Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr1
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: 96304692
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2448173 characters in sequence are not A, C, G, or T
File 11 of 313
Found at i:3566004 original size:21 final size:22
Alignment explanation
Indices: 3565978--3566019 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
3565968 GCACTTTTTA
3565978 AAAATTTA-AAAA-ATTATAAAC
1 AAAATTTATAAAACATT-TAAAC
3565999 AAAATTTATAAAACATTTAAA
1 AAAATTTATAAAACATTTAAA
3566020 ATTATAATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 8 0.42
22 8 0.42
23 3 0.16
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.31
Consensus pattern (22 bp):
AAAATTTATAAAACATTTAAAC
Found at i:3575762 original size:32 final size:32
Alignment explanation
Indices: 3575721--3575782 Score: 115
Period size: 32 Copynumber: 1.9 Consensus size: 32
3575711 CATCTATTTT
3575721 CATTGTTCAACTCTTTGACAACACGAAAAATC
1 CATTGTTCAACTCTTTGACAACACGAAAAATC
*
3575753 CATTGTTCAACTCTTTGACAACATGAAAAA
1 CATTGTTCAACTCTTTGACAACACGAAAAA
3575783 ACCAAAAGCT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.39, C:0.23, G:0.10, T:0.29
Consensus pattern (32 bp):
CATTGTTCAACTCTTTGACAACACGAAAAATC
Found at i:3577564 original size:5 final size:5
Alignment explanation
Indices: 3577554--3577582 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
3577544 GGGAGAGTTC
3577554 TTTCT TTTCT TTTCT TTTCT TTT-T TTTCT
1 TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT
3577583 AAATGGAAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.17
5 19 0.83
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (5 bp):
TTTCT
Found at i:3579610 original size:30 final size:31
Alignment explanation
Indices: 3579566--3579628 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 31
3579556 ATGATATTAA
3579566 CAATTTATGAAAATTAAATCAAA-AAAAAATT
1 CAATTTATGAAAATTAAA-CAAATAAAAAATT
* **
3579597 CAATTT-TTAAAATTGTACAAATAAAAAATT
1 CAATTTATGAAAATTAAACAAATAAAAAATT
3579627 CA
1 CA
3579629 TAACATTTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
29 4 0.14
30 18 0.64
31 6 0.21
ACGTcount: A:0.57, C:0.08, G:0.03, T:0.32
Consensus pattern (31 bp):
CAATTTATGAAAATTAAACAAATAAAAAATT
Found at i:3584537 original size:12 final size:12
Alignment explanation
Indices: 3584520--3584549 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
3584510 AAAACATAAT
3584520 TTGAAATATTTA
1 TTGAAATATTTA
3584532 TTGAAATATTTA
1 TTGAAATATTTA
3584544 TTGAAA
1 TTGAAA
3584550 GAAATTAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.43, C:0.00, G:0.10, T:0.47
Consensus pattern (12 bp):
TTGAAATATTTA
Found at i:3584709 original size:20 final size:19
Alignment explanation
Indices: 3584684--3584727 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
3584674 TGGAGAATGA
3584684 TTTCTGAAAAATGATTTACT
1 TTTCTG-AAAATGATTTACT
*
3584704 TTTCTGGAAATGATTTACT
1 TTTCTGAAAATGATTTACT
3584723 TTTCT
1 TTTCT
3584728 AGTGTTTGGA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 17 0.74
20 6 0.26
ACGTcount: A:0.27, C:0.11, G:0.11, T:0.50
Consensus pattern (19 bp):
TTTCTGAAAATGATTTACT
Found at i:3585885 original size:23 final size:24
Alignment explanation
Indices: 3585859--3585908 Score: 93
Period size: 23 Copynumber: 2.1 Consensus size: 24
3585849 AATATTGTGA
3585859 TTTAACTCTTAAT-TTTATAAAAT
1 TTTAACTCTTAATATTTATAAAAT
3585882 TTTAACTCTTAATATTTATAAAAT
1 TTTAACTCTTAATATTTATAAAAT
3585906 TTT
1 TTT
3585909 CTTTCCCTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 13 0.50
24 13 0.50
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (24 bp):
TTTAACTCTTAATATTTATAAAAT
Found at i:3589744 original size:14 final size:14
Alignment explanation
Indices: 3589725--3589751 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
3589715 AGAAAAGCCT
3589725 GAAAAGCTTTTACG
1 GAAAAGCTTTTACG
3589739 GAAAAGCTTTTAC
1 GAAAAGCTTTTAC
3589752 AGGTTACCAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.15, G:0.19, T:0.30
Consensus pattern (14 bp):
GAAAAGCTTTTACG
Found at i:3592017 original size:20 final size:19
Alignment explanation
Indices: 3591976--3592018 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
3591966 AAAAAAATAA
** *
3591976 TTAAAAATCATAAATTTTT
1 TTAAAAATCATAAAAATCT
3591995 TTAAAAATTCATAAAAATCT
1 TTAAAAA-TCATAAAAATCT
3592015 TTAA
1 TTAA
3592019 GGGTAAAGTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.51, C:0.07, G:0.00, T:0.42
Consensus pattern (19 bp):
TTAAAAATCATAAAAATCT
Found at i:3595169 original size:34 final size:34
Alignment explanation
Indices: 3595126--3595193 Score: 109
Period size: 34 Copynumber: 2.0 Consensus size: 34
3595116 TCAATTGAAA
* * *
3595126 AAGTTGGAAATATCAAATGTCATGGCCTTGACTT
1 AAGTTGGAAATATCAAATGCCATGACATTGACTT
3595160 AAGTTGGAAATATCAAATGCCATGACATTGACTT
1 AAGTTGGAAATATCAAATGCCATGACATTGACTT
3595194 GCAATCTCTC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.35, C:0.15, G:0.19, T:0.31
Consensus pattern (34 bp):
AAGTTGGAAATATCAAATGCCATGACATTGACTT
Found at i:3595517 original size:22 final size:23
Alignment explanation
Indices: 3595492--3595534 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
3595482 GGTCGATGAG
*
3595492 AAAAAATAAATAT-AAATTATAA
1 AAAAAATAAACATAAAATTATAA
*
3595514 AAAAAGTAAACATAAAATTAT
1 AAAAAATAAACATAAAATTAT
3595535 TTTAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 11 0.61
23 7 0.39
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.26
Consensus pattern (23 bp):
AAAAAATAAACATAAAATTATAA
Found at i:3595531 original size:23 final size:21
Alignment explanation
Indices: 3595492--3595534 Score: 59
Period size: 23 Copynumber: 2.0 Consensus size: 21
3595482 GGTCGATGAG
*
3595492 AAAAAATAAATATAAATTATA
1 AAAAAATAAACATAAATTATA
3595513 AAAAAAGTAAACATAAAATTAT
1 AAAAAA-TAAACAT-AAATTAT
3595535 TTTAAATATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 6 0.32
22 6 0.32
23 7 0.37
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.26
Consensus pattern (21 bp):
AAAAAATAAACATAAATTATA
Found at i:3595565 original size:20 final size:20
Alignment explanation
Indices: 3595528--3595575 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
3595518 AGTAAACATA
3595528 AAATTATTTTAAATATTTTT
1 AAATTATTTTAAATATTTTT
*
3595548 AAATATATTTTATA-ATTTTT
1 AAAT-TATTTTAAATATTTTT
3595568 AGAATTAT
1 A-AATTAT
3595576 AATTAAAATG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
20 14 0.56
21 11 0.44
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (20 bp):
AAATTATTTTAAATATTTTT
Found at i:3599050 original size:56 final size:56
Alignment explanation
Indices: 3598989--3599099 Score: 143
Period size: 56 Copynumber: 2.0 Consensus size: 56
3598979 TTTTAAAATT
* * * *
3598989 TTATAACTTTTATTACTCAG-GGTTTGTTTAGGGTTACACACAAAATTAATGAAAAA
1 TTATAACCTCTATTACT-AGCGGTTTGCTTAAGGTTACACACAAAATTAATGAAAAA
* * *
3599045 TTATAACCTCTGTTGCTTGCGGTTTGCTTAAGGTTACACACAAAATTAATGAAAA
1 TTATAACCTCTATTACTAGCGGTTTGCTTAAGGTTACACACAAAATTAATGAAAA
3599100 TAATTATAGC
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
55 1 0.02
56 46 0.98
ACGTcount: A:0.35, C:0.14, G:0.15, T:0.36
Consensus pattern (56 bp):
TTATAACCTCTATTACTAGCGGTTTGCTTAAGGTTACACACAAAATTAATGAAAAA
Found at i:3602701 original size:30 final size:30
Alignment explanation
Indices: 3602667--3602727 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
3602657 TCCTTAACTC
3602667 AAACTTTGGAAAAATTACAATTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
* * * * *
3602697 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
3602727 A
1 A
3602728 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (30 bp):
AAACTTTGGAAAAATTACAATTTTGCCCCT
Found at i:3605262 original size:13 final size:13
Alignment explanation
Indices: 3605230--3605267 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
3605220 CAGTTAATTA
3605230 AATTAT-TTAATTT
1 AATTATATT-ATTT
3605243 AATTTATATTATTT
1 AA-TTATATTATTT
3605257 AATTATATTAT
1 AATTATATTAT
3605268 ACATTTTGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 11 0.48
14 10 0.43
15 2 0.09
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (13 bp):
AATTATATTATTT
Found at i:3607239 original size:18 final size:18
Alignment explanation
Indices: 3607216--3607255 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
3607206 AATAAAAAAG
3607216 TAAAAAAATAAGAAATAT
1 TAAAAAAATAAGAAATAT
* *
3607234 TAAAAAGATAATAAATAT
1 TAAAAAAATAAGAAATAT
3607252 TAAA
1 TAAA
3607256 CATTTATTGC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.70, C:0.00, G:0.05, T:0.25
Consensus pattern (18 bp):
TAAAAAAATAAGAAATAT
Found at i:3610256 original size:27 final size:27
Alignment explanation
Indices: 3610225--3610402 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
3610215 TAAATTGTAC
3610225 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
3610252 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
3610278 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
3610306 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
3610334 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
3610361 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
3610388 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
3610403 GACTCAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:3610339 original size:82 final size:81
Alignment explanation
Indices: 3610226--3610381 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
3610216 AAATTGTACA
* *
3610226 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
3610290 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
3610307 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
3610372 TGCGAGTTGA
65 TGCGAATTGA
3610382 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:3610393 original size:82 final size:81
Alignment explanation
Indices: 3610222--3610402 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
3610212 GATTAAATTG
* *
3610222 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
3610287 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
3610303 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
3610367 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
3610385 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
3610403 GACTCAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:3618319 original size:27 final size:27
Alignment explanation
Indices: 3618288--3618465 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
3618278 TAAATTGTAC
3618288 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
3618315 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
3618341 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
3618369 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
3618397 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
3618424 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
3618451 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
3618466 GACTCAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:3618402 original size:82 final size:81
Alignment explanation
Indices: 3618289--3618444 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
3618279 AAATTGTACA
* *
3618289 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
3618353 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
3618370 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
3618435 TGCGAGTTGA
65 TGCGAATTGA
3618445 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:3618456 original size:82 final size:81
Alignment explanation
Indices: 3618285--3618465 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
3618275 GATTAAATTG
* *
3618285 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
3618350 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
3618366 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
3618430 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
3618448 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
3618466 GACTCAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:3626382 original size:27 final size:27
Alignment explanation
Indices: 3626351--3626528 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
3626341 TAAATTGTAC
3626351 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
3626378 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
3626404 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
3626432 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
3626460 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
3626487 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
3626514 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
3626529 GACTCAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:3626465 original size:82 final size:81
Alignment explanation
Indices: 3626352--3626507 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
3626342 AAATTGTACA
* *
3626352 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
3626416 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
3626433 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
3626498 TGCGAGTTGA
65 TGCGAATTGA
3626508 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:3626519 original size:82 final size:81
Alignment explanation
Indices: 3626348--3626528 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
3626338 GATTAAATTG
* *
3626348 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
3626413 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
3626429 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
3626493 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
3626511 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
3626529 GACTCAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:3628191 original size:14 final size:14
Alignment explanation
Indices: 3628153--3628195 Score: 54
Period size: 13 Copynumber: 3.1 Consensus size: 14
3628143 CAAAATTTAC
3628153 AATATAATTAAA-T
1 AATATAATTAAATT
3628166 AATATAAATTAAATT
1 AATAT-AATTAAATT
*
3628181 AA-ATAATTTAATT
1 AATATAATTAAATT
3628194 AA
1 AA
3628196 CTGTTTACCT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
13 15 0.56
14 9 0.33
15 3 0.11
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (14 bp):
AATATAATTAAATT
Found at i:3638987 original size:21 final size:21
Alignment explanation
Indices: 3638963--3639005 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
3638953 CTCCTCTTTT
3638963 TGTCTATTTTCTTTGTGTTGC
1 TGTCTATTTTCTTTGTGTTGC
3638984 TGTCTATTTTCTTTGTGTTGC
1 TGTCTATTTTCTTTGTGTTGC
3639005 T
1 T
3639006 TTCTTTCAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.05, C:0.14, G:0.19, T:0.63
Consensus pattern (21 bp):
TGTCTATTTTCTTTGTGTTGC
Found at i:3642491 original size:6 final size:6
Alignment explanation
Indices: 3642475--3642512 Score: 51
Period size: 6 Copynumber: 6.3 Consensus size: 6
3642465 TGAGTATTGG
*
3642475 TTTTAT TTTTTT ATTTTAT TTTTAT TTTTA- TTTTAT TT
1 TTTTAT TTTTAT -TTTTAT TTTTAT TTTTAT TTTTAT TT
3642513 GGTTAAGTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
5 5 0.18
6 18 0.64
7 5 0.18
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTTAT
Found at i:3653649 original size:27 final size:27
Alignment explanation
Indices: 3653619--3653790 Score: 245
Period size: 27 Copynumber: 6.4 Consensus size: 27
3653609 ATACTAGACC
* *
3653619 CCCTTATGTGATAAAATAACTATTTTG
1 CCCTTATGTGGTAAAATGACTATTTTG
* * *
3653646 CCCTTATATAGTAAAATGACTGTTTTG
1 CCCTTATGTGGTAAAATGACTATTTTG
* *
3653673 CCCTCATGTGGTAAAATGACTATTTTA
1 CCCTTATGTGGTAAAATGACTATTTTG
* *
3653700 CCCTTATATGGTAAAATGACTGTTTTG
1 CCCTTATGTGGTAAAATGACTATTTTG
*
3653727 CCCTCATGTGGTAAAATGACTATTTTG
1 CCCTTATGTGGTAAAATGACTATTTTG
3653754 CCCTTATGTGGTAAAATGACTATTTTG
1 CCCTTATGTGGTAAAATGACTATTTTG
*
3653781 CCCCTATGTG
1 CCCTTATGTG
3653791 ATATATGTTT
Statistics
Matches: 126, Mismatches: 19, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 126 1.00
ACGTcount: A:0.27, C:0.17, G:0.16, T:0.39
Consensus pattern (27 bp):
CCCTTATGTGGTAAAATGACTATTTTG
Found at i:3656591 original size:22 final size:22
Alignment explanation
Indices: 3656566--3656609 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
3656556 TAGTCATATA
3656566 ATAAATTATTAATATAATAAAT
1 ATAAATTATTAATATAATAAAT
* * *
3656588 ATAATTTATTATTTTAATAAAT
1 ATAAATTATTAATATAATAAAT
3656610 TATTTAATAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
ATAAATTATTAATATAATAAAT
Found at i:3656645 original size:13 final size:14
Alignment explanation
Indices: 3656629--3656670 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 14
3656619 TTTCAATTTT
3656629 ATTTTAATAATA-A
1 ATTTTAATAATATA
*
3656642 ATTTTAAAAATAATA
1 ATTTTAATAAT-ATA
3656657 ATTTTAAATAATAT
1 ATTTT-AATAATAT
3656671 TATTCACATA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
13 10 0.42
14 1 0.04
15 8 0.33
16 5 0.21
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
ATTTTAATAATATA
Found at i:3656655 original size:16 final size:16
Alignment explanation
Indices: 3656633--3656669 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
3656623 AATTTTATTT
3656633 TAATAATAAATTTTAAA
1 TAATAAT-AATTTTAAA
3656650 -AATAATAATTTTAAA
1 TAATAATAATTTTAAA
3656665 TAATA
1 TAATA
3656670 TTATTCACAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TAATAATAATTTTAAA
Found at i:3659073 original size:20 final size:19
Alignment explanation
Indices: 3659039--3659078 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
3659029 CATTTCAATT
*
3659039 TCATTTATCATTTCACATG
1 TCATTTATCAATTCACATG
*
3659058 TCATTTAATCAATTCATATG
1 TCATTT-ATCAATTCACATG
3659078 T
1 T
3659079 TTATAACCCT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.30, C:0.17, G:0.05, T:0.47
Consensus pattern (19 bp):
TCATTTATCAATTCACATG
Found at i:3660463 original size:63 final size:63
Alignment explanation
Indices: 3660354--3660472 Score: 177
Period size: 63 Copynumber: 1.9 Consensus size: 63
3660344 CAAGTTGTGA
* * *
3660354 AACTCACTGTTTGTGATTTAGGGTCACATGAGGTAGGGACATGGGCGTGTGTCCAGACTGTTT
1 AACTCACTATTTGTGATTTAGGGTCACATGAGGTAGAGACACGGGCGTGTGTCCAGACTGTTT
* *
3660417 AACTCACTATTTGTGATTTAGTGTCACATG-GGTCATAGACACGGGCGTGTGTCCAG
1 AACTCACTATTTGTGATTTAGGGTCACATGAGGT-AGAGACACGGGCGTGTGTCCAG
3660473 GTTGTGTGAG
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
62 3 0.06
63 47 0.94
ACGTcount: A:0.22, C:0.18, G:0.29, T:0.31
Consensus pattern (63 bp):
AACTCACTATTTGTGATTTAGGGTCACATGAGGTAGAGACACGGGCGTGTGTCCAGACTGTTT
Found at i:3661626 original size:22 final size:21
Alignment explanation
Indices: 3661578--3661628 Score: 57
Period size: 22 Copynumber: 2.4 Consensus size: 21
3661568 ATAAACTATT
3661578 ACTATTTTAGGGAAAAATAAC
1 ACTATTTTAGGGAAAAATAAC
* * * *
3661599 AATATTTTAGAGTAACAATATC
1 ACTATTTTAG-GGAAAAATAAC
3661621 ACTATTTT
1 ACTATTTT
3661629 CGCCTGGAGG
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
21 9 0.38
22 15 0.62
ACGTcount: A:0.43, C:0.10, G:0.10, T:0.37
Consensus pattern (21 bp):
ACTATTTTAGGGAAAAATAAC
Found at i:3662500 original size:14 final size:14
Alignment explanation
Indices: 3662483--3662510 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
3662473 ACTAATTTGT
3662483 TTGAAAAAATTACA
1 TTGAAAAAATTACA
3662497 TTGAAAAAATTACA
1 TTGAAAAAATTACA
3662511 AGTGTACTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.07, G:0.07, T:0.29
Consensus pattern (14 bp):
TTGAAAAAATTACA
Found at i:3664158 original size:23 final size:23
Alignment explanation
Indices: 3664131--3664175 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
3664121 TTGTATTAAT
3664131 TTACTAAATTAAACTTAAAAATG
1 TTACTAAATTAAACTTAAAAATG
* *
3664154 TTACTAAATTTATCTTAAAAAT
1 TTACTAAATTAAACTTAAAAAT
3664176 TATAATTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.49, C:0.09, G:0.02, T:0.40
Consensus pattern (23 bp):
TTACTAAATTAAACTTAAAAATG
Found at i:3669040 original size:25 final size:25
Alignment explanation
Indices: 3668991--3669138 Score: 101
Period size: 25 Copynumber: 6.0 Consensus size: 25
3668981 TGTCATTAGA
*
3668991 TTACCGAT-TCTCAGCTCG-AGAGAGC
1 TTACCGATAT-TCAGCTCGTA-TGAGC
3669016 TTACCGATATTCAGCTCGTATGAGC
1 TTACCGATATTCAGCTCGTATGAGC
* * * * *
3669041 TTATCGTTATTCAACTTGTATGAGT
1 TTACCGATATTCAGCTCGTATGAGC
* *
3669066 TTA-CTATTACTCAGCTCGTATGAGC
1 TTACCGA-TATTCAGCTCGTATGAGC
*
3669091 TTACC-A-ATTACAGCTCGTAAGAGC
1 TTACCGATATT-CAGCTCGTATGAGC
* * *
3669115 ATACCAAT-TTAGAGCTCGTATGAG
1 TTACCGATATT-CAGCTCGTATGAG
3669139 TATACATGTA
Statistics
Matches: 99, Mismatches: 17, Indels: 14
0.76 0.13 0.11
Matches are distributed among these distances:
23 2 0.02
24 18 0.18
25 76 0.77
26 3 0.03
ACGTcount: A:0.27, C:0.22, G:0.19, T:0.32
Consensus pattern (25 bp):
TTACCGATATTCAGCTCGTATGAGC
Found at i:3669143 original size:25 final size:24
Alignment explanation
Indices: 3669077--3669143 Score: 82
Period size: 24 Copynumber: 2.8 Consensus size: 24
3669067 TACTATTACT
3669077 CAGCTCGTATGAGCT-TACCAATTA
1 CAGCTCGTATGAG-TATACCAATTA
* *
3669101 CAGCTCGTAAGAGCATACCAATTTA
1 CAGCTCGTATGAGTATACCAA-TTA
*
3669126 GAGCTCGTATGAGTATAC
1 CAGCTCGTATGAGTATAC
3669144 ATGTACAGGA
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
24 18 0.50
25 18 0.50
ACGTcount: A:0.31, C:0.22, G:0.19, T:0.27
Consensus pattern (24 bp):
CAGCTCGTATGAGTATACCAATTA
Found at i:3669850 original size:10 final size:10
Alignment explanation
Indices: 3669835--3669873 Score: 78
Period size: 10 Copynumber: 3.9 Consensus size: 10
3669825 ATTTGGAAGA
3669835 GTTTAAAATT
1 GTTTAAAATT
3669845 GTTTAAAATT
1 GTTTAAAATT
3669855 GTTTAAAATT
1 GTTTAAAATT
3669865 GTTTAAAAT
1 GTTTAAAAT
3669874 CCTACTATGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 29 1.00
ACGTcount: A:0.41, C:0.00, G:0.10, T:0.49
Consensus pattern (10 bp):
GTTTAAAATT
Found at i:3673144 original size:52 final size:52
Alignment explanation
Indices: 3673086--3673286 Score: 159
Period size: 52 Copynumber: 4.0 Consensus size: 52
3673076 GATGGAAAAT
* *
3673086 ATGTGATATGTGCTTCCGTAAAAGACCATAGCTAGGCTATGGCATCGGTACA
1 ATGTGATATGTGCTTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTACA
* * * * ***
3673138 ATGTGAT-TCGAG-TTCCCGTATAAGACCATGGCTGGGCAATAGCATCGGTGTG
1 ATGTGATAT-GTGCTT-CCGTATAAGACCATAGCTGGGCTATGGCATCGGTACA
* * *
3673190 ATGTGATAATATGAC-TCCGTATAAGACCATATCTGGGATATGGCATCGGT---
1 ATGTGAT-ATGTG-CTTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTACA
* * * *
3673240 ATGT--TATGTG-ATCCGTATAAGACCATGGCAGGGCTATGGCTTCGGTA
1 ATGTGATATGTGCTTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTA
3673287 TGTGATGTGT
Statistics
Matches: 119, Mismatches: 22, Indels: 21
0.73 0.14 0.13
Matches are distributed among these distances:
46 30 0.25
47 4 0.03
48 1 0.01
50 4 0.03
51 3 0.03
52 45 0.38
53 30 0.25
54 2 0.02
ACGTcount: A:0.26, C:0.18, G:0.27, T:0.28
Consensus pattern (52 bp):
ATGTGATATGTGCTTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTACA
Found at i:3673278 original size:46 final size:46
Alignment explanation
Indices: 3673205--3673295 Score: 128
Period size: 46 Copynumber: 2.0 Consensus size: 46
3673195 ATAATATGAC
* * *
3673205 TCCGTATAAGACCATATCTGGGATATGGCATCGGTATGTTATGTGA
1 TCCGTATAAGACCATAGCAGGGATATGGCATCGGTATGTGATGTGA
* * *
3673251 TCCGTATAAGACCATGGCAGGGCTATGGCTTCGGTATGTGATGTG
1 TCCGTATAAGACCATAGCAGGGATATGGCATCGGTATGTGATGTG
3673296 TGACAATGTG
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
46 39 1.00
ACGTcount: A:0.23, C:0.16, G:0.30, T:0.31
Consensus pattern (46 bp):
TCCGTATAAGACCATAGCAGGGATATGGCATCGGTATGTGATGTGA
Found at i:3673336 original size:28 final size:28
Alignment explanation
Indices: 3673296--3673358 Score: 117
Period size: 28 Copynumber: 2.2 Consensus size: 28
3673286 ATGTGATGTG
3673296 TGACAATGTGAAAGTCCATAGTTTACTA
1 TGACAATGTGAAAGTCCATAGTTTACTA
3673324 TGACAATGTGAAAGTCCATAGTTTACTA
1 TGACAATGTGAAAGTCCATAGTTTACTA
*
3673352 TGGCAAT
1 TGACAAT
3673359 ATGATAATGA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.32
Consensus pattern (28 bp):
TGACAATGTGAAAGTCCATAGTTTACTA
Found at i:3676809 original size:24 final size:23
Alignment explanation
Indices: 3676777--3676827 Score: 84
Period size: 24 Copynumber: 2.2 Consensus size: 23
3676767 TTAGTACTTA
*
3676777 TTTTTTTCTTCTTTTTTTTCTTCT
1 TTTTTTTCTTCTTTTTTTTATT-T
3676801 TTTTTTTCTTCTTTTTTTTATTT
1 TTTTTTTCTTCTTTTTTTTATTT
3676824 TTTT
1 TTTT
3676828 AAATTTTATT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
23 5 0.19
24 21 0.81
ACGTcount: A:0.02, C:0.12, G:0.00, T:0.86
Consensus pattern (23 bp):
TTTTTTTCTTCTTTTTTTTATTT
Found at i:3676827 original size:12 final size:12
Alignment explanation
Indices: 3676777--3676819 Score: 86
Period size: 12 Copynumber: 3.6 Consensus size: 12
3676767 TTAGTACTTA
3676777 TTTTTTTCTTCT
1 TTTTTTTCTTCT
3676789 TTTTTTTCTTCT
1 TTTTTTTCTTCT
3676801 TTTTTTTCTTCT
1 TTTTTTTCTTCT
3676813 TTTTTTT
1 TTTTTTT
3676820 ATTTTTTTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 31 1.00
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (12 bp):
TTTTTTTCTTCT
Found at i:3679661 original size:82 final size:82
Alignment explanation
Indices: 3679524--3679686 Score: 308
Period size: 82 Copynumber: 2.0 Consensus size: 82
3679514 GCTTGTTGTG
*
3679524 GAGTCATGTTGACTAACGCTCCTCCACTCGCGGCATCTACCATATTCATCTCCATGGGTTTCAAG
1 GAGTCATGTTAACTAACGCTCCTCCACTCGCGGCATCTACCATATTCATCTCCATGGGTTTCAAG
3679589 CCTTCATAAAAGTACTA
66 CCTTCATAAAAGTACTA
*
3679606 GAGTCATGTTAACTAACGCTCCTTCACTCGCGGCATCTACCATATTCATCTCCATGGGTTTCAAG
1 GAGTCATGTTAACTAACGCTCCTCCACTCGCGGCATCTACCATATTCATCTCCATGGGTTTCAAG
3679671 CCTTCATAAAAGTACT
66 CCTTCATAAAAGTACT
3679687 GGAGCAAAGA
Statistics
Matches: 79, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
82 79 1.00
ACGTcount: A:0.26, C:0.29, G:0.15, T:0.30
Consensus pattern (82 bp):
GAGTCATGTTAACTAACGCTCCTCCACTCGCGGCATCTACCATATTCATCTCCATGGGTTTCAAG
CCTTCATAAAAGTACTA
Found at i:3681344 original size:283 final size:283
Alignment explanation
Indices: 3680835--3681401 Score: 1019
Period size: 283 Copynumber: 2.0 Consensus size: 283
3680825 TCCAGCCTCC
**
3680835 GGTTGTCTCATTCTTCCTTGGGCTCAATCCTTGGCTTTTGGATGATCCACTCTCGACTCAAGTAA
1 GGTTGTCTCATTCCGCCTTGGGCTCAATCCTTGGCTTTTGGATGATCCACTCTCGACTCAAGTAA
3680900 GCCAGTTATAGTGGAAGAGGACGCCTATGACCACCAGCTCCAAAGATTAGATTTACGATTTTTAG
66 GCCAGTTATAGTGGAAGAGGACGCCTATGACCACCAGCTCCAAAGATTAGATTTACGATTTTTAG
* * * *
3680965 GGAACCTGACTCTAGCCAGTACTCTATTCTAGATCAACGCTTCTCAATGGCGAATCCCACGCTAT
131 GGAACCTGACTCTAGCCAGTAATCTATGCTAGAGCAACGCTTCTCAATGGCGAATCCCACGCCAT
*
3681030 TTTGTCTCTTTGGCTCGCCAACCTCTGACGCAGTAAGTTAACAAACCGACTATGCAGTCCTTCCA
196 TTTGTCTCTTTGGCTCGCCAACCTCTGACGCAGTAAGTTAACAAACCGACTATGCAATCCTTCCA
3681095 AAACATACAAAGCGGCCGCCTTT
261 AAACATACAAAGCGGCCGCCTTT
*
3681118 GNGTTGTCTCATTCCGCCTTGGGCTCAATCCTTGGCTTTTGGATGATCC-TTCTCGACTCAAGTA
1 G-GTTGTCTCATTCCGCCTTGGGCTCAATCCTTGGCTTTTGGATGATCCACTCTCGACTCAAGTA
3681182 AGCCAGTTATAGTGGAAGAGGACGCCTATGACCACCAGCTCCAAAGATTAGATTTACGATTTTTA
65 AGCCAGTTATAGTGGAAGAGGACGCCTATGACCACCAGCTCCAAAGATTAGATTTACGATTTTTA
* *
3681247 GGGAATCTGACTCTAGCTAGTAATCTATGCTAGAGCAACGCTTCTCAATGGCGAATCCCACGCCA
130 GGGAACCTGACTCTAGCCAGTAATCTATGCTAGAGCAACGCTTCTCAATGGCGAATCCCACGCCA
*
3681312 TTTTGTCTCTTTGGCTCGCCAACCTCTGACGCAGTAAGTTAACGAACCGACTATGCAATCCTTCC
195 TTTTGTCTCTTTGGCTCGCCAACCTCTGACGCAGTAAGTTAACAAACCGACTATGCAATCCTTCC
3681377 AAAACATACAAAGCGGCCGCCTTT
260 AAAACATACAAAGCGGCCGCCTTT
3681401 G
1 G
3681402 CATATGCTGA
Statistics
Matches: 272, Mismatches: 11, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
283 227 0.83
284 45 0.17
ACGTcount: A:0.25, C:0.27, G:0.20, T:0.28
Consensus pattern (283 bp):
GGTTGTCTCATTCCGCCTTGGGCTCAATCCTTGGCTTTTGGATGATCCACTCTCGACTCAAGTAA
GCCAGTTATAGTGGAAGAGGACGCCTATGACCACCAGCTCCAAAGATTAGATTTACGATTTTTAG
GGAACCTGACTCTAGCCAGTAATCTATGCTAGAGCAACGCTTCTCAATGGCGAATCCCACGCCAT
TTTGTCTCTTTGGCTCGCCAACCTCTGACGCAGTAAGTTAACAAACCGACTATGCAATCCTTCCA
AAACATACAAAGCGGCCGCCTTT
Found at i:3682923 original size:25 final size:25
Alignment explanation
Indices: 3682890--3683122 Score: 76
Period size: 25 Copynumber: 9.4 Consensus size: 25
3682880 ACAATACTTT
* *
3682890 ACAAGGGTTTCTCACAAGATTAGCC
1 ACAAAGGTTTCTCACAAGAATAGCC
* * *
3682915 ACAAAGGTTTTTCATAGGAATAGCC
1 ACAAAGGTTTCTCACAAGAATAGCC
* *
3682940 ACAAAGGTTT-TC-CATATAATATACC
1 ACAAAGGTTTCTCACA-AGAATA-GCC
* *
3682965 ATAAAGGCTTTC-CA-AAAAATA-CC
1 ACAAAGG-TTTCTCACAAGAATAGCC
* * *
3682988 ACAAAAACG-TT-TCATAAGATTAGCC
1 AC--AAAGGTTTCTCACAAGAATAGCC
* * *
3683013 ACAAAGGCTTTCT-A-GATAATACACC
1 ACAAAGG-TTTCTCACAAGAATA-GCC
* * * *
3683038 ACAAATGCTTCTCATAAGATTAGCC
1 ACAAAGGTTTCTCACAAGAATAGCC
* *
3683063 ATAAAGGCTTTC-CA-AATAATATGCC
1 ACAAAGG-TTTCTCACAAGAATA-GCC
* * *
3683088 AAAAAGGCTTT-TCATAAGATTAGCC
1 ACAAAGG-TTTCTCACAAGAATAGCC
3683113 ACAAAGGTTT
1 ACAAAGGTTT
3683123 TCTAGATAAT
Statistics
Matches: 153, Mismatches: 35, Indels: 41
0.67 0.15 0.18
Matches are distributed among these distances:
23 12 0.08
24 27 0.18
25 96 0.63
26 18 0.12
ACGTcount: A:0.39, C:0.20, G:0.14, T:0.27
Consensus pattern (25 bp):
ACAAAGGTTTCTCACAAGAATAGCC
Found at i:3683055 original size:50 final size:50
Alignment explanation
Indices: 3682999--3683132 Score: 187
Period size: 50 Copynumber: 2.7 Consensus size: 50
3682989 CAAAAACGTT
* *
3682999 TCATAAGATTAGCCACAAAGGCTTTCTAGATAATACACCACAAATGCTTC
1 TCATAAGATTAGCCACAAAGGCTTTCTAGATAATACACCAAAAAGGCTTC
* * * ** *
3683049 TCATAAGATTAGCCATAAAGGCTTTCCAAATAATATGCCAAAAAGGCTTT
1 TCATAAGATTAGCCACAAAGGCTTTCTAGATAATACACCAAAAAGGCTTC
*
3683099 TCATAAGATTAGCCACAAAGGTTTTCTAGATAAT
1 TCATAAGATTAGCCACAAAGGCTTTCTAGATAAT
3683133 CCATTTTTAC
Statistics
Matches: 72, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
50 72 1.00
ACGTcount: A:0.39, C:0.19, G:0.13, T:0.28
Consensus pattern (50 bp):
TCATAAGATTAGCCACAAAGGCTTTCTAGATAATACACCAAAAAGGCTTC
Found at i:3685504 original size:29 final size:29
Alignment explanation
Indices: 3685472--3685539 Score: 68
Period size: 29 Copynumber: 2.3 Consensus size: 29
3685462 ATACTATTAT
*
3685472 TATTTATATAATTTTTAT-TTATCTATTTA
1 TATTTATATAATTATTATATT-TCTATTTA
* *
3685501 TATTTCTACT-ATTATTATATTTCTATTTC
1 TATTTATA-TAATTATTATATTTCTATTTA
*
3685530 TATTCATATA
1 TATTTATATA
3685540 CTAATATTAT
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
28 1 0.03
29 27 0.87
30 3 0.10
ACGTcount: A:0.29, C:0.09, G:0.00, T:0.62
Consensus pattern (29 bp):
TATTTATATAATTATTATATTTCTATTTA
Found at i:3685513 original size:23 final size:23
Alignment explanation
Indices: 3685463--3685531 Score: 65
Period size: 23 Copynumber: 3.1 Consensus size: 23
3685453 GTTATTCCAA
*
3685463 TACTATTATTAT-TTATATAATTTT
1 TACTATTATTATATT-TAT-ATTTC
*
3685487 TA-T-TTA-TCTATTTATATTTC
1 TACTATTATTATATTTATATTTC
*
3685507 TACTATTATTATATTTCTATTTC
1 TACTATTATTATATTTATATTTC
3685530 TA
1 TA
3685532 TTCATATACT
Statistics
Matches: 37, Mismatches: 4, Indels: 9
0.74 0.08 0.18
Matches are distributed among these distances:
20 6 0.16
21 6 0.16
22 8 0.22
23 15 0.41
24 2 0.05
ACGTcount: A:0.29, C:0.09, G:0.00, T:0.62
Consensus pattern (23 bp):
TACTATTATTATATTTATATTTC
Found at i:3685533 original size:17 final size:18
Alignment explanation
Indices: 3685491--3685538 Score: 55
Period size: 17 Copynumber: 2.7 Consensus size: 18
3685481 AATTTTTATT
3685491 TATCTATTTATATTTCTAC
1 TATCTA-TTATATTTCTAC
3685510 TAT-TATTATATTTCTA-
1 TATCTATTATATTTCTAC
*
3685526 TTTCTATTCATAT
1 TATCTATT-ATAT
3685539 ACTAATATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
16 2 0.08
17 15 0.58
18 6 0.23
19 3 0.12
ACGTcount: A:0.27, C:0.12, G:0.00, T:0.60
Consensus pattern (18 bp):
TATCTATTATATTTCTAC
Found at i:3685688 original size:3 final size:3
Alignment explanation
Indices: 3685673--3685783 Score: 55
Period size: 3 Copynumber: 36.3 Consensus size: 3
3685663 TTTAAAACTT
* * * * *
3685673 TTA TTA CTA TTA TTA TTA TTA -TA TTTA TGTA TCA ATA TCA TT- TTT
1 TTA TTA TTA TTA TTA TTA TTA TTA -TTA T-TA TTA TTA TTA TTA TTA
* * * * * *
3685718 TTA TATA TTA TTA TCA TTA TTA TTA TTG CTA TTA GTA CTA TTA TTC
1 TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
3685764 TTT TCTA TTA TTA TTT TTA T
1 TTA T-TA TTA TTA TTA TTA T
3685784 ATTTATTTAT
Statistics
Matches: 79, Mismatches: 23, Indels: 12
0.69 0.20 0.11
Matches are distributed among these distances:
2 4 0.05
3 65 0.82
4 10 0.13
ACGTcount: A:0.29, C:0.07, G:0.03, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:3687947 original size:19 final size:19
Alignment explanation
Indices: 3687923--3687967 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
3687913 CGTCTCTTTT
*
3687923 TGCATT-CATTTCATGCATC
1 TGCATTGCATTTCAT-CATA
3687942 TGCATTGCATTTCATCATA
1 TGCATTGCATTTCATCATA
3687961 TGCATTG
1 TGCATTG
3687968 AATGTCACAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 16 0.67
20 8 0.33
ACGTcount: A:0.22, C:0.22, G:0.13, T:0.42
Consensus pattern (19 bp):
TGCATTGCATTTCATCATA
Found at i:3691427 original size:11 final size:11
Alignment explanation
Indices: 3691411--3691438 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
3691401 TAATAATAAT
3691411 AAAAAAATCAA
1 AAAAAAATCAA
3691422 AAAAAAATCAA
1 AAAAAAATCAA
3691433 AAAAAA
1 AAAAAA
3691439 GATAAGAAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.86, C:0.07, G:0.00, T:0.07
Consensus pattern (11 bp):
AAAAAAATCAA
Found at i:3692961 original size:46 final size:44
Alignment explanation
Indices: 3692901--3693015 Score: 149
Period size: 44 Copynumber: 2.6 Consensus size: 44
3692891 ACAGGACAGA
* *
3692901 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATT--AAATATGGCATTGGAG
* *
3692947 ACAGGATTGAGCCATGTAAGTCCATATTATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAATATGGCATTGGAG
* **
3692991 ACAGGAATAATTCATGTAAGTCCAT
1 ACAGGAATGAGCCATGTAAGTCCAT
3693016 GTCAAAGACA
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
44 35 0.57
46 26 0.43
ACGTcount: A:0.36, C:0.14, G:0.23, T:0.28
Consensus pattern (44 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAATATGGCATTGGAG
Found at i:3692996 original size:44 final size:45
Alignment explanation
Indices: 3692901--3693034 Score: 153
Period size: 46 Copynumber: 3.0 Consensus size: 45
3692891 ACAGGACAGA
* *
3692901 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTA-AAATATGGCATTGGAG
* *
3692947 ACAGGATTGAGCCATGTAAGTCCATATT-ATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
* ** * * *
3692991 ACAGGAATAATTCATGTAAGTCCATGTCAAAGACATGGCATTGG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAA-ATATGGCATTGG
3693035 CAGGGTATTG
Statistics
Matches: 74, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
44 36 0.49
45 1 0.01
46 37 0.50
ACGTcount: A:0.35, C:0.14, G:0.24, T:0.27
Consensus pattern (45 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
Found at i:3693059 original size:14 final size:15
Alignment explanation
Indices: 3693035--3693068 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
3693025 ATGGCATTGG
*
3693035 CAGGGTATTGATAGA
1 CAGGATATTGATAGA
3693050 -AGGATATTGATAGA
1 CAGGATATTGATAGA
3693064 CAGGA
1 CAGGA
3693069 ACAACCCTAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
14 13 0.76
15 4 0.24
ACGTcount: A:0.38, C:0.06, G:0.32, T:0.24
Consensus pattern (15 bp):
CAGGATATTGATAGA
Found at i:3695246 original size:44 final size:44
Alignment explanation
Indices: 3695198--3695537 Score: 183
Period size: 44 Copynumber: 7.7 Consensus size: 44
3695188 AGCCACCAGC
* *
3695198 CTTAT-TTCCCTGAGGTAGCAAAGGAGTAGGCTGAAGATTGTAGT
1 CTTATCTT-CCTGAGGTAGCAAAGGAGCAGGCTGAAGATTGAAGT
** * *
3695242 CTTATCTTTTTGAGGTAGCAAGGGAGCAGACTGAAGATTGAAGAT
1 CTTATCTTCCTGAGGTAGCAAAGGAGCAGGCTGAAGATTGAAG-T
* ** * * * *
3695287 CTTATC-TCTCTGAGATAGCAGTGGAGTA-GATCGAATA-TGACAAAT
1 CTTATCTTC-CTGAGGTAGCAAAGGAGCAGGCT-GAAGATTG--AAGT
* * ** ** ***** *
3695332 CTTATCTTCCCGAGGTAGCAGAGGAGCAGATTTTAGCCACCAGC
1 CTTATCTTCCTGAGGTAGCAAAGGAGCAGGCTGAAGATTGAAGT
* * * *
3695376 CTTAT-TTCCCTGAGGTAGCAAGGGAGTAGGCTAAAGATTGCAGT
1 CTTATCTT-CCTGAGGTAGCAAAGGAGCAGGCTGAAGATTGAAGT
* * *
3695420 CTTATCTTTCTGAGGTAGCAAAGGAACAGACTGAAGATTGAAGAT
1 CTTATCTTCCTGAGGTAGCAAAGGAGCAGGCTGAAGATTGAAG-T
* * * * *
3695465 CTTGTATTCCTGA-GCAGCAATA-GAGCAGGCTGAGGATTGTAGAT
1 CTTATCTTCCTGAGGTAGCAA-AGGAGCAGGCTGAAGATTGAAG-T
*
3695509 CTTATCTTCATGAGGTAGCAATA-GAGCAG
1 CTTATCTTCCTGAGGTAGCAA-AGGAGCAG
3695538 ATCGAAGATG
Statistics
Matches: 219, Mismatches: 63, Indels: 27
0.71 0.20 0.09
Matches are distributed among these distances:
43 2 0.01
44 134 0.61
45 78 0.36
46 5 0.02
ACGTcount: A:0.30, C:0.16, G:0.27, T:0.27
Consensus pattern (44 bp):
CTTATCTTCCTGAGGTAGCAAAGGAGCAGGCTGAAGATTGAAGT
Found at i:3695402 original size:89 final size:88
Alignment explanation
Indices: 3695151--3695449 Score: 255
Period size: 88 Copynumber: 3.4 Consensus size: 88
3695141 CAAAACAGCG
* *
3695151 AATCTTATCTTCCCGAGGTAGCAGGGGAGTAGATTTTAGCCACCAGCCTTATTTCCCTGAGGTAG
1 AATCTTATCTTCCCGAGGTAGCAGAGGAGCAGATTTTAGCCACCAGCCTTATTTCCCTGAGGTAG
* *
3695216 CAAAGGAGTAGGCTGAAGATTGT
66 CAAGGGAGTAGGCTGAAGATTGA
* *** * ** ***** * * * *
3695239 AGTCTTATCTTTTTGAGGTAGCA-AGGGAGCAGACTGAAGATTGAAGATCTTATCTCTCTGAGAT
1 AATCTTATCTTCCCGAGGTAGCAGA-GGAGCAGATTTTAGCCACCAG-CCTTATTTCCCTGAGGT
* *
3695303 AGC-AGTGGAGTA-GATCGAATA-TGACA
64 AGCAAG-GGAGTAGGCT-GAAGATTG--A
3695329 AATCTTATCTTCCCGAGGTAGCAGAGGAGCAGATTTTAGCCACCAGCCTTATTTCCCTGAGGTAG
1 AATCTTATCTTCCCGAGGTAGCAGAGGAGCAGATTTTAGCCACCAGCCTTATTTCCCTGAGGTAG
* *
3695394 CAAGGGAGTAGGCTAAAGATTGC
66 CAAGGGAGTAGGCTGAAGATTGA
* * * * *
3695417 AGTCTTATCTTTCTGAGGTAGCAAAGGAACAGA
1 AATCTTATCTTCCCGAGGTAGCAGAGGAGCAGA
3695450 CTGAAGATTG
Statistics
Matches: 154, Mismatches: 47, Indels: 20
0.70 0.21 0.09
Matches are distributed among these distances:
88 64 0.42
89 51 0.33
90 38 0.25
91 1 0.01
ACGTcount: A:0.29, C:0.18, G:0.26, T:0.27
Consensus pattern (88 bp):
AATCTTATCTTCCCGAGGTAGCAGAGGAGCAGATTTTAGCCACCAGCCTTATTTCCCTGAGGTAG
CAAGGGAGTAGGCTGAAGATTGA
Found at i:3695557 original size:222 final size:222
Alignment explanation
Indices: 3695207--3695610 Score: 519
Period size: 222 Copynumber: 1.8 Consensus size: 222
3695197 CCTTATTTCC
** * * * ** * *
3695207 CTGAGGTAGCAAAGGAGTAGGCTGAAGATTGTAGTCTTATCTTTTTGAGGTAGCAAGGGAGCAGA
1 CTGAGGTAGCAAAGGAACAGACTGAAGATTGAAGTCTTATATTCCTGAGGCAGCAAGAGAGCAGA
* * * *
3695272 CTGAAGATTGAAGATCTTATCTCTCTGAGATAGCAGTGGAGTAGATCGAATATGACAAATCTTAT
66 CTGAAGATTGAAGATCTTATCTCTCTGAGATAGCAATAGAGCAGATCGAAGATGACAAATCTTAT
* * *
3695337 CTTCC-CGAGGTAGCAGA-GGAGCAGATTTTAGCCACCAGCCTTATTTCCCTGAGGTAGCAAGGG
131 C-TCCACAAGGTAGCA-ATGGAGCAGATTTAAGCCACCAGCCTTATCTCCCTGAGGTAGCAAGGG
3695400 AGTAGGCTAAAGATTGCAGTCTTATCTTT
194 AGTAGGCTAAAGATTGCAGTCTTATCTTT
* *
3695429 CTGAGGTAGCAAAGGAACAGACTGAAGATTGAAGATCTTGTATTCCTGA-GCAGCAATAGAGCAG
1 CTGAGGTAGCAAAGGAACAGACTGAAGATTGAAG-TCTTATATTCCTGAGGCAGCAAGAGAGCAG
* * * * * *
3695493 GCTGAGGATTGTAGATCTTATCT-TCATGAGGTAGCAATAGAGCAGATCGAAGATGGCGAATCTT
65 ACTGAAGATTGAAGATCTTATCTCTC-TGAGATAGCAATAGAGCAGATCGAAGATGACAAATCTT
*
3695557 ATCTCCATAAGGTAGCAATGGAGCAGATTTAAGCCACCAGCCTTATCTCCCTGA
129 ATCTCCACAAGGTAGCAATGGAGCAGATTTAAGCCACCAGCCTTATCTCCCTGA
3695611 AGTTGCAGTG
Statistics
Matches: 153, Mismatches: 25, Indels: 8
0.82 0.13 0.04
Matches are distributed among these distances:
221 6 0.04
222 137 0.90
223 10 0.07
ACGTcount: A:0.30, C:0.17, G:0.26, T:0.26
Consensus pattern (222 bp):
CTGAGGTAGCAAAGGAACAGACTGAAGATTGAAGTCTTATATTCCTGAGGCAGCAAGAGAGCAGA
CTGAAGATTGAAGATCTTATCTCTCTGAGATAGCAATAGAGCAGATCGAAGATGACAAATCTTAT
CTCCACAAGGTAGCAATGGAGCAGATTTAAGCCACCAGCCTTATCTCCCTGAGGTAGCAAGGGAG
TAGGCTAAAGATTGCAGTCTTATCTTT
Found at i:3695722 original size:45 final size:45
Alignment explanation
Indices: 3695597--3696059 Score: 228
Period size: 44 Copynumber: 10.4 Consensus size: 45
3695587 AAGCCACCAG
* *
3695597 CCTTATCTCCCTGAAGTTGCAGTGGAGCAGGTCGAA-ATTACAAA
1 CCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATTACAAA
* * *
3695641 CCTTATCTCCCTGAAGTTGCATTGGAGTAGACTGAAGA-TAGCAAA
1 CCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATTA-CAAA
* * * * *
3695686 TCTTATTTCCCTGAAGATGCAGTGGAACAGATTGAAGCTATAAATAAACAGA
1 CCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAG--AT---T--ACAAA
* * * *
3695738 TCTTATCTCTCTGAA-TTGCAGTAGAGCAGA-T---CA-TAGCAAA
1 CCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATTA-CAAA
* * * **
3695778 CTTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAG-TAACAGG
1 CCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATTACAAA
* * * * * * ** * *
3695822 TCTTATCTCCTTGAGGTAGCAG-GGAAGAAGATTTAAG-CCACCAG
1 CCTTATCTCCCTGAAGTTGCAGTGG-AGCAGATTGAAGATTACAAA
* * *
3695866 CCTTATCTCCCTGAA-TTACAGTGGAGCA-AGTTG-ACATTACCAAT
1 CCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-TTGAAGATTA-CAAA
* * * * * *
3695910 CCTTATCTCCCTAAAGTTGTAGTGGAGCA-A--GAAAATAAACGAG
1 CCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGAT-TACAAA
* * * *
3695953 TCTTATCTCCCTGAAGTTGTAGTGGAGCA-AGTTGAAG-TCACGAA
1 CCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-TTGAAGATTACAAA
* * *
3695997 CCTTATCTCCCTGAAGTTGTAGTGGAGCAGGTTGAA-ATTATCAAT
1 CCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATTA-CAAA
* *
3696042 TCTTATCTCCTTGAAGTT
1 CCTTATCTCCCTGAAGTT
3696060 TCAGCAGAGT
Statistics
Matches: 316, Mismatches: 72, Indels: 61
0.70 0.16 0.14
Matches are distributed among these distances:
39 1 0.00
40 15 0.05
41 14 0.04
42 4 0.01
43 45 0.14
44 134 0.42
45 68 0.22
46 3 0.01
47 1 0.00
50 1 0.00
51 13 0.04
52 16 0.05
53 1 0.00
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.29
Consensus pattern (45 bp):
CCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATTACAAA
Found at i:3695960 original size:87 final size:87
Alignment explanation
Indices: 3695867--3696025 Score: 241
Period size: 87 Copynumber: 1.8 Consensus size: 87
3695857 AGCCACCAGC
*
3695867 CTTATCTCCCTGAA-TTACAGTGGAGCAAGTTGACA-TTACCAATCCTTATCTCCCTAAAGTTGT
1 CTTATCTCCCTGAAGTTACAGTGGAGCAAGTTGA-AGTCACCAA-CCTTATCTCCCTAAAGTTGT
3695930 AGTGGAGCAAGAAAATAAACGAGT
64 AGTGGAGCAAGAAAATAAACGAGT
** * *
3695954 CTTATCTCCCTGAAGTTGTAGTGGAGCAAGTTGAAGTCACGAACCTTATCTCCCTGAAGTTGTAG
1 CTTATCTCCCTGAAGTTACAGTGGAGCAAGTTGAAGTCACCAACCTTATCTCCCTAAAGTTGTAG
3696019 TGGAGCA
66 TGGAGCA
3696026 GGTTGAAATT
Statistics
Matches: 65, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
87 43 0.66
88 22 0.34
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.28
Consensus pattern (87 bp):
CTTATCTCCCTGAAGTTACAGTGGAGCAAGTTGAAGTCACCAACCTTATCTCCCTAAAGTTGTAG
TGGAGCAAGAAAATAAACGAGT
Found at i:3696503 original size:19 final size:19
Alignment explanation
Indices: 3696479--3696534 Score: 58
Period size: 19 Copynumber: 2.8 Consensus size: 19
3696469 AGGAAGATAA
* * *
3696479 TTATTTGTTTTTGTTTTAT
1 TTATTTATTTTTATTTCAT
3696498 TTATTTATTTTTATTTCAT
1 TTATTTATTTTTATTTCAT
*
3696517 TTCATTTTATTTTAATTT
1 TT-A-TTTATTTTTATTT
3696535 ATTAAATTAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
19 18 0.58
20 1 0.03
21 12 0.39
ACGTcount: A:0.18, C:0.04, G:0.04, T:0.75
Consensus pattern (19 bp):
TTATTTATTTTTATTTCAT
Found at i:3697107 original size:15 final size:14
Alignment explanation
Indices: 3697081--3697167 Score: 70
Period size: 15 Copynumber: 6.0 Consensus size: 14
3697071 TATTCTAATA
*
3697081 CTATTATTATTTAT
1 CTATTTTTATTTAT
3697095 CTAATTTTTATTTAT
1 CT-ATTTTTATTTAT
* *
3697110 CTATTTATATTTCT
1 CTATTTTTATTTAT
*
3697124 ACTATTATTATATT-T
1 -CTATTTTTAT-TTAT
3697139 CTATTTATTATATT-T
1 CTATTT-TTAT-TTAT
*
3697154 CTATTTGTATTTAT
1 CTATTTTTATTTAT
3697168 ATACTAATAT
Statistics
Matches: 61, Mismatches: 7, Indels: 10
0.78 0.09 0.13
Matches are distributed among these distances:
13 2 0.03
14 21 0.34
15 36 0.59
16 2 0.03
ACGTcount: A:0.26, C:0.08, G:0.01, T:0.64
Consensus pattern (14 bp):
CTATTTTTATTTAT
Found at i:3697120 original size:29 final size:28
Alignment explanation
Indices: 3697053--3697189 Score: 93
Period size: 29 Copynumber: 4.6 Consensus size: 28
3697043 ATTGCTATTA
*
3697053 TTATTATGTTTCTATTGTTATTCTAATACTA-
1 TTATTAT-TTTCTATTTTTATT-T-AT-CTAT
3697084 TTATTATTTATCTAATTTTTATTTATCTAT
1 TTATTATTT-TCT-ATTTTTATTTATCTAT
*
3697114 TTA-TATTTCTACTATTATTATATT-TCTAT
1 TTATTATTT-T-CTATTTTTAT-TTATCTAT
* *
3697143 TTATTATATTTCTATTTGTATTTATATACT
1 TTATTAT-TTTCTATTTTTATTTATCTA-T
*
3697173 AATATTATTTTC-ATTTT
1 -TTATTATTTTCTATTTT
3697190 AGTTTTCTTA
Statistics
Matches: 88, Mismatches: 8, Indels: 22
0.75 0.07 0.19
Matches are distributed among these distances:
28 2 0.02
29 39 0.44
30 20 0.23
31 19 0.22
32 8 0.09
ACGTcount: A:0.27, C:0.08, G:0.02, T:0.63
Consensus pattern (28 bp):
TTATTATTTTCTATTTTTATTTATCTAT
Found at i:3697136 original size:17 final size:15
Alignment explanation
Indices: 3697114--3697159 Score: 74
Period size: 15 Copynumber: 2.9 Consensus size: 15
3697104 ATTTATCTAT
3697114 TTATATTTCTACTATTA
1 TTATATTTCTA-T-TTA
3697131 TTATATTTCTATTTA
1 TTATATTTCTATTTA
3697146 TTATATTTCTATTT
1 TTATATTTCTATTT
3697160 GTATTTATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
15 17 0.59
16 1 0.03
17 11 0.38
ACGTcount: A:0.26, C:0.09, G:0.00, T:0.65
Consensus pattern (15 bp):
TTATATTTCTATTTA
Found at i:3697157 original size:44 final size:44
Alignment explanation
Indices: 3697053--3697182 Score: 133
Period size: 44 Copynumber: 2.8 Consensus size: 44
3697043 ATTGCTATTA
3697053 TTATTATGTTTCTATTGTTATTCTAATACTATTATTATTTATCTAAT
1 TTATTAT-TTTCTATT-TTATT-TAATACTATTATTATTTATCTAAT
*
3697100 TT-TTATTTATCTATTTATATTT-CTACTATTATTATATT-TCT-AT
1 TTATTATTT-TCTATTT-TATTTAATACTATTATTAT-TTATCTAAT
*
3697143 TTATTATATTTCTATTTGTATTTATATACTAATATTATTT
1 TTATTAT-TTTCTATTT-TATTTA-ATACTATTATTATTT
3697183 TCATTTTAGT
Statistics
Matches: 72, Mismatches: 4, Indels: 16
0.78 0.04 0.17
Matches are distributed among these distances:
43 4 0.06
44 31 0.43
45 10 0.14
46 25 0.35
47 2 0.03
ACGTcount: A:0.28, C:0.08, G:0.02, T:0.62
Consensus pattern (44 bp):
TTATTATTTTCTATTTTATTTAATACTATTATTATTTATCTAAT
Found at i:3697310 original size:3 final size:3
Alignment explanation
Indices: 3697295--3697469 Score: 200
Period size: 3 Copynumber: 59.3 Consensus size: 3
3697285 TTTAAAACTT
*
3697295 TTA TTA CTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * *
3697343 TTA TTA TTA TTA TTA TTA TTA -TA TATA TGTA TCA ATA TCA TTA TT-
1 TTA TTA TTA TTA TTA TTA TTA TTA T-TA T-TA TTA TTA TTA TTA TTA
*
3697388 TTA TT- TTA TT- TTA TTA TATA TTA TTA TTA TCA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA
* * * *
3697432 CTA TTA GTA CTA TTA TTA TT- TT- TTA TTA TTA TTT TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
3697470 ATTTATTTAT
Statistics
Matches: 147, Mismatches: 18, Indels: 14
0.82 0.10 0.08
Matches are distributed among these distances:
2 12 0.08
3 126 0.86
4 9 0.06
ACGTcount: A:0.32, C:0.03, G:0.01, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:3699118 original size:27 final size:26
Alignment explanation
Indices: 3699077--3699152 Score: 127
Period size: 27 Copynumber: 2.9 Consensus size: 26
3699067 CCCTCCCAAA
3699077 AAAAAACCTAACCCCCAAAAAAAAAG
1 AAAAAACCTAACCCCCAAAAAAAAAG
*
3699103 AAAAAACCTAACCCCCCCAAAAAAAAG
1 AAAAAACCTAA-CCCCCAAAAAAAAAG
3699130 AAAAAACCTAA-CCCCAAAAAAAA
1 AAAAAACCTAACCCCCAAAAAAAA
3699153 CCAAGAAACT
Statistics
Matches: 47, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
25 11 0.23
26 11 0.23
27 25 0.53
ACGTcount: A:0.64, C:0.29, G:0.03, T:0.04
Consensus pattern (26 bp):
AAAAAACCTAACCCCCAAAAAAAAAG
Found at i:3714391 original size:13 final size:13
Alignment explanation
Indices: 3714373--3714422 Score: 57
Period size: 13 Copynumber: 3.8 Consensus size: 13
3714363 TATATACATC
3714373 ATAATAAAAAAAT
1 ATAATAAAAAAAT
*
3714386 ATAATAAAAATAT
1 ATAATAAAAAAAT
*
3714399 ATATACAAAACAAAT
1 ATA-ATAAAA-AAAT
3714414 ATAA-AAAAA
1 ATAATAAAAA
3714423 TTACCTTTTC
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
12 1 0.03
13 19 0.59
14 6 0.19
15 6 0.19
ACGTcount: A:0.74, C:0.04, G:0.00, T:0.22
Consensus pattern (13 bp):
ATAATAAAAAAAT
Found at i:3714888 original size:21 final size:23
Alignment explanation
Indices: 3714862--3714904 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
3714852 ATACTTCTTG
*
3714862 TATATT-TCT-ATGTATATACTT
1 TATATTGTCTCATGTACATACTT
3714883 TATATTGTCTCATGTACATACT
1 TATATTGTCTCATGTACATACT
3714905 CCGAAATACT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 6 0.32
22 3 0.16
23 10 0.53
ACGTcount: A:0.28, C:0.14, G:0.07, T:0.51
Consensus pattern (23 bp):
TATATTGTCTCATGTACATACTT
Found at i:3715242 original size:16 final size:15
Alignment explanation
Indices: 3715218--3715252 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
3715208 TAATTATTAT
3715218 TATTCTAATATTTTGA
1 TATTCTAATATTTT-A
*
3715234 TATTTTAATATTTTA
1 TATTCTAATATTTTA
3715249 TATT
1 TATT
3715253 ATTCACATCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 5 0.28
16 13 0.72
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.63
Consensus pattern (15 bp):
TATTCTAATATTTTA
Found at i:3717109 original size:17 final size:17
Alignment explanation
Indices: 3717078--3717114 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
3717068 TTAAAATAAA
3717078 AATAAAAATCTTAAAAC
1 AATAAAAATCTTAAAAC
*
3717095 AATAATAAATCTAAAAAC
1 AATAA-AAATCTTAAAAC
3717113 AA
1 AA
3717115 AGTTTTAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 5 0.28
18 13 0.72
ACGTcount: A:0.68, C:0.11, G:0.00, T:0.22
Consensus pattern (17 bp):
AATAAAAATCTTAAAAC
Found at i:3717259 original size:7 final size:7
Alignment explanation
Indices: 3717247--3717276 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
3717237 AAATTATAAA
3717247 AATTATT
1 AATTATT
3717254 AATTATT
1 AATTATT
3717261 AATTATT
1 AATTATT
*
3717268 AGTTATT
1 AATTATT
3717275 AA
1 AA
3717277 AAATTCTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.53
Consensus pattern (7 bp):
AATTATT
Found at i:3717281 original size:17 final size:17
Alignment explanation
Indices: 3717238--3717281 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 17
3717228 AATTATAAAA
3717238 AATTA-TAAAAATTATT
1 AATTATTAAAAATTATT
3717254 AATTATT---AATTATT
1 AATTATTAAAAATTATT
*
3717268 AGTTATTAAAAATT
1 AATTATTAAAAATT
3717282 CTAAATATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 7
0.74 0.03 0.23
Matches are distributed among these distances:
14 13 0.57
16 5 0.22
17 5 0.22
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (17 bp):
AATTATTAAAAATTATT
Found at i:3726980 original size:9 final size:9
Alignment explanation
Indices: 3726958--3727001 Score: 63
Period size: 9 Copynumber: 4.9 Consensus size: 9
3726948 TGACATGTAC
3726958 AATTAAAAA
1 AATTAAAAA
3726967 CAATTAAAAA
1 -AATTAAAAA
3726977 AATTAAAAA
1 AATTAAAAA
*
3726986 AA-CAAAAA
1 AATTAAAAA
3726994 AATTAAAA
1 AATTAAAA
3727002 TACAAAAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
8 7 0.23
9 15 0.48
10 9 0.29
ACGTcount: A:0.77, C:0.05, G:0.00, T:0.18
Consensus pattern (9 bp):
AATTAAAAA
Found at i:3727012 original size:17 final size:17
Alignment explanation
Indices: 3726958--3727011 Score: 65
Period size: 16 Copynumber: 3.1 Consensus size: 17
3726948 TGACATGTAC
*
3726958 AATTAAAAACAATTAAAAA
1 AATTAAAAA-AA-CAAAAA
3726977 AATTAAAAAAACAAAAA
1 AATTAAAAAAACAAAAA
*
3726994 AATT-AAAATACAAAAA
1 AATTAAAAAAACAAAAA
3727010 AA
1 AA
3727012 AAACACTGGT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
16 13 0.39
17 9 0.27
18 2 0.06
19 9 0.27
ACGTcount: A:0.78, C:0.06, G:0.00, T:0.17
Consensus pattern (17 bp):
AATTAAAAAAACAAAAA
Found at i:3727125 original size:3 final size:3
Alignment explanation
Indices: 3727119--3727167 Score: 50
Period size: 3 Copynumber: 16.7 Consensus size: 3
3727109 CCGACTCCTC
*
3727119 CTT CTT C-T CTT CTTT CTT -TT CTT CTT CTC CTT CTTT CTT -TT CTT
1 CTT CTT CTT CTT C-TT CTT CTT CTT CTT CTT CTT C-TT CTT CTT CTT
3727163 CTT CT
1 CTT CT
3727168 CTTTCTTTAT
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
2 6 0.15
3 27 0.69
4 6 0.15
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
CTT
Found at i:3727141 original size:12 final size:12
Alignment explanation
Indices: 3727120--3727171 Score: 56
Period size: 12 Copynumber: 4.5 Consensus size: 12
3727110 CGACTCCTCC
*
3727120 TTCTTCTCTTCT
1 TTCTTTTCTTCT
3727132 TTCTTTTCTTC-
1 TTCTTTTCTTCT
*
3727143 TTC--TCCTTCT
1 TTCTTTTCTTCT
3727153 TTCTTTTCTTCT
1 TTCTTTTCTTCT
3727165 TCTCTTT
1 T-TCTTT
3727172 CTTTATTTTC
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
9 5 0.15
10 3 0.09
11 3 0.09
12 17 0.52
13 5 0.15
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (12 bp):
TTCTTTTCTTCT
Found at i:3727142 original size:17 final size:17
Alignment explanation
Indices: 3727120--3727175 Score: 60
Period size: 17 Copynumber: 3.1 Consensus size: 17
3727110 CGACTCCTCC
3727120 TTCTTCTCTTCTTTCTTTT
1 TTCTTCTCTTCTTTC--TT
3727139 CTTCTTCTCCTTCTTTCTT
1 -TTCTTCT-CTTCTTTCTT
3727158 TTCTTCT-TCTCTTTCTT
1 TTCTTCTCT-TCTTTCTT
3727175 T
1 T
3727176 ATTTTCCTCT
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
16 1 0.03
17 9 0.26
18 7 0.21
19 2 0.06
20 7 0.21
21 8 0.24
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (17 bp):
TTCTTCTCTTCTTTCTT
Found at i:3727153 original size:21 final size:21
Alignment explanation
Indices: 3727119--3727208 Score: 137
Period size: 21 Copynumber: 4.3 Consensus size: 21
3727109 CCGACTCCTC
3727119 CTTCTTCT-CTTCTTTCTTTT
1 CTTCTTCTCCTTCTTTCTTTT
3727139 CTTCTTCTCCTTCTTTCTTTT
1 CTTCTTCTCCTTCTTTCTTTT
* *
3727160 CTTCTTCTCTTTCTTTATTTT
1 CTTCTTCTCCTTCTTTCTTTT
* *
3727181 CCTCTTCTCCTTATTTCTTTT
1 CTTCTTCTCCTTCTTTCTTTT
3727202 CTTCTTC
1 CTTCTTC
3727209 CCGAAATGGA
Statistics
Matches: 62, Mismatches: 7, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
20 8 0.13
21 54 0.87
ACGTcount: A:0.02, C:0.31, G:0.00, T:0.67
Consensus pattern (21 bp):
CTTCTTCTCCTTCTTTCTTTT
Found at i:3727172 original size:12 final size:12
Alignment explanation
Indices: 3727119--3727174 Score: 54
Period size: 9 Copynumber: 5.2 Consensus size: 12
3727109 CCGACTCCTC
3727119 CTTCTTCTC-TT
1 CTTCTTCTCTTT
3727130 C-T-TTCT-TTT
1 CTTCTTCTCTTT
*
3727139 CTTCTTCTCCTT
1 CTTCTTCTCTTT
3727151 C-T-TTCT-TTT
1 CTTCTTCTCTTT
3727160 CTTCTTCTCTTT
1 CTTCTTCTCTTT
3727172 CTT
1 CTT
3727175 TATTTTCCTC
Statistics
Matches: 36, Mismatches: 2, Indels: 13
0.71 0.04 0.25
Matches are distributed among these distances:
9 10 0.28
10 7 0.19
11 10 0.28
12 9 0.25
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (12 bp):
CTTCTTCTCTTT
Found at i:3727490 original size:9 final size:9
Alignment explanation
Indices: 3727468--3727511 Score: 63
Period size: 9 Copynumber: 4.9 Consensus size: 9
3727458 TGACATGTAC
3727468 AATTAAAAA
1 AATTAAAAA
3727477 CAATTAAAAA
1 -AATTAAAAA
3727487 AATTAAAAA
1 AATTAAAAA
*
3727496 AA-CAAAAA
1 AATTAAAAA
3727504 AATTAAAA
1 AATTAAAA
3727512 TACAAAAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
8 7 0.23
9 15 0.48
10 9 0.29
ACGTcount: A:0.77, C:0.05, G:0.00, T:0.18
Consensus pattern (9 bp):
AATTAAAAA
Found at i:3727522 original size:17 final size:17
Alignment explanation
Indices: 3727468--3727521 Score: 65
Period size: 16 Copynumber: 3.1 Consensus size: 17
3727458 TGACATGTAC
*
3727468 AATTAAAAACAATTAAAAA
1 AATTAAAAA-AA-CAAAAA
3727487 AATTAAAAAAACAAAAA
1 AATTAAAAAAACAAAAA
*
3727504 AATT-AAAATACAAAAA
1 AATTAAAAAAACAAAAA
3727520 AA
1 AA
3727522 AAACACTGGT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
16 13 0.39
17 9 0.27
18 2 0.06
19 9 0.27
ACGTcount: A:0.78, C:0.06, G:0.00, T:0.17
Consensus pattern (17 bp):
AATTAAAAAAACAAAAA
Found at i:3727635 original size:3 final size:3
Alignment explanation
Indices: 3727629--3727677 Score: 50
Period size: 3 Copynumber: 16.7 Consensus size: 3
3727619 CCGACTCCTC
*
3727629 CTT CTT C-T CTT CTTT CTT -TT CTT CTT CTC CTT CTTT CTT -TT CTT
1 CTT CTT CTT CTT C-TT CTT CTT CTT CTT CTT CTT C-TT CTT CTT CTT
3727673 CTT CT
1 CTT CT
3727678 CTTTCTTTAT
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
2 6 0.15
3 27 0.69
4 6 0.15
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
CTT
Found at i:3727651 original size:12 final size:12
Alignment explanation
Indices: 3727630--3727681 Score: 56
Period size: 12 Copynumber: 4.5 Consensus size: 12
3727620 CGACTCCTCC
*
3727630 TTCTTCTCTTCT
1 TTCTTTTCTTCT
3727642 TTCTTTTCTTC-
1 TTCTTTTCTTCT
*
3727653 TTC--TCCTTCT
1 TTCTTTTCTTCT
3727663 TTCTTTTCTTCT
1 TTCTTTTCTTCT
3727675 TCTCTTT
1 T-TCTTT
3727682 CTTTATTTTC
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
9 5 0.15
10 3 0.09
11 3 0.09
12 17 0.52
13 5 0.15
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (12 bp):
TTCTTTTCTTCT
Found at i:3727652 original size:17 final size:17
Alignment explanation
Indices: 3727630--3727685 Score: 60
Period size: 17 Copynumber: 3.1 Consensus size: 17
3727620 CGACTCCTCC
3727630 TTCTTCTCTTCTTTCTTTT
1 TTCTTCTCTTCTTTC--TT
3727649 CTTCTTCTCCTTCTTTCTT
1 -TTCTTCT-CTTCTTTCTT
3727668 TTCTTCT-TCTCTTTCTT
1 TTCTTCTCT-TCTTTCTT
3727685 T
1 T
3727686 ATTTTCCTCT
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
16 1 0.03
17 9 0.26
18 7 0.21
19 2 0.06
20 7 0.21
21 8 0.24
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (17 bp):
TTCTTCTCTTCTTTCTT
Found at i:3727663 original size:21 final size:21
Alignment explanation
Indices: 3727629--3727718 Score: 137
Period size: 21 Copynumber: 4.3 Consensus size: 21
3727619 CCGACTCCTC
3727629 CTTCTTCT-CTTCTTTCTTTT
1 CTTCTTCTCCTTCTTTCTTTT
3727649 CTTCTTCTCCTTCTTTCTTTT
1 CTTCTTCTCCTTCTTTCTTTT
* *
3727670 CTTCTTCTCTTTCTTTATTTT
1 CTTCTTCTCCTTCTTTCTTTT
* *
3727691 CCTCTTCTCCTTATTTCTTTT
1 CTTCTTCTCCTTCTTTCTTTT
3727712 CTTCTTC
1 CTTCTTC
3727719 CCGAAATGGA
Statistics
Matches: 62, Mismatches: 7, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
20 8 0.13
21 54 0.87
ACGTcount: A:0.02, C:0.31, G:0.00, T:0.67
Consensus pattern (21 bp):
CTTCTTCTCCTTCTTTCTTTT
Found at i:3727682 original size:12 final size:12
Alignment explanation
Indices: 3727629--3727684 Score: 54
Period size: 9 Copynumber: 5.2 Consensus size: 12
3727619 CCGACTCCTC
3727629 CTTCTTCTC-TT
1 CTTCTTCTCTTT
3727640 C-T-TTCT-TTT
1 CTTCTTCTCTTT
*
3727649 CTTCTTCTCCTT
1 CTTCTTCTCTTT
3727661 C-T-TTCT-TTT
1 CTTCTTCTCTTT
3727670 CTTCTTCTCTTT
1 CTTCTTCTCTTT
3727682 CTT
1 CTT
3727685 TATTTTCCTC
Statistics
Matches: 36, Mismatches: 2, Indels: 13
0.71 0.04 0.25
Matches are distributed among these distances:
9 10 0.28
10 7 0.19
11 10 0.28
12 9 0.25
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (12 bp):
CTTCTTCTCTTT
Found at i:3727781 original size:510 final size:510
Alignment explanation
Indices: 3726822--3727844 Score: 2028
Period size: 510 Copynumber: 2.0 Consensus size: 510
3726812 TTTTCTCTTT
3726822 CAACATCAAAAAAAATGTATAAAATAATTTAAAAAATACCAAAATGGTACTAATAGCAAATTATT
1 CAACATCAAAAAAAATGTATAAAATAATTTAAAAAATACCAAAATGGTACTAATAGCAAATTATT
3726887 GACGAAAATGTTACGGGGAGGGTGGTGCCGCGTATGGAAGAGGCGTGACCACCTTCCCAGCTGAC
66 GACGAAAATGTTACGGGGAGGGTGGTGCCGCGTATGGAAGAGGCGTGACCACCTTCCCAGCTGAC
3726952 ATGTACAATTAAAAACAATTAAAAAAATTAAAAAAACAAAAAAATTAAAATACAAAAAAAAAACA
131 ATGTACAATTAAAAACAATTAAAAAAATTAAAAAAACAAAAAAATTAAAATACAAAAAAAAAACA
3727017 CTGGTCAAACTGACATGCCAACTTTCTTTTTCCTTCCTTCCTTCCCTCCCTCTTCTTCTCCTTCT
196 CTGGTCAAACTGACATGCCAACTTTCTTTTTCCTTCCTTCCTTCCCTCCCTCTTCTTCTCCTTCT
3727082 CTTTTTCATTTTTCTTTCCCTCATCAGCCGACTCCTCCTTCTTCTCTTCTTTCTTTTCTTCTTCT
261 CTTTTTCATTTTTCTTTCCCTCATCAGCCGACTCCTCCTTCTTCTCTTCTTTCTTTTCTTCTTCT
3727147 CCTTCTTTCTTTTCTTCTTCTCTTTCTTTATTTTCCTCTTCTCCTTATTTCTTTTCTTCTTCCCG
326 CCTTCTTTCTTTTCTTCTTCTCTTTCTTTATTTTCCTCTTCTCCTTATTTCTTTTCTTCTTCCCG
3727212 AAATGGAGTTGGGGACCATAATATATGGTCCCAACACAGAAAAAACAAGGTGTGCATGCAGGAGA
391 AAATGGAGTTGGGGACCATAATATATGGTCCCAACACAGAAAAAACAAGGTGTGCATGCAGGAGA
* *
3727277 CCGGTCCTGCCTCTGCCATTGGCACCATCGGTGCCGCCTGTGGCAGGGACACCCC
456 CCGGTCCTGCCTCTGCCATTGGCACCATCGGTGCCGCCTGTGGCAGGCACACCAC
3727332 CAACATCAAAAAAAATGTATAAAATAATTTAAAAAATACCAAAATGGTACTAATAGCAAATTATT
1 CAACATCAAAAAAAATGTATAAAATAATTTAAAAAATACCAAAATGGTACTAATAGCAAATTATT
3727397 GACGAAAATGTTACGGGGAGGGTGGTGCCGCGTATGGAAGAGGCGTGACCACCTTCCCAGCTGAC
66 GACGAAAATGTTACGGGGAGGGTGGTGCCGCGTATGGAAGAGGCGTGACCACCTTCCCAGCTGAC
3727462 ATGTACAATTAAAAACAATTAAAAAAATTAAAAAAACAAAAAAATTAAAATACAAAAAAAAAACA
131 ATGTACAATTAAAAACAATTAAAAAAATTAAAAAAACAAAAAAATTAAAATACAAAAAAAAAACA
3727527 CTGGTCAAACTGACATGCCAACTTTCTTTTTCCTTCCTTCCTTCCCTCCCTCTTCTTCTCCTTCT
196 CTGGTCAAACTGACATGCCAACTTTCTTTTTCCTTCCTTCCTTCCCTCCCTCTTCTTCTCCTTCT
3727592 CTTTTTCATTTTTCTTTCCCTCATCAGCCGACTCCTCCTTCTTCTCTTCTTTCTTTTCTTCTTCT
261 CTTTTTCATTTTTCTTTCCCTCATCAGCCGACTCCTCCTTCTTCTCTTCTTTCTTTTCTTCTTCT
3727657 CCTTCTTTCTTTTCTTCTTCTCTTTCTTTATTTTCCTCTTCTCCTTATTTCTTTTCTTCTTCCCG
326 CCTTCTTTCTTTTCTTCTTCTCTTTCTTTATTTTCCTCTTCTCCTTATTTCTTTTCTTCTTCCCG
3727722 AAATGGAGTTGGGGACCATAATATATGGTCCCAACACAGAAAAAACAAGGTGTGCATGCAGGAGA
391 AAATGGAGTTGGGGACCATAATATATGGTCCCAACACAGAAAAAACAAGGTGTGCATGCAGGAGA
3727787 CCGGTCCTGCCTCTGCCATTGGCACCATCGGTGCCGCCTGTGGCAGGCACACCAC
456 CCGGTCCTGCCTCTGCCATTGGCACCATCGGTGCCGCCTGTGGCAGGCACACCAC
3727842 CAA
1 CAA
3727845 TCCAGCTTTT
Statistics
Matches: 511, Mismatches: 2, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
510 511 1.00
ACGTcount: A:0.29, C:0.26, G:0.14, T:0.32
Consensus pattern (510 bp):
CAACATCAAAAAAAATGTATAAAATAATTTAAAAAATACCAAAATGGTACTAATAGCAAATTATT
GACGAAAATGTTACGGGGAGGGTGGTGCCGCGTATGGAAGAGGCGTGACCACCTTCCCAGCTGAC
ATGTACAATTAAAAACAATTAAAAAAATTAAAAAAACAAAAAAATTAAAATACAAAAAAAAAACA
CTGGTCAAACTGACATGCCAACTTTCTTTTTCCTTCCTTCCTTCCCTCCCTCTTCTTCTCCTTCT
CTTTTTCATTTTTCTTTCCCTCATCAGCCGACTCCTCCTTCTTCTCTTCTTTCTTTTCTTCTTCT
CCTTCTTTCTTTTCTTCTTCTCTTTCTTTATTTTCCTCTTCTCCTTATTTCTTTTCTTCTTCCCG
AAATGGAGTTGGGGACCATAATATATGGTCCCAACACAGAAAAAACAAGGTGTGCATGCAGGAGA
CCGGTCCTGCCTCTGCCATTGGCACCATCGGTGCCGCCTGTGGCAGGCACACCAC
Found at i:3727872 original size:20 final size:20
Alignment explanation
Indices: 3727847--3727896 Score: 75
Period size: 19 Copynumber: 2.5 Consensus size: 20
3727837 ACCACCAATC
3727847 CAGCTTTTTTTTTTCAAATT
1 CAGCTTTTTTTTTTCAAATT
**
3727867 CAGC-TTTTTTTTTCAGTTT
1 CAGCTTTTTTTTTTCAAATT
3727886 CAGCTTTTTTT
1 CAGCTTTTTTT
3727897 CAGCTACTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
19 17 0.63
20 10 0.37
ACGTcount: A:0.14, C:0.16, G:0.08, T:0.62
Consensus pattern (20 bp):
CAGCTTTTTTTTTTCAAATT
Found at i:3728812 original size:20 final size:20
Alignment explanation
Indices: 3728787--3728854 Score: 54
Period size: 20 Copynumber: 3.5 Consensus size: 20
3728777 TTTAAGATAC
3728787 AACAATTATTACTATTTTTT
1 AACAATTATTACTATTTTTT
* *
3728807 AACAATCTTTTA-TAATTTTT
1 AACAAT-TATTACTATTTTTT
* * *
3728827 AATAATT-CTACGATTTTTT
1 AACAATTATTACTATTTTTT
3728846 -ACAA-TATTA
1 AACAATTATTA
3728855 TACAATTTCT
Statistics
Matches: 37, Mismatches: 8, Indels: 8
0.70 0.15 0.15
Matches are distributed among these distances:
17 1 0.03
18 7 0.19
19 7 0.19
20 18 0.49
21 4 0.11
ACGTcount: A:0.37, C:0.10, G:0.01, T:0.51
Consensus pattern (20 bp):
AACAATTATTACTATTTTTT
Found at i:3729925 original size:27 final size:27
Alignment explanation
Indices: 3729877--3729928 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
3729867 CGATATCATA
*
3729877 AATAGTTTGACGAGACATTAAACATGG
1 AATAGTTTGACGAGACACTAAACATGG
* * *
3729904 AATAGTTTGATGGGACGCTAAACAT
1 AATAGTTTGACGAGACACTAAACAT
3729929 CATCTAGTAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.38, C:0.12, G:0.23, T:0.27
Consensus pattern (27 bp):
AATAGTTTGACGAGACACTAAACATGG
Found at i:3730711 original size:30 final size:29
Alignment explanation
Indices: 3730677--3730742 Score: 89
Period size: 30 Copynumber: 2.2 Consensus size: 29
3730667 CCCAGCCACC
3730677 CCCAATCC-AGATAAAAATTTATAAACCCAA
1 CCCAATCCGA-ATAAAAATTTAT-AACCCAA
*
3730707 CCCAATTCGAATAAAAATTTATAACCCAA
1 CCCAATCCGAATAAAAATTTATAACCCAA
*
3730736 TCCAATC
1 CCCAATC
3730743 TAAATAATTA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
29 12 0.38
30 19 0.59
31 1 0.03
ACGTcount: A:0.47, C:0.27, G:0.03, T:0.23
Consensus pattern (29 bp):
CCCAATCCGAATAAAAATTTATAACCCAA
Found at i:3733027 original size:54 final size:54
Alignment explanation
Indices: 3732968--3733076 Score: 209
Period size: 54 Copynumber: 2.0 Consensus size: 54
3732958 TTAGTGAAAC
*
3732968 TGTGAAATTGGTTTGAAATTAAGATGATTCATGTTATTATATGAATTAAATGAG
1 TGTGAAATTGGTTTGAAATTAAGATGATTCATGCTATTATATGAATTAAATGAG
3733022 TGTGAAATTGGTTTGAAATTAAGATGATTCATGCTATTATATGAATTAAATGAG
1 TGTGAAATTGGTTTGAAATTAAGATGATTCATGCTATTATATGAATTAAATGAG
3733076 T
1 T
3733077 ATTTGATTAA
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 54 1.00
ACGTcount: A:0.37, C:0.03, G:0.20, T:0.40
Consensus pattern (54 bp):
TGTGAAATTGGTTTGAAATTAAGATGATTCATGCTATTATATGAATTAAATGAG
Found at i:3733068 original size:27 final size:26
Alignment explanation
Indices: 3732984--3733074 Score: 76
Period size: 27 Copynumber: 3.4 Consensus size: 26
3732974 ATTGGTTTGA
*
3732984 AATTAAGATGATTCATGTTATTATATG
1 AATTAA-ATGATTCATGATATTATATG
* * * * *
3733011 AATTAAATGAGT-GTGAAATTGGTTTG
1 AATTAAATGATTCATGATATT-ATATG
*
3733037 AAATTAAGATGATTCATGCTATTATATG
1 -AATTAA-ATGATTCATGATATTATATG
3733065 AATTAAATGA
1 AATTAAATGA
3733075 GTATTTGATT
Statistics
Matches: 48, Mismatches: 12, Indels: 9
0.70 0.17 0.13
Matches are distributed among these distances:
25 5 0.10
26 12 0.25
27 18 0.38
28 8 0.17
29 5 0.10
ACGTcount: A:0.40, C:0.03, G:0.18, T:0.40
Consensus pattern (26 bp):
AATTAAATGATTCATGATATTATATG
Found at i:3733707 original size:26 final size:30
Alignment explanation
Indices: 3733651--3733707 Score: 68
Period size: 30 Copynumber: 2.0 Consensus size: 30
3733641 TAAATTGATT
**
3733651 AAATGTTGATTGATTATGTGAATGACACTG
1 AAATGTTGATTGATTATGTGAACAACACTG
3733681 AAATGTTGATT-A-TATGT-AACAAC-CTG
1 AAATGTTGATTGATTATGTGAACAACACTG
3733707 A
1 A
3733708 TTTTGGGCTT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
26 4 0.16
27 4 0.16
28 5 0.20
29 1 0.04
30 11 0.44
ACGTcount: A:0.37, C:0.09, G:0.19, T:0.35
Consensus pattern (30 bp):
AAATGTTGATTGATTATGTGAACAACACTG
Found at i:3733824 original size:38 final size:38
Alignment explanation
Indices: 3733771--3733843 Score: 137
Period size: 38 Copynumber: 1.9 Consensus size: 38
3733761 AAGAATTTTA
3733771 TTATTATTTTAGAGTTATAGCATGTTTATATTAGTATT
1 TTATTATTTTAGAGTTATAGCATGTTTATATTAGTATT
*
3733809 TTATTATTTTGGAGTTATAGCATGTTTATATTAGT
1 TTATTATTTTAGAGTTATAGCATGTTTATATTAGT
3733844 GCATGAAAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.27, C:0.03, G:0.15, T:0.55
Consensus pattern (38 bp):
TTATTATTTTAGAGTTATAGCATGTTTATATTAGTATT
Found at i:3733856 original size:38 final size:38
Alignment explanation
Indices: 3733776--3733858 Score: 103
Period size: 38 Copynumber: 2.2 Consensus size: 38
3733766 TTTTATTATT
* ** * **
3733776 ATTTTAGAGTTATAGCATGTTTATATTAGTATTTTATT
1 ATTTTGGAGTTATAGCATGTTTATATTAGTACATGAAA
*
3733814 ATTTTGGAGTTATAGCATGTTTATATTAGTGCATGAAA
1 ATTTTGGAGTTATAGCATGTTTATATTAGTACATGAAA
3733852 ATTTTGG
1 ATTTTGG
3733859 TGAAGTAATT
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.29, C:0.04, G:0.18, T:0.49
Consensus pattern (38 bp):
ATTTTGGAGTTATAGCATGTTTATATTAGTACATGAAA
Found at i:3735007 original size:48 final size:48
Alignment explanation
Indices: 3734947--3735066 Score: 143
Period size: 48 Copynumber: 2.5 Consensus size: 48
3734937 GTTGTGTGCG
**
3734947 AGTGTAAGACATGTCTAGGACATGCATCGGCCTCGAGATATTTAAGCC
1 AGTGTAAGACATGTCTAGGACATGCATCGGCCTCGAGATATACAAGCC
* * ** * *
3734995 AGTTTAAGACATGTTTACTACATGCATCGGCCTCGCGATATACAAGCT
1 AGTGTAAGACATGTCTAGGACATGCATCGGCCTCGAGATATACAAGCC
*
3735043 AGTGTAAGACCTGTCT-GAGACATG
1 AGTGTAAGACATGTCTAG-GACATG
3735067 GCGTCAGCTT
Statistics
Matches: 58, Mismatches: 13, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
48 58 1.00
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.27
Consensus pattern (48 bp):
AGTGTAAGACATGTCTAGGACATGCATCGGCCTCGAGATATACAAGCC
Found at i:3735148 original size:49 final size:49
Alignment explanation
Indices: 3735086--3735211 Score: 182
Period size: 49 Copynumber: 2.6 Consensus size: 49
3735076 TGTGGTTTAT
* *
3735086 CAGTGTAAGACCTGTCTGGGACATGGCATCGACAC-CTATAGATGAGAGC
1 CAGTGTAAGACCTGTCTGGGACATGGCATCGAC-CTCAATAGATGAAAGC
* * *
3735135 CAGTGTAAAACCTGTCTGGGACATGGCATCGGCCTCAATATATGAAAGC
1 CAGTGTAAGACCTGTCTGGGACATGGCATCGACCTCAATAGATGAAAGC
3735184 CAGTGTAAGACCATGTCTGGGACATGGC
1 CAGTGTAAGACC-TGTCTGGGACATGGC
3735212 GTTGGTATCT
Statistics
Matches: 69, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
48 1 0.01
49 53 0.77
50 15 0.22
ACGTcount: A:0.29, C:0.22, G:0.28, T:0.21
Consensus pattern (49 bp):
CAGTGTAAGACCTGTCTGGGACATGGCATCGACCTCAATAGATGAAAGC
Found at i:3741553 original size:61 final size:61
Alignment explanation
Indices: 3741488--3741675 Score: 145
Period size: 61 Copynumber: 3.1 Consensus size: 61
3741478 TTCAAATTAT
* *
3741488 ATTTTATAGTATCATATATTATAATTTTAGTAAATTCATATAAGAATAAAGAATATTAAGA
1 ATTTTATAGTATCATATATTATAATTTAAGTAAATTAATATAAGAATAAAGAATATTAAGA
* * * * * * * * * *
3741549 ATTTTATTA-AATCATATATTTTAATTAAAATATATTTA-ATAATAATTATGTTAAT-TT-A-T
1 ATTTTA-TAGTATCATATATTATAATTTAAGTAAATTAATATAAGAATAAAG--AATATTAAGA
* * * * *
3741608 ATTTTACAGTATCATATATTATGATTTCAGTAAATTAATATAAGAATATTA-ATTATTAAGA
1 ATTTTATAGTATCATATATTATAATTTAAGTAAATTAATATAAGAATA-AAGAATATTAAGA
3741669 ATTTTAT
1 ATTTTAT
3741676 TAAATTATAT
Statistics
Matches: 91, Mismatches: 27, Indels: 18
0.67 0.20 0.13
Matches are distributed among these distances:
58 3 0.03
59 29 0.32
60 18 0.20
61 36 0.40
62 5 0.05
ACGTcount: A:0.45, C:0.03, G:0.06, T:0.46
Consensus pattern (61 bp):
ATTTTATAGTATCATATATTATAATTTAAGTAAATTAATATAAGAATAAAGAATATTAAGA
Found at i:3741609 original size:120 final size:121
Alignment explanation
Indices: 3741452--3741725 Score: 419
Period size: 120 Copynumber: 2.3 Consensus size: 121
3741442 ATATATCACT
* * * *
3741452 ATTAAATTATATTTAATATTAATTAT-TTCAAATTATATTTTATAGTATCATATATTATAATTTT
1 ATTAAAATATATTTAATAATAATTATGTTCAAATTATATTTTACAGTATCATATATTATAATTTC
*
3741516 AGTAAATTCATATAAGAATA-AAGAATATTAAGAATTTTATTAAATCATATATTTTA
66 AGTAAATTAATATAAGAATATAA-AATATTAAGAATTTTATTAAATCATATATTTTA
* *
3741572 ATTAAAATATATTTAATAATAATTATGTT-AATTTATATTTTACAGTATCATATATTATGATTTC
1 ATTAAAATATATTTAATAATAATTATGTTCAAATTATATTTTACAGTATCATATATTATAATTTC
* * *
3741636 AGTAAATTAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATATTTTA
66 AGTAAATTAATATAAGAATATAAAATATTAAGAATTTTATTAAATCATATATTTTA
*
3741692 ATTAAAATATATTTAATAATAATTATGTTTAAAT
1 ATTAAAATATATTTAATAATAATTATGTTCAAAT
3741726 ATGATTAAAT
Statistics
Matches: 140, Mismatches: 11, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
120 134 0.96
121 6 0.04
ACGTcount: A:0.45, C:0.03, G:0.04, T:0.48
Consensus pattern (121 bp):
ATTAAAATATATTTAATAATAATTATGTTCAAATTATATTTTACAGTATCATATATTATAATTTC
AGTAAATTAATATAAGAATATAAAATATTAAGAATTTTATTAAATCATATATTTTA
Found at i:3741697 original size:18 final size:17
Alignment explanation
Indices: 3741669--3741703 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
3741659 ATTATTAAGA
*
3741669 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
3741686 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
3741704 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:3741917 original size:44 final size:45
Alignment explanation
Indices: 3741868--3741958 Score: 121
Period size: 45 Copynumber: 2.0 Consensus size: 45
3741858 ACCTCTATTC
* * *
3741868 CATTCAACCAAACACAAGATTA-CTATTACGCCTCTATTCCATTA
1 CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
***
3741912 CATTCAACCAAACAGTGGATTAGCTATTACACCTCTAATCCAATA
1 CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
3741957 CA
1 CA
3741959 CCTCTAATCC
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 19 0.47
45 21 0.52
ACGTcount: A:0.37, C:0.29, G:0.07, T:0.27
Consensus pattern (45 bp):
CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
Found at i:3741960 original size:16 final size:16
Alignment explanation
Indices: 3741939--3742007 Score: 129
Period size: 16 Copynumber: 4.2 Consensus size: 16
3741929 GATTAGCTAT
3741939 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
3741955 TACACCTCTAATCCCAA
1 TACACCTCTAAT-CCAA
3741972 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
3741988 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
3742004 TACA
1 TACA
3742008 GCGAACCAAA
Statistics
Matches: 52, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
16 36 0.69
17 16 0.31
ACGTcount: A:0.38, C:0.38, G:0.00, T:0.25
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:3741981 original size:33 final size:32
Alignment explanation
Indices: 3741939--3742007 Score: 129
Period size: 33 Copynumber: 2.1 Consensus size: 32
3741929 GATTAGCTAT
3741939 TACACCTCTAATCCAATACACCTCTAATCCCAA
1 TACACCTCTAATCCAATACACCTCTAAT-CCAA
3741972 TACACCTCTAATCCAATACACCTCTAATCCAA
1 TACACCTCTAATCCAATACACCTCTAATCCAA
3742004 TACA
1 TACA
3742008 GCGAACCAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 8 0.22
33 28 0.78
ACGTcount: A:0.38, C:0.38, G:0.00, T:0.25
Consensus pattern (32 bp):
TACACCTCTAATCCAATACACCTCTAATCCAA
Found at i:3742828 original size:12 final size:12
Alignment explanation
Indices: 3742811--3742839 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
3742801 AGTGTATCCA
3742811 AGGGTGAAAGTG
1 AGGGTGAAAGTG
3742823 AGGGTGAAAGTG
1 AGGGTGAAAGTG
3742835 AGGGT
1 AGGGT
3742840 TCAAGAAGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.31, C:0.00, G:0.52, T:0.17
Consensus pattern (12 bp):
AGGGTGAAAGTG
Found at i:3749215 original size:5 final size:5
Alignment explanation
Indices: 3749205--3749230 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
3749195 GAGATGGAAT
3749205 TCGAA TCGAA TCGAA TCGAA TCGAA T
1 TCGAA TCGAA TCGAA TCGAA TCGAA T
3749231 ATATTTGTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.23
Consensus pattern (5 bp):
TCGAA
Found at i:3749776 original size:15 final size:15
Alignment explanation
Indices: 3749741--3749799 Score: 66
Period size: 15 Copynumber: 4.0 Consensus size: 15
3749731 AAGAGTGAGA
**
3749741 AGTAAAATTTTAGAA
1 AGTAAAATTTTAGGG
3749756 AGTAAAATTTTAGGG
1 AGTAAAATTTTAGGG
* *
3749771 A-TTAAATTTAAGGG
1 AGTAAAATTTTAGGG
*
3749785 GGTAAAATTTTAGGG
1 AGTAAAATTTTAGGG
3749800 GAAAATAAAA
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
14 11 0.31
15 25 0.69
ACGTcount: A:0.42, C:0.00, G:0.24, T:0.34
Consensus pattern (15 bp):
AGTAAAATTTTAGGG
Found at i:3759563 original size:55 final size:55
Alignment explanation
Indices: 3759441--3759570 Score: 136
Period size: 55 Copynumber: 2.4 Consensus size: 55
3759431 TGCGACATAG
* * * * *
3759441 CCGTGGTCAAACCTGTCAAAACAACACGGGCGTTAGACACGCCCGTGTGGAAGAA
1 CCGTGGTCGAACCTGTCAAAACAACAAGGGCGTGAGACACGCCCGTGTCGAACAA
* * * * * * *
3759496 CTGTGGGT-GAACCTGTTAAAATAGCAAGGGCGTGCGACACGCCCGTGTCTAACAC
1 CCGT-GGTCGAACCTGTCAAAACAACAAGGGCGTGAGACACGCCCGTGTCGAACAA
3759551 CCGTGGTCGAACCTGTCAAA
1 CCGTGGTCGAACCTGTCAAA
3759571 TTAACACGGG
Statistics
Matches: 59, Mismatches: 14, Indels: 4
0.77 0.18 0.05
Matches are distributed among these distances:
54 3 0.05
55 53 0.90
56 3 0.05
ACGTcount: A:0.28, C:0.27, G:0.28, T:0.18
Consensus pattern (55 bp):
CCGTGGTCGAACCTGTCAAAACAACAAGGGCGTGAGACACGCCCGTGTCGAACAA
Found at i:3769680 original size:19 final size:19
Alignment explanation
Indices: 3769642--3769699 Score: 59
Period size: 19 Copynumber: 3.1 Consensus size: 19
3769632 TCTTTATATA
* *
3769642 TTATAAAT-TTTGGAATTT
1 TTATAAATATTTTGTATTT
3769660 TTATAAATATTTTGTATTT
1 TTATAAATATTTTGTATTT
3769679 TTGA-AAATTATTTT-TATTT
1 TT-ATAAA-TATTTTGTATTT
3769698 TT
1 TT
3769700 TGTAATTTAT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
18 8 0.23
19 20 0.57
20 7 0.20
ACGTcount: A:0.31, C:0.00, G:0.07, T:0.62
Consensus pattern (19 bp):
TTATAAATATTTTGTATTT
Found at i:3769680 original size:20 final size:19
Alignment explanation
Indices: 3769657--3769700 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
3769647 AATTTTGGAA
3769657 TTTTTATAAA-TATTTTGTAT
1 TTTTTA-AAATTATTTT-TAT
*
3769677 TTTTGAAAATTATTTTTAT
1 TTTTTAAAATTATTTTTAT
3769696 TTTTT
1 TTTTT
3769701 GTAATTTATG
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
19 10 0.48
20 11 0.52
ACGTcount: A:0.27, C:0.00, G:0.05, T:0.68
Consensus pattern (19 bp):
TTTTTAAAATTATTTTTAT
Found at i:3769706 original size:19 final size:19
Alignment explanation
Indices: 3769656--3769706 Score: 50
Period size: 20 Copynumber: 2.6 Consensus size: 19
3769646 AAATTTTGGA
* *
3769656 ATTTTTATAAATATTTTGT
1 ATTTTTGTAATTATTTTGT
*
3769675 ATTTTTGAAAATTATTTT-T
1 ATTTTTG-TAATTATTTTGT
3769694 ATTTTTTGTAATT
1 A-TTTTTGTAATT
3769707 TATGTTGAGA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
19 12 0.46
20 14 0.54
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (19 bp):
ATTTTTGTAATTATTTTGT
Found at i:3773818 original size:18 final size:18
Alignment explanation
Indices: 3773782--3773827 Score: 58
Period size: 18 Copynumber: 2.5 Consensus size: 18
3773772 ATTCGAAAAA
3773782 AATTCGAGTTAACTTAAAT
1 AATTCGA-TTAACTTAAAT
3773801 AATTCGATTAA-TTCAAAT
1 AATTCGATTAACTT-AAAT
*
3773819 AACTCGATT
1 AATTCGATT
3773828 CGTTTAACTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
17 2 0.08
18 16 0.64
19 7 0.28
ACGTcount: A:0.41, C:0.13, G:0.09, T:0.37
Consensus pattern (18 bp):
AATTCGATTAACTTAAAT
Found at i:3780759 original size:19 final size:18
Alignment explanation
Indices: 3780729--3780778 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
3780719 ATATGAATTG
*
3780729 AAAAATAAATATTCACATAT
1 AAAAAT-AATATTCAC-TAA
* *
3780749 AAAAATTATATTTACTAA
1 AAAAATAATATTCACTAA
3780767 AAAAATAATATT
1 AAAAATAATATT
3780779 TACAATAATT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
18 13 0.50
19 7 0.27
20 6 0.23
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.34
Consensus pattern (18 bp):
AAAAATAATATTCACTAA
Found at i:3781228 original size:16 final size:16
Alignment explanation
Indices: 3781204--3781234 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3781194 ATATATCGAT
3781204 AAATATAAAAAAATTA
1 AAATATAAAAAAATTA
*
3781220 AAATTTAAAAAAATT
1 AAATATAAAAAAATT
3781235 CAACCCAAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (16 bp):
AAATATAAAAAAATTA
Found at i:3783103 original size:11 final size:11
Alignment explanation
Indices: 3783089--3783122 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
3783079 TTTCTCTTAT
*
3783089 TCTTCTTTTTC
1 TCTTCTTCTTC
*
3783100 TCTTCTTCTCC
1 TCTTCTTCTTC
3783111 TCTTCTTCTTC
1 TCTTCTTCTTC
3783122 T
1 T
3783123 TCGACTGTCC
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:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (11 bp):
TCTTCTTCTTC
Done.