Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D04
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: 52479919
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Warning! 336953 characters in sequence are not A, C, G, or T
File 91 of 173
Found at i:28538559 original size:79 final size:77
Alignment explanation
Indices: 28538421--28538637 Score: 267
Period size: 79 Copynumber: 2.7 Consensus size: 77
28538411 ATACAATCAG
* * * * *
28538421 GGGCACATATGTTCATTCAAAGGTACCGAAGTACAAATAGGGGCATGTATGTGCATTCAGGGGTA
1 GGGCACATATGTGCATTC-AGGGTA-CAAAGTACAAATAGGGGCACGTATGTGCATTCAGGAGTA
28538486 -CTAAAGTACAAATA
64 TC-AAAGTACAAATA
* *
28538500 GGGACACATATGTGCATTCAGGGTATCAAAGTACAAATAGCGGCACGTATGTGAATTCAGGAGTA
1 GGG-CACATATGTGCATTCAGGGTA-CAAAGTACAAATAGGGGCACGTATGTGCATTCAGGAGTA
28538565 TCAAAGTACAAATA
64 TCAAAGTACAAATA
* *
28538579 CGGGCA-AGTATGTGCATTTAGGGGTACCAAGTACAAATAGGGGCACGTATGTGCATTCA
1 -GGGCACA-TATGTGCATTCA-GGGTACAAAGTACAAATAGGGGCACGTATGTGCATTCA
28538638 CTCAATAATT
Statistics
Matches: 121, Mismatches: 12, Indels: 10
0.85 0.08 0.07
Matches are distributed among these distances:
78 1 0.01
79 97 0.80
80 23 0.19
ACGTcount: A:0.35, C:0.16, G:0.26, T:0.24
Consensus pattern (77 bp):
GGGCACATATGTGCATTCAGGGTACAAAGTACAAATAGGGGCACGTATGTGCATTCAGGAGTATC
AAAGTACAAATA
Found at i:28539049 original size:21 final size:20
Alignment explanation
Indices: 28539023--28539063 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
28539013 CAATATATTC
28539023 TAAATTCAACACATTTACCCA
1 TAAATTCAA-ACATTTACCCA
* *
28539044 TAAATTCTAGCATTTACCCA
1 TAAATTCAAACATTTACCCA
28539064 ATTTAACCCA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.39, C:0.27, G:0.02, T:0.32
Consensus pattern (20 bp):
TAAATTCAAACATTTACCCA
Found at i:28544949 original size:21 final size:20
Alignment explanation
Indices: 28544899--28544949 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 20
28544889 GTTAAGTTTT
*
28544899 GTTAAATTTTAATTTATTTA
1 GTTAAATTTTAATTAATTTA
**
28544919 GTTATGTTTTCAATTAATTTA
1 GTTAAATTTT-AATTAATTTA
*
28544940 TTTAAATTTT
1 GTTAAATTTT
28544950 TGAAATCCCC
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
20 8 0.33
21 16 0.67
ACGTcount: A:0.31, C:0.02, G:0.06, T:0.61
Consensus pattern (20 bp):
GTTAAATTTTAATTAATTTA
Found at i:28545672 original size:21 final size:21
Alignment explanation
Indices: 28545648--28545687 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
28545638 GCCACATGGT
28545648 CATG-TCCTTCAGGCACACGGG
1 CATGTTCCTT-AGGCACACGGG
*
28545669 CATGTTCCTTAGTCACACG
1 CATGTTCCTTAGGCACACG
28545688 AGCGTGTGCT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.20, C:0.33, G:0.23, T:0.25
Consensus pattern (21 bp):
CATGTTCCTTAGGCACACGGG
Found at i:28545714 original size:21 final size:22
Alignment explanation
Indices: 28545677--28545732 Score: 64
Period size: 21 Copynumber: 2.6 Consensus size: 22
28545667 GGCATGTTCC
28545677 TTAGTCACACGAG-CGTGT-GCT
1 TTAGTCACACG-GTCGTGTAGCT
*
28545698 TTAGTCACACGGTCGTGTATCT
1 TTAGTCACACGGTCGTGTAGCT
*
28545720 CT-GTCACACGGTC
1 TTAGTCACACGGTC
28545733 TTGATCTTCT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 1 0.03
21 27 0.87
22 3 0.10
ACGTcount: A:0.18, C:0.27, G:0.25, T:0.30
Consensus pattern (22 bp):
TTAGTCACACGGTCGTGTAGCT
Found at i:28545747 original size:19 final size:21
Alignment explanation
Indices: 28545702--28545748 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
28545692 TGTGCTTTAG
*
28545702 TCACACGGTCGTGTATCTCTG
1 TCACACGGTCGTGTATCTCTC
*
28545723 TCACACGGTCTTG-ATCT-TC
1 TCACACGGTCGTGTATCTCTC
28545742 TCACACG
1 TCACACG
28545749 CCCTGGCCAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 8 0.33
20 4 0.17
21 12 0.50
ACGTcount: A:0.17, C:0.32, G:0.19, T:0.32
Consensus pattern (21 bp):
TCACACGGTCGTGTATCTCTC
Found at i:28545873 original size:19 final size:20
Alignment explanation
Indices: 28545836--28545880 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
28545826 AGCAATACTC
28545836 TACATGTTTAACCTGTTATA
1 TACATGTTTAACCTGTTATA
*
28545856 TACATGTTTAA-GTGTTATA
1 TACATGTTTAACCTGTTATA
28545875 TA-ATGT
1 TACATGT
28545881 GTTATGTTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 4 0.17
19 9 0.38
20 11 0.46
ACGTcount: A:0.31, C:0.09, G:0.13, T:0.47
Consensus pattern (20 bp):
TACATGTTTAACCTGTTATA
Found at i:28547721 original size:30 final size:29
Alignment explanation
Indices: 28547538--28547854 Score: 194
Period size: 30 Copynumber: 11.1 Consensus size: 29
28547528 CAAAAAACGT
*
28547538 AAAAACCTTTGTGGCAAACCTCTGTAAAAAG
1 AAAAGCCTTTGTGGCAAACCTCTGT--AAAG
* *
28547569 AAGAGCCTTTGTGGCAAATCTCTGTAAAGG
1 AAAAGCCTTTGTGGCAAACCTCTGTAAA-G
* * * *
28547599 AAAAACCTTTATGGCGAACCTTTG-AATAG
1 AAAAGCCTTTGTGGCAAACCTCTGTAA-AG
28547628 -AAAGCCTTTGTGG-AATA--T-T-TAAAAG
1 AAAAGCCTTTGTGGCAA-ACCTCTGT-AAAG
* *
28547653 AAAAGCCTTTGAGGCAAACCTCTGTACAG
1 AAAAGCCTTTGTGGCAAACCTCTGTAAAG
* * * *
28547682 AAAAACCTTTGTGGCAAATCTTTGTTAAGG
1 AAAAGCCTTTGTGGCAAACCTCTG-TAAAG
*
28547712 AAAAGCCTTTGTGGGAAACCTC--TAAA-
1 AAAAGCCTTTGTGGCAAACCTCTGTAAAG
* * * *
28547738 CAGAGCCTTTGTGGCATA--TCT-AAAAG
1 AAAAGCCTTTGTGGCAAACCTCTGTAAAG
* * * *
28547764 AAAAACCTTTCTGGAAAACCTCTGTATAG
1 AAAAGCCTTTGTGGCAAACCTCTGTAAAG
* *
28547793 AAAAGCCTTTATGGCAAATCC-CCGTAAAAG
1 AAAAGCCTTTGTGGCAAA-CCTCTGT-AAAG
* * ** *
28547823 AAAAACCTTTATGGTGAACCTTTGTAAAG
1 AAAAGCCTTTGTGGCAAACCTCTGTAAAG
28547852 AAA
1 AAA
28547855 GCCCATTTGG
Statistics
Matches: 218, Mismatches: 48, Indels: 42
0.71 0.16 0.14
Matches are distributed among these distances:
24 2 0.01
25 6 0.03
26 42 0.19
27 6 0.03
28 16 0.07
29 60 0.28
30 64 0.29
31 22 0.10
ACGTcount: A:0.37, C:0.18, G:0.19, T:0.26
Consensus pattern (29 bp):
AAAAGCCTTTGTGGCAAACCTCTGTAAAG
Found at i:28547786 original size:111 final size:112
Alignment explanation
Indices: 28547538--28547843 Score: 357
Period size: 111 Copynumber: 2.7 Consensus size: 112
28547528 CAAAAAACGT
*
28547538 AAAAACCTTTGTGGCAAACCTCTGTAAAAAGAAGAGCCTTTGTGGCAAATCTCTGTAAAGGAAAA
1 AAAAACCTTTGTGGCAAACCTCTGTAAGAA-AA-A-CCTTTGTGGCAAATCTCTGTAAAGGAAAA
* * *
28547603 ACCTTTATGGCGAACCTTTGAATAGAAAGCCTTTGTGGAATATTTAAAAG
63 ACCTTTATGGCGAACCTCTGAATACAAAGCCTTTGTGGAATATCTAAAAG
* * * * *
28547653 AAAAGCCTTTGAGGCAAACCTCTGTACAGAAAAACCTTTGTGGCAAATCTTTGTTAAGGAAAAGC
1 AAAAACCTTTGTGGCAAACCTCTGTA-AGAAAAACCTTTGTGGCAAATCTCTGTAAAGGAAAAAC
* * *
28547718 CTTTGTGG-GAAACCTCT-AA-ACAGAGCCTTTGTGGCATATCTAAAAG
65 CTTTATGGCG-AACCTCTGAATACAAAGCCTTTGTGGAATATCTAAAAG
* * * * * * *
28547764 AAAAACCTTTCTGGAAAACCTCTGTATAGAAAAGCCTTTATGGCAAATCCCCGTAAAAGAAAAAC
1 AAAAACCTTTGTGGCAAACCTCTGTA-AGAAAAACCTTTGTGGCAAATCTCTGTAAAGGAAAAAC
*
28547829 CTTTATGGTGAACCT
65 CTTTATGGCGAACCT
28547844 TTGTAAAGAA
Statistics
Matches: 162, Mismatches: 26, Indels: 10
0.82 0.13 0.05
Matches are distributed among these distances:
111 87 0.54
112 4 0.02
113 41 0.25
114 1 0.01
115 26 0.16
116 3 0.02
ACGTcount: A:0.37, C:0.18, G:0.19, T:0.26
Consensus pattern (112 bp):
AAAAACCTTTGTGGCAAACCTCTGTAAGAAAAACCTTTGTGGCAAATCTCTGTAAAGGAAAAACC
TTTATGGCGAACCTCTGAATACAAAGCCTTTGTGGAATATCTAAAAG
Found at i:28547843 original size:59 final size:57
Alignment explanation
Indices: 28547538--28547854 Score: 233
Period size: 59 Copynumber: 5.6 Consensus size: 57
28547528 CAAAAAACGT
* * *
28547538 AAAAACCTTTGTGGCAAACCTCTGTAAAAAGAAGAGCCTTTGTGGCAAATCTCTGTAAAGG
1 AAAAACCTTTATGGCAAACCTCTGT--AAAGAAAAGCCTTTGTGGCAAATC-C-GTAAAAG
* * *
28547599 AAAAACCTTTATGGCGAACCTTTG-AATAG-AAAGCCTTTGTGG-AATAT--TTAAAAG
1 AAAAACCTTTATGGCAAACCTCTGTAA-AGAAAAGCCTTTGTGGCAA-ATCCGTAAAAG
* * * * * *
28547653 AAAAGCCTTTGA-GGCAAACCTCTGTACAGAAAAACCTTTGTGGCAAATCTTTGTTAAGG
1 AAAAACCTTT-ATGGCAAACCTCTGTAAAGAAAAGCCTTTGTGGCAAATC--CGTAAAAG
* * * * * *
28547712 AAAAGCCTTTGTGGGAAACCTC--TAAA-CAGAGCCTTTGTGGCATAT-C-TAAAAG
1 AAAAACCTTTATGGCAAACCTCTGTAAAGAAAAGCCTTTGTGGCAAATCCGTAAAAG
* * * *
28547764 AAAAACCTTTCTGGAAAACCTCTGTATAGAAAAGCCTTTATGGCAAATCCCCGTAAAAG
1 AAAAACCTTTATGGCAAACCTCTGTAAAGAAAAGCCTTTGTGGCAAAT--CCGTAAAAG
** *
28547823 AAAAACCTTTATGGTGAACCTTTGTAAAGAAA
1 AAAAACCTTTATGGCAAACCTCTGTAAAGAAA
28547855 GCCCATTTGG
Statistics
Matches: 201, Mismatches: 37, Indels: 38
0.73 0.13 0.14
Matches are distributed among these distances:
52 23 0.11
54 29 0.14
55 31 0.15
56 17 0.08
57 5 0.02
58 17 0.08
59 58 0.29
61 21 0.10
ACGTcount: A:0.37, C:0.18, G:0.19, T:0.26
Consensus pattern (57 bp):
AAAAACCTTTATGGCAAACCTCTGTAAAGAAAAGCCTTTGTGGCAAATCCGTAAAAG
Found at i:28553014 original size:31 final size:32
Alignment explanation
Indices: 28552943--28553014 Score: 78
Period size: 32 Copynumber: 2.3 Consensus size: 32
28552933 CTTTTTTTAT
28552943 AGCTAAATTTGACACTCAACCATTTAAAAAAA
1 AGCTAAATTTGACACTCAACCATTTAAAAAAA
* **
28552975 AG-TCAAATTTGACCAC-CAACC-TTTCAGCAAA
1 AGCT-AAATTTGA-CACTCAACCATTTAAAAAAA
28553006 AGCTAAATT
1 AGCTAAATT
28553015 GTTGGTTTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
31 15 0.44
32 16 0.47
33 3 0.09
ACGTcount: A:0.44, C:0.22, G:0.08, T:0.25
Consensus pattern (32 bp):
AGCTAAATTTGACACTCAACCATTTAAAAAAA
Found at i:28563758 original size:25 final size:25
Alignment explanation
Indices: 28563730--28563786 Score: 78
Period size: 25 Copynumber: 2.3 Consensus size: 25
28563720 CTATAAACAA
**
28563730 TAAGCTCATACGAGTTGAATATCAG
1 TAAGCTCATACGAACTGAATATCAG
* *
28563755 TAAGCTCATGCGAACTGAATATCGG
1 TAAGCTCATACGAACTGAATATCAG
28563780 TAAGCTC
1 TAAGCTC
28563787 TCTTGAGCTG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.26
Consensus pattern (25 bp):
TAAGCTCATACGAACTGAATATCAG
Found at i:28566752 original size:18 final size:18
Alignment explanation
Indices: 28566729--28566765 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
28566719 AGTGTAAGAA
28566729 AACCGTTTTCAAATCGGG
1 AACCGTTTTCAAATCGGG
28566747 AACCGTTTTCAAATCGGG
1 AACCGTTTTCAAATCGGG
28566765 A
1 A
28566766 TTTTTTTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.30, C:0.22, G:0.22, T:0.27
Consensus pattern (18 bp):
AACCGTTTTCAAATCGGG
Found at i:28575859 original size:13 final size:13
Alignment explanation
Indices: 28575841--28575866 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
28575831 CATGTGTGAC
28575841 ACACGGCCATGCG
1 ACACGGCCATGCG
28575854 ACACGGCCATGCG
1 ACACGGCCATGCG
28575867 TCCCCTGTAG
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:0.38, G:0.31, T:0.08
Consensus pattern (13 bp):
ACACGGCCATGCG
Found at i:28583582 original size:20 final size:20
Alignment explanation
Indices: 28583554--28583591 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
28583544 TTGAAACCAA
*
28583554 TAATTATGTGTGTGTTTCAC
1 TAATCATGTGTGTGTTTCAC
28583574 TAATCATGTGTGTGTTTC
1 TAATCATGTGTGTGTTTC
28583592 GCTACAGAGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.18, C:0.11, G:0.21, T:0.50
Consensus pattern (20 bp):
TAATCATGTGTGTGTTTCAC
Found at i:28586609 original size:33 final size:32
Alignment explanation
Indices: 28586572--28586684 Score: 118
Period size: 33 Copynumber: 3.4 Consensus size: 32
28586562 ACCTATATTT
*
28586572 TGTGTTTACTATCGTAACAAACTTTCTTTGTTC
1 TGTGTTTACTATC-CAACAAACTTTCTTTGTTC
* * *
28586605 TGTGTTTACTATCCCATCACACTTTCTCTGTTC
1 TGTGTTTACTAT-CCAACAAACTTTCTTTGTTC
* ** *
28586638 TGTGTTTACTGTTCCAACGGACTATCTTTGTTC
1 TGTGTTTACT-ATCCAACAAACTTTCTTTGTTC
*
28586671 TATGTTTACTATCC
1 TGTGTTTACTATCC
28586685 CTACGGACTA
Statistics
Matches: 66, Mismatches: 12, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
32 3 0.05
33 61 0.92
34 2 0.03
ACGTcount: A:0.18, C:0.23, G:0.12, T:0.47
Consensus pattern (32 bp):
TGTGTTTACTATCCAACAAACTTTCTTTGTTC
Found at i:28586691 original size:33 final size:33
Alignment explanation
Indices: 28586596--28586697 Score: 118
Period size: 33 Copynumber: 3.1 Consensus size: 33
28586586 TAACAAACTT
*
28586596 TCTTTGTTCTGTGTTTACTATCCCATCAC--ACTT
1 TCTTTGTTCTGTGTTTACTATCCC-T-ACGGACTA
* * * *
28586629 TCTCTGTTCTGTGTTTACTGTTCCAACGGACTA
1 TCTTTGTTCTGTGTTTACTATCCCTACGGACTA
*
28586662 TCTTTGTTCTATGTTTACTATCCCTACGGACTA
1 TCTTTGTTCTGTGTTTACTATCCCTACGGACTA
28586695 TCT
1 TCT
28586698 CTGTGGATGC
Statistics
Matches: 57, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
31 2 0.04
33 55 0.96
ACGTcount: A:0.16, C:0.25, G:0.13, T:0.46
Consensus pattern (33 bp):
TCTTTGTTCTGTGTTTACTATCCCTACGGACTA
Found at i:28597068 original size:30 final size:30
Alignment explanation
Indices: 28597023--28597089 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 30
28597013 ATTTCCCCGG
* * * *
28597023 GCATCAGCATTGACTATTGTATAGGTATCT
1 GCATCGGCATCGACTATTGCATAGGCATCT
*
28597053 GCATCGGCATCGACTATTGCATGGGCATCT
1 GCATCGGCATCGACTATTGCATAGGCATCT
*
28597083 GTATCGG
1 GCATCGG
28597090 TACCGTCATC
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.22, C:0.21, G:0.25, T:0.31
Consensus pattern (30 bp):
GCATCGGCATCGACTATTGCATAGGCATCT
Found at i:28598673 original size:16 final size:16
Alignment explanation
Indices: 28598652--28598687 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
28598642 TTTAAACGAA
28598652 TAAAACATGAGATAAT
1 TAAAACATGAGATAAT
28598668 TAAAACATGAGATAAT
1 TAAAACATGAGATAAT
28598684 TAAA
1 TAAA
28598688 TGAAAATATC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.58, C:0.06, G:0.11, T:0.25
Consensus pattern (16 bp):
TAAAACATGAGATAAT
Found at i:28600085 original size:9 final size:9
Alignment explanation
Indices: 28600059--28600100 Score: 50
Period size: 9 Copynumber: 4.4 Consensus size: 9
28600049 ACAATTCTCA
28600059 CAAATTCTCT
1 CAAATT-TCT
28600069 CAAAATTTCT
1 C-AAATTTCT
28600079 CAAATTTCT
1 CAAATTTCT
28600088 CACAA-TTCT
1 CA-AATTTCT
28600097 CAAA
1 CAAA
28600101 AAGCTCTCAA
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
8 2 0.07
9 16 0.53
10 7 0.23
11 5 0.17
ACGTcount: A:0.38, C:0.26, G:0.00, T:0.36
Consensus pattern (9 bp):
CAAATTTCT
Found at i:28603472 original size:46 final size:46
Alignment explanation
Indices: 28603397--28603511 Score: 176
Period size: 46 Copynumber: 2.5 Consensus size: 46
28603387 CCACACTAAT
* *
28603397 ATGTAGCCAAAGCTACCACTAATACGTAGCTGTAGCTACCACTGAA
1 ATGTAGCCAAAGCTACCACTGATACGTAGCCGTAGCTACCACTGAA
*
28603443 ATGTAGCCAAAGCTACCACTGATATGTAGCCGTAGCTACCACTGAA
1 ATGTAGCCAAAGCTACCACTGATACGTAGCCGTAGCTACCACTGAA
* **
28603489 ATGCAGCTGAAGCTACCACTGAT
1 ATGTAGCCAAAGCTACCACTGAT
28603512 CAATAACACT
Statistics
Matches: 63, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 63 1.00
ACGTcount: A:0.33, C:0.26, G:0.19, T:0.22
Consensus pattern (46 bp):
ATGTAGCCAAAGCTACCACTGATACGTAGCCGTAGCTACCACTGAA
Found at i:28603509 original size:23 final size:23
Alignment explanation
Indices: 28603397--28603510 Score: 131
Period size: 23 Copynumber: 5.0 Consensus size: 23
28603387 CCACACTAAT
*
28603397 ATGTAGCCAAAGCTACCACT-AA
1 ATGTAGCCGAAGCTACCACTGAA
* * *
28603419 TACGTAGCTGTAGCTACCACTGAA
1 -ATGTAGCCGAAGCTACCACTGAA
* *
28603443 ATGTAGCCAAAGCTACCACTGAT
1 ATGTAGCCGAAGCTACCACTGAA
*
28603466 ATGTAGCCGTAGCTACCACTGAA
1 ATGTAGCCGAAGCTACCACTGAA
* *
28603489 ATGCAGCTGAAGCTACCACTGA
1 ATGTAGCCGAAGCTACCACTGA
28603511 TCAATAACAC
Statistics
Matches: 75, Mismatches: 15, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
23 73 0.97
24 2 0.03
ACGTcount: A:0.33, C:0.26, G:0.19, T:0.21
Consensus pattern (23 bp):
ATGTAGCCGAAGCTACCACTGAA
Found at i:28605848 original size:9 final size:9
Alignment explanation
Indices: 28605834--28605891 Score: 98
Period size: 9 Copynumber: 6.4 Consensus size: 9
28605824 TTTGGTTAAA
28605834 AATTAACCG
1 AATTAACCG
28605843 AATTAACCG
1 AATTAACCG
*
28605852 AATTAATCG
1 AATTAACCG
*
28605861 AATTACCCG
1 AATTAACCG
28605870 AATTAACCG
1 AATTAACCG
28605879 AATTAACCG
1 AATTAACCG
28605888 AATT
1 AATT
28605892 GAATCACTAC
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 45 1.00
ACGTcount: A:0.43, C:0.21, G:0.10, T:0.26
Consensus pattern (9 bp):
AATTAACCG
Found at i:28605947 original size:11 final size:11
Alignment explanation
Indices: 28605931--28605955 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
28605921 ACTTTTAGAC
28605931 TTTAGTTTTAG
1 TTTAGTTTTAG
28605942 TTTAGTTTTAG
1 TTTAGTTTTAG
28605953 TTT
1 TTT
28605956 TAGAATTTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.16, C:0.00, G:0.16, T:0.68
Consensus pattern (11 bp):
TTTAGTTTTAG
Found at i:28607185 original size:42 final size:42
Alignment explanation
Indices: 28607105--28607186 Score: 103
Period size: 42 Copynumber: 2.0 Consensus size: 42
28607095 CGTTTTTTCT
* * **
28607105 ATGCCATAGTCCAATTATGGTCTTACACATATTTACATATTG
1 ATGCCATAGCCCAACTATGGTCTTACACATATGCACATATTG
*
28607147 ATGCCATAGCCCAGCTATGGTCTTACACAGTA-GCACATAT
1 ATGCCATAGCCCAACTATGGTCTTACACA-TATGCACATAT
28607187 CACACCGATG
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
42 32 0.94
43 2 0.06
ACGTcount: A:0.30, C:0.23, G:0.15, T:0.32
Consensus pattern (42 bp):
ATGCCATAGCCCAACTATGGTCTTACACATATGCACATATTG
Found at i:28607213 original size:47 final size:48
Alignment explanation
Indices: 28607146--28607238 Score: 116
Period size: 47 Copynumber: 2.0 Consensus size: 48
28607136 TTTACATATT
* *
28607146 GATGCCATAGCCCAGCTATGGTCTTACACAG-TAGCACATATCACACC
1 GATGCCATAGCCCAGATATGGTCTTACACAGAAAGCACATATCACACC
* * * * *
28607193 GATGCCATATCCCGGATATGGTTTTATACAGAAATCACATATCACA
1 GATGCCATAGCCCAGATATGGTCTTACACAGAAAGCACATATCACA
28607239 TGTTGTCATG
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
47 26 0.68
48 12 0.32
ACGTcount: A:0.32, C:0.27, G:0.16, T:0.25
Consensus pattern (48 bp):
GATGCCATAGCCCAGATATGGTCTTACACAGAAAGCACATATCACACC
Found at i:28609900 original size:46 final size:46
Alignment explanation
Indices: 28609828--28609939 Score: 179
Period size: 46 Copynumber: 2.4 Consensus size: 46
28609818 CACTAATATG
* *
28609828 TAGCCGAAGCTACCACTAATACGTAGCTGTAGCTACCACTGAAATA
1 TAGCCGAAGCTACCACTGATACGTAGCCGTAGCTACCACTGAAATA
* * *
28609874 TAGCCGAAGCTACCACTGGTATGTAGCCGTAGCTACCACTGAAATG
1 TAGCCGAAGCTACCACTGATACGTAGCCGTAGCTACCACTGAAATA
28609920 TAGCCGAAGCTACCACTGAT
1 TAGCCGAAGCTACCACTGAT
28609940 CAATAACACT
Statistics
Matches: 60, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 60 1.00
ACGTcount: A:0.31, C:0.27, G:0.21, T:0.21
Consensus pattern (46 bp):
TAGCCGAAGCTACCACTGATACGTAGCCGTAGCTACCACTGAAATA
Found at i:28609937 original size:23 final size:23
Alignment explanation
Indices: 28609825--28609938 Score: 149
Period size: 23 Copynumber: 5.0 Consensus size: 23
28609815 CCACACTAAT
28609825 ATGTAGCCGAAGCTACCACT-AA
1 ATGTAGCCGAAGCTACCACTGAA
* * *
28609847 TACGTAGCTGTAGCTACCACTGAA
1 -ATGTAGCCGAAGCTACCACTGAA
* **
28609871 ATATAGCCGAAGCTACCACTGGT
1 ATGTAGCCGAAGCTACCACTGAA
*
28609894 ATGTAGCCGTAGCTACCACTGAA
1 ATGTAGCCGAAGCTACCACTGAA
28609917 ATGTAGCCGAAGCTACCACTGA
1 ATGTAGCCGAAGCTACCACTGA
28609939 TCAATAACAC
Statistics
Matches: 76, Mismatches: 14, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
23 74 0.97
24 2 0.03
ACGTcount: A:0.32, C:0.26, G:0.21, T:0.21
Consensus pattern (23 bp):
ATGTAGCCGAAGCTACCACTGAA
Found at i:28610191 original size:18 final size:17
Alignment explanation
Indices: 28610165--28610203 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
28610155 ATTTTCCTTC
28610165 CACATTC-AATATTAATT
1 CACATTCAAATA-TAATT
28610182 CACATATCAAATATAATT
1 CACAT-TCAAATATAATT
28610200 CACA
1 CACA
28610204 ATTTATAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 5 0.25
18 11 0.55
19 4 0.20
ACGTcount: A:0.46, C:0.21, G:0.00, T:0.33
Consensus pattern (17 bp):
CACATTCAAATATAATT
Found at i:28613572 original size:3 final size:3
Alignment explanation
Indices: 28613564--28613589 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
28613554 GAATCATGGA
28613564 TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TC
28613590 ATTTTCATCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
TCT
Found at i:28615387 original size:3 final size:3
Alignment explanation
Indices: 28615379--28615414 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
28615369 GATATCATGT
*
28615379 TTA TTA TTA CTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
28615415 GTAGTAGTAG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:28617498 original size:13 final size:14
Alignment explanation
Indices: 28617467--28617499 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
28617457 TTCAGACCCT
*
28617467 CTAAACCCTAAATC
1 CTAAACCATAAATC
28617481 CTAAACCATAAA-C
1 CTAAACCATAAATC
28617494 CTAAAC
1 CTAAAC
28617500 ATTTTAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 7 0.39
14 11 0.61
ACGTcount: A:0.48, C:0.33, G:0.00, T:0.18
Consensus pattern (14 bp):
CTAAACCATAAATC
Found at i:28618610 original size:6 final size:6
Alignment explanation
Indices: 28618599--28618635 Score: 56
Period size: 6 Copynumber: 6.2 Consensus size: 6
28618589 TTTTTCAACC
* *
28618599 CCAAAT CCAAAT CCAAAT CCAAAC CCAAAC CCAAAT C
1 CCAAAT CCAAAT CCAAAT CCAAAT CCAAAT CCAAAT C
28618636 TAATTCCCAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.49, C:0.41, G:0.00, T:0.11
Consensus pattern (6 bp):
CCAAAT
Found at i:28623176 original size:15 final size:16
Alignment explanation
Indices: 28623141--28623174 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
28623131 TCATTTGTTG
28623141 TTTAAAATTGTTATTA
1 TTTAAAATTGTTATTA
28623157 TTTAAATATTGTT-TTA
1 TTTAAA-ATTGTTATTA
28623173 TT
1 TT
28623175 AATTAAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 11 0.65
17 6 0.35
ACGTcount: A:0.32, C:0.00, G:0.06, T:0.62
Consensus pattern (16 bp):
TTTAAAATTGTTATTA
Found at i:28623519 original size:27 final size:27
Alignment explanation
Indices: 28623461--28623523 Score: 76
Period size: 27 Copynumber: 2.3 Consensus size: 27
28623451 TTAAATTATT
**
28623461 TATATTTTATAATTCAATATTTTTGTA
1 TATATTTTATAATTCAATATTTTAATA
28623488 TATATTTT-TAATTCAATATCATTTAATA
1 TATATTTTATAATTCAATAT--TTTAATA
28623516 -ATATTTTA
1 TATATTTTA
28623524 AACCCTACTT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
26 11 0.35
27 15 0.48
28 5 0.16
ACGTcount: A:0.37, C:0.05, G:0.02, T:0.57
Consensus pattern (27 bp):
TATATTTTATAATTCAATATTTTAATA
Found at i:28623759 original size:19 final size:19
Alignment explanation
Indices: 28623728--28623778 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
28623718 GTTTATGGTA
*
28623728 ATTA-AATAATATTTATTT
1 ATTATAATAATATTTATCT
*
28623746 ATTATAATAGTATTTATCT
1 ATTATAATAATATTTATCT
28623765 -TTATAATAAATATT
1 ATTATAAT-AATATT
28623779 AAATTTAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
18 11 0.39
19 17 0.61
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (19 bp):
ATTATAATAATATTTATCT
Found at i:28624026 original size:162 final size:160
Alignment explanation
Indices: 28623858--28624171 Score: 431
Period size: 163 Copynumber: 1.9 Consensus size: 160
28623848 AATTTTGAAA
*
28623858 TTTAAACTA-ATTTCTTTAAAGATGAATAAA-A-ATATTATTTAAATTAAATTTTCTA-TGAAAG
1 TTTAAACTATATTT-TTTAAAGATAAATAAAGATATATT-TTTAAATTAAATTTTCTAGT-AAAG
* * *
28623919 TTTTAACTTTAAACTAAATATTAAAATTAGTAAATTTATAATTTATAATTTA-AATAAAAAATAT
63 TTTTAACTTTAAACTAAATATTAAAATTA-AAAATTT-TAATTAAGAATTTAGAAT-AAAAATAT
28623983 TAAAATTAAATTATGTTATAGATTTTTATGAAAGGAT
125 TAAAATT-AATTATGTTATAGATTTTTATGAAAGGAT
* * *
28624020 TTTAAACTATATTTTTTAATGATAAATAAAGATATATTTTTAAATTAAATTTTCTAGTAGATTTT
1 TTTAAACTATATTTTTTAAAGATAAATAAAGATATATTTTTAAATTAAATTTTCTAGTAAAGTTT
*
28624085 TAACTTTAAACTAAATATTAAAATTAAAAATTTTAATTAAGAATTTAGAATAAAAATATTGAAAT
66 TAACTTTAAACTAAATATTAAAATTAAAAATTTTAATTAAGAATTTAGAATAAAAATATTAAAAT
* * *
28624150 TAATTTTTTTATGGATTTTTAT
131 TAATTATGTTATAGATTTTTAT
28624172 TAAAATTAAT
Statistics
Matches: 136, Mismatches: 11, Indels: 12
0.86 0.07 0.08
Matches are distributed among these distances:
160 18 0.13
161 26 0.19
162 32 0.24
163 54 0.40
164 6 0.04
ACGTcount: A:0.46, C:0.03, G:0.06, T:0.45
Consensus pattern (160 bp):
TTTAAACTATATTTTTTAAAGATAAATAAAGATATATTTTTAAATTAAATTTTCTAGTAAAGTTT
TAACTTTAAACTAAATATTAAAATTAAAAATTTTAATTAAGAATTTAGAATAAAAATATTAAAAT
TAATTATGTTATAGATTTTTATGAAAGGAT
Found at i:28624308 original size:13 final size:13
Alignment explanation
Indices: 28624277--28624309 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
28624267 ATGATAGATA
*
28624277 TTAAATTTAAAAT
1 TTAAATATAAAAT
28624290 TT-AATATAAAAT
1 TTAAATATAAAAT
28624302 TTAAATAT
1 TTAAATAT
28624310 TATTTAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (13 bp):
TTAAATATAAAAT
Found at i:28631490 original size:18 final size:18
Alignment explanation
Indices: 28631469--28631506 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
28631459 TTCCAAAACA
*
28631469 TTATTC-ATTTACAAATTG
1 TTATTCAATTT-CAAAATG
28631487 TTATTCAATTTCAAAATG
1 TTATTCAATTTCAAAATG
28631505 TT
1 TT
28631507 TTTTTATTGC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.34, C:0.11, G:0.05, T:0.50
Consensus pattern (18 bp):
TTATTCAATTTCAAAATG
Found at i:28634216 original size:29 final size:28
Alignment explanation
Indices: 28634184--28634254 Score: 106
Period size: 29 Copynumber: 2.5 Consensus size: 28
28634174 AGCCGAAGTT
*
28634184 ATCCCTTTTCATATTTAATGGTCGTCACA
1 ATCCCTTTTCATATTT-ATGATCGTCACA
*
28634213 ATCCCTTTTCATGATTTATGATCGTCACC
1 ATCCCTTTTCAT-ATTTATGATCGTCACA
28634242 ATCCCTTTTCATA
1 ATCCCTTTTCATA
28634255 ATCGATAGTC
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
28 1 0.03
29 34 0.87
30 4 0.10
ACGTcount: A:0.23, C:0.27, G:0.08, T:0.42
Consensus pattern (28 bp):
ATCCCTTTTCATATTTATGATCGTCACA
Found at i:28634304 original size:29 final size:29
Alignment explanation
Indices: 28634242--28634311 Score: 86
Period size: 29 Copynumber: 2.4 Consensus size: 29
28634232 GATCGTCACC
*
28634242 ATCCCTTTTCATAATCGATAGTCGAAACT
1 ATCCCTTTTCATAATCGATAGCCGAAACT
* * * * *
28634271 CTCCCTTTTCATATTCGATGGCCGGAGCT
1 ATCCCTTTTCATAATCGATAGCCGAAACT
28634300 ATCCCTTTTCAT
1 ATCCCTTTTCAT
28634312 TGGTCAATGA
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.21, C:0.29, G:0.13, T:0.37
Consensus pattern (29 bp):
ATCCCTTTTCATAATCGATAGCCGAAACT
Found at i:28639494 original size:50 final size:50
Alignment explanation
Indices: 28639369--28639662 Score: 363
Period size: 50 Copynumber: 5.8 Consensus size: 50
28639359 GATCATAACA
* ** * *
28639369 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTTTCATATCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATCTCGG
* * **
28639420 TGCCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* ** * * *
28639470 TGCCAACGCCATGTCCCAGGCATGGTCTTACATGGGATGTTTTCATATCAG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATCTCGG
* * ** *
28639521 TGCCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTTGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
28639571 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* * *
28639621 TGCCAACACCATGTCCTAGACATGGTCTTACATGGGATCTCT
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
28639663 TTACCCAAAT
Statistics
Matches: 205, Mismatches: 37, Indels: 3
0.84 0.15 0.01
Matches are distributed among these distances:
50 132 0.64
51 73 0.36
ACGTcount: A:0.20, C:0.30, G:0.23, T:0.27
Consensus pattern (50 bp):
TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:28639544 original size:101 final size:101
Alignment explanation
Indices: 28639369--28639651 Score: 451
Period size: 101 Copynumber: 2.8 Consensus size: 101
28639359 GATCATAACA
*
28639369 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTTTCATATCGGTGCCCATGCCATGT
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGATGTTTTCATATCGGTGCCCATGCCATGT
28639434 CCCAGACATGGTCTTACGGGGGACCTCTCATCTCGG
66 CCCAGACATGGTCTTACGGGGGACCTCTCATCTCGG
* *
28639470 TGCCAACGCCATGTCCCAGGCATGGTCTTACATGGGATGTTTTCATATCAGTGCCCATGCCATGT
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGATGTTTTCATATCGGTGCCCATGCCATGT
*
28639535 CCCAGACATGGTCTTACGGGGGACCTCTCATCTTGG
66 CCCAGACATGGTCTTACGGGGGACCTCTCATCTCGG
** * * * **
28639571 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATCTCGGTGCCAACACCATGT
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGATGTTTTCATATCGGTGCCCATGCCATGT
*
28639635 CCTAGACATGGTCTTAC
66 CCCAGACATGGTCTTAC
28639652 ATGGGATCTC
Statistics
Matches: 168, Mismatches: 14, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
100 35 0.21
101 133 0.79
ACGTcount: A:0.20, C:0.30, G:0.23, T:0.27
Consensus pattern (101 bp):
TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGATGTTTTCATATCGGTGCCCATGCCATGT
CCCAGACATGGTCTTACGGGGGACCTCTCATCTCGG
Found at i:28639635 original size:151 final size:152
Alignment explanation
Indices: 28639376--28639658 Score: 433
Period size: 151 Copynumber: 1.9 Consensus size: 152
28639366 ACATGCCAAA
* ** * * *
28639376 GCCATGTCCCAGACATGGTCTTACATGGGATGTTTTCATATCGGTGCCCATGCCATGTCCCAGAC
1 GCCATGTCCCAGACATGGTCTTACAGGGGATCCTCTCATATCGGTGCCAACGCCATGTCCCAGAC
* * *
28639441 ATGGTCTTACGGGGGACCTCTCATCTCGGTGCCAACGCCATGTCCCAGGCATGGTCTTACATGGG
66 ATGGTCTTACAGGGGACCTCTCATCTCGGTGCCAACACCATGTCCCAGACATGGTCTTACATGGG
28639506 ATGTTTTCATATCAGTGCCCAT
131 ATGTTTTCATATCAGTGCCCAT
* * *
28639528 GCCATGTCCCAGACATGGTCTTACGGGGGA-CCTCTCATCTTGGTGCCAACGCCATGTCCCAGAC
1 GCCATGTCCCAGACATGGTCTTACAGGGGATCCTCTCATATCGGTGCCAACGCCATGTCCCAGAC
* *
28639592 ATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACACCATGTCCTAGACATGGTCTTACATGGG
66 ATGGTCTTACAGGGGACCTCTCATCTCGGTGCCAACACCATGTCCCAGACATGGTCTTACATGGG
28639657 AT
131 AT
28639659 CTCTTTACCC
Statistics
Matches: 117, Mismatches: 14, Indels: 1
0.89 0.11 0.01
Matches are distributed among these distances:
151 89 0.76
152 28 0.24
ACGTcount: A:0.20, C:0.29, G:0.24, T:0.27
Consensus pattern (152 bp):
GCCATGTCCCAGACATGGTCTTACAGGGGATCCTCTCATATCGGTGCCAACGCCATGTCCCAGAC
ATGGTCTTACAGGGGACCTCTCATCTCGGTGCCAACACCATGTCCCAGACATGGTCTTACATGGG
ATGTTTTCATATCAGTGCCCAT
Found at i:28656682 original size:37 final size:37
Alignment explanation
Indices: 28656641--28656714 Score: 139
Period size: 37 Copynumber: 2.0 Consensus size: 37
28656631 TGTTGTCATG
28656641 ATTAGTCTTCAATCACATCCTCAATTACAATAACAAT
1 ATTAGTCTTCAATCACATCCTCAATTACAATAACAAT
*
28656678 ATTAGTCTTCAATCACATCTTCAATTACAATAACAAT
1 ATTAGTCTTCAATCACATCCTCAATTACAATAACAAT
28656715 CACAATCTCT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.41, C:0.23, G:0.03, T:0.34
Consensus pattern (37 bp):
ATTAGTCTTCAATCACATCCTCAATTACAATAACAAT
Found at i:28673685 original size:70 final size:69
Alignment explanation
Indices: 28673537--28674197 Score: 490
Period size: 70 Copynumber: 9.5 Consensus size: 69
28673527 CAGTTAGTGC
** * * * * *** * * *
28673537 GAGCTCAAGCTCTTAGCTGTGATTTTAAGGCTCACAGTTTCAATGCGCAACCTCCAAAATAGTTA
1 GAGCTCAAGCTCCCAACTGTGATCTTAAGGCTCGCAGGTTCAACATGTAGCCTCTAAAATAGTTA
*
28673602 GCAC
66 GCAT
* * *
28673606 GAGCTCAAGCTTCCAACTGTGGTCTTAAGGCTCGCAGGTTCAACACTGTAACCTCTAAAATAGTT
1 GAGCTCAAGCTCCCAACTGTGATCTTAAGGCTCGCAGGTTCAACA-TGTAGCCTCTAAAATAGTT
**
28673671 AGTGT
65 AGCAT
* ** ** * * * *
28673676 TAGCTCAAGCTCTTAGTTGTGATTTTAAGGCTCGTAGGTTCAACATCATAGCCTCCAAAATAGTT
1 GAGCTCAAGCTCCCAACTGTGATCTTAAGGCTCGCAGGTTCAACAT-GTAGCCTCTAAAATAGTT
28673741 AGCAT
65 AGCAT
* * * * * * *
28673746 GAGCTCGAGCTCCTAACTGTGATATTAAGGCTCGCAAGTTCACCACCGTAGCCTCCAAAATAGTT
1 GAGCTCAAGCTCCCAACTGTGATCTTAAGGCTCGCAGGTTCAACA-TGTAGCCTCTAAAATAGTT
**
28673811 AGCGC
65 AGCAT
* * *
28673816 GAGCTCAAGCTCCCAACTGTGATCTTAAAGCTCACAGGTTCAACATTGTAGCCTCTAAAATAGCT
1 GAGCTCAAGCTCCCAACTGTGATCTTAAGGCTCGCAGGTTCAACA-TGTAGCCTCTAAAATAGTT
28673881 AGCAT
65 AGCAT
* * * ** *
28673886 GAGATCAAGCTCCCAACTGTGATCTTAAGGCTCGTATGTTCAACATCACAGCCTCTAAAACAGTT
1 GAGCTCAAGCTCCCAACTGTGATCTTAAGGCTCGCAGGTTCAACAT-GTAGCCTCTAAAATAGTT
28673951 AGCAT
65 AGCAT
* * * * * *
28673956 GAGCTCAAACTCCCAATTGTGATCTTAAGGCTTGCAGGTTTAACATCGCAACCTCCTAAACA-A-
1 GAGCTCAAGCTCCCAACTGTGATCTTAAGGCTCGCAGGTTCAACAT-GTAGCCT-CTAAA-ATAG
**
28674019 TTAGCGC
63 TTAGCAT
* * * * * * *
28674026 AAGCTCAAGCTCCCAGCTGTGATCTTAATGCTCGTAAGTTCAATGC-TGCA-CCTCCAAAATAGT
1 GAGCTCAAGCTCCCAACTGTGATCTTAAGGCTCGCAGGTTCAA--CATGTAGCCTCTAAAATAGT
* **
28674089 TAACGC
64 TAGCAT
* * * * ** *
28674095 GAGGTCAAACTCTCAACTGTGATCTTAAGGCTCACAATTTCAACACTGGAGCCTCCTAAACA-A-
1 GAGCTCAAGCTCCCAACTGTGATCTTAAGGCTCGCAGGTTCAACA-TGTAGCCT-CTAAA-ATAG
28674158 TTAGC-T
63 TTAGCAT
* * *
28674164 AGAGCTTAAACTCCCAGCTGTGATCTTAAGGCTC
1 -GAGCTCAAGCTCCCAACTGTGATCTTAAGGCTC
28674198 ATAGGCTCAA
Statistics
Matches: 472, Mismatches: 104, Indels: 31
0.78 0.17 0.05
Matches are distributed among these distances:
67 2 0.00
68 5 0.01
69 83 0.18
70 367 0.78
71 12 0.03
72 3 0.01
ACGTcount: A:0.29, C:0.25, G:0.18, T:0.27
Consensus pattern (69 bp):
GAGCTCAAGCTCCCAACTGTGATCTTAAGGCTCGCAGGTTCAACATGTAGCCTCTAAAATAGTTA
GCAT
Found at i:28673953 original size:210 final size:210
Alignment explanation
Indices: 28673582--28674197 Score: 617
Period size: 210 Copynumber: 2.9 Consensus size: 210
28673572 AGTTTCAATG
* * * * *
28673582 CGCAACCTCCAAAATAGTTAGCACGAGCTCAAGCTTCCAACTGTGGTCTTAAGGCTCGCAGGTTC
1 CGCAACCTCCAAAATAGTTAGCGCGAGCTCAAGCTCCCAACTGTGATCTTAAAGCTCACAGGTTC
* ** * * ** ** *
28673647 AACACTGTAACCTCTAAAATAGTTAGTGTTAGCTCAAGCTCTTAGTTGTGATTTTAAGGCTCGTA
66 AACACTGTAACCTCTAAAATAGCTAGCATGAGATCAAGCTCCCAACTGTGATCTTAAGGCTCGTA
* * * * *
28673712 GGTTCAACATCATAGCCTCCAAAATAGTTAGCATGAGCTCGAGCTCCTAACTGTGATATTAAGGC
131 GGTTCAACATCACAGCCTCCAAAACAGTTAGCATGAGCTCAAACTCCCAACTGTGATATTAAGGC
*
28673777 TCGCAAGTTCACCAC
196 TCGCAAGTTCAACAC
* *
28673792 CGTAGCCTCCAAAATAGTTAGCGCGAGCTCAAGCTCCCAACTGTGATCTTAAAGCTCACAGGTTC
1 CGCAACCTCCAAAATAGTTAGCGCGAGCTCAAGCTCCCAACTGTGATCTTAAAGCTCACAGGTTC
* *
28673857 AACATTGTAGCCTCTAAAATAGCTAGCATGAGATCAAGCTCCCAACTGTGATCTTAAGGCTCGTA
66 AACACTGTAACCTCTAAAATAGCTAGCATGAGATCAAGCTCCCAACTGTGATCTTAAGGCTCGTA
* * * *
28673922 TGTTCAACATCACAGCCTCTAAAACAGTTAGCATGAGCTCAAACTCCCAATTGTGATCTTAAGGC
131 GGTTCAACATCACAGCCTCCAAAACAGTTAGCATGAGCTCAAACTCCCAACTGTGATATTAAGGC
* * * *
28673987 TTGCAGGTTTAACAT
196 TCGCAAGTTCAACAC
* * * * * * ** *
28674002 CGCAACCTCCTAAACAATTAGCGCAAGCTCAAGCTCCCAGCTGTGATCTTAATGCTCGTAAGTTC
1 CGCAACCTCCAAAATAGTTAGCGCGAGCTCAAGCTCCCAACTGTGATCTTAAAGCTCACAGGTTC
** * * * * ** * * * **
28674067 AATGCTG-CACCTCCAAAATAGTTAACGCGAGGTCAAACTCTCAACTGTGATCTTAAGGCTCACA
66 AACACTGTAACCTCTAAAATAGCTAGCATGAGATCAAGCTCCCAACTGTGATCTTAAGGCTCGTA
** ** * * * * *
28674131 ATTTCAACA-CTGGAGCCTCCTAAACAATTAGC-TAGAGCTTAAACTCCCAGCTGTGATCTTAAG
131 GGTTCAACATC-ACAGCCTCCAAAACAGTTAGCAT-GAGCTCAAACTCCCAACTGTGATATTAAG
28674194 GCTC
194 GCTC
28674198 ATAGGCTCAA
Statistics
Matches: 334, Mismatches: 70, Indels: 5
0.82 0.17 0.01
Matches are distributed among these distances:
208 2 0.01
209 97 0.29
210 235 0.70
ACGTcount: A:0.30, C:0.26, G:0.18, T:0.26
Consensus pattern (210 bp):
CGCAACCTCCAAAATAGTTAGCGCGAGCTCAAGCTCCCAACTGTGATCTTAAAGCTCACAGGTTC
AACACTGTAACCTCTAAAATAGCTAGCATGAGATCAAGCTCCCAACTGTGATCTTAAGGCTCGTA
GGTTCAACATCACAGCCTCCAAAACAGTTAGCATGAGCTCAAACTCCCAACTGTGATATTAAGGC
TCGCAAGTTCAACAC
Found at i:28676060 original size:8 final size:8
Alignment explanation
Indices: 28676049--28676073 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
28676039 TTTTTCATAA
28676049 TTTCACTT
1 TTTCACTT
28676057 TTTCACTT
1 TTTCACTT
28676065 TTTCACTT
1 TTTCACTT
28676073 T
1 T
28676074 CAATCACTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.12, C:0.24, G:0.00, T:0.64
Consensus pattern (8 bp):
TTTCACTT
Found at i:28676392 original size:51 final size:51
Alignment explanation
Indices: 28676335--28676474 Score: 185
Period size: 50 Copynumber: 2.8 Consensus size: 51
28676325 TTGGTTCACA
*
28676335 TAGTAGCCTACACATAGTACTACACATGTGACCATCACTATCCGATACAAG
1 TAGTAGCCTGCACATAGTACTACACATGTGACCATCACTATCCGATACAAG
* * * * * *
28676386 TAGTAGCCTGCACATAGTACTACACATGCGATC-T-ATCTTTCTGGTACACG
1 TAGTAGCCTGCACATAGTACTACACATGTGACCATCA-CTATCCGATACAAG
*
28676436 TAGTAGCCTGCACATACTACTACACATGTGACCATCACT
1 TAGTAGCCTGCACATAGTACTACACATGTGACCATCACT
28676475 TTCACTTTCA
Statistics
Matches: 76, Mismatches: 10, Indels: 6
0.83 0.11 0.07
Matches are distributed among these distances:
49 1 0.01
50 41 0.54
51 33 0.43
52 1 0.01
ACGTcount: A:0.31, C:0.28, G:0.15, T:0.26
Consensus pattern (51 bp):
TAGTAGCCTGCACATAGTACTACACATGTGACCATCACTATCCGATACAAG
Found at i:28680648 original size:39 final size:39
Alignment explanation
Indices: 28680599--28681090 Score: 714
Period size: 39 Copynumber: 12.6 Consensus size: 39
28680589 CATATTCACT
** *
28680599 TTTAAGCATATATCACTTTACACATATAATCACATAACA
1 TTTAAGCATATATCACAATACTCATATAATCACATAACA
* * *
28680638 TTTAAACATATATCACAATACTTATATAATCACATAACG
1 TTTAAGCATATATCACAATACTCATATAATCACATAACA
* *
28680677 TTTAAGCATATTTCACAATACTCATATAATCACATAAAA
1 TTTAAGCATATATCACAATACTCATATAATCACATAACA
*
28680716 TTTAAGCATATATCACAGTACTCATATAATCACATAACA
1 TTTAAGCATATATCACAATACTCATATAATCACATAACA
* *
28680755 TTTAAACAAATATCACAATACTCATATAATCACATAACA
1 TTTAAGCATATATCACAATACTCATATAATCACATAACA
*
28680794 TTTAAGCATATTTCACAATACTCATATAATCACATAACA
1 TTTAAGCATATATCACAATACTCATATAATCACATAACA
*
28680833 TTTAAGCATATATCACAGTACTCATATAATCACATAACA
1 TTTAAGCATATATCACAATACTCATATAATCACATAACA
* * **
28680872 TTTAAGCATATATCATAGTACTCATATAATCACATAATG
1 TTTAAGCATATATCACAATACTCATATAATCACATAACA
* * *
28680911 TTTAAGCATATATCACATTGCTCATATAATCACATAACG
1 TTTAAGCATATATCACAATACTCATATAATCACATAACA
* *
28680950 TTGAAGTATATATCACAATACTCATATAATCACATAACA
1 TTTAAGCATATATCACAATACTCATATAATCACATAACA
* * * **
28680989 CTTAAGCCTATATCACAATACTCATATAATCACAAAATG
1 TTTAAGCATATATCACAATACTCATATAATCACATAACA
*
28681028 TTTAAGCATATATCACAATACTCATATAATTACATAACA
1 TTTAAGCATATATCACAATACTCATATAATCACATAACA
* *
28681067 TTAAAACATATATCACAATACTCA
1 TTTAAGCATATATCACAATACTCA
28681091 AAAACATATT
Statistics
Matches: 404, Mismatches: 49, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 404 1.00
ACGTcount: A:0.45, C:0.20, G:0.04, T:0.32
Consensus pattern (39 bp):
TTTAAGCATATATCACAATACTCATATAATCACATAACA
Found at i:28684801 original size:39 final size:39
Alignment explanation
Indices: 28684758--28684848 Score: 112
Period size: 39 Copynumber: 2.3 Consensus size: 39
28684748 CATATTCACT
* * *
28684758 TTTAAGCATGTATCACATTACAT-ATATAATTACATAACA
1 TTTAAGCATATATCACAATAC-TCATATAATCACATAACA
**
28684797 TTTAAGTGTATATCACAATACTCATATAATCACATAACA
1 TTTAAGCATATATCACAATACTCATATAATCACATAACA
*
28684836 TTTAAACATATAT
1 TTTAAGCATATAT
28684849 GTCGCATGTG
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
38 1 0.02
39 42 0.98
ACGTcount: A:0.44, C:0.15, G:0.04, T:0.36
Consensus pattern (39 bp):
TTTAAGCATATATCACAATACTCATATAATCACATAACA
Found at i:28690948 original size:126 final size:121
Alignment explanation
Indices: 28690767--28691025 Score: 392
Period size: 126 Copynumber: 2.1 Consensus size: 121
28690757 ACTAATTCCC
28690767 AACCTTTAATCTACAATATAATACTCAATTCATAGTATCGACTTTTTGACATGTTTTATAGCTAT
1 AACCTTTAATCTACAATATAATACTCAATTCATAGTATCGACTTTTTGACATGTTTTATAGCTAT
* * * * * * *
28690832 TTTTTGAAAATTCATTGAAACCTTAATAAATTTTTAACGAAAATTCAACGTAAGTTTAGA
66 TTTCTAAAAACTCATTAAAACCTAAAGAAATTTTTAACAAAAATT-AA---AAGTTTAGA
*
28690892 AACCTCTTAATCTACAATATAATACTCAATTCATAGTATCGACTTTTTGACATGTTTTATGGCTA
1 AACCT-TTAATCTACAATATAATACTCAATTCATAGTATCGACTTTTTGACATGTTTTATAGCTA
28690957 TTTTCTAAAAACTCATTAAAACCTAAAGAAATTTTTAACAAAAATTAAAAGTTTAGA
65 TTTTCTAAAAACTCATTAAAACCTAAAGAAATTTTTAACAAAAATTAAAAGTTTAGA
28691014 AACCTATTAATC
1 AACCT-TTAATC
28691026 ATGTGAAAAC
Statistics
Matches: 124, Mismatches: 9, Indels: 5
0.90 0.07 0.04
Matches are distributed among these distances:
122 20 0.16
125 7 0.06
126 97 0.78
ACGTcount: A:0.39, C:0.15, G:0.08, T:0.38
Consensus pattern (121 bp):
AACCTTTAATCTACAATATAATACTCAATTCATAGTATCGACTTTTTGACATGTTTTATAGCTAT
TTTCTAAAAACTCATTAAAACCTAAAGAAATTTTTAACAAAAATTAAAAGTTTAGA
Found at i:28692732 original size:14 final size:14
Alignment explanation
Indices: 28692713--28692739 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
28692703 TGTGAATCGA
28692713 AACCAGGCATGTGT
1 AACCAGGCATGTGT
28692727 AACCAGGCATGTG
1 AACCAGGCATGTG
28692740 GCCGCCCGTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.22, G:0.30, T:0.19
Consensus pattern (14 bp):
AACCAGGCATGTGT
Found at i:28695062 original size:20 final size:21
Alignment explanation
Indices: 28695012--28695062 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
28695002 TGTCAGTCCT
* *
28695012 ATGAATAGTGGGGTCAAGTCC
1 ATGAATAGTGGAGTCAAATCC
28695033 AT-ATATAGTGGAGTCAAAT-C
1 ATGA-ATAGTGGAGTCAAATCC
28695053 ATGAATAGTG
1 ATGAATAGTG
28695063 ATGATATGTA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
20 10 0.38
21 16 0.62
ACGTcount: A:0.35, C:0.10, G:0.27, T:0.27
Consensus pattern (21 bp):
ATGAATAGTGGAGTCAAATCC
Found at i:28696214 original size:18 final size:19
Alignment explanation
Indices: 28696168--28696214 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 19
28696158 GTTCCCTAAG
*
28696168 TTAATTCAATTTATTCAAT
1 TTAATTCAATTAATTCAAT
* *
28696187 TTAAAT-AATTAATTTAAT
1 TTAATTCAATTAATTCAAT
28696205 TT-ATTCAATT
1 TTAATTCAATT
28696215 TTCAAAATAA
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
17 2 0.09
18 16 0.70
19 5 0.22
ACGTcount: A:0.40, C:0.06, G:0.00, T:0.53
Consensus pattern (19 bp):
TTAATTCAATTAATTCAAT
Found at i:28699917 original size:28 final size:28
Alignment explanation
Indices: 28699885--28700003 Score: 145
Period size: 28 Copynumber: 4.3 Consensus size: 28
28699875 TTCAAATATC
28699885 GCCACAAAGGCTGA-TCTTTTCATACTTT
1 GCCACAAAGGCT-ATTCTTTTCATACTTT
*
28699913 TCCACAAAGGCTATTCTTTTCATACTTT
1 GCCACAAAGGCTATTCTTTTCATACTTT
* * **
28699941 GCCACAAAGGTTATTATTTTCATACTCC
1 GCCACAAAGGCTATTCTTTTCATACTTT
*
28699969 GCCACAAAGGCT-TTCATTTCATGA-TTT
1 GCCACAAAGGCTATTCTTTTCAT-ACTTT
28699996 GCCACAAA
1 GCCACAAA
28700004 AGCATCATTT
Statistics
Matches: 78, Mismatches: 11, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
27 18 0.23
28 60 0.77
ACGTcount: A:0.28, C:0.25, G:0.12, T:0.35
Consensus pattern (28 bp):
GCCACAAAGGCTATTCTTTTCATACTTT
Found at i:28702462 original size:25 final size:25
Alignment explanation
Indices: 28702436--28702527 Score: 103
Period size: 25 Copynumber: 3.7 Consensus size: 25
28702426 TTCGACCCAT
* *
28702436 AGCTCATGTGAGCATATCGATTTAT
1 AGCTCATGTGAGCATACCGATTTAC
* * *
28702461 AGCTCGTGAGAGCATACCGATATAC
1 AGCTCATGTGAGCATACCGATTTAC
* * *
28702486 AACTCAAGTGAGCATACCGATTCAC
1 AGCTCATGTGAGCATACCGATTTAC
*
28702511 AGCTCATATGAGCATAC
1 AGCTCATGTGAGCATAC
28702528 ATGTACATGA
Statistics
Matches: 53, Mismatches: 14, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
25 53 1.00
ACGTcount: A:0.33, C:0.23, G:0.20, T:0.25
Consensus pattern (25 bp):
AGCTCATGTGAGCATACCGATTTAC
Found at i:28704416 original size:42 final size:43
Alignment explanation
Indices: 28704313--28704418 Score: 110
Period size: 42 Copynumber: 2.5 Consensus size: 43
28704303 GGCTGAAAGC
*
28704313 GCACTTTGTAGAACACATTTTCACTGACACGAGAGTAACAACAT
1 GCAC-TTGTAGAACACATTTTCACTGACACGAGACTAACAACAT
* ** * **
28704357 GCAC-TGTAGGATGCATTTTCACTGACACGATACTGAA-AATGT
1 GCACTTGTAGAACACATTTTCACTGACACGAGACT-AACAACAT
28704399 GC-CTTGTAGAACACATTTTC
1 GCACTTGTAGAACACATTTTC
28704419 CTTTCTCTCT
Statistics
Matches: 50, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
41 1 0.02
42 43 0.86
43 2 0.04
44 4 0.08
ACGTcount: A:0.32, C:0.22, G:0.18, T:0.28
Consensus pattern (43 bp):
GCACTTGTAGAACACATTTTCACTGACACGAGACTAACAACAT
Found at i:28709057 original size:57 final size:57
Alignment explanation
Indices: 28708988--28709101 Score: 228
Period size: 57 Copynumber: 2.0 Consensus size: 57
28708978 CCATATCTAC
28708988 CTGTATGAGACATTATTTTATAATCTTTTTTTACCTCATCATTTATGGTCTTTACCA
1 CTGTATGAGACATTATTTTATAATCTTTTTTTACCTCATCATTTATGGTCTTTACCA
28709045 CTGTATGAGACATTATTTTATAATCTTTTTTTACCTCATCATTTATGGTCTTTACCA
1 CTGTATGAGACATTATTTTATAATCTTTTTTTACCTCATCATTTATGGTCTTTACCA
28709102 ATAAAACCAA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 57 1.00
ACGTcount: A:0.25, C:0.18, G:0.09, T:0.49
Consensus pattern (57 bp):
CTGTATGAGACATTATTTTATAATCTTTTTTTACCTCATCATTTATGGTCTTTACCA
Found at i:28710552 original size:20 final size:20
Alignment explanation
Indices: 28710519--28710557 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
28710509 AATAATTGCT
28710519 TGATGATTATATTTGAATGA
1 TGATGATTATATTTGAATGA
*
28710539 TGATAGATTA-ATTTTAATG
1 TGAT-GATTATATTTGAATG
28710558 TTATAAATTG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.36, C:0.00, G:0.18, T:0.46
Consensus pattern (20 bp):
TGATGATTATATTTGAATGA
Found at i:28713388 original size:40 final size:40
Alignment explanation
Indices: 28713342--28713418 Score: 120
Period size: 40 Copynumber: 1.9 Consensus size: 40
28713332 ACTCCTCGTT
*
28713342 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATT-TAGTAACTCGCA
*
28713382 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTC
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTC
28713419 TAGCACGTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
40 32 0.94
41 2 0.06
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
Found at i:28713459 original size:27 final size:27
Alignment explanation
Indices: 28713421--28713479 Score: 118
Period size: 27 Copynumber: 2.2 Consensus size: 27
28713411 AGTAACTCTA
28713421 GCACGTATAGCATAAGCTCTAGCAGGC
1 GCACGTATAGCATAAGCTCTAGCAGGC
28713448 GCACGTATAGCATAAGCTCTAGCAGGC
1 GCACGTATAGCATAAGCTCTAGCAGGC
28713475 GCACG
1 GCACG
28713480 AGCCTCGGAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.29, C:0.27, G:0.27, T:0.17
Consensus pattern (27 bp):
GCACGTATAGCATAAGCTCTAGCAGGC
Found at i:28716271 original size:39 final size:40
Alignment explanation
Indices: 28716187--28716369 Score: 216
Period size: 40 Copynumber: 4.7 Consensus size: 40
28716177 GCTCCTCGTT
*
28716187 CAAATGCCTTC-GGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
*
28716226 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* *
28716266 C-AATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * * * *
28716304 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAAC-TCGCA
28716345 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
28716370 CATCATTCAA
Statistics
Matches: 124, Mismatches: 13, Indels: 13
0.83 0.09 0.09
Matches are distributed among these distances:
38 25 0.20
39 32 0.26
40 54 0.44
41 13 0.10
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:28716285 original size:78 final size:79
Alignment explanation
Indices: 28716189--28716369 Score: 215
Period size: 78 Copynumber: 2.3 Consensus size: 79
28716179 TCCTCGTTCA
* * *
28716189 AATGCCTTCGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGGA
1 AATGCCTTCGGGCTTAGCCCGGAAT-TAGTAACTCGCACAAATGCCTTC-GGATCTTAACCCGGA
* *
28716252 TTTAGTAAC-TCGCAC
64 TATAGTAACTTAGCAC
* **
28716267 AATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCGGATA
1 AATGCCTTCGGGCTTAGCCCGGAATTAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGATA
* *
28716332 TGGTCACTTAGCAC
66 TAGTAACTTAGCAC
*
28716346 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGG-CTTAGCCCGGA
28716370 CATCATTCAA
Statistics
Matches: 88, Mismatches: 11, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
77 3 0.03
78 57 0.65
79 17 0.19
80 11 0.12
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (79 bp):
AATGCCTTCGGGCTTAGCCCGGAATTAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGATA
TAGTAACTTAGCAC
Found at i:28734210 original size:19 final size:19
Alignment explanation
Indices: 28734186--28734222 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
28734176 TGTGTGATAG
28734186 GTGATAGAGATAGACCCAA
1 GTGATAGAGATAGACCCAA
*
28734205 GTGATAGAGGTAGACCCA
1 GTGATAGAGATAGACCCA
28734223 TTACAGAACA
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:0.38, C:0.16, G:0.30, T:0.16
Consensus pattern (19 bp):
GTGATAGAGATAGACCCAA
Found at i:28757245 original size:17 final size:18
Alignment explanation
Indices: 28757218--28757258 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
28757208 AAGGCCATTT
28757218 TGGGTCGTGTGGG-CCACA
1 TGGG-CGTGTGGGCCCACA
28757236 TGGGCGTGTGGGCCCACA
1 TGGGCGTGTGGGCCCACA
28757254 TGGGC
1 TGGGC
28757259 ATGCAACATG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 8 0.36
18 14 0.64
ACGTcount: A:0.10, C:0.24, G:0.46, T:0.20
Consensus pattern (18 bp):
TGGGCGTGTGGGCCCACA
Found at i:28757793 original size:34 final size:34
Alignment explanation
Indices: 28757733--28757798 Score: 82
Period size: 34 Copynumber: 1.9 Consensus size: 34
28757723 ACTGTACTGT
* *
28757733 AATGGGCTAAGGCCCTAATGCTTACTGTTACTAA
1 AATGGGCTAAGGCCCTAATGCATACTGATACTAA
28757767 AATGGGCTAAGG-CCTAAACTG-ATACTGATACT
1 AATGGGCTAAGGCCCT-AA-TGCATACTGATACT
28757799 GATATTGAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
33 3 0.11
34 23 0.82
35 2 0.07
ACGTcount: A:0.32, C:0.20, G:0.21, T:0.27
Consensus pattern (34 bp):
AATGGGCTAAGGCCCTAATGCATACTGATACTAA
Found at i:28759788 original size:14 final size:14
Alignment explanation
Indices: 28759769--28759795 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
28759759 GCTACCATTT
28759769 TACTATTTTGTTGC
1 TACTATTTTGTTGC
28759783 TACTATTTTGTTG
1 TACTATTTTGTTG
28759796 TTATTGTTTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.15, C:0.11, G:0.15, T:0.59
Consensus pattern (14 bp):
TACTATTTTGTTGC
Found at i:28760358 original size:31 final size:29
Alignment explanation
Indices: 28760323--28760393 Score: 79
Period size: 31 Copynumber: 2.3 Consensus size: 29
28760313 AAGTCCACTC
* *
28760323 ATTTTTTTAAATTTTTAAATATATTTATATT
1 ATTTTTTTAAATATTT-AATAAATTTATA-T
*
28760354 ATTTTTATTTAATATTTAATAAATTTATAT
1 ATTTTT-TTAAATATTTAATAAATTTATAT
28760384 ATTTTATTTA
1 ATTTT-TTTA
28760394 TTAAAATGTT
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
30 8 0.24
31 18 0.53
32 8 0.24
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (29 bp):
ATTTTTTTAAATATTTAATAAATTTATAT
Found at i:28761387 original size:97 final size:88
Alignment explanation
Indices: 28761125--28761397 Score: 287
Period size: 88 Copynumber: 3.0 Consensus size: 88
28761115 ATTTCAGACC
* ** * *
28761125 ACTTAATTTGGAGTTGAAATGGTAATTTTTCTTTTCACCTTTATACTTAAAATCAGTATTTTTTT
1 ACTTAATTTGAAAATGAAATGGTAATTTTCCTTTTCACCTTTATACTTGAAATCAGTATTTTTTT
*
28761190 TTTCAATTGAACGCTGAACTTGT
66 TTTCAATTGAACTCTGAACTTGT
* * * * * *
28761213 ACTTAATTTGAAATTCAAATGGTTATTTTCCTTTTCACCTTTATAATTGAAATTAGTTTTTTTTT
1 ACTTAATTTGAAAATGAAATGGTAATTTTCCTTTTCACCTTTATACTTGAAATCAG--TATTTTT
*
28761278 TTTTTCAGTTGAACT-TCGAACTTGT
64 TTTTTCAATTGAACTCT-GAACTTGT
* *
28761303 ACTTAATTTGGAGTTGAAAATGAAATGGTAATTTTCCTTTTTCACCTTTACACTTGAAATCAATA
1 ACTTAA--T----TTGAAAATGAAATGGTAATTTTCC-TTTTCACCTTTATACTTGAAATCAGT-
*
28761368 CATATTTTTTTTCAATTGAACTCTGAACTT
58 -ATTTTTTTTTTCAATTGAACTCTGAACTT
28761398 AAATTTATTG
Statistics
Matches: 151, Mismatches: 21, Indels: 17
0.80 0.11 0.09
Matches are distributed among these distances:
88 48 0.32
89 1 0.01
90 33 0.22
92 1 0.01
95 1 0.01
96 21 0.14
97 45 0.30
98 1 0.01
ACGTcount: A:0.28, C:0.13, G:0.11, T:0.48
Consensus pattern (88 bp):
ACTTAATTTGAAAATGAAATGGTAATTTTCCTTTTCACCTTTATACTTGAAATCAGTATTTTTTT
TTTCAATTGAACTCTGAACTTGT
Found at i:28761923 original size:39 final size:38
Alignment explanation
Indices: 28761827--28761936 Score: 107
Period size: 39 Copynumber: 2.8 Consensus size: 38
28761817 AGCGTTTGGA
*
28761827 TAAAAAACGCGCTAAAAATCGAGCATCAGCGGCGCTTT
1 TAAAAAACGCGCTAAAAATAGAGCATCAGCGGCGCTTT
* * * * *
28761865 TAGGAAGACGTTGCT-AAAATAGAGTA-CTAGTGGCGCTTT
1 TA-AAAAACG-CGCTAAAAATAGAGCATC-AGCGGCGCTTT
*
28761904 TAAAAAACGCCGCTAAAAATAGAGCATTAGCGG
1 TAAAAAACG-CGCTAAAAATAGAGCATCAGCGG
28761937 TGTTTTCCAG
Statistics
Matches: 54, Mismatches: 13, Indels: 9
0.71 0.17 0.12
Matches are distributed among these distances:
38 11 0.20
39 40 0.74
40 3 0.06
ACGTcount: A:0.37, C:0.18, G:0.24, T:0.21
Consensus pattern (38 bp):
TAAAAAACGCGCTAAAAATAGAGCATCAGCGGCGCTTT
Found at i:28762024 original size:41 final size:41
Alignment explanation
Indices: 28761959--28762137 Score: 254
Period size: 41 Copynumber: 4.4 Consensus size: 41
28761949 AGCACCGCAA
* * *
28761959 GCGCCGCTAATGCTCTGGGCTTTAGCGGCGTTTTTTAAAAG
1 GCGCCGCTAATGCTCTGGGCTTTAGCGGCATTTTTGAAAAT
* *
28762000 GCGCCGCTAATGCTCTAGGATTTAGCGGCATTTTTGAAAAT
1 GCGCCGCTAATGCTCTGGGCTTTAGCGGCATTTTTGAAAAT
* *
28762041 ACGCCGCTAATACTCTGGGCTTTAGCGGCATTTTTGAAAAT
1 GCGCCGCTAATGCTCTGGGCTTTAGCGGCATTTTTGAAAAT
*
28762082 GCGCCGCTAATGCTCTGGGCTTTAG-AGCATTTTTGAAAA-
1 GCGCCGCTAATGCTCTGGGCTTTAGCGGCATTTTTGAAAAT
* *
28762121 GTGCTGCTAATGCTCTG
1 GCGCCGCTAATGCTCTG
28762138 TTTTTGAAAA
Statistics
Matches: 124, Mismatches: 14, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
39 15 0.12
40 13 0.10
41 96 0.77
ACGTcount: A:0.21, C:0.21, G:0.26, T:0.32
Consensus pattern (41 bp):
GCGCCGCTAATGCTCTGGGCTTTAGCGGCATTTTTGAAAAT
Found at i:28762529 original size:14 final size:14
Alignment explanation
Indices: 28762510--28762629 Score: 84
Period size: 14 Copynumber: 8.4 Consensus size: 14
28762500 TATCACTATA
*
28762510 GTTTAGGGTTTTTG
1 GTTTAGGGTTTATG
*
28762524 GTTTAGGGTATATG
1 GTTTAGGGTTTATG
* *
28762538 GTTTAGAGTTTAAG
1 GTTTAGGGTTTATG
*
28762552 GTTTAGGTGTTACCAT-
1 GTTTAGG-GTT--TATG
*
28762568 -TTTAAGGTTTATG
1 GTTTAGGGTTTATG
*
28762581 GATTATGGGTTTATGG
1 GTTTA-GGGTTTAT-G
28762597 GTTTATGGG-TTATG
1 GTTTA-GGGTTTATG
* *
28762611 ATTTATGGTTTATG
1 GTTTAGGGTTTATG
28762625 GTTTA
1 GTTTA
28762630 AAGACTGGGA
Statistics
Matches: 82, Mismatches: 16, Indels: 16
0.72 0.14 0.14
Matches are distributed among these distances:
12 2 0.02
13 2 0.02
14 49 0.60
15 19 0.23
16 9 0.11
17 1 0.01
ACGTcount: A:0.19, C:0.02, G:0.30, T:0.49
Consensus pattern (14 bp):
GTTTAGGGTTTATG
Found at i:28762593 original size:15 final size:15
Alignment explanation
Indices: 28762573--28762625 Score: 58
Period size: 15 Copynumber: 3.6 Consensus size: 15
28762563 ACCATTTTAA
28762573 GGTTTATGGATTATG
1 GGTTTATGGATTATG
*
28762588 GGTTTATGGGTTTATG
1 GGTTTAT-GGATTATG
28762604 GG-TTAT-GATTTAT-
1 GGTTTATGGA-TTATG
28762617 GGTTTATGG
1 GGTTTATGG
28762626 TTTAAAGACT
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
13 3 0.09
14 8 0.25
15 12 0.38
16 9 0.28
ACGTcount: A:0.17, C:0.00, G:0.34, T:0.49
Consensus pattern (15 bp):
GGTTTATGGATTATG
Found at i:28762596 original size:8 final size:7
Alignment explanation
Indices: 28762510--28762629 Score: 73
Period size: 7 Copynumber: 16.7 Consensus size: 7
28762500 TATCACTATA
*
28762510 GTTTAGG
1 GTTTATG
*
28762517 GTTTTTG
1 GTTTATG
*
28762524 GTTTAGG
1 GTTTATG
*
28762531 GTATATG
1 GTTTATG
28762538 GTTTA-G
1 GTTTATG
*
28762544 AGTTTAAG
1 -GTTTATG
28762552 GTTTA-G
1 GTTTATG
**
28762558 GTGTTACCA
1 GT-TTA-TG
* *
28762567 TTTTAAG
1 GTTTATG
28762574 GTTTATG
1 GTTTATG
*
28762581 GATTATGG
1 GTTTAT-G
28762589 GTTTATGG
1 GTTTAT-G
28762597 GTTTATG
1 GTTTATG
*
28762604 GGTTATG
1 GTTTATG
*
28762611 ATTTATG
1 GTTTATG
28762618 GTTTATG
1 GTTTATG
28762625 GTTTA
1 GTTTA
28762630 AAGACTGGGA
Statistics
Matches: 88, Mismatches: 19, Indels: 12
0.74 0.16 0.10
Matches are distributed among these distances:
6 4 0.05
7 65 0.74
8 18 0.20
9 1 0.01
ACGTcount: A:0.19, C:0.02, G:0.30, T:0.49
Consensus pattern (7 bp):
GTTTATG
Found at i:28762804 original size:15 final size:14
Alignment explanation
Indices: 28762781--28762879 Score: 67
Period size: 14 Copynumber: 7.0 Consensus size: 14
28762771 GAGTTACTAT
*
28762781 ATTAAGGTTTATGG
1 ATTAGGGTTTATGG
*
28762795 ATTATGGGTTTAGGG
1 ATTA-GGGTTTATGG
* *
28762810 ATTAGGGATTAGGG
1 ATTAGGGTTTATGG
* *
28762824 GTTAAGGGTTTATAG
1 ATT-AGGGTTTATGG
* *
28762839 TTTATGGTTTAT-G
1 ATTAGGGTTTATGG
*
28762852 ATTCAGGGTTTAAGG
1 ATT-AGGGTTTATGG
*
28762867 A-TAGGGGTTATGG
1 ATTAGGGTTTATGG
28762880 GTTTAGATTG
Statistics
Matches: 67, Mismatches: 14, Indels: 9
0.74 0.16 0.10
Matches are distributed among these distances:
13 12 0.18
14 31 0.46
15 24 0.36
ACGTcount: A:0.24, C:0.01, G:0.35, T:0.39
Consensus pattern (14 bp):
ATTAGGGTTTATGG
Found at i:28766628 original size:20 final size:20
Alignment explanation
Indices: 28766591--28766628 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
28766581 TCTAGATATT
* *
28766591 TTTTTGTTGGTGGTTAGAGA
1 TTTTTGTTGCTGGATAGAGA
28766611 TTTTTGTTGCTGGATAGA
1 TTTTTGTTGCTGGATAGA
28766629 AATGTGTTTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.16, C:0.03, G:0.32, T:0.50
Consensus pattern (20 bp):
TTTTTGTTGCTGGATAGAGA
Found at i:28768656 original size:23 final size:24
Alignment explanation
Indices: 28768630--28768689 Score: 70
Period size: 23 Copynumber: 2.5 Consensus size: 24
28768620 TTAATACTAA
28768630 TTAATTTTTTATA-TTAATAATGT
1 TTAATTTTTTATATTTAATAATGT
* * *
28768653 TTAA-TTTTAATATTTAATATTTT
1 TTAATTTTTTATATTTAATAATGT
28768676 TTAATGTTTTTATA
1 TTAAT-TTTTTATA
28768690 AAGAATGGTA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
22 7 0.23
23 16 0.53
25 7 0.23
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.63
Consensus pattern (24 bp):
TTAATTTTTTATATTTAATAATGT
Found at i:28779979 original size:26 final size:26
Alignment explanation
Indices: 28779943--28779999 Score: 114
Period size: 26 Copynumber: 2.2 Consensus size: 26
28779933 AATTAAGATT
28779943 AACATCATTACAGGTAAGATAAAACC
1 AACATCATTACAGGTAAGATAAAACC
28779969 AACATCATTACAGGTAAGATAAAACC
1 AACATCATTACAGGTAAGATAAAACC
28779995 AACAT
1 AACAT
28780000 TTTTCCGGCC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.51, C:0.19, G:0.11, T:0.19
Consensus pattern (26 bp):
AACATCATTACAGGTAAGATAAAACC
Found at i:28780496 original size:24 final size:22
Alignment explanation
Indices: 28780465--28780584 Score: 89
Period size: 22 Copynumber: 5.2 Consensus size: 22
28780455 AAAATAATCA
*
28780465 AAAAAAATTTTGAATTACAGGGAC
1 AAAAAAA--TTGAATTATAGGGAC
* *
28780489 AAAAAAATTGATTTATAGGGAT
1 AAAAAAATTGAATTATAGGGAC
* **
28780511 AAACAAATCAAATTATAGGGAC
1 AAAAAAATTGAATTATAGGGAC
* * *
28780533 AAAAAAACGTTAAATTACAAGGAC
1 AAAAAAA--TTGAATTATAGGGAC
*
28780557 ATAAAAAGGTTGAATTATAGGGA-
1 A-AAAAA-ATTGAATTATAGGGAC
28780580 AAAAA
1 AAAAA
28780585 TCGACTTACA
Statistics
Matches: 76, Mismatches: 16, Indels: 10
0.75 0.16 0.10
Matches are distributed among these distances:
22 39 0.51
23 1 0.01
24 31 0.41
25 5 0.07
ACGTcount: A:0.54, C:0.07, G:0.17, T:0.23
Consensus pattern (22 bp):
AAAAAAATTGAATTATAGGGAC
Found at i:28780499 original size:22 final size:22
Alignment explanation
Indices: 28780465--28780695 Score: 84
Period size: 22 Copynumber: 10.4 Consensus size: 22
28780455 AAAATAATCA
28780465 AAAAAAATTTTGAATTACAGGGAC
1 AAAAAAA--TTGAATTACAGGGAC
* * *
28780489 AAAAAAATTGATTTATAGGGAT
1 AAAAAAATTGAATTACAGGGAC
* ** *
28780511 AAACAAATCAAATTATAGGGAC
1 AAAAAAATTGAATTACAGGGAC
* *
28780533 AAAAAAACGTTAAATTACAAGGAC
1 AAAAAAA--TTGAATTACAGGGAC
* *
28780557 ATAAAAAGGTTGAATTATAGGG--
1 A-AAAAA-ATTGAATTACAGGGAC
* *
28780579 -AAAAAATCGACTTACA-GGA-
1 AAAAAAATTGAATTACAGGGAC
* *
28780598 AAAAAAA--GAACTAC-GCGAAC
1 AAAAAAATTGAATTACAG-GGAC
** *
28780618 TAAAAATTTTGAATTATAGGGAC
1 -AAAAAAATTGAATTACAGGGAC
* * *
28780641 -AAAAAGTTCAATTTACAGTGAC
1 AAAAAAATTGAA-TTACAGGGAC
* * *
28780663 AAAAAAAAGTCGAATTACAAGGAG
1 -AAAAAAA-TTGAATTACAGGGAC
28780687 AAAAAAATT
1 AAAAAAATT
28780696 TTGACTTATA
Statistics
Matches: 150, Mismatches: 40, Indels: 36
0.66 0.18 0.16
Matches are distributed among these distances:
18 7 0.05
19 9 0.06
20 11 0.07
21 13 0.09
22 44 0.29
23 15 0.10
24 43 0.29
25 8 0.05
ACGTcount: A:0.53, C:0.09, G:0.16, T:0.22
Consensus pattern (22 bp):
AAAAAAATTGAATTACAGGGAC
Found at i:28780728 original size:70 final size:71
Alignment explanation
Indices: 28780619--28780756 Score: 156
Period size: 70 Copynumber: 2.0 Consensus size: 71
28780609 TACGCGAACT
** ** * *
28780619 AAAAATTTTGAATTATAGGGACAAAAAGTTCAATTTACAGTG-ACAAAAAA-AAGTCGAATTACA
1 AAAAATTTTGAATTATAGGGACAAAAAGAACAAACTACAG-GAACAAAAAAGAAATAGAATTACA
28780682 AGGAGAA
65 AGGAGAA
* * *
28780689 AAAAATTTTGACTTATAGGGAGAACAAA-AACAAACTACAGGAACAAAAAAGAAATAGAATTATA
1 AAAAATTTTGAATTATAGGGACAA-AAAGAACAAACTACAGGAACAAAAAAGAAATAGAATTACA
28780753 AGGA
65 AGGA
28780757 TCGAAAATTC
Statistics
Matches: 56, Mismatches: 9, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
69 1 0.02
70 38 0.68
71 17 0.30
ACGTcount: A:0.54, C:0.09, G:0.17, T:0.20
Consensus pattern (71 bp):
AAAAATTTTGAATTATAGGGACAAAAAGAACAAACTACAGGAACAAAAAAGAAATAGAATTACAA
GGAGAA
Found at i:28783686 original size:31 final size:29
Alignment explanation
Indices: 28783643--28783710 Score: 75
Period size: 30 Copynumber: 2.3 Consensus size: 29
28783633 TTTTATAAAT
* *
28783643 AATTAATATTTAT-TAATTAAAAATATTTAC
1 AATTTATATTTATAT-ATT-AAAATATTAAC
28783673 AATTTATATTTTATATATTAAAATATTAAC
1 AATTTATA-TTTATATATTAAAATATTAAC
*
28783703 AAGTTATA
1 AATTTATA
28783711 ATAATTTTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
30 24 0.73
31 8 0.24
32 1 0.03
ACGTcount: A:0.49, C:0.03, G:0.01, T:0.47
Consensus pattern (29 bp):
AATTTATATTTATATATTAAAATATTAAC
Found at i:28783889 original size:13 final size:13
Alignment explanation
Indices: 28783873--28783920 Score: 51
Period size: 13 Copynumber: 3.7 Consensus size: 13
28783863 TAAATCAAAT
*
28783873 TTTTTAAAAACAC
1 TTTTCAAAAACAC
*
28783886 TTTTCAAAATCAC
1 TTTTCAAAAACAC
* **
28783899 TTTTCTACGACAC
1 TTTTCAAAAACAC
28783912 TTTTCAAAA
1 TTTTCAAAA
28783921 TTCTCACAGT
Statistics
Matches: 26, Mismatches: 9, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.38, C:0.21, G:0.02, T:0.40
Consensus pattern (13 bp):
TTTTCAAAAACAC
Found at i:28790193 original size:62 final size:59
Alignment explanation
Indices: 28790073--28790197 Score: 135
Period size: 62 Copynumber: 2.1 Consensus size: 59
28790063 ATATTTGTAC
* * * ****
28790073 AAATTGTTTTTATATTGTTTCATTTAATAAAATAAAAGTTGTTTTGAATATTTTAATAG
1 AAATTATTTTTATATTGTTTCATTTAATAAAATAAAAGTTCTTTTAAATAAGGCAATAG
*
28790132 TAAATTATTTTTATATT-TTGTCCTATTTAATAAAATAGAAGTTCTTTTAAATAAGGCAATAG
1 -AAATTATTTTTATATTGTT-T-C-ATTTAATAAAATAAAAGTTCTTTTAAATAAGGCAATAG
28790194 AAAT
1 AAAT
28790198 AATGCAATAG
Statistics
Matches: 54, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
59 2 0.04
60 16 0.30
61 5 0.09
62 31 0.57
ACGTcount: A:0.39, C:0.04, G:0.10, T:0.47
Consensus pattern (59 bp):
AAATTATTTTTATATTGTTTCATTTAATAAAATAAAAGTTCTTTTAAATAAGGCAATAG
Found at i:28790199 original size:14 final size:14
Alignment explanation
Indices: 28790180--28790218 Score: 69
Period size: 14 Copynumber: 2.8 Consensus size: 14
28790170 AAGTTCTTTT
*
28790180 AAATAAGGCAATAG
1 AAATAATGCAATAG
28790194 AAATAATGCAATAG
1 AAATAATGCAATAG
28790208 AAATAATGCAA
1 AAATAATGCAA
28790219 CATAATTTCA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.59, C:0.08, G:0.15, T:0.18
Consensus pattern (14 bp):
AAATAATGCAATAG
Found at i:28793384 original size:126 final size:126
Alignment explanation
Indices: 28793221--28793588 Score: 498
Period size: 126 Copynumber: 3.0 Consensus size: 126
28793211 TAAGGCCAAA
** *
28793221 CAGGAACTACTGT--AAAAAAA--GTCCACGT-GAGAGCTTTTTTCAGTAATTTTTTTGGCAGTG
1 CAGGAACTACTGTAGAAAAAAAGCGTCCACGTAG-GAGCTTTTTTCAGTAATTTTGCTGACAGTG
* * *
28793281 CATCTTGCTTGACGCGTTTTTGACATTATTTTTTCAGAATCGTCTTCTCAAAATTATTTTTT
65 CATCATGCTTGAAGCGTTTTTGACATTATTTTTTCAGAACCGTCTTCTCAAAATTATTTTTT
* *
28793343 CAGGAACTACTGTAGAAAAAAAGCGTCCACATAGGAGCTTTTTTCAGTAATTTTGCTAACAGTGC
1 CAGGAACTACTGTAGAAAAAAAGCGTCCACGTAGGAGCTTTTTTCAGTAATTTTGCTGACAGTGC
* * *
28793408 ATCCTGCTTGAAGCGTTTTTGAAACTATTTTTTTCAGAACCGTCTTCTCAAAATTATTTTTT
66 ATCATGCTTGAAGCGTTTTTGACATTA-TTTTTTCAGAACCGTCTTCTCAAAATTATTTTTT
** *
28793470 CAAAAACTACTGTAGAAAAAGAGCGTCCACGTAGGAG-TCTTTTT-AGTAATTTTGCTGACAGTG
1 CAGGAACTACTGTAGAAAAAAAGCGTCCACGTAGGAGCT-TTTTTCAGTAATTTTGCTGACAGTG
* * * *
28793533 CATCATGTTTGAAGTGTTTTCGACATTATCTTTTCAGAACCGTCTTCTCAAAATTA
65 CATCATGCTTGAAGCGTTTTTGACATTATTTTTTCAGAACCGTCTTCTCAAAATTA
28793589 ACTTTTCTAA
Statistics
Matches: 217, Mismatches: 22, Indels: 11
0.87 0.09 0.04
Matches are distributed among these distances:
122 13 0.06
124 7 0.03
125 27 0.12
126 98 0.45
127 72 0.33
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.38
Consensus pattern (126 bp):
CAGGAACTACTGTAGAAAAAAAGCGTCCACGTAGGAGCTTTTTTCAGTAATTTTGCTGACAGTGC
ATCATGCTTGAAGCGTTTTTGACATTATTTTTTCAGAACCGTCTTCTCAAAATTATTTTTT
Found at i:28793716 original size:34 final size:33
Alignment explanation
Indices: 28793671--28793794 Score: 122
Period size: 34 Copynumber: 3.7 Consensus size: 33
28793661 CTAAACACAA
*
28793671 AATTATTTTAAAAAAACTAAACCCTAATTTAATT
1 AATT-TTTTAAAAACACTAAACCCTAATTTAATT
* *
28793705 AATTTTCTTAAAAACTCTAAACCTTAATTTAATT
1 AATTTT-TTAAAAACACTAAACCCTAATTTAATT
* * * * *
28793739 AATTTATTTTAAACCCCTAAAACCTAATTGAATT
1 AATTT-TTTAAAAACACTAAACCCTAATTTAATT
* **
28793773 AATTTTTTTAAAATTCTAAACC
1 AATTTTTTAAAAACACTAAACC
28793795 TTGATTTATT
Statistics
Matches: 75, Mismatches: 13, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
33 15 0.20
34 59 0.79
35 1 0.01
ACGTcount: A:0.44, C:0.15, G:0.01, T:0.41
Consensus pattern (33 bp):
AATTTTTTAAAAACACTAAACCCTAATTTAATT
Found at i:28795021 original size:20 final size:20
Alignment explanation
Indices: 28794996--28795038 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
28794986 TTTTTTGGTA
28794996 AAATAACAAAATATAGTAAT
1 AAATAACAAAATATAGTAAT
*
28795016 AAATAACAAAATATGGTAAT
1 AAATAACAAAATATAGTAAT
28795036 AAA
1 AAA
28795039 ACATCATGAC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.65, C:0.05, G:0.07, T:0.23
Consensus pattern (20 bp):
AAATAACAAAATATAGTAAT
Found at i:28798220 original size:268 final size:265
Alignment explanation
Indices: 28797726--28798230 Score: 708
Period size: 268 Copynumber: 1.9 Consensus size: 265
28797716 TAAACTTGCT
* * *
28797726 TAATAAAAGTACTTGTATATCATTTTAGTCATTTTATTTTATGTTAATAATATATATGCATATAT
1 TAATAAAAGTACTTGTACATCATTTTAGTCATTTTATTTTATGTTAATAATATATATGAATAAAT
* * * * * *
28797791 ATATTACTTCGCTAATGGATAGGTTATGAGTGAAGGTTTTGGAAATGTGACCAAATTGAGTAACC
66 ATACTACTCCACTAATGAATAGGTTATGAGTGAAGATTTTGGAAATGTGACCAAATTAAGTAACC
* *
28797856 GAGATAAGGTGCTTGAGTTGTCATCTCACCTCGCGTAAAAAGATTCAAGTGACGAACCAAAACCT
131 GAGATAAGGTGCTTGAGTTGTCATCTCACCTCGCATAAAAAGATCCAAGTGACGAACCAAAACCT
* * * *
28797921 GCAAACACTCTGCTAGCCGAGTTTCCATGAGTAGGGGAAAAATAATTCGTTTAGAGACGTATCAA
196 GCAAACACTCTGCTAACCAAGTGTCCATGAGTA-AGGAAAAATAATTCGTTTAGAGACGTATCAA
28797986 ATCGAG
260 ATCGAG
*
28797992 TAATAAAAGTACTTGTACCTCATTTTAGTCATTTTATTTTATGTTAATAATATATATAAGAATAA
1 TAATAAAAGTACTTGTACATCATTTTAGTCATTTTATTTTATGTTAATAATATATAT--GAATAA
* * *
28798057 ATATACTACTCCATTGATGAATAGGTTATGAGTGAAGATTTTGGAAATGTGAGCAAATTAAGTAA
64 ATATACTACTCCACTAATGAATAGGTTATGAGTGAAGATTTTGGAAATGTGACCAAATTAAGTAA
* * * * *
28798122 CCGAGATAAGGTTCTTGGGTTGTTC-TCTCACCTTGCATAAAAAGATCCGAGTGACGAACCGAAA
129 CCGAGATAAGGTGCTTGAGTTG-TCATCTCACCTCGCATAAAAAGATCCAAGTGACGAACCAAAA
* * *
28798186 CTTGCAAACACTCTGGTAATCAAGCTGT-CATGAGTAAGGAAAAAT
193 CCTGCAAACACTCTGCTAACCAAG-TGTCCATGAGTAAGGAAAAAT
28798231 TGAGTAACCT
Statistics
Matches: 208, Mismatches: 27, Indels: 7
0.86 0.11 0.03
Matches are distributed among these distances:
266 55 0.26
267 8 0.04
268 141 0.68
269 4 0.02
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.32
Consensus pattern (265 bp):
TAATAAAAGTACTTGTACATCATTTTAGTCATTTTATTTTATGTTAATAATATATATGAATAAAT
ATACTACTCCACTAATGAATAGGTTATGAGTGAAGATTTTGGAAATGTGACCAAATTAAGTAACC
GAGATAAGGTGCTTGAGTTGTCATCTCACCTCGCATAAAAAGATCCAAGTGACGAACCAAAACCT
GCAAACACTCTGCTAACCAAGTGTCCATGAGTAAGGAAAAATAATTCGTTTAGAGACGTATCAAA
TCGAG
Found at i:28805694 original size:45 final size:45
Alignment explanation
Indices: 28805630--28805719 Score: 180
Period size: 45 Copynumber: 2.0 Consensus size: 45
28805620 TCAGCAAATC
28805630 CTGTTCTTCATTCCAAGATGAAACATGTTGAACTTGATCTTCATT
1 CTGTTCTTCATTCCAAGATGAAACATGTTGAACTTGATCTTCATT
28805675 CTGTTCTTCATTCCAAGATGAAACATGTTGAACTTGATCTTCATT
1 CTGTTCTTCATTCCAAGATGAAACATGTTGAACTTGATCTTCATT
28805720 TTGTCCGGGA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.27, C:0.20, G:0.13, T:0.40
Consensus pattern (45 bp):
CTGTTCTTCATTCCAAGATGAAACATGTTGAACTTGATCTTCATT
Found at i:28808056 original size:7 final size:7
Alignment explanation
Indices: 28808046--28808090 Score: 54
Period size: 7 Copynumber: 6.3 Consensus size: 7
28808036 GTTTTTGGGT
*
28808046 TTTATGG
1 TTTAGGG
28808053 TTTAGGG
1 TTTAGGG
28808060 TTTAGGG
1 TTTAGGG
*
28808067 TTTTAGAG
1 -TTTAGGG
*
28808075 TTTGGGG
1 TTTAGGG
28808082 TTTAGGG
1 TTTAGGG
28808089 TT
1 TT
28808091 AAAAATTAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
7 26 0.81
8 6 0.19
ACGTcount: A:0.13, C:0.00, G:0.38, T:0.49
Consensus pattern (7 bp):
TTTAGGG
Found at i:28808067 original size:22 final size:22
Alignment explanation
Indices: 28808042--28808090 Score: 73
Period size: 22 Copynumber: 2.2 Consensus size: 22
28808032 GCTTGTTTTT
28808042 GGGTTTTATG-GTTTAGGGTTTA
1 GGGTTTTA-GAGTTTAGGGTTTA
*
28808064 GGGTTTTAGAGTTTGGGGTTTA
1 GGGTTTTAGAGTTTAGGGTTTA
28808086 GGGTT
1 GGGTT
28808091 AAAAATTAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 1 0.04
22 24 0.96
ACGTcount: A:0.12, C:0.00, G:0.41, T:0.47
Consensus pattern (22 bp):
GGGTTTTAGAGTTTAGGGTTTA
Found at i:28809217 original size:225 final size:225
Alignment explanation
Indices: 28808489--28809271 Score: 1228
Period size: 225 Copynumber: 3.4 Consensus size: 225
28808479 GAACACCTCT
*
28808489 AGTTTAGGGTTTTTCAATTAAATTATTTAAAAAAATTTCAAAATTGGATTAGTTTTCGTGTTTAT
1 AGTTTAGGGTTTGTCAATTAAATTATTTAAAAAAATTTCAAAATTGGATTAGTTTTCGTGTTTAT
* *
28808554 TATTTTTTAAGAAAAAATCAATTAAATTATGGTTTAGGGTTACTTGAGTAATTTAATTTAAAAAA
66 TATTTTTTAAGAAAAAATCAATTAAATTAGGGTTTAGGGTTACTTGAGTAATTTAATTAAAAAAA
* ***
28808619 TTTTAAAGATTAGATTAGGGTTAGGGTTTTTGTTAGGGTTTTGGTGTTTTTAAGTTAAGGGTTTT
131 TTTTAAAAATTAGATTAGGGTTAGGGTTAGGGTTAGGGTTTTGGTGTTTTTAAGTTAAGGGTTTT
* * *
28808684 CATGGAAAAATCAAATAAGTTAGGGTTTAA
196 TAAGGAAAAATCAAATAAGTTAGGGTTTAG
*
28808714 AGTTTAGGGTTTGTCAATTAAATTATTTAAAAAAATTT-AAAATTGGATTAGTTTTCATGTTTAT
1 AGTTTAGGGTTTGTCAATTAAATTATTTAAAAAAATTTCAAAATTGGATTAGTTTTCGTGTTTAT
*
28808778 TATTTTTTAAGAAAAAATCAATTAAATTAGGATTTAGGGTTACTTGAGTAATTTAATTAAAAAAA
66 TATTTTTTAAGAAAAAATCAATTAAATTAGGGTTTAGGGTTACTTGAGTAATTTAATTAAAAAAA
* *
28808843 TTAAAAATTAAAAATTAGATTAGGGTTAGGGTTAGTGTTTTTTAGGGTTTTTGTGTTTTTAAGTT
131 TT-----TTAAAAATTAGATTAGGGTTAGGGTTAG-G---GTTAGGGTTTTGGTGTTTTTAAGTT
* *
28808908 AATGATTTTTAAGGAAAAATCAAATAAGTTAGGGTTTAG
187 AAGGGTTTTTAAGGAAAAATCAAATAAGTTAGGGTTTAG
28808947 AGTTTAGGGTTTGTCAATTAAATTATTTAAAAAAATTTCAAAATTGGATTAGTTTTCGTGTTTAT
1 AGTTTAGGGTTTGTCAATTAAATTATTTAAAAAAATTTCAAAATTGGATTAGTTTTCGTGTTTAT
* *
28809012 TA-TTTTTAAGAAAAAATTAATTAAATTGGGGTTTAGGGTTACTTGAGTAATTTAATTAAAAAAA
66 TATTTTTTAAGAAAAAATCAATTAAATTAGGGTTTAGGGTTACTTGAGTAATTTAATT-AAAAAA
*
28809076 ATTTTAAAAATTAGATTAGGGTTAGGGTTAGGGTTAGAGTTTTGGTGTTTTTAAGTTAAGGGTTT
130 ATTTTAAAAATTAGATTAGGGTTAGGGTTAGGGTTAGGGTTTTGGTGTTTTTAAGTTAAGGGTTT
28809141 TTAAGGAAAAATCAAATAAGTTAGGGTTTAG
195 TTAAGGAAAAATCAAATAAGTTAGGGTTTAG
**** *
28809172 AGTTTAGGGTTTGTCAATTAAATTATTTAAATTTTTTTTAAAATTGGATTAGTTTTCGTGTTTAT
1 AGTTTAGGGTTTGTCAATTAAATTATTTAAAAAAATTTCAAAATTGGATTAGTTTTCGTGTTTAT
* *
28809237 TATTTTTTAAGAAAATATGAATTAAATTAGGGTTT
66 TATTTTTTAAGAAAAAATCAATTAAATTAGGGTTT
28809272 TGGTGTTTTT
Statistics
Matches: 513, Mismatches: 33, Indels: 23
0.90 0.06 0.04
Matches are distributed among these distances:
224 89 0.17
225 158 0.31
226 29 0.06
228 1 0.00
229 53 0.10
233 147 0.29
234 36 0.07
ACGTcount: A:0.36, C:0.02, G:0.18, T:0.44
Consensus pattern (225 bp):
AGTTTAGGGTTTGTCAATTAAATTATTTAAAAAAATTTCAAAATTGGATTAGTTTTCGTGTTTAT
TATTTTTTAAGAAAAAATCAATTAAATTAGGGTTTAGGGTTACTTGAGTAATTTAATTAAAAAAA
TTTTAAAAATTAGATTAGGGTTAGGGTTAGGGTTAGGGTTTTGGTGTTTTTAAGTTAAGGGTTTT
TAAGGAAAAATCAAATAAGTTAGGGTTTAG
Found at i:28813350 original size:50 final size:50
Alignment explanation
Indices: 28813275--28813562 Score: 397
Period size: 50 Copynumber: 5.8 Consensus size: 50
28813265 ATTTGGGTAA
28813275 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** *
28813325 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGTGTTGGCACCGAGATA
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
*
28813375 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGAGAT-
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* * *
28813424 -GA---CCCATGTAAGACCATGTCTGGGACATTGCATTGGCACCGAAAGG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* ** * *
28813470 AGATGTCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCACCGATATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** *
28813520 AGAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
28813563 TGTTATTATC
Statistics
Matches: 210, Mismatches: 22, Indels: 11
0.86 0.09 0.05
Matches are distributed among these distances:
45 39 0.19
47 2 0.01
48 2 0.01
50 133 0.63
51 34 0.16
ACGTcount: A:0.26, C:0.23, G:0.30, T:0.21
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
Found at i:28813494 original size:95 final size:97
Alignment explanation
Indices: 28813274--28813562 Score: 366
Period size: 95 Copynumber: 2.9 Consensus size: 97
28813264 CATTTGGGTA
*
28813274 AAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCCCATGTA
1 AAGAGGTCCCACGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGAT-AGA-G-CCCATGTA
** * *
28813339 AGACCATGTCTGGGACATGGTGTTGGCACCGAGAT
63 AGACCATGTCTGGGACATGGCATTGGCACCGAAAG
* *
28813374 AAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGAGAT-GA-CCCATGTAAGA
1 AAGAGGTCCCACGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATAGAGCCCATGTAAGA
*
28813437 CCATGTCTGGGACATTGCATTGGCACCGAAAG
66 CCATGTCTGGGACATGGCATTGGCACCGAAAG
* * * * * *
28813469 GAGATGTCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCACCGATATGAGAACATCCCATGT
1 AAGAGGTCCCACGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGAT-AG---AGCCCATGT
*
28813534 AAGACCATGTCTGGGACATGGCTTTGGCA
62 AAGACCATGTCTGGGACATGGCATTGGCA
28813563 TGTTATTATC
Statistics
Matches: 168, Mismatches: 15, Indels: 11
0.87 0.08 0.06
Matches are distributed among these distances:
95 81 0.48
97 1 0.01
98 2 0.01
100 50 0.30
101 34 0.20
ACGTcount: A:0.27, C:0.22, G:0.30, T:0.21
Consensus pattern (97 bp):
AAGAGGTCCCACGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATAGAGCCCATGTAAGA
CCATGTCTGGGACATGGCATTGGCACCGAAAG
Found at i:28817736 original size:22 final size:22
Alignment explanation
Indices: 28817711--28817753 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
28817701 TCGTCAGCAA
28817711 ATATGTGAGGCTCAAAAAAATG
1 ATATGTGAGGCTCAAAAAAATG
28817733 ATATGTGAGGCTCAAAAAAAT
1 ATATGTGAGGCTCAAAAAAAT
28817754 AATGAGAAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.47, C:0.09, G:0.21, T:0.23
Consensus pattern (22 bp):
ATATGTGAGGCTCAAAAAAATG
Found at i:28820288 original size:13 final size:13
Alignment explanation
Indices: 28820270--28820296 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
28820260 TTTCCAGCAA
28820270 TTATGCATTTATT
1 TTATGCATTTATT
28820283 TTATGCATTTATT
1 TTATGCATTTATT
28820296 T
1 T
28820297 AATCTTGACT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.07, G:0.07, T:0.63
Consensus pattern (13 bp):
TTATGCATTTATT
Found at i:28820460 original size:50 final size:50
Alignment explanation
Indices: 28820400--28820683 Score: 335
Period size: 50 Copynumber: 5.8 Consensus size: 50
28820390 GGGTAAAGAT
* *
28820400 GTCCCATGTAATACCATATCTGGGACATGGCGTTGGCACCGAGATGAGAG
1 GTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAG
* *
28820450 GTCCCATGTAAGAGCATGTCTGGGACATGGTGTTGGCACCGAGATGAGAG
1 GTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAG
* * *
28820500 GTCCCATGTAAGACCATGTTTGGGACATGGCATTGGAACCGAGAT--GA-
1 GTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAG
* *
28820547 --CCCATGTAAGACCATGTCTGGGACATGGTGTTGGCACCGAGACGAGAG
1 GTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAG
** * * * * * *
28820595 GTCCCCCGTAAGACCATGTCTGGGACGTGACATTGGTACCGAAATGAGAAC
1 GTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAG-AG
* * * *
28820646 ATCCCATGTAAGACCATGTTTAGGACATGGCTTTGGCA
1 GTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA
28820684 TGTTATTATC
Statistics
Matches: 195, Mismatches: 33, Indels: 11
0.82 0.14 0.05
Matches are distributed among these distances:
45 38 0.19
47 2 0.01
48 2 0.01
50 123 0.63
51 30 0.15
ACGTcount: A:0.26, C:0.21, G:0.30, T:0.22
Consensus pattern (50 bp):
GTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAG
Found at i:28820573 original size:95 final size:96
Alignment explanation
Indices: 28820400--28820683 Score: 329
Period size: 95 Copynumber: 2.9 Consensus size: 96
28820390 GGGTAAAGAT
* * * * *
28820400 GTCCCATGTAATACCATATCTGGGACATGGCGTTGGCACCGAGATGAGAGGTCCCATGTAAGAGC
1 GTCCCATGTAAGACCATGTCTGGGACATGGCATTGGAACCGAGAT--GA-G-CCCATGTAAGACC
*
28820465 ATGTCTGGGACATGGTGTTGGCACCGAGATGAGAG
62 ATGTCTGGGACATGGTGTTGGCACCGAGACGAGAG
*
28820500 GTCCCATGTAAGACCATGTTTGGGACATGGCATTGGAACCGAGATGA-CCCATGTAAGACCATGT
1 GTCCCATGTAAGACCATGTCTGGGACATGGCATTGGAACCGAGATGAGCCCATGTAAGACCATGT
28820564 CTGGGACATGGTGTTGGCACCGAGACGAGAG
66 CTGGGACATGGTGTTGGCACCGAGACGAGAG
** * * * *
28820595 GTCCCCCGTAAGACCATGTCTGGGACGTGACATTGGTACCGAAATGAGAACATCCCATGTAAGAC
1 GTCCCATGTAAGACCATGTCTGGGACATGGCATTGGAACCGAGATGAG-----CCCATGTAAGAC
* *
28820660 CATGTTTAGGACATGGCT-TTGGCA
61 CATGTCTGGGACATGG-TGTTGGCA
28820684 TGTTATTATC
Statistics
Matches: 161, Mismatches: 16, Indels: 13
0.85 0.08 0.07
Matches are distributed among these distances:
95 86 0.53
98 2 0.01
100 40 0.25
101 32 0.20
102 1 0.01
ACGTcount: A:0.26, C:0.21, G:0.30, T:0.22
Consensus pattern (96 bp):
GTCCCATGTAAGACCATGTCTGGGACATGGCATTGGAACCGAGATGAGCCCATGTAAGACCATGT
CTGGGACATGGTGTTGGCACCGAGACGAGAG
Found at i:28820643 original size:145 final size:146
Alignment explanation
Indices: 28820396--28820681 Score: 403
Period size: 145 Copynumber: 2.0 Consensus size: 146
28820386 ATTTGGGTAA
* * * *
28820396 AGATGTCCCATGTAATACCATATCTGGGACATGGCGTTGGCACCGAGATGAGAGGTCCCATGTAA
1 AGATGACCCATGTAAGACCATATCTGGGACATGGCGTTGGCACCGAGACGAGAGGTCCCACGTAA
* *** * ** *
28820461 GAGCATGTCTGGGACATGGTGTTGGCACCGAGATGAG-AGGTCCCATGTAAGACCATGTTTGGGA
66 GACCATGTCTGGGACATGACATTGGCACCGAAATGAGAACATCCCATGTAAGACCATGTTTAGGA
28820525 CATGGCATTGGAACCG
131 CATGGCATTGGAACCG
* * *
28820541 AGATGACCCATGTAAGACCATGTCTGGGACATGGTGTTGGCACCGAGACGAGAGGTCCCCCGTAA
1 AGATGACCCATGTAAGACCATATCTGGGACATGGCGTTGGCACCGAGACGAGAGGTCCCACGTAA
* *
28820606 GACCATGTCTGGGACGTGACATTGGTACCGAAATGAGAACATCCCATGTAAGACCATGTTTAGGA
66 GACCATGTCTGGGACATGACATTGGCACCGAAATGAGAACATCCCATGTAAGACCATGTTTAGGA
*
28820671 CATGGCTTTGG
131 CATGGCATTGG
28820682 CATGTTATTA
Statistics
Matches: 122, Mismatches: 18, Indels: 1
0.87 0.13 0.01
Matches are distributed among these distances:
145 88 0.72
146 34 0.28
ACGTcount: A:0.26, C:0.21, G:0.30, T:0.22
Consensus pattern (146 bp):
AGATGACCCATGTAAGACCATATCTGGGACATGGCGTTGGCACCGAGACGAGAGGTCCCACGTAA
GACCATGTCTGGGACATGACATTGGCACCGAAATGAGAACATCCCATGTAAGACCATGTTTAGGA
CATGGCATTGGAACCG
Found at i:28822570 original size:41 final size:40
Alignment explanation
Indices: 28822396--28822622 Score: 291
Period size: 40 Copynumber: 5.7 Consensus size: 40
28822386 TTGAATGATG
* * * *
28822396 ATCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCAT
1 ATCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAA
* *
28822436 ATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAA
1 ATCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAA
* *
28822476 TTCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAA
1 ATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAA
*
28822515 ATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 ATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT-AA
*
28822556 ATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA
1 ATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-A
*
28822597 A-CCGGGCTATGTCCCGAAGGCATTTG
1 ATCCGGGCTAAGTCCCGAAGGCATTTG
28822623 AACGAGGAGC
Statistics
Matches: 166, Mismatches: 15, Indels: 12
0.86 0.08 0.06
Matches are distributed among these distances:
39 34 0.20
40 82 0.49
41 50 0.30
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
ATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAA
Found at i:28830466 original size:40 final size:40
Alignment explanation
Indices: 28830382--28830606 Score: 296
Period size: 40 Copynumber: 5.7 Consensus size: 40
28830372 TTGAATGATG
* * * *
28830382 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* * *
28830422 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
*
28830462 TCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
28830501 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
28830541 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
28830582 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
28830607 AACGAGGAGC
Statistics
Matches: 165, Mismatches: 15, Indels: 10
0.87 0.08 0.05
Matches are distributed among these distances:
39 34 0.21
40 121 0.73
41 10 0.06
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:28830628 original size:119 final size:119
Alignment explanation
Indices: 28830382--28830639 Score: 283
Period size: 119 Copynumber: 2.2 Consensus size: 119
28830372 TTGAATGATG
* *
28830382 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCTTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATTT
* ** *
28830447 GTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAAA
66 GTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTGACTAAA
* * * **
28830501 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCAT
1 TCCGGGTTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCAT
* * * *
28830564 TTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-GAGCTATA
64 TTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTGGAACGAGTGA-CTAAA
* *
28830621 TCC-GGTTAAATTCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
28830640 TACGTGATTT
Statistics
Matches: 117, Mismatches: 17, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
118 3 0.03
119 83 0.71
120 31 0.26
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.25
Consensus pattern (119 bp):
TCCGGGTTAAGTCCCGAAGGCTTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATTT
GTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTGACTAAA
Found at i:28836822 original size:84 final size:85
Alignment explanation
Indices: 28836680--28836849 Score: 288
Period size: 84 Copynumber: 2.0 Consensus size: 85
28836670 ATATGTGTGT
*
28836680 TGAAGGATACAGAGCTCATATAGAAAATTTTACACGAGGCCCACAGAGGTACTATGTCTGTACAT
1 TGAAGGATACAGAGCTCATACAGAAAATTTTACACGAGGCCCACAGAGGTACTATGTCTGTACAT
28836745 CCGGGGAGTAATAAAATGTA
66 CCGGGGAGTAATAAAATGTA
* * **
28836765 TGAAGGATACAGAGCTCATACA-AAAATTTTACATGTGGCCCACAGCTGTACTATGTCTGTACAT
1 TGAAGGATACAGAGCTCATACAGAAAATTTTACACGAGGCCCACAGAGGTACTATGTCTGTACAT
28836829 CCGGGGAGTAATAAAATGTA
66 CCGGGGAGTAATAAAATGTA
28836849 T
1 T
28836850 AATGATCTGA
Statistics
Matches: 80, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
84 59 0.74
85 21 0.26
ACGTcount: A:0.35, C:0.17, G:0.22, T:0.25
Consensus pattern (85 bp):
TGAAGGATACAGAGCTCATACAGAAAATTTTACACGAGGCCCACAGAGGTACTATGTCTGTACAT
CCGGGGAGTAATAAAATGTA
Found at i:28839375 original size:50 final size:50
Alignment explanation
Indices: 28839298--28839579 Score: 376
Period size: 50 Copynumber: 5.7 Consensus size: 50
28839288 GGGTAAAGAG
* *
28839298 GTCCCATGTAAGACCATGTCTGAGACATGGCGCTGGCACCGAGATGAGAA
1 GTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAA
* *
28839348 GTCCCATGTAAGACCATGTCTGGGACATGGTGTTGGCACCGAGATGAGAG
1 GTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAA
* *
28839398 GTCCCATGTAAGACCATGTTTGGGACATGGCATTGGCACCGAGAT--G-A
1 GTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAA
* *
28839445 --CCCATGTAAGACCATGTTTGGGACATGGCGTTGGCACCGAGATGAGAG
1 GTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAA
* * ** * *
28839493 GTCCCCTGTAATACCATGTCTGGGACATGGAATGGGCACCGATATGAGAA
1 GTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAA
* *
28839543 CATCCCATGTAAGACCATGTCTGGGACATGGCTTTGG
1 -GTCCCATGTAAGACCATGTCTGGGACATGGCGTTGG
28839580 ATGTTATTAT
Statistics
Matches: 202, Mismatches: 24, Indels: 11
0.85 0.10 0.05
Matches are distributed among these distances:
45 42 0.21
47 1 0.00
48 1 0.00
50 128 0.63
51 30 0.15
ACGTcount: A:0.26, C:0.22, G:0.30, T:0.22
Consensus pattern (50 bp):
GTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAA
Found at i:28839491 original size:95 final size:98
Alignment explanation
Indices: 28839294--28839579 Score: 398
Period size: 95 Copynumber: 2.9 Consensus size: 98
28839284 ATTTGGGTAA
* **
28839294 AGAGGTCCCATGTAAGACCATGTCTGAGACATGGCGCTGGCACCGAGATGAGAAGTCCCATGTAA
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGAT-AGAA-TCCCATGTAA
*
28839359 GACCATGTCTGGGACATGGTGTTGGCACCGAGATG
64 GACCATGTCTGGGACATGGCGTTGGCACCGAGATG
*
28839394 AGAGGTCCCATGTAAGACCATGTTTGGGACATGGCATTGGCACCGAGAT-G-A-CCCATGTAAGA
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATAGAATCCCATGTAAGA
*
28839456 CCATGTTTGGGACATGGCGTTGGCACCGAGATG
66 CCATGTCTGGGACATGGCGTTGGCACCGAGATG
* * * * *
28839489 AGAGGTCCCCTGTAATACCATGTCTGGGACATGGAATGGGCACCGATATGAGAACATCCCATGTA
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGAT-AG-A-ATCCCATGTA
*
28839554 AGACCATGTCTGGGACATGGCTTTGG
63 AGACCATGTCTGGGACATGGCGTTGG
28839580 ATGTTATTAT
Statistics
Matches: 166, Mismatches: 14, Indels: 11
0.87 0.07 0.06
Matches are distributed among these distances:
95 85 0.51
97 2 0.01
98 1 0.01
100 46 0.28
101 32 0.19
ACGTcount: A:0.26, C:0.22, G:0.31, T:0.22
Consensus pattern (98 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATAGAATCCCATGTAAGA
CCATGTCTGGGACATGGCGTTGGCACCGAGATG
Found at i:28841985 original size:11 final size:12
Alignment explanation
Indices: 28841966--28842006 Score: 52
Period size: 11 Copynumber: 3.7 Consensus size: 12
28841956 AAAAATAGGG
*
28841966 ATTTAAGAG-AA
1 ATTTGAGAGCAA
28841977 ATTTGAGAGCAA
1 ATTTGAGAGCAA
28841989 A-TTGAGAGCAA
1 ATTTGAGAGCAA
28842000 A-TTGAGA
1 ATTTGAGA
28842007 AGAAATTGAA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
11 25 0.89
12 3 0.11
ACGTcount: A:0.46, C:0.05, G:0.24, T:0.24
Consensus pattern (12 bp):
ATTTGAGAGCAA
Found at i:28842012 original size:11 final size:10
Alignment explanation
Indices: 28841971--28842020 Score: 55
Period size: 11 Copynumber: 4.6 Consensus size: 10
28841961 TAGGGATTTA
28841971 AGAGAAATTTG
1 AGAGAAA-TTG
28841982 AGAGCAAATTG
1 AGAG-AAATTG
28841993 AGAGCAAATTG
1 AGAG-AAATTG
28842004 AGAAGAAATTG
1 AG-AGAAATTG
*
28842015 AAAGAA
1 AGAGAA
28842021 TAATAGAGAA
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
10 4 0.11
11 27 0.75
12 5 0.14
ACGTcount: A:0.52, C:0.04, G:0.26, T:0.18
Consensus pattern (10 bp):
AGAGAAATTG
Found at i:28845081 original size:6 final size:6
Alignment explanation
Indices: 28845070--28845097 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
28845060 ATACGAAATG
28845070 AAATTT AAATTT AAATTT AAATTT AAAT
1 AAATTT AAATTT AAATTT AAATTT AAAT
28845098 GTTCAAACTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (6 bp):
AAATTT
Found at i:28845111 original size:96 final size:96
Alignment explanation
Indices: 28845006--28845181 Score: 293
Period size: 96 Copynumber: 1.8 Consensus size: 96
28844996 ATCAATAAAT
* *
28845006 AAACTAATCAATGTTCAAACTTTGAACATGCTTTATTAAACCT-TCAATTTCA-TTATACGAAAT
1 AAACTAATCAATGTTCAAACTTTGAACATGCTTTAATAAA-CTATCAATAT-ATTTATACGAAAT
28845069 GAAATTTAAATTTAAATTTAAATTTAAATGTTC
64 GAAATTTAAATTTAAATTTAAATTTAAATGTTC
28845102 AAACTAATCAATGTTCAAACTTTGAACATGCTTTAATAAACTAATCAATATATTTATACGAAATG
1 AAACTAATCAATGTTCAAACTTTGAACATGCTTTAATAAACT-ATCAATATATTTATACGAAATG
28845167 AAATTTAAATTTAAA
65 AAATTTAAATTTAAA
28845182 ATGTTATAAA
Statistics
Matches: 75, Mismatches: 2, Indels: 5
0.91 0.02 0.06
Matches are distributed among these distances:
95 2 0.03
96 40 0.53
97 33 0.44
ACGTcount: A:0.44, C:0.12, G:0.06, T:0.38
Consensus pattern (96 bp):
AAACTAATCAATGTTCAAACTTTGAACATGCTTTAATAAACTATCAATATATTTATACGAAATGA
AATTTAAATTTAAATTTAAATTTAAATGTTC
Found at i:28848571 original size:47 final size:47
Alignment explanation
Indices: 28848519--28848663 Score: 158
Period size: 47 Copynumber: 3.1 Consensus size: 47
28848509 TCATTTAAGA
*
28848519 ATATTTATTATTAAGAATTTTATGAAATTATATATCATTATTAAATT
1 ATATTTATTATTAAGAATTTTATGAAATTATATATAATTATTAAATT
* **
28848566 ATATTTAATATTAATTA-TTT-T-AAATTATATA-AATTCATATAAGA--
1 ATATTTATTATTAAGAATTTTATGAAATTATATATAATT-AT-TAA-ATT
* * *
28848610 AAATTTATTATCAAGAATTTTATGAAATTATATATTATTATTAAATT
1 ATATTTATTATTAAGAATTTTATGAAATTATATATAATTATTAAATT
28848657 ATATTTA
1 ATATTTA
28848664 ATAATAATTA
Statistics
Matches: 78, Mismatches: 11, Indels: 18
0.73 0.10 0.17
Matches are distributed among these distances:
43 3 0.04
44 24 0.31
45 8 0.10
46 8 0.10
47 32 0.41
48 3 0.04
ACGTcount: A:0.45, C:0.02, G:0.03, T:0.50
Consensus pattern (47 bp):
ATATTTATTATTAAGAATTTTATGAAATTATATATAATTATTAAATT
Found at i:28848593 original size:44 final size:44
Alignment explanation
Indices: 28848543--28848691 Score: 144
Period size: 44 Copynumber: 3.3 Consensus size: 44
28848533 GAATTTTATG
*
28848543 AAATTATATATCATTATTAAATTATATTTAATATTAATTATTTT
1 AAATTATATATAATTATTAAATTATATTTAATATTAATTATTTT
* * * **
28848587 AAATTATATA-AATTCATATAAGA--AAATTTATTATCAAGAATTTTAT
1 AAATTATATATAATT-AT-TAA-ATTATATTTAATATTAATTA-TTT-T
* *
28848633 GAAATTATATATTATTATTAAATTATATTTAATAATAATTATTTT
1 -AAATTATATATAATTATTAAATTATATTTAATATTAATTATTTT
28848678 AAATTATATA-AATT
1 AAATTATATATAATT
28848692 CATATAAGAA
Statistics
Matches: 82, Mismatches: 14, Indels: 19
0.71 0.12 0.17
Matches are distributed among these distances:
43 6 0.07
44 34 0.41
45 8 0.10
46 8 0.10
47 23 0.28
48 3 0.04
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (44 bp):
AAATTATATATAATTATTAAATTATATTTAATATTAATTATTTT
Found at i:28848616 original size:91 final size:91
Alignment explanation
Indices: 28848504--28848719 Score: 369
Period size: 91 Copynumber: 2.4 Consensus size: 91
28848494 ATGATTTTAG
* *
28848504 TAAATTCATTTAAGAATATTTATTATTAAGAATTTTATGAAATTATATATCATTATTAAATTATA
1 TAAATTCATATAAGAAAATTTATTATTAAGAATTTTATGAAATTATATATCATTATTAAATTATA
*
28848569 TTTAATATTAATTATTTTAAATTATA
66 TTTAATAATAATTATTTTAAATTATA
* *
28848595 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATTATTATTAAATTATA
1 TAAATTCATATAAGAAAATTTATTATTAAGAATTTTATGAAATTATATATCATTATTAAATTATA
28848660 TTTAATAATAATTATTTTAAATTATA
66 TTTAATAATAATTATTTTAAATTATA
* *
28848686 TAAATTCATATAAGAAAATTTATTAGTAATAATT
1 TAAATTCATATAAGAAAATTTATTATTAAGAATT
28848720 ATTTTAAATT
Statistics
Matches: 117, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
91 117 1.00
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.48
Consensus pattern (91 bp):
TAAATTCATATAAGAAAATTTATTATTAAGAATTTTATGAAATTATATATCATTATTAAATTATA
TTTAATAATAATTATTTTAAATTATA
Found at i:28848616 original size:101 final size:97
Alignment explanation
Indices: 28848511--28848787 Score: 315
Period size: 91 Copynumber: 2.9 Consensus size: 97
28848501 TAGTAAATTC
28848511 ATTTAAGAATATTTATTATTAAGAATTTTATGAAATTATATATCATTATTAAATTATATTTAATA
1 ATTTAAGAATATTTATTATTAAGAATTTTATGAAATTATATAT-ATTATTAAATTATATTTAATA
28848576 TTAATTATTTTAAATTATATAAATTCATATAAG
65 TTAATTATTTTAAATTATATAAATTCATATAAG
*
28848609 -----A-AA-ATTTATTATCAAGAATTTTATGAAATTATATATTATTATTAAATTATATTTAATA
1 ATTTAAGAATATTTATTATTAAGAATTTTATGAAATTATATA-TATTATTAAATTATATTTAATA
*
28848667 ATAATTATTTTAAATTATATAAATTCATATAAG
65 TTAATTATTTTAAATTATATAAATTCATATAAG
* * ** * *
28848700 AAAATTTATTAGTAATAATTATT-TT-A-AATTTTATTAAATCGTATATTTTAATTAAAATATAT
1 ---ATTTA--AG-AATATTTATTATTAAGAATTTTATGAAATTATATATATT-ATTAAATTATAT
28848762 TTAATAATT-ATTATTTTAAATTATAT
59 TTAAT-ATTAATTATTTTAAATTATAT
28848788 TTTATAGTAT
Statistics
Matches: 153, Mismatches: 10, Indels: 29
0.80 0.05 0.15
Matches are distributed among these distances:
91 84 0.55
92 3 0.02
93 1 0.01
100 3 0.02
101 50 0.33
102 3 0.02
103 3 0.02
104 6 0.04
ACGTcount: A:0.45, C:0.02, G:0.03, T:0.49
Consensus pattern (97 bp):
ATTTAAGAATATTTATTATTAAGAATTTTATGAAATTATATATATTATTAAATTATATTTAATAT
TAATTATTTTAAATTATATAAATTCATATAAG
Found at i:28848677 original size:47 final size:47
Alignment explanation
Indices: 28848535--28848678 Score: 140
Period size: 47 Copynumber: 3.1 Consensus size: 47
28848525 ATTATTAAGA
* *
28848535 ATTTTATGAAATTATATATCATTATTAAATTATATTTAATATTAATT
1 ATTTTATGAAATTATATATAATTATTAAATTATATTTAATAATAATT
* * **
28848582 A-TTT-T-AAATTATATA-AATTCATATAAGA--AAATTT-ATTATCAAGA
1 ATTTTATGAAATTATATATAATT-AT-TAA-ATTATATTTAATAAT-AATT
*
28848626 ATTTTATGAAATTATATATTATTATTAAATTATATTTAATAATAATT
1 ATTTTATGAAATTATATATAATTATTAAATTATATTTAATAATAATT
28848673 ATTTTA
1 ATTTTA
28848679 AATTATATAA
Statistics
Matches: 75, Mismatches: 11, Indels: 22
0.69 0.10 0.20
Matches are distributed among these distances:
43 6 0.08
44 20 0.27
45 8 0.11
46 8 0.11
47 26 0.35
48 7 0.09
ACGTcount: A:0.45, C:0.02, G:0.03, T:0.50
Consensus pattern (47 bp):
ATTTTATGAAATTATATATAATTATTAAATTATATTTAATAATAATT
Found at i:28848718 original size:47 final size:46
Alignment explanation
Indices: 28848577--28848738 Score: 174
Period size: 47 Copynumber: 3.5 Consensus size: 46
28848567 TATTTAATAT
28848577 TAATTATTTTAAATTATATAAATTCATATAAGAAAATTTATTATCAA
1 TAATTATTTTAAATTATATAAATTCATATAAGAAAATTTATTAT-AA
* * **
28848624 GAATT-TTATGAAATTATAT--ATT-AT-T-ATTAAATTATATTTAATAA
1 TAATTATT-TTAAATTATATAAATTCATATAAGAAAATT-TA-TT-ATAA
28848668 TAATTATTTTAAATTATATAAATTCATATAAGAAAATTTATTAGTAA
1 TAATTATTTTAAATTATATAAATTCATATAAGAAAATTTATTA-TAA
*
28848715 TAATTATTTTAAATTTTATTAAAT
1 TAATTATTTTAAATTATA-TAAAT
28848739 CGTATATTTT
Statistics
Matches: 94, Mismatches: 9, Indels: 23
0.75 0.07 0.18
Matches are distributed among these distances:
42 6 0.06
43 3 0.03
44 20 0.21
45 7 0.07
46 6 0.06
47 38 0.40
48 8 0.09
49 6 0.06
ACGTcount: A:0.47, C:0.02, G:0.03, T:0.48
Consensus pattern (46 bp):
TAATTATTTTAAATTATATAAATTCATATAAGAAAATTTATTATAA
Found at i:28848790 original size:59 final size:59
Alignment explanation
Indices: 28848727--28849134 Score: 240
Period size: 59 Copynumber: 6.8 Consensus size: 59
28848717 ATTATTTTAA
* *
28848727 ATTTTATTAAATCGTATATTTTAATTAAAATATATTTAATAATTATTATTTTAAATTAT
1 ATTTTATTAAATCATATATTTTATTTAAAATATATTTAATAATTATTATTTTAAATTAT
* * * * *
28848786 ATTTTA-TAGTATCATATATTATGATTTTAGTAAAT-TCATATAAGAA-TATTGATTATT-AA-G
1 ATTTTATTA-AATCATATATT-TTA-TTTA--AAATAT-ATTTAATAATTATT-ATT-TTAAATT
28848846 A-
58 AT
* * *
28848847 ATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAATAATTATTTCAAATTAT
1 ATTTTATTAAATCATATATTTTATTTAAAATATATTTAATAATTATTATTTTAAATTAT
* * * * *
28848906 ATTTTA-TAGTATCATATATTATGATTTTAGTAAAT-TCATATAAGAA-TATTGATTATT-AA-G
1 ATTTTATTA-AATCATATATT-TTA-TTTA--AAATAT-ATTTAATAATTATT-ATT-TTAAATT
28848966 A-
58 AT
* *
28848967 ATTTTATTAAATCATATATTTTATTTAAAATATATTTAATAATAATTATTTCAAATTAT
1 ATTTTATTAAATCATATATTTTATTTAAAATATATTTAATAATTATTATTTTAAATTAT
* * * * * *
28849026 ATTTTA-TAGTATCATATATTATGATTTGAGTAAAT-TCATATAAGAA-AATTGATTATT-AA-G
1 ATTTTATTA-AATCATATATT-TTATTT-A--AAATAT-ATTTAATAATTATT-ATT-TTAAATT
28849086 A-
58 AT
* * *
28849087 ATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTA
1 ATTTTATTAAATCATATATTTTATTTAAAATATATTTAATAATTATTA
28849135 AGTTAAAATA
Statistics
Matches: 268, Mismatches: 42, Indels: 80
0.69 0.11 0.21
Matches are distributed among these distances:
56 2 0.01
57 44 0.16
58 21 0.08
59 55 0.21
60 17 0.06
61 54 0.20
62 23 0.09
63 48 0.18
64 4 0.01
ACGTcount: A:0.43, C:0.03, G:0.05, T:0.49
Consensus pattern (59 bp):
ATTTTATTAAATCATATATTTTATTTAAAATATATTTAATAATTATTATTTTAAATTAT
Found at i:28848858 original size:120 final size:120
Alignment explanation
Indices: 28848726--28849134 Score: 755
Period size: 120 Copynumber: 3.4 Consensus size: 120
28848716 AATTATTTTA
* * *
28848726 AATTTTATTAAATCGTATATTTTAATTAAAATATATTTAATAATTATTATTTTAAATTATATTTT
1 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAATAATTATTTCAAATTATATTTT
28848791 ATAGTATCATATATTATGATTTTAGTAAATTCATATAAGAATATTGATTATTAAG
66 ATAGTATCATATATTATGATTTTAGTAAATTCATATAAGAATATTGATTATTAAG
28848846 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAATAATTATTTCAAATTATATTTT
1 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAATAATTATTTCAAATTATATTTT
28848911 ATAGTATCATATATTATGATTTTAGTAAATTCATATAAGAATATTGATTATTAAG
66 ATAGTATCATATATTATGATTTTAGTAAATTCATATAAGAATATTGATTATTAAG
*
28848966 AATTTTATTAAATCATATATTTTATTTAAAATATATTTAATAATAATTATTTCAAATTATATTTT
1 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAATAATTATTTCAAATTATATTTT
* *
28849031 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAAAATTGATTATTAAG
66 ATAGTATCATATATTATGATTTTAGTAAATTCATATAAGAATATTGATTATTAAG
*
28849086 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTA
1 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAATAATTA
28849135 AGTTAAAATA
Statistics
Matches: 281, Mismatches: 8, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
120 281 1.00
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.49
Consensus pattern (120 bp):
AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAATAATTATTTCAAATTATATTTT
ATAGTATCATATATTATGATTTTAGTAAATTCATATAAGAATATTGATTATTAAG
Found at i:28848861 original size:61 final size:61
Alignment explanation
Indices: 28848796--28849106 Score: 261
Period size: 61 Copynumber: 5.2 Consensus size: 61
28848786 ATTTTATAGT
28848796 ATCATATATTATGATTTTAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAA
1 ATCATATATTATGATTTTAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAA
* * ** * * * * * * * *
28848857 ATCATATATTTTAATTAAAATATATTTA-ATAATAATTATTTCA-AATT-A-TATTTTA-TAGT
1 ATCATATATTATGATTTTAGTAAATTCATATAAGAA-TA-TTGATTATTAAGAATTTTATTA-A
28848916 ATCATATATTATGATTTTAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAA
1 ATCATATATTATGATTTTAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAA
* * * * *
28848977 ATCATATATT-TTA-TTTA--AAATAT-ATTTAATAATAATT-ATT-TCAAATTATATTTTA-TA
1 ATCATATATTATGATTTTAGTAAAT-TCATATAAGAAT-ATTGATTAT-TAA-GA-ATTTTATTA
*
28849034 GT
61 -A
* *
28849036 ATCATATATTATGATTTGAGTAAATTCATATAAGAAAATTGATTATTAAGAATTTTATTAA
1 ATCATATATTATGATTTTAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAA
*
28849097 ATTATATATT
1 ATCATATATT
28849107 TTAATTAAAA
Statistics
Matches: 189, Mismatches: 39, Indels: 44
0.69 0.14 0.16
Matches are distributed among these distances:
56 1 0.01
57 17 0.09
58 12 0.06
59 52 0.28
60 18 0.10
61 60 0.32
62 12 0.06
63 16 0.08
64 1 0.01
ACGTcount: A:0.43, C:0.03, G:0.06, T:0.48
Consensus pattern (61 bp):
ATCATATATTATGATTTTAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAA
Done.