542141 TGTTATGT
1 T-TTAAGG
*
52542149 TTTTAGG
1 TTTAAGG
52542156 TTT-AGAG
1 TTTAAG-G
52542163 TTTAAGG
1 TTTAAGG
*
52542170 TTTTAAAG
1 -TTTAAGG
52542178 TTTAAAGG
1 TTT-AAGG
*
52542186 TTT-AGA
1 TTTAAGG
*
52542192 TTTATGG
1 TTTAAGG
* *
52542199 TTTATGA
1 TTTAAGG
*
52542206 TTTAGAGT
1 TTTA-AGG
*
52542214 TTTATGG
1 TTTAAGG
52542221 TTT-AGAG
1 TTTAAG-G
*
52542228 TTTAGGG
1 TTTAAGG
*
52542235 TTTAGGG
1 TTTAAGG
52542242 TTT
1 TTT
52542245 TTTAGTTTAG
Statistics
Matches: 156, Mismatches: 27, Indels: 38
0.71 0.12 0.17
Matches are distributed among these distances:
5 3 0.02
6 14 0.09
7 105 0.67
8 30 0.19
10 4 0.03
ACGTcount: A:0.23, C:0.00, G:0.27, T:0.50
Consensus pattern (7 bp):
TTTAAGG
Found at i:52542059 original size:14 final size:14
Alignment explanation
Indices: 52542036--52542517 Score: 98
Period size: 14 Copynumber: 33.7 Consensus size: 14
52542026 GTTTAGAGTT
* *
52542036 TTTAATGTTTAGTG
1 TTTAAGGTTTAGGG
*
52542050 TTTAAGGTTTAAGGT
1 TTTAAGGTTT-AGGG
*
52542065 TTTTAGGTTTAGGG
1 TTTAAGGTTTAGGG
*
52542079 TTTAGGGTTTAGGG
1 TTTAAGGTTTAGGG
*
52542093 TTTAAGGTTTATGG
1 TTTAAGGTTTAGGG
*
52542107 -TTAATGGTTTTTA-AG
1 TTTAA-GG--TTTAGGG
* *
52542122 -TTAGGGTTTAAGG
1 TTTAAGGTTTAGGG
* * *
52542135 TTTAA-ATGTTATGT
1 TTTAAGGT-TTAGGG
* *
52542149 TTTTAGGTTTAGAG
1 TTTAAGGTTTAGGG
**
52542163 TTTAAGGTTTTAAAG
1 TTTAAGG-TTTAGGG
*
52542178 TTTAAAGGTTTA-GA
1 TTT-AAGGTTTAGGG
* * *
52542192 TTTATGGTTTATGA
1 TTTAAGGTTTAGGG
* *
52542206 TTTAGAGTTTTATGG
1 TTTA-AGGTTTAGGG
52542221 TTT-AGAGTTTAGGG
1 TTTAAG-GTTTAGGG
* ***
52542235 TTTAGGGTTTTTTAG
1 TTTAAGG-TTTAGGG
*
52542250 TTT-AGGGTTAGGG
1 TTTAAGGTTTAGGG
*
52542263 -TTAGAGTTTTTAGTGAAG
1 TTTA-AG-GTTTAG-G--G
* *
52542281 GTT-AGGATTAGGG
1 TTTAAGGTTTAGGG
*
52542294 -TT-AGTGTTTTA-AG
1 TTTAAG-G-TTTAGGG
* *
52542307 -TTAAGGGTTATGG
1 TTTAAGGTTTAGGG
*
52542320 TTTTAGGTTTAGGG
1 TTTAAGGTTTAGGG
* ***
52542334 TTTATGGTTTTAAAT
1 TTTAAGG-TTTAGGG
*
52542349 TTTAAAGTTTAGGG
1 TTTAAGGTTTAGGG
* *
52542363 TTTTCATGTTTAGGG
1 -TTTAAGGTTTAGGG
* **
52542378 TTTAGGGTTTAATGTTT
1 TTTAAGGTTT-A-G-GG
*
52542395 TTTAA-GTTAAGGG
1 TTTAAGGTTTAGGG
* * *
52542408 -TTATGATTTATGG
1 TTTAAGGTTTAGGG
* **
52542421 TTTAGGGTTTATGTTT
1 TTTAAGGTTTA-G-GG
*
52542437 TTTAA-GTTTAGAG
1 TTTAAGGTTTAGGG
** *
52542450 TTTATGATTTTTTA-AG
1 TTTA--A-GGTTTAGGG
52542466 TTTAAGGTTTAGGG
1 TTTAAGGTTTAGGG
52542480 TTTAAGGTTTAGGG
1 TTTAAGGTTTAGGG
*
52542494 TTTAAGGTTTAAGG
1 TTTAAGGTTTAGGG
52542508 TTTAAGGTTT
1 TTTAAGGTTT
52542518 TTAAGTTAAG
Statistics
Matches: 338, Mismatches: 89, Indels: 82
0.66 0.17 0.16
Matches are distributed among these distances:
12 16 0.05
13 38 0.11
14 163 0.48
15 81 0.24
16 27 0.08
17 10 0.03
18 1 0.00
19 2 0.01
ACGTcount: A:0.23, C:0.00, G:0.28, T:0.49
Consensus pattern (14 bp):
TTTAAGGTTTAGGG
Found at i:52542082 original size:22 final size:22
Alignment explanation
Indices: 52541974--52542088 Score: 71
Period size: 22 Copynumber: 5.2 Consensus size: 22
52541964 TTAGGATTAG
* * *
52541974 GGTTTTTAAGTTAAGGG-TTAT
1 GGTTTTTAGGTTTAGGGTTTAA
52541995 GGTTTTTAGGTTTAGGGTTTTTAA
1 GGTTTTTAGGTTTAGGG--TTTAA
*
52542019 ---TTTTATGGTTTAGAGTTTTTAA
1 GGTTTTTA-GGTTTAG-G-GTTTAA
* *
52542041 --TGTTTAGTGTTTAAGGTTTAA
1 GGTTTTTAG-GTTTAGGGTTTAA
*
52542062 GGTTTTTAGGTTTAGGGTTTAG
1 GGTTTTTAGGTTTAGGGTTTAA
52542084 GGTTT
1 GGTTT
52542089 AGGGTTTAAG
Statistics
Matches: 74, Mismatches: 10, Indels: 19
0.72 0.10 0.18
Matches are distributed among these distances:
21 25 0.34
22 30 0.41
23 16 0.22
24 3 0.04
ACGTcount: A:0.19, C:0.00, G:0.28, T:0.53
Consensus pattern (22 bp):
GGTTTTTAGGTTTAGGGTTTAA
Found at i:52542096 original size:21 final size:21
Alignment explanation
Indices: 52542042--52542642 Score: 116
Period size: 21 Copynumber: 28.6 Consensus size: 21
52542032 AGTTTTTAAT
*
52542042 GTTTAGTGTTTAAGGTTTAAGG
1 GTTTAGGGTTTAAGGTTT-AGG
* *
52542064 TTTTTA-GGTTTAGGGTTTAGG
1 -GTTTAGGGTTTAAGGTTTAGG
*
52542085 GTTTAGGGTTTAAGGTTTATG
1 GTTTAGGGTTTAAGGTTTAGG
* *
52542106 GTTAATGGTTTTTAA-G-TTAGG
1 GTTTA-GG-GTTTAAGGTTTAGG
* * *
52542127 GTTTAAGGTTTAA-ATGTTATGT
1 GTTTAGGGTTTAAGGT-TTA-GG
*
52542149 TTTTA-GGTTT-AGAGTTTAAGG
1 GTTTAGGGTTTAAG-GTTT-AGG
* **
52542170 TTTTAAAGTTTAAAGGTTTA-G
1 GTTTAGGGTTT-AAGGTTTAGG
* * * *
52542191 ATTTATGGTTTATGATTTAGAG
1 GTTTAGGGTTTAAGGTTTAG-G
* *
52542213 TTTTATGGTTT-AGAGTTTAGG
1 GTTTAGGGTTTAAG-GTTTAGG
*
52542234 GTTTAGGGTTTTTTA-GTTTAGG
1 GTTTAGGG--TTTAAGGTTTAGG
*
52542256 G-TTAGGG-TTAGAGTTTTTA--
1 GTTTAGGGTTTA-AG-GTTTAGG
* * *
52542275 G-TGAAGG-TT-AGGATTAGG
1 GTTTAGGGTTTAAGGTTTAGG
* *
52542293 G-TTAGTGTTTTAA-GTTAAGG
1 GTTTAG-GGTTTAAGGTTTAGG
* *
52542313 G-TTATGGTTTTAGGTTTAGG
1 GTTTAGGGTTTAAGGTTTAGG
* ** **
52542333 GTTTATGGTTTTAAATTTTAAA
1 GTTTA-GGGTTTAAGGTTTAGG
* *
52542355 GTTTAGGGTTTTCATGTTTAGG
1 GTTTAGGG-TTTAAGGTTTAGG
* *
52542377 GTTTAGGGTTTAATGTTTTTTA-A
1 GTTTAGGGTTTAA-G--GTTTAGG
* * * *
52542400 GTTAAGGG-TTATGATTTATG
1 GTTTAGGGTTTAAGGTTTAGG
* * *
52542420 GTTTAGGGTTTATGTTTTTTA-A
1 GTTTAGGGTTTAAG--GTTTAGG
* * *
52542442 GTTTAGAGTTTATGATTT---
1 GTTTAGGGTTTAAGGTTTAGG
*
52542460 -TTTA-AGTTTAAGGTTTAGG
1 GTTTAGGGTTTAAGGTTTAGG
* * *
52542479 GTTTAAGGTTTAGGGTTTAAG
1 GTTTAGGGTTTAAGGTTTAGG
* *
52542500 GTTTAAGGTTTAAGGTTTTTA-A
1 GTTTAGGGTTTAAGG--TTTAGG
* *
52542522 GTTAAGGG-TTAA-GATTAGG
1 GTTTAGGGTTTAAGGTTTAGG
* *
52542541 G-TTAGGATTTTTAA-GTTAAGG
1 GTTTAGG--GTTTAAGGTTTAGG
52542562 GTTAGAACTAGGGTTTAAGGTTTAGG
1 GTT-----TAGGGTTTAAGGTTTAGG
* * *
52542588 GTTTATGTTTTTAGGTTTAGG
1 GTTTAGGGTTTAAGGTTTAGG
*
52542609 G-TTAGAGTTTTAAGGTTTTAGG
1 GTTTAG-GGTTTAAGG-TTTAGG
52542631 GTTTAGGGTTTA
1 GTTTAGGGTTTA
52542643 TGATTTTTAA
Statistics
Matches: 428, Mismatches: 92, Indels: 117
0.67 0.14 0.18
Matches are distributed among these distances:
16 13 0.03
17 6 0.01
18 12 0.03
19 24 0.06
20 48 0.11
21 151 0.35
22 114 0.27
23 35 0.08
24 7 0.02
25 5 0.01
26 9 0.02
27 4 0.01
ACGTcount: A:0.23, C:0.00, G:0.29, T:0.48
Consensus pattern (21 bp):
GTTTAGGGTTTAAGGTTTAGG
Found at i:52542126 original size:35 final size:34
Alignment explanation
Indices: 52542085--52542172 Score: 108
Period size: 35 Copynumber: 2.5 Consensus size: 34
52542075 AGGGTTTAGG
52542085 GTTTAGGGTTTAAGGTTT-ATGGTTAATGGTTTTTAA
1 GTTTAGGGTTTAAGGTTTAAT-GTT-AT-GTTTTTAA
*
52542121 G-TTAGGGTTTAAGGTTTAAATGTTATGTTTTTAG
1 GTTTAGGGTTTAAGGTTT-AATGTTATGTTTTTAA
*
52542155 GTTTAGAGTTTAAGGTTT
1 GTTTAGGGTTTAAGGTTT
52542173 TAAAGTTTAA
Statistics
Matches: 47, Mismatches: 2, Indels: 7
0.84 0.04 0.12
Matches are distributed among these distances:
34 8 0.17
35 33 0.70
36 4 0.09
37 2 0.04
ACGTcount: A:0.23, C:0.00, G:0.27, T:0.50
Consensus pattern (34 bp):
GTTTAGGGTTTAAGGTTTAATGTTATGTTTTTAA
Found at i:52542292 original size:31 final size:31
Alignment explanation
Indices: 52542251--52542312 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
52542241 GTTTTTTAGT
* *
52542251 TTAGGGTTAGGGTTAGAGTTTTTAGTGAAGG
1 TTAGGATTAGGGTTAGAGTTTTAAGTGAAGG
* *
52542282 TTAGGATTAGGGTTAGTGTTTTAAGTTAAGG
1 TTAGGATTAGGGTTAGAGTTTTAAGTGAAGG
52542313 GTTATGGTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.24, C:0.00, G:0.35, T:0.40
Consensus pattern (31 bp):
TTAGGATTAGGGTTAGAGTTTTAAGTGAAGG
Found at i:52542409 original size:23 final size:22
Alignment explanation
Indices: 52542381--52542476 Score: 90
Period size: 23 Copynumber: 4.4 Consensus size: 22
52542371 TTTAGGGTTT
52542381 AGGGTTTAATGTTTTTTAAGTTA
1 AGGGTTT-ATGTTTTTTAAGTTA
* * * *
52542404 AGGG-TTATGATTTAT-GGTTT
1 AGGGTTTATGTTTTTTAAGTTA
*
52542424 AGGGTTTATGTTTTTTAAGTTT
1 AGGGTTTATGTTTTTTAAGTTA
*
52542446 AGAGTTTATGATTTTTTAAGTTTA
1 AGGGTTTATG-TTTTTTAAG-TTA
52542470 A-GGTTTA
1 AGGGTTTA
52542477 GGGTTTAAGG
Statistics
Matches: 59, Mismatches: 10, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
20 7 0.12
21 16 0.27
22 15 0.25
23 18 0.31
24 3 0.05
ACGTcount: A:0.24, C:0.00, G:0.23, T:0.53
Consensus pattern (22 bp):
AGGGTTTATGTTTTTTAAGTTA
Found at i:52542423 original size:94 final size:95
Alignment explanation
Indices: 52542300--52542489 Score: 258
Period size: 94 Copynumber: 2.0 Consensus size: 95
52542290 AGGGTTAGTG
* * *
52542300 TTTTAAGTTAAGGGTTATGGTTTTAGGTTTAGGGTTTATGGTTTTAAATTTTAAAGTTTA-GGGT
1 TTTTAAGTTAAGGGTTATGATTTTAGGTTTAGGGTTTATGGTTTTAAAGTTTAAAGTTTATGAGT
* * *
52542364 TTTCATGTTTAGGGTTTAGGGTTTAATGTT
66 TTTCAAGTTTAAGGTTTAGGGTTTAAGGTT
* * * *
52542394 TTTTAAGTTAAGGGTTATGA-TTTATGGTTTAGGGTTTATGTTTTTTAAGTTTAGAGTTTATGAT
1 TTTTAAGTTAAGGGTTATGATTTTA-GGTTTAGGGTTTATGGTTTTAAAGTTTAAAGTTTATGAG
*
52542458 TTTTTAAGTTTAAGGTTTAGGGTTTAAGGTT
65 TTTTCAAGTTTAAGGTTTAGGGTTTAAGGTT
52542489 T
1 T
52542490 AGGGTTTAAG
Statistics
Matches: 83, Mismatches: 11, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
93 4 0.05
94 50 0.60
95 29 0.35
ACGTcount: A:0.22, C:0.01, G:0.25, T:0.52
Consensus pattern (95 bp):
TTTTAAGTTAAGGGTTATGATTTTAGGTTTAGGGTTTATGGTTTTAAAGTTTAAAGTTTATGAGT
TTTCAAGTTTAAGGTTTAGGGTTTAAGGTT
Found at i:52542424 original size:65 final size:66
Alignment explanation
Indices: 52542349--52542497 Score: 169
Period size: 65 Copynumber: 2.3 Consensus size: 66
52542339 GGTTTTAAAT
* * *
52542349 TTTAAAGTTTAGGGTTT-TCATGTTTAGGGTTTAGGGTTTAATG-TTTTTTAAG-TTAAGGGTTA
1 TTTAAGGTTTAGGGTTTATCATGTTTA-AGTTTAGAGTTT-ATGATTTTTTAAGTTTAAGGGTTA
*
52542411 TGA
64 GGA
* ** * *
52542414 TTTATGGTTTAGGGTTTATGTTTTTTAAGTTTAGAGTTTATGATTTTTTAAGTTTAAGGTTTAGG
1 TTTAAGGTTTAGGGTTTATCATGTTTAAGTTTAGAGTTTATGATTTTTTAAGTTTAAGGGTTAGG
*
52542479 G
66 A
52542480 TTTAAGGTTTAGGGTTTA
1 TTTAAGGTTTAGGGTTTA
52542498 AGGTTTAAGG
Statistics
Matches: 70, Mismatches: 11, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
64 3 0.04
65 34 0.49
66 33 0.47
ACGTcount: A:0.22, C:0.01, G:0.26, T:0.52
Consensus pattern (66 bp):
TTTAAGGTTTAGGGTTTATCATGTTTAAGTTTAGAGTTTATGATTTTTTAAGTTTAAGGGTTAGG
A
Found at i:52542439 original size:43 final size:44
Alignment explanation
Indices: 52542371--52542459 Score: 137
Period size: 43 Copynumber: 2.1 Consensus size: 44
52542361 GGTTTTCATG
52542371 TTTAGGGTTTAGGGTTTAATGTTTTTTAAGTTAAG-GGTTATGA
1 TTTAGGGTTTAGGGTTTAATGTTTTTTAAGTTAAGAGGTTATGA
* * *
52542414 TTTATGGTTTAGGGTTT-ATGTTTTTTAAGTTTAGAGTTTATGA
1 TTTAGGGTTTAGGGTTTAATGTTTTTTAAGTTAAGAGGTTATGA
52542457 TTT
1 TTT
52542460 TTTAAGTTTA
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
42 16 0.38
43 26 0.62
ACGTcount: A:0.21, C:0.00, G:0.25, T:0.54
Consensus pattern (44 bp):
TTTAGGGTTTAGGGTTTAATGTTTTTTAAGTTAAGAGGTTATGA
Found at i:52542481 original size:7 final size:7
Alignment explanation
Indices: 52542460--52542517 Score: 91
Period size: 7 Copynumber: 8.4 Consensus size: 7
52542450 TTTATGATTT
52542460 TTTAA-G
1 TTTAAGG
52542466 TTTAAGG
1 TTTAAGG
*
52542473 TTTAGGG
1 TTTAAGG
52542480 TTTAAGG
1 TTTAAGG
*
52542487 TTTAGGG
1 TTTAAGG
52542494 TTTAAGG
1 TTTAAGG
52542501 TTTAAGG
1 TTTAAGG
52542508 TTTAAGG
1 TTTAAGG
52542515 TTT
1 TTT
52542518 TTAAGTTAAG
Statistics
Matches: 47, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
6 5 0.11
7 42 0.89
ACGTcount: A:0.24, C:0.00, G:0.29, T:0.47
Consensus pattern (7 bp):
TTTAAGG
Found at i:52542589 original size:14 final size:14
Alignment explanation
Indices: 52542570--52542642 Score: 60
Period size: 14 Copynumber: 5.1 Consensus size: 14
52542560 GGGTTAGAAC
52542570 TAGGGTTTAAGGTT
1 TAGGGTTTAAGGTT
* *
52542584 TAGGGTTTATGTTTT
1 TAGGGTTTAAG-GTT
*
52542599 TA-GGTTT-AGGGT
1 TAGGGTTTAAGGTT
*
52542611 TAGAGTTTTAAGGTTT
1 TAG-GGTTTAAGG-TT
*
52542627 TAGGGTTTAGGGTT
1 TAGGGTTTAAGGTT
52542641 TA
1 TA
52542643 TGATTTTTAA
Statistics
Matches: 45, Mismatches: 9, Indels: 10
0.70 0.14 0.16
Matches are distributed among these distances:
12 3 0.07
13 1 0.02
14 23 0.51
15 14 0.31
16 4 0.09
ACGTcount: A:0.19, C:0.00, G:0.33, T:0.48
Consensus pattern (14 bp):
TAGGGTTTAAGGTT
Found at i:52542691 original size:29 final size:29
Alignment explanation
Indices: 52542570--52542700 Score: 90
Period size: 29 Copynumber: 4.6 Consensus size: 29
52542560 GGGTTAGAAC
* *** *
52542570 TAGGGTTTAAGGTTTAGGGTTTATGTTTT
1 TAGGGTTTAGGGTTTAATATTTATGATTT
* *
52542599 TA-GGTTTAGGG-TTAGAGT-TTTAAGGTTT
1 TAGGGTTTAGGGTTTA-A-TATTTATGATTT
* * **
52542627 TAGGGTTTAGGGTTT-ATGATTTTTAAGCT
1 TAGGGTTTAGGGTTTAAT-ATTTATGATTT
*
52542656 TAAGGTTTAGGGTTTAATATTTATGATTT
1 TAGGGTTTAGGGTTTAATATTTATGATTT
*
52542685 TAGGGTTTAGAGTTTA
1 TAGGGTTTAGGGTTTA
52542701 GAGGTTAAAG
Statistics
Matches: 77, Mismatches: 18, Indels: 14
0.71 0.17 0.13
Matches are distributed among these distances:
27 4 0.05
28 19 0.25
29 50 0.65
30 4 0.05
ACGTcount: A:0.22, C:0.01, G:0.28, T:0.49
Consensus pattern (29 bp):
TAGGGTTTAGGGTTTAATATTTATGATTT
Found at i:52542776 original size:22 final size:22
Alignment explanation
Indices: 52542739--52542791 Score: 72
Period size: 22 Copynumber: 2.5 Consensus size: 22
52542729 AAGGTTAGGA
52542739 TTAGGG-TTAGTATTTTTAGAT
1 TTAGGGTTTAGTATTTTTAGAT
* *
52542760 TTAGGGTTTAGTGTTTTTAGGT
1 TTAGGGTTTAGTATTTTTAGAT
*
52542782 TTAAGGTTTA
1 TTAGGGTTTA
52542792 AGGTTTAAGG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
21 6 0.21
22 22 0.79
ACGTcount: A:0.21, C:0.00, G:0.26, T:0.53
Consensus pattern (22 bp):
TTAGGGTTTAGTATTTTTAGAT
Found at i:52542825 original size:7 final size:7
Alignment explanation
Indices: 52542778--52542832 Score: 67
Period size: 7 Copynumber: 7.9 Consensus size: 7
52542768 TAGTGTTTTT
52542778 AGGTTTA
1 AGGTTTA
52542785 AGGTTTA
1 AGGTTTA
52542792 AGGTTTA
1 AGGTTTA
52542799 AGGTTT-
1 AGGTTTA
52542805 AGTGTTTA
1 AG-GTTTA
*
52542813 GGGTTTA
1 AGGTTTA
*
52542820 AAGTTTA
1 AGGTTTA
*
52542827 GGGTTT
1 AGGTTT
52542833 TTAAGTTATG
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
6 2 0.05
7 38 0.93
8 1 0.02
ACGTcount: A:0.24, C:0.00, G:0.31, T:0.45
Consensus pattern (7 bp):
AGGTTTA
Found at i:52542882 original size:22 final size:22
Alignment explanation
Indices: 52542864--52542942 Score: 72
Period size: 22 Copynumber: 3.5 Consensus size: 22
52542854 ATAGTTTAGG
52542864 GTTTAGGTTTTTTAGGTTTAAA
1 GTTTAGGTTTTTTAGGTTTAAA
* *
52542886 GTTT-GTGGTTTTTAAGTTTAAA
1 GTTTAG-GTTTTTTAGGTTTAAA
* **
52542908 GTTTAGG-GTTTTATGGTTTATG
1 GTTTAGGTTTTTTA-GGTTTAAA
52542930 GTTTAAGGTTTTT
1 GTTT-AGGTTTTT
52542943 AAGTTAAGGG
Statistics
Matches: 45, Mismatches: 7, Indels: 8
0.75 0.12 0.13
Matches are distributed among these distances:
21 6 0.13
22 32 0.71
23 4 0.09
24 3 0.07
ACGTcount: A:0.19, C:0.00, G:0.25, T:0.56
Consensus pattern (22 bp):
GTTTAGGTTTTTTAGGTTTAAA
Found at i:52542912 original size:44 final size:44
Alignment explanation
Indices: 52542864--52542947 Score: 107
Period size: 44 Copynumber: 1.9 Consensus size: 44
52542854 ATAGTTTAGG
* **
52542864 GTTTA-GGTTTTTTAGGTTTAAAGTTTGTGGTTTTTAAGTTTAAA
1 GTTTAGGGTTTTAT-GGTTTAAAGTTTAAGGTTTTTAAGTTTAAA
**
52542908 GTTTAGGGTTTTATGGTTTATGGTTTAAGGTTTTTAAGTT
1 GTTTAGGGTTTTATGGTTTAAAGTTTAAGGTTTTTAAGTT
52542948 AAGGGTTAGG
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
44 27 0.79
45 7 0.21
ACGTcount: A:0.20, C:0.00, G:0.25, T:0.55
Consensus pattern (44 bp):
GTTTAGGGTTTTATGGTTTAAAGTTTAAGGTTTTTAAGTTTAAA
Found at i:52542980 original size:33 final size:33
Alignment explanation
Indices: 52542938--52543000 Score: 117
Period size: 33 Copynumber: 1.9 Consensus size: 33
52542928 TGGTTTAAGG
*
52542938 TTTTTAAGTTAAGGGTTAGGATTAGGGTTTGGA
1 TTTTTAAGTTAAGGGTTAGAATTAGGGTTTGGA
52542971 TTTTTAAGTTAAGGGTTAGAATTAGGGTTT
1 TTTTTAAGTTAAGGGTTAGAATTAGGGTTT
52543001 AGTGTTTAGG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.25, C:0.00, G:0.30, T:0.44
Consensus pattern (33 bp):
TTTTTAAGTTAAGGGTTAGAATTAGGGTTTGGA
Found at i:52543002 original size:7 final size:7
Alignment explanation
Indices: 52542992--52543043 Score: 52
Period size: 7 Copynumber: 7.3 Consensus size: 7
52542982 AGGGTTAGAA
52542992 TTAGGGT
1 TTAGGGT
*
52542999 TTAGTGT
1 TTAGGGT
52543006 TTAGGGT
1 TTAGGGT
52543013 TTAGGGTTT
1 TTAGGG--T
52543022 TTA-GGT
1 TTAGGGT
*
52543028 TTAGTGT
1 TTAGGGT
*
52543035 TTAAGGT
1 TTAGGGT
52543042 TT
1 TT
52543044 TAAAGTTCAA
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
6 4 0.11
7 27 0.73
8 2 0.05
9 4 0.11
ACGTcount: A:0.15, C:0.00, G:0.33, T:0.52
Consensus pattern (7 bp):
TTAGGGT
Found at i:52543011 original size:14 final size:14
Alignment explanation
Indices: 52542992--52543043 Score: 61
Period size: 14 Copynumber: 3.6 Consensus size: 14
52542982 AGGGTTAGAA
52542992 TTAGGGTTTAGTGT
1 TTAGGGTTTAGTGT
*
52543006 TTAGGGTTTAGGGTTT
1 TTAGGGTTTA--GTGT
52543022 TTA-GGTTTAGTGT
1 TTAGGGTTTAGTGT
*
52543035 TTAAGGTTT
1 TTAGGGTTT
52543044 TAAAGTTCAA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
13 6 0.18
14 15 0.45
15 6 0.18
16 6 0.18
ACGTcount: A:0.15, C:0.00, G:0.33, T:0.52
Consensus pattern (14 bp):
TTAGGGTTTAGTGT
Found at i:52543019 original size:33 final size:31
Alignment explanation
Indices: 52542940--52543043 Score: 79
Period size: 33 Copynumber: 3.3 Consensus size: 31
52542930 GTTTAAGGTT
* * * *
52542940 TTTAAGTTAAGGGTTAGGATTAGGGTTTGGATT
1 TTTAGGTTTAGGGTTA-GATTAGGGTTTAG-TG
* *
52542973 TTTAAGTTAAGGGTTAGAATTAGGGTTTAGTG
1 TTTAGGTTTAGGGTTAG-ATTAGGGTTTAGTG
*
52543005 TTTAGGGTTTAGGGTT--TTTA-GGTTTAGTG
1 TTTA-GGTTTAGGGTTAGATTAGGGTTTAGTG
52543034 TTTAAGGTTT
1 TTT-AGGTTT
52543044 TAAAGTTCAA
Statistics
Matches: 63, Mismatches: 5, Indels: 10
0.81 0.06 0.13
Matches are distributed among these distances:
29 17 0.27
30 4 0.06
32 6 0.10
33 36 0.57
ACGTcount: A:0.22, C:0.00, G:0.32, T:0.46
Consensus pattern (31 bp):
TTTAGGTTTAGGGTTAGATTAGGGTTTAGTG
Found at i:52543030 original size:15 final size:16
Alignment explanation
Indices: 52542992--52543036 Score: 51
Period size: 15 Copynumber: 3.0 Consensus size: 16
52542982 AGGGTTAGAA
*
52542992 TTAGGGTTTA--GTGT
1 TTAGGGTTTAGGGTTT
52543006 TTAGGGTTTAGGGTTT
1 TTAGGGTTTAGGGTTT
*
52543022 TTA-GGTTTAGTGTTT
1 TTAGGGTTTAGGGTTT
52543037 AAGGTTTTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
14 10 0.37
15 11 0.41
16 6 0.22
ACGTcount: A:0.13, C:0.00, G:0.33, T:0.53
Consensus pattern (16 bp):
TTAGGGTTTAGGGTTT
Found at i:52543036 original size:22 final size:23
Alignment explanation
Indices: 52542998--52543044 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
52542988 AGAATTAGGG
*
52542998 TTTAGTGTTTAGGGTTTAGGGTT
1 TTTAGTGTTTAGGGTTTAAGGTT
*
52543021 TTTAG-GTTTAGTGTTTAAGGTT
1 TTTAGTGTTTAGGGTTTAAGGTT
52543043 TT
1 TT
52543045 AAAGTTCAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 17 0.77
23 5 0.23
ACGTcount: A:0.15, C:0.00, G:0.30, T:0.55
Consensus pattern (23 bp):
TTTAGTGTTTAGGGTTTAAGGTT
Found at i:52543094 original size:22 final size:22
Alignment explanation
Indices: 52543004--52543108 Score: 83
Period size: 22 Copynumber: 4.8 Consensus size: 22
52542994 AGGGTTTAGT
* * * *
52543004 GTTTAGGGTTTAGGGTTTTTAG
1 GTTTAAGGTTTAGGATTTTAAA
52543026 GTTT-AGTGTTTAAGG-TTTTAAA
1 GTTTAAG-GTTT-AGGATTTTAAA
* *
52543048 GTTCAAGGATTTAGGGTTTTAAA
1 GTTTAAGG-TTTAGGATTTTAAA
52543071 GTTTAAGGTTTAGGATTTGT-AA
1 GTTTAAGGTTTAGGATTT-TAAA
*
52543093 G-TTAAGGGTTAGGATT
1 GTTTAAGGTTTAGGATT
52543109 AAGGTTAGGG
Statistics
Matches: 70, Mismatches: 7, Indels: 13
0.78 0.08 0.14
Matches are distributed among these distances:
21 15 0.21
22 32 0.46
23 23 0.33
ACGTcount: A:0.25, C:0.01, G:0.30, T:0.45
Consensus pattern (22 bp):
GTTTAAGGTTTAGGATTTTAAA
Found at i:52543095 original size:45 final size:44
Alignment explanation
Indices: 52543012--52543099 Score: 101
Period size: 45 Copynumber: 2.0 Consensus size: 44
52543002 GTGTTTAGGG
* *
52543012 TTTAGGGTTTTTAGGTTTAGTGTTTAAGGTTTTAAAGTTCAAGGA
1 TTTAGGGTTTTAAAGTTTAGTGTTTAAGGTTTTAAAGTT-AAGGA
52543057 TTTAGGGTTTTAAAGTTTAAG-GTTT-AGGATTTGT-AAGTTAAGG
1 TTTAGGGTTTTAAAGTTT-AGTGTTTAAGG-TTT-TAAAGTTAAGG
52543100 GTTAGGATTA
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
44 7 0.18
45 28 0.74
46 3 0.08
ACGTcount: A:0.26, C:0.01, G:0.27, T:0.45
Consensus pattern (44 bp):
TTTAGGGTTTTAAAGTTTAGTGTTTAAGGTTTTAAAGTTAAGGA
Found at i:52543096 original size:148 final size:147
Alignment explanation
Indices: 52542857--52543144 Score: 389
Period size: 148 Copynumber: 2.0 Consensus size: 147
52542847 ATGATTTATA
* ** * * *
52542857 GTTTAGGGTTTAGGTTTTTTAGGTTTAAAGTTTGTGGTTTTTAAGTTTAAAGTTTAGGGTTTTAT
1 GTTTAGGGTTTAGGGTTTTTAGGTTTAAAGTTTAAGGTTTTAAAGTTCAAAGTTTAGGGTTTTAA
* * * * * *
52542922 GGTTTATGGTTTAAGGTTTTTAAGTTAAGGGTTAGGATTAGGGTTTGGATTTTTAAGTTAAGGGT
66 AGTTTAAGGTTTAAGGTTTGTAAGTTAAGGGTTAGGATTAAGGTTAGGATTTTTAAGTTAAGAGT
52542987 TAGAATTAGGGTTTAGT
131 TAGAATTAGGGTTTAGT
** *
52543004 GTTTAGGGTTTAGGGTTTTTAGGTTTAGTGTTTAAGGTTTTAAAGTTCAAGGATTTAGGGTTTTA
1 GTTTAGGGTTTAGGGTTTTTAGGTTTAAAGTTTAAGGTTTTAAAGTTCAAAG-TTTAGGGTTTTA
* *
52543069 AAGTTTAAGGTTT-AGGATTTGTAAGTTAAGGGTTAGGATTAAGGTTAGGGTTTTTAAGTTAATA
65 AAGTTTAAGGTTTAAGG-TTTGTAAGTTAAGGGTTAGGATTAAGGTTAGGATTTTTAAGTTAAGA
*
52543133 GTTAGGATTAGG
129 GTTAGAATTAGG
52543145 ATTAGAGTTT
Statistics
Matches: 121, Mismatches: 18, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
147 47 0.39
148 74 0.61
ACGTcount: A:0.24, C:0.00, G:0.30, T:0.46
Consensus pattern (147 bp):
GTTTAGGGTTTAGGGTTTTTAGGTTTAAAGTTTAAGGTTTTAAAGTTCAAAGTTTAGGGTTTTAA
AGTTTAAGGTTTAAGGTTTGTAAGTTAAGGGTTAGGATTAAGGTTAGGATTTTTAAGTTAAGAGT
TAGAATTAGGGTTTAGT
Found at i:52543127 original size:33 final size:34
Alignment explanation
Indices: 52543073--52543169 Score: 117
Period size: 33 Copynumber: 2.9 Consensus size: 34
52543063 GTTTTAAAGT
* * *
52543073 TTAAGGTTTAGGATTTGTAAGTTAAGGGTTAGGA
1 TTAAGGATTAGGGTTTTTAAGTTAAGGGTTAGGA
**
52543107 TTAAGG-TTAGGGTTTTTAAGTTAATAGTTAGGA
1 TTAAGGATTAGGGTTTTTAAGTTAAGGGTTAGGA
* *
52543140 TT-AGGATTAGAGTTTTTAAGTTTAGGGTTA
1 TTAAGGATTAGGGTTTTTAAGTTAAGGGTTA
52543170 TGGTTTTTTG
Statistics
Matches: 54, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
32 3 0.06
33 45 0.83
34 6 0.11
ACGTcount: A:0.29, C:0.00, G:0.29, T:0.42
Consensus pattern (34 bp):
TTAAGGATTAGGGTTTTTAAGTTAAGGGTTAGGA
Found at i:52543197 original size:22 final size:21
Alignment explanation
Indices: 52543140--52543201 Score: 63
Period size: 21 Copynumber: 2.9 Consensus size: 21
52543130 ATAGTTAGGA
* *
52543140 TTAGGATTAGAGTTTTTAAGT
1 TTAGGGTTAGAGTTTTTTAGT
*
52543161 TTAGGGTTATG-GTTTTTTGGT
1 TTAGGGTTA-GAGTTTTTTAGT
*
52543182 TTAAGGTTTAGAGTTTTTTA
1 TT-AGGGTTAGAGTTTTTTA
52543202 ATTATAAAGT
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
21 19 0.58
22 14 0.42
ACGTcount: A:0.21, C:0.00, G:0.26, T:0.53
Consensus pattern (21 bp):
TTAGGGTTAGAGTTTTTTAGT
Found at i:52543301 original size:15 final size:15
Alignment explanation
Indices: 52543268--52543309 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
52543258 AAAATCCAAA
*
52543268 GGTTTA-AGGTTTAG
1 GGTTTAGAGTTTTAG
*
52543282 AGTTTAGAGTTTTAG
1 GGTTTAGAGTTTTAG
*
52543297 GGTTTAGTGTTTT
1 GGTTTAGAGTTTT
52543310 TAAGTTAAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
14 5 0.22
15 18 0.78
ACGTcount: A:0.19, C:0.00, G:0.31, T:0.50
Consensus pattern (15 bp):
GGTTTAGAGTTTTAG
Found at i:52543345 original size:33 final size:32
Alignment explanation
Indices: 52543300--52543422 Score: 183
Period size: 33 Copynumber: 3.7 Consensus size: 32
52543290 GTTTTAGGGT
** *
52543300 TTAGTGTTTTTAAGTTAAATGTTAGGATTAGGG
1 TTAG-GTTTTTAAGTTAAGGGTTAGGATTAGGA
52543333 TTAGAGTTTTTAAGTTAAGGGTTAGGATTAGGA
1 TTAG-GTTTTTAAGTTAAGGGTTAGGATTAGGA
52543366 TTAGGGTTTTTAAGTTAAGGGTTAGGATTAGGA
1 TTA-GGTTTTTAAGTTAAGGGTTAGGATTAGGA
52543399 TTAGGATTTTTAAGTTAAGGGTTA
1 TTAGG-TTTTTAAGTTAAGGGTTA
52543423 TGGTTTTTAG
Statistics
Matches: 84, Mismatches: 4, Indels: 4
0.91 0.04 0.04
Matches are distributed among these distances:
32 2 0.02
33 81 0.96
34 1 0.01
ACGTcount: A:0.28, C:0.00, G:0.29, T:0.42
Consensus pattern (32 bp):
TTAGGTTTTTAAGTTAAGGGTTAGGATTAGGA
Found at i:52543381 original size:66 final size:68
Alignment explanation
Indices: 52543300--52543447 Score: 203
Period size: 66 Copynumber: 2.2 Consensus size: 68
52543290 GTTTTAGGGT
* * *
52543300 TTAGTGTTTTTAAGTTAAATGTTAGGATTAGGGTTA-GAGTTTTTAAGTTAAGGGTTA-GG-ATT
1 TTAGGGTTTTTAAGTTAAAGGTTAGGATTAGGATTAGGA-TTTTTAAGTTAAGGGTTATGGTATT
52543362 AGGA
65 AGGA
* *
52543366 TTAGGGTTTTTAAGTTAAGGGTTAGGATTAGGATTAGGATTTTTAAGTTAAGGGTTATGGTTTTT
1 TTAGGGTTTTTAAGTTAAAGGTTAGGATTAGGATTAGGATTTTTAAGTTAAGGGTTATGG-TATT
*
52543431 AGGT
65 AGGA
52543435 TTAGGGTTTTTAA
1 TTAGGGTTTTTAA
52543448 TTTTATGGTT
Statistics
Matches: 72, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
66 50 0.69
67 4 0.06
69 18 0.25
ACGTcount: A:0.26, C:0.00, G:0.29, T:0.45
Consensus pattern (68 bp):
TTAGGGTTTTTAAGTTAAAGGTTAGGATTAGGATTAGGATTTTTAAGTTAAGGGTTATGGTATTA
GGA
Found at i:52543451 original size:22 final size:22
Alignment explanation
Indices: 52543426--52543531 Score: 78
Period size: 22 Copynumber: 4.8 Consensus size: 22
52543416 AGGGTTATGG
52543426 TTTTTAGGTTTAGGGTTTTTAA
1 TTTTTAGGTTTAGGGTTTTTAA
*
52543448 -TTTTATGGTTTAGAGTTTTTAA
1 TTTTTA-GGTTTAGGGTTTTTAA
* *
52543470 TGTTTAGTGTTTAAGG--TTTAA
1 TTTTTAG-GTTTAGGGTTTTTAA
* *
52543491 GGTTTTTAGGTTTAAGG--TTTAG
1 --TTTTTAGGTTTAGGGTTTTTAA
*
52543513 TATTTAGGGTTTAGGGTTT
1 TTTTTA-GGTTTAGGGTTT
52543532 AGGGTTTATG
Statistics
Matches: 68, Mismatches: 8, Indels: 15
0.75 0.09 0.16
Matches are distributed among these distances:
20 5 0.07
21 18 0.26
22 28 0.41
23 17 0.25
ACGTcount: A:0.20, C:0.00, G:0.25, T:0.55
Consensus pattern (22 bp):
TTTTTAGGTTTAGGGTTTTTAA
Found at i:52543475 original size:7 final size:7
Alignment explanation
Indices: 52543465--52543568 Score: 63
Period size: 7 Copynumber: 14.7 Consensus size: 7
52543455 GTTTAGAGTT
*
52543465 TTTAATG
1 TTTAAGG
52543472 TTT-AGTG
1 TTTAAG-G
52543479 TTTAAGG
1 TTTAAGG
52543486 TTTAAGG
1 TTTAAGG
*
52543493 TTTTTAGG
1 -TTTAAGG
52543501 TTTAAGG
1 TTTAAGG
*
52543508 TTT-AGTA
1 TTTAAG-G
*
52543515 TTTAGGG
1 TTTAAGG
*
52543522 TTTAGGG
1 TTTAAGG
*
52543529 TTTAGGG
1 TTTAAGG
*
52543536 TTTATGG
1 TTTAAGG
52543543 TTTTTAA-G
1 --TTTAAGG
*
52543551 -TTAGGG
1 TTTAAGG
52543557 TTTAAGG
1 TTTAAGG
52543564 TTTAA
1 TTTAA
52543569 ATGTTATGTT
Statistics
Matches: 78, Mismatches: 10, Indels: 18
0.74 0.09 0.17
Matches are distributed among these distances:
5 3 0.04
6 4 0.05
7 57 0.73
8 10 0.13
9 4 0.05
ACGTcount: A:0.22, C:0.00, G:0.28, T:0.50
Consensus pattern (7 bp):
TTTAAGG
Found at i:52543488 original size:14 final size:14
Alignment explanation
Indices: 52543478--52543673 Score: 84
Period size: 14 Copynumber: 13.8 Consensus size: 14
52543468 AATGTTTAGT
*
52543478 GTTTAAGGTTTAAG
1 GTTTAGGGTTTAAG
52543492 GTTTTTA-GGTTTAAG
1 G--TTTAGGGTTTAAG
** *
52543507 GTTTAGTATTTAGG
1 GTTTAGGGTTTAAG
*
52543521 GTTTAGGGTTTAGG
1 GTTTAGGGTTTAAG
*
52543535 GTTTATGGTTTTTAA-
1 GTTTA-GG-GTTTAAG
52543550 G-TTAGGGTTTAAG
1 GTTTAGGGTTTAAG
** *
52543563 GTTTA-AATGTTATG
1 GTTTAGGGT-TTAAG
*
52543577 TTTTTA-GGTTT-AG
1 -GTTTAGGGTTTAAG
*
52543590 AGTTTAGGGTTTTAAA
1 -GTTTAGGG-TTTAAG
*
52543606 GTTTAAAGGTTT-AG
1 GTTT-AGGGTTTAAG
*
52543620 ATTTAGGGTTTATA-
1 GTTTAGGGTTTA-AG
* *
52543634 ATTTAGGGTTTTAGG
1 GTTTAGGG-TTTAAG
* *
52543649 GTTTAGAGTTTAAA
1 GTTTAGGGTTTAAG
52543663 GTTTAGGGTTT
1 GTTTAGGGTTT
52543674 TTTTAGTTTA
Statistics
Matches: 137, Mismatches: 28, Indels: 34
0.69 0.14 0.17
Matches are distributed among these distances:
12 5 0.04
13 19 0.14
14 63 0.46
15 38 0.28
16 12 0.09
ACGTcount: A:0.23, C:0.00, G:0.28, T:0.48
Consensus pattern (14 bp):
GTTTAGGGTTTAAG
Found at i:52543495 original size:21 final size:21
Alignment explanation
Indices: 52543465--52543619 Score: 71
Period size: 21 Copynumber: 7.6 Consensus size: 21
52543455 GTTTAGAGTT
*
52543465 TTTAATGTTTAGTGTTTAAGG
1 TTTAAGGTTTAGTGTTTAAGG
52543486 TTTAAGG--T--T-TTT-AGG
1 TTTAAGGTTTAGTGTTTAAGG
* *
52543501 TTTAAGGTTTAGTATTTAGGG
1 TTTAAGGTTTAGTGTTTAAGG
* * *
52543522 TTTAGGGTTTAGGGTTTATGG
1 TTTAAGGTTTAGTGTTTAAGG
*
52543543 TTTTTAA-G-TTAGGGTTTAAGG
1 --TTTAAGGTTTAGTGTTTAAGG
* *
52543564 TTTAA-ATGTTA-TGTTTTTAGG
1 TTTAAGGT-TTAGTG-TTTAAGG
* *
52543585 TTT-AGAGTTTAGGGTTTTAAAG
1 TTTAAG-GTTTAGTG-TTTAAGG
52543607 TTTAAAGGTTTAG
1 TTT-AAGGTTTAG
52543620 ATTTAGGGTT
Statistics
Matches: 103, Mismatches: 15, Indels: 30
0.70 0.10 0.20
Matches are distributed among these distances:
15 10 0.10
16 3 0.03
17 2 0.02
19 7 0.07
20 5 0.05
21 52 0.50
22 12 0.12
23 10 0.10
24 2 0.02
ACGTcount: A:0.23, C:0.00, G:0.27, T:0.50
Consensus pattern (21 bp):
TTTAAGGTTTAGTGTTTAAGG
Found at i:52543596 original size:7 final size:7
Alignment explanation
Indices: 52543579--52543673 Score: 59
Period size: 7 Copynumber: 13.4 Consensus size: 7
52543569 ATGTTATGTT
52543579 TTTAG-G
1 TTTAGAG
52543585 TTTAGAG
1 TTTAGAG
*
52543592 TTTAGGG
1 TTTAGAG
*
52543599 TTTTAAAG
1 -TTTAGAG
*
52543607 TTTAAAGG
1 TTTAGA-G
52543615 TTTAGA-
1 TTTAGAG
*
52543621 TTTAGGG
1 TTTAGAG
* *
52543628 TTTATAA
1 TTTAGAG
*
52543635 TTTAGGG
1 TTTAGAG
*
52543642 TTTTAGGG
1 -TTTAGAG
52543650 TTTAGAG
1 TTTAGAG
*
52543657 TTTAAAG
1 TTTAGAG
*
52543664 TTTAGGG
1 TTTAGAG
52543671 TTT
1 TTT
52543674 TTTTAGTTTA
Statistics
Matches: 69, Mismatches: 15, Indels: 9
0.74 0.16 0.10
Matches are distributed among these distances:
6 10 0.14
7 41 0.59
8 18 0.26
ACGTcount: A:0.25, C:0.00, G:0.27, T:0.47
Consensus pattern (7 bp):
TTTAGAG
Found at i:52543630 original size:43 final size:43
Alignment explanation
Indices: 52543579--52543673 Score: 113
Period size: 43 Copynumber: 2.2 Consensus size: 43
52543569 ATGTTATGTT
* *
52543579 TTTA-GGTTTAGAGTTTAGGGTTTTAAAGTTTAAAGGTTTAGA-
1 TTTAGGGTTTAGAATTTAGGGTTTTAAAGTTTAAA-GTTTAAAG
* ** *
52543621 TTTAGGGTTTATAATTTAGGGTTTTAGGGTTTAGAGTTTAAAG
1 TTTAGGGTTTAGAATTTAGGGTTTTAAAGTTTAAAGTTTAAAG
52543664 TTTAGGGTTT
1 TTTAGGGTTT
52543674 TTTTAGTTTA
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
42 10 0.22
43 35 0.78
ACGTcount: A:0.25, C:0.00, G:0.27, T:0.47
Consensus pattern (43 bp):
TTTAGGGTTTAGAATTTAGGGTTTTAAAGTTTAAAGTTTAAAG
Found at i:52543722 original size:31 final size:32
Alignment explanation
Indices: 52543681--52543766 Score: 93
Period size: 31 Copynumber: 2.7 Consensus size: 32
52543671 TTTTTTTAGT
* *
52543681 TTAGGGTTAGGGTTAGAGTTTTTAGTGAA-GG
1 TTAGGATTAGGGTTAGAGTTTTAAGTGAAGGG
* *
52543712 TTAGGATTAGGGTTAGTGTTTTAAGTTAAGGG
1 TTAGGATTAGGGTTAGAGTTTTAAGTGAAGGG
* *
52543744 TTATGGTTTTAGGTTTAGAGTTT
1 TTA-GG-ATTAGGGTTAGAGTTT
52543767 AGGGTTTTAA
Statistics
Matches: 45, Mismatches: 7, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
31 25 0.56
32 5 0.11
33 2 0.04
34 13 0.29
ACGTcount: A:0.22, C:0.00, G:0.34, T:0.44
Consensus pattern (32 bp):
TTAGGATTAGGGTTAGAGTTTTAAGTGAAGGG
Found at i:52543788 original size:22 final size:22
Alignment explanation
Indices: 52543724--52543824 Score: 88
Period size: 22 Copynumber: 4.8 Consensus size: 22
52543714 AGGATTAGGG
* *
52543724 TTAGTGTTTTAA-G-TTAAGGG
1 TTAGGGTTTTAATGTTTAAGGT
* *
52543744 TTATGGTTTT-AGGTTT-AGAGT
1 TTAGGGTTTTAATGTTTAAG-GT
52543765 TTAGGGTTTTAAAT-TTTAAGGT
1 TTAGGGTTTT-AATGTTTAAGGT
* *
52543787 TTAGGGTTTTCATGTTTAGGGT
1 TTAGGGTTTTAATGTTTAAGGT
52543809 TTAGGG-TTTAATGTTT
1 TTAGGGTTTTAATGTTT
52543825 TTTAAGTTAA
Statistics
Matches: 66, Mismatches: 8, Indels: 13
0.76 0.09 0.15
Matches are distributed among these distances:
19 1 0.02
20 11 0.17
21 23 0.35
22 28 0.42
23 3 0.05
ACGTcount: A:0.21, C:0.01, G:0.28, T:0.50
Consensus pattern (22 bp):
TTAGGGTTTTAATGTTTAAGGT
Found at i:52543839 original size:23 final size:22
Alignment explanation
Indices: 52543811--52543906 Score: 81
Period size: 23 Copynumber: 4.4 Consensus size: 22
52543801 TTTAGGGTTT
52543811 AGGGTTTAATGTTTTTTAAGTTA
1 AGGGTTT-ATGTTTTTTAAGTTA
* * * *
52543834 AGGG-TTATGATTTAT-GGTTT
1 AGGGTTTATGTTTTTTAAGTTA
* *
52543854 AGGGTTTAGGTTTTTTAAGTTT
1 AGGGTTTATGTTTTTTAAGTTA
*
52543876 AGAGTTTATGATTTTTTAAGTTTA
1 AGGGTTTATG-TTTTTTAAG-TTA
52543900 A-GGTTTA
1 AGGGTTTA
52543907 GGGTTTAGGG
Statistics
Matches: 57, Mismatches: 12, Indels: 8
0.74 0.16 0.10
Matches are distributed among these distances:
20 7 0.12
21 15 0.26
22 14 0.25
23 18 0.32
24 3 0.05
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.52
Consensus pattern (22 bp):
AGGGTTTATGTTTTTTAAGTTA
Found at i:52543854 original size:43 final size:43
Alignment explanation
Indices: 52543801--52543889 Score: 126
Period size: 43 Copynumber: 2.1 Consensus size: 43
52543791 GGTTTTCATG
*
52543801 TTTAGGGTTTAGGGTTTAATGTTTTTTAAGTTAAG-GGTTATGA
1 TTTAGGGTTTAGGGTTT-AGGTTTTTTAAGTTAAGAGGTTATGA
* * *
52543844 TTTATGGTTTAGGGTTTAGGTTTTTTAAGTTTAGAGTTTATGA
1 TTTAGGGTTTAGGGTTTAGGTTTTTTAAGTTAAGAGGTTATGA
52543887 TTT
1 TTT
52543890 TTTAAGTTTA
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
42 15 0.37
43 26 0.63
ACGTcount: A:0.21, C:0.00, G:0.26, T:0.53
Consensus pattern (43 bp):
TTTAGGGTTTAGGGTTTAGGTTTTTTAAGTTAAGAGGTTATGA
Found at i:52543855 original size:94 final size:95
Alignment explanation
Indices: 52543730--52543913 Score: 239
Period size: 94 Copynumber: 1.9 Consensus size: 95
52543720 AGGGTTAGTG
* * *
52543730 TTTTAAGTTAAGGGTTATGGTTTTAGGTTTAGAGTTTAGGGTTTTAAATTTTA-AGGTTTA-GGG
1 TTTTAAGTTAAGGGTTATGATTTTAGGTTTAGAGTTTAGGGTTTTAAAGTTTAGA-GTTTATGAG
* *
52543793 TTTTCATGTTTAGGGTTTAGGGTTTAATGTT
65 TTTTCAAGTTTAAGGTTTAGGGTTTAATGTT
* * * *
52543824 TTTTAAGTTAAGGGTTATGA-TTTATGGTTTAGGGTTTAGGTTTTTTAAGTTTAGAGTTTATGAT
1 TTTTAAGTTAAGGGTTATGATTTTA-GGTTTAGAGTTTAGGGTTTTAAAGTTTAGAGTTTATGAG
*
52543888 TTTTTAAGTTTAAGGTTTAGGGTTTA
65 TTTTCAAGTTTAAGGTTTAGGGTTTA
52543914 GGGTTTAGTG
Statistics
Matches: 77, Mismatches: 10, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
93 4 0.05
94 48 0.62
95 25 0.32
ACGTcount: A:0.22, C:0.01, G:0.26, T:0.51
Consensus pattern (95 bp):
TTTTAAGTTAAGGGTTATGATTTTAGGTTTAGAGTTTAGGGTTTTAAAGTTTAGAGTTTATGAGT
TTTCAAGTTTAAGGTTTAGGGTTTAATGTT
Found at i:52543918 original size:14 final size:14
Alignment explanation
Indices: 52543895--52543933 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
52543885 GATTTTTTAA
52543895 GTTTAAGGTTTAGG
1 GTTTAAGGTTTAGG
* *
52543909 GTTTAGGGTTTAGT
1 GTTTAAGGTTTAGG
52543923 GTTTAAGGTTT
1 GTTTAAGGTTT
52543934 TTAAGTTAAG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.18, C:0.00, G:0.33, T:0.49
Consensus pattern (14 bp):
GTTTAAGGTTTAGG
Found at i:52543927 original size:66 final size:65
Alignment explanation
Indices: 52543807--52543940 Score: 173
Period size: 66 Copynumber: 2.0 Consensus size: 65
52543797 CATGTTTAGG
* * *
52543807 GTTTAGGGTTTAATGTTTTTTAAGTTAAGGGTTATGATTTATGGTTTAGGGTTT-AGGTTTTTTA
1 GTTTAGAGTTTAATGTTTTTTAAGTTAAGGGTTAGGATTTAGGGTTTAGGGTTTAAGG-TTTTTA
52543871 A
65 A
* * *
52543872 GTTTAGAGTTT-ATGATTTTTTAAGTTTAAGGTTTAGGGTTTAGGGTTTAGTGTTTAAGGTTTTT
1 GTTTAGAGTTTAATG-TTTTTTAAG-TTAAGGGTTAGGATTTAGGGTTTAGGGTTTAAGGTTTTT
52543936 AA
64 AA
52543938 GTT
1 GTT
52543941 AAGGGTTAAG
Statistics
Matches: 60, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
64 3 0.05
65 19 0.32
66 35 0.58
67 3 0.05
ACGTcount: A:0.22, C:0.00, G:0.26, T:0.52
Consensus pattern (65 bp):
GTTTAGAGTTTAATGTTTTTTAAGTTAAGGGTTAGGATTTAGGGTTTAGGGTTTAAGGTTTTTAA
Found at i:52544005 original size:14 final size:14
Alignment explanation
Indices: 52543986--52544257 Score: 86
Period size: 14 Copynumber: 19.6 Consensus size: 14
52543976 GGGTTAGAAC
52543986 TAGGGTTTAAGGTT
1 TAGGGTTTAAGGTT
* *
52544000 TAGGGTTTATGTTTT
1 TAGGGTTTAAG-GTT
*
52544015 TA-GGTTTAGGGTT
1 TAGGGTTTAAGGTT
52544028 TAGGGTTTTAAGGTTT
1 TAGGG-TTTAAGG-TT
* *
52544044 TAGGGTTTAGGGCT
1 TAGGGTTTAAGGTT
* *
52544058 TATGATTT----TT
1 TAGGGTTTAAGGTT
* *
52544068 TA-AGCTTAAGGTT
1 TAGGGTTTAAGGTT
*
52544081 TAGGGTTTATGGTT
1 TAGGGTTTAAGGTT
*** * *
52544095 TAATATTTATGATTT
1 TAGGGTTTAAG-GTT
52544110 TAGGGTTT-AGAGTT
1 TAGGGTTTAAG-GTT
*
52544124 TAGAGG-TTAAAGTT
1 TAG-GGTTTAAGGTT
*
52544138 TAGTGTTTTTAA-GTT
1 TAG-G-GTTTAAGGTT
* * *
52544153 AAAGG-TT-AGGAT
1 TAGGGTTTAAGGTT
**
52544165 TAGGG-TTAGTATTTT
1 TAGGGTTTA--AGGTT
*
52544180 TA-GGTTTAGGGTT
1 TAGGGTTTAAGGTT
* *
52544193 TAGTGTTTTTAGGTT
1 TAG-GGTTTAAGGTT
*
52544208 TAAGGTTTAAGGTT
1 TAGGGTTTAAGGTT
*
52544222 TAAGGTTT-AGTGTT
1 TAGGGTTTAAG-GTT
*
52544236 TAGGGTTTAAAGTT
1 TAGGGTTTAAGGTT
52544250 TAGGGTTT
1 TAGGGTTT
52544258 TTAAGTTATG
Statistics
Matches: 187, Mismatches: 48, Indels: 46
0.67 0.17 0.16
Matches are distributed among these distances:
9 2 0.01
10 3 0.02
11 1 0.01
12 9 0.05
13 14 0.07
14 99 0.53
15 48 0.26
16 11 0.06
ACGTcount: A:0.22, C:0.01, G:0.29, T:0.48
Consensus pattern (14 bp):
TAGGGTTTAAGGTT
Found at i:52544052 original size:7 final size:7
Alignment explanation
Indices: 52543986--52544055 Score: 70
Period size: 7 Copynumber: 9.7 Consensus size: 7
52543976 GGGTTAGAAC
52543986 TAGGGTT
1 TAGGGTT
*
52543993 TAAGGTT
1 TAGGGTT
52544000 TAGGGTT
1 TAGGGTT
**
52544007 TATGTTTT
1 TA-GGGTT
52544015 TA-GGTT
1 TAGGGTT
52544021 TAGGGTT
1 TAGGGTT
52544028 TAGGGTTT
1 TAGGG-TT
*
52544036 TAAGGTTT
1 T-AGGGTT
52544044 TAGGGTT
1 TAGGGTT
52544051 TAGGG
1 TAGGG
52544056 CTTATGATTT
Statistics
Matches: 51, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
6 4 0.08
7 33 0.65
8 11 0.22
9 3 0.06
ACGTcount: A:0.17, C:0.00, G:0.36, T:0.47
Consensus pattern (7 bp):
TAGGGTT
Found at i:52544194 original size:7 final size:7
Alignment explanation
Indices: 52544178--52544257 Score: 65
Period size: 7 Copynumber: 11.4 Consensus size: 7
52544168 GGTTAGTATT
52544178 TTTA-GG
1 TTTAGGG
52544184 TTTAGGG
1 TTTAGGG
*
52544191 TTTAGTGTT
1 TTTAG-G-G
52544200 TTTA-GG
1 TTTAGGG
*
52544206 TTTAAGG
1 TTTAGGG
*
52544213 TTTAAGG
1 TTTAGGG
*
52544220 TTTAAGG
1 TTTAGGG
*
52544227 TTTAGTG
1 TTTAGGG
52544234 TTTAGGG
1 TTTAGGG
**
52544241 TTTAAAG
1 TTTAGGG
52544248 TTTAGGG
1 TTTAGGG
52544255 TTT
1 TTT
52544258 TTAAGTTATG
Statistics
Matches: 61, Mismatches: 9, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
6 8 0.13
7 48 0.79
8 1 0.02
9 4 0.07
ACGTcount: A:0.20, C:0.00, G:0.30, T:0.50
Consensus pattern (7 bp):
TTTAGGG
Found at i:52544308 original size:22 final size:22
Alignment explanation
Indices: 52544289--52544365 Score: 86
Period size: 22 Copynumber: 3.5 Consensus size: 22
52544279 ATAATTTAGG
52544289 GTTTA-GGTTTTTTAGGTTTAAA
1 GTTTATGG-TTTTTAGGTTTAAA
*
52544311 GTTTATGGTTTTTAAGTTTAAA
1 GTTTATGGTTTTTAGGTTTAAA
* **
52544333 GTTTA-GGGTTTTATGGTTTATG
1 GTTTATGGTTTTTA-GGTTTAAA
52544355 GTTTATGGTTT
1 GTTTATGGTTT
52544366 ATGGTTTTTA
Statistics
Matches: 46, Mismatches: 6, Indels: 5
0.81 0.11 0.09
Matches are distributed among these distances:
21 7 0.15
22 33 0.72
23 6 0.13
ACGTcount: A:0.19, C:0.00, G:0.25, T:0.56
Consensus pattern (22 bp):
GTTTATGGTTTTTAGGTTTAAA
Found at i:52544343 original size:7 final size:7
Alignment explanation
Indices: 52544342--52544372 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
52544332 AGTTTAGGGT
52544342 TTTATGG
1 TTTATGG
52544349 TTTATGG
1 TTTATGG
52544356 TTTATGG
1 TTTATGG
52544363 TTTATGG
1 TTTATGG
52544370 TTT
1 TTT
52544373 TTAAGTTAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.13, C:0.00, G:0.26, T:0.61
Consensus pattern (7 bp):
TTTATGG
Found at i:52544407 original size:33 final size:33
Alignment explanation
Indices: 52544370--52544432 Score: 108
Period size: 33 Copynumber: 1.9 Consensus size: 33
52544360 TGGTTTATGG
* *
52544370 TTTTTAAGTTAAGGGTTAGGATTAGGGTTTGGA
1 TTTTTAAGTTAAAGGTTAGAATTAGGGTTTGGA
52544403 TTTTTAAGTTAAAGGTTAGAATTAGGGTTT
1 TTTTTAAGTTAAAGGTTAGAATTAGGGTTT
52544433 AGGGTTTAGG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.27, C:0.00, G:0.29, T:0.44
Consensus pattern (33 bp):
TTTTTAAGTTAAAGGTTAGAATTAGGGTTTGGA
Found at i:52544439 original size:74 final size:73
Alignment explanation
Indices: 52544354--52544583 Score: 190
Period size: 74 Copynumber: 3.0 Consensus size: 73
52544344 TATGGTTTAT
* *
52544354 GGTTTATGGTTTATGGTTTTTAAGTTAAGGGTTAGGATTAGGGTTTGGATTTTTAAGTTAAAGGT
1 GGTTTAAGGTTTA-GGTTTTTAAGTTAAGGGTTAGGATTAAGGTTTGGATTTTTAAGTTAAAGGT
*
52544419 TAGAATTAG
65 TAGGATTAG
* * * * * * ** ** *
52544428 GGTTTAGGGTTTAGGGTTTTTAGGTTTAGTGTTTAAGGTTTTAAAGTTTAAAGATTTAGGGTTTT
1 GGTTTAAGGTTTA-GGTTTTTAAGTTAAG-GGTT-AGG-ATTAAGGTTTGGATTTTTA-AG--TT
* *
52544493 AAAGTTTAAGGTTTAG
59 AAAGGTT-AGGATTAG
* * * *
52544509 AGTTTAAGGTTTAGAATTTTTAAGTTAAGGGTTAGGATTAAGGTTTGGGTTTTTAAGTTAATGGT
1 GGTTTAAGGTTTAG-GTTTTTAAGTTAAGGGTTAGGATTAAGGTTTGGATTTTTAAGTTAAAGGT
52544574 TAGGATTAG
65 TAGGATTAG
52544583 G
1 G
52544584 ATTAGAGTTT
Statistics
Matches: 114, Mismatches: 34, Indels: 16
0.70 0.21 0.10
Matches are distributed among these distances:
74 32 0.28
75 10 0.09
76 3 0.03
77 13 0.11
78 13 0.11
79 3 0.03
80 12 0.11
81 28 0.25
ACGTcount: A:0.26, C:0.00, G:0.29, T:0.45
Consensus pattern (73 bp):
GGTTTAAGGTTTAGGTTTTTAAGTTAAGGGTTAGGATTAAGGTTTGGATTTTTAAGTTAAAGGTT
AGGATTAG
Found at i:52544454 original size:22 final size:22
Alignment explanation
Indices: 52544428--52544522 Score: 93
Period size: 22 Copynumber: 4.3 Consensus size: 22
52544418 TTAGAATTAG
*
52544428 GGTTTAGGGTTTAGGGTTTTTA
1 GGTTTAGGGTTTAGGGTTTTAA
* *
52544450 GGTTTAGTGTTTAAGGTTTTAA
1 GGTTTAGGGTTTAGGGTTTTAA
* * *
52544472 AGTTTAAAGATTTAGGGTTTTAA
1 GGTTT-AGGGTTTAGGGTTTTAA
* * *
52544495 AGTTTAAGGTTTAGAG-TTTAA
1 GGTTTAGGGTTTAGGGTTTTAA
52544516 GGTTTAG
1 GGTTTAG
52544523 AATTTTTAAG
Statistics
Matches: 60, Mismatches: 12, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
21 10 0.17
22 32 0.53
23 18 0.30
ACGTcount: A:0.25, C:0.00, G:0.28, T:0.46
Consensus pattern (22 bp):
GGTTTAGGGTTTAGGGTTTTAA
Found at i:52544523 original size:14 final size:14
Alignment explanation
Indices: 52544467--52544521 Score: 65
Period size: 14 Copynumber: 3.8 Consensus size: 14
52544457 TGTTTAAGGT
*
52544467 TTTAAAGTTTAAAG
1 TTTAAGGTTTAAAG
*
52544481 ATTTAGGGTTTTAAAG
1 -TTTAAGG-TTTAAAG
*
52544497 TTTAAGGTTTAGAG
1 TTTAAGGTTTAAAG
52544511 TTTAAGGTTTA
1 TTTAAGGTTTA
52544522 GAATTTTTAA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
14 17 0.49
15 11 0.31
16 7 0.20
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.45
Consensus pattern (14 bp):
TTTAAGGTTTAAAG
Found at i:52544562 original size:155 final size:147
Alignment explanation
Indices: 52544283--52544583 Score: 399
Period size: 155 Copynumber: 2.0 Consensus size: 147
52544273 TGATTTATAA
* * *
52544283 TTTAGGGTTTAGGTTTTTTAGGTTTAAAGTTTATGGTTTTTAAGTTTAAAGTTTAGGGTTTTATG
1 TTTAGGGTTTAGGGTTTTTAGGTTTAAAGTTTAAGGTTTTAAAGTTTAAAGTTTAGGGTTTTATG
* * *
52544348 GTTTATGGTTTATGGTTTATGGTTTTTAAGTTAAGGGTTAGGATTAGGGTTTGGATTTTTAAGTT
66 GTTTATGGTTTAAGGTTTATGATTTTTAAGTTAAGGGTTAGGATTAAGGTTTGGATTTTTAAGTT
52544413 AAAGGTTAGAATTAGGG
131 AAAGGTTAGAATTAGGG
**
52544430 TTTAGGGTTTAGGGTTTTTAGGTTTAGTGTTTAAGGTTTTAAAGTTTAAAGATTTAGGGTTTTAA
1 TTTAGGGTTTAGGGTTTTTAGGTTTAAAGTTTAAGGTTTTAAAGTTTAAAG-TTTAGGGTTTT--
*
52544495 AGTTTAAGGTTTA-GAGTTTAAGGTTTA-GAATTTTTAAGTTAAGGGTTAGGATTAAGGTTTGGG
63 A---T--GGTTTATG-GTTTAAGGTTTATG-ATTTTTAAGTTAAGGGTTAGGATTAAGGTTTGGA
* *
52544558 TTTTTAAGTTAATGGTTAGGATTAGG
121 TTTTTAAGTTAAAGGTTAGAATTAGG
52544584 ATTAGAGTTT
Statistics
Matches: 133, Mismatches: 11, Indels: 12
0.85 0.07 0.08
Matches are distributed among these distances:
147 46 0.35
148 11 0.08
150 1 0.01
153 1 0.01
154 2 0.02
155 72 0.54
ACGTcount: A:0.25, C:0.00, G:0.28, T:0.47
Consensus pattern (147 bp):
TTTAGGGTTTAGGGTTTTTAGGTTTAAAGTTTAAGGTTTTAAAGTTTAAAGTTTAGGGTTTTATG
GTTTATGGTTTAAGGTTTATGATTTTTAAGTTAAGGGTTAGGATTAAGGTTTGGATTTTTAAGTT
AAAGGTTAGAATTAGGG
Found at i:52544566 original size:33 final size:33
Alignment explanation
Indices: 52544488--52544608 Score: 127
Period size: 33 Copynumber: 3.6 Consensus size: 33
52544478 AAGATTTAGG
* * *
52544488 GTTTTAAAGTTTAAGGTTTAGAGTTTAAGGTTTAGA
1 GTTTTTAAG-TTAAGGGTTAG-GATTAAGGTTT-GA
* *
52544524 ATTTTTAAGTTAAGGGTTAGGATTAAGGTTTGG
1 GTTTTTAAGTTAAGGGTTAGGATTAAGGTTTGA
* *
52544557 GTTTTTAAGTTAATGGTTAGGATT-AGGATTAGA
1 GTTTTTAAGTTAAGGGTTAGGATTAAGG-TTTGA
*
52544590 GTTTTTAAGTTTAGGGTTA
1 GTTTTTAAGTTAAGGGTTA
52544609 TGGTTTTTTG
Statistics
Matches: 73, Mismatches: 11, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
32 3 0.04
33 43 0.59
34 10 0.14
35 10 0.14
36 7 0.10
ACGTcount: A:0.28, C:0.00, G:0.27, T:0.45
Consensus pattern (33 bp):
GTTTTTAAGTTAAGGGTTAGGATTAAGGTTTGA
Found at i:52544614 original size:21 final size:22
Alignment explanation
Indices: 52544585--52544640 Score: 60
Period size: 21 Copynumber: 2.6 Consensus size: 22
52544575 AGGATTAGGA
*
52544585 TTAGAGTTTTTAAGTTT-AGGG
1 TTAGGGTTTTTAAGTTTAAGGG
* ** *
52544606 TTATGGTTTTTTGGTTTAAGGT
1 TTAGGGTTTTTAAGTTTAAGGG
52544628 TTAGGGTTTTTAA
1 TTAGGGTTTTTAA
52544641 TTATAGAGTT
Statistics
Matches: 26, Mismatches: 8, Indels: 1
0.74 0.23 0.03
Matches are distributed among these distances:
21 13 0.50
22 13 0.50
ACGTcount: A:0.20, C:0.00, G:0.27, T:0.54
Consensus pattern (22 bp):
TTAGGGTTTTTAAGTTTAAGGG
Found at i:52544675 original size:225 final size:224
Alignment explanation
Indices: 52544444--52544853 Score: 594
Period size: 225 Copynumber: 1.8 Consensus size: 224
52544434 GGGTTTAGGG
* * *
52544444 TTTTTAGGTTT-AGTGTTTAAGGTTTTAAAGTT-TAAAGATTTAGGGTTTTAAAGTTTAAGGTTT
1 TTTTTAGGTTTAAG-GTTTAAGGTTTTAAAATTCAAAAG-TTTAGGG-TTTAAAGTTTAAAGTTT
* *
52544507 AGAG-TTTAAGGTTTAGAATTTTTAAGTTAAGGGTTAGGATTAAGGTTTGGGTTTTTAAG-TTAA
63 AGAGTTTTAAGGTTTAGAATTTTTAAGTTAAAGGTTAGGATTAAGGTTAGGGTTTTTAAGTTTAA
* * * *
52544570 TGGTTAGGATTAGGATTAGAGTTTTTAAGTTTAGGGTTATGGTTTTTTGGTTTAAGGTTTAGGGT
128 -GATTAGG-GTAGGATTAGAGTTTTTAAGTTAAGGGTTATGGTTTTTAGGTTTAAGGTTTAGGGT
52544635 TTTTAATTATAGAGTTTAGTGTTTAGTGTTTAAT
191 TTTTAATTATAGAGTTTAGTGTTTAGTGTTTAAT
** *
52544669 TTTTTAGGTTTAAGGTTTGGGGTTTTAAAATTCAAAAGTTTAGGGTTTAAGGTTTAAAGTTTAGA
1 TTTTTAGGTTTAAGGTTTAAGGTTTTAAAATTCAAAAGTTTAGGGTTTAAAGTTTAAAGTTTAGA
** *
52544734 GTTTTAAGGTTTAGTGTTTTTAAGTTAAAGGTTAGGATTAGGGTTAGGGTTTTTAAGTTTAAGAT
66 GTTTTAAGGTTTAGAATTTTTAAGTTAAAGGTTAGGATTAAGGTTAGGGTTTTTAAGTTTAAGAT
* *
52544799 TAGGGTAGGATTAGGGTTTTTAAGTTAAGGGTTATGGTTTTTAGGTTTAGGGTTT
131 TAGGGTAGGATTAGAGTTTTTAAGTTAAGGGTTATGGTTTTTAGGTTTAAGGTTT
52544854 TAAATTTTAT
Statistics
Matches: 164, Mismatches: 17, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
224 65 0.40
225 89 0.54
226 10 0.06
ACGTcount: A:0.26, C:0.00, G:0.27, T:0.47
Consensus pattern (224 bp):
TTTTTAGGTTTAAGGTTTAAGGTTTTAAAATTCAAAAGTTTAGGGTTTAAAGTTTAAAGTTTAGA
GTTTTAAGGTTTAGAATTTTTAAGTTAAAGGTTAGGATTAAGGTTAGGGTTTTTAAGTTTAAGAT
TAGGGTAGGATTAGAGTTTTTAAGTTAAGGGTTATGGTTTTTAGGTTTAAGGTTTAGGGTTTTTA
ATTATAGAGTTTAGTGTTTAGTGTTTAAT
Found at i:52544739 original size:22 final size:21
Alignment explanation
Indices: 52544703--52544746 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 21
52544693 TTAAAATTCA
52544703 AAAGTTTAGGGTTTAAGGTTT
1 AAAGTTTAGGGTTTAAGGTTT
*
52544724 AAAGTTTAGAGTTTTAAGGTTT
1 AAAGTTTAG-GGTTTAAGGTTT
52544746 A
1 A
52544747 GTGTTTTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 9 0.43
22 12 0.57
ACGTcount: A:0.32, C:0.00, G:0.25, T:0.43
Consensus pattern (21 bp):
AAAGTTTAGGGTTTAAGGTTT
Found at i:52544757 original size:16 final size:15
Alignment explanation
Indices: 52544707--52544753 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 15
52544697 AATTCAAAAG
* *
52544707 TTTAGGGTTTA-AGG
1 TTTAAGGTTTAGAGT
*
52544721 TTTAAAGTTTAGAGT
1 TTTAAGGTTTAGAGT
*
52544736 TTTAAGGTTTAGTGT
1 TTTAAGGTTTAGAGT
52544751 TTT
1 TTT
52544754 TAAGTTAAAG
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
14 9 0.33
15 18 0.67
ACGTcount: A:0.23, C:0.00, G:0.26, T:0.51
Consensus pattern (15 bp):
TTTAAGGTTTAGAGT
Found at i:52544787 original size:33 final size:32
Alignment explanation
Indices: 52544744--52544832 Score: 115
Period size: 32 Copynumber: 2.8 Consensus size: 32
52544734 GTTTTAAGGT
* * *
52544744 TTAGTGTTTTTAAGTTAAAGGTTAGGATTAGGG
1 TTAGGGTTTTTAAGTTAAAGGTTAGG-GTAGGA
* *
52544777 TTAGGGTTTTTAAGTTTAAGATTAGGGTAGGA
1 TTAGGGTTTTTAAGTTAAAGGTTAGGGTAGGA
*
52544809 TTAGGGTTTTTAAGTTAAGGGTTA
1 TTAGGGTTTTTAAGTTAAAGGTTA
52544833 TGGTTTTTAG
Statistics
Matches: 48, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
32 25 0.52
33 23 0.48
ACGTcount: A:0.27, C:0.00, G:0.30, T:0.43
Consensus pattern (32 bp):
TTAGGGTTTTTAAGTTAAAGGTTAGGGTAGGA
Found at i:52544818 original size:32 final size:33
Alignment explanation
Indices: 52544744--52544826 Score: 114
Period size: 33 Copynumber: 2.5 Consensus size: 33
52544734 GTTTTAAGGT
* * * *
52544744 TTAGTGTTTTTAAGTTAAAGGTTAGGATTAGGG
1 TTAGGGTTTTTAAGTTAAAGATTAGGAGTAGGA
*
52544777 TTAGGGTTTTTAAGTTTAAGATTAGG-GTAGGA
1 TTAGGGTTTTTAAGTTAAAGATTAGGAGTAGGA
52544809 TTAGGGTTTTTAAGTTAA
1 TTAGGGTTTTTAAGTTAA
52544827 GGGTTATGGT
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
32 21 0.48
33 23 0.52
ACGTcount: A:0.28, C:0.00, G:0.29, T:0.43
Consensus pattern (33 bp):
TTAGGGTTTTTAAGTTAAAGATTAGGAGTAGGA
Found at i:52544837 original size:21 final size:21
Alignment explanation
Indices: 52544813--52544852 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
52544803 GTAGGATTAG
52544813 GGTTTTTAAGTTAAGGGTTAT
1 GGTTTTTAAGTTAAGGGTTAT
* *
52544834 GGTTTTTAGGTTTAGGGTT
1 GGTTTTTAAGTTAAGGGTT
52544853 TTAAATTTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.17, C:0.00, G:0.33, T:0.50
Consensus pattern (21 bp):
GGTTTTTAAGTTAAGGGTTAT
Found at i:52544861 original size:22 final size:22
Alignment explanation
Indices: 52544836--52544916 Score: 85
Period size: 22 Copynumber: 3.6 Consensus size: 22
52544826 AGGGTTATGG
52544836 TTTTTAGGTTTAGGGTTTTAAA
1 TTTTTAGGTTTAGGGTTTTAAA
*
52544858 -TTTTATGGTTTAGGGTTTTTAA
1 TTTTTA-GGTTTAGGGTTTTAAA
* * *
52544880 TGTTTAGTGTTTAAGG-TTTAAGG
1 TTTTTAG-GTTTAGGGTTTTAA-A
52544903 TTTTTAGGTTTAGG
1 TTTTTAGGTTTAGG
52544917 TTTAGTATTT
Statistics
Matches: 48, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
21 5 0.10
22 26 0.54
23 17 0.35
ACGTcount: A:0.20, C:0.00, G:0.26, T:0.54
Consensus pattern (22 bp):
TTTTTAGGTTTAGGGTTTTAAA
Found at i:52544885 original size:7 final size:7
Alignment explanation
Indices: 52544875--52545096 Score: 57
Period size: 7 Copynumber: 31.4 Consensus size: 7
52544865 GTTTAGGGTT
*
52544875 TTTAATG
1 TTTAAGG
52544882 TTT-AGTG
1 TTTAAG-G
52544889 TTTAAGG
1 TTTAAGG
52544896 TTTAAGG
1 TTTAAGG
*
52544903 TTTTTAGG
1 -TTTAAGG
52544911 TTT-AGG
1 TTTAAGG
*
52544917 TTT-AGTA
1 TTTAAG-G
*
52544924 TTTAGGG
1 TTTAAGG
*
52544931 TTTAAAG
1 TTTAAGG
*
52544938 TTTAGGG
1 TTTAAGG
*
52544945 TTTAGGG
1 TTTAAGG
*
52544952 TTTAGAGTT
1 TTTA-AG-G
52544961 TTTAA-G
1 TTTAAGG
*
52544967 -TTAGGG
1 TTTAAGG
**
52544973 TTTACTG
1 TTTAAGG
*
52544980 TTTAA-A
1 TTTAAGG
* *
52544986 TGTTATGT
1 T-TTAAGG
*
52544994 TTTTAGG
1 TTTAAGG
*
52545001 TTTAGGG
1 TTTAAGG
*
52545008 TTTAGGG
1 TTTAAGG
*
52545015 TTTTAAAG
1 -TTTAAGG
52545023 TTTAAGAG
1 TTTAAG-G
*
52545031 TTTAA-A
1 TTTAAGG
52545037 TTT-AGTG
1 TTTAAG-G
* *
52545044 TTTATGA
1 TTTAAGG
*
52545051 TTTAGGG
1 TTTAAGG
*
52545058 TTTTATGG
1 -TTTAAGG
52545066 TTT-AGAG
1 TTTAAG-G
*
52545073 TTTATGG
1 TTTAAGG
52545080 TTTAAGG
1 TTTAAGG
*
52545087 TTTAGGG
1 TTTAAGG
52545094 TTT
1 TTT
52545097 TTTAGTTAAG
Statistics
Matches: 158, Mismatches: 38, Indels: 38
0.68 0.16 0.16
Matches are distributed among these distances:
5 4 0.03
6 15 0.09
7 104 0.66
8 31 0.20
9 4 0.03
ACGTcount: A:0.23, C:0.00, G:0.27, T:0.50
Consensus pattern (7 bp):
TTTAAGG
Found at i:52544940 original size:21 final size:21
Alignment explanation
Indices: 52544882--52544961 Score: 65
Period size: 21 Copynumber: 3.8 Consensus size: 21
52544872 GTTTTTAATG
* * *
52544882 TTTAGTGTTTAAGGTTTAAGGTT
1 TTTAGGGTTTAAAGTTT-A-GTA
*
52544905 TTTA-GGTTT-AGGTTTAGTA
1 TTTAGGGTTTAAAGTTTAGTA
**
52544924 TTTAGGGTTTAAAGTTTAGGG
1 TTTAGGGTTTAAAGTTTAGTA
*
52544945 TTTAGGGTTTAGAGTTT
1 TTTAGGGTTTAAAGTTT
52544962 TTAAGTTAGG
Statistics
Matches: 49, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
19 6 0.12
20 6 0.12
21 29 0.59
22 4 0.08
23 4 0.08
ACGTcount: A:0.21, C:0.00, G:0.29, T:0.50
Consensus pattern (21 bp):
TTTAGGGTTTAAAGTTTAGTA
Found at i:52545064 original size:15 final size:15
Alignment explanation
Indices: 52545044--52545089 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
52545034 AAATTTAGTG
*
52545044 TTTATGATTTAGGGT
1 TTTATGGTTTAGGGT
*
52545059 TTTATGGTTTAGAG-
1 TTTATGGTTTAGGGT
*
52545073 TTTATGGTTTAAGGT
1 TTTATGGTTTAGGGT
52545088 TT
1 TT
52545090 AGGGTTTTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
14 12 0.46
15 14 0.54
ACGTcount: A:0.20, C:0.00, G:0.26, T:0.54
Consensus pattern (15 bp):
TTTATGGTTTAGGGT
Found at i:52545089 original size:14 final size:14
Alignment explanation
Indices: 52544823--52545096 Score: 57
Period size: 14 Copynumber: 19.1 Consensus size: 14
52544813 GGTTTTTAAG
*
52544823 TTAAGGGTTATGGTT
1 TTAAGGTTTATGG-T
* *
52544838 TTTAGGTTTAGGGTT
1 TTAAGGTTTATGG-T
**
52544853 TTAAATTTTATGGT
1 TTAAGGTTTATGGT
*
52544867 TTAGGGTTTTTAAT-GT
1 TTAAGG--TTT-ATGGT
*
52544883 TT-AGTGTTTAAGGT
1 TTAAG-GTTTATGGT
*
52544897 TTAAGGTTTTTAGGT
1 TTAAGGTTTAT-GGT
*
52544912 TT-AGGTTTA-GTAT
1 TTAAGGTTTATG-GT
* **
52544925 TTAGGGTTTAAAGT
1 TTAAGGTTTATGGT
* *
52544939 TTAGGGTTTAGGGT
1 TTAAGGTTTATGGT
* *
52544953 TT-AGAGTTTTTAAG-
1 TTAAG-GTTTAT-GGT
*
52544967 TTAGGGTTTACT-GT
1 TTAAGGTTTA-TGGT
* *
52544981 TTAA-ATGTTATGTT
1 TTAAGGT-TTATGGT
* *
52544995 TTTAGGTTTAGGGT
1 TTAAGGTTTATGGT
* **
52545009 TTAGGGTTTTAAAGT
1 TTAAGG-TTTATGGT
**
52545024 TTAAGAGTTTA-AAT
1 TTAAG-GTTTATGGT
*
52545038 TT-AGTGTTTATGAT
1 TTAAG-GTTTATGGT
*
52545052 TTAGGGTTTTATGGT
1 TTAAGG-TTTATGGT
52545067 TT-AGAGTTTATGGT
1 TTAAG-GTTTATGGT
*
52545081 TTAAGGTTTAGGGT
1 TTAAGGTTTATGGT
52545095 TT
1 TT
52545097 TTTAGTTAAG
Statistics
Matches: 188, Mismatches: 46, Indels: 51
0.66 0.16 0.18
Matches are distributed among these distances:
12 1 0.01
13 15 0.08
14 101 0.54
15 60 0.32
16 9 0.05
17 2 0.01
ACGTcount: A:0.22, C:0.00, G:0.27, T:0.51
Consensus pattern (14 bp):
TTAAGGTTTATGGT
Found at i:52545123 original size:27 final size:27
Alignment explanation
Indices: 52545088--52545149 Score: 106
Period size: 27 Copynumber: 2.3 Consensus size: 27
52545078 GGTTTAAGGT
* *
52545088 TTAGGGTTTTTTAGTTAAGGGTTAGGG
1 TTAGGGTTTTTTAGTGAAGGGTTAGGA
52545115 TTAGGGTTTTTTAGTGAAGGGTTAGGA
1 TTAGGGTTTTTTAGTGAAGGGTTAGGA
52545142 TTAGGGTT
1 TTAGGGTT
52545150 AGTGTTTTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.19, C:0.00, G:0.37, T:0.44
Consensus pattern (27 bp):
TTAGGGTTTTTTAGTGAAGGGTTAGGA
Done.