Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A08
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: 123748673
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 5630000 characters in sequence are not A, C, G, or T
File 19 of 373
Found at i:5407329 original size:21 final size:21
Alignment explanation
Indices: 5407277--5407317 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
5407267 ACAACTGACG
5407277 TTGGTTGTGGCTTGTGGAACC
1 TTGGTTGTGGCTTGTGGAACC
*
5407298 TTGTTTGTGGCTTGTGGAAC
1 TTGGTTGTGGCTTGTGGAAC
5407318 TGTGGTCGTG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.10, C:0.12, G:0.37, T:0.41
Consensus pattern (21 bp):
TTGGTTGTGGCTTGTGGAACC
Found at i:5407480 original size:35 final size:36
Alignment explanation
Indices: 5407434--5407504 Score: 135
Period size: 36 Copynumber: 2.0 Consensus size: 36
5407424 TAAAGAAGAA
5407434 AGGAAAAATTGGGGGA-GGGGTGGGAATTTGGAACG
1 AGGAAAAATTGGGGGAGGGGGTGGGAATTTGGAACG
5407469 AGGAAAAATTGGGGGAGGGGGTGGGAATTTGGAACG
1 AGGAAAAATTGGGGGAGGGGGTGGGAATTTGGAACG
5407505 GCAGAAAGAA
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
35 16 0.46
36 19 0.54
ACGTcount: A:0.31, C:0.03, G:0.49, T:0.17
Consensus pattern (36 bp):
AGGAAAAATTGGGGGAGGGGGTGGGAATTTGGAACG
Found at i:5407743 original size:11 final size:12
Alignment explanation
Indices: 5407714--5407745 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
5407704 TCAAAATTTA
*
5407714 AATTTTTTATCG
1 AATTTTTCATCG
5407726 AATTTTTCATCG
1 AATTTTTCATCG
5407738 AATTTTTC
1 AATTTTTC
5407746 GAATCGAGTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.25, C:0.12, G:0.06, T:0.56
Consensus pattern (12 bp):
AATTTTTCATCG
Found at i:5407838 original size:64 final size:64
Alignment explanation
Indices: 5407737--5407863 Score: 254
Period size: 64 Copynumber: 2.0 Consensus size: 64
5407727 ATTTTTCATC
5407737 GAATTTTTCGAATCGAGTCGGATTTTACTCACCCCTACTTGCAAACAAGCTAAAGAGGTTGTAT
1 GAATTTTTCGAATCGAGTCGGATTTTACTCACCCCTACTTGCAAACAAGCTAAAGAGGTTGTAT
5407801 GAATTTTTCGAATCGAGTCGGATTTTACTCACCCCTACTTGCAAACAAGCTAAAGAGGTTGTA
1 GAATTTTTCGAATCGAGTCGGATTTTACTCACCCCTACTTGCAAACAAGCTAAAGAGGTTGTA
5407864 AAAATCGGCT
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
64 63 1.00
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.31
Consensus pattern (64 bp):
GAATTTTTCGAATCGAGTCGGATTTTACTCACCCCTACTTGCAAACAAGCTAAAGAGGTTGTAT
Found at i:5410488 original size:41 final size:43
Alignment explanation
Indices: 5410412--5410495 Score: 154
Period size: 42 Copynumber: 2.0 Consensus size: 43
5410402 TACAATGACT
5410412 AATTTGTCAATTTTTTTAATAAATGGGGAGAAATGCAATCTAA
1 AATTTGTCAATTTTTTTAATAAATGGGGAGAAATGCAATCTAA
5410455 AATTTGTCAA-TTTTTTAATAAATGGGGAG-AATGCAATCTAA
1 AATTTGTCAATTTTTTTAATAAATGGGGAGAAATGCAATCTAA
5410496 CTCCTAAAAG
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
41 12 0.29
42 19 0.46
43 10 0.24
ACGTcount: A:0.39, C:0.07, G:0.17, T:0.37
Consensus pattern (43 bp):
AATTTGTCAATTTTTTTAATAAATGGGGAGAAATGCAATCTAA
Found at i:5410583 original size:18 final size:18
Alignment explanation
Indices: 5410556--5410595 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
5410546 CCTCCGTAAA
*
5410556 ATTACTTGCA-AAATTAAG
1 ATTACATGCATAAA-TAAG
5410574 ATTACATGCATAAATAAG
1 ATTACATGCATAAATAAG
5410592 ATTA
1 ATTA
5410596 AAAAACTTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 17 0.85
19 3 0.15
ACGTcount: A:0.47, C:0.10, G:0.10, T:0.33
Consensus pattern (18 bp):
ATTACATGCATAAATAAG
Found at i:5421759 original size:13 final size:14
Alignment explanation
Indices: 5421725--5421759 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
5421715 TTTTTTAAAG
5421725 TTTTAAA-TATTAT
1 TTTTAAATTATTAT
5421738 TTTTAAATTATT-T
1 TTTTAAATTATTAT
5421751 TTTTAAATT
1 TTTTAAATT
5421760 TTAAATGTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 17 0.81
14 4 0.19
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (14 bp):
TTTTAAATTATTAT
Found at i:5421760 original size:21 final size:23
Alignment explanation
Indices: 5421736--5421781 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 23
5421726 TTTAAATATT
*
5421736 ATTTTTAAAT-TAT-TTTTTTAA
1 ATTTTTAAATGTATATTTTTGAA
5421757 A-TTTTAAATGTATATTTTTGAA
1 ATTTTTAAATGTATATTTTTGAA
5421779 ATT
1 ATT
5421782 ATTTCTTATA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
20 8 0.38
21 4 0.19
22 8 0.38
23 1 0.05
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.61
Consensus pattern (23 bp):
ATTTTTAAATGTATATTTTTGAA
Found at i:5421798 original size:36 final size:33
Alignment explanation
Indices: 5421713--5421849 Score: 143
Period size: 36 Copynumber: 4.0 Consensus size: 33
5421703 TTATAATATA
5421713 TATTTTT-TAAAGTTTTAAATATTATTTTTAAAT
1 TATTTTTATAAA-TTTTAAATATTATTTTTAAAT
* *
5421746 TATTTTTTTAAATTTTAAATGTATATTTTTGAAAT
1 TATTTTTATAAATTTTAAATAT-TATTTTT-AAAT
* *
5421781 TATTTCTTATAAATTTTAAAAATATATATTTGAAAT
1 TATTT-TTATAAATTTTAAATAT-TAT-TTTTAAAT
* *
5421817 CATTTTT-TAAAATATTAAATATTATTTTTAAAT
1 TATTTTTAT-AAATTTTAAATATTATTTTTAAAT
5421850 ACTGAATATA
Statistics
Matches: 89, Mismatches: 9, Indels: 12
0.81 0.08 0.11
Matches are distributed among these distances:
33 23 0.26
34 15 0.17
35 22 0.25
36 26 0.29
37 3 0.03
ACGTcount: A:0.39, C:0.01, G:0.03, T:0.56
Consensus pattern (33 bp):
TATTTTTATAAATTTTAAATATTATTTTTAAAT
Found at i:5421846 original size:21 final size:20
Alignment explanation
Indices: 5421820--5421873 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 20
5421810 TTGAAATCAT
5421820 TTTTTAAAATATTAAATATTA
1 TTTTTAAAATATTAAATA-TA
* *
5421841 TTTTT-AAATACTGAATATA
1 TTTTTAAAATATTAAATATA
5421860 TTTTTAATAATATT
1 TTTTTAA-AATATT
5421874 TAAACATTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
19 7 0.25
20 11 0.39
21 10 0.36
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.54
Consensus pattern (20 bp):
TTTTTAAAATATTAAATATA
Found at i:5421946 original size:14 final size:15
Alignment explanation
Indices: 5421927--5421955 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
5421917 ATCTTTAAAA
5421927 ATAA-TTAAAAAATT
1 ATAATTTAAAAAATT
5421941 ATAATTTAAAAAATT
1 ATAATTTAAAAAATT
5421956 CTGAAAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 4 0.29
15 10 0.71
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
ATAATTTAAAAAATT
Found at i:5422090 original size:19 final size:20
Alignment explanation
Indices: 5422068--5422112 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
5422058 TAATTTGTTT
5422068 TTTTTTACTTTTT-TTTAAC
1 TTTTTTACTTTTTCTTTAAC
* *
5422087 TTTTGT-CTTTTTCTTTAAT
1 TTTTTTACTTTTTCTTTAAC
5422106 TTTTTTA
1 TTTTTTA
5422113 AAGTTTTATA
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
18 6 0.29
19 15 0.71
ACGTcount: A:0.13, C:0.09, G:0.02, T:0.76
Consensus pattern (20 bp):
TTTTTTACTTTTTCTTTAAC
Found at i:5422112 original size:28 final size:27
Alignment explanation
Indices: 5422061--5422113 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 27
5422051 TTTTCTTTAA
*
5422061 TTTGTTTTTTTTTACTTTTTTTTAACT
1 TTTGTTTTTTTTTACATTTTTTTAACT
5422088 TTTGTCTTTTTCTTTA-ATTTTTTTAA
1 TTTGT-TTTTT-TTTACATTTTTTTAA
5422114 AGTTTTATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
27 5 0.22
28 14 0.61
29 4 0.17
ACGTcount: A:0.13, C:0.08, G:0.04, T:0.75
Consensus pattern (27 bp):
TTTGTTTTTTTTTACATTTTTTTAACT
Found at i:5422119 original size:29 final size:27
Alignment explanation
Indices: 5422061--5422128 Score: 73
Period size: 29 Copynumber: 2.4 Consensus size: 27
5422051 TTTTCTTTAA
* *
5422061 TTTGTTTTTTTTTACTTTTTTTTAACT
1 TTTGTTTTTTTTTAATTTTTTTAAACT
*
5422088 TTTGTCTTTTTCTTTAATTTTTTTAAAGT
1 TTTGT-TTTTT-TTTAATTTTTTTAAACT
* *
5422117 TTTATATTTTTT
1 TTTGTTTTTTTT
5422129 CTTATTCTAT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
27 7 0.21
28 9 0.26
29 18 0.53
ACGTcount: A:0.15, C:0.06, G:0.04, T:0.75
Consensus pattern (27 bp):
TTTGTTTTTTTTTAATTTTTTTAAACT
Found at i:5422224 original size:23 final size:23
Alignment explanation
Indices: 5422192--5422247 Score: 71
Period size: 22 Copynumber: 2.5 Consensus size: 23
5422182 ATTTGAAATG
5422192 TTTTATAATATATATATTTTAAAA
1 TTTTA-AATATATATATTTTAAAA
*
5422216 TTTTAAATAT-TATTTTTTAAAA
1 TTTTAAATATATATATTTTAAAA
*
5422238 -ATTAAATATA
1 TTTTAAATATA
5422248 GTTTTTAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
21 8 0.28
22 11 0.38
23 5 0.17
24 5 0.17
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (23 bp):
TTTTAAATATATATATTTTAAAA
Found at i:5422236 original size:22 final size:22
Alignment explanation
Indices: 5422198--5422269 Score: 76
Period size: 22 Copynumber: 3.3 Consensus size: 22
5422188 AATGTTTTAT
* *
5422198 AATATATATATTTTAAAATTTTA
1 AATAT-TATTTTTTAAAATATTA
5422221 AATATTATTTTTTAAAA-ATTA
1 AATATTATTTTTTAAAATATTA
* *
5422242 AATA-TAGTTTTTAATAATATGA
1 AATATTATTTTTTAA-AATATTA
5422264 AATATT
1 AATATT
5422270 TAAACATTTA
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
20 9 0.21
21 9 0.21
22 18 0.43
23 6 0.14
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (22 bp):
AATATTATTTTTTAAAATATTA
Found at i:5422370 original size:21 final size:21
Alignment explanation
Indices: 5422328--5422370 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
5422318 TTTTAATAAT
* * **
5422328 ATAAAACATTTAAAATTTTTA
1 ATAAAAAATTAAAAATGGTTA
5422349 ATAAAAAATTAAAAATGGTTA
1 ATAAAAAATTAAAAATGGTTA
5422370 A
1 A
5422371 ATATATTAAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.58, C:0.02, G:0.05, T:0.35
Consensus pattern (21 bp):
ATAAAAAATTAAAAATGGTTA
Found at i:5422472 original size:13 final size:13
Alignment explanation
Indices: 5422454--5422486 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
5422444 AAACCTTTTT
5422454 AATTTT-TTATAAA
1 AATTTTATT-TAAA
5422467 AATTTTATTTAAA
1 AATTTTATTTAAA
5422480 AATTTTA
1 AATTTTA
5422487 ATGTTTAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 17 0.89
14 2 0.11
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (13 bp):
AATTTTATTTAAA
Found at i:5422526 original size:20 final size:21
Alignment explanation
Indices: 5422501--5422551 Score: 77
Period size: 21 Copynumber: 2.4 Consensus size: 21
5422491 TTAAATATTA
*
5422501 TTAAAAAAT-ATATTTAATAT
1 TTAAAAAATAATATTTAAAAT
5422521 TTAAAAAATAATATTTAAAAT
1 TTAAAAAATAATATTTAAAAT
5422542 TTAGAAAAAT
1 TTA-AAAAAT
5422552 TAATTTCAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
20 9 0.32
21 13 0.46
22 6 0.21
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (21 bp):
TTAAAAAATAATATTTAAAAT
Found at i:5422534 original size:21 final size:20
Alignment explanation
Indices: 5422501--5422681 Score: 92
Period size: 22 Copynumber: 8.7 Consensus size: 20
5422491 TTAAATATTA
*
5422501 TTAAAAAATATATTTAATAT
1 TTAAAAAATATATTTAAAAT
5422521 TTAAAAAATAATATTTAAAAT
1 TTAAAAAAT-ATATTTAAAAT
5422542 TTAGAAAAAT-TAATTTCAAAAATACATTT
1 TTA-AAAAATAT-ATTT----AA-A-A--T
** * *
5422571 TTAAAATTTATAATAAATAAT
1 TTAAAAAATATATTTAA-AAT
5422592 TTAAAAATATATATTTAAAATT
1 TTAAAAA-ATATATTTAAAA-T
5422614 TTAAAAAATA-A--T----T
1 TTAAAAAATATATTTAAAAT
*
5422627 TTAAAATA-ATATTTAAAATT
1 TTAAAAAATATATTTAAAA-T
5422647 TTAAAAAATAATATTTAAAATT
1 TTAAAAAAT-ATATTTAAAA-T
5422669 TTAAAAAATATAT
1 TTAAAAAATATAT
5422682 ATTATAAAAC
Statistics
Matches: 126, Mismatches: 11, Indels: 47
0.68 0.06 0.26
Matches are distributed among these distances:
12 1 0.01
13 9 0.07
15 1 0.01
18 1 0.01
20 19 0.15
21 33 0.26
22 42 0.33
23 1 0.01
24 4 0.03
25 2 0.02
26 1 0.01
27 1 0.01
28 6 0.05
29 5 0.04
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.41
Consensus pattern (20 bp):
TTAAAAAATATATTTAAAAT
Found at i:5422598 original size:35 final size:33
Alignment explanation
Indices: 5422519--5422667 Score: 183
Period size: 35 Copynumber: 4.3 Consensus size: 33
5422509 TATATTTAAT
5422519 ATTTAAAAAATAATATTTAAAA-TTTAGAAAAATTA
1 ATTT-AAAAATAATATTTAAAATTTTA-AAAAA-TA
* *
5422554 ATTTCAAAAATACATTTTTAAAATTTATAATAAATA
1 ATTT-AAAAATA-ATATTTAAAATTT-TAAAAAATA
5422590 ATTTAAAAATATATATTTAAAATTTTAAAAAATA
1 ATTTAAAAATA-ATATTTAAAATTTTAAAAAATA
*
5422624 ATTTTAAAATAATATTTAAAATTTTAAAAAATA
1 ATTTAAAAATAATATTTAAAATTTTAAAAAATA
*
5422657 ATATTTAAAAT
1 AT-TTAAAAAT
5422668 TTTAAAAAAT
Statistics
Matches: 103, Mismatches: 7, Indels: 9
0.87 0.06 0.08
Matches are distributed among these distances:
33 24 0.23
34 26 0.25
35 30 0.29
36 15 0.15
37 6 0.06
38 2 0.02
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.41
Consensus pattern (33 bp):
ATTTAAAAATAATATTTAAAATTTTAAAAAATA
Found at i:5422626 original size:13 final size:14
Alignment explanation
Indices: 5422610--5422645 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
5422600 ATATATTTAA
5422610 AATTTTAAAA-AAT
1 AATTTTAAAATAAT
5422623 AATTTTAAAATAAT
1 AATTTTAAAATAAT
5422637 -A-TTTAAAAT
1 AATTTTAAAAT
5422646 TTTAAAAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 8 0.36
13 11 0.50
14 3 0.14
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (14 bp):
AATTTTAAAATAAT
Found at i:5422683 original size:23 final size:22
Alignment explanation
Indices: 5422629--5422690 Score: 106
Period size: 22 Copynumber: 2.7 Consensus size: 22
5422619 AAATAATTTT
5422629 AAAATAATATTTAAAATTTTAA
1 AAAATAATATTTAAAATTTTAA
5422651 AAAATAATATTTAAAATTTTAA
1 AAAATAATATTTAAAATTTTAA
5422673 AAAATATATATTATAAAA
1 AAAATA-ATATT-TAAAA
5422691 CATTTCAAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
22 28 0.74
23 5 0.13
24 5 0.13
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (22 bp):
AAAATAATATTTAAAATTTTAA
Found at i:5422743 original size:14 final size:13
Alignment explanation
Indices: 5422720--5422767 Score: 51
Period size: 14 Copynumber: 3.5 Consensus size: 13
5422710 AAATTTTTTT
*
5422720 AAAATTAATAACAA
1 AAAATAAATAA-AA
*
5422734 AAAATAAATAAAT
1 AAAATAAATAAAA
5422747 AAAATAAAATAAGAA
1 AAAAT-AAATAA-AA
5422762 AAAATA
1 AAAATA
5422768 TAAAACTTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
13 6 0.21
14 17 0.59
15 6 0.21
ACGTcount: A:0.77, C:0.02, G:0.02, T:0.19
Consensus pattern (13 bp):
AAAATAAATAAAA
Found at i:5422747 original size:18 final size:18
Alignment explanation
Indices: 5422721--5422758 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
5422711 AATTTTTTTA
*
5422721 AAATTAATAACAA-AAAAT
1 AAATAAATAA-AATAAAAT
5422739 AAATAAATAAAATAAAAT
1 AAATAAATAAAATAAAAT
5422757 AA
1 AA
5422759 GAAAAAATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 2 0.11
18 16 0.89
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.21
Consensus pattern (18 bp):
AAATAAATAAAATAAAAT
Found at i:5424400 original size:21 final size:21
Alignment explanation
Indices: 5424376--5424418 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
5424366 AAAGTTGGTG
5424376 ATCAACTAAGTAGTTTATCTT
1 ATCAACTAAGTAGTTTATCTT
5424397 ATCAACTAAGTAGTTTATCTT
1 ATCAACTAAGTAGTTTATCTT
5424418 A
1 A
5424419 CTTTTTATTT
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:0.35, C:0.14, G:0.09, T:0.42
Consensus pattern (21 bp):
ATCAACTAAGTAGTTTATCTT
Found at i:5427906 original size:25 final size:25
Alignment explanation
Indices: 5427861--5427920 Score: 61
Period size: 25 Copynumber: 2.4 Consensus size: 25
5427851 TAATAATAAG
* *
5427861 AATAATA-TAAATAATAGTAAATAT
1 AATAATATTAAATAACAGTAAAAAT
* *
5427885 AATAATATTAAGTAACATTAAAAAT
1 AATAATATTAAATAACAGTAAAAAT
5427910 AATTAAT-TTAA
1 AA-TAATATTAA
5427921 TAATAAAGAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
24 7 0.23
25 19 0.63
26 4 0.13
ACGTcount: A:0.60, C:0.02, G:0.03, T:0.35
Consensus pattern (25 bp):
AATAATATTAAATAACAGTAAAAAT
Found at i:5428521 original size:23 final size:21
Alignment explanation
Indices: 5428478--5428521 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 21
5428468 CAGGAAAATG
5428478 TAATTTTTCTTTTTATTTTTT
1 TAATTTTTCTTTTTATTTTTT
*
5428499 TAATTATTTGTTTTATATTTTTT
1 TAATT-TTTCTTTT-TATTTTTT
5428522 ATGTTTTAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 5 0.25
22 7 0.35
23 8 0.40
ACGTcount: A:0.18, C:0.02, G:0.02, T:0.77
Consensus pattern (21 bp):
TAATTTTTCTTTTTATTTTTT
Found at i:5428918 original size:12 final size:13
Alignment explanation
Indices: 5428891--5428916 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5428881 GGTGGTGGCA
5428891 GAGGCAAGTGGGG
1 GAGGCAAGTGGGG
5428904 GAGGCAAGTGGGG
1 GAGGCAAGTGGGG
5428917 AGCTAGGGTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.08, G:0.62, T:0.08
Consensus pattern (13 bp):
GAGGCAAGTGGGG
Found at i:5429854 original size:14 final size:14
Alignment explanation
Indices: 5429835--5429869 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
5429825 GTTGATTTTT
*
5429835 TTGAAAAGCAGAAA
1 TTGAAAAGAAGAAA
5429849 TTGAAAAGAAGAAA
1 TTGAAAAGAAGAAA
5429863 TTGAAAA
1 TTGAAAA
5429870 TTCCTCAGCG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.60, C:0.03, G:0.20, T:0.17
Consensus pattern (14 bp):
TTGAAAAGAAGAAA
Found at i:5429982 original size:73 final size:72
Alignment explanation
Indices: 5429849--5430090 Score: 272
Period size: 73 Copynumber: 3.3 Consensus size: 72
5429839 AAAGCAGAAA
* *
5429849 TTGAAAAGAAGAAATTGAAAATT-CCTCAGCGTG-CCATGAGGCTCAACTCATCTCTCGCAATAT
1 TTGAAAA-CAGAAATTG-AAATTACCTCAGCGTGTCC-TGAGGCTCAACTCACCTCTCGCAATAT
5429912 GAGTTAATTT
63 GAGTTAATTT
* *
5429922 TTGACAAACAGAAGTTGAAATTACCTCAGCGTGTCCTAAGGCTCAACTCACCTCTCGCAATATGA
1 TTGA-AAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGA
*
5429987 GTTGATTTTTT
65 GTT-A--ATTT
* * * * *
5429998 TTGAAAGATAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTAGCAATATGA
1 TTGAAA-ACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGA
* *
5430063 ATTGATTT
65 GTTAATTT
*
5430071 TTGAAAAACATAAATTGAAA
1 TTG-AAAACAGAAATTGAAA
5430091 AACAGAATTT
Statistics
Matches: 144, Mismatches: 17, Indels: 16
0.81 0.10 0.09
Matches are distributed among these distances:
72 5 0.03
73 68 0.47
74 9 0.06
75 2 0.01
76 60 0.42
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.30
Consensus pattern (72 bp):
TTGAAAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAG
TTAATTT
Found at i:5430090 original size:14 final size:14
Alignment explanation
Indices: 5430071--5430105 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
5430061 GAATTGATTT
*
5430071 TTGAAAAACATAAA
1 TTGAAAAACAGAAA
*
5430085 TTGAAAAACAGAAT
1 TTGAAAAACAGAAA
5430099 TTGAAAA
1 TTGAAAA
5430106 TACCTCAGCG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.60, C:0.06, G:0.11, T:0.23
Consensus pattern (14 bp):
TTGAAAAACAGAAA
Found at i:5430112 original size:163 final size:155
Alignment explanation
Indices: 5429853--5430393 Score: 549
Period size: 163 Copynumber: 3.5 Consensus size: 155
5429843 CAGAAATTGA
* * * * * *
5429853 AAAGA-AGAAATTGAAAATTCCTCAGCGTGCCATGAGGCTCAACTCATCTCTCGCAATATGAGTT
1 AAAGATAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTAGCAATATGAGTT
* * * *
5429917 -A-ATT-----TTTGACAAACAGAAGTTGAAATTACCTCAGCGTGTCCTAAGGCTCAACTCACCT
66 GATTTTGAAAATTTGAAAAACAGAA-TTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCT
5429975 CTCGCAATATGAGTTGATTTTTTTTG
130 CTCGCAATATGAGTTGATTTTTTTTG
*
5430001 AAAGATAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTAGCAATATGAATT
1 AAAGATAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTAGCAATATGAGTT
5430066 GATTTTTGAAAAACATAAATTGAAAAACAGAATTTGAAAATACCTCAGCGTGTCCTGAGGCTCAA
66 GA-TTTTG--AAA-AT---TTGAAAAACAGAA-TTGAAAATACCTCAGCGTGTCCTGAGGCTCAA
5430131 CTCACCTCTCGCAATATGAGTTGA---TTTTTG
123 CTCACCTCTCGCAATATGAGTTGATTTTTTTTG
* * * * *
5430161 ACAA-ATAGAAATTGAAAATACCTCAGCGTGGCCTGATGCTCAACTCACCTCTCGCAATATGAGT
1 A-AAGATAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTAGCAATATGAGT
* * *
5430225 TGATTTT-----TTTGAAAAACAGGAATTAAAAATACCACAGCGTGACCTGAGGCTCAACTCACC
65 TGATTTTGAAAATTTGAAAAACA-GAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACC
5430285 TCTCGCAATATGAGTAGATTGATTTTTTTTTG
129 TCTCGCAATAT--G-AG-TTGA-TTTTTTTTG
** * * * * ** *
5430317 AGTGACAGAAATAGAAAATACCTCAATGTTTCTTGAGGCTCAACTCATTTCTTGCAATATGAGTT
1 AAAGATAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTAGCAATATGAG-T
*
5430382 TAATTTTGAAAA
65 TGATTTTGAAAA
5430394 CAGAAATAAA
Statistics
Matches: 326, Mismatches: 35, Indels: 50
0.79 0.09 0.12
Matches are distributed among these distances:
148 61 0.19
149 55 0.17
150 2 0.01
151 3 0.01
152 6 0.02
156 55 0.17
157 7 0.02
159 4 0.01
160 65 0.20
161 2 0.01
163 66 0.20
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.30
Consensus pattern (155 bp):
AAAGATAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTAGCAATATGAGTT
GATTTTGAAAATTTGAAAAACAGAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTC
TCGCAATATGAGTTGATTTTTTTTG
Found at i:5430142 original size:236 final size:236
Alignment explanation
Indices: 5429721--5430297 Score: 777
Period size: 236 Copynumber: 2.4 Consensus size: 236
5429711 GTGACCCGAT
* * *
5429721 GCTCAACTCACTTCTCACAATATGAGTTGATTTTTTTTTGAAAAAAAAGAAACTG-AAATACCTC
1 GCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTTTG-AAAAAAAGAAATTGAAAATACCTC
* * * * *
5429785 AGTATGTGAGCTGGGGCTCAACTCACCTCTCGTAATATGAGTTGATTTTTTTGAAAAGCAGAAAT
64 A--ACGTGA-CTGAGGCTCAACTCACCTCTCGCAATATGAATTGA-TTTTTTGAAAAACAGAAAT
* *
5429850 TGAAAAGAAGAAATTGAAAATTCCTCAGCGTGCCATGAGGCTCAACTCATCTCTCGCAATATGAG
125 TGAAAAGAAGAAATTGAAAATACCTCAGCGTGCCATGAGGCTCAACTCACCTCTCGCAATATGAG
* * *
5429915 TTAATTTTTGACAAACAGAAGTTGAAATTACCTCAGCGTGTCCTAAG
190 TTAATTTTTGACAAACAGAAATTGAAAATACCTCAGCGTGGCCTAAG
* *
5429962 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTGAAAGATAGAAATTGAAAATACCTCAA
1 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTGAAAAAAAGAAATTGAAAATACCTCAA
* * *
5430027 CGTGTCTTGAGGCTCAACTCACCTCTAGCAATATGAATTGA-TTTTTGAAAAACATAAATTGAAA
66 CGTGAC-TGAGGCTCAACTCACCTCTCGCAATATGAATTGATTTTTTGAAAAACAGAAATTGAAA
* *
5430091 A-ACAGAATTTGAAAATACCTCAGCGTGTCC-TGAGGCTCAACTCACCTCTCGCAATATGAGTTG
130 AGA-AGAAATTGAAAATACCTCAGCGTG-CCATGAGGCTCAACTCACCTCTCGCAATATGAGTTA
* * *
5430154 ATTTTTGACAAATAGAAATTGAAAATACCTCAGCGTGGCCTGAT
193 ATTTTTGACAAACAGAAATTGAAAATACCTCAGCGTGGCCTAAG
* * * * *
5430198 GCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTTGAAAAACAGGAATTAAAAATACCACAG
1 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTGAAAAAAAGAAATTGAAAATACCTCAA
5430262 CGTGACCTGAGGCTCAACTCACCTCTCGCAATATGA
66 CGTGA-CTGAGGCTCAACTCACCTCTCGCAATATGA
5430298 GTAGATTGAT
Statistics
Matches: 300, Mismatches: 31, Indels: 16
0.86 0.09 0.05
Matches are distributed among these distances:
235 61 0.20
236 144 0.48
237 3 0.01
238 34 0.11
239 11 0.04
240 19 0.06
241 28 0.09
ACGTcount: A:0.34, C:0.20, G:0.17, T:0.29
Consensus pattern (236 bp):
GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTGAAAAAAAGAAATTGAAAATACCTCAA
CGTGACTGAGGCTCAACTCACCTCTCGCAATATGAATTGATTTTTTGAAAAACAGAAATTGAAAA
GAAGAAATTGAAAATACCTCAGCGTGCCATGAGGCTCAACTCACCTCTCGCAATATGAGTTAATT
TTTGACAAACAGAAATTGAAAATACCTCAGCGTGGCCTAAG
Found at i:5430145 original size:87 final size:87
Alignment explanation
Indices: 5429998--5430178 Score: 272
Period size: 87 Copynumber: 2.1 Consensus size: 87
5429988 TTGATTTTTT
* * *
5429998 TTGAAAGATAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTAGCAATATGA
1 TTGAAAAACAGAAATTGAAAATACCTCAACGTGTCCTGAGGCTCAACTCACCTCTAGCAATATGA
*
5430063 ATTGATTTTTGAAAAACATAAA
66 ATTGATTTTTGAAAAACAGAAA
* * *
5430085 TTGAAAAACAGAATTTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGA
1 TTGAAAAACAGAAATTGAAAATACCTCAACGTGTCCTGAGGCTCAACTCACCTCTAGCAATATGA
* * *
5430150 GTTGATTTTTGACAAATAGAAA
66 ATTGATTTTTGAAAAACAGAAA
5430172 TTGAAAA
1 TTGAAAA
5430179 TACCTCAGCG
Statistics
Matches: 84, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
87 84 1.00
ACGTcount: A:0.39, C:0.17, G:0.16, T:0.28
Consensus pattern (87 bp):
TTGAAAAACAGAAATTGAAAATACCTCAACGTGTCCTGAGGCTCAACTCACCTCTAGCAATATGA
ATTGATTTTTGAAAAACAGAAA
Found at i:5430218 original size:73 final size:73
Alignment explanation
Indices: 5430085--5430304 Score: 332
Period size: 73 Copynumber: 3.0 Consensus size: 73
5430075 AAAACATAAA
* *
5430085 TTGAAAAACAGAATTTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGA
1 TTGAAAAACAGAAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGA
5430150 GTTGATTT
66 GTTGATTT
* * * *
5430158 TTGACAAATAGAAATTGAAAATACCTCAGCGTGGCCTGATGCTCAACTCACCTCTCGCAATATGA
1 TTGAAAAACAGAAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGA
5430223 GTTGATTTTT
66 GTTGA--TTT
* * *
5430233 TTGAAAAACAGGAATTAAAAATACCACAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGA
1 TTGAAAAACAGAAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGA
*
5430298 GTAGATT
66 GTTGATT
5430305 GATTTTTTTT
Statistics
Matches: 132, Mismatches: 13, Indels: 4
0.89 0.09 0.03
Matches are distributed among these distances:
73 67 0.51
75 65 0.49
ACGTcount: A:0.33, C:0.22, G:0.18, T:0.27
Consensus pattern (73 bp):
TTGAAAAACAGAAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGA
GTTGATTT
Found at i:5430278 original size:75 final size:75
Alignment explanation
Indices: 5430085--5430304 Score: 329
Period size: 75 Copynumber: 3.0 Consensus size: 75
5430075 AAAACATAAA
*
5430085 TTGAAAAACA-GAATTTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATG
1 TTGAAAAACAGGAA-TTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATG
5430149 AGTTGA--TTT
65 AGTTGATTTTT
* * * * *
5430158 TTGACAAATAGAAATTGAAAATACCTCAGCGTGGCCTGATGCTCAACTCACCTCTCGCAATATGA
1 TTGAAAAACAGGAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGA
5430223 GTTGATTTTT
66 GTTGATTTTT
* *
5430233 TTGAAAAACAGGAATTAAAAATACCACAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGA
1 TTGAAAAACAGGAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGA
*
5430298 GTAGATT
66 GTTGATT
5430305 GATTTTTTTT
Statistics
Matches: 131, Mismatches: 13, Indels: 4
0.89 0.09 0.03
Matches are distributed among these distances:
73 62 0.47
74 2 0.02
75 67 0.51
ACGTcount: A:0.33, C:0.22, G:0.18, T:0.27
Consensus pattern (75 bp):
TTGAAAAACAGGAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGA
GTTGATTTTT
Found at i:5452191 original size:18 final size:18
Alignment explanation
Indices: 5452168--5452260 Score: 141
Period size: 18 Copynumber: 5.2 Consensus size: 18
5452158 CCCAACTACT
* *
5452168 GTATACGTGAACAGTATC
1 GTATACGTGAATAGTACC
*
5452186 GTATACGTGAATAGTGCC
1 GTATACGTGAATAGTACC
*
5452204 GTATACGTGAATAGTACT
1 GTATACGTGAATAGTACC
*
5452222 GTATACGTGAATAGTGCC
1 GTATACGTGAATAGTACC
5452240 GTATACGTGAATAGTACC
1 GTATACGTGAATAGTACC
5452258 GTA
1 GTA
5452261 AACGGTCGTA
Statistics
Matches: 67, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 67 1.00
ACGTcount: A:0.31, C:0.15, G:0.25, T:0.29
Consensus pattern (18 bp):
GTATACGTGAATAGTACC
Found at i:5452226 original size:36 final size:37
Alignment explanation
Indices: 5452168--5452260 Score: 156
Period size: 36 Copynumber: 2.6 Consensus size: 37
5452158 CCCAACTACT
*
5452168 GTATACGTGAACAGTA-TCGTATACGTGAATAGTGCC
1 GTATACGTGAATAGTACTCGTATACGTGAATAGTGCC
5452204 GTATACGTGAATAGTACT-GTATACGTGAATAGTGCC
1 GTATACGTGAATAGTACTCGTATACGTGAATAGTGCC
5452240 GTATACGTGAATAGTAC-CGTA
1 GTATACGTGAATAGTACTCGTA
5452261 AACGGTCGTA
Statistics
Matches: 54, Mismatches: 1, Indels: 4
0.92 0.02 0.07
Matches are distributed among these distances:
36 53 0.98
37 1 0.02
ACGTcount: A:0.31, C:0.15, G:0.25, T:0.29
Consensus pattern (37 bp):
GTATACGTGAATAGTACTCGTATACGTGAATAGTGCC
Found at i:5454297 original size:14 final size:14
Alignment explanation
Indices: 5454261--5454302 Score: 68
Period size: 14 Copynumber: 3.1 Consensus size: 14
5454251 CTAAATCATA
5454261 ATTTTAGTAAAAT-
1 ATTTTAGTAAAATC
5454274 ATTTTAGTAAAATC
1 ATTTTAGTAAAATC
*
5454288 ATTTTGGTAAAATC
1 ATTTTAGTAAAATC
5454302 A
1 A
5454303 AGATTAAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
13 13 0.48
14 14 0.52
ACGTcount: A:0.43, C:0.05, G:0.10, T:0.43
Consensus pattern (14 bp):
ATTTTAGTAAAATC
Found at i:5471897 original size:24 final size:26
Alignment explanation
Indices: 5471851--5471908 Score: 75
Period size: 24 Copynumber: 2.3 Consensus size: 26
5471841 TTAATAAATT
* *
5471851 AAAACATTATATTGAAAATAATGAAA
1 AAAATATTAGATTGAAAATAATGAAA
5471877 AAAATATTAGATT-AAAA-AATGAAA
1 AAAATATTAGATTGAAAATAATGAAA
*
5471901 AAGATATT
1 AAAATATT
5471909 TTCTATAAGA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
24 14 0.48
25 4 0.14
26 11 0.38
ACGTcount: A:0.62, C:0.02, G:0.09, T:0.28
Consensus pattern (26 bp):
AAAATATTAGATTGAAAATAATGAAA
Found at i:5472816 original size:17 final size:18
Alignment explanation
Indices: 5472780--5472830 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 18
5472770 TAGGGGTGTG
*
5472780 CAAAATTCGGGTAAAACCGA
1 CAAAATTC-GGT-TAACCGA
5472800 -AAAATTCGGTTAACCGA
1 CAAAATTCGGTTAACCGA
*
5472817 CAGAATTCGGTTAA
1 CAAAATTCGGTTAA
5472831 TCGGTCGGTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
17 6 0.21
18 15 0.54
19 7 0.25
ACGTcount: A:0.41, C:0.18, G:0.20, T:0.22
Consensus pattern (18 bp):
CAAAATTCGGTTAACCGA
Found at i:5473055 original size:13 final size:13
Alignment explanation
Indices: 5473037--5473061 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5473027 CAAGTACCCA
5473037 ACCCAACCCAATT
1 ACCCAACCCAATT
5473050 ACCCAACCCAAT
1 ACCCAACCCAAT
5473062 CATAAAAATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.48, G:0.00, T:0.12
Consensus pattern (13 bp):
ACCCAACCCAATT
Found at i:5473099 original size:5 final size:6
Alignment explanation
Indices: 5473086--5473126 Score: 55
Period size: 6 Copynumber: 6.5 Consensus size: 6
5473076 ATAATTTAAT
*
5473086 AAATAA AAATAA AAATTTAA AACTAA AAATAA AAATAA AAA
1 AAATAA AAATAA AAA--TAA AAATAA AAATAA AAATAA AAA
5473127 ATATATAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
6 26 0.84
8 5 0.16
ACGTcount: A:0.78, C:0.02, G:0.00, T:0.20
Consensus pattern (6 bp):
AAATAA
Found at i:5473114 original size:20 final size:21
Alignment explanation
Indices: 5473078--5473121 Score: 72
Period size: 20 Copynumber: 2.1 Consensus size: 21
5473068 AATGACAAAT
5473078 AATTTAATAAATAAAAATAAA
1 AATTTAATAAATAAAAATAAA
*
5473099 AATTTAA-AACTAAAAATAAA
1 AATTTAATAAATAAAAATAAA
5473119 AAT
1 AAT
5473122 AAAAAATATA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 15 0.68
21 7 0.32
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.27
Consensus pattern (21 bp):
AATTTAATAAATAAAAATAAA
Found at i:5473127 original size:20 final size:20
Alignment explanation
Indices: 5473089--5473127 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
5473079 ATTTAATAAA
**
5473089 TAAAAATAAAAATTTAAAAC
1 TAAAAATAAAAATAAAAAAC
5473109 TAAAAATAAAAATAAAAAA
1 TAAAAATAAAAATAAAAAA
5473128 TATATAATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.77, C:0.03, G:0.00, T:0.21
Consensus pattern (20 bp):
TAAAAATAAAAATAAAAAAC
Found at i:5473160 original size:9 final size:9
Alignment explanation
Indices: 5473146--5473222 Score: 93
Period size: 9 Copynumber: 8.6 Consensus size: 9
5473136 TTTATACAAA
5473146 TAATTCGGT
1 TAATTCGGT
*
5473155 TAATTCAGT
1 TAATTCGGT
* *
5473164 TAATTTGGG
1 TAATTCGGT
5473173 TAATTCAGG-
1 TAATTC-GGT
5473182 TAATTCGGT
1 TAATTCGGT
*
5473191 TAATTCGAT
1 TAATTCGGT
*
5473200 TAATTTGGT
1 TAATTCGGT
5473209 TAATTCGGT
1 TAATTCGGT
5473218 TAATT
1 TAATT
5473223 TTATACTTAT
Statistics
Matches: 57, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
8 2 0.04
9 53 0.93
10 2 0.04
ACGTcount: A:0.27, C:0.08, G:0.19, T:0.45
Consensus pattern (9 bp):
TAATTCGGT
Found at i:5474807 original size:16 final size:17
Alignment explanation
Indices: 5474788--5474819 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
5474778 CTATTTTCAT
5474788 GTATTATTT-TTTTTAC
1 GTATTATTTATTTTTAC
5474804 GTATTATTTATTTTTA
1 GTATTATTTATTTTTA
5474820 AAAGTTGTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.22, C:0.03, G:0.06, T:0.69
Consensus pattern (17 bp):
GTATTATTTATTTTTAC
Found at i:5480302 original size:44 final size:45
Alignment explanation
Indices: 5480201--5482026 Score: 806
Period size: 44 Copynumber: 41.6 Consensus size: 45
5480191 ATACAGGGAT
* * * *
5480201 AAGATCTGCTTTCTTCGATCTACTTCACCACCAGTATGGGAAGAC
1 AAGATCTGCTATCTTCGATCTACTTCACTACCAATATAGGAAGAC
* * * *
5480246 AAGATCTG-TATCTTGGATCCACTTC-CTATCAATATAGGAAGAT
1 AAGATCTGCTATCTTCGATCTACTTCACTACCAATATAGGAAGAC
* * * * *
5480289 AGGACCTGCTATCTTCGATCTACTTCAC-GCCAATACATGAAGAC
1 AAGATCTGCTATCTTCGATCTACTTCACTACCAATATAGGAAGAC
* * * * * *
5480333 AAGATCTGCTTTCTGCGATCTACTTCGCCACTAATATGGGAAGAC
1 AAGATCTGCTATCTTCGATCTACTTCACTACCAATATAGGAAGAC
* * *
5480378 AAGATCTGC-ATCTTCGATCCACTTC-TTACCAATATAGGAAGAT
1 AAGATCTGCTATCTTCGATCTACTTCACTACCAATATAGGAAGAC
* * * *
5480421 AAGATCAGCTATCTTCGATCTACTTCAC-GCCAATACATGAAGAC
1 AAGATCTGCTATCTTCGATCTACTTCACTACCAATATAGGAAGAC
* * * * * *
5480465 AAGATCTACTTTCTGCGATCTACTTCGCCACCAATATGGGAAGAC
1 AAGATCTGCTATCTTCGATCTACTTCACTACCAATATAGGAAGAC
* * *
5480510 AAGATCTGC-ATCTTCGATCCATTTC-CTACCAATATAGGAAGAT
1 AAGATCTGCTATCTTCGATCTACTTCACTACCAATATAGGAAGAC
* * * * *
5480553 AGGATCAGCTATCTTCGATCTACTTCAC-GCCAATACATGAAGAC
1 AAGATCTGCTATCTTCGATCTACTTCACTACCAATATAGGAAGAC
* * * *
5480597 AAGATCTGCTTTCTTCGATCTACTTCGCCACCAATATGGGAAGAC
1 AAGATCTGCTATCTTCGATCTACTTCACTACCAATATAGGAAGAC
* *
5480642 AAGATCTGC-ATCTTCGATCTATTTC-CTACCAATATAGGAAGAT
1 AAGATCTGCTATCTTCGATCTACTTCACTACCAATATAGGAAGAC
* * * * ** *
5480685 AGGATCAGCTATCTTCGATCTACTTC-TTGCC----CCGGGAGA-
1 AAGATCTGCTATCTTCGATCTACTTCACTACCAATATAGGAAGAC
* * * * * * * ** * * **
5480724 TAGAACT-ATCAGCTTCAATGTACTCCACT-GTAAT-CAGGGAGGT
1 AAGATCTGCT-ATCTTCGATCTACTTCACTACCAATATAGGAAGAC
* ** * * * ** * * *
5480767 AAAATCTGCCGTCTTCAACCTGCTTTGCTGCCAAATACAGGAAGGC
1 AAGATCTGCTATCTTCGATCTACTTCACTACC-AATATAGGAAGAC
* * * * *
5480813 AAGATCTGCAATCTTCAATCTA-TTCCACTACCAAATACAGGGAGAT
1 AAGATCTGCTATCTTCGATCTACTT-CACTACC-AATATAGGAAGAC
* * ** * * * **** * * **
5480859 AGAGTTAT-C-GGCTTCAATGTACTCCACT-GTGGT-CAGGGAGGT
1 A-AGATCTGCTATCTTCGATCTACTTCACTACCAATATAGGAAGAC
* * * * * * * *
5480901 AAAATCTGCCATCTTTGATCTGCTTCGCTGCCAAATACAGGAAGGC
1 AAGATCTGCTATCTTCGATCTACTTCACTACC-AATATAGGAAGAC
* * * * * * *
5480947 AAGATCTGCAATCCTCAATCTA-TTCCACTGTCAAATACAGG--GAT
1 AAGATCTGCTATCTTCGATCTACTT-CACT-ACCAATATAGGAAGAC
* * * * * *
5480991 AAGATCTGCTTTCTTCAATCTACTTCACCACTAGTATGGGAAGAC
1 AAGATCTGCTATCTTCGATCTACTTCACTACCAATATAGGAAGAC
* * * *
5481036 AAGATCTG-TATCTTGGATCCACTTC-CTATCAATATAGGAAGAT
1 AAGATCTGCTATCTTCGATCTACTTCACTACCAATATAGGAAGAC
* * * * *
5481079 AGGACCTGCTATCTTCGATCTACTTCAC-GCCAATACATGAAGAC
1 AAGATCTGCTATCTTCGATCTACTTCACTACCAATATAGGAAGAC
* * * * *
5481123 AAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGAC
1 AAGATCTGCTATCTTCGATCTACTTCACTACCAATATAGGAAGAC
* * *
5481168 AAGATCTG-TATCTTCGATCCACTTC-TTACCAATATAGGAAGAT
1 AAGATCTGCTATCTTCGATCTACTTCACTACCAATATAGGAAGAC
* * * *
5481211 AAGATCAGCTATCTTCGATCTACTTCAC-GCCAATACATGAAGAC
1 AAGATCTGCTATCTTCGATCTACTTCACTACCAATATAGGAAGAC
* * * *
5481255 AAGATCTGCTTTCTTCGATCTACTTCGCCACCAATATGGGAAGAC
1 AAGATCTGCTATCTTCGATCTACTTCACTACCAATATAGGAAGAC
* * *
5481300 AAGATCTGC-ATCTTCGATCCATTTC-CTACCAATATAGGAAGAT
1 AAGATCTGCTATCTTCGATCTACTTCACTACCAATATAGGAAGAC
* * * * ** *
5481343 AGGATCAGCTATCTTCGATCTACTTC-TTGCC----CCGGGAGA-
1 AAGATCTGCTATCTTCGATCTACTTCACTACCAATATAGGAAGAC
* * * * * * * ** * * **
5481382 TAGAACT-ATCAGCTTCAATGTACTCCACT-GTAAT-CAGGGAGGT
1 AAGATCTGCT-ATCTTCGATCTACTTCACTACCAATATAGGAAGAC
* ** ** * * * ** * * *
5481425 AAAATCCACCGTCTTCAACCTGCTTTGCTGCCAAATATAGAAAGGC
1 AAGATCTGCTATCTTCGATCTACTTCACTACC-AATATAGGAAGAC
* * * * * *
5481471 AAGATCTACAATCTTCAATCTA-TTCCACTGCCAAATACAGTG-AGAT
1 AAGATCTGCTATCTTCGATCTACTT-CACTACC-AATATAG-GAAGAC
* * ** * * * **** * * **
5481517 AGAGTTAT-C-GGCTTCAATGTACTCCACT-GTGGT-CAGGGAGGT
1 A-AGATCTGCTATCTTCGATCTACTTCACTACCAATATAGGAAGAC
* * * * * * * *
5481559 AAAATCTGCCATCTTTGATCTGCTTCGCTGCCAAATACAGGAAGGC
1 AAGATCTGCTATCTTCGATCTACTTCACTACC-AATATAGGAAGAC
* * * * * * *
5481605 AAGATCTGCAATCCTCAATCTA-TTCCACTGTCAAATACAGG--GAT
1 AAGATCTGCTATCTTCGATCTACTT-CACT-ACCAATATAGGAAGAC
* * * *
5481649 AAGATCTGCTTTCTTCGATCTACTTCACCACCAGTATGGGAAGAC
1 AAGATCTGCTATCTTCGATCTACTTCACTACCAATATAGGAAGAC
* * * *
5481694 AAGATCTG-TATCTTGGATCCACTTC-CTATCAATATAGGAAGAT
1 AAGATCTGCTATCTTCGATCTACTTCACTACCAATATAGGAAGAC
* * * * *
5481737 AGGACCTGCTATCTTCGATCTACTTCAC-GCCAATACATGAAGAC
1 AAGATCTGCTATCTTCGATCTACTTCACTACCAATATAGGAAGAC
* * * * *
5481781 AAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGAC
1 AAGATCTGCTATCTTCGATCTACTTCACTACCAATATAGGAAGAC
* * *
5481826 AAGATCTGC-ATCTTCGATCCACTTC-TTACCAATATAGGAAGAT
1 AAGATCTGCTATCTTCGATCTACTTCACTACCAATATAGGAAGAC
* * * * *
5481869 AAGATCAGCTATCTTCGATCTACTTCAC-GCCAATACATGAAGAT
1 AAGATCTGCTATCTTCGATCTACTTCACTACCAATATAGGAAGAC
* * * *
5481913 AAGATCTGCTTTCTTCGATCTACTTCGCCACCAATATGGGAAGAC
1 AAGATCTGCTATCTTCGATCTACTTCACTACCAATATAGGAAGAC
*** *
5481958 AAGATCTGC-ATCTTCGATCCGTTTC-CTACCAATATAGGAAGAT
1 AAGATCTGCTATCTTCGATCTACTTCACTACCAATATAGGAAGAC
* *
5482001 AGGATCAGCTATCTTCGATCTACTTC
1 AAGATCTGCTATCTTCGATCTACTTC
5482027 TTGCCCCGGG
Statistics
Matches: 1311, Mismatches: 398, Indels: 145
0.71 0.21 0.08
Matches are distributed among these distances:
38 2 0.00
39 30 0.02
40 12 0.01
41 7 0.01
42 30 0.02
43 273 0.21
44 578 0.44
45 221 0.17
46 148 0.11
47 10 0.01
ACGTcount: A:0.30, C:0.25, G:0.17, T:0.28
Consensus pattern (45 bp):
AAGATCTGCTATCTTCGATCTACTTCACTACCAATATAGGAAGAC
Found at i:5480391 original size:132 final size:132
Alignment explanation
Indices: 5480201--5482026 Score: 1497
Period size: 132 Copynumber: 13.9 Consensus size: 132
5480191 ATACAGGGAT
* * * *
5480201 AAGATCTGCTTTCTTCGATCTACTTCACCACCAGTATGGGAAGACAAGATCTGTATCTTGGATCC
1 AAGATCTGCTTTCTTCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTCGATCC
* * * *
5480266 ACTTCCTATCAATATAGGAAGATAGGACCTGCTATCTTCGATCTACTTCACGCCAATACATGAAG
66 ACTTCCTACCAATATAGGAAGATAAGATCAGCTATCTTCGATCTACTTCACGCCAATACATGAAG
5480331 AC
131 AC
* *
5480333 AAGATCTGCTTTCTGCGATCTACTTCGCCACTAATATGGGAAGACAAGATCTGCATCTTCGATCC
1 AAGATCTGCTTTCTTCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTCGATCC
*
5480398 ACTTCTTACCAATATAGGAAGATAAGATCAGCTATCTTCGATCTACTTCACGCCAATACATGAAG
66 ACTTCCTACCAATATAGGAAGATAAGATCAGCTATCTTCGATCTACTTCACGCCAATACATGAAG
5480463 AC
131 AC
* *
5480465 AAGATCTACTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTCGATCC
1 AAGATCTGCTTTCTTCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTCGATCC
* *
5480530 ATTTCCTACCAATATAGGAAGATAGGATCAGCTATCTTCGATCTACTTCACGCCAATACATGAAG
66 ACTTCCTACCAATATAGGAAGATAAGATCAGCTATCTTCGATCTACTTCACGCCAATACATGAAG
5480595 AC
131 AC
*
5480597 AAGATCTGCTTTCTTCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTCGATCT
1 AAGATCTGCTTTCTTCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTCGATCC
* * ** ** *
5480662 ATTTCCTACCAATATAGGAAGATAGGATCAGCTATCTTCGATCTACTTCTTGCC----CCGGGAG
66 ACTTCCTACCAATATAGGAAGATAAGATCAGCTATCTTCGATCTACTTCACGCCAATACATGAAG
5480723 A-
131 AC
* * * ** * * * * *
5480724 TAGAACT-ATCAGCTTCAATGTAC-T--CCACTGTAATCA-GGGAGGTA-AA-ATCTGCCGTCTT
1 AAGATCTGCT-TTCTTCGATCTACTTCGCCAC--CAAT-ATGGGAAG-ACAAGATCTG-CATCTT
* * * * * ** * * * *
5480782 C-AACCTGCTTTGCTGCCAAATACAGGAAGGCAAGATCTGCAATCTTCAATCTA-TTCCACTACC
60 CGATCC-AC-TTCCTACC-AATATAGGAAGATAAGATCAGCTATCTTCGATCTACTT-CAC-GCC
* * *
5480845 AAATACAGGGAGAT
120 -AATACATGAAGAC
* * ** * * ** * *
5480859 AGAGTTAT-C-GGCTTCAATGTAC-T--CCA-CTGTGGTCAGGGAGGTA-AA-ATCTGCCATCTT
1 A-AGATCTGCTTTCTTCGATCTACTTCGCCACCAAT-AT--GGGAAG-ACAAGATCTG-CATCTT
* ** * * ** * * * * *
5480916 TGATCTGCTTCGCTGCCAAATACAGGAAGGCAAGATCTGCAATCCTCAATCTA-TTCCACTGTCA
60 CGATCCACTTC-CTACC-AATATAGGAAGATAAGATCAGCTATCTTCGATCTACTT-CAC-G-CC
* *
5480980 AATACA-G-GGAT
120 AATACATGAAGAC
* * * * * *
5480991 AAGATCTGCTTTCTTCAATCTACTTCACCACTAGTATGGGAAGACAAGATCTGTATCTTGGATCC
1 AAGATCTGCTTTCTTCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTCGATCC
* * * *
5481056 ACTTCCTATCAATATAGGAAGATAGGACCTGCTATCTTCGATCTACTTCACGCCAATACATGAAG
66 ACTTCCTACCAATATAGGAAGATAAGATCAGCTATCTTCGATCTACTTCACGCCAATACATGAAG
5481121 AC
131 AC
* *
5481123 AAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGTATCTTCGATCC
1 AAGATCTGCTTTCTTCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTCGATCC
*
5481188 ACTTCTTACCAATATAGGAAGATAAGATCAGCTATCTTCGATCTACTTCACGCCAATACATGAAG
66 ACTTCCTACCAATATAGGAAGATAAGATCAGCTATCTTCGATCTACTTCACGCCAATACATGAAG
5481253 AC
131 AC
5481255 AAGATCTGCTTTCTTCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTCGATCC
1 AAGATCTGCTTTCTTCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTCGATCC
* * ** ** *
5481320 ATTTCCTACCAATATAGGAAGATAGGATCAGCTATCTTCGATCTACTTCTTGCC----CCGGGAG
66 ACTTCCTACCAATATAGGAAGATAAGATCAGCTATCTTCGATCTACTTCACGCCAATACATGAAG
5481381 A-
131 AC
* * * ** * * * * ** *
5481382 TAGAACT-ATCAGCTTCAATGTAC-T--CCACTGTAATCA-GGGAGGTA-AA-ATCCACCGTCTT
1 AAGATCTGCT-TTCTTCGATCTACTTCGCCAC--CAAT-ATGGGAAG-ACAAGAT-CTGCATCTT
* * * * * ** * *
5481440 C-AACCTGCTTTGCTGCCAAATATAGAAAGGCAAGATCTA-CAATCTTCAATCTA-TTCCACTGC
60 CGATCC-AC-TTCCTACC-AATATAGGAAGATAAGATC-AGCTATCTTCGATCTACTT-CAC-GC
*
5481502 CAAATACAGTG-AGAT
119 C-AATACA-TGAAGAC
* * ** * * ** * *
5481517 AGAGTTAT-C-GGCTTCAATGTAC-T--CCA-CTGTGGTCAGGGAGGTA-AA-ATCTGCCATCTT
1 A-AGATCTGCTTTCTTCGATCTACTTCGCCACCAAT-AT--GGGAAG-ACAAGATCTG-CATCTT
* ** * * ** * * * * *
5481574 TGATCTGCTTCGCTGCCAAATACAGGAAGGCAAGATCTGCAATCCTCAATCTA-TTCCACTGTCA
60 CGATCCACTTC-CTACC-AATATAGGAAGATAAGATCAGCTATCTTCGATCTACTT-CAC-G-CC
* *
5481638 AATACA-G-GGAT
120 AATACATGAAGAC
* * * *
5481649 AAGATCTGCTTTCTTCGATCTACTTCACCACCAGTATGGGAAGACAAGATCTGTATCTTGGATCC
1 AAGATCTGCTTTCTTCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTCGATCC
* * * *
5481714 ACTTCCTATCAATATAGGAAGATAGGACCTGCTATCTTCGATCTACTTCACGCCAATACATGAAG
66 ACTTCCTACCAATATAGGAAGATAAGATCAGCTATCTTCGATCTACTTCACGCCAATACATGAAG
5481779 AC
131 AC
*
5481781 AAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTCGATCC
1 AAGATCTGCTTTCTTCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTCGATCC
*
5481846 ACTTCTTACCAATATAGGAAGATAAGATCAGCTATCTTCGATCTACTTCACGCCAATACATGAAG
66 ACTTCCTACCAATATAGGAAGATAAGATCAGCTATCTTCGATCTACTTCACGCCAATACATGAAG
*
5481911 AT
131 AC
5481913 AAGATCTGCTTTCTTCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTCGATCC
1 AAGATCTGCTTTCTTCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTCGATCC
** *
5481978 GTTTCCTACCAATATAGGAAGATAGGATCAGCTATCTTCGATCTACTTC
66 ACTTCCTACCAATATAGGAAGATAAGATCAGCTATCTTCGATCTACTTC
5482027 TTGCCCCGGG
Statistics
Matches: 1409, Mismatches: 211, Indels: 148
0.80 0.12 0.08
Matches are distributed among these distances:
124 8 0.01
125 12 0.01
126 37 0.03
127 48 0.03
128 67 0.05
129 6 0.00
130 14 0.01
131 14 0.01
132 900 0.64
133 37 0.03
134 230 0.16
135 17 0.01
136 14 0.01
137 5 0.00
ACGTcount: A:0.30, C:0.25, G:0.17, T:0.28
Consensus pattern (132 bp):
AAGATCTGCTTTCTTCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTCGATCC
ACTTCCTACCAATATAGGAAGATAAGATCAGCTATCTTCGATCTACTTCACGCCAATACATGAAG
AC
Found at i:5480958 original size:134 final size:134
Alignment explanation
Indices: 5480718--5480989 Score: 427
Period size: 134 Copynumber: 2.0 Consensus size: 134
5480708 TTCTTGCCCC
*
5480718 GGGAGATAGAACTATCAGCTTCAATGTACTCCACTGTAATCAGGGAGGTAAAATCTGCCGTCTTC
1 GGGAGATAGAACTATCAGCTTCAATGTACTCCACTGTAATCAGGGAGGTAAAATCTGCCATCTTC
* *
5480783 AACCTGCTTTGCTGCCAAATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCACTACCAAA
66 AACCTGCTTCGCTGCCAAATACAGGAAGGCAAGATCTGCAATCCTCAATCTATTCCACTACCAAA
5480848 TACA
131 TACA
** * ** *
5480852 GGGAGATAGAGTTATCGGCTTCAATGTACTCCACTGTGGTCAGGGAGGTAAAATCTGCCATCTTT
1 GGGAGATAGAACTATCAGCTTCAATGTACTCCACTGTAATCAGGGAGGTAAAATCTGCCATCTTC
* * **
5480917 GATCTGCTTCGCTGCCAAATACAGGAAGGCAAGATCTGCAATCCTCAATCTATTCCACTGTCAAA
66 AACCTGCTTCGCTGCCAAATACAGGAAGGCAAGATCTGCAATCCTCAATCTATTCCACTACCAAA
5480982 TACA
131 TACA
5480986 GGGA
1 GGGA
5480990 TAAGATCTGC
Statistics
Matches: 125, Mismatches: 13, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
134 125 1.00
ACGTcount: A:0.30, C:0.24, G:0.21, T:0.26
Consensus pattern (134 bp):
GGGAGATAGAACTATCAGCTTCAATGTACTCCACTGTAATCAGGGAGGTAAAATCTGCCATCTTC
AACCTGCTTCGCTGCCAAATACAGGAAGGCAAGATCTGCAATCCTCAATCTATTCCACTACCAAA
TACA
Found at i:5481163 original size:658 final size:658
Alignment explanation
Indices: 5480074--5482580 Score: 3779
Period size: 658 Copynumber: 3.8 Consensus size: 658
5480064 GAGGTAGAGT
* * * * * * *
5480074 TATCGGCTTCAATGTACTCCACTGTAGTCAGGGAGGTAAAATCCGCCATCGTCGATCTGCTTCGC
1 TATCAGCTTCAATGTACTCCACTGTAATCAGGGAGGTAAAATCCGCCGTCTTCAACCTGCTTTGC
* * *
5480139 TGCCAAATACAGGAAGGCAAGATCTGCAATCCTCAATCTATTCCACTGTCAAATACAGGGATA-A
66 TGCCAAATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCACTGCCAAATACAGGGAGATA
* ** * * * **** * * *
5480203 GA-TCT-GCTTTCTTCGATCTACTTCACCACCAGT-ATGGGAAG-ACAAGATCTG-TATCTTGGA
131 GAGT-TATC-GGCTTCAATGTACTCCA-CTGTGGTCA-GGGAGGTA-AA-ATCTGCCATCTTTGA
** ** * ** * * * * * *
5480263 TCCACTTC-CTATC-AATATAGGAAGATAGGACCTGCTATCTTCGATCTACTT-CAC-G-CCAAT
190 TCTGCTTCGCTGCCAAATACAGGAAGGCAAGATCTGCAATCCTCAATCTA-TTCCACTGTCAAAT
* * * * * *
5480323 ACATGAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCACTAATATGGGAAGACAAGATCTGCA
254 ACA-G-GGATAAGATCTGCTTTCTTCAATCTACTTCACCACTAGTATGGGAAGACAAGATCTGCA
* * * *
5480388 TCTTCGATCCACTTCTTACCAATATAGGAAGATAAGATCAGCTATCTTCGATCTACTTCACGCCA
317 TCTTGGATCCACTTCCTACCAATATAGGAAGATAAGACCTGCTATCTTCGATCTACTTCACGCCA
*
5480453 ATACATGAAGACAAGATCTACTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTG
382 ATACATGAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTG
* *
5480518 CATCTTCGATCCATTTCCTACCAATATAGGAAGATAGGATCAGCTATCTTCGATCTACTTCACGC
447 CATCTTCGATCCACTTCCTACCAATATAGGAAGATAAGATCAGCTATCTTCGATCTACTTCACGC
5480583 CAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCAATATGGGAAGACAAGATC
512 CAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCAATATGGGAAGACAAGATC
*
5480648 TGCATCTTCGATCTATTTCCTACCAATATAGGAAGATAGGATCAGCTATCTTCGATCTACTTCTT
577 TGCATCTTCGATCCATTTCCTACCAATATAGGAAGATAGGATCAGCTATCTTCGATCTACTTCTT
5480713 GCCCCGGGAGATAGAAC
642 GCCCCGGGAGATAGAAC
*
5480730 TATCAGCTTCAATGTACTCCACTGTAATCAGGGAGGTAAAATCTGCCGTCTTCAACCTGCTTTGC
1 TATCAGCTTCAATGTACTCCACTGTAATCAGGGAGGTAAAATCCGCCGTCTTCAACCTGCTTTGC
*
5480795 TGCCAAATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCACTACCAAATACAGGGAGATA
66 TGCCAAATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCACTGCCAAATACAGGGAGATA
5480860 GAGTTATCGGCTTCAATGTACTCCACTGTGGTCAGGGAGGTAAAATCTGCCATCTTTGATCTGCT
131 GAGTTATCGGCTTCAATGTACTCCACTGTGGTCAGGGAGGTAAAATCTGCCATCTTTGATCTGCT
5480925 TCGCTGCCAAATACAGGAAGGCAAGATCTGCAATCCTCAATCTATTCCACTGTCAAATACAGGGA
196 TCGCTGCCAAATACAGGAAGGCAAGATCTGCAATCCTCAATCTATTCCACTGTCAAATACAGGGA
*
5480990 TAAGATCTGCTTTCTTCAATCTACTTCACCACTAGTATGGGAAGACAAGATCTGTATCTTGGATC
261 TAAGATCTGCTTTCTTCAATCTACTTCACCACTAGTATGGGAAGACAAGATCTGCATCTTGGATC
* *
5481055 CACTTCCTATCAATATAGGAAGATAGGACCTGCTATCTTCGATCTACTTCACGCCAATACATGAA
326 CACTTCCTACCAATATAGGAAGATAAGACCTGCTATCTTCGATCTACTTCACGCCAATACATGAA
*
5481120 GACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGTATCTTCGA
391 GACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTCGA
*
5481185 TCCACTTCTTACCAATATAGGAAGATAAGATCAGCTATCTTCGATCTACTTCACGCCAATACATG
456 TCCACTTCCTACCAATATAGGAAGATAAGATCAGCTATCTTCGATCTACTTCACGCCAATACATG
5481250 AAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTC
521 AAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTC
5481315 GATCCATTTCCTACCAATATAGGAAGATAGGATCAGCTATCTTCGATCTACTTCTTGCCCCGGGA
586 GATCCATTTCCTACCAATATAGGAAGATAGGATCAGCTATCTTCGATCTACTTCTTGCCCCGGGA
5481380 GATAGAAC
651 GATAGAAC
*
5481388 TATCAGCTTCAATGTACTCCACTGTAATCAGGGAGGTAAAATCCACCGTCTTCAACCTGCTTTGC
1 TATCAGCTTCAATGTACTCCACTGTAATCAGGGAGGTAAAATCCGCCGTCTTCAACCTGCTTTGC
* * * *
5481453 TGCCAAATATAGAAAGGCAAGATCTACAATCTTCAATCTATTCCACTGCCAAATACAGTGAGATA
66 TGCCAAATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCACTGCCAAATACAGGGAGATA
5481518 GAGTTATCGGCTTCAATGTACTCCACTGTGGTCAGGGAGGTAAAATCTGCCATCTTTGATCTGCT
131 GAGTTATCGGCTTCAATGTACTCCACTGTGGTCAGGGAGGTAAAATCTGCCATCTTTGATCTGCT
5481583 TCGCTGCCAAATACAGGAAGGCAAGATCTGCAATCCTCAATCTATTCCACTGTCAAATACAGGGA
196 TCGCTGCCAAATACAGGAAGGCAAGATCTGCAATCCTCAATCTATTCCACTGTCAAATACAGGGA
* * *
5481648 TAAGATCTGCTTTCTTCGATCTACTTCACCACCAGTATGGGAAGACAAGATCTGTATCTTGGATC
261 TAAGATCTGCTTTCTTCAATCTACTTCACCACTAGTATGGGAAGACAAGATCTGCATCTTGGATC
* *
5481713 CACTTCCTATCAATATAGGAAGATAGGACCTGCTATCTTCGATCTACTTCACGCCAATACATGAA
326 CACTTCCTACCAATATAGGAAGATAAGACCTGCTATCTTCGATCTACTTCACGCCAATACATGAA
5481778 GACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTCGA
391 GACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTCGA
*
5481843 TCCACTTCTTACCAATATAGGAAGATAAGATCAGCTATCTTCGATCTACTTCACGCCAATACATG
456 TCCACTTCCTACCAATATAGGAAGATAAGATCAGCTATCTTCGATCTACTTCACGCCAATACATG
*
5481908 AAGATAAGATCTGCTTTCTTCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTC
521 AAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTC
*
5481973 GATCCGTTTCCTACCAATATAGGAAGATAGGATCAGCTATCTTCGATCTACTTCTTGCCCCGGGA
586 GATCCATTTCCTACCAATATAGGAAGATAGGATCAGCTATCTTCGATCTACTTCTTGCCCCGGGA
5482038 GATAGAAC
651 GATAGAAC
5482046 TATCAGCTTCAATGTACTCCACTGTAATCAGGGAGGTAAAATCCGCCGTCTTCAACCTGCTTTGC
1 TATCAGCTTCAATGTACTCCACTGTAATCAGGGAGGTAAAATCCGCCGTCTTCAACCTGCTTTGC
5482111 TGCCAAATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCACTGCCAAATACAGGGAGATA
66 TGCCAAATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCACTGCCAAATACAGGGAGATA
5482176 GAGTTATCGGCTTCAATGTACTCCACTGTGGTCAGGGAGGTAAAATCTGCCATCTTTGATCTGCT
131 GAGTTATCGGCTTCAATGTACTCCACTGTGGTCAGGGAGGTAAAATCTGCCATCTTTGATCTGCT
* * * **
5482241 TCACTGCCAAATACAGGAAGGAAAGATCTGCAATCTTCAATCTATTCCACTACCAAATACAGGGA
196 TCGCTGCCAAATACAGGAAGGCAAGATCTGCAATCCTCAATCTATTCCACTGTCAAATACAGGGA
* * ** * * ** * *
5482306 GATAGAGT-T-ATCGGCTTCAATGTACTCCA-CTGTGGTCA-GGGAGGTA-AA-ATCTGCCATCT
261 TA-AGA-TCTGCT-TTCTTCAATCTACTTCACCACTAGT-ATGGGAAG-ACAAGATCTG-CATCT
* ** * * ** * * * *
5482365 TTGATCTGCTTCGCTGCCAAATACAGGAAGGCAAGATCTGCAATATTCGATCTACTTCACTCCAA
320 TGGATCCACTTC-CTACC-AATATAGGAAGATAAGACCTGCTATCTTCGATCTACTTCACGCCAA
* * *
5482430 TACATGAAGATAAGATCTGCTTTCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGC
383 TACATGAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGC
* * ** * * * *
5482495 ATCGTCAATCCACTTCCTACCAATATAGGAAGATCGGACCTGTTATCTTTGATCTACTTCACGCC
448 ATCTTCGATCCACTTCCTACCAATATAGGAAGATAAGATCAGCTATCTTCGATCTACTTCACGCC
5482560 AATACATGAAGACAAGATCTG
513 AATACATGAAGACAAGATCTG
5482581 TTTTAATGAC
Statistics
Matches: 1714, Mismatches: 118, Indels: 34
0.92 0.06 0.02
Matches are distributed among these distances:
655 5 0.00
656 139 0.08
657 28 0.02
658 1335 0.78
659 23 0.01
660 184 0.11
ACGTcount: A:0.30, C:0.25, G:0.18, T:0.28
Consensus pattern (658 bp):
TATCAGCTTCAATGTACTCCACTGTAATCAGGGAGGTAAAATCCGCCGTCTTCAACCTGCTTTGC
TGCCAAATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCACTGCCAAATACAGGGAGATA
GAGTTATCGGCTTCAATGTACTCCACTGTGGTCAGGGAGGTAAAATCTGCCATCTTTGATCTGCT
TCGCTGCCAAATACAGGAAGGCAAGATCTGCAATCCTCAATCTATTCCACTGTCAAATACAGGGA
TAAGATCTGCTTTCTTCAATCTACTTCACCACTAGTATGGGAAGACAAGATCTGCATCTTGGATC
CACTTCCTACCAATATAGGAAGATAAGACCTGCTATCTTCGATCTACTTCACGCCAATACATGAA
GACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTCGA
TCCACTTCCTACCAATATAGGAAGATAAGATCAGCTATCTTCGATCTACTTCACGCCAATACATG
AAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTC
GATCCATTTCCTACCAATATAGGAAGATAGGATCAGCTATCTTCGATCTACTTCTTGCCCCGGGA
GATAGAAC
Found at i:5481787 original size:790 final size:789
Alignment explanation
Indices: 5480201--5482580 Score: 2756
Period size: 790 Copynumber: 3.0 Consensus size: 789
5480191 ATACAGGGAT
5480201 AAGATCTGCTTTCTTCGATCTACTTCACCACCAGTATGGGAAGACAAGATCTGTATCTTGGATCC
1 AAGATCTGCTTTCTTCGATCTACTTCACCACCAGTATGGGAAGACAAGATCTGTATCTTGGATCC
5480266 ACTTCCTATCAATATAGGAAGATAGGACCTGCTATCTTCGATCTACTTCACGCCAATACATGAAG
66 ACTTCCTATCAATATAGGAAGATAGGACCTGCTATCTTCGATCTACTTCACGCCAATACATGAAG
*
5480331 ACAAGATCTGCTTTCTGCGATCTACTTCGCCACTAATATGGGAAGACAAGATCTGCATCTTCGAT
131 ACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTCGAT
5480396 CCACTTCTTACCAATATAGGAAGATAAGATCAGCTATCTTCGATCTACTTCACGCCAATACATGA
196 CCACTTCTTACCAATATAGGAAGATAAGATCAGCTATCTTCGATCTACTTCACGCCAATACATGA
*
5480461 AGACAAGATCTACTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTCG
261 AGACAAGATCT-CTTTCTTCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTCG
* *
5480526 ATCCATTTCCTACCAATATAGGAAGATAGGATCAGCTATCTTCGATCTACTTCACGCCAATACAT
325 ATCCATTTCCTACCAATATAGGAAGATAGGATCAGCTATCTTCGATCTACTTCATGCC---ACAG
* * * * ** * * * * **
5480591 GAAGACAAGATCT-GCTTTCTTCGATCTACTTCGCCAC--CAAT-ATGGGAAG-ACAAGAT-CTG
387 GGAGA-TAGAACTATC-AGCTTCAATGTAC-T--CCACTGTAATCA-GGGAGGTA-AA-ATCCAC
* * * * * *
5480650 CATCTTCGATCT-ATTTCCTACC-AATATAGGAA-GATAGGATC-AGCTATCTTCGATCTACTT-
444 CATCTTCGATCTGCTTTACTGCCAAATATAGGAAGGA-AAGATCTA-CAATCTTCAATCTA-TTC
* * ** * **
5480710 C-TTGCC-----CCGGGAGATAGAACTATCAGCTTCAATGTACTCCACTGTAATCAGGGAGGTAA
506 CACTGCCAAATACAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTGTGGTCAGGGAGGTAA
* ** * *
5480769 AATCTGCCGTCTTCAACCTGCTTTGCTGCCAAATACAGGAAGGCAAGATCTGCAATCTTCAATCT
571 AATCTGCCATCTTTGATCTGCTTCGCTGCCAAATACAGGAAGGCAAGATCTGCAATCTTCAATCT
* * * ** * * * ****
5480834 ATTCCACTACCAAATACAGGGAGATAGAGT-T-ATCGGCTTCAATGTACTCCA-CTGTGGTCA-G
636 ATTCCACT-TCAAATACAGGGATA-AGA-TCTGCT-TTCTTCGATCTACTTCACCACCAGT-ATG
* * ** * * ** * * *
5480895 GGAGGTA-AA-ATCTGCCATCTTTGATCTGCTTCGCTGCCAAATACAGGAAGGCAAGATCTGCAA
696 GGAAG-ACAAGATCTG-CATCTTCGATCCACTTC-CTACC-AATATAGGAAGATAGGACCTGCTA
* * * * *
5480958 TCCTCAATCTA-TTCCACTGTCAAATACA-G-GGAT
757 TCTTCGATCTACTT-CAC-G-CCAATACATGAAGAC
* *
5480991 AAGATCTGCTTTCTTCAATCTACTTCACCACTAGTATGGGAAGACAAGATCTGTATCTTGGATCC
1 AAGATCTGCTTTCTTCGATCTACTTCACCACCAGTATGGGAAGACAAGATCTGTATCTTGGATCC
5481056 ACTTCCTATCAATATAGGAAGATAGGACCTGCTATCTTCGATCTACTTCACGCCAATACATGAAG
66 ACTTCCTATCAATATAGGAAGATAGGACCTGCTATCTTCGATCTACTTCACGCCAATACATGAAG
*
5481121 ACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGTATCTTCGAT
131 ACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTCGAT
5481186 CCACTTCTTACCAATATAGGAAGATAAGATCAGCTATCTTCGATCTACTTCACGCCAATACATGA
196 CCACTTCTTACCAATATAGGAAGATAAGATCAGCTATCTTCGATCTACTTCACGCCAATACATGA
5481251 AGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTCG
261 AGACAAGATCT-CTTTCTTCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTCG
* *
5481316 ATCCATTTCCTACCAATATAGGAAGATAGGATCAGCTATCTTCGATCTACTTCTTGCC-CCGGGA
325 ATCCATTTCCTACCAATATAGGAAGATAGGATCAGCTATCTTCGATCTACTTCATGCCACAGGGA
* * *
5481380 GATAGAACTATCAGCTTCAATGTACTCCACTGTAATCAGGGAGGTAAAATCCACCGTCTTCAACC
390 GATAGAACTATCAGCTTCAATGTACTCCACTGTAATCAGGGAGGTAAAATCCACCATCTTCGATC
* * *
5481445 TGCTTTGCTGCCAAATATAGAAAGGCAAGATCTACAATCTTCAATCTATTCCACTGCCAAATACA
455 TGCTTTACTGCCAAATATAGGAAGGAAAGATCTACAATCTTCAATCTATTCCACTGCCAAATACA
*
5481510 GTGAGATAGAGTTATCGGCTTCAATGTACTCCACTGTGGTCAGGGAGGTAAAATCTGCCATCTTT
520 GGGAGATAGAGTTATCGGCTTCAATGTACTCCACTGTGGTCAGGGAGGTAAAATCTGCCATCTTT
*
5481575 GATCTGCTTCGCTGCCAAATACAGGAAGGCAAGATCTGCAATCCTCAATCTATTCCACTGTCAAA
585 GATCTGCTTCGCTGCCAAATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCACT-TCAAA
*
5481640 TACAGGGATAAGATCTGCTTTCTTCGATCTACTTCACCACCAGTATGGGAAGACAAGATCTGTAT
649 TACAGGGATAAGATCTGCTTTCTTCGATCTACTTCACCACCAGTATGGGAAGACAAGATCTGCAT
* *
5481705 CTTGGATCCACTTCCTATCAATATAGGAAGATAGGACCTGCTATCTTCGATCTACTTCACGCCAA
714 CTTCGATCCACTTCCTACCAATATAGGAAGATAGGACCTGCTATCTTCGATCTACTTCACGCCAA
5481770 TACATGAAGAC
779 TACATGAAGAC
* * * * *
5481781 AAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTCGATCC
1 AAGATCTGCTTTCTTCGATCTACTTCACCACCAGTATGGGAAGACAAGATCTGTATCTTGGATCC
* * * * *
5481846 ACTTCTTACCAATATAGGAAGATAAGATCAGCTATCTTCGATCTACTTCACGCCAATACATGAAG
66 ACTTCCTATCAATATAGGAAGATAGGACCTGCTATCTTCGATCTACTTCACGCCAATACATGAAG
* *
5481911 ATAAGATCTGCTTTCTTCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTCGAT
131 ACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTCGAT
** * * ** ** *
5481976 CCGTTTCCTACCAATATAGGAAGATAGGATCAGCTATCTTCGATCTACTTCTTGCC----CCGGG
196 CCACTTCTTACCAATATAGGAAGATAAGATCAGCTATCTTCGATCTACTTCACGCCAATACATGA
* * * ** * * * * * *
5482037 AGA-TAGAACTATCAGCTTCAATGTAC-T--CCACTGTAATCA-GGGAGGTA-AA-ATCCGCCGT
261 AGACAAGATCTCT-TTCTTCGATCTACTTCGCCAC--CAAT-ATGGGAAG-ACAAGATCTG-CAT
* * * * * ** * * * *
5482095 CTTC-AACCTGCTTTGCTGCCAAATACAGGAAGGCAAGATCTGCAATCTTCAATCTA-TTCCACT
320 CTTCGATCC--ATTTCCTACC-AATATAGGAAGATAGGATCAGCTATCTTCGATCTACTT-CA-T
** * **
5482158 GCCAAATACAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTGTGGTCAGGGAGGTAAAATC
380 GCC----ACAGGGAGATAGAACTATCAGCTTCAATGTACTCCACTGTAATCAGGGAGGTAAAATC
** * * * *
5482223 TGCCATCTTTGATCTGCTTCACTGCCAAATACAGGAAGGAAAGATCTGCAATCTTCAATCTATTC
441 CACCATCTTCGATCTGCTTTACTGCCAAATATAGGAAGGAAAGATCTACAATCTTCAATCTATTC
*
5482288 CACTACCAAATACAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTGTGGTCAGGGAGGTAA
506 CACTGCCAAATACAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTGTGGTCAGGGAGGTAA
* *
5482353 AATCTGCCATCTTTGATCTGCTTCGCTGCCAAATACAGGAAGGCAAGATCTGCAATATTCGATCT
571 AATCTGCCATCTTTGATCTGCTTCGCTGCCAAATACAGGAAGGCAAGATCTGCAATCTTCAATCT
* * *
5482418 ACTT-CAC-TCCAATACATGAAGATAAGATCTGCTTTCTTCGATCTACTTCGCCACCAGTATGGG
636 A-TTCCACTTCAAATACA-G-GGATAAGATCTGCTTTCTTCGATCTACTTCACCACCAGTATGGG
* * * * *
5482481 AAGACAAGATCTGCATCGTCAATCCACTTCCTACCAATATAGGAAGATCGGACCTGTTATCTTTG
698 AAGACAAGATCTGCATCTTCGATCCACTTCCTACCAATATAGGAAGATAGGACCTGCTATCTTCG
5482546 ATCTACTTCACGCCAATACATGAAGAC
763 ATCTACTTCACGCCAATACATGAAGAC
5482573 AAGATCTG
1 AAGATCTG
5482581 TTTTAATGAC
Statistics
Matches: 1386, Mismatches: 159, Indels: 88
0.85 0.10 0.05
Matches are distributed among these distances:
782 8 0.01
783 9 0.01
784 39 0.03
785 50 0.04
786 67 0.05
787 10 0.01
788 7 0.01
789 2 0.00
790 646 0.47
791 24 0.02
792 517 0.37
793 7 0.01
ACGTcount: A:0.30, C:0.25, G:0.18, T:0.28
Consensus pattern (789 bp):
AAGATCTGCTTTCTTCGATCTACTTCACCACCAGTATGGGAAGACAAGATCTGTATCTTGGATCC
ACTTCCTATCAATATAGGAAGATAGGACCTGCTATCTTCGATCTACTTCACGCCAATACATGAAG
ACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTCGAT
CCACTTCTTACCAATATAGGAAGATAAGATCAGCTATCTTCGATCTACTTCACGCCAATACATGA
AGACAAGATCTCTTTCTTCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTCGA
TCCATTTCCTACCAATATAGGAAGATAGGATCAGCTATCTTCGATCTACTTCATGCCACAGGGAG
ATAGAACTATCAGCTTCAATGTACTCCACTGTAATCAGGGAGGTAAAATCCACCATCTTCGATCT
GCTTTACTGCCAAATATAGGAAGGAAAGATCTACAATCTTCAATCTATTCCACTGCCAAATACAG
GGAGATAGAGTTATCGGCTTCAATGTACTCCACTGTGGTCAGGGAGGTAAAATCTGCCATCTTTG
ATCTGCTTCGCTGCCAAATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCACTTCAAATA
CAGGGATAAGATCTGCTTTCTTCGATCTACTTCACCACCAGTATGGGAAGACAAGATCTGCATCT
TCGATCCACTTCCTACCAATATAGGAAGATAGGACCTGCTATCTTCGATCTACTTCACGCCAATA
CATGAAGAC
Found at i:5482161 original size:46 final size:46
Alignment explanation
Indices: 5482110--5482303 Score: 148
Period size: 46 Copynumber: 4.3 Consensus size: 46
5482100 ACCTGCTTTG
*
5482110 CTGCCAAATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCA
1 CTGCCAAATACAGGAAGGTAAGATCTGCAATCTTCAATCTATTCCA
* * * * ** * *
5482156 CTGCCAAATACAGGGAGATAGAGTTAT-C-GGCTTCAATGTACTCCA
1 CTGCCAAATACAGGAAGGTA-AGATCTGCAATCTTCAATCTATTCCA
*** * * * ** *
5482201 CTG--TGGT-CAGGGAGGTAAAATCTGCCATCTTTGATCTGCTT-CA
1 CTGCCAAATACAGGAAGGTAAGATCTGCAATCTTCAATCT-ATTCCA
*
5482244 CTGCCAAATACAGGAAGGAAAGATCTGCAATCTTCAATCTATTCCA
1 CTGCCAAATACAGGAAGGTAAGATCTGCAATCTTCAATCTATTCCA
*
5482290 CTACCAAATACAGG
1 CTGCCAAATACAGG
5482304 GAGATAGAGT
Statistics
Matches: 106, Mismatches: 34, Indels: 16
0.68 0.22 0.10
Matches are distributed among these distances:
41 3 0.03
42 10 0.09
43 12 0.11
44 1 0.01
45 19 0.18
46 57 0.54
47 4 0.04
ACGTcount: A:0.32, C:0.24, G:0.19, T:0.25
Consensus pattern (46 bp):
CTGCCAAATACAGGAAGGTAAGATCTGCAATCTTCAATCTATTCCA
Found at i:5482528 original size:88 final size:89
Alignment explanation
Indices: 5482390--5482554 Score: 192
Period size: 88 Copynumber: 1.9 Consensus size: 89
5482380 GCCAAATACA
* * * * * *
5482390 GGAAGGCAAGATCTGCAATATTCGATCTACTTCACTCCAATACATGAAGATAAGATCTGCTT-TC
1 GGAAGACAAGATCTGCAATAGTCAATCCACTTCACTCCAATACAGGAAGATAAGACCTG-TTATC
5482454 TTCGATCTACTTCGCCACCAGTATG
65 TTCGATCTACTTCGCCACCAGTATG
* * **
5482479 GGAAGACAAGATCTGC-ATCGTCAATCCACTTC-CTACCAATATAGGAAGATCGGACCTGTTATC
1 GGAAGACAAGATCTGCAATAGTCAATCCACTTCACT-CCAATACAGGAAGATAAGACCTGTTATC
*
5482542 TTTGATCTACTTC
65 TTCGATCTACTTC
5482555 ACGCCAATAC
Statistics
Matches: 63, Mismatches: 11, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
87 4 0.06
88 44 0.70
89 15 0.24
ACGTcount: A:0.29, C:0.25, G:0.17, T:0.29
Consensus pattern (89 bp):
GGAAGACAAGATCTGCAATAGTCAATCCACTTCACTCCAATACAGGAAGATAAGACCTGTTATCT
TCGATCTACTTCGCCACCAGTATG
Found at i:5482582 original size:44 final size:44
Alignment explanation
Indices: 5482384--5482582 Score: 145
Period size: 44 Copynumber: 4.5 Consensus size: 44
5482374 TTCGCTGCCA
* ** * *
5482384 AATACAGGAAGGCAAGATCTGCAATATTCGATCTACTTCACTCC
1 AATACAGGAAGACAAGATCTGTTATCTTCGATCTACTTCACACC
* * *
5482428 AATACATGAAGATAAGATCTGCTT-TCTTCGATCTACTTCGCCACC
1 AATACAGGAAGACAAGATCTG-TTATCTTCGATCTACTTC-ACACC
* ** * * * *
5482473 AGTATGGGAAGACAAGATCTG-CATCGTCAATCCACTTC-CTACC
1 AATACAGGAAGACAAGATCTGTTATCTTCGATCTACTTCAC-ACC
* * * * *
5482516 AATATAGGAAGATC-GGACCTGTTATCTTTGATCTACTTCACGCC
1 AATACAGGAAGA-CAAGATCTGTTATCTTCGATCTACTTCACACC
*
5482560 AATACATGAAGACAAGATCTGTT
1 AATACAGGAAGACAAGATCTGTT
5482583 TTAATGACTT
Statistics
Matches: 116, Mismatches: 31, Indels: 16
0.71 0.19 0.10
Matches are distributed among these distances:
42 1 0.01
43 19 0.16
44 76 0.66
45 20 0.17
ACGTcount: A:0.32, C:0.24, G:0.17, T:0.28
Consensus pattern (44 bp):
AATACAGGAAGACAAGATCTGTTATCTTCGATCTACTTCACACC
Found at i:5483604 original size:7 final size:7
Alignment explanation
Indices: 5483588--5483637 Score: 61
Period size: 7 Copynumber: 7.4 Consensus size: 7
5483578 TGGCCTCTCC
5483588 TTTTTC-
1 TTTTTCT
5483594 TTTTTCT
1 TTTTTCT
5483601 TTTTTC-
1 TTTTTCT
5483607 -TTTTCT
1 TTTTTCT
5483613 TTTTTCAT
1 TTTTTC-T
*
5483621 TTTTTCA
1 TTTTTCT
5483628 TTTTTCT
1 TTTTTCT
5483635 TTT
1 TTT
5483638 CGTTTTTTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
5 5 0.13
6 6 0.16
7 20 0.53
8 7 0.18
ACGTcount: A:0.04, C:0.14, G:0.00, T:0.82
Consensus pattern (7 bp):
TTTTTCT
Found at i:5483644 original size:7 final size:6
Alignment explanation
Indices: 5483587--5483637 Score: 50
Period size: 6 Copynumber: 7.8 Consensus size: 6
5483577 TTGGCCTCTC
5483587 CTTTTT CTTTTT CTTTTT -TCTTTT CTTTTTT CATTTTTT CATTTTT CTTTT
1 CTTTTT CTTTTT CTTTTT CT-TTTT C-TTTTT C--TTTTT C-TTTTT CTTTT
5483638 CGTTTTTTTT
Statistics
Matches: 40, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
5 1 0.03
6 20 0.50
7 11 0.28
8 8 0.20
ACGTcount: A:0.04, C:0.16, G:0.00, T:0.80
Consensus pattern (6 bp):
CTTTTT
Found at i:5483644 original size:12 final size:13
Alignment explanation
Indices: 5483588--5483637 Score: 66
Period size: 12 Copynumber: 3.8 Consensus size: 13
5483578 TGGCCTCTCC
5483588 TTTTTCTTTTTCT
1 TTTTTCTTTTTCT
5483601 TTTTTC-TTTTCT
1 TTTTTCTTTTTCT
*
5483613 TTTTTCATTTTTTCA
1 TTTTTC--TTTTTCT
5483628 TTTTTCTTTT
1 TTTTTCTTTT
5483638 CGTTTTTTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
12 12 0.36
13 10 0.30
15 11 0.33
ACGTcount: A:0.04, C:0.14, G:0.00, T:0.82
Consensus pattern (13 bp):
TTTTTCTTTTTCT
Found at i:5484081 original size:15 final size:16
Alignment explanation
Indices: 5484055--5484085 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
5484045 CTCAAGTAGA
5484055 GGTTTTTCTTTTATTT
1 GGTTTTTCTTTTATTT
5484071 GGTTTTT-TTTTATTT
1 GGTTTTTCTTTTATTT
5484086 TCTCGTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.53
16 7 0.47
ACGTcount: A:0.06, C:0.03, G:0.13, T:0.77
Consensus pattern (16 bp):
GGTTTTTCTTTTATTT
Found at i:5484106 original size:12 final size:11
Alignment explanation
Indices: 5484057--5484133 Score: 66
Period size: 11 Copynumber: 6.4 Consensus size: 11
5484047 CAAGTAGAGG
5484057 TTTTTCTTTTAT
1 TTTTTCTTTT-T
*
5484069 TTGGTTTTTTTTT
1 TT--TTTCTTTTT
5484082 ATTTTCTCGTTTTT
1 -TTTT-TC-TTTTT
5484096 TTTTTACTTTTT
1 TTTTT-CTTTTT
5484108 TTTTGTC-TTTT
1 TTTT-TCTTTTT
5484119 TTTTTCTTTTT
1 TTTTTCTTTTT
5484130 TTTT
1 TTTT
5484134 GCCTCCACTG
Statistics
Matches: 55, Mismatches: 2, Indels: 17
0.74 0.03 0.23
Matches are distributed among these distances:
10 2 0.04
11 16 0.29
12 15 0.27
13 8 0.15
14 14 0.25
ACGTcount: A:0.04, C:0.08, G:0.05, T:0.83
Consensus pattern (11 bp):
TTTTTCTTTTT
Found at i:5484131 original size:22 final size:23
Alignment explanation
Indices: 5484092--5484134 Score: 79
Period size: 22 Copynumber: 1.9 Consensus size: 23
5484082 ATTTTCTCGT
5484092 TTTTTTTTTACTTTTTTTTTGTC
1 TTTTTTTTTACTTTTTTTTTGTC
5484115 TTTTTTTTT-CTTTTTTTTTG
1 TTTTTTTTTACTTTTTTTTTG
5484135 CCTCCACTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 11 0.55
23 9 0.45
ACGTcount: A:0.02, C:0.07, G:0.05, T:0.86
Consensus pattern (23 bp):
TTTTTTTTTACTTTTTTTTTGTC
Found at i:5484133 original size:10 final size:10
Alignment explanation
Indices: 5484057--5484133 Score: 57
Period size: 10 Copynumber: 7.5 Consensus size: 10
5484047 CAAGTAGAGG
5484057 TTTTTCTTTT
1 TTTTTCTTTT
* **
5484067 ATTTGGTTTT
1 TTTTTCTTTT
*
5484077 TTTTTATTTT
1 TTTTTCTTTT
**
5484087 CTCGTT-TTTT
1 -TTTTTCTTTT
*
5484097 TTTTACTTTTT
1 TTTTTC-TTTT
5484108 TTTTGTCTTTT
1 TTTT-TCTTTT
5484119 TTTTTCTTTT
1 TTTTTCTTTT
5484129 TTTTT
1 TTTTT
5484134 GCCTCCACTG
Statistics
Matches: 51, Mismatches: 12, Indels: 8
0.72 0.17 0.11
Matches are distributed among these distances:
9 2 0.04
10 29 0.57
11 19 0.37
12 1 0.02
ACGTcount: A:0.04, C:0.08, G:0.05, T:0.83
Consensus pattern (10 bp):
TTTTTCTTTT
Found at i:5486051 original size:266 final size:266
Alignment explanation
Indices: 5485577--5486108 Score: 992
Period size: 266 Copynumber: 2.0 Consensus size: 266
5485567 GCGGATACAT
* * * *
5485577 ATACGGCTTTGCTCTCATATGCGGAGACATTCGATCATTTTCTTCGTTCGAGCGTTAAGATAAGT
1 ATACGGCTTTGCCCTCATATGCAGAGACATTCGATCATTTTCTTCATTCGAGCGTTAAAATAAGT
*
5485642 CTCACGAACTCTTCAAAAGGGACGTATCTTATATCTCCTTTTTACTCAATCCGGGTCGTGACTCG
66 CTCACGAACTCTTCAAAAGGGACGTATCTTATATCTCCTTTTTACTCAATCCGGGCCGTGACTCG
*
5485707 TTGCTCACTAAACCTCATGGTGCTCGTTGGCTTCTCTTTTAAAAAAGTTCAGCGGCTCTCGAATA
131 TTGCTCACTAAACCTCATGGTGCTCGTTGGCTTCTCTTTTAAAAAAGTTCAGCGGCTCTCAAATA
*
5485772 ATCCTTGTCACATTAAATTCTCGGGCCACGGAGCAATGGTTGTGTGGTCCTCTATTAAACTATCA
196 ATCCTTGTCACATTAAATTCTCGGGCCACGGAGCAATGGTTGTGTGGTCCTCCATTAAACTATCA
5485837 TCCTTC
261 TCCTTC
5485843 ATACGGCTTTGCCCTCATATGCAGAGACATTCGATCATTTTCTTCATTCGAGCGTTAAAATAAGT
1 ATACGGCTTTGCCCTCATATGCAGAGACATTCGATCATTTTCTTCATTCGAGCGTTAAAATAAGT
5485908 CTCACGAACTCTTCAAAAGGGACGTATCTTATATCTCCTTTTTACTCAATCCGGGCCGTGACTCG
66 CTCACGAACTCTTCAAAAGGGACGTATCTTATATCTCCTTTTTACTCAATCCGGGCCGTGACTCG
*
5485973 TTGCTCACTAAACCTCATGGTGCTCGTTGGCTTCTCTTTTAAGAAAGTTCAGCGGCTCTCAAATA
131 TTGCTCACTAAACCTCATGGTGCTCGTTGGCTTCTCTTTTAAAAAAGTTCAGCGGCTCTCAAATA
5486038 ATCCTTGTCACATTAAATTCTCGGGCCACGGAGCAATGGTTGTGTGGTCCTCCATTAAACTATCA
196 ATCCTTGTCACATTAAATTCTCGGGCCACGGAGCAATGGTTGTGTGGTCCTCCATTAAACTATCA
5486103 TCCTTC
261 TCCTTC
5486109 TCTTATCACG
Statistics
Matches: 258, Mismatches: 8, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
266 258 1.00
ACGTcount: A:0.23, C:0.25, G:0.18, T:0.33
Consensus pattern (266 bp):
ATACGGCTTTGCCCTCATATGCAGAGACATTCGATCATTTTCTTCATTCGAGCGTTAAAATAAGT
CTCACGAACTCTTCAAAAGGGACGTATCTTATATCTCCTTTTTACTCAATCCGGGCCGTGACTCG
TTGCTCACTAAACCTCATGGTGCTCGTTGGCTTCTCTTTTAAAAAAGTTCAGCGGCTCTCAAATA
ATCCTTGTCACATTAAATTCTCGGGCCACGGAGCAATGGTTGTGTGGTCCTCCATTAAACTATCA
TCCTTC
Found at i:5487627 original size:15 final size:15
Alignment explanation
Indices: 5487603--5487636 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
5487593 AACAATTACG
*
5487603 ATAATGCGAGCAAAA
1 ATAATACGAGCAAAA
5487618 ATAATACGAGCAAAA
1 ATAATACGAGCAAAA
5487633 ATAA
1 ATAA
5487637 CAAAAATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.59, C:0.12, G:0.15, T:0.15
Consensus pattern (15 bp):
ATAATACGAGCAAAA
Found at i:5491383 original size:6 final size:6
Alignment explanation
Indices: 5491353--5491422 Score: 50
Period size: 6 Copynumber: 10.3 Consensus size: 6
5491343 TTACGTTAAA
* *
5491353 AATTTT AAATTT AGTTTCT ATATTTT AATTTT ATTACTTTT AATTTT AAATTTT
1 AATTTT AATTTT AATTT-T A-ATTTT AATTTT A--A-TTTT AATTTT -AATTTT
5491407 AAAATTTT AATTTT AA
1 --AATTTT AATTTT AA
5491423 CTCAAATGGT
Statistics
Matches: 53, Mismatches: 4, Indels: 14
0.75 0.06 0.20
Matches are distributed among these distances:
6 26 0.49
7 11 0.21
8 11 0.21
9 5 0.09
ACGTcount: A:0.36, C:0.03, G:0.01, T:0.60
Consensus pattern (6 bp):
AATTTT
Found at i:5491400 original size:21 final size:20
Alignment explanation
Indices: 5491374--5491422 Score: 62
Period size: 21 Copynumber: 2.4 Consensus size: 20
5491364 TAGTTTCTAT
* *
5491374 ATTTTAATTTTATTACTTTTA
1 ATTTTAATTTTA-AAATTTTA
5491395 ATTTTAAATTTTAAAATTTTA
1 ATTTT-AATTTTAAAATTTTA
5491416 ATTTTAA
1 ATTTTAA
5491423 CTCAAATGGT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 2 0.08
21 16 0.64
22 7 0.28
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (20 bp):
ATTTTAATTTTAAAATTTTA
Found at i:5491420 original size:14 final size:15
Alignment explanation
Indices: 5491394--5491422 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
5491384 TATTACTTTT
5491394 AATTTTAAATTTTAA
1 AATTTTAAATTTTAA
5491409 AATTTT-AATTTTAA
1 AATTTTAAATTTTAA
5491423 CTCAAATGGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
AATTTTAAATTTTAA
Found at i:5498313 original size:27 final size:27
Alignment explanation
Indices: 5498275--5498330 Score: 64
Period size: 27 Copynumber: 2.1 Consensus size: 27
5498265 ATTAGGATTA
5498275 AACTTAGATTATA-AAATAGATAAAA-AC
1 AACTTAGATTATACAAA-AGA-AAAATAC
5498302 AACTATAG-TTATACAAAAGAAAAATAC
1 AACT-TAGATTATACAAAAGAAAAATAC
5498329 AA
1 AA
5498331 GGGGATGCTA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
26 4 0.15
27 16 0.62
28 6 0.23
ACGTcount: A:0.61, C:0.09, G:0.07, T:0.23
Consensus pattern (27 bp):
AACTTAGATTATACAAAAGAAAAATAC
Found at i:5502072 original size:12 final size:12
Alignment explanation
Indices: 5502055--5502089 Score: 54
Period size: 12 Copynumber: 2.9 Consensus size: 12
5502045 TTTATGCATA
5502055 TATATTTATTAT
1 TATATTTATTAT
5502067 TATATTTATTAT
1 TATATTTATTAT
5502079 TA-ATATTATTA
1 TATAT-TTATTA
5502090 GCATTAGCAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 2 0.09
12 20 0.91
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (12 bp):
TATATTTATTAT
Found at i:5502621 original size:52 final size:52
Alignment explanation
Indices: 5502525--5502623 Score: 119
Period size: 52 Copynumber: 1.9 Consensus size: 52
5502515 ATGTTATTTG
* * * *
5502525 TTATATATTTCTTTTACTATTTCATGTATATGTTTTTTAAATACCATAATAT
1 TTATATATTTCTTTTACTATCTCACGTATATATTTTATAAATACCATAATAT
* **
5502577 TTATAT-TTTTTTTGTACTATCTCACGTATATATTTTATCCATACCAT
1 TTATATATTTCTTT-TACTATCTCACGTATATATTTTATAAATACCAT
5502624 TATGAAGAAT
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
51 6 0.15
52 33 0.85
ACGTcount: A:0.28, C:0.13, G:0.04, T:0.55
Consensus pattern (52 bp):
TTATATATTTCTTTTACTATCTCACGTATATATTTTATAAATACCATAATAT
Found at i:5510902 original size:17 final size:18
Alignment explanation
Indices: 5510861--5510902 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
5510851 TAATATCGAA
* *
5510861 GATAAAAAAAATTTAATT
1 GATAAAAAAAACTAAATT
*
5510879 GAGAAAAAAAACTAAATT
1 GATAAAAAAAACTAAATT
5510897 G-TAAAA
1 GATAAAA
5510903 GTGTTGAACA
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
17 4 0.20
18 16 0.80
ACGTcount: A:0.64, C:0.02, G:0.10, T:0.24
Consensus pattern (18 bp):
GATAAAAAAAACTAAATT
Found at i:5514211 original size:15 final size:15
Alignment explanation
Indices: 5514188--5514240 Score: 58
Period size: 14 Copynumber: 3.7 Consensus size: 15
5514178 TTTTTAGGCT
5514188 AAAAT-ATTTTTCGG
1 AAAATGATTTTTCGG
5514202 AAAATGA-TTTTCTGG
1 AAAATGATTTTTC-GG
* *
5514217 AAAATAATTTAT-GG
1 AAAATGATTTTTCGG
5514231 AAAATGATTT
1 AAAATGATTT
5514241 ATTTTTCTGG
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
14 21 0.64
15 9 0.27
16 3 0.09
ACGTcount: A:0.42, C:0.04, G:0.15, T:0.40
Consensus pattern (15 bp):
AAAATGATTTTTCGG
Found at i:5514241 original size:14 final size:14
Alignment explanation
Indices: 5514200--5514242 Score: 59
Period size: 14 Copynumber: 3.0 Consensus size: 14
5514190 AATATTTTTC
*
5514200 GGAAAATGATTTTCT
1 GGAAAATGA-TTTAT
*
5514215 GGAAAATAATTTAT
1 GGAAAATGATTTAT
5514229 GGAAAATGATTTAT
1 GGAAAATGATTTAT
5514243 TTTTCTGGTG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
14 17 0.68
15 8 0.32
ACGTcount: A:0.42, C:0.02, G:0.19, T:0.37
Consensus pattern (14 bp):
GGAAAATGATTTAT
Found at i:5514724 original size:22 final size:22
Alignment explanation
Indices: 5514699--5514784 Score: 88
Period size: 22 Copynumber: 4.0 Consensus size: 22
5514689 ATCCAAGTGC
5514699 ATAACTAATATTACACCACATG
1 ATAACTAATATTACACCACATG
* *
5514721 ATAACTAATATTACAGCACATT
1 ATAACTAATATTACACCACATG
* **
5514743 ATAAC-AACATT-GTCCA-AGTG
1 ATAACTAATATTACACCACA-TG
5514763 CATAACTAATATTACACCACAT
1 -ATAACTAATATTACACCACAT
5514785 TATCAATATC
Statistics
Matches: 49, Mismatches: 10, Indels: 9
0.72 0.15 0.13
Matches are distributed among these distances:
19 1 0.02
20 3 0.06
21 10 0.20
22 30 0.61
23 4 0.08
24 1 0.02
ACGTcount: A:0.44, C:0.22, G:0.06, T:0.28
Consensus pattern (22 bp):
ATAACTAATATTACACCACATG
Found at i:5515775 original size:32 final size:32
Alignment explanation
Indices: 5515729--5515789 Score: 104
Period size: 32 Copynumber: 1.9 Consensus size: 32
5515719 TGTCAATCAT
5515729 TTCAATATCCAACAAGCTTAAAACATAATAAA
1 TTCAATATCCAACAAGCTTAAAACATAATAAA
* *
5515761 TTCAATATCTAACAAGCTTGAAACATAAT
1 TTCAATATCCAACAAGCTTAAAACATAAT
5515790 CAATATCTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.49, C:0.18, G:0.05, T:0.28
Consensus pattern (32 bp):
TTCAATATCCAACAAGCTTAAAACATAATAAA
Found at i:5515796 original size:27 final size:30
Alignment explanation
Indices: 5515729--5515802 Score: 91
Period size: 32 Copynumber: 2.5 Consensus size: 30
5515719 TGTCAATCAT
*
5515729 TTCAATATCCAACAAGCTTAAAACATAATAAA
1 TTCAATATCTAACAAGCTTAAAAC--AATAAA
*
5515761 TTCAATATCTAACAAGCTTGAAAC-AT-AA
1 TTCAATATCTAACAAGCTTAAAACAATAAA
5515789 -TCAATATCTAACAA
1 TTCAATATCTAACAA
5515803 AATCAAGACA
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
27 14 0.35
28 2 0.05
29 2 0.05
32 22 0.55
ACGTcount: A:0.50, C:0.19, G:0.04, T:0.27
Consensus pattern (30 bp):
TTCAATATCTAACAAGCTTAAAACAATAAA
Found at i:5522959 original size:27 final size:29
Alignment explanation
Indices: 5522917--5522972 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 29
5522907 AAAAAACTAA
* *
5522917 AAAAAAAATCATTTC-TCTTTTTTGTTTT
1 AAAAAAAATCACTTCTTCTTTTTTATTTT
5522945 AAAAAAAATC-CTTCTTCTTTTTTATTTT
1 AAAAAAAATCACTTCTTCTTTTTTATTTT
5522973 TTCTCAACTC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 3 0.12
28 22 0.88
ACGTcount: A:0.32, C:0.12, G:0.02, T:0.54
Consensus pattern (29 bp):
AAAAAAAATCACTTCTTCTTTTTTATTTT
Found at i:5539180 original size:38 final size:38
Alignment explanation
Indices: 5539122--5539198 Score: 127
Period size: 38 Copynumber: 2.0 Consensus size: 38
5539112 ATCATCAAGG
* * *
5539122 TTGGATCCATTGAGGTGTTTAATTGGGTAGAAAACAAA
1 TTGGATCCATTAAGGCGTTTAATTAGGTAGAAAACAAA
5539160 TTGGATCCATTAAGGCGTTTAATTAGGTAGAAAACAAA
1 TTGGATCCATTAAGGCGTTTAATTAGGTAGAAAACAAA
5539198 T
1 T
5539199 GTTTGAGACC
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.36, C:0.09, G:0.23, T:0.31
Consensus pattern (38 bp):
TTGGATCCATTAAGGCGTTTAATTAGGTAGAAAACAAA
Found at i:5541530 original size:21 final size:21
Alignment explanation
Indices: 5541513--5541566 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
5541503 TTTAACCCTA
5541513 AACCCTTAAACCGAAACCTTG
1 AACCCTTAAACCGAAACCTTG
* *
5541534 AA-CCTCAAATCCGAAACTTTG
1 AACCCTTAAA-CCGAAACCTTG
5541555 AACCCTTAAACC
1 AACCCTTAAACC
5541567 TTGAACCTAC
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
20 6 0.21
21 16 0.57
22 6 0.21
ACGTcount: A:0.39, C:0.33, G:0.07, T:0.20
Consensus pattern (21 bp):
AACCCTTAAACCGAAACCTTG
Found at i:5544605 original size:28 final size:28
Alignment explanation
Indices: 5544550--5544604 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
5544540 TTTAATTCTA
* *
5544550 AGTTTTAATATTTTTTTATTTTTAAAAT
1 AGTTTTAATATTTTTTAAATTTTAAAAT
*
5544578 AGTTTTTATATTTTTTGAAATTTTAAA
1 AGTTTTAATATTTTTT-AAATTTTAAA
5544605 TTTAAAAATT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 15 0.65
29 8 0.35
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (28 bp):
AGTTTTAATATTTTTTAAATTTTAAAAT
Found at i:5549593 original size:36 final size:36
Alignment explanation
Indices: 5549541--5549613 Score: 119
Period size: 36 Copynumber: 2.0 Consensus size: 36
5549531 TGATTTTCCA
* * *
5549541 TCTTCAAAAGAAGCGAATAGCTTTGTGCTTTGTTGG
1 TCTTAAAAAGAAGCGAATAGCCTTGTGCTTTGGTGG
5549577 TCTTAAAAAGAAGCGAATAGCCTTGTGCTTTGGTGG
1 TCTTAAAAAGAAGCGAATAGCCTTGTGCTTTGGTGG
5549613 T
1 T
5549614 TTACATCTGT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.26, C:0.14, G:0.26, T:0.34
Consensus pattern (36 bp):
TCTTAAAAAGAAGCGAATAGCCTTGTGCTTTGGTGG
Found at i:5561268 original size:19 final size:18
Alignment explanation
Indices: 5561244--5561291 Score: 69
Period size: 19 Copynumber: 2.6 Consensus size: 18
5561234 ACGTAAAAAG
5561244 TAAAAAGTAAAAGATGAAA
1 TAAAAA-TAAAAGATGAAA
5561263 TAAAAATAAAAAGATGAAA
1 TAAAAAT-AAAAGATGAAA
*
5561282 TGAAAATAAA
1 TAAAAATAAA
5561292 TAACAAAATG
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
18 4 0.15
19 23 0.85
ACGTcount: A:0.71, C:0.00, G:0.12, T:0.17
Consensus pattern (18 bp):
TAAAAATAAAAGATGAAA
Found at i:5562212 original size:16 final size:16
Alignment explanation
Indices: 5562182--5562229 Score: 57
Period size: 15 Copynumber: 3.1 Consensus size: 16
5562172 AGAAATTAAT
5562182 ATAAAATCT-AAAAT-A
1 ATAAAAT-TAAAAATAA
5562197 ATAATAATTAAAAATAA
1 ATAA-AATTAAAAATAA
5562214 ATAAAATT-AAAATAA
1 ATAAAATTAAAAATAA
5562229 A
1 A
5562230 CTTAAAATAG
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
15 13 0.43
16 12 0.40
17 5 0.17
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (16 bp):
ATAAAATTAAAAATAA
Found at i:5562228 original size:11 final size:11
Alignment explanation
Indices: 5562174--5562243 Score: 56
Period size: 11 Copynumber: 6.5 Consensus size: 11
5562164 ATAGCTTAAG
*
5562174 AAATTAATATA
1 AAATTAAAATA
5562185 AAATCTAAAATA
1 AAAT-TAAAATA
*
5562197 ATAA-T-AATTA
1 A-AATTAAAATA
*
5562207 AAAAT-AAATA
1 AAATTAAAATA
5562217 AAATTAAAATA
1 AAATTAAAATA
*
5562228 AACTTAAAATA
1 AAATTAAAATA
*
5562239 GAATT
1 AAATT
5562244 TCCTATTTTT
Statistics
Matches: 48, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
9 2 0.04
10 14 0.29
11 23 0.48
12 7 0.15
13 2 0.04
ACGTcount: A:0.66, C:0.03, G:0.01, T:0.30
Consensus pattern (11 bp):
AAATTAAAATA
Found at i:5566460 original size:19 final size:18
Alignment explanation
Indices: 5566436--5566483 Score: 69
Period size: 19 Copynumber: 2.6 Consensus size: 18
5566426 ACGTAAAAAG
5566436 TAAAAAGTAAAAGATGAAA
1 TAAAAA-TAAAAGATGAAA
5566455 TAAAAATAAAAAGATGAAA
1 TAAAAAT-AAAAGATGAAA
*
5566474 TGAAAATAAA
1 TAAAAATAAA
5566484 TAACAAAATG
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
18 4 0.15
19 23 0.85
ACGTcount: A:0.71, C:0.00, G:0.12, T:0.17
Consensus pattern (18 bp):
TAAAAATAAAAGATGAAA
Found at i:5567380 original size:16 final size:16
Alignment explanation
Indices: 5567350--5567397 Score: 57
Period size: 15 Copynumber: 3.1 Consensus size: 16
5567340 GAAAATTAAT
5567350 ATAAAATCT-AAAAT-A
1 ATAAAAT-TAAAAATAA
5567365 ATAATAATTAAAAATAA
1 ATAA-AATTAAAAATAA
5567382 ATAAAATT-AAAATAA
1 ATAAAATTAAAAATAA
5567397 A
1 A
5567398 CTTAAAATAG
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
15 13 0.43
16 12 0.40
17 5 0.17
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (16 bp):
ATAAAATTAAAAATAA
Found at i:5567396 original size:11 final size:11
Alignment explanation
Indices: 5567341--5567411 Score: 58
Period size: 11 Copynumber: 6.5 Consensus size: 11
5567331 ATAGCTTAAG
*
5567341 AAAATTAATAT
1 AAAATTAAAAT
5567352 AAAATCTAAAAT
1 AAAAT-TAAAAT
*
5567364 AATAA-T-AATT
1 AA-AATTAAAAT
*
5567374 AAAAAT-AAAT
1 AAAATTAAAAT
5567384 AAAATTAAAAT
1 AAAATTAAAAT
*
5567395 AAACTTAAAAT
1 AAAATTAAAAT
*
5567406 AGAATT
1 AAAATT
5567412 TCCTATTTTT
Statistics
Matches: 49, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
9 2 0.04
10 14 0.29
11 24 0.49
12 7 0.14
13 2 0.04
ACGTcount: A:0.66, C:0.03, G:0.01, T:0.30
Consensus pattern (11 bp):
AAAATTAAAAT
Found at i:5569754 original size:14 final size:14
Alignment explanation
Indices: 5569703--5569762 Score: 61
Period size: 14 Copynumber: 4.2 Consensus size: 14
5569693 AAGTTTGAAT
5569703 AAAATATTAAAATTA
1 AAAAT-TTAAAATTA
*
5569718 ATAAATTT-AAATTC
1 A-AAATTTAAAATTA
*
5569732 AGAATTTAAAA-TA
1 AAAATTTAAAATTA
5569745 AAAATATTAAAATTA
1 AAAAT-TTAAAATTA
5569760 AAA
1 AAA
5569763 GTGTGTTATG
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
13 10 0.27
14 15 0.41
15 8 0.22
16 4 0.11
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (14 bp):
AAAATTTAAAATTA
Found at i:5569871 original size:15 final size:15
Alignment explanation
Indices: 5569841--5569890 Score: 52
Period size: 13 Copynumber: 3.5 Consensus size: 15
5569831 CATGAGACCT
*
5569841 TATAATAT-AATATA
1 TATAATATGAATTTA
5569855 TAT-ATAT-AATTTA
1 TATAATATGAATTTA
*
5569868 TATAATATGAATTCA
1 TATAATATGAATTTA
*
5569883 AATAATAT
1 TATAATAT
5569891 TTACAGTTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
13 12 0.39
14 7 0.23
15 12 0.39
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (15 bp):
TATAATATGAATTTA
Found at i:5576122 original size:14 final size:14
Alignment explanation
Indices: 5576103--5576148 Score: 56
Period size: 14 Copynumber: 3.2 Consensus size: 14
5576093 CCATTGTTGA
5576103 AAATTTTTAAATTT
1 AAATTTTTAAATTT
* **
5576117 AAATTTTGAAAAAT
1 AAATTTTTAAATTT
5576131 AAATTTTTAAATATT
1 AAATTTTTAAAT-TT
5576146 AAA
1 AAA
5576149 ATTCAAAATT
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
14 21 0.84
15 4 0.16
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (14 bp):
AAATTTTTAAATTT
Found at i:5576156 original size:28 final size:28
Alignment explanation
Indices: 5576103--5576156 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
5576093 CCATTGTTGA
* *
5576103 AAATTTTTAAATTTAAATTTTGAAAAAT
1 AAATTTTTAAATTTAAATATTCAAAAAT
5576131 AAATTTTTAAATATTAAA-ATTCAAAA
1 AAATTTTTAAAT-TTAAATATTCAAAA
5576157 TTTTGGTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
28 18 0.78
29 5 0.22
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.43
Consensus pattern (28 bp):
AAATTTTTAAATTTAAATATTCAAAAAT
Found at i:5576216 original size:14 final size:14
Alignment explanation
Indices: 5576197--5576228 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
5576187 ATTTTAACAT
5576197 TTTATTTAATTTAA
1 TTTATTTAATTTAA
*
5576211 TTTATTTAATTTAT
1 TTTATTTAATTTAA
5576225 TTTA
1 TTTA
5576229 ATGTTTTGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (14 bp):
TTTATTTAATTTAA
Found at i:5577176 original size:13 final size:13
Alignment explanation
Indices: 5577141--5577180 Score: 62
Period size: 14 Copynumber: 2.9 Consensus size: 13
5577131 AAAATTTTTA
5577141 ATTTTAAGAAAAAT
1 ATTTTAA-AAAAAT
5577155 ATTTGTAAAAAAAT
1 ATTT-TAAAAAAAT
5577169 ATTTTAAAAAAA
1 ATTTTAAAAAAA
5577181 ATCGACGGGC
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
13 8 0.32
14 14 0.56
15 3 0.12
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.35
Consensus pattern (13 bp):
ATTTTAAAAAAAT
Found at i:5577225 original size:8 final size:8
Alignment explanation
Indices: 5577212--5577239 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
5577202 TTATTTAATT
5577212 TTTTTATA
1 TTTTTATA
5577220 TTTTTATA
1 TTTTTATA
5577228 TTTTTATA
1 TTTTTATA
5577236 TTTT
1 TTTT
5577240 CAAATTTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (8 bp):
TTTTTATA
Found at i:5577246 original size:16 final size:16
Alignment explanation
Indices: 5577212--5577247 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
5577202 TTATTTAATT
* *
5577212 TTTTTATATTTTTATA
1 TTTTTATATTTTCAAA
5577228 TTTTTATATTTTCAAA
1 TTTTTATATTTTCAAA
5577244 TTTT
1 TTTT
5577248 AATAAATTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.25, C:0.03, G:0.00, T:0.72
Consensus pattern (16 bp):
TTTTTATATTTTCAAA
Found at i:5585514 original size:51 final size:51
Alignment explanation
Indices: 5585438--5585551 Score: 183
Period size: 51 Copynumber: 2.2 Consensus size: 51
5585428 AGTGACAATC
* *
5585438 GACAAGCGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCCGATCAGT
1 GACAAGTGATAAGTGATAAGTGGTAGCTTTAGCTACACTTATCCGATCAGT
* * *
5585489 GACAAGTGATAAGTGATAAGTGGTAGTTTTAGCTACACTTATCTGATCTGT
1 GACAAGTGATAAGTGATAAGTGGTAGCTTTAGCTACACTTATCCGATCAGT
5585540 GACAAGTGATAA
1 GACAAGTGATAA
5585552 ATGTGATCAG
Statistics
Matches: 58, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
51 58 1.00
ACGTcount: A:0.32, C:0.15, G:0.24, T:0.29
Consensus pattern (51 bp):
GACAAGTGATAAGTGATAAGTGGTAGCTTTAGCTACACTTATCCGATCAGT
Found at i:5586621 original size:13 final size:13
Alignment explanation
Indices: 5586605--5586632 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
5586595 ATAAATAAAT
5586605 TATTAATTAAAAA
1 TATTAATTAAAAA
5586618 TATTAATTAAAAA
1 TATTAATTAAAAA
5586631 TA
1 TA
5586633 AAATAAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (13 bp):
TATTAATTAAAAA
Found at i:5589772 original size:22 final size:21
Alignment explanation
Indices: 5589738--5589792 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 21
5589728 GGTTATTAAA
*
5589738 TTTTAATAAAATATTAAATATAT
1 TTTTAAT-TAATATTAAATAT-T
**
5589761 TTTTAATTAATATTTTATATT
1 TTTTAATTAATATTAAATATT
5589782 TTTTAAATTAA
1 TTTT-AATTAA
5589793 AAACTAAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
21 5 0.18
22 16 0.57
23 7 0.25
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
TTTTAATTAATATTAAATATT
Found at i:5603969 original size:14 final size:14
Alignment explanation
Indices: 5603926--5603969 Score: 54
Period size: 14 Copynumber: 3.0 Consensus size: 14
5603916 TAAAATGGTA
5603926 AAATTTTAATTTA-
1 AAATTTTAATTTAT
5603939 AACATTTTATAATTTAT
1 AA-A-TTT-TAATTTAT
5603956 AAATTTTAATTTAT
1 AAATTTTAATTTAT
5603970 TAATGATAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
13 2 0.07
14 9 0.33
15 6 0.22
16 8 0.30
17 2 0.07
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (14 bp):
AAATTTTAATTTAT
Found at i:5607413 original size:21 final size:22
Alignment explanation
Indices: 5607374--5607414 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
5607364 CAGTTTTTAA
5607374 TAATAAAAATAGATAAATTTTT
1 TAATAAAAATAGATAAATTTTT
*
5607396 TAATAAAAATA-ATCAATTT
1 TAATAAAAATAGATAAATTT
5607415 GCTCTTTGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.39
Consensus pattern (22 bp):
TAATAAAAATAGATAAATTTTT
Found at i:5609196 original size:23 final size:23
Alignment explanation
Indices: 5609152--5609201 Score: 59
Period size: 23 Copynumber: 2.1 Consensus size: 23
5609142 ATTAAACTGA
5609152 AAAATTCATCCGTACAATTGCA-T
1 AAAATTCA-CCGTACAATTGCACT
5609175 AAAATTCA-CGTATCAATGTGCACT
1 AAAATTCACCGTA-CAAT-TGCACT
5609199 AAA
1 AAA
5609202 TGAAGGGTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
21 4 0.17
22 4 0.17
23 12 0.50
24 4 0.17
ACGTcount: A:0.42, C:0.20, G:0.10, T:0.28
Consensus pattern (23 bp):
AAAATTCACCGTACAATTGCACT
Found at i:5615286 original size:11 final size:12
Alignment explanation
Indices: 5615263--5615287 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5615253 AATCCCTTCC
5615263 AAAACATTAAAA
1 AAAACATTAAAA
5615275 AAAACATTAAAA
1 AAAACATTAAAA
5615287 A
1 A
5615288 GAAGAAAACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.76, C:0.08, G:0.00, T:0.16
Consensus pattern (12 bp):
AAAACATTAAAA
Found at i:5615974 original size:19 final size:21
Alignment explanation
Indices: 5615929--5615999 Score: 51
Period size: 21 Copynumber: 3.5 Consensus size: 21
5615919 TCGTATCATC
*
5615929 TTATATTTTTTATCAATTATT
1 TTATATTATTTATCAATTATT
* *
5615950 TAATATTATTT-T-AATTTTT
1 TTATATTATTTATCAATTATT
* *
5615969 TTATATCA-TTAACACATTATT
1 TTATATTATTTATCA-ATTATT
*
5615990 TT-TATAATTT
1 TTATATTATTT
5616000 TTTAAGGTAA
Statistics
Matches: 38, Mismatches: 8, Indels: 8
0.70 0.15 0.15
Matches are distributed among these distances:
18 2 0.05
19 12 0.32
20 6 0.16
21 18 0.47
ACGTcount: A:0.32, C:0.06, G:0.00, T:0.62
Consensus pattern (21 bp):
TTATATTATTTATCAATTATT
Found at i:5624088 original size:20 final size:20
Alignment explanation
Indices: 5624050--5624104 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
5624040 TTAAAGCTAG
5624050 AGAAAAAGAA-AAAAAAAGA
1 AGAAAAAGAAGAAAAAAAGA
* * *
5624069 AGAAGAAGAGGAAAATAAGA
1 AGAAAAAGAAGAAAAAAAGA
5624089 AGAAAAAGAAGAAAAA
1 AGAAAAAGAAGAAAAA
5624105 TTGTTATGCC
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
19 8 0.28
20 21 0.72
ACGTcount: A:0.76, C:0.00, G:0.22, T:0.02
Consensus pattern (20 bp):
AGAAAAAGAAGAAAAAAAGA
Found at i:5624097 original size:23 final size:22
Alignment explanation
Indices: 5624057--5624100 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
5624047 TAGAGAAAAA
*
5624057 GAAAAAAAAAGAAGAAGAAGAG
1 GAAAAAAAAAGAAAAAGAAGAG
*
5624079 GAAAATAAGAAGAAAAAGAAGA
1 GAAAA-AAAAAGAAAAAGAAGA
5624101 AAAATTGTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.73, C:0.00, G:0.25, T:0.02
Consensus pattern (22 bp):
GAAAAAAAAAGAAAAAGAAGAG
Found at i:5624102 original size:9 final size:9
Alignment explanation
Indices: 5624050--5624104 Score: 56
Period size: 9 Copynumber: 5.8 Consensus size: 9
5624040 TTAAAGCTAG
5624050 AGAAAAAGAA
1 AGAAAAAG-A
*
5624060 AAAAAAAGA
1 AGAAAAAGA
*
5624069 AGAAGAAGA
1 AGAAAAAGA
*
5624078 GGAAAATAAGA
1 AG-AAA-AAGA
5624089 AGAAAAAGA
1 AGAAAAAGA
5624098 AGAAAAA
1 AGAAAAA
5624105 TTGTTATGCC
Statistics
Matches: 37, Mismatches: 6, Indels: 5
0.77 0.12 0.10
Matches are distributed among these distances:
9 20 0.54
10 12 0.32
11 5 0.14
ACGTcount: A:0.76, C:0.00, G:0.22, T:0.02
Consensus pattern (9 bp):
AGAAAAAGA
Found at i:5631869 original size:32 final size:32
Alignment explanation
Indices: 5631828--5631891 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
5631818 ACTGTCATCG
5631828 TCTATCCAAATGGAATTTAAAAAGCTCTAAAA
1 TCTATCCAAATGGAATTTAAAAAGCTCTAAAA
*
5631860 TCTATCCAAATGGAATTTATAAAGCTCTAAAA
1 TCTATCCAAATGGAATTTAAAAAGCTCTAAAA
5631892 GAGAATCTTA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.45, C:0.16, G:0.09, T:0.30
Consensus pattern (32 bp):
TCTATCCAAATGGAATTTAAAAAGCTCTAAAA
Found at i:5638687 original size:20 final size:20
Alignment explanation
Indices: 5638648--5638693 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
5638638 TTTAATAGTA
5638648 ATTTAATATTAAAATGATAT
1 ATTTAATATTAAAATGATAT
* * *
5638668 ATTTGATATTAAATTTATAT
1 ATTTAATATTAAAATGATAT
5638688 -TTTAAT
1 ATTTAAT
5638694 TGAATTATCA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 5 0.23
20 17 0.77
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.52
Consensus pattern (20 bp):
ATTTAATATTAAAATGATAT
Found at i:5655936 original size:46 final size:46
Alignment explanation
Indices: 5655662--5655936 Score: 390
Period size: 46 Copynumber: 6.0 Consensus size: 46
5655652 TTCGACATGA
* * * * *
5655662 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TATCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATATCAGGT
* ** ** *
5655708 TGCCATGGTATCATTCAACCATGGTCTTATTCATTTCCCCATCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTT-CATATCAGGT
* * *
5655755 TGCCATGGTATCTTTCAACCATGGTCTTACACGTTTCATGTCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
5655801 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
5655847 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
*
5655893 TGCCATGGTATCTTTCAACTATGGTCTTACACATTTCATATCAG
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
5655937 AGAGCACACT
Statistics
Matches: 209, Mismatches: 18, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
45 3 0.01
46 168 0.80
47 38 0.18
ACGTcount: A:0.22, C:0.25, G:0.15, T:0.39
Consensus pattern (46 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
Found at i:5658088 original size:11 final size:11
Alignment explanation
Indices: 5658072--5658123 Score: 52
Period size: 11 Copynumber: 4.7 Consensus size: 11
5658062 TATACTAAAT
5658072 AAATAATAATA
1 AAATAATAATA
*
5658083 AAATAAT-ATT
1 AAATAATAATA
* *
5658093 AAATATCTCATA
1 AAATA-ATAATA
*
5658105 AAATATTAATA
1 AAATAATAATA
5658116 AAATAATA
1 AAATAATA
5658124 TTTATCTAAT
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
10 7 0.21
11 19 0.58
12 7 0.21
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (11 bp):
AAATAATAATA
Found at i:5663326 original size:18 final size:18
Alignment explanation
Indices: 5663303--5663344 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
5663293 CTCCATACAT
5663303 TGTACACACATTCCAATC
1 TGTACACACATTCCAATC
* *
5663321 TGTACATACGTTCCAATC
1 TGTACACACATTCCAATC
*
5663339 TATACA
1 TGTACA
5663345 AGCGTGTACT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.33, C:0.29, G:0.07, T:0.31
Consensus pattern (18 bp):
TGTACACACATTCCAATC
Found at i:5666466 original size:17 final size:17
Alignment explanation
Indices: 5666444--5666476 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
5666434 ATATACAATA
5666444 TATTCACAATTTACTTG
1 TATTCACAATTTACTTG
*
5666461 TATTCACACTTTACTT
1 TATTCACAATTTACTT
5666477 CTTAACAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.27, C:0.21, G:0.03, T:0.48
Consensus pattern (17 bp):
TATTCACAATTTACTTG
Found at i:5666592 original size:13 final size:14
Alignment explanation
Indices: 5666576--5666611 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
5666566 CAATCTCATA
5666576 TCTCAATTTCAA-T
1 TCTCAATTTCAATT
5666589 TCTCAA-TTCAATT
1 TCTCAATTTCAATT
5666602 TCTC-ATTTCA
1 TCTCAATTTCA
5666612 TTCCAATAGC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
12 6 0.29
13 15 0.71
ACGTcount: A:0.28, C:0.25, G:0.00, T:0.47
Consensus pattern (14 bp):
TCTCAATTTCAATT
Found at i:5666601 original size:18 final size:19
Alignment explanation
Indices: 5666563--5666603 Score: 59
Period size: 18 Copynumber: 2.2 Consensus size: 19
5666553 TGGTTCATGT
5666563 TTTCAATCTCATATCTCAA
1 TTTCAATCTCATATCTCAA
5666582 TTTCAATTCTCA-AT-TCAA
1 TTTCAA-TCTCATATCTCAA
5666600 TTTC
1 TTTC
5666604 TCATTTCATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 8 0.38
20 5 0.24
ACGTcount: A:0.29, C:0.24, G:0.00, T:0.46
Consensus pattern (19 bp):
TTTCAATCTCATATCTCAA
Found at i:5666867 original size:23 final size:22
Alignment explanation
Indices: 5666764--5666871 Score: 114
Period size: 21 Copynumber: 5.0 Consensus size: 22
5666754 CCTGATCAGT
* *
5666764 ATACGACACATAAAGTGCCT-A
1 ATACGACACATGAGGTGCCTGA
* *
5666785 AAACGACACATGAGGTGCTTG-
1 ATACGACACATGAGGTGCCTGA
*
5666806 ATACGACACACGAGGTGCCTG-
1 ATACGACACATGAGGTGCCTGA
*
5666827 ATACGACACACGAGGTGCCTGAA
1 ATACGACACATGAGGTGCCTG-A
* *
5666850 ATACGACACATAAAGTGCCTGA
1 ATACGACACATGAGGTGCCTGA
5666872 TCGATAAAGC
Statistics
Matches: 74, Mismatches: 10, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
21 55 0.74
22 1 0.01
23 18 0.24
ACGTcount: A:0.36, C:0.24, G:0.23, T:0.17
Consensus pattern (22 bp):
ATACGACACATGAGGTGCCTGA
Found at i:5666868 original size:44 final size:42
Alignment explanation
Indices: 5666764--5666872 Score: 137
Period size: 42 Copynumber: 2.5 Consensus size: 42
5666754 CCTGATCAGT
* * * *
5666764 ATACGACACATAAAGTGCCTAAAACGACACATGAGGTGCTTG
1 ATACGACACATAAAGTGCCTGATACGACACACGAGGTGCCTG
** *
5666806 ATACGACACACGAGGTGCCTGATACGACACACGAGGTGCCTG
1 ATACGACACATAAAGTGCCTGATACGACACACGAGGTGCCTG
5666848 AAATACGACACATAAAGTGCCTGAT
1 --ATACGACACATAAAGTGCCTGAT
5666873 CGATAAAGCC
Statistics
Matches: 55, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
42 35 0.64
44 20 0.36
ACGTcount: A:0.36, C:0.24, G:0.23, T:0.17
Consensus pattern (42 bp):
ATACGACACATAAAGTGCCTGATACGACACACGAGGTGCCTG
Found at i:5667242 original size:2 final size:2
Alignment explanation
Indices: 5667235--5667276 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
5667225 TACATAGATC
5667235 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5667276 A
1 A
5667277 ATTTCAATCA
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5667291 original size:15 final size:15
Alignment explanation
Indices: 5667273--5667322 Score: 73
Period size: 15 Copynumber: 3.3 Consensus size: 15
5667263 ATATATATAT
5667273 TATAATTTCAATCAA
1 TATAATTTCAATCAA
*
5667288 TATAAATTCAATCAA
1 TATAATTTCAATCAA
* *
5667303 AATGATTTCAATCAA
1 TATAATTTCAATCAA
5667318 TATAA
1 TATAA
5667323 ATTTGATAAA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 29 1.00
ACGTcount: A:0.50, C:0.12, G:0.02, T:0.36
Consensus pattern (15 bp):
TATAATTTCAATCAA
Found at i:5668025 original size:6 final size:6
Alignment explanation
Indices: 5668014--5668050 Score: 58
Period size: 6 Copynumber: 6.2 Consensus size: 6
5668004 AAACCCCAAA
5668014 TTTTTC TTTTTC TTTTTC TTTTTC TTTCTT- TTTTTC T
1 TTTTTC TTTTTC TTTTTC TTTTTC TTT-TTC TTTTTC T
5668051 CCCCTGTTTC
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
5 2 0.07
6 25 0.86
7 2 0.07
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTTTC
Done.