Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr6
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: 47432654
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2298022 characters in sequence are not A, C, G, or T
File 105 of 136
Found at i:35437628 original size:14 final size:15
Alignment explanation
Indices: 35437599--35437630 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
35437589 AAAAACATCA
35437599 TAATTTTATCTATTT
1 TAATTTTATCTATTT
35437614 TAATTTTAT-TATTT
1 TAATTTTATCTATTT
35437628 TAA
1 TAA
35437631 CTATAACCAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (15 bp):
TAATTTTATCTATTT
Found at i:35442363 original size:44 final size:44
Alignment explanation
Indices: 35442313--35442403 Score: 166
Period size: 44 Copynumber: 2.1 Consensus size: 44
35442303 GTGTTTCTTT
35442313 TTTCCTAAAATTTCCTCTTTC-TGACATTTTTCTCTCCTCCCTTG
1 TTTCCTAAAATTTCCTCTTTCTTG-CATTTTTCTCTCCTCCCTTG
35442357 TTTCCTAAAATTTCCTCTTTCTTGCATTTTTCTCTCCTCCCTTG
1 TTTCCTAAAATTTCCTCTTTCTTGCATTTTTCTCTCCTCCCTTG
35442401 TTT
1 TTT
35442404 TCTCACTTTT
Statistics
Matches: 46, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
44 44 0.96
45 2 0.04
ACGTcount: A:0.12, C:0.31, G:0.04, T:0.53
Consensus pattern (44 bp):
TTTCCTAAAATTTCCTCTTTCTTGCATTTTTCTCTCCTCCCTTG
Found at i:35450033 original size:21 final size:23
Alignment explanation
Indices: 35450009--35450052 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
35449999 TCTTATGGTT
35450009 TTCTT-AACATCAC-ATTTATAC
1 TTCTTAAACATCACAATTTATAC
35450030 TTCTTACAACATCACAATTTATA
1 TTCTTA-AACATCACAATTTATA
35450053 TAAAAAAATC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 5 0.25
23 8 0.40
24 7 0.35
ACGTcount: A:0.36, C:0.23, G:0.00, T:0.41
Consensus pattern (23 bp):
TTCTTAAACATCACAATTTATAC
Found at i:35450744 original size:28 final size:28
Alignment explanation
Indices: 35450712--35450769 Score: 89
Period size: 28 Copynumber: 2.1 Consensus size: 28
35450702 AAACATGTCC
*
35450712 TTAGTTTAATCGAAAATGAGCAAATTAA
1 TTAGTCTAATCGAAAATGAGCAAATTAA
* *
35450740 TTAGTCTAATTGGAAATGAGCAAATTAA
1 TTAGTCTAATCGAAAATGAGCAAATTAA
35450768 TT
1 TT
35450770 GAAAGACTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.43, C:0.07, G:0.16, T:0.34
Consensus pattern (28 bp):
TTAGTCTAATCGAAAATGAGCAAATTAA
Found at i:35458748 original size:13 final size:13
Alignment explanation
Indices: 35458732--35458763 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
35458722 TAGTGTGTAT
35458732 ATTTAAACCTAAA
1 ATTTAAACCTAAA
*
35458745 ATTTAAACCTTAA
1 ATTTAAACCTAAA
35458758 ATTTAA
1 ATTTAA
35458764 TATTAATGCC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.00, T:0.38
Consensus pattern (13 bp):
ATTTAAACCTAAA
Found at i:35470880 original size:72 final size:72
Alignment explanation
Indices: 35470790--35470929 Score: 217
Period size: 72 Copynumber: 1.9 Consensus size: 72
35470780 AATAGGTAAA
* * *
35470790 AAAAAATCTGGTAAGTTAATTTATTGAAAACAATATTAAATTTAAAAGAGTTCTAAAATTCTTAA
1 AAAAAATCTGCTAAGTTAATTTATTGAAAACAAAATTAAATCTAAAAGAGTTCTAAAATTCTTAA
35470855 AAAAGGT
66 AAAAGGT
* * * *
35470862 AAAAAATCTGCTATGTTAATTTATTGAAAACAAAATTATATCTAAAAGAGTTTTCAAATTCTTAA
1 AAAAAATCTGCTAAGTTAATTTATTGAAAACAAAATTAAATCTAAAAGAGTTCTAAAATTCTTAA
35470927 AAA
66 AAA
35470930 GAAAATAGAT
Statistics
Matches: 61, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
72 61 1.00
ACGTcount: A:0.49, C:0.07, G:0.09, T:0.34
Consensus pattern (72 bp):
AAAAAATCTGCTAAGTTAATTTATTGAAAACAAAATTAAATCTAAAAGAGTTCTAAAATTCTTAA
AAAAGGT
Found at i:35478931 original size:29 final size:30
Alignment explanation
Indices: 35478899--35478961 Score: 101
Period size: 30 Copynumber: 2.1 Consensus size: 30
35478889 AGCTTTGGCT
35478899 ATCGATT-ATGAAAAGGGATGGTGACAACC
1 ATCGATTAATGAAAAGGGATGGTGACAACC
* *
35478928 ATCGATTAATGAAAAGGGATGGTTACCACC
1 ATCGATTAATGAAAAGGGATGGTGACAACC
35478958 ATCG
1 ATCG
35478962 TTTAGCACAC
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
29 7 0.23
30 24 0.77
ACGTcount: A:0.37, C:0.16, G:0.25, T:0.22
Consensus pattern (30 bp):
ATCGATTAATGAAAAGGGATGGTGACAACC
Found at i:35489164 original size:26 final size:26
Alignment explanation
Indices: 35489106--35489171 Score: 78
Period size: 26 Copynumber: 2.5 Consensus size: 26
35489096 ACCATAACAC
*
35489106 AAATCAGTCATTTACCCACGAAGAGCA
1 AAAT-AGTCATTTACCCACCAAGAGCA
* *
35489133 AAATAGTCATTTACCCTCCAAGGGCA
1 AAATAGTCATTTACCCACCAAGAGCA
**
35489159 TTATAGTCATTTA
1 AAATAGTCATTTA
35489172 ACAACCTTTC
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 30 0.88
27 4 0.12
ACGTcount: A:0.36, C:0.23, G:0.14, T:0.27
Consensus pattern (26 bp):
AAATAGTCATTTACCCACCAAGAGCA
Found at i:35498991 original size:2 final size:2
Alignment explanation
Indices: 35498984--35499020 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
35498974 AGTATGGTTG
35498984 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
35499021 GAGTTTAGAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:35505725 original size:27 final size:27
Alignment explanation
Indices: 35505672--35505985 Score: 377
Period size: 27 Copynumber: 11.7 Consensus size: 27
35505662 GGTATAACAG
*
35505672 TCATTTTACCCTAT-G-GGGTATTACGA
1 TCATTTTACCC-ATCGAGGGTATTTCGA
* *
35505698 TCATTTTATCCTTCGAGGGTATTTCGA
1 TCATTTTACCCATCGAGGGTATTTCGA
*
35505725 TCGTTTTACCCATCGAGGGTATTTC-A
1 TCATTTTACCCATCGAGGGTATTTCGA
*
35505751 GTCATTTTACACATCGAGGGTATTTCGA
1 -TCATTTTACCCATCGAGGGTATTTCGA
* *
35505779 TCATTTTACCCATCGAGGGTATCTCGG
1 TCATTTTACCCATCGAGGGTATTTCGA
* * *
35505806 TAATTTTACCCATCAAGGGTATTTTGA
1 TCATTTTACCCATCGAGGGTATTTCGA
*
35505833 TTATTTTACCCATCGAGGGTATTTC-A
1 TCATTTTACCCATCGAGGGTATTTCGA
* *
35505859 GTGATTTTATCCATCGAGGGTATTTCGA
1 -TCATTTTACCCATCGAGGGTATTTCGA
* * *
35505887 TCATTTTACCCATCGAAGGTATTTTGG
1 TCATTTTACCCATCGAGGGTATTTCGA
* * *
35505914 TCATTTTACCCATTGAGGGTATTTTGG
1 TCATTTTACCCATCGAGGGTATTTCGA
35505941 TCATTTTACCCATCGAGGGTATTTC-A
1 TCATTTTACCCATCGAGGGTATTTCGA
*
35505967 GTCATTTTACCCATTGAGG
1 -TCATTTTACCCATCGAGG
35505986 TTGTTTCAGT
Statistics
Matches: 249, Mismatches: 32, Indels: 13
0.85 0.11 0.04
Matches are distributed among these distances:
25 1 0.00
26 13 0.05
27 233 0.94
28 2 0.01
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.39
Consensus pattern (27 bp):
TCATTTTACCCATCGAGGGTATTTCGA
Found at i:35514146 original size:28 final size:28
Alignment explanation
Indices: 35514111--35514226 Score: 151
Period size: 28 Copynumber: 4.1 Consensus size: 28
35514101 CATGTAGTAG
* * **
35514111 CAGTGTGGGCCTGAGCCCTATACAGCAA
1 CAGTGTGGGCCTTAGCCCAATACAATAA
* *
35514139 CGGTGTGGGCCTTAGCCCAACACAATAA
1 CAGTGTGGGCCTTAGCCCAATACAATAA
*
35514167 CAGTGTAGGCCTTAGCCCAATACAATAA
1 CAGTGTGGGCCTTAGCCCAATACAATAA
* *
35514195 CAGTGTGGGCCTTAGCCAAATACAGTAA
1 CAGTGTGGGCCTTAGCCCAATACAATAA
35514223 CAGT
1 CAGT
35514227 ACAATGCAGT
Statistics
Matches: 76, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 76 1.00
ACGTcount: A:0.30, C:0.26, G:0.24, T:0.20
Consensus pattern (28 bp):
CAGTGTGGGCCTTAGCCCAATACAATAA
Found at i:35514591 original size:27 final size:27
Alignment explanation
Indices: 35514557--35514995 Score: 470
Period size: 27 Copynumber: 16.3 Consensus size: 27
35514547 GAATATAACA
*
35514557 GTCATTTTACCCTATAG-GGGTATTTTG
1 GTCATTTTACCC-ATCGAGGGTATTTTG
* * * **
35514584 GTTATTTTACCCTTCGGGGGTATTTCA
1 GTCATTTTACCCATCGAGGGTATTTTG
* *
35514611 ATCATTTTACCCATGGAGGGTATTTTG
1 GTCATTTTACCCATCGAGGGTATTTTG
*
35514638 ATCATTTTACCCATCGAGGGTATTTCT-
1 GTCATTTTACCCATCGAGGGTATTT-TG
* *
35514665 GTCATTTTATCCATCGAGGGTATTTCG
1 GTCATTTTACCCATCGAGGGTATTTTG
*
35514692 ATCATTTTACCCATCGAGGGTATTTTG
1 GTCATTTTACCCATCGAGGGTATTTTG
* *
35514719 GTCATTTTAACCATTGAGGGTATTTTG
1 GTCATTTTACCCATCGAGGGTATTTTG
* * *
35514746 GTCATTTAACCCATCAAGGGTATTTCG
1 GTCATTTTACCCATCGAGGGTATTTTG
* * **
35514773 ATCATTTTATCCATCGAGGGTATTTCA
1 GTCATTTTACCCATCGAGGGTATTTTG
* * * * * **
35514800 ATTATTTTACCAATTGATGGTATTTCA
1 GTCATTTTACCCATCGAGGGTATTTTG
* * *
35514827 GTCATTTTATCCATCGAGGGAATTTCG
1 GTCATTTTACCCATCGAGGGTATTTTG
* *
35514854 ATCATTTTACCCATCGAAGGTATTTCT-
1 GTCATTTTACCCATCGAGGGTATTT-TG
* *
35514881 ATTATTTTACCCATCGAGGGTATTTTG
1 GTCATTTTACCCATCGAGGGTATTTTG
* *
35514908 GTCATTTTATCCATCGAGGGTATTTCG
1 GTCATTTTACCCATCGAGGGTATTTTG
* *
35514935 ATCATTTTACCCATCGAGGGTATTTCG
1 GTCATTTTACCCATCGAGGGTATTTTG
*
35514962 GTCATTTTACCCATCGAGGGTATTTCG
1 GTCATTTTACCCATCGAGGGTATTTTG
35514989 GTCATTT
1 GTCATTT
35514996 GCCCATGAAT
Statistics
Matches: 348, Mismatches: 59, Indels: 10
0.83 0.14 0.02
Matches are distributed among these distances:
26 3 0.01
27 344 0.99
28 1 0.00
ACGTcount: A:0.22, C:0.18, G:0.19, T:0.41
Consensus pattern (27 bp):
GTCATTTTACCCATCGAGGGTATTTTG
Found at i:35514621 original size:54 final size:54
Alignment explanation
Indices: 35514558--35514995 Score: 522
Period size: 54 Copynumber: 8.1 Consensus size: 54
35514548 AATATAACAG
* * * * * * *
35514558 TCATTTTACCCTATAG-GGGTATTTTGGTTATTTTACCCTTCGGGGGTATTTCAA
1 TCATTTTACCC-ATCGAGGGTATTTCGATCATTTTACCCATCGAGGGTATTTCGA
* *
35514612 TCATTTTACCCATGGAGGGTATTTTGATCATTTTACCCATCGAGGGTATTTCTG-
1 TCATTTTACCCATCGAGGGTATTTCGATCATTTTACCCATCGAGGGTATTTC-GA
* * *
35514666 TCATTTTATCCATCGAGGGTATTTCGATCATTTTACCCATCGAGGGTATTTTGG
1 TCATTTTACCCATCGAGGGTATTTCGATCATTTTACCCATCGAGGGTATTTCGA
* * * * * *
35514720 TCATTTTAACCATTGAGGGTATTTTGGTCATTTAACCCATCAAGGGTATTTCGA
1 TCATTTTACCCATCGAGGGTATTTCGATCATTTTACCCATCGAGGGTATTTCGA
* * * * * *
35514774 TCATTTTATCCATCGAGGGTATTTCAATTATTTTACCAATTGATGGTATTTC-A
1 TCATTTTACCCATCGAGGGTATTTCGATCATTTTACCCATCGAGGGTATTTCGA
* * * *
35514827 GTCATTTTATCCATCGAGGGAATTTCGATCATTTTACCCATCGAAGGTATTTCTA
1 -TCATTTTACCCATCGAGGGTATTTCGATCATTTTACCCATCGAGGGTATTTCGA
* * * *
35514882 TTATTTTACCCATCGAGGGTATTTTGGTCATTTTATCCATCGAGGGTATTTCGA
1 TCATTTTACCCATCGAGGGTATTTCGATCATTTTACCCATCGAGGGTATTTCGA
* *
35514936 TCATTTTACCCATCGAGGGTATTTCGGTCATTTTACCCATCGAGGGTATTTCGG
1 TCATTTTACCCATCGAGGGTATTTCGATCATTTTACCCATCGAGGGTATTTCGA
35514990 TCATTT
1 TCATTT
35514996 GCCCATGAAT
Statistics
Matches: 332, Mismatches: 47, Indels: 10
0.85 0.12 0.03
Matches are distributed among these distances:
53 5 0.02
54 326 0.98
55 1 0.00
ACGTcount: A:0.22, C:0.18, G:0.19, T:0.41
Consensus pattern (54 bp):
TCATTTTACCCATCGAGGGTATTTCGATCATTTTACCCATCGAGGGTATTTCGA
Found at i:35514672 original size:81 final size:81
Alignment explanation
Indices: 35514558--35514995 Score: 576
Period size: 81 Copynumber: 5.4 Consensus size: 81
35514548 AATATAACAG
* * * * * *
35514558 TCATTTTACCCTATAG-GGGTATTTTGGTTATTTTACCCTTCGGGGGTATTTCAATCATTTTACC
1 TCATTTTACCC-ATCGAGGGTATTTTGGTCATTTTATCCATCGAGGGTATTTCGATCATTTTACC
*
35514622 CATGGAGGGTATTTTGA
65 CATCGAGGGTATTTTGA
35514639 TCATTTTACCCATCGAGGGTATTTCT-GTCATTTTATCCATCGAGGGTATTTCGATCATTTTACC
1 TCATTTTACCCATCGAGGGTATTT-TGGTCATTTTATCCATCGAGGGTATTTCGATCATTTTACC
*
35514703 CATCGAGGGTATTTTGG
65 CATCGAGGGTATTTTGA
* * * * * *
35514720 TCATTTTAACCATTGAGGGTATTTTGGTCATTTAACCCATCAAGGGTATTTCGATCATTTTATCC
1 TCATTTTACCCATCGAGGGTATTTTGGTCATTTTATCCATCGAGGGTATTTCGATCATTTTACCC
**
35514785 ATCGAGGGTATTTCAA
66 ATCGAGGGTATTTTGA
* * * * ** *
35514801 TTATTTTACCAATTGATGGTATTTCAGTCATTTTATCCATCGAGGGAATTTCGATCATTTTACCC
1 TCATTTTACCCATCGAGGGTATTTTGGTCATTTTATCCATCGAGGGTATTTCGATCATTTTACCC
*
35514866 ATCGAAGGTATTTCT-A
66 ATCGAGGGTATTT-TGA
*
35514882 TTATTTTACCCATCGAGGGTATTTTGGTCATTTTATCCATCGAGGGTATTTCGATCATTTTACCC
1 TCATTTTACCCATCGAGGGTATTTTGGTCATTTTATCCATCGAGGGTATTTCGATCATTTTACCC
* *
35514947 ATCGAGGGTATTTCGG
66 ATCGAGGGTATTTTGA
*
35514963 TCATTTTACCCATCGAGGGTATTTCGGTCATTT
1 TCATTTTACCCATCGAGGGTATTTTGGTCATTT
35514996 GCCCATGAAT
Statistics
Matches: 311, Mismatches: 41, Indels: 10
0.86 0.11 0.03
Matches are distributed among these distances:
80 4 0.01
81 306 0.98
82 1 0.00
ACGTcount: A:0.22, C:0.18, G:0.19, T:0.41
Consensus pattern (81 bp):
TCATTTTACCCATCGAGGGTATTTTGGTCATTTTATCCATCGAGGGTATTTCGATCATTTTACCC
ATCGAGGGTATTTTGA
Found at i:35518839 original size:21 final size:23
Alignment explanation
Indices: 35518813--35518854 Score: 61
Period size: 21 Copynumber: 1.9 Consensus size: 23
35518803 CAGAGATGCT
*
35518813 CTCTTAGTTTT-GTGT-TTTGTG
1 CTCTTAATTTTGGTGTGTTTGTG
35518834 CTCTTAATTTTGGTGTGTTTG
1 CTCTTAATTTTGGTGTGTTTG
35518855 AAGTGTAGCT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 10 0.56
22 4 0.22
23 4 0.22
ACGTcount: A:0.07, C:0.10, G:0.24, T:0.60
Consensus pattern (23 bp):
CTCTTAATTTTGGTGTGTTTGTG
Found at i:35525587 original size:51 final size:52
Alignment explanation
Indices: 35525447--35525639 Score: 200
Period size: 51 Copynumber: 3.8 Consensus size: 52
35525437 NNNNNNNNNN
*
35525447 ATAGCTTAGGTCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGAA
1 ATAGCTTAGGTCACGTGTGTAGTACTATGTGCAGGCTACTACGCGTACCGAA
* * * * *
35525499 AT-G-ATAGGTCGCATGTGTAGTACTATGTGCAGGCTACTATGCGTACC-AC
1 ATAGCTTAGGTCACGTGTGTAGTACTATGTGCAGGCTACTACGCGTACCGAA
* * * *
35525548 ATAGCTTCGATCACGTGTGTAGTACTATGTGCAGGCTACTAC-CTGTATCG-G
1 ATAGCTTAGGTCACGTGTGTAGTACTATGTGCAGGCTACTACGC-GTACCGAA
*** *
35525599 AT-GAAAATGGTCACATGTGTAGTACTATGTGCAGGCTACTA
1 ATAGCTTA-GGTCACGTGTGTAGTACTATGTGCAGGCTACTA
35525640 TGTGAATCGG
Statistics
Matches: 116, Mismatches: 20, Indels: 11
0.79 0.14 0.07
Matches are distributed among these distances:
49 3 0.03
50 42 0.36
51 69 0.59
52 2 0.02
ACGTcount: A:0.25, C:0.19, G:0.26, T:0.30
Consensus pattern (52 bp):
ATAGCTTAGGTCACGTGTGTAGTACTATGTGCAGGCTACTACGCGTACCGAA
Found at i:35543428 original size:14 final size:15
Alignment explanation
Indices: 35543406--35543482 Score: 61
Period size: 14 Copynumber: 5.0 Consensus size: 15
35543396 CAATCAAACA
35543406 CCAGAAAAT-ATTTT
1 CCAGAAAATCATTTT
*
35543420 CCAGTAAATCATTTT
1 CCAGAAAATCATTTT
*
35543435 ACAGAAAAGTAAAACATTTT
1 CCAGAAAA-T----CATTTT
35543455 CCAG-AAATCATTTT
1 CCAGAAAATCATTTT
*
35543469 ACAGAAAA-CATTTT
1 CCAGAAAATCATTTT
35543483 ACTGGCAATC
Statistics
Matches: 51, Mismatches: 5, Indels: 14
0.73 0.07 0.20
Matches are distributed among these distances:
14 23 0.45
15 14 0.27
16 1 0.02
18 1 0.02
19 3 0.06
20 9 0.18
ACGTcount: A:0.44, C:0.16, G:0.08, T:0.32
Consensus pattern (15 bp):
CCAGAAAATCATTTT
Found at i:35543447 original size:20 final size:20
Alignment explanation
Indices: 35543422--35543461 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
35543412 AATATTTTCC
*
35543422 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
35543442 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
35543462 TCATTTTACA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:35543467 original size:34 final size:35
Alignment explanation
Indices: 35543410--35543476 Score: 118
Period size: 34 Copynumber: 1.9 Consensus size: 35
35543400 CAAACACCAG
*
35543410 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
35543445 AAAACATTTTCCAG-AAATCATTTTACAGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
35543477 CATTTTACTG
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
34 18 0.58
35 13 0.42
ACGTcount: A:0.48, C:0.13, G:0.07, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:35543483 original size:14 final size:14
Alignment explanation
Indices: 35543445--35543484 Score: 62
Period size: 14 Copynumber: 2.9 Consensus size: 14
35543435 ACAGAAAAGT
*
35543445 AAAACATTTTCCAG
1 AAAACATTTTACAG
*
35543459 AAATCATTTTACAG
1 AAAACATTTTACAG
35543473 AAAACATTTTAC
1 AAAACATTTTAC
35543485 TGGCAATCAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.45, C:0.17, G:0.05, T:0.33
Consensus pattern (14 bp):
AAAACATTTTACAG
Found at i:35557061 original size:98 final size:99
Alignment explanation
Indices: 35556925--35557122 Score: 389
Period size: 98 Copynumber: 2.0 Consensus size: 99
35556915 CAAATCTTAC
35556925 GGTGTCACATTGAGGTGTTTAGCGAAAATTGAACTCGTTGGTAAAAATTTGTTTCTAGGTTTAAA
1 GGTGTCACATTGAGGTGTTTAGCGAAAATTGAACTCGTTGGTAAAAATTTGTTTCTAGGTTTAAA
35556990 AAACCTTTTTTATTATTATTTAACAAACCATCTA
66 AAACCTTTTTTATTATTATTTAACAAACCATCTA
35557024 GGTGTCACA-TGAGGTGTTTAGCGAAAATTGAACTCGTTGGTAAAAATTTGTTTCTAGGTTTAAA
1 GGTGTCACATTGAGGTGTTTAGCGAAAATTGAACTCGTTGGTAAAAATTTGTTTCTAGGTTTAAA
35557088 AAACCTTTTTTATTATTATTTAACAAACCATCTA
66 AAACCTTTTTTATTATTATTTAACAAACCATCTA
35557122 G
1 G
35557123 TCAAAAACCT
Statistics
Matches: 99, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
98 90 0.91
99 9 0.09
ACGTcount: A:0.32, C:0.12, G:0.17, T:0.39
Consensus pattern (99 bp):
GGTGTCACATTGAGGTGTTTAGCGAAAATTGAACTCGTTGGTAAAAATTTGTTTCTAGGTTTAAA
AAACCTTTTTTATTATTATTTAACAAACCATCTA
Found at i:35558190 original size:27 final size:27
Alignment explanation
Indices: 35558160--35558659 Score: 521
Period size: 27 Copynumber: 18.7 Consensus size: 27
35558150 TCATCTCTTA
** *
35558160 GGGGTATAACAGTCATTTTACCTTATG
1 GGGGTATTTCAGTCATTTTACCCTATG
* *
35558187 GGGGTATTTCGGTTATTTTACCCTATG
1 GGGGTATTTCAGTCATTTTACCCTATG
**
35558214 AAGGTATTTC-GATCATTTTACCCTATG
1 GGGGTATTTCAG-TCATTTTACCCTATG
* ** **
35558241 GGGTTATTTTGGTCATTCAACCCTATG
1 GGGGTATTTCAGTCATTTTACCCTATG
* * * *
35558268 GGGTTATTTCGGTTATTTTACCCTATA
1 GGGGTATTTCAGTCATTTTACCCTATG
* *
35558295 AGGGTATTTCAATCATTTTACCCTAT-
1 GGGGTATTTCAGTCATTTTACCCTATG
* *
35558321 GGGGTATTTCAGTCAATTTATCCTATG
1 GGGGTATTTCAGTCATTTTACCCTATG
* * * * *
35558348 AGGGTATTTCGGTCATTTTATCTTATA
1 GGGGTATTTCAGTCATTTTACCCTATG
*
35558375 GGGGTA-TTCCGATCATTTTACCCTATG
1 GGGGTATTTCAG-TCATTTTACCCTATG
*
35558402 GGGGTATTTTAGTCATTTTACCCTATG
1 GGGGTATTTCAGTCATTTTACCCTATG
*
35558429 AGGGTATTTCAGTCATTTTACCCTAT-
1 GGGGTATTTCAGTCATTTTACCCTATG
35558455 GGGGTATTTCAGTCATTTTACCCTAT-
1 GGGGTATTTCAGTCATTTTACCCTATG
35558481 GGGGTATTTCAGTCATTTTACCCTAT-
1 GGGGTATTTCAGTCATTTTACCCTATG
*
35558507 GGGGTATTTCAGTCATTTTACCCTATA
1 GGGGTATTTCAGTCATTTTACCCTATG
* * *
35558534 GGGGTATTTCGGTCATTTTACCTTACG
1 GGGGTATTTCAGTCATTTTACCCTATG
* * * *
35558561 AGGGTATTT-TGATTATTTTGCCCTATG
1 GGGGTATTTCAG-TCATTTTACCCTATG
* *
35558588 GGGGTATTTCGGTCATTTTATCCTATG
1 GGGGTATTTCAGTCATTTTACCCTATG
*
35558615 GGAGTATTTC-GATCATTTTACCCTATG
1 GGGGTATTTCAG-TCATTTTACCCTATG
*** *
35558642 AATGTATTTCGGTCATTT
1 GGGGTATTTCAGTCATTT
35558660 ATCGACCTCT
Statistics
Matches: 400, Mismatches: 63, Indels: 20
0.83 0.13 0.04
Matches are distributed among these distances:
26 106 0.26
27 288 0.72
28 6 0.01
ACGTcount: A:0.20, C:0.17, G:0.20, T:0.43
Consensus pattern (27 bp):
GGGGTATTTCAGTCATTTTACCCTATG
Found at i:35558650 original size:81 final size:81
Alignment explanation
Indices: 35558169--35558641 Score: 588
Period size: 81 Copynumber: 5.9 Consensus size: 81
35558159 AGGGGTATAA
* * *
35558169 CAGTCATTTTACCTTATGGGGGTATTTCGGTTATTTTACCCTAT-GAAGGTATTTCGATCATTTT
1 CAGTCATTTTACCCTATGGGGGTATTTCGGTCATTTTACCCTATAG-GGGTATTTCGATCATTTT
35558233 ACCCTATGGGGTTATTTT
65 ACCCTATGGGG-TATTTT
* ** * * * *
35558251 -GGTCATTCAACCCTATGGGGTTATTTCGGTTATTTTACCCTATAAGGGTATTTCAATCATTTTA
1 CAGTCATTTTACCCTATGGGGGTATTTCGGTCATTTTACCCTATAGGGGTATTTCGATCATTTTA
35558315 CCCTATGGGGTA-TTT
66 CCCTATGGGGTATTTT
* * * * * *
35558330 CAGTCAATTTATCCTATGAGGGTATTTCGGTCATTTTATCTTATAGGGGTATTCCGATCATTTTA
1 CAGTCATTTTACCCTATGGGGGTATTTCGGTCATTTTACCCTATAGGGGTATTTCGATCATTTTA
35558395 CCCTATGGGGGTATTTT
66 CCCTAT-GGGGTATTTT
* *
35558412 -AGTCATTTTACCCTATGAGGGTATTTCAGTCATTTTACCCTAT-GGGGTATTTC-AGTCATTTT
1 CAGTCATTTTACCCTATGGGGGTATTTCGGTCATTTTACCCTATAGGGGTATTTCGA-TCATTTT
35558474 ACCCTATGGGGTA-TTT
65 ACCCTATGGGGTATTTT
* *
35558490 CAGTCATTTTACCCTAT-GGGGTATTTCAGTCATTTTACCCTATAGGGGTATTTCGGTCATTTTA
1 CAGTCATTTTACCCTATGGGGGTATTTCGGTCATTTTACCCTATAGGGGTATTTCGATCATTTTA
* *
35558554 CCTTACGAGGGTATTTT
66 CCCTATG-GGGTATTTT
* * * *
35558571 GA-TTATTTTGCCCTATGGGGGTATTTCGGTCATTTTATCCTAT-GGGAGTATTTCGATCATTTT
1 CAGTCATTTTACCCTATGGGGGTATTTCGGTCATTTTACCCTATAGGG-GTATTTCGATCATTTT
35558634 ACCCTATG
65 ACCCTATG
35558642 AATGTATTTC
Statistics
Matches: 340, Mismatches: 39, Indels: 25
0.84 0.10 0.06
Matches are distributed among these distances:
78 28 0.08
79 49 0.14
80 102 0.30
81 158 0.46
82 3 0.01
ACGTcount: A:0.20, C:0.17, G:0.20, T:0.43
Consensus pattern (81 bp):
CAGTCATTTTACCCTATGGGGGTATTTCGGTCATTTTACCCTATAGGGGTATTTCGATCATTTTA
CCCTATGGGGTATTTT
Found at i:35559944 original size:11 final size:11
Alignment explanation
Indices: 35559925--35559955 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
35559915 TCCTCCCAAC
35559925 AACTCCATTCA
1 AACTCCATTCA
*
35559936 AATTCCATTCA
1 AACTCCATTCA
35559947 AACTCCATT
1 AACTCCATT
35559956 GACCTGTGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.35, C:0.32, G:0.00, T:0.32
Consensus pattern (11 bp):
AACTCCATTCA
Found at i:35566536 original size:25 final size:25
Alignment explanation
Indices: 35566491--35566541 Score: 59
Period size: 25 Copynumber: 2.0 Consensus size: 25
35566481 ACTCTTCCTA
* *
35566491 TCTCTTCACTTCTCTCTCATTTTTC
1 TCTCTTCACTTCCCTCTCATTATTC
*
35566516 TCTCTTCATTTCCCT-TCCATTATTC
1 TCTCTTCACTTCCCTCT-CATTATTC
35566541 T
1 T
35566542 TAATTCCTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
24 1 0.05
25 21 0.95
ACGTcount: A:0.10, C:0.35, G:0.00, T:0.55
Consensus pattern (25 bp):
TCTCTTCACTTCCCTCTCATTATTC
Found at i:35568360 original size:21 final size:21
Alignment explanation
Indices: 35568336--35568387 Score: 52
Period size: 22 Copynumber: 2.4 Consensus size: 21
35568326 AGTGTGTTCC
*
35568336 TTTTATGTTGATTG-TTTTAG
1 TTTTATGTTGAATGCTTTTAG
*
35568356 ATTTTCTTGTTGAATGCTTTTAG
1 -TTTT-ATGTTGAATGCTTTTAG
*
35568379 TTTCATGTT
1 TTTTATGTT
35568388 ATTTAAGTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
21 8 0.32
22 11 0.44
23 6 0.24
ACGTcount: A:0.15, C:0.06, G:0.17, T:0.62
Consensus pattern (21 bp):
TTTTATGTTGAATGCTTTTAG
Found at i:35571571 original size:139 final size:139
Alignment explanation
Indices: 35571321--35571593 Score: 510
Period size: 139 Copynumber: 2.0 Consensus size: 139
35571311 TAAGAACTAA
**
35571321 TGGGGTATTTTAAGTTATATAGTAGGGTATTATTAGGGTTTAATCTGGGTAAAATGGGTTTATAG
1 TGGGGTATTTTAAGTTATATAGTAGGGTATTATTAGGGTTTAATCTGGGTAAAAAAGGTTTATAG
35571386 CCTAACGGGTCATGTCACGGGTCGAGCAAAAATTATAAATTTTCGCAGTGATGTCGCAACACAGG
66 CCTAACGGGTCATGTCACGGGTCGAGCAAAAATTATAAATTTTCGCAGTGATGTCGCAACACAGG
35571451 AGTTGTGAC
131 AGTTGTGAC
35571460 TGGGGTATTTTAAGTTATATAGTAGGGTATTATTAGGGTTTAATCTGGGTAAAAAAGGTTTATAG
1 TGGGGTATTTTAAGTTATATAGTAGGGTATTATTAGGGTTTAATCTGGGTAAAAAAGGTTTATAG
* *
35571525 CCTGACGGGTCATGTCACGGGTCGAGCAAAAATTATAGATTTTCGCAGTGATGTCGCAACACAGG
66 CCTAACGGGTCATGTCACGGGTCGAGCAAAAATTATAAATTTTCGCAGTGATGTCGCAACACAGG
35571590 AGTT
131 AGTT
35571594 TTGTGTCACA
Statistics
Matches: 130, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
139 130 1.00
ACGTcount: A:0.29, C:0.11, G:0.27, T:0.32
Consensus pattern (139 bp):
TGGGGTATTTTAAGTTATATAGTAGGGTATTATTAGGGTTTAATCTGGGTAAAAAAGGTTTATAG
CCTAACGGGTCATGTCACGGGTCGAGCAAAAATTATAAATTTTCGCAGTGATGTCGCAACACAGG
AGTTGTGAC
Found at i:35575889 original size:25 final size:25
Alignment explanation
Indices: 35575861--35575917 Score: 98
Period size: 25 Copynumber: 2.3 Consensus size: 25
35575851 ACCTTATCAA
35575861 AGTCCTCA-TACTCAAGCAACATGTT
1 AGTCCTCACT-CTCAAGCAACATGTT
35575886 AGTCCTCACTCTCAAGCAACATGTT
1 AGTCCTCACTCTCAAGCAACATGTT
35575911 AGTCCTC
1 AGTCCTC
35575918 CCTTAGGCCT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
25 30 0.97
26 1 0.03
ACGTcount: A:0.28, C:0.32, G:0.12, T:0.28
Consensus pattern (25 bp):
AGTCCTCACTCTCAAGCAACATGTT
Found at i:35577903 original size:20 final size:20
Alignment explanation
Indices: 35577878--35577974 Score: 69
Period size: 20 Copynumber: 4.9 Consensus size: 20
35577868 CTTATACTGG
35577878 TTGCACTTCAGTGCCCCTGA
1 TTGCACTTCAGTGCCCCTGA
* **
35577898 TTGCAC-TCTAGTGCCCTTTT
1 TTGCACTTC-AGTGCCCCTGA
* *
35577918 TTACACTTTAGTG-CCCT-A
1 TTGCACTTCAGTGCCCCTGA
35577936 TTTGCACTTC-GATGCCCCTGA
1 -TTGCACTTCAG-TGCCCCTGA
*
35577957 TTGCA-TTCTGGTGCCCCT
1 TTGCACTTC-AGTGCCCCT
35577975 ATTCAGCACT
Statistics
Matches: 60, Mismatches: 9, Indels: 16
0.71 0.11 0.19
Matches are distributed among these distances:
18 1 0.02
19 17 0.28
20 39 0.65
21 3 0.05
ACGTcount: A:0.13, C:0.32, G:0.18, T:0.37
Consensus pattern (20 bp):
TTGCACTTCAGTGCCCCTGA
Found at i:35579911 original size:11 final size:11
Alignment explanation
Indices: 35579895--35579931 Score: 60
Period size: 11 Copynumber: 3.5 Consensus size: 11
35579885 TAACAATAAC
35579895 AATATTAAAAT
1 AATATTAAAAT
35579906 AATATTAAAAT
1 AATATTAAAAT
35579917 AATA--AAAAT
1 AATATTAAAAT
35579926 AATATT
1 AATATT
35579932 TGTAATAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
9 9 0.38
11 15 0.62
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (11 bp):
AATATTAAAAT
Found at i:35580626 original size:27 final size:27
Alignment explanation
Indices: 35580590--35580658 Score: 104
Period size: 27 Copynumber: 2.6 Consensus size: 27
35580580 AAATTAAAAA
*
35580590 TTACCAAAATGT-TATAATTTTTTTTAT
1 TTACCAAAATATATATAA-TTTTTTTAT
35580617 TTACCAAAATATATATAATTTTTTTAT
1 TTACCAAAATATATATAATTTTTTTAT
*
35580644 TTACTAAAATATATA
1 TTACCAAAATATATA
35580659 AAAAACCAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
27 34 0.87
28 5 0.13
ACGTcount: A:0.41, C:0.07, G:0.01, T:0.51
Consensus pattern (27 bp):
TTACCAAAATATATATAATTTTTTTAT
Found at i:35580764 original size:27 final size:27
Alignment explanation
Indices: 35580722--35580801 Score: 124
Period size: 27 Copynumber: 3.0 Consensus size: 27
35580712 ACTCCCTGGG
**
35580722 ACAAGGGAACATTGTTGGCGGCACCAA
1 ACAAGGGAACCCTGTTGGCGGCACCAA
35580749 ACAAGGGAACCCTGTTGGCGGCACCAA
1 ACAAGGGAACCCTGTTGGCGGCACCAA
**
35580776 ACAAGGGTTCCCTGTTGGCGGCACCA
1 ACAAGGGAACCCTGTTGGCGGCACCA
35580802 NNNNNNNNNN
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 49 1.00
ACGTcount: A:0.28, C:0.28, G:0.30, T:0.15
Consensus pattern (27 bp):
ACAAGGGAACCCTGTTGGCGGCACCAA
Found at i:35583502 original size:18 final size:18
Alignment explanation
Indices: 35583476--35583513 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
35583466 ATCCAAATGA
* *
35583476 TCGCCACCACCTTCTTCT
1 TCGCAACCACATTCTTCT
35583494 TCGCAACCACATTCTTCT
1 TCGCAACCACATTCTTCT
35583512 TC
1 TC
35583514 ACCACCAACC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.16, C:0.45, G:0.05, T:0.34
Consensus pattern (18 bp):
TCGCAACCACATTCTTCT
Found at i:35583520 original size:18 final size:18
Alignment explanation
Indices: 35583479--35583520 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
35583469 CAAATGATCG
* *
35583479 CCACCACCTTCTTCTTCG
1 CCACCACATTCTTCTTCA
*
35583497 CAACCACATTCTTCTTCA
1 CCACCACATTCTTCTTCA
35583515 CCACCA
1 CCACCA
35583521 ACCATATCAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.21, C:0.48, G:0.02, T:0.29
Consensus pattern (18 bp):
CCACCACATTCTTCTTCA
Found at i:35584095 original size:3 final size:3
Alignment explanation
Indices: 35584087--35584136 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
35584077 NCTAACATCT
35584087 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
35584135 TA
1 TA
35584137 CTATAAAATT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:35584495 original size:27 final size:27
Alignment explanation
Indices: 35584422--35584501 Score: 133
Period size: 27 Copynumber: 3.0 Consensus size: 27
35584412 ATAACACGAG
**
35584422 TGGTGCCGCCAACAGGGAACCCTTGTT
1 TGGTGCCGCCAACAGGGTTCCCTTGTT
35584449 TGGTGCCGCCAACAGGGTTCCCTTGTT
1 TGGTGCCGCCAACAGGGTTCCCTTGTT
*
35584476 TGGTGCCGCCAACAGTGTTCCCTTGT
1 TGGTGCCGCCAACAGGGTTCCCTTGT
35584502 CCCAGGGAGT
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 50 1.00
ACGTcount: A:0.14, C:0.30, G:0.29, T:0.28
Consensus pattern (27 bp):
TGGTGCCGCCAACAGGGTTCCCTTGTT
Found at i:35584554 original size:18 final size:17
Alignment explanation
Indices: 35584528--35584564 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
35584518 ATCAGTCCAG
35584528 TTTTTTTTTTCTGTTTT
1 TTTTTTTTTTCTGTTTT
*
35584545 TTTTTGTTTTTTTGTTTT
1 TTTTT-TTTTTCTGTTTT
35584563 TT
1 TT
35584565 ATATATTTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 5 0.28
18 13 0.72
ACGTcount: A:0.00, C:0.03, G:0.08, T:0.89
Consensus pattern (17 bp):
TTTTTTTTTTCTGTTTT
Found at i:35584594 original size:27 final size:28
Alignment explanation
Indices: 35584564--35584634 Score: 99
Period size: 27 Copynumber: 2.5 Consensus size: 28
35584554 TTTTGTTTTT
35584564 TATATATTTTGGTAAATAAAAAAAT-TA
1 TATATATTTTGGTAAATAAAAAAATATA
* *
35584591 TATATTTTTTGGTAAATAAAAAAATATT
1 TATATATTTTGGTAAATAAAAAAATATA
*
35584619 TATAACATTTTGGTAA
1 TAT-ATATTTTGGTAA
35584635 TTTTTAATTT
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
27 24 0.63
28 4 0.11
29 10 0.26
ACGTcount: A:0.46, C:0.01, G:0.08, T:0.44
Consensus pattern (28 bp):
TATATATTTTGGTAAATAAAAAAATATA
Found at i:35585273 original size:9 final size:10
Alignment explanation
Indices: 35585259--35585283 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
35585249 AGAAAAGTTA
35585259 TAAAAAATAT
1 TAAAAAATAT
35585269 TAAAAAATAT
1 TAAAAAATAT
35585279 TAAAA
1 TAAAA
35585284 TTTTTTGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (10 bp):
TAAAAAATAT
Found at i:35585574 original size:13 final size:13
Alignment explanation
Indices: 35585556--35585587 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
35585546 AAATGTCACA
35585556 TTTATTTATATTT
1 TTTATTTATATTT
*
35585569 TTTATTTTTATTT
1 TTTATTTATATTT
35585582 TTTATT
1 TTTATT
35585588 ACACCTTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (13 bp):
TTTATTTATATTT
Found at i:35586053 original size:17 final size:17
Alignment explanation
Indices: 35586033--35586078 Score: 56
Period size: 17 Copynumber: 2.7 Consensus size: 17
35586023 AGATTAATTA
*
35586033 TATAAATTATTTAATAT
1 TATAAATTATTTAAAAT
* *
35586050 TATAAAATAATTAAAAT
1 TATAAATTATTTAAAAT
*
35586067 TACAAATTATTT
1 TATAAATTATTT
35586079 TATAAATTTT
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (17 bp):
TATAAATTATTTAAAAT
Found at i:35586127 original size:11 final size:10
Alignment explanation
Indices: 35586113--35586160 Score: 51
Period size: 10 Copynumber: 4.5 Consensus size: 10
35586103 TTTTTATGTT
35586113 ATTTTCTATAA
1 ATTTTCTAT-A
35586124 ATTTTTCTATA
1 A-TTTTCTATA
* *
35586135 TTTTTTTATA
1 ATTTTCTATA
35586145 ATATTTCTATA
1 AT-TTTCTATA
35586156 ATTTT
1 ATTTT
35586161 TAATAATCAA
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
10 12 0.39
11 11 0.35
12 8 0.26
ACGTcount: A:0.29, C:0.06, G:0.00, T:0.65
Consensus pattern (10 bp):
ATTTTCTATA
Found at i:35586136 original size:21 final size:21
Alignment explanation
Indices: 35586112--35586167 Score: 62
Period size: 21 Copynumber: 2.7 Consensus size: 21
35586102 ATTTTTATGT
*
35586112 TATTTTCTATA-AATTTTTCTA
1 TATTTT-TATATAATATTTCTA
*
35586133 TATTTTTTTATAATATTTCTA
1 TATTTTTATATAATATTTCTA
35586154 TAATTTTTA-ATAAT
1 T-ATTTTTATATAAT
35586168 CAATCAATTG
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
20 3 0.10
21 21 0.70
22 6 0.20
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.62
Consensus pattern (21 bp):
TATTTTTATATAATATTTCTA
Found at i:35586139 original size:22 final size:22
Alignment explanation
Indices: 35586114--35586161 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
35586104 TTTTATGTTA
*
35586114 TTTTCTATAAATTTTTCTAT-AT
1 TTTTCTAT-AATATTTCTATAAT
*
35586136 TTTTTTATAATATTTCTATAAT
1 TTTTCTATAATATTTCTATAAT
35586158 TTTT
1 TTTT
35586162 AATAATCAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 10 0.43
22 13 0.57
ACGTcount: A:0.27, C:0.06, G:0.00, T:0.67
Consensus pattern (22 bp):
TTTTCTATAATATTTCTATAAT
Found at i:35594382 original size:20 final size:20
Alignment explanation
Indices: 35594348--35594389 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
35594338 AACTATTTAA
** *
35594348 ATAATATTACTTGAATAGTT
1 ATAATATTAAATGAATAATT
35594368 ATAATATTAAATGAATAATT
1 ATAATATTAAATGAATAATT
35594388 AT
1 AT
35594390 GTGTTTATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.48, C:0.02, G:0.07, T:0.43
Consensus pattern (20 bp):
ATAATATTAAATGAATAATT
Found at i:35597080 original size:17 final size:17
Alignment explanation
Indices: 35597060--35597092 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
35597050 AAAATAAATA
*
35597060 AAGACATAAAAAATAAC
1 AAGAAATAAAAAATAAC
35597077 AAGAAATAAAAAATAA
1 AAGAAATAAAAAATAA
35597093 AAATAATATA
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:0.76, C:0.06, G:0.06, T:0.12
Consensus pattern (17 bp):
AAGAAATAAAAAATAAC
Found at i:35597182 original size:4 final size:4
Alignment explanation
Indices: 35597173--35597206 Score: 59
Period size: 4 Copynumber: 8.5 Consensus size: 4
35597163 AAAAGGGAGT
*
35597173 AATA AATA AATA AATG AATA AATA AATA AATA AA
1 AATA AATA AATA AATA AATA AATA AATA AATA AA
35597207 ATTTGTAGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.24
Consensus pattern (4 bp):
AATA
Found at i:35600883 original size:26 final size:26
Alignment explanation
Indices: 35600847--35600896 Score: 100
Period size: 26 Copynumber: 1.9 Consensus size: 26
35600837 TTCAGTGATA
35600847 CGGGGAATCAGCACTTAGCAACCCCT
1 CGGGGAATCAGCACTTAGCAACCCCT
35600873 CGGGGAATCAGCACTTAGCAACCC
1 CGGGGAATCAGCACTTAGCAACCC
35600897 TTTTAGAGTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.28, C:0.34, G:0.24, T:0.14
Consensus pattern (26 bp):
CGGGGAATCAGCACTTAGCAACCCCT
Found at i:35600935 original size:67 final size:67
Alignment explanation
Indices: 35600808--35600968 Score: 241
Period size: 67 Copynumber: 2.4 Consensus size: 67
35600798 AGGATTAGGT
* * * * * *
35600808 GGAATCAACACTTAGCAACCACCTTTATATTCAGTGATACGGGGAATCAGCACTTAGCAACCCCT
1 GGAATCAGCACTTAGCAACC-CTTTTAGAGTCAATAATACGGGGAATCAGCACTTAGCAACCCCT
35600873 CGG
65 CGG
* *
35600876 GGAATCAGCACTTAGCAACCCTTTTAGAGTCAATAATTCGTGGAATCAGCACTTAGCAACCCCTC
1 GGAATCAGCACTTAGCAACCCTTTTAGAGTCAATAATACGGGGAATCAGCACTTAGCAACCCCTC
35600941 GG
66 GG
35600943 GGAATCAGCACTTAGCAACCCTTTTA
1 GGAATCAGCACTTAGCAACCCTTTTA
35600969 TATTCAGTAT
Statistics
Matches: 85, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
67 66 0.78
68 19 0.22
ACGTcount: A:0.30, C:0.27, G:0.19, T:0.24
Consensus pattern (67 bp):
GGAATCAGCACTTAGCAACCCTTTTAGAGTCAATAATACGGGGAATCAGCACTTAGCAACCCCTC
GG
Found at i:35602057 original size:11 final size:12
Alignment explanation
Indices: 35602029--35602061 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
35602019 GCCCAAATGT
35602029 CGAAATTTTCGAA
1 CGAAATTTTC-AA
35602042 CGAAATTTTC-A
1 CGAAATTTTCAA
35602053 CGAAATTTT
1 CGAAATTTT
35602062 TCCGTGAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 10 0.50
13 10 0.50
ACGTcount: A:0.36, C:0.15, G:0.12, T:0.36
Consensus pattern (12 bp):
CGAAATTTTCAA
Found at i:35606380 original size:43 final size:41
Alignment explanation
Indices: 35606292--35606521 Score: 198
Period size: 43 Copynumber: 5.5 Consensus size: 41
35606282 CTCGGTGGAT
* *
35606292 TCAGCACTTAGCAACCACC-ATA-AATTC-AGTGATACAGGGAA
1 TCAGCACTTAGCAACC-CCTTTACAA-TCAAG-GATACGGGGAA
* * *
35606333 TCAGCACATAGCAACCCCTTTCACAATTAAGGATTCGGTGGAA
1 TCAGCACTTAGCAACCCCTTT-ACAATCAAGGATACGG-GGAA
* *
35606376 TCAGCACTTAGCAACCACCTTTATATTC-AGTGATACGGGGAA
1 TCAGCACTTAGCAACC-CCTTTACAATCAAG-GATACGGGGAA
* *
35606418 TCAGCACTTAGCAACCCCTTTCACAATCAAAGATACGGTGGGA
1 TCAGCACTTAGCAACCCCTTT-ACAATCAAGGATACGG-GGAA
* * * ** **
35606461 TCAGCACATAGCAACCACCTTTAGAGTCAATAATTTGGGGAA
1 TCAGCACTTAGCAACC-CCTTTACAATCAAGGATACGGGGAA
35606503 TCAGCACTTAGCAACCCCT
1 TCAGCACTTAGCAACCCCT
35606522 CGGGGAATCA
Statistics
Matches: 155, Mismatches: 23, Indels: 22
0.77 0.12 0.11
Matches are distributed among these distances:
40 2 0.01
41 24 0.15
42 58 0.37
43 61 0.39
44 10 0.06
ACGTcount: A:0.33, C:0.26, G:0.18, T:0.23
Consensus pattern (41 bp):
TCAGCACTTAGCAACCCCTTTACAATCAAGGATACGGGGAA
Found at i:35606425 original size:42 final size:42
Alignment explanation
Indices: 35606292--35606518 Score: 221
Period size: 42 Copynumber: 5.4 Consensus size: 42
35606282 CTCGGTGGAT
* *
35606292 TCAGCACTTAGCAACCACC-ATAAATTCAGTGATACAGGGAA
1 TCAGCACTTAGCAACCACCTTTAAATTCAGTGATACGGGGAA
* * *
35606333 TCAGCACATAGCAACC-CCTTTCACAATTAAG-GATTCGGTGGAA
1 TCAGCACTTAGCAACCACCTTT-A-AATTCAGTGATACGG-GGAA
*
35606376 TCAGCACTTAGCAACCACCTTTATATTCAGTGATACGGGGAA
1 TCAGCACTTAGCAACCACCTTTAAATTCAGTGATACGGGGAA
** *
35606418 TCAGCACTTAGCAACC-CCTTTCACAA-TCAAAGATACGGTGGGA
1 TCAGCACTTAGCAACCACCTTT-A-AATTCAGTGATACGG-GGAA
* * * * * **
35606461 TCAGCACATAGCAACCACCTTTAGAGTCAATAATTTGGGGAA
1 TCAGCACTTAGCAACCACCTTTAAATTCAGTGATACGGGGAA
35606503 TCAGCACTTAGCAACC
1 TCAGCACTTAGCAACC
35606519 CCTCGGGGAA
Statistics
Matches: 154, Mismatches: 21, Indels: 21
0.79 0.11 0.11
Matches are distributed among these distances:
40 2 0.01
41 21 0.14
42 61 0.40
43 60 0.39
44 10 0.06
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.22
Consensus pattern (42 bp):
TCAGCACTTAGCAACCACCTTTAAATTCAGTGATACGGGGAA
Found at i:35606430 original size:85 final size:85
Alignment explanation
Indices: 35606283--35606521 Score: 327
Period size: 85 Copynumber: 2.8 Consensus size: 85
35606273 TATCCGTTAC
* * * *
35606283 TCGGTGGATTCAGCACTTAGCAACCACC-ATAAATTCAGTGATACAGGGAATCAGCACATAGCAA
1 TCGGTGGAATCAGCACTTAGCAACCACCTTTAAATTCAGTGATACGGGGAATCAGCACTTAGCAA
* *
35606347 CCCCTTTCACAATTAAGGAT
66 CCCCTTTCACAATCAAAGAT
*
35606367 TCGGTGGAATCAGCACTTAGCAACCACCTTTATATTCAGTGATACGGGGAATCAGCACTTAGCAA
1 TCGGTGGAATCAGCACTTAGCAACCACCTTTAAATTCAGTGATACGGGGAATCAGCACTTAGCAA
35606432 CCCCTTTCACAATCAAAGAT
66 CCCCTTTCACAATCAAAGAT
* * * * * * * **
35606452 ACGGTGGGATCAGCACATAGCAACCACCTTTAGAGTCAATAATTTGGGGAATCAGCACTTAGCAA
1 TCGGTGGAATCAGCACTTAGCAACCACCTTTAAATTCAGTGATACGGGGAATCAGCACTTAGCAA
35606517 CCCCT
66 CCCCT
35606522 CGGGGAATCA
Statistics
Matches: 138, Mismatches: 16, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
84 27 0.20
85 111 0.80
ACGTcount: A:0.33, C:0.26, G:0.19, T:0.23
Consensus pattern (85 bp):
TCGGTGGAATCAGCACTTAGCAACCACCTTTAAATTCAGTGATACGGGGAATCAGCACTTAGCAA
CCCCTTTCACAATCAAAGAT
Found at i:35606526 original size:26 final size:26
Alignment explanation
Indices: 35606497--35606547 Score: 102
Period size: 26 Copynumber: 2.0 Consensus size: 26
35606487 TCAATAATTT
35606497 GGGGAATCAGCACTTAGCAACCCCTC
1 GGGGAATCAGCACTTAGCAACCCCTC
35606523 GGGGAATCAGCACTTAGCAACCCCT
1 GGGGAATCAGCACTTAGCAACCCCT
35606548 TTAGAGTCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.27, C:0.33, G:0.24, T:0.16
Consensus pattern (26 bp):
GGGGAATCAGCACTTAGCAACCCCTC
Found at i:35606570 original size:67 final size:67
Alignment explanation
Indices: 35606460--35606619 Score: 250
Period size: 67 Copynumber: 2.4 Consensus size: 67
35606450 ATACGGTGGG
* *
35606460 ATCAGCACATAGCAACCACCTTTAGAGTCAATAATTTGGGGAATCAGC-ACTTAGCAACCCCTCG
1 ATCAGCACTTAGCAACC-CCTTTAGAGTCAATAATTCGGGGAATCAGCAACTTAGCAA-CCCTCG
35606524 GGGA
64 GGGA
* *
35606528 ATCAGCACTTAGCAACCCCTTTAGAGTCAATAATTCGTGGAATCAGCAACTTAGCAACCCTCTGG
1 ATCAGCACTTAGCAACCCCTTTAGAGTCAATAATTCGGGGAATCAGCAACTTAGCAACCCTCGGG
35606593 GA
66 GA
*
35606595 ATCAGCACTTAGCAACCCTTTTAGA
1 ATCAGCACTTAGCAACCCCTTTAGA
35606620 TTCAGTATAT
Statistics
Matches: 86, Mismatches: 5, Indels: 3
0.91 0.05 0.03
Matches are distributed among these distances:
67 61 0.71
68 25 0.29
ACGTcount: A:0.32, C:0.27, G:0.18, T:0.23
Consensus pattern (67 bp):
ATCAGCACTTAGCAACCCCTTTAGAGTCAATAATTCGGGGAATCAGCAACTTAGCAACCCTCGGG
GA
Found at i:35607663 original size:11 final size:12
Alignment explanation
Indices: 35607635--35607667 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
35607625 GCCCAAACGT
35607635 CGAAATTTTCGAA
1 CGAAATTTTC-AA
35607648 CGAAATTTTC-A
1 CGAAATTTTCAA
35607659 CGAAATTTT
1 CGAAATTTT
35607668 TCTGTGAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 10 0.50
13 10 0.50
ACGTcount: A:0.36, C:0.15, G:0.12, T:0.36
Consensus pattern (12 bp):
CGAAATTTTCAA
Found at i:35611007 original size:17 final size:17
Alignment explanation
Indices: 35610967--35610999 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
35610957 GCAAAAGAGA
35610967 AAATCAAATAAGAAATC
1 AAATCAAATAAGAAATC
35610984 AAATCAAATAAGAAAT
1 AAATCAAATAAGAAAT
35611000 TGAGTCAACA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.67, C:0.09, G:0.06, T:0.18
Consensus pattern (17 bp):
AAATCAAATAAGAAATC
Found at i:35615065 original size:24 final size:24
Alignment explanation
Indices: 35615033--35615082 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
35615023 AAAGCATGTG
35615033 TTGAGAATCTTTAATTATTTGATA
1 TTGAGAATCTTTAATTATTTGATA
* *
35615057 TTGAGAATCTTTGATTATTTTATA
1 TTGAGAATCTTTAATTATTTGATA
35615081 TT
1 TT
35615083 ATTAAATAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.30, C:0.04, G:0.12, T:0.54
Consensus pattern (24 bp):
TTGAGAATCTTTAATTATTTGATA
Found at i:35620052 original size:27 final size:27
Alignment explanation
Indices: 35620000--35620052 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 27
35619990 GCTCACATGA
*
35620000 GCTTCCCATTATATGGCTCGAGAGAGG
1 GCTTCCCATTATATGGCTCGAAAGAGG
* *
35620027 GCTTCCCTATTATGT-GCTCTAAAGAG
1 GCTTCCC-ATTATATGGCTCGAAAGAG
35620053 CACTCTCGAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
27 16 0.73
28 6 0.27
ACGTcount: A:0.23, C:0.23, G:0.25, T:0.30
Consensus pattern (27 bp):
GCTTCCCATTATATGGCTCGAAAGAGG
Found at i:35620688 original size:25 final size:25
Alignment explanation
Indices: 35620641--35620703 Score: 65
Period size: 25 Copynumber: 2.5 Consensus size: 25
35620631 TATTTATCTC
*
35620641 TTATGAGCTTCCCGATACTTGGCTT
1 TTATGAGCTTCCCGATACATGGCTT
* *
35620666 TTATGAGCTTCCTGATTA-ATGGCTC
1 TTATGAGCTTCCCGA-TACATGGCTT
* *
35620691 GTAGGAGCTTCCC
1 TTATGAGCTTCCC
35620704 AATATTTGGC
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
25 29 0.94
26 2 0.06
ACGTcount: A:0.17, C:0.24, G:0.22, T:0.37
Consensus pattern (25 bp):
TTATGAGCTTCCCGATACATGGCTT
Found at i:35620702 original size:50 final size:50
Alignment explanation
Indices: 35620645--35620775 Score: 140
Period size: 50 Copynumber: 2.6 Consensus size: 50
35620635 TATCTCTTAT
* ** *
35620645 GAGCTTCCCGATACTTGGCTTTTATGAGCTTCCTGATTA-ATGGCTCGTAG
1 GAGCTTCCCAATACTTGGCTCGTAAGAGCTTCCT-ATTACATGGCTCGTAG
* ** *
35620695 GAGCTTCCCAATATTTGGCTCGTAAGAGCTTCCTATTACATGGCTCACAT
1 GAGCTTCCCAATACTTGGCTCGTAAGAGCTTCCTATTACATGGCTCGTAG
* *
35620745 GAGCTTCCCATTA-TATGGCTCGAAAGAGCTT
1 GAGCTTCCCAATACT-TGGCTCGTAAGAGCTT
35620776 TTCGATTACA
Statistics
Matches: 69, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
49 5 0.07
50 64 0.93
ACGTcount: A:0.22, C:0.24, G:0.21, T:0.33
Consensus pattern (50 bp):
GAGCTTCCCAATACTTGGCTCGTAAGAGCTTCCTATTACATGGCTCGTAG
Found at i:35620738 original size:25 final size:25
Alignment explanation
Indices: 35620670--35620775 Score: 106
Period size: 25 Copynumber: 4.2 Consensus size: 25
35620660 TGGCTTTTAT
* *
35620670 GAGCTTCCTGATTA-ATGGCTCGTAG
1 GAGCTTCC-CATTATATGGCTCGTAA
* *
35620695 GAGCTTCCCAATATTTGGCTCGTAA
1 GAGCTTCCCATTATATGGCTCGTAA
* * ** *
35620720 GAGCTTCCTATTACATGGCTCACAT
1 GAGCTTCCCATTATATGGCTCGTAA
*
35620745 GAGCTTCCCATTATATGGCTCGAAA
1 GAGCTTCCCATTATATGGCTCGTAA
35620770 GAGCTT
1 GAGCTT
35620776 TTCGATTACA
Statistics
Matches: 64, Mismatches: 16, Indels: 2
0.78 0.20 0.02
Matches are distributed among these distances:
24 3 0.05
25 61 0.95
ACGTcount: A:0.24, C:0.24, G:0.22, T:0.31
Consensus pattern (25 bp):
GAGCTTCCCATTATATGGCTCGTAA
Found at i:35620792 original size:50 final size:50
Alignment explanation
Indices: 35620695--35620794 Score: 130
Period size: 50 Copynumber: 2.0 Consensus size: 50
35620685 TGGCTCGTAG
* * * *
35620695 GAGCTTCCCAATATTTGGCTCGTAAGAGCTTCCTATTACATGGCTCACAT
1 GAGCTTCCCAATATATGGCTCGAAAGAGCTTCCGATTACATGACTCACAT
* *
35620745 GAGCTTCCCATTATATGGCTCGAAAGAGCTTTTCGATTACAT-ACTCACAT
1 GAGCTTCCCAATATATGGCTCGAAAGAGC-TTCCGATTACATGACTCACAT
35620795 AGGCATACCT
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
50 33 0.77
51 10 0.23
ACGTcount: A:0.26, C:0.25, G:0.17, T:0.32
Consensus pattern (50 bp):
GAGCTTCCCAATATATGGCTCGAAAGAGCTTCCGATTACATGACTCACAT
Found at i:35628549 original size:32 final size:29
Alignment explanation
Indices: 35628511--35628574 Score: 83
Period size: 32 Copynumber: 2.1 Consensus size: 29
35628501 TTTATTATAT
* *
35628511 AAACAATTTTTAAAATATAGTATATCAAATTG
1 AAACAATTCTTAAAATA-A-TA-AACAAATTG
35628543 AAACAATTCTTAAAATAATAAACAAATTG
1 AAACAATTCTTAAAATAATAAACAAATTG
35628572 AAA
1 AAA
35628575 ATACAATAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
29 11 0.37
30 2 0.07
31 1 0.03
32 16 0.53
ACGTcount: A:0.56, C:0.08, G:0.05, T:0.31
Consensus pattern (29 bp):
AAACAATTCTTAAAATAATAAACAAATTG
Found at i:35628690 original size:23 final size:23
Alignment explanation
Indices: 35628664--35628720 Score: 78
Period size: 23 Copynumber: 2.5 Consensus size: 23
35628654 TCTACAATAT
*
35628664 CCAAATAATATTATAAACGACAA
1 CCAAATAATATTAAAAACGACAA
*
35628687 CCAAATAATATTAAAAAGGACAA
1 CCAAATAATATTAAAAACGACAA
* *
35628710 CGAAACAATAT
1 CCAAATAATAT
35628721 AATAGCTGCG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.58, C:0.16, G:0.07, T:0.19
Consensus pattern (23 bp):
CCAAATAATATTAAAAACGACAA
Found at i:35628911 original size:3 final size:3
Alignment explanation
Indices: 35628903--35628966 Score: 112
Period size: 3 Copynumber: 21.3 Consensus size: 3
35628893 AACATCGTCC
35628903 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
35628951 TCA TCA TTC- TCA TCA T
1 TCA TCA -TCA TCA TCA T
35628967 TCCTGAACCA
Statistics
Matches: 59, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.03
3 55 0.93
4 2 0.03
ACGTcount: A:0.31, C:0.33, G:0.00, T:0.36
Consensus pattern (3 bp):
TCA
Found at i:35635612 original size:18 final size:18
Alignment explanation
Indices: 35635589--35635626 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
35635579 CAAGGGTTTC
35635589 TCAATTGGTACTTATCAA
1 TCAATTGGTACTTATCAA
35635607 TCAATTGGTACTTATCAA
1 TCAATTGGTACTTATCAA
35635625 TC
1 TC
35635627 GCATTTTGAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.32, C:0.18, G:0.11, T:0.39
Consensus pattern (18 bp):
TCAATTGGTACTTATCAA
Found at i:35636139 original size:17 final size:17
Alignment explanation
Indices: 35636119--35636165 Score: 67
Period size: 17 Copynumber: 2.8 Consensus size: 17
35636109 ATCTCTTAAA
*
35636119 AGAGTTCATCAAACCCT
1 AGAGTTCACCAAACCCT
*
35636136 AGAGTTCACCAAACCTT
1 AGAGTTCACCAAACCCT
*
35636153 AGAGTTCGCCAAA
1 AGAGTTCACCAAA
35636166 TGAAAAATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.36, C:0.28, G:0.15, T:0.21
Consensus pattern (17 bp):
AGAGTTCACCAAACCCT
Found at i:35640312 original size:22 final size:23
Alignment explanation
Indices: 35640287--35640337 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 23
35640277 CACGTATATT
*
35640287 TTAAAAT-ATATCAAACATTT-CA
1 TTAAAATGA-ATCAAACATTTGAA
*
35640309 TTAAAATGAGTCAAACATTTGAA
1 TTAAAATGAATCAAACATTTGAA
35640332 TTAAAA
1 TTAAAA
35640338 CCATCAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 17 0.68
23 8 0.32
ACGTcount: A:0.51, C:0.10, G:0.06, T:0.33
Consensus pattern (23 bp):
TTAAAATGAATCAAACATTTGAA
Found at i:35640344 original size:22 final size:21
Alignment explanation
Indices: 35640296--35640345 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 21
35640286 TTTAAAATAT
* **
35640296 ATCAAACATTTCATTAAAATG
1 ATCAAACATTTAATTAAAACC
35640317 AGTCAAACATTTGAATTAAAACC
1 A-TCAAACATTT-AATTAAAACC
35640340 ATCAAA
1 ATCAAA
35640346 ATTGATGGTT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
21 1 0.04
22 15 0.62
23 8 0.33
ACGTcount: A:0.50, C:0.16, G:0.06, T:0.28
Consensus pattern (21 bp):
ATCAAACATTTAATTAAAACC
Found at i:35641977 original size:50 final size:50
Alignment explanation
Indices: 35641922--35642149 Score: 258
Period size: 50 Copynumber: 4.4 Consensus size: 50
35641912 CAATGTCATA
* * * ** * * * *
35641922 TCCCAGATATAGTCTTACATGAGAGTTCTCATATCGGTGCCCATGTCATG
1 TCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATG
* *
35641972 TCCCAGACATGGTCTTACGTGGGACCTCTTATCTCGGTGCCAACGCCATG
1 TCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATG
*
35642022 TCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGGTGCCAACGCCATG
1 TCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATG
* * *
35642072 TCCCAGACATGGTTTTACATAGGACCTCTCATGATCTCAAGGATGCCAATGCCATG
1 TCCCAGACATGGTCTTACATGGGACCTCTC---ATCTC--GG-TGCCAACGCCATG
*
35642128 TCCCAGACATGGTTTTACATGG
1 TCCCAGACATGGTCTTACATGG
35642150 AATCTCTTTA
Statistics
Matches: 153, Mismatches: 19, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
50 114 0.75
53 4 0.03
55 2 0.01
56 33 0.22
ACGTcount: A:0.22, C:0.29, G:0.22, T:0.28
Consensus pattern (50 bp):
TCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATG
Found at i:35644735 original size:28 final size:28
Alignment explanation
Indices: 35644704--35644807 Score: 79
Period size: 28 Copynumber: 3.8 Consensus size: 28
35644694 TAAAAAATAA
*
35644704 AATAAACATACATTACCAAAACTATCTT
1 AATAAACATACACTACCAAAACTATCTT
* ** ** ** *
35644732 AATACACA-ATTCTAATAATTCTA-CTAA
1 AATAAACATACACTACCAAAACTATCT-T
*
35644759 AATAAACATGCACTACCAAAACTATCTT
1 AATAAACATACACTACCAAAACTATCTT
*
35644787 AATAAGCATACACTA-CAAAAC
1 AATAAACATACACTACCAAAAC
35644808 AAACATACAT
Statistics
Matches: 53, Mismatches: 20, Indels: 7
0.66 0.25 0.09
Matches are distributed among these distances:
26 2 0.04
27 21 0.40
28 28 0.53
29 2 0.04
ACGTcount: A:0.50, C:0.22, G:0.02, T:0.26
Consensus pattern (28 bp):
AATAAACATACACTACCAAAACTATCTT
Found at i:35644946 original size:19 final size:19
Alignment explanation
Indices: 35644919--35644955 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
35644909 CTAAAGAAAA
35644919 TTTTAACACAAATCTAAAT
1 TTTTAACACAAATCTAAAT
*
35644938 TTTTGACACAAATCTAAA
1 TTTTAACACAAATCTAAA
35644956 CTAATAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.46, C:0.16, G:0.03, T:0.35
Consensus pattern (19 bp):
TTTTAACACAAATCTAAAT
Found at i:35646495 original size:19 final size:19
Alignment explanation
Indices: 35646471--35646507 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
35646461 TCATTTAAAA
35646471 ATTTTAAAAAATAAAAATC
1 ATTTTAAAAAATAAAAATC
* *
35646490 ATTTTAGAAAATTAAAAT
1 ATTTTAAAAAATAAAAAT
35646508 TATTAAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.59, C:0.03, G:0.03, T:0.35
Consensus pattern (19 bp):
ATTTTAAAAAATAAAAATC
Found at i:35651354 original size:29 final size:30
Alignment explanation
Indices: 35651289--35651354 Score: 89
Period size: 30 Copynumber: 2.2 Consensus size: 30
35651279 TACAAACTCC
*
35651289 ACTTGATTGCATTAATATAAGTAAATTATT
1 ACTTGATTGCATTAATATAAATAAATTATT
** *
35651319 TGTTGATTGTATTAATATAAAT-AATTATT
1 ACTTGATTGCATTAATATAAATAAATTATT
35651348 ACTTGAT
1 ACTTGAT
35651355 AGACGTAATA
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
29 12 0.40
30 18 0.60
ACGTcount: A:0.38, C:0.05, G:0.11, T:0.47
Consensus pattern (30 bp):
ACTTGATTGCATTAATATAAATAAATTATT
Found at i:35653035 original size:18 final size:19
Alignment explanation
Indices: 35653014--35653060 Score: 55
Period size: 18 Copynumber: 2.6 Consensus size: 19
35653004 GTCATTTATA
35653014 AAAATATTTTAATT-CAAT
1 AAAATATTTTAATTACAAT
35653032 AAAA-ATATTTAATTACAAT
1 AAAATAT-TTTAATTACAAT
*
35653051 GAAAT-TTTTA
1 AAAATATTTTA
35653061 TTATTTTTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
17 2 0.08
18 15 0.60
19 8 0.32
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (19 bp):
AAAATATTTTAATTACAAT
Found at i:35653035 original size:19 final size:19
Alignment explanation
Indices: 35653011--35653050 Score: 64
Period size: 19 Copynumber: 2.1 Consensus size: 19
35653001 AAAGTCATTT
35653011 ATAAAAATATTTTAATT-CA
1 ATAAAAATA-TTTAATTACA
35653030 ATAAAAATATTTAATTACA
1 ATAAAAATATTTAATTACA
35653049 AT
1 AT
35653051 GAAATTTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 7 0.35
19 13 0.65
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.40
Consensus pattern (19 bp):
ATAAAAATATTTAATTACA
Found at i:35658108 original size:16 final size:16
Alignment explanation
Indices: 35658087--35658125 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
35658077 AAAACCTACT
35658087 CACCACGTTGGCACAA
1 CACCACGTTGGCACAA
35658103 CACCACGTTGGCACAA
1 CACCACGTTGGCACAA
35658119 CTACCAC
1 C-ACCAC
35658126 TACCAACAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 17 0.77
17 5 0.23
ACGTcount: A:0.31, C:0.41, G:0.15, T:0.13
Consensus pattern (16 bp):
CACCACGTTGGCACAA
Found at i:35661928 original size:267 final size:268
Alignment explanation
Indices: 35661442--35661976 Score: 1063
Period size: 267 Copynumber: 2.0 Consensus size: 268
35661432 AAAAATTATA
35661442 AAAATATTGACTATTAAAATAATAAAATTATATTTTTACTATCGTAAAAATTACAATTCACCTCC
1 AAAATATTGACTATTAAAATAATAAAATTATATTTTTACTATCGTAAAAATTACAATTCACCTCC
35661507 TTAAAATATTTTCCTAATTTCACCCTTGCTAGTAGGGTTCTAACTTCCCTATTGTACCACAATTT
66 TTAAAATATTTTCCTAATTTCACCCTTGCTAGTAGGGTTCTAACTTCCCTATTGTACCACAATTT
35661572 TCAATTTTCAAGTTCAATGACACTACTCATCAGTTTTTTTTTTTTTTTTACTATTGATCGCATCT
131 TCAATTTTCAAGTTCAATGACACTACTCATCAGTTTTTTTTTTTTTTTTACTATTGATCGCATCT
35661637 CAATTTGGTAACTTCACTTTTTGTTTTTTTGGATCATATTCAACTTTAAGGTTCACATTTGTTAT
196 CAATTTGGTAACTTCACTTTTTGTTTTTTTGGATCATATTCAACTTTAAGGTTCACATTTGTTAT
35661702 ATAAATTG
261 ATAAATTG
35661710 AAAATATTGA-TATTAAAATAATAAAATTATATTTTTACTATCGTAAAAATTACAATTCACCTCC
1 AAAATATTGACTATTAAAATAATAAAATTATATTTTTACTATCGTAAAAATTACAATTCACCTCC
35661774 TTAAAATATTTTCCTAATTTCACCCTTGCTAGTAGGGTTCTAACTTCCCTATTGTACCACAATTT
66 TTAAAATATTTTCCTAATTTCACCCTTGCTAGTAGGGTTCTAACTTCCCTATTGTACCACAATTT
35661839 TCAATTTTCAAGTTCAATGACACTACTCATCAGTTTTTTTTTTTTTTTTACTATTGATCGCATCT
131 TCAATTTTCAAGTTCAATGACACTACTCATCAGTTTTTTTTTTTTTTTTACTATTGATCGCATCT
35661904 CAATTTGGTAACTTCACTTTTTGTTTTTTTGGATCATATTCAACTTTAAGGTTCACATTTGTTAT
196 CAATTTGGTAACTTCACTTTTTGTTTTTTTGGATCATATTCAACTTTAAGGTTCACATTTGTTAT
35661969 ATAAATTG
261 ATAAATTG
35661977 GTTCCTCTTA
Statistics
Matches: 267, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
267 257 0.96
268 10 0.04
ACGTcount: A:0.30, C:0.17, G:0.08, T:0.45
Consensus pattern (268 bp):
AAAATATTGACTATTAAAATAATAAAATTATATTTTTACTATCGTAAAAATTACAATTCACCTCC
TTAAAATATTTTCCTAATTTCACCCTTGCTAGTAGGGTTCTAACTTCCCTATTGTACCACAATTT
TCAATTTTCAAGTTCAATGACACTACTCATCAGTTTTTTTTTTTTTTTTACTATTGATCGCATCT
CAATTTGGTAACTTCACTTTTTGTTTTTTTGGATCATATTCAACTTTAAGGTTCACATTTGTTAT
ATAAATTG
Found at i:35662450 original size:9 final size:9
Alignment explanation
Indices: 35662438--35662505 Score: 50
Period size: 9 Copynumber: 7.3 Consensus size: 9
35662428 ATTTAGACTA
35662438 TTTTTATAT
1 TTTTTATAT
35662447 TTTTTATAT
1 TTTTTATAT
35662456 TTCTTT-T-T
1 TT-TTTATAT
*
35662464 TTTTTGTAATT
1 TTTTTAT-A-T
* *
35662475 TTTTTAAAA
1 TTTTTATAT
*
35662484 TTTTAACTAT
1 TTTTTA-TAT
35662494 TTTTTATAT
1 TTTTTATAT
35662503 TTT
1 TTT
35662506 GAAATATACA
Statistics
Matches: 46, Mismatches: 7, Indels: 12
0.71 0.11 0.18
Matches are distributed among these distances:
7 3 0.07
8 4 0.09
9 23 0.50
10 10 0.22
11 6 0.13
ACGTcount: A:0.22, C:0.03, G:0.01, T:0.74
Consensus pattern (9 bp):
TTTTTATAT
Found at i:35663538 original size:23 final size:24
Alignment explanation
Indices: 35663486--35663540 Score: 67
Period size: 25 Copynumber: 2.3 Consensus size: 24
35663476 ATGATATTTT
*
35663486 TTAAAATATATATATTTTTATAAG
1 TTAAAATATATATATTTATATAAG
* *
35663510 TATAAAATATTTATATTTATATCA-
1 T-TAAAATATATATATTTATATAAG
35663534 TTAAAAT
1 TTAAAAT
35663541 TTAAAATTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
23 6 0.22
24 2 0.07
25 19 0.70
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (24 bp):
TTAAAATATATATATTTATATAAG
Found at i:35663777 original size:9 final size:9
Alignment explanation
Indices: 35663763--35663793 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
35663753 GTTAAACGAA
35663763 TCGAGTTAT
1 TCGAGTTAT
*
35663772 TCGAGTTAA
1 TCGAGTTAT
35663781 TCGAGTTAT
1 TCGAGTTAT
35663790 TCGA
1 TCGA
35663794 ATCAAATCGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:35663862 original size:9 final size:9
Alignment explanation
Indices: 35663845--35663881 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
35663835 TGAGTTTTCG
35663845 AATTCGAAT
1 AATTCGAAT
*
35663854 AACTCGAAT
1 AATTCGAAT
35663863 AATTCGAAT
1 AATTCGAAT
35663872 AATTCGAAT
1 AATTCGAAT
35663881 A
1 A
35663882 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:35665488 original size:67 final size:68
Alignment explanation
Indices: 35665374--35665508 Score: 247
Period size: 67 Copynumber: 2.0 Consensus size: 68
35665364 CGGACGAGGG
35665374 ACACCTGGTTTCAGCTGTCACTGTAGAACCTTCAAGAATATAAAGACTGTCGGTCCTTTTACCTT
1 ACACCTGGTTTCAGCTGTCACTGTAGAACCTTCAAGAATATAAAGACTGTCGGTCCTTTTACCTT
35665439 TTA
66 TTA
35665442 ACACC-GGTTTCAG-TGGTCACTGTAGAACCTTCAAGAATATAAAGACTGTCGGTCCTTTTACCT
1 ACACCTGGTTTCAGCT-GTCACTGTAGAACCTTCAAGAATATAAAGACTGTCGGTCCTTTTACCT
35665505 TTTA
65 TTTA
35665509 CCTTTTACTT
Statistics
Matches: 66, Mismatches: 0, Indels: 3
0.96 0.00 0.04
Matches are distributed among these distances:
66 1 0.02
67 60 0.91
68 5 0.08
ACGTcount: A:0.27, C:0.23, G:0.17, T:0.33
Consensus pattern (68 bp):
ACACCTGGTTTCAGCTGTCACTGTAGAACCTTCAAGAATATAAAGACTGTCGGTCCTTTTACCTT
TTA
Found at i:35674897 original size:28 final size:30
Alignment explanation
Indices: 35674866--35674927 Score: 78
Period size: 28 Copynumber: 2.2 Consensus size: 30
35674856 TTCAAAAATT
35674866 AAATAACATA-TTTAAT-ATGTAAAA-ATAA
1 AAATAACATATTTTAATAATG-AAAATATAA
*
35674894 AAAT-ATATATTTTAATAATGAAAATATAA
1 AAATAACATATTTTAATAATGAAAATATAA
35674923 AAATA
1 AAATA
35674928 TGTGGTGCAT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
27 4 0.14
28 14 0.48
29 11 0.38
ACGTcount: A:0.61, C:0.02, G:0.03, T:0.34
Consensus pattern (30 bp):
AAATAACATATTTTAATAATGAAAATATAA
Found at i:35675140 original size:9 final size:9
Alignment explanation
Indices: 35675126--35675156 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
35675116 GTTAAACGAA
35675126 TCGAGTTAT
1 TCGAGTTAT
*
35675135 TCGAGTTAA
1 TCGAGTTAT
35675144 TCGAGTTAT
1 TCGAGTTAT
35675153 TCGA
1 TCGA
35675157 ATCAACTCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:35675227 original size:9 final size:9
Alignment explanation
Indices: 35675210--35675246 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
35675200 TGAGTTTTCG
35675210 AATTCGAAT
1 AATTCGAAT
*
35675219 AACTCGAAT
1 AATTCGAAT
35675228 AATTCGAAT
1 AATTCGAAT
35675237 AATTCGAAT
1 AATTCGAAT
35675246 A
1 A
35675247 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:35698697 original size:44 final size:43
Alignment explanation
Indices: 35698631--35698796 Score: 163
Period size: 44 Copynumber: 3.8 Consensus size: 43
35698621 GGAAATGGTG
35698631 AATCTTATCTCCCTGATGTTACAGTGGAGCAGATTGAAGCTAAA
1 AATCTTATCTCCCTGA-GTTACAGTGGAGCAGATTGAAGCTAAA
* * **
35698675 AATCTTATCTCCATGAGATTACAGCGGAGCAGATTGAAGCTAGT
1 AATCTTATCTCCCTGAG-TTACAGTGGAGCAGATTGAAGCTAAA
* ** **
35698719 AATCCTATCTCCCTGAGGTTACAGTGGAGTGGATT-AAAATAAA
1 AATCTTATCTCCCTGA-GTTACAGTGGAGCAGATTGAAGCTAAA
* * * *
35698762 GGATCTTATCTCTCTGAAGTTACAGTAGAGTAGAT
1 -AATCTTATCTCCCTG-AGTTACAGTGGAGCAGAT
35698797 CGCAGCAGAT
Statistics
Matches: 100, Mismatches: 18, Indels: 8
0.79 0.14 0.06
Matches are distributed among these distances:
43 5 0.05
44 93 0.93
45 2 0.02
ACGTcount: A:0.32, C:0.17, G:0.22, T:0.30
Consensus pattern (43 bp):
AATCTTATCTCCCTGAGTTACAGTGGAGCAGATTGAAGCTAAA
Found at i:35710231 original size:86 final size:85
Alignment explanation
Indices: 35710083--35710251 Score: 230
Period size: 86 Copynumber: 2.0 Consensus size: 85
35710073 TAAGGTCTTT
* * * **
35710083 CCTTTTAGAGTCTTGCCACAAAGCCATCATTTAAGAGGTTCACCGCAAAGGTTTACCCTTCCAGA
1 CCTTCTAGAGTCTTGCCACAAAGCCATCATTTAACAGGTTCACCACAAAGGCCTACCCTTCCAGA
*
35710148 GTTTTGGCACAAAGGTTTAC
66 GTTTTGCCACAAAGGTTTAC
* ** * *
35710168 CCTTCTAGAGTTTTGCCACAAAGGCTGTCCTTTAACAGGTTCACCACAAAGGCCTACCTTTCCAG
1 CCTTCTAGAGTCTTGCCACAAA-GCCATCATTTAACAGGTTCACCACAAAGGCCTACCCTTCCAG
35710233 AGTTTTGCCACAAAGGTTT
65 AGTTTTGCCACAAAGGTTT
35710252 TCCTTTAATA
Statistics
Matches: 72, Mismatches: 11, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
85 20 0.28
86 52 0.72
ACGTcount: A:0.26, C:0.26, G:0.18, T:0.30
Consensus pattern (85 bp):
CCTTCTAGAGTCTTGCCACAAAGCCATCATTTAACAGGTTCACCACAAAGGCCTACCCTTCCAGA
GTTTTGCCACAAAGGTTTAC
Found at i:35710235 original size:57 final size:57
Alignment explanation
Indices: 35710155--35710355 Score: 258
Period size: 57 Copynumber: 3.5 Consensus size: 57
35710145 AGAGTTTTGG
* * * * * *
35710155 CACAAAGGTTTACCCTTCTAGAGTTTTGCCACAAAGGCTGTCCTTTAACAGGTTCAC
1 CACAAAGGCTTACCTTTCCAGAGTTTTGCCACAAAGGTTTTCCTTTAATAGGTTCAC
*
35710212 CACAAAGGCCTACCTTTCCAGAGTTTTGCCACAAAGGTTTTCCTTTAATAGGTTCAC
1 CACAAAGGCTTACCTTTCCAGAGTTTTGCCACAAAGGTTTTCCTTTAATAGGTTCAC
* * ** * **
35710269 TACAAAGACTTACCTTTCTTGAGTTTTTCCACAAAGGTTTTCCTTTAATAGGTTTGC
1 CACAAAGGCTTACCTTTCCAGAGTTTTGCCACAAAGGTTTTCCTTTAATAGGTTCAC
* *
35710326 CACAAAGGCTTACCTTTCCAAAATTTTGCC
1 CACAAAGGCTTACCTTTCCAGAGTTTTGCC
35710356 TAAACTCACA
Statistics
Matches: 122, Mismatches: 22, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
57 122 1.00
ACGTcount: A:0.26, C:0.25, G:0.15, T:0.34
Consensus pattern (57 bp):
CACAAAGGCTTACCTTTCCAGAGTTTTGCCACAAAGGTTTTCCTTTAATAGGTTCAC
Found at i:35710256 original size:29 final size:29
Alignment explanation
Indices: 35710128--35710355 Score: 142
Period size: 29 Copynumber: 8.0 Consensus size: 29
35710118 AGGTTCACCG
* * *
35710128 CAAAGGTTTACCCTTCCAGAGTTTTGGCA
1 CAAAGGCTTACCTTTCCAGAGTTTTGCCA
* * *
35710157 CAAAGGTTTACCCTTCTAGAGTTTTGCCA
1 CAAAGGCTTACCTTTCCAGAGTTTTGCCA
* **
35710186 CAAAGGCTGT-CCTTTAACAG-G-TTCACCA
1 CAAAGGCT-TACCTTT-CCAGAGTTTTGCCA
*
35710214 CAAAGGCCTACCTTTCCAGAGTTTTGCCA
1 CAAAGGCTTACCTTTCCAGAGTTTTGCCA
* * * * * ** *
35710243 CAAAGGTTTTCCTTT-AATAGGTTCACTA
1 CAAAGGCTTACCTTTCCAGAGTTTTGCCA
* ** *
35710271 CAAAGACTTACCTTTCTTGAGTTTTTCCA
1 CAAAGGCTTACCTTTCCAGAGTTTTGCCA
* * * * *
35710300 CAAAGGTTTTCCTTT-AATAGGTTTGCCA
1 CAAAGGCTTACCTTTCCAGAGTTTTGCCA
* *
35710328 CAAAGGCTTACCTTTCCAAAATTTTGCC
1 CAAAGGCTTACCTTTCCAGAGTTTTGCC
35710356 TAAACTCACA
Statistics
Matches: 147, Mismatches: 45, Indels: 14
0.71 0.22 0.07
Matches are distributed among these distances:
27 4 0.03
28 58 0.39
29 82 0.56
30 3 0.02
ACGTcount: A:0.26, C:0.25, G:0.16, T:0.34
Consensus pattern (29 bp):
CAAAGGCTTACCTTTCCAGAGTTTTGCCA
Found at i:35710333 original size:28 final size:28
Alignment explanation
Indices: 35710179--35710342 Score: 123
Period size: 28 Copynumber: 5.8 Consensus size: 28
35710169 CTTCTAGAGT
*
35710179 TTTGCCACAAAGGCTGT-CCTTTAACAGG
1 TTTGCCACAAAGGCT-TACCTTTAATAGG
** * * * *
35710207 TTCACCACAAAGGCCTACCTTTCCAGAGT
1 TTTGCCACAAAGGCTTACCTTT-AATAGG
* *
35710236 TTTGCCACAAAGGTTTTCCTTTAATAGG
1 TTTGCCACAAAGGCTTACCTTTAATAGG
** * * ** *
35710264 TTCACTACAAAGACTTACCTTTCTTGAGT
1 TTTGCCACAAAGGCTTACCTTTAAT-AGG
* * *
35710293 TTTTCCACAAAGGTTTTCCTTTAATAGG
1 TTTGCCACAAAGGCTTACCTTTAATAGG
35710321 TTTGCCACAAAGGCTTACCTTT
1 TTTGCCACAAAGGCTTACCTTT
35710343 CCAAAATTTT
Statistics
Matches: 98, Mismatches: 35, Indels: 6
0.71 0.25 0.04
Matches are distributed among these distances:
27 1 0.01
28 58 0.59
29 39 0.40
ACGTcount: A:0.26, C:0.24, G:0.15, T:0.35
Consensus pattern (28 bp):
TTTGCCACAAAGGCTTACCTTTAATAGG
Found at i:35713154 original size:5 final size:5
Alignment explanation
Indices: 35713144--35713196 Score: 58
Period size: 5 Copynumber: 10.6 Consensus size: 5
35713134 ATGAAGTAAA
35713144 AAAAG AAAAG AAAAG AAAAG AAAAG -AAAG AAACA- AAACA- AAGAAG
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAA-AG AAA-AG AA-AAG
35713189 AAAAG AAA
1 AAAAG AAA
35713197 CAGAGAGCAA
Statistics
Matches: 44, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
4 4 0.09
5 36 0.82
6 4 0.09
ACGTcount: A:0.79, C:0.04, G:0.17, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:35713245 original size:11 final size:11
Alignment explanation
Indices: 35713219--35713253 Score: 52
Period size: 12 Copynumber: 3.0 Consensus size: 11
35713209 CGAAATAGGG
35713219 GAAAAGAAAGAA
1 GAAAAGAAA-AA
35713231 GAAAAGAAAAA
1 GAAAAGAAAAA
35713242 GAAAAGGAAAAA
1 GAAAA-GAAAAA
35713254 CTAGGGTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 7 0.32
12 15 0.68
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (11 bp):
GAAAAGAAAAA
Found at i:35721075 original size:20 final size:20
Alignment explanation
Indices: 35721026--35721064 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
35721016 TGGAGCAGGA
*
35721026 ATATCGATACCTTAGGAAAT
1 ATATCGATACCTTAAGAAAT
35721046 ATATCGATACCTTAAGAAA
1 ATATCGATACCTTAAGAAA
35721065 AGTATTGATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.44, C:0.15, G:0.13, T:0.28
Consensus pattern (20 bp):
ATATCGATACCTTAAGAAAT
Found at i:35723066 original size:6 final size:6
Alignment explanation
Indices: 35723055--35723105 Score: 50
Period size: 6 Copynumber: 8.3 Consensus size: 6
35723045 AATTAAATAA
* * *
35723055 AATATT AATATT AATATT AA-ATA AAAATAA ATATATT AATATT AATATT
1 AATATT AATATT AATATT AATATT AATAT-T A-ATATT AATATT AATATT
35723104 AA
1 AA
35723106 ATAAAAAAGT
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
5 4 0.10
6 29 0.74
7 3 0.08
8 3 0.08
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (6 bp):
AATATT
Found at i:35723090 original size:25 final size:24
Alignment explanation
Indices: 35723046--35723109 Score: 76
Period size: 25 Copynumber: 2.6 Consensus size: 24
35723036 ATTTAATTTA
*
35723046 ATTAAATAAAATATTAATATTAAT
1 ATTAAATAAAATAATAATATTAAT
35723070 ATTAAATAAAAATAA-ATATATTAAT
1 ATTAAAT-AAAATAATA-ATATTAAT
*
35723095 ATTAATATTAAATAA
1 ATTAA-ATAAAATAA
35723110 AAAAGTGGTA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
24 8 0.23
25 25 0.71
26 2 0.06
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (24 bp):
ATTAAATAAAATAATAATATTAAT
Found at i:35723094 original size:31 final size:30
Alignment explanation
Indices: 35723049--35723112 Score: 119
Period size: 31 Copynumber: 2.1 Consensus size: 30
35723039 TAATTTAATT
35723049 AAATAAAATATTAATATTAATATTAAATAA
1 AAATAAAATATTAATATTAATATTAAATAA
35723079 AAATAAATATATTAATATTAATATTAAATAA
1 AAATAAA-ATATTAATATTAATATTAAATAA
35723110 AAA
1 AAA
35723113 AGTGGTAAAG
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 7 0.21
31 26 0.79
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (30 bp):
AAATAAAATATTAATATTAATATTAAATAA
Found at i:35729618 original size:31 final size:31
Alignment explanation
Indices: 35729543--35729618 Score: 89
Period size: 31 Copynumber: 2.5 Consensus size: 31
35729533 GATATGAAAT
* *
35729543 ATTACAGGGTATGAAAATGAAAATGTGAATC
1 ATTACAGGGTGTGAAAATGAAAACGTGAATC
* * * * *
35729574 ATTATAGGATGTGAAAATGCAAACGTGACTG
1 ATTACAGGGTGTGAAAATGAAAACGTGAATC
35729605 ATTACAGGGTGTGA
1 ATTACAGGGTGTGA
35729619 TATGTAGATG
Statistics
Matches: 36, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.39, C:0.08, G:0.26, T:0.26
Consensus pattern (31 bp):
ATTACAGGGTGTGAAAATGAAAACGTGAATC
Found at i:35730134 original size:183 final size:185
Alignment explanation
Indices: 35729808--35730168 Score: 474
Period size: 183 Copynumber: 2.0 Consensus size: 185
35729798 GACAGGTTAA
* * * **
35729808 ATCAAGATCTAGCATTTTTTTTGCAGATCATCGAGTATTATTTGTCTCTATGGAGACTTTTTTTG
1 ATCAAGATCTAGCA-TTTTGTTGCAGATCATCGAGTACTATTTGTCTCTATGAAGACTTTTGGTG
* * * * *
35729873 TGGTGGAGGGATGTAATTGAAAATTTTTAAACATTTGATGTCTACGGGTTTTACACTTAGATACC
65 TAGTAGAGGGATGTAATTGAAAATGTTTAAACATTTGATGTCTACAGGCTTTACACTTAGATACC
* * *
35729938 TTGGTGCGGTGTAGTTTAAGCTCGTACGAGTTATTTAGTATGGTGTAGTGGAGGAT
130 TTGGTACGGTGTAGTTTAAGCTCATACGAGCTATTTAGTATGGTGTAGTGGAGGAT
*
35729994 ATCAAGATCTAGCA-TTTGTTGCGGATCATCGAGTACTATTTGTCTCTATGAAGAC-TTTGGTGT
1 ATCAAGATCTAGCATTTTGTTGCAGATCATCGAGTACTATTTGTCTCTATGAAGACTTTTGGTGT
* * * * * * *
35730057 AGTAGAGGGGTTTAATTGAAAATGTTTAAATATTTGATGTCTACAGGCTTTACATTTTGGTGCCT
66 AGTAGAGGGATGTAATTGAAAATGTTTAAACATTTGATGTCTACAGGCTTTACACTTAGATACCT
* * * *
35730122 TGGTATGGTGTAGTTTACGCTCATACGAGCTATTTGGTGTGGTGTAG
131 TGGTACGGTGTAGTTTAAGCTCATACGAGCTATTTAGTATGGTGTAG
35730169 CTCACCCATG
Statistics
Matches: 150, Mismatches: 25, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
183 99 0.66
184 37 0.25
186 14 0.09
ACGTcount: A:0.24, C:0.11, G:0.25, T:0.40
Consensus pattern (185 bp):
ATCAAGATCTAGCATTTTGTTGCAGATCATCGAGTACTATTTGTCTCTATGAAGACTTTTGGTGT
AGTAGAGGGATGTAATTGAAAATGTTTAAACATTTGATGTCTACAGGCTTTACACTTAGATACCT
TGGTACGGTGTAGTTTAAGCTCATACGAGCTATTTAGTATGGTGTAGTGGAGGAT
Found at i:35758846 original size:27 final size:27
Alignment explanation
Indices: 35758816--35758883 Score: 91
Period size: 27 Copynumber: 2.5 Consensus size: 27
35758806 TATAGAGTAA
* *
35758816 GCCACCAAGGCATTCCATTCAGAATTT
1 GCCACAAAGGAATTCCATTCAGAATTT
* * *
35758843 GCCACAAAGGAATTCCTTTTAGAGTTT
1 GCCACAAAGGAATTCCATTCAGAATTT
35758870 GCCACAAAGGAATT
1 GCCACAAAGGAATT
35758884 TCTTAACTAT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.32, C:0.24, G:0.18, T:0.26
Consensus pattern (27 bp):
GCCACAAAGGAATTCCATTCAGAATTT
Found at i:35767024 original size:66 final size:66
Alignment explanation
Indices: 35766943--35767071 Score: 231
Period size: 66 Copynumber: 2.0 Consensus size: 66
35766933 GGAATGTCGA
* *
35766943 AGTTTTGTTATGTTGGTGTATAGTATTCGCCTATGTGACACACCTTTGGCATATTGAGTTTGTTA
1 AGTTTTGTTATGTTGGTGTATAGTATTCGCCCATGTGACACACCATTGGCATATTGAGTTTGTTA
35767008 G
66 G
*
35767009 AGTTTTGTTATGTTGGTGTATAGTATTTGCCCATGTGACACACCATTGGCATATTGAGTTTGT
1 AGTTTTGTTATGTTGGTGTATAGTATTCGCCCATGTGACACACCATTGGCATATTGAGTTTGT
35767072 CTCAGTTTTG
Statistics
Matches: 60, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
66 60 1.00
ACGTcount: A:0.20, C:0.12, G:0.24, T:0.43
Consensus pattern (66 bp):
AGTTTTGTTATGTTGGTGTATAGTATTCGCCCATGTGACACACCATTGGCATATTGAGTTTGTTA
G
Found at i:35767079 original size:66 final size:66
Alignment explanation
Indices: 35766943--35767087 Score: 229
Period size: 66 Copynumber: 2.2 Consensus size: 66
35766933 GGAATGTCGA
* *
35766943 AGTTTTGTTATGTTGGTGTATAGTATTCGCCTATGTGACACACCTTTGGCATATTGAGTTTGTTA
1 AGTTTTGTTATGTTGGTGTATAGTATTCGCCCATGTGACACACCATTGGCATATTGAGTTTGTTA
*
35767008 G
66 C
*
35767009 AGTTTTGTTATGTTGGTGTATAGTATTTGCCCATGTGACACACCATTGGCATATTGAGTTTGTCT
1 AGTTTTGTTATGTTGGTGTATAGTATTCGCCCATGTGACACACCATTGGCATATTGAGTTTGT-T
35767074 -C
65 AC
35767075 AGTTTTGTATATG
1 AGTTTTGT-TATG
35767088 CCATTGGGCA
Statistics
Matches: 73, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
66 68 0.93
67 5 0.07
ACGTcount: A:0.20, C:0.12, G:0.23, T:0.44
Consensus pattern (66 bp):
AGTTTTGTTATGTTGGTGTATAGTATTCGCCCATGTGACACACCATTGGCATATTGAGTTTGTTA
C
Found at i:35768832 original size:159 final size:159
Alignment explanation
Indices: 35768543--35768861 Score: 602
Period size: 159 Copynumber: 2.0 Consensus size: 159
35768533 CGGTAAGATT
*
35768543 TCGGGGACGAAAATCCCTGAGGGGGGAGAATTGTCACAGCCCGATTCTGGGCCTAGTCGGAACAG
1 TCGGGGACGAAAATCCCTGAGGGGGGAGAATTGTAACAGCCCGATTCTGGGCCTAGTCGGAACAG
*
35768608 TGGTTTTGGGAACACAAATCTGACAAGGGAAAATATGACTATTATTATATTTTTATGGTCTACAA
66 TGGTTTCGGGAACACAAATCTGACAAGGGAAAATATGACTATTATTATATTTTTATGGTCTACAA
35768673 TTTTAGGGAAAAATTTCGTAAAAATTTCG
131 TTTTAGGGAAAAATTTCGTAAAAATTTCG
*
35768702 TCGGGGACGAAAATCCCTGAGGGGGGAGAATTGTAACCGCCCGATTCTGGGCCTAGTCGGAACAG
1 TCGGGGACGAAAATCCCTGAGGGGGGAGAATTGTAACAGCCCGATTCTGGGCCTAGTCGGAACAG
*
35768767 TGGTTTCGGGACCACAAATCTGACAAGGGAAAATATGACTATTATTATATTTTTATGGTCTACAA
66 TGGTTTCGGGAACACAAATCTGACAAGGGAAAATATGACTATTATTATATTTTTATGGTCTACAA
35768832 TTTTAGGGAAAAATTTCGTAAAAATTTCG
131 TTTTAGGGAAAAATTTCGTAAAAATTTCG
35768861 T
1 T
35768862 TCAAAAATTT
Statistics
Matches: 156, Mismatches: 4, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
159 156 1.00
ACGTcount: A:0.31, C:0.16, G:0.25, T:0.28
Consensus pattern (159 bp):
TCGGGGACGAAAATCCCTGAGGGGGGAGAATTGTAACAGCCCGATTCTGGGCCTAGTCGGAACAG
TGGTTTCGGGAACACAAATCTGACAAGGGAAAATATGACTATTATTATATTTTTATGGTCTACAA
TTTTAGGGAAAAATTTCGTAAAAATTTCG
Found at i:35768856 original size:11 final size:13
Alignment explanation
Indices: 35768840--35768873 Score: 54
Period size: 11 Copynumber: 2.8 Consensus size: 13
35768830 AATTTTAGGG
35768840 AAAAATTTCG-T-
1 AAAAATTTCGTTC
35768851 AAAAATTTCGTTC
1 AAAAATTTCGTTC
35768864 AAAAATTTCG
1 AAAAATTTCG
35768874 ACGTTTGGGC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 10 0.48
12 1 0.05
13 10 0.48
ACGTcount: A:0.44, C:0.12, G:0.09, T:0.35
Consensus pattern (13 bp):
AAAAATTTCGTTC
Found at i:35769888 original size:103 final size:103
Alignment explanation
Indices: 35769706--35769908 Score: 370
Period size: 103 Copynumber: 2.0 Consensus size: 103
35769696 ATTGAATATG
35769706 AAGGGGTTGCTAAGTGCTGATTCCCCGACTCATTAGTGGTTGCTAAGTGCTGATTCCACCGTATC
1 AAGGGGTTGCTAAGTGCTGATTCCCCGACTCATTAGTGGTTGCTAAGTGCTGATTCCACCGTATC
35769771 TTTAAATATAAAGGGGGTTGCTAAGTGCTGATTCCCCC
66 TTTAAATATAAAGGGGGTTGCTAAGTGCTGATTCCCCC
* *
35769809 AAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
1 AAGGGGTTGCTAAGTGCTGATTCCCCGACTCATTAGTGGTTGCTAAGTGCTGATTCCACCGTATC
* *
35769874 TTTAAATTTGAAGGGGGTTGCTAAGTGCTGATTCC
66 TTTAAATATAAAGGGGGTTGCTAAGTGCTGATTCC
35769909 TCGAATGATT
Statistics
Matches: 96, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 96 1.00
ACGTcount: A:0.21, C:0.20, G:0.27, T:0.33
Consensus pattern (103 bp):
AAGGGGTTGCTAAGTGCTGATTCCCCGACTCATTAGTGGTTGCTAAGTGCTGATTCCACCGTATC
TTTAAATATAAAGGGGGTTGCTAAGTGCTGATTCCCCC
Found at i:35769902 original size:76 final size:76
Alignment explanation
Indices: 35769811--35770062 Score: 405
Period size: 76 Copynumber: 3.3 Consensus size: 76
35769801 ATTCCCCCAA
35769811 GGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATCTT
1 GGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATCTT
*
35769876 TAAATTTGAAG
66 TAAATATGAAG
* * * * * *
35769887 GGGGTTGCTAAGTGCTGATTCCTCGAATGATTGGTGGTTGCTACGTGTTGATTCCACCATATCTT
1 GGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATCTT
* * *
35769952 TGAATGTGAAA
66 TAAATATGAAG
35769963 GGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATCTT
1 GGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATCTT
*
35770028 TAAATATAAAG
66 TAAATATGAAG
35770039 GGGGTTGCTAAGTGCTGATTCCCC
1 GGGGTTGCTAAGTGCTGATTCCCC
35770063 CAAGGGGTTG
Statistics
Matches: 157, Mismatches: 19, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
76 157 1.00
ACGTcount: A:0.20, C:0.18, G:0.27, T:0.35
Consensus pattern (76 bp):
GGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATCTT
TAAATATGAAG
Found at i:35769907 original size:43 final size:41
Alignment explanation
Indices: 35769846--35770060 Score: 156
Period size: 43 Copynumber: 5.5 Consensus size: 41
35769836 ATTCATTGGT
35769846 GGTTGCTAAGTGCTGATTCCACCGTATCTTTAAATTTGAAGGG
1 GGTTGCTAAGTGCTGATTCCACCGTATCTTT-AATTT-AAGGG
* * * *
35769889 GGTTGCTAAGTGCTGATTCC-TCG-A---ATGA-TT--GGT
1 GGTTGCTAAGTGCTGATTCCACCGTATCTTTAATTTAAGGG
* * * * *
35769922 GGTTGCTACGTGTTGATTCCACCATATCTTTGAATGTGAAAGG
1 GGTTGCTAAGTGCTGATTCCACCGTATCTTT-AAT-TTAAGGG
* *
35769965 GGTTGCTAAGTGCTGATTCC-CCG-A---TTCA-TT--GGT
1 GGTTGCTAAGTGCTGATTCCACCGTATCTTTAATTTAAGGG
*
35769998 GGTTGCTAAGTGCTGATTCCACCGTATCTTTAAATATAAAGGG
1 GGTTGCTAAGTGCTGATTCCACCGTATCTTT-AAT-TTAAGGG
35770041 GGTTGCTAAGTGCTGATTCC
1 GGTTGCTAAGTGCTGATTCC
35770061 CCCAAGGGGT
Statistics
Matches: 129, Mismatches: 23, Indels: 40
0.67 0.12 0.21
Matches are distributed among these distances:
33 41 0.32
34 4 0.03
35 3 0.02
36 2 0.02
37 2 0.02
38 6 0.05
39 2 0.02
41 4 0.03
42 4 0.03
43 61 0.47
ACGTcount: A:0.21, C:0.17, G:0.27, T:0.35
Consensus pattern (41 bp):
GGTTGCTAAGTGCTGATTCCACCGTATCTTTAATTTAAGGG
Found at i:35783670 original size:29 final size:29
Alignment explanation
Indices: 35783635--35783701 Score: 116
Period size: 29 Copynumber: 2.3 Consensus size: 29
35783625 ATTTTGCTTC
35783635 AATAAAAAATATATGTAGTGTATTTTAAA
1 AATAAAAAATATATGTAGTGTATTTTAAA
* *
35783664 CATAAAAAATATCTGTAGTGTATTTTAAA
1 AATAAAAAATATATGTAGTGTATTTTAAA
35783693 AATAAAAAA
1 AATAAAAAA
35783702 AAATTAATCT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.54, C:0.03, G:0.09, T:0.34
Consensus pattern (29 bp):
AATAAAAAATATATGTAGTGTATTTTAAA
Found at i:35783819 original size:21 final size:21
Alignment explanation
Indices: 35783795--35783847 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
35783785 CATTGTTTCT
*
35783795 AATCTCACCGCTACAGTATCC
1 AATCTCACCGCTACAGTAACC
*
35783816 AATCTCACCGCTACAGTAACT
1 AATCTCACCGCTACAGTAACC
35783837 AATCTCACCGC
1 AATCTCACCGC
35783848 CACCGCTGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.30, C:0.38, G:0.09, T:0.23
Consensus pattern (21 bp):
AATCTCACCGCTACAGTAACC
Found at i:35790271 original size:67 final size:65
Alignment explanation
Indices: 35790089--35790301 Score: 216
Period size: 68 Copynumber: 3.2 Consensus size: 65
35790079 AGGAGGTTTA
* * * *
35790089 AGGTGTAAGACCATAGCTTGATTATGACAATTAATATAGTCTGCCAGGACATTAAACATGGGGTT
1 AGGTGTAAGACCATAGCTCGA-TATGACAA-CAATAGATTCTGCCAGGACATTAAACATGGGGTT
*
35790154 AT
64 AC
* *
35790156 A-ATAAGTAAGACCATAGCTCGGATATGACAAC-ATAGGGAGTT-TGCCAGGATATTAAACATGG
1 AGGT--GTAAGACCATAGCTC-GATATGACAACAATA--GA-TTCTGCCAGGACATTAAACATGG
35790218 GGTTAC
60 GGTTAC
* *
35790224 AGGTGTAAGACCATATCTCGACTATGATAACCAATAGATTCTGCCAGGACATTAAACATGGGGGT
1 AGGTGTAAGACCATAGCTCGA-TATGACAA-CAATAGATTCTGCCAGGACATTAAACAT-GGGGT
35790289 TAC
63 TAC
*
35790292 AAGTGTAAGA
1 AGGTGTAAGA
35790302 ATATAGCTTG
Statistics
Matches: 122, Mismatches: 12, Indels: 23
0.78 0.08 0.15
Matches are distributed among these distances:
66 8 0.07
67 41 0.34
68 66 0.54
69 7 0.06
ACGTcount: A:0.36, C:0.15, G:0.23, T:0.26
Consensus pattern (65 bp):
AGGTGTAAGACCATAGCTCGATATGACAACAATAGATTCTGCCAGGACATTAAACATGGGGTTAC
Found at i:35790344 original size:68 final size:67
Alignment explanation
Indices: 35790091--35790369 Score: 178
Period size: 68 Copynumber: 4.1 Consensus size: 67
35790081 GAGGTTTAAG
* * * * ** * * * *
35790091 GTGTAAGACCATAGCTTGATTATGACAATTAATATAGTCTGCCAGGACATTAAACATGGGGTTAT
1 GTGTAAGAACATAGCTCGACTATGATAACCAATAAATTCTGCCAGAACATTAAACATGGGGTTAC
35790156 AA
66 AA
* * * * *
35790158 -TAAGTAAGACCATAGCTCGGA-TATGACAA-C-ATAGGGAGTT-TGCCAGGATATTAAACATGG
1 GT--GTAAGAACATAGCTC-GACTATGATAACCAATA---AATTCTGCCAGAACATTAAACATGG
*
35790218 GGTTACAG
60 GGTTACAA
* * * *
35790226 GTGTAAGACCATATCTCGACTATGATAACCAATAGATTCTGCCAGGACATTAAACATGGGGGTTA
1 GTGTAAGAACATAGCTCGACTATGATAACCAATAAATTCTGCCAGAACATTAAACAT-GGGGTTA
35790291 CAA
65 CAA
* * * * *
35790294 GTGTAAGAATATAGCTTGACTATGGA-AACTAATAAAGTT-TGTCCA-AACATTAAACATGAGAT
1 GTGTAAGAACATAGCTCGACTAT-GATAACCAATAAA-TTCTG-CCAGAACATTAAACATGGGGT
35790356 TACAA
63 TACAA
35790361 TGTGTAAGA
1 -GTGTAAGA
35790370 CTATGGATCG
Statistics
Matches: 173, Mismatches: 23, Indels: 31
0.76 0.10 0.14
Matches are distributed among these distances:
66 8 0.05
67 46 0.27
68 105 0.61
69 14 0.08
ACGTcount: A:0.37, C:0.14, G:0.22, T:0.27
Consensus pattern (67 bp):
GTGTAAGAACATAGCTCGACTATGATAACCAATAAATTCTGCCAGAACATTAAACATGGGGTTAC
AA
Found at i:35793037 original size:12 final size:13
Alignment explanation
Indices: 35793020--35793055 Score: 56
Period size: 14 Copynumber: 2.8 Consensus size: 13
35793010 CGAAAGAAGG
35793020 AAAAATGGAAA-A
1 AAAAATGGAAATA
35793032 AAAAATGGAGAATA
1 AAAAATGGA-AATA
35793046 AAAAATGGAA
1 AAAAATGGAA
35793056 GCAACTTATG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 9 0.41
13 3 0.14
14 10 0.45
ACGTcount: A:0.69, C:0.00, G:0.19, T:0.11
Consensus pattern (13 bp):
AAAAATGGAAATA
Found at i:35795369 original size:43 final size:43
Alignment explanation
Indices: 35795287--35795401 Score: 128
Period size: 43 Copynumber: 2.7 Consensus size: 43
35795277 TTTTCGGAAA
**
35795287 GTGTTTTTGTGTAAGACCACGTCTGGGACGTTGGTATCGA-CTT
1 GTGTTTTTGTGTAAGACCACGTCTGGGACGTTGACATCGATC-T
35795330 GTGTTTTTGTGTAAGACC-CTGTCTGGGACAG-TGACATCGATCT
1 GTGTTTTTGTGTAAGACCAC-GTCTGGGAC-GTTGACATCGATCT
*** *
35795373 GTGTTTACATGTAAGACCACGTCTAGGAC
1 GTGTTTTTGTGTAAGACCACGTCTGGGAC
35795402 ATTGGCATTG
Statistics
Matches: 62, Mismatches: 6, Indels: 8
0.82 0.08 0.11
Matches are distributed among these distances:
42 1 0.02
43 58 0.94
44 3 0.05
ACGTcount: A:0.20, C:0.18, G:0.28, T:0.34
Consensus pattern (43 bp):
GTGTTTTTGTGTAAGACCACGTCTGGGACGTTGACATCGATCT
Found at i:35795627 original size:28 final size:29
Alignment explanation
Indices: 35795586--35795642 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 29
35795576 TTAAATTATA
35795586 AATGTGAACTATGTGTATACATATGTGGT
1 AATGTGAACTATGTGTATACATATGTGGT
* * *
35795615 AATGT-AATTATGTGTATGCATATTTGGT
1 AATGTGAACTATGTGTATACATATGTGGT
35795643 GATGCATAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
28 20 0.80
29 5 0.20
ACGTcount: A:0.30, C:0.05, G:0.23, T:0.42
Consensus pattern (29 bp):
AATGTGAACTATGTGTATACATATGTGGT
Found at i:35798876 original size:40 final size:40
Alignment explanation
Indices: 35798755--35798894 Score: 137
Period size: 40 Copynumber: 3.5 Consensus size: 40
35798745 GACTTTGAGT
* *
35798755 CGATGAGACACTGGGTGTCAAATTATTACTTCGGATTTATT
1 CGATGAGACACTAGGTGTCAAATTATTACTTC-GATTTATC
** * * * *
35798796 CGATGAGGTAGTAGGTG-CCAA-T-TTACTTCGGTTTAGC
1 CGATGAGACACTAGGTGTCAAATTATTACTTCGATTTATC
*
35798833 CGATGAGACACTAGGTGTCAAATTATTACTTCGAATTATC
1 CGATGAGACACTAGGTGTCAAATTATTACTTCGATTTATC
35798873 CGATGATG-CACT-GGCTGTCAAA
1 CGATGA-GACACTAGG-TGTCAAA
35798895 CTGGTGTGTT
Statistics
Matches: 79, Mismatches: 15, Indels: 11
0.75 0.14 0.10
Matches are distributed among these distances:
37 19 0.24
38 10 0.13
39 4 0.05
40 32 0.41
41 14 0.18
ACGTcount: A:0.27, C:0.17, G:0.24, T:0.32
Consensus pattern (40 bp):
CGATGAGACACTAGGTGTCAAATTATTACTTCGATTTATC
Found at i:35802449 original size:24 final size:26
Alignment explanation
Indices: 35802422--35802473 Score: 72
Period size: 25 Copynumber: 2.1 Consensus size: 26
35802412 CTCGTTAAGT
35802422 GCTCTTTG-GAGCTACCCGATA-TAA
1 GCTCTTTGTGAGCTACCCGATATTAA
* *
35802446 GCTCTTTGTGAGCTTCCCGTTATTAA
1 GCTCTTTGTGAGCTACCCGATATTAA
35802472 GC
1 GC
35802474 CCAGATAAGC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 8 0.33
25 11 0.46
26 5 0.21
ACGTcount: A:0.19, C:0.25, G:0.21, T:0.35
Consensus pattern (26 bp):
GCTCTTTGTGAGCTACCCGATATTAA
Found at i:35807157 original size:98 final size:99
Alignment explanation
Indices: 35807019--35807218 Score: 393
Period size: 98 Copynumber: 2.0 Consensus size: 99
35807009 TTATAATATT
35807019 ATATAATATTAACACTTAATGTTTAAGTATATATATTATATATTATATTATAATATAAAACAAAG
1 ATATAATATTAACACTTAATGTTTAAGTATATATATTATATATTATATTATAATATAAAACAAAG
35807084 AAATAAAAGAAAAAGAAATAGTAAAAGAAACAAG
66 AAATAAAAGAAAAAGAAATAGTAAAAGAAACAAG
35807118 ATATAATATT-ACACTTAATGTTTAAGTATATATATTATATATTATATTATAATATAAAACAAAG
1 ATATAATATTAACACTTAATGTTTAAGTATATATATTATATATTATATTATAATATAAAACAAAG
35807182 AAATAAAAGAAAAAGAAATAGTAAAAGAAACAAG
66 AAATAAAAGAAAAAGAAATAGTAAAAGAAACAAG
35807216 ATA
1 ATA
35807219 GAAACGAAAC
Statistics
Matches: 101, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
98 91 0.90
99 10 0.10
ACGTcount: A:0.57, C:0.04, G:0.08, T:0.30
Consensus pattern (99 bp):
ATATAATATTAACACTTAATGTTTAAGTATATATATTATATATTATATTATAATATAAAACAAAG
AAATAAAAGAAAAAGAAATAGTAAAAGAAACAAG
Found at i:35809422 original size:26 final size:26
Alignment explanation
Indices: 35809387--35809444 Score: 75
Period size: 29 Copynumber: 2.2 Consensus size: 26
35809377 TTCAGTAGAA
35809387 ATAAAATTTTA-A-TTATTATTTAATT
1 ATAAAATTTTATAGTTATTATTTAA-T
35809412 ATAACAATTTTATATGTTATTATTTAAT
1 ATAA-AATTTTATA-GTTATTATTTAAT
35809440 ATAAA
1 ATAAA
35809445 TCTAATACAA
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
25 4 0.14
26 7 0.24
27 2 0.07
28 5 0.17
29 11 0.38
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (26 bp):
ATAAAATTTTATAGTTATTATTTAAT
Found at i:35809919 original size:14 final size:13
Alignment explanation
Indices: 35809900--35809929 Score: 51
Period size: 14 Copynumber: 2.2 Consensus size: 13
35809890 TTCAAAACTT
35809900 AATTTTTTAAAATA
1 AATTTTTTAAAA-A
35809914 AATTTTTTAAAAA
1 AATTTTTTAAAAA
35809927 AAT
1 AAT
35809930 AAACTTTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.25
14 12 0.75
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (13 bp):
AATTTTTTAAAAA
Done.