Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008562.1 Hibiscus syriacus cultivar Beakdansim tig00111471_pilon, whole genome shotgun sequence
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: 208436
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.34
Found at i:17458 original size:35 final size:35
Alignment explanation
Indices: 17414--17482 Score: 120
Period size: 35 Copynumber: 2.0 Consensus size: 35
17404 TGAACACTTA
*
17414 ATGACTCTTGGTCTCTTGGAATTGATTGTTTTTTG
1 ATGAATCTTGGTCTCTTGGAATTGATTGTTTTTTG
*
17449 ATGAATCTTGTTCTCTTGGAATTGATTGTTTTTT
1 ATGAATCTTGGTCTCTTGGAATTGATTGTTTTTT
17483 CATTTCCTCA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.16, C:0.10, G:0.20, T:0.54
Consensus pattern (35 bp):
ATGAATCTTGGTCTCTTGGAATTGATTGTTTTTTG
Found at i:18212 original size:21 final size:21
Alignment explanation
Indices: 18186--18252 Score: 107
Period size: 21 Copynumber: 3.2 Consensus size: 21
18176 ATGCGCCTCG
*
18186 AACAAACGAGACCACGTGTCA
1 AACAAACGAGGCCACGTGTCA
18207 AACAAACGAGGCCACGTGTCA
1 AACAAACGAGGCCACGTGTCA
**
18228 AACAAACGAGGGTACGTGTCA
1 AACAAACGAGGCCACGTGTCA
18249 AACA
1 AACA
18253 GACTAGGTTA
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 43 1.00
ACGTcount: A:0.42, C:0.25, G:0.22, T:0.10
Consensus pattern (21 bp):
AACAAACGAGGCCACGTGTCA
Found at i:20794 original size:17 final size:18
Alignment explanation
Indices: 20763--20808 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
20753 ATTTAAAACG
*
20763 TTTATTTTTTCATTT-TAA
1 TTTATTTTTT-ATTTGCAA
20781 TTTATTTTTTATTTGCAA
1 TTTATTTTTTATTTGCAA
20799 TTT-TTTTTTA
1 TTTATTTTTTA
20809 ATATTAAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
17 11 0.42
18 15 0.58
ACGTcount: A:0.20, C:0.04, G:0.02, T:0.74
Consensus pattern (18 bp):
TTTATTTTTTATTTGCAA
Found at i:23483 original size:13 final size:13
Alignment explanation
Indices: 23467--23566 Score: 128
Period size: 13 Copynumber: 7.7 Consensus size: 13
23457 GTCATAAATC
*
23467 TATGTCGCGCATT
1 TATGACGCGCATT
*
23480 TATGACACGCATT
1 TATGACGCGCATT
*
23493 TATGACGCTCATT
1 TATGACGCGCATT
23506 TATGACGCGCATT
1 TATGACGCGCATT
**
23519 TATGACGATCATT
1 TATGACGCGCATT
*
23532 TATGATGCGCATT
1 TATGACGCGCATT
**
23545 TATGACGATCATT
1 TATGACGCGCATT
23558 TATGACGCG
1 TATGACGCG
23567 TATTGCGCGT
Statistics
Matches: 72, Mismatches: 15, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
13 72 1.00
ACGTcount: A:0.25, C:0.20, G:0.20, T:0.35
Consensus pattern (13 bp):
TATGACGCGCATT
Found at i:23496 original size:26 final size:26
Alignment explanation
Indices: 23476--23566 Score: 155
Period size: 26 Copynumber: 3.5 Consensus size: 26
23466 CTATGTCGCG
* *
23476 CATTTATGACACGCATTTATGACGCT
1 CATTTATGACGCGCATTTATGACGAT
23502 CATTTATGACGCGCATTTATGACGAT
1 CATTTATGACGCGCATTTATGACGAT
*
23528 CATTTATGATGCGCATTTATGACGAT
1 CATTTATGACGCGCATTTATGACGAT
23554 CATTTATGACGCG
1 CATTTATGACGCG
23567 TATTGCGCGT
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 61 1.00
ACGTcount: A:0.26, C:0.20, G:0.19, T:0.35
Consensus pattern (26 bp):
CATTTATGACGCGCATTTATGACGAT
Found at i:23806 original size:2 final size:2
Alignment explanation
Indices: 23799--23830 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
23789 ATAATACTAA
23799 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
23831 TGTAGATTGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:23832 original size:85 final size:85
Alignment explanation
Indices: 23727--23914 Score: 340
Period size: 85 Copynumber: 2.2 Consensus size: 85
23717 TGTCATAAAT
* *
23727 TATATATATATATATATATTGTAGATTGACAAATAATCAAACTAAATCACATTTAATGCCTCATA
1 TATATATATATATATATATTGTAGATTGACAAATAATCAAACTAAATCACATTTAATGCCTAAAA
23792 ATACTAAATATATATATATA
66 ATACTAAATATATATATATA
*
23812 TATATATATATATATATATTGTAGATTGACAAATAATCAAACTAGATCACATTTAATGCCTAAAA
1 TATATATATATATATATATTGTAGATTGACAAATAATCAAACTAAATCACATTTAATGCCTAAAA
23877 ATACTAAATATATATATATA
66 ATACTAAATATATATATATA
23897 TATATATATATATCATAT
1 TATATATATATAT-ATAT
23915 TATATATAAG
Statistics
Matches: 99, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
85 95 0.96
86 4 0.04
ACGTcount: A:0.47, C:0.10, G:0.05, T:0.38
Consensus pattern (85 bp):
TATATATATATATATATATTGTAGATTGACAAATAATCAAACTAAATCACATTTAATGCCTAAAA
ATACTAAATATATATATATA
Found at i:23891 original size:2 final size:2
Alignment explanation
Indices: 23884--23922 Score: 62
Period size: 2 Copynumber: 19.5 Consensus size: 2
23874 AAAATACTAA
23884 AT AT AT AT AT AT AT AT AT AT AT AT AT CAT AT -T AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT A
23923 AGCAATCCAT
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 1 0.03
2 32 0.91
3 2 0.06
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:29644 original size:32 final size:32
Alignment explanation
Indices: 29608--29673 Score: 82
Period size: 32 Copynumber: 2.1 Consensus size: 32
29598 CAAAAAGGGC
* *
29608 AAAAACAAA-AAAGAA-AAGAAGCAAAAAAGAA
1 AAAAAAAAAGAAAGAACAAAAAGC-AAAAAGAA
*
29639 AAAAAAAAAGAAAGAACAAAAATCAAAAAGAA
1 AAAAAAAAAGAAAGAACAAAAAGCAAAAAGAA
29671 AAA
1 AAA
29674 GGGACAAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
31 8 0.27
32 17 0.57
33 5 0.17
ACGTcount: A:0.82, C:0.06, G:0.11, T:0.02
Consensus pattern (32 bp):
AAAAAAAAAGAAAGAACAAAAAGCAAAAAGAA
Found at i:29652 original size:16 final size:15
Alignment explanation
Indices: 29608--29673 Score: 60
Period size: 16 Copynumber: 4.2 Consensus size: 15
29598 CAAAAAGGGC
*
29608 AAAAACAAAAAAGAA
1 AAAAAAAAAAAAGAA
**
29623 AAGAAGCAAAAAAGAA
1 AA-AAAAAAAAAAGAA
29639 AAAAAAAAAGAAAGAA
1 AAAAAAAAA-AAAGAA
**
29655 CAAAAATCAAAAAGAA
1 -AAAAAAAAAAAAGAA
29671 AAA
1 AAA
29674 GGGACAAAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
15 10 0.23
16 26 0.60
17 7 0.16
ACGTcount: A:0.82, C:0.06, G:0.11, T:0.02
Consensus pattern (15 bp):
AAAAAAAAAAAAGAA
Found at i:29660 original size:20 final size:19
Alignment explanation
Indices: 29608--29673 Score: 62
Period size: 20 Copynumber: 3.3 Consensus size: 19
29598 CAAAAAGGGC
29608 AAAAACAAAAAAGAAAAGAAG
1 AAAAACAAAAAA-AAAA-AAG
29629 CAAAAA-AGAAAAAAAAAAAG
1 -AAAAACA-AAAAAAAAAAAG
**
29649 AAAGAACAAAAATCAAAAAG
1 AAA-AACAAAAAAAAAAAAG
29669 AAAAA
1 AAAAA
29674 GGGACAAAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
19 5 0.13
20 18 0.46
21 6 0.15
22 10 0.26
ACGTcount: A:0.82, C:0.06, G:0.11, T:0.02
Consensus pattern (19 bp):
AAAAACAAAAAAAAAAAAG
Found at i:30307 original size:22 final size:22
Alignment explanation
Indices: 30279--30333 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
30269 GCTACCCCAT
30279 CAAACCTTTGAGCATCAAATGC
1 CAAACCTTTGAGCATCAAATGC
*
30301 CAAACCTTTGAGCATCAAATGT
1 CAAACCTTTGAGCATCAAATGC
30323 CAAACCTTTGA
1 CAAACCTTTGA
30334 CCAAACATAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.36, C:0.25, G:0.13, T:0.25
Consensus pattern (22 bp):
CAAACCTTTGAGCATCAAATGC
Found at i:30743 original size:24 final size:24
Alignment explanation
Indices: 30673--30745 Score: 60
Period size: 24 Copynumber: 3.0 Consensus size: 24
30663 TCTCAATTGT
*
30673 AAAACTCTTTTAATTGATATTTTC
1 AAAAATCTTTTAATTGATATTTTC
** ** *
30697 -AAAA-CTTTGGATCAAACATTTTTC
1 AAAAATCTTTTAAT-TGATA-TTTTC
30721 AAAAATCTTTTAATTGATATTTTC
1 AAAAATCTTTTAATTGATATTTTC
30745 A
1 A
30746 TAACTTTGAA
Statistics
Matches: 34, Mismatches: 11, Indels: 8
0.64 0.21 0.15
Matches are distributed among these distances:
22 6 0.18
23 5 0.15
24 11 0.32
25 6 0.18
26 6 0.18
ACGTcount: A:0.37, C:0.12, G:0.05, T:0.45
Consensus pattern (24 bp):
AAAAATCTTTTAATTGATATTTTC
Found at i:31535 original size:106 final size:106
Alignment explanation
Indices: 31336--32820 Score: 2121
Period size: 106 Copynumber: 14.1 Consensus size: 106
31326 CCACTCAAGG
* * * * * * *
31336 CAACACAAGTTCAACTTCACAACGAATGGACGGCTGGTTGTCAA-CAACAATTTTCAAATTTCAG
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAG
* *
31400 AGCCAATTTCAACTTCACAACAAAGGATATTGGACTCCAGA
66 AGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGA
* * *
31441 CAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACCATTTCCCAATTTCAA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAG
*
31506 ATCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGA
66 AGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGA
* * *
31547 CAACACAAGTTCAACTTCACGACGAAGGGACCGCTGATTGTCAATAAACAACTTT-CCAATTTAA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAA-TTTCCCAATTTCA
*
31611 GAGCCAATTTCAACTTCACAGCGAAAGATATTGGACTCCAGA
65 GAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGA
* * * * *
31653 CAACGCAAGTTCAACTTCACAACGAAGGGACCGCTGGTTGTCAACAAATAACTTCTCAATTTCAG
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAG
** *
31718 AGCCAATTTCAACTTCACAATGAAGGATATTGGATTCCAGA
66 AGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGA
* * *
31759 CAACACAAGTTCAATTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTTCAG
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAG
31824 AGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGA
66 AGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGA
* * * *
31865 CAACGCAAGTTCAACTTCACGACGAAGGGACCGTTGGTTGTCAACAAACAACTTCTCAATTTCAG
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAG
* *
31930 TGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
66 AGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGA
* * * *
31971 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTTAG
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAG
*
32036 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
66 AGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGA
* *
32077 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCTCAATTTCAG
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAG
*
32142 AGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGA
66 AGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGA
*
32183 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTTCAG
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAG
*
32248 AGCCAATTTCAACTTCACAGCGAAGGATATTGGACACCAGA
66 AGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGA
* *
32289 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTT-TCAATTTCA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAA-TTTCCCAATTTCA
*
32353 GAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
65 GAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGA
*
32395 CAACGCAAGTTCAACTTCACGACGAAGGAACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAG
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAG
* *
32460 AGCCAATTTCAACTTCACAGCGTAGGATATTGGACTCAAGA
66 AGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGA
** * *
32501 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTTATTGTCAATAAAGAACTTT-CCAATTTTA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAA-TTTCCCAATTTCA
* * *
32565 GAGCCAATTTTAACTTCTCAGCGAAGGATCTTGGAC-CCAAGA
65 GAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCC-AGA
* * * * * * *
32607 CAACACAAGCTCAACTTCACGACGAAGGGGCGGCTGATTGTGAA-CAA-AATTT--C-A-TTCAG
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAG
* * *
32666 AGTCAATTTCAACTTAACAGCGAAGGATATTGGACTCGAGA
66 AGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGA
* * * * * ** *
32707 CAACACAAGTTCAACTTCACAACGAAGGGA-CGACTGGTTATCAACAAATAATTTCCCGGTTCCA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCG-CTGGTTGTCAATAAACAATTTCCCAATTTCA
* * * *
32771 GAGTCAATTTCAACTTCACAGCAAAGGATATTGGCCTCGAGA
65 GAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGA
*
32813 CAATGCAA
1 CAACGCAA
32821 CTTGCATTGG
Statistics
Matches: 1256, Mismatches: 109, Indels: 29
0.90 0.08 0.02
Matches are distributed among these distances:
99 1 0.00
100 72 0.06
101 4 0.00
102 6 0.00
103 3 0.00
104 3 0.00
105 47 0.04
106 1112 0.89
107 8 0.01
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (106 bp):
CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAG
AGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGA
Found at i:34544 original size:4 final size:4
Alignment explanation
Indices: 34519--34593 Score: 51
Period size: 4 Copynumber: 16.8 Consensus size: 4
34509 ATTGTTTCTT
* * *
34519 TTTA TTTA TATA TGTA TATTA TTTA TATTA TTTTA TCTTCC TTATA CTTTA
1 TTTA TTTA TTTA TTTA T-TTA TTTA T-TTA -TTTA T-TT-A TT-TA -TTTA
34570 TTTA TTTA TTTA TTTA TTTTA TTT
1 TTTA TTTA TTTA TTTA -TTTA TTT
34594 TCTTCTTGTT
Statistics
Matches: 58, Mismatches: 5, Indels: 16
0.73 0.06 0.20
Matches are distributed among these distances:
4 35 0.60
5 18 0.31
6 5 0.09
ACGTcount: A:0.25, C:0.05, G:0.01, T:0.68
Consensus pattern (4 bp):
TTTA
Found at i:34654 original size:9 final size:9
Alignment explanation
Indices: 34640--34671 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
34630 ATTATTTTCC
34640 TTTATTTTA
1 TTTATTTTA
34649 TTTATTTTA
1 TTTATTTTA
*
34658 TCTATTTTA
1 TTTATTTTA
34667 TTTAT
1 TTTAT
34672 CTCTTCTCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.22, C:0.03, G:0.00, T:0.75
Consensus pattern (9 bp):
TTTATTTTA
Found at i:36469 original size:2 final size:2
Alignment explanation
Indices: 36462--36497 Score: 63
Period size: 2 Copynumber: 17.5 Consensus size: 2
36452 TACAACTAAT
36462 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA GTA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA T
36498 GGGTAATGTG
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 31 0.94
3 2 0.06
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:39395 original size:15 final size:14
Alignment explanation
Indices: 39366--39403 Score: 60
Period size: 15 Copynumber: 2.7 Consensus size: 14
39356 GATTTTGAGA
39366 TTTTGAAA-TCAAG
1 TTTTGAAATTCAAG
39379 TTTTGAAATTACAAG
1 TTTTGAAATT-CAAG
39394 TTTTGAAATT
1 TTTTGAAATT
39404 TGAAATTACT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 8 0.35
14 1 0.04
15 14 0.61
ACGTcount: A:0.37, C:0.05, G:0.13, T:0.45
Consensus pattern (14 bp):
TTTTGAAATTCAAG
Found at i:41506 original size:20 final size:20
Alignment explanation
Indices: 41469--41507 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
41459 AGATTGAGTG
* * *
41469 GATTTTGATGTTGTTTGCAC
1 GATTTTAATGATGATTGCAC
41489 GATTTTAATGATGATTGCA
1 GATTTTAATGATGATTGCA
41508 AGTTTAGGAG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.23, C:0.08, G:0.23, T:0.46
Consensus pattern (20 bp):
GATTTTAATGATGATTGCAC
Found at i:41687 original size:21 final size:21
Alignment explanation
Indices: 41663--41702 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
41653 CAGAACCTCA
*
41663 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
41684 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
41703 TCAAAGGGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.25, G:0.40, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:41730 original size:20 final size:21
Alignment explanation
Indices: 41685--41745 Score: 88
Period size: 20 Copynumber: 2.9 Consensus size: 21
41675 TTCCCCTGTG
41685 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGGTT-CCC-TCAAA
41708 GGGGGAATCGGTTCCCT-AAA
1 GGGGGAATCGGTTCCCTCAAA
*
41728 GGGGGAATCGATTCCCTC
1 GGGGGAATCGGTTCCCTC
41746 TGCACCAAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
20 19 0.53
21 1 0.03
22 3 0.08
23 13 0.36
ACGTcount: A:0.21, C:0.25, G:0.33, T:0.21
Consensus pattern (21 bp):
GGGGGAATCGGTTCCCTCAAA
Found at i:51839 original size:82 final size:82
Alignment explanation
Indices: 51685--51842 Score: 194
Period size: 82 Copynumber: 1.9 Consensus size: 82
51675 ACTTCAGAAT
* * * * *
51685 AAATCAGACTTGATCTGTTCCATTTTTTCGGGTAGACATATCAATTTTAGAAGACAGAATTGCTT
1 AAATCAGACTCGATCTGTGCCATTTTTTCGGGCAGACATATCAATTTTAGAAAACAGAATTGCTC
* *
51750 TATTATTCATTTAGGAA
66 CACTATTCATTTAGGAA
* **
51767 AAATCAGACTCGATCTGTGCC-TCTTTTTCGGGCAGACATATCAATTTTGGAAAAC-GTGTCTGC
1 AAATCAGACTCGATCTGTGCCAT-TTTTTCGGGCAGACATATCAATTTTAGAAAACAGAAT-TGC
51830 TCCACTATTCATT
64 TCCACTATTCATT
51843 CATGGGAAAT
Statistics
Matches: 64, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
81 3 0.05
82 61 0.95
ACGTcount: A:0.28, C:0.18, G:0.16, T:0.37
Consensus pattern (82 bp):
AAATCAGACTCGATCTGTGCCATTTTTTCGGGCAGACATATCAATTTTAGAAAACAGAATTGCTC
CACTATTCATTTAGGAA
Found at i:52128 original size:24 final size:24
Alignment explanation
Indices: 52107--52153 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
52097 TATTTATTTG
52107 TTCTTTCTCCTTTATTATTATTTCA
1 TTCTTTCT-CTTTATTATTATTTCA
* *
52132 TTTTTTCTTTTTATTATTATTT
1 TTCTTTCTCTTTATTATTATTT
52154 TTTAAATGAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 13 0.65
25 7 0.35
ACGTcount: A:0.15, C:0.13, G:0.00, T:0.72
Consensus pattern (24 bp):
TTCTTTCTCTTTATTATTATTTCA
Found at i:53065 original size:236 final size:236
Alignment explanation
Indices: 52155--53607 Score: 1710
Period size: 236 Copynumber: 6.2 Consensus size: 236
52145 TTATTATTTT
* * * * ** *
52155 TTAAATGAGAAACTTTGAAAATAGCTTTCTCATTTCCTTACAAATAC-CGTACGAAAGCATATTA
1 TTAAATGAGAAACTTTGAAAATCGCTTTCTCATTT--TT-CAAATTCATGT--GAAAACATCCTG
* * * * * *
52219 CCCGAAGGTATTATAGATGTCCCAAATGACTTATCATCTTGCTTGAAAGACTTACAGATAACCCG
61 CCCGAAGGTCTTATGGATG-GCCGAAGGACTTATCATCTTGCTTGAAAGACTTACAGATGACCCG
* * ** * * *
52284 AATGATTTAATCATCATGCTCGAAAGATTTACTGTTGGCCCAAAGGATTTAATAAGTAAAAAACT
125 AAGGATTTAATCATCATGCTCGAAAGACTTACTGACGGCCCGAAGGACTTACTAAGTAAAAAACT
*
52349 TTGGAAATCGTTTTCTTACTTTTCAAAAATTTT-ATTTTCTGATAAACA
190 TTGGAAATCGCTTTCTTACTTTTC-AAAATTTTCATTTTCTGA-AAACA
* * * *
52397 TTAAATGAGAAACTTTGAAAATCGCTTTCTCATTTGTCAAATTCATGTAAAAACATCATACCCGA
1 TTAAATGAGAAACTTTGAAAATCGCTTTCTCATTTTTCAAATTCATGTGAAAACATCCTGCCCGA
* * * * * * *
52462 AGGTATTATGGATGGCCGAAGGACTTATCATCTTGCTCGAATGGCTTATAGATGACCCAAAGAAT
66 AGGTCTTATGGATGGCCGAAGGACTTATCATCTTGCTTGAAAGACTTACAGATGACCCGAAGGAT
* * *
52527 TTAATCATCATGCTTGAAA-A--TA-T-ACTGCCCGAAGGAATTACTAAGTAAAAAACTTTGGAA
131 TTAATCATCATGCTCGAAAGACTTACTGACGGCCCGAAGGACTTACTAAGTAAAAAACTTTGGAA
52587 ATCGCTTTCTTA-----C----TTTTCATTTTCTGAAAACA
196 ATCGCTTTCTTACTTTTCAAAATTTTCATTTTCTGAAAACA
* * * * *
52619 TTAAATGAGAAACTTTGAAAATTGTTTTCTCATTTTT-AAATTCATTTGAAAACATCCTTCCTGA
1 TTAAATGAGAAACTTTGAAAATCGCTTTCTCATTTTTCAAATTCATGTGAAAACATCCTGCCCGA
* * *** * *
52683 AGGCCTTAAGGATTGATAGAAGGACTTATCATCTTGCTTGTAAGATTTACAGATGACCCGAAGGA
66 AGGTCTTATGGA-TGGCCGAAGGACTTATCATCTTGCTTGAAAGACTTACAGATGACCCGAAGGA
* * * * * *
52748 TTTAATCATAATGCTCGAAAGACATACTGATGGTCTGAAAGACTTACTAAGTAAAAAACTTTGGA
130 TTTAATCATCATGCTCGAAAGACTTACTGACGGCCCGAAGGACTTACTAAGTAAAAAACTTTGGA
*
52813 AATCGCTTTTTTACTTTTCAAAATTTTCATTTTCTGAAAACA
195 AATCGCTTTCTTACTTTTCAAAATTTTCATTTTCTGAAAACA
* * *
52855 ATAAATGAGAAACTTTGAAAATCGCTTTCTTATTTTTCAAATTCATGTGAAAACATCCTGCCCAA
1 TTAAATGAGAAACTTTGAAAATCGCTTTCTCATTTTTCAAATTCATGTGAAAACATCCTGCCCGA
* *
52920 AGGTCTTATGGATGGTCTGAAGGACTTAACATCTTGCTTGAAAGACTTACAGATGACCCGAAGGA
66 AGGTCTTATGGATGG-CCGAAGGACTTATCATCTTGCTTGAAAGACTTACAGATGACCCGAAGGA
* * * ** *
52985 TTTAATCATCATGCTCGAATGACTGA-TGGCCCCCCGAAGGACTTACTAAGTAAGAAACTTTGGA
130 TTTAATCATCATGCTCGAAAGACTTACTGACGGCCCGAAGGACTTACTAAGTAAAAAACTTTGGA
*
53049 AATCGTTTTCTTACTTTTCAAACA-TTTCATTTTCTGAAAACA
195 AATCGCTTTCTTACTTTTCAAA-ATTTTCATTTTCTGAAAACA
* *
53091 TTAGATGAGAAACTTTGAAAACCGCTTTCTCATTTTTCAAATTCATGTGAAAA-ATCCTGCCCGA
1 TTAAATGAGAAACTTTGAAAATCGCTTTCTCATTTTTCAAATTCATGTGAAAACATCCTGCCCGA
* * * *
53155 ATGTCTTATGGATGGCACGAACGACTTATCATCTTGCTCGGAAGACTTACAGATGACCCGAAGGA
66 AGGTCTTATGGATGGC-CGAAGGACTTATCATCTTGCTTGAAAGACTTACAGATGACCCGAAGGA
* * * * * *
53220 TTTAATCATCATGCTAGAAAGACTTACTGATGGCCCAAAGGACATACTAAGTAAGAAACTTTGAA
130 TTTAATCATCATGCTCGAAAGACTTACTGACGGCCCGAAGGACTTACTAAGTAAAAAACTTTGGA
* * *
53285 AATCACTTTC-TAATTTTCAAAAATTTCATTTTCTGAAAACA
195 AATCGCTTTCTTACTTTTCAAAATTTTCATTTTCTGAAAACA
* * *
53326 TTAAATGAAAAACTTTGAAAATTGCTTTCTCATTTTTCAAATTCATGTGAAAACATCCTGCTCGA
1 TTAAATGAGAAACTTTGAAAATCGCTTTCTCATTTTTCAAATTCATGTGAAAACATCCTGCCCGA
* * * * *
53391 AGGACTTATGGATGGCATGAAGGACTTATCATCTTGCTGGAAAGACTTATAGATGATCCGAAGGA
66 AGGTCTTATGGATGGC-CGAAGGACTTATCATCTTGCTTGAAAGACTTACAGATGACCCGAAGGA
* *
53456 TTTAATCATCATGCTCGAAGGACTTACTAACGGCCCGAAGGACTTACTAAGTAAGAAAA-TTTGG
130 TTTAATCATCATGCTCGAAAGACTTACTGACGGCCCGAAGGACTTACTAAGTAA-AAAACTTTGG
** * *** *
53520 AAATAACTTTCTTACTTTTCAAAAATTTCA-TTTAAAAAAAAA
194 AAATCGCTTTCTTACTTTTCAAAATTTTCATTTTCTGAAAACA
* * *
53562 TTAAATGAGAAACTTTGGAAATCGCTTTCTCATTTTTAAAAGTCAT
1 TTAAATGAGAAACTTTGAAAATCGCTTTCTCATTTTTCAAATTCAT
53608 TTAATGGTTT
Statistics
Matches: 1040, Mismatches: 145, Indels: 58
0.84 0.12 0.05
Matches are distributed among these distances:
221 31 0.03
222 102 0.10
223 10 0.01
225 2 0.00
226 1 0.00
227 43 0.04
232 43 0.04
233 1 0.00
234 4 0.00
235 167 0.16
236 389 0.37
237 178 0.17
238 26 0.03
239 6 0.01
240 3 0.00
242 34 0.03
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Consensus pattern (236 bp):
TTAAATGAGAAACTTTGAAAATCGCTTTCTCATTTTTCAAATTCATGTGAAAACATCCTGCCCGA
AGGTCTTATGGATGGCCGAAGGACTTATCATCTTGCTTGAAAGACTTACAGATGACCCGAAGGAT
TTAATCATCATGCTCGAAAGACTTACTGACGGCCCGAAGGACTTACTAAGTAAAAAACTTTGGAA
ATCGCTTTCTTACTTTTCAAAATTTTCATTTTCTGAAAACA
Found at i:53242 original size:42 final size:42
Alignment explanation
Indices: 53182--53261 Score: 106
Period size: 42 Copynumber: 1.9 Consensus size: 42
53172 CGAACGACTT
* * * *
53182 ATCATCTTGCTCGGAAGACTTACAGATGACCCGAAGGATTTA
1 ATCATCATGCTAGAAAGACTTACAGATGACCCAAAGGATTTA
* *
53224 ATCATCATGCTAGAAAGACTTACTGATGGCCCAAAGGA
1 ATCATCATGCTAGAAAGACTTACAGATGACCCAAAGGA
53262 CATACTAAGT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 32 1.00
ACGTcount: A:0.34, C:0.21, G:0.21, T:0.24
Consensus pattern (42 bp):
ATCATCATGCTAGAAAGACTTACAGATGACCCAAAGGATTTA
Found at i:58822 original size:21 final size:21
Alignment explanation
Indices: 58805--58848 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
58795 GGGTTAATTA
*
58805 AAATTATATATATATTAACTT
1 AAATCATATATATATTAACTT
* *
58826 TAATCATATATATACTTCACTT
1 AAATCATATATATA-TTAACTT
58848 A
1 A
58849 TGTACAATTA
Statistics
Matches: 18, Mismatches: 4, Indels: 1
0.78 0.17 0.04
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.43, C:0.11, G:0.00, T:0.45
Consensus pattern (21 bp):
AAATCATATATATATTAACTT
Found at i:66318 original size:21 final size:22
Alignment explanation
Indices: 66279--66322 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
66269 AAACCATTCA
*
66279 GGGGGGAATCGGTACCCCTTTG
1 GGGGGGAATCAGTACCCCTTTG
*
66301 GGGGGGAATCAGT-TCCCTTTG
1 GGGGGGAATCAGTACCCCTTTG
66322 G
1 G
66323 AAAAACTGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 8 0.40
22 12 0.60
ACGTcount: A:0.14, C:0.20, G:0.41, T:0.25
Consensus pattern (22 bp):
GGGGGGAATCAGTACCCCTTTG
Found at i:68962 original size:23 final size:21
Alignment explanation
Indices: 68933--68980 Score: 69
Period size: 23 Copynumber: 2.2 Consensus size: 21
68923 ATTCCCCTAT
68933 GGGGAATCAGTTCCCCTTCAAAG
1 GGGGAATCAGTT-CCCTTC-AAG
*
68956 GGGGAATCGGTTCCCTTCAAG
1 GGGGAATCAGTTCCCTTCAAG
68977 GGGG
1 GGGG
68981 TATCGATTCC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 7 0.29
22 6 0.25
23 11 0.46
ACGTcount: A:0.21, C:0.23, G:0.35, T:0.21
Consensus pattern (21 bp):
GGGGAATCAGTTCCCTTCAAG
Found at i:68979 original size:21 final size:22
Alignment explanation
Indices: 68933--68992 Score: 77
Period size: 21 Copynumber: 2.7 Consensus size: 22
68923 ATTCCCCTAT
*
68933 GGGGAATCAGTTCCCCTTCAAAG
1 GGGGAATCGGTT-CCCTTCAAAG
68956 GGGGAATCGGTTCCCTTC-AAG
1 GGGGAATCGGTTCCCTTCAAAG
* *
68977 GGGGTATCGATTCCCT
1 GGGGAATCGGTTCCCT
68993 CTGCACCAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
21 17 0.50
22 6 0.18
23 11 0.32
ACGTcount: A:0.20, C:0.25, G:0.30, T:0.25
Consensus pattern (22 bp):
GGGGAATCGGTTCCCTTCAAAG
Found at i:83130 original size:90 final size:89
Alignment explanation
Indices: 82978--83150 Score: 292
Period size: 90 Copynumber: 1.9 Consensus size: 89
82968 ACACACCCTT
*
82978 TTATAGCCAAGTTACCCTAATCATATTATGGTTTTATTATTTCAAATTAATTAAATCTATATTTA
1 TTATAGCCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATATTTA
* *
83043 ATTAATTGTAATTTAATAATCCTC
66 ATTAATTGAAATTAAATAATCCTC
* *
83067 TTATATCCAAGTTACCCTAATCATATTGGGGATTTTATTATTTCAAATTAATTAAATCTATATTT
1 TTATAGCCAAGTTACCCTAATCATATTAGGG-TTTTATTATTTCAAATTAATTAAATCTATATTT
83132 AATTAATTGAAATTAAATA
65 AATTAATTGAAATTAAATA
83151 TTCGGGATTA
Statistics
Matches: 78, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
89 28 0.36
90 50 0.64
ACGTcount: A:0.38, C:0.11, G:0.06, T:0.45
Consensus pattern (89 bp):
TTATAGCCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATATTTA
ATTAATTGAAATTAAATAATCCTC
Found at i:89945 original size:90 final size:89
Alignment explanation
Indices: 89793--89965 Score: 285
Period size: 90 Copynumber: 1.9 Consensus size: 89
89783 ACACACCCTT
*
89793 TTATAGCCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATATTTA
1 TTATAGCCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATATTAA
* *
89858 ATTAATTGGAATTTAATAATCCTC
66 ATTAATTGAAATTAAATAATCCTC
*
89882 TTATATCCAAGTTACCCTAATCATATT-GTGGATTTTATTATTTCAAATTAATTAAATCTATATT
1 TTATAGCCAAGTTACCCTAATCATATTAG-GG-TTTTATTATTTCAAATTAATTAAATCTATATT
89946 AAATTAATTGAAATTAAATA
64 AAATTAATTGAAATTAAATA
89966 TTCGGGATTA
Statistics
Matches: 78, Mismatches: 4, Indels: 3
0.92 0.05 0.04
Matches are distributed among these distances:
88 1 0.01
89 28 0.36
90 49 0.63
ACGTcount: A:0.38, C:0.11, G:0.07, T:0.44
Consensus pattern (89 bp):
TTATAGCCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATATTAA
ATTAATTGAAATTAAATAATCCTC
Found at i:92795 original size:13 final size:13
Alignment explanation
Indices: 92773--92803 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
92763 ACTATTTTCT
*
92773 GAAAATAAAAATA
1 GAAAACAAAAATA
92786 GAAAACAAAAATA
1 GAAAACAAAAATA
92799 GAAAA
1 GAAAA
92804 AAATTCTAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.77, C:0.03, G:0.10, T:0.10
Consensus pattern (13 bp):
GAAAACAAAAATA
Found at i:98782 original size:61 final size:61
Alignment explanation
Indices: 98703--98843 Score: 183
Period size: 61 Copynumber: 2.3 Consensus size: 61
98693 CACTAGTCAA
* * *
98703 ATATGCATTAAAGTGCTAATAAACATAAGGTTGTGCCCACCATATACACTAAGTGTCATTT
1 ATATACATTATAGTGCTAATAAACATAAGGTCGTGCCCACCATATACACTAAGTGTCATTT
* * * * *
98764 ATATACATTATAGTGCTAATACACATAAGGTCGTGCCTATCGTATGCACTAAGTGTCATTT
1 ATATACATTATAGTGCTAATAAACATAAGGTCGTGCCCACCATATACACTAAGTGTCATTT
* * *
98825 ATAAACACTATAATGCTAA
1 ATATACATTATAGTGCTAA
98844 ATTGGATATG
Statistics
Matches: 69, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
61 69 1.00
ACGTcount: A:0.36, C:0.18, G:0.14, T:0.32
Consensus pattern (61 bp):
ATATACATTATAGTGCTAATAAACATAAGGTCGTGCCCACCATATACACTAAGTGTCATTT
Found at i:100398 original size:20 final size:20
Alignment explanation
Indices: 100375--100413 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
100365 GTCTAATTTC
100375 ACATTCTAACATCAAATTCA
1 ACATTCTAACATCAAATTCA
*
100395 ACATTCTAACATTAAATTC
1 ACATTCTAACATCAAATTC
100414 CAGTACATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.44, C:0.23, G:0.00, T:0.33
Consensus pattern (20 bp):
ACATTCTAACATCAAATTCA
Found at i:101104 original size:20 final size:22
Alignment explanation
Indices: 101056--101120 Score: 62
Period size: 21 Copynumber: 2.9 Consensus size: 22
101046 TCAGATTATC
*
101056 CAGGGGGAACCGATTCCCCCCCCCT
1 CAGGGGGAACAGATT---CCCCCCT
101081 CA-GGGGAACAGATTCCCCCC-
1 CAGGGGGAACAGATTCCCCCCT
* *
101101 CAGGGGGTACCGATTCCCCC
1 CAGGGGGAACAGATTCCCCC
101121 TGTCTAATGG
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
20 2 0.06
21 21 0.58
24 11 0.31
25 2 0.06
ACGTcount: A:0.18, C:0.43, G:0.26, T:0.12
Consensus pattern (22 bp):
CAGGGGGAACAGATTCCCCCCT
Found at i:101504 original size:34 final size:32
Alignment explanation
Indices: 101465--101534 Score: 104
Period size: 34 Copynumber: 2.1 Consensus size: 32
101455 TTTTGTAAAG
*
101465 GGGAAAGGTTCTAGCTTAGCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTTAGCCCG-G-AAAAACTA
*
101499 GGGAAAGGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
101531 GGGA
1 GGGA
101535 GTTTGCAAGG
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 11 0.32
33 1 0.03
34 22 0.65
ACGTcount: A:0.31, C:0.16, G:0.31, T:0.21
Consensus pattern (32 bp):
GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
Found at i:102237 original size:15 final size:15
Alignment explanation
Indices: 102217--102248 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
102207 AACCAACAAA
102217 GGTGGTGTCTCTAAT
1 GGTGGTGTCTCTAAT
102232 GGTGGTGTCTCTAAT
1 GGTGGTGTCTCTAAT
102247 GG
1 GG
102249 CTCTTGAAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.12, C:0.12, G:0.38, T:0.38
Consensus pattern (15 bp):
GGTGGTGTCTCTAAT
Found at i:103916 original size:21 final size:20
Alignment explanation
Indices: 103873--103951 Score: 122
Period size: 20 Copynumber: 3.9 Consensus size: 20
103863 AGATTGTCCA
103873 GGGGTACAGATTCCCCCCAG
1 GGGGTACAGATTCCCCCCAG
*
103893 GGGGTACCGATTCCCCCCAG
1 GGGGTACAGATTCCCCCCAG
*
103913 GGGGAACAGATTCCCCCCCAG
1 GGGGTACAGATT-CCCCCCAG
*
103934 GGGGTACCGATTCCCCCC
1 GGGGTACAGATTCCCCCC
103952 TGTCTAACGG
Statistics
Matches: 53, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
20 35 0.66
21 18 0.34
ACGTcount: A:0.18, C:0.39, G:0.29, T:0.14
Consensus pattern (20 bp):
GGGGTACAGATTCCCCCCAG
Found at i:103938 original size:41 final size:40
Alignment explanation
Indices: 103873--103951 Score: 140
Period size: 41 Copynumber: 1.9 Consensus size: 40
103863 AGATTGTCCA
*
103873 GGGGTACAGATTCCCCCCAGGGGGTACCGATTCCCCCCAG
1 GGGGAACAGATTCCCCCCAGGGGGTACCGATTCCCCCCAG
103913 GGGGAACAGATTCCCCCCCAGGGGGTACCGATTCCCCCC
1 GGGGAACAGATT-CCCCCCAGGGGGTACCGATTCCCCCC
103952 TGTCTAACGG
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
40 11 0.30
41 26 0.70
ACGTcount: A:0.18, C:0.39, G:0.29, T:0.14
Consensus pattern (40 bp):
GGGGAACAGATTCCCCCCAGGGGGTACCGATTCCCCCCAG
Found at i:105294 original size:24 final size:25
Alignment explanation
Indices: 105231--105295 Score: 70
Period size: 20 Copynumber: 2.8 Consensus size: 25
105221 TTTAACACTT
105231 TTACCTACACGTGAAAATCATATAA
1 TTACCTACACGTGAAAATCATATAA
**
105256 TTA---ACA--TGAAAATCA-ATTG
1 TTACCTACACGTGAAAATCATATAA
105275 TTACCTACACGTGAAAATCAT
1 TTACCTACACGTGAAAATCAT
105296 CACACACTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 12
0.70 0.04 0.26
Matches are distributed among these distances:
19 5 0.16
20 9 0.28
22 6 0.19
24 9 0.28
25 3 0.09
ACGTcount: A:0.43, C:0.18, G:0.09, T:0.29
Consensus pattern (25 bp):
TTACCTACACGTGAAAATCATATAA
Found at i:105995 original size:23 final size:22
Alignment explanation
Indices: 105967--106012 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 22
105957 ATATATTTCA
105967 AAAGATTAACCTCACTAAGCTTC
1 AAAGATTAACCTCAC-AAGCTTC
* *
105990 AAAGATTAGCCTCACATGCTTC
1 AAAGATTAACCTCACAAGCTTC
106012 A
1 A
106013 CACTTGCTCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 7 0.33
23 14 0.67
ACGTcount: A:0.37, C:0.26, G:0.11, T:0.26
Consensus pattern (22 bp):
AAAGATTAACCTCACAAGCTTC
Found at i:108112 original size:21 final size:21
Alignment explanation
Indices: 108086--108132 Score: 94
Period size: 21 Copynumber: 2.2 Consensus size: 21
108076 TGATACTATA
108086 AGAAAGACTTTATCACCTTCT
1 AGAAAGACTTTATCACCTTCT
108107 AGAAAGACTTTATCACCTTCT
1 AGAAAGACTTTATCACCTTCT
108128 AGAAA
1 AGAAA
108133 TTCAATATCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.38, C:0.21, G:0.11, T:0.30
Consensus pattern (21 bp):
AGAAAGACTTTATCACCTTCT
Found at i:108141 original size:21 final size:21
Alignment explanation
Indices: 108086--108141 Score: 58
Period size: 21 Copynumber: 2.7 Consensus size: 21
108076 TGATACTATA
**
108086 AGAAAGACTTTATCACCTTCT
1 AGAAAGACAATATCACCTTCT
**
108107 AGAAAGACTTTATCACCTTCT
1 AGAAAGACAATATCACCTTCT
**
108128 AGAAATTCAATATC
1 AGAAAGACAATATC
108142 TTTTCGCTTC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.38, C:0.21, G:0.09, T:0.32
Consensus pattern (21 bp):
AGAAAGACAATATCACCTTCT
Found at i:117521 original size:20 final size:20
Alignment explanation
Indices: 117496--117543 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
117486 ATATTTCATT
117496 TTCATCCTCAAGCTATGATC
1 TTCATCCTCAAGCTATGATC
*
117516 TTCATCCCCAAGCTATGATC
1 TTCATCCTCAAGCTATGATC
117536 TTCATCCT
1 TTCATCCT
117544 AAATTGGTCC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.23, C:0.33, G:0.08, T:0.35
Consensus pattern (20 bp):
TTCATCCTCAAGCTATGATC
Found at i:117816 original size:60 final size:60
Alignment explanation
Indices: 117737--117870 Score: 146
Period size: 60 Copynumber: 2.2 Consensus size: 60
117727 TGAATGATCT
* * * * * *
117737 AAAAGTTTAGGGACTAATTTAGAATGAGATTTATAG-TTAGGGGATGAAATAT-AAATGTTC
1 AAAAGTTTAAGGACCAATTTAGAATGAGAGTCATAGCTTA-AGGATGAAAT-TGAAATATTC
* * * *
117797 AAAAGTTTAAGGACCAATTTCGATTGAGAGTCATAGCTTAAGGATGAAATTGGAATATTT
1 AAAAGTTTAAGGACCAATTTAGAATGAGAGTCATAGCTTAAGGATGAAATTGAAATATTC
117857 AAAAGTTTAAGGAC
1 AAAAGTTTAAGGAC
117871 TACTTTGAGA
Statistics
Matches: 62, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
59 1 0.02
60 58 0.94
61 3 0.05
ACGTcount: A:0.40, C:0.06, G:0.22, T:0.31
Consensus pattern (60 bp):
AAAAGTTTAAGGACCAATTTAGAATGAGAGTCATAGCTTAAGGATGAAATTGAAATATTC
Found at i:118656 original size:48 final size:48
Alignment explanation
Indices: 118580--118725 Score: 184
Period size: 48 Copynumber: 3.0 Consensus size: 48
118570 TATACCCTAA
* * * * *
118580 CCGACCTAACTTACTATATACCCAAATAAAATAAAAAACTGAAATGAC
1 CCGACCCAACTTACTATAGACCCGAATAAAATCAAAAACCGAAATGAC
* * *
118628 CCGACCCAACTTACTATAGACCCGAATAAAACCAAAACCCGAAATAAC
1 CCGACCCAACTTACTATAGACCCGAATAAAATCAAAAACCGAAATGAC
* ** *
118676 CGGACCCAACTTACTATAGACTGGAATAAAATCAAAATCCGAAATGAC
1 CCGACCCAACTTACTATAGACCCGAATAAAATCAAAAACCGAAATGAC
118724 CC
1 CC
118726 AACTCTACCC
Statistics
Matches: 83, Mismatches: 15, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
48 83 1.00
ACGTcount: A:0.46, C:0.27, G:0.10, T:0.17
Consensus pattern (48 bp):
CCGACCCAACTTACTATAGACCCGAATAAAATCAAAAACCGAAATGAC
Found at i:119033 original size:55 final size:55
Alignment explanation
Indices: 118974--119083 Score: 220
Period size: 55 Copynumber: 2.0 Consensus size: 55
118964 GTGATTGGAT
118974 CACCCAGATATATTTGGTTATTTTAATAAAATTTAATTTTTAAAATTACTAAAAC
1 CACCCAGATATATTTGGTTATTTTAATAAAATTTAATTTTTAAAATTACTAAAAC
119029 CACCCAGATATATTTGGTTATTTTAATAAAATTTAATTTTTAAAATTACTAAAAC
1 CACCCAGATATATTTGGTTATTTTAATAAAATTTAATTTTTAAAATTACTAAAAC
119084 AACGTTTAAG
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 55 1.00
ACGTcount: A:0.42, C:0.11, G:0.05, T:0.42
Consensus pattern (55 bp):
CACCCAGATATATTTGGTTATTTTAATAAAATTTAATTTTTAAAATTACTAAAAC
Found at i:122360 original size:95 final size:95
Alignment explanation
Indices: 122155--122417 Score: 341
Period size: 95 Copynumber: 2.7 Consensus size: 95
122145 GGCTAGCTGA
* * *
122155 ATCCATAAAG-CTGGGGTGTTTAACCAATTGCTCTAGAGGGATAACTTAATATCATTGTATAG-A
1 ATCCATAAAGAC-GGGGTGTTTAACCAATTGCTCTAGAGGGATAAC-TCA-AGC-TT-TATTGTA
*
122218 TATTATAATCACCTTTATCAGGCTAGCTGAATATT
61 TATTATAATCACCTTTATCAGGCTAACTGAATATT
122253 ATCCATAAAGACGGGGTGTTTAACCAATTGCTCTAGAGGGATAACTCAAGCTTTATTGTATATTA
1 ATCCATAAAGACGGGGTGTTTAACCAATTGCTCTAGAGGGATAACTCAAGCTTTATTGTATATTA
* *
122318 TAATCACCTTTATCAGGTTAACTGAATTTT
66 TAATCACCTTTATCAGGCTAACTGAATATT
* ** ** * *
122348 ATCTATAAAGACGGGACGTTTAAGTAATTGCTTTAGAGGGACAACTCAAGCTTTATTGTATATAT
1 ATCCATAAAGACGGGGTGTTTAACCAATTGCTCTAGAGGGATAACTCAAGCTTTATTGTATAT-T
122413 ATAAT
65 ATAAT
122418 ATTATAATCT
Statistics
Matches: 149, Mismatches: 13, Indels: 8
0.88 0.08 0.05
Matches are distributed among these distances:
94 4 0.03
95 91 0.61
96 8 0.05
97 2 0.01
98 43 0.29
99 1 0.01
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.35
Consensus pattern (95 bp):
ATCCATAAAGACGGGGTGTTTAACCAATTGCTCTAGAGGGATAACTCAAGCTTTATTGTATATTA
TAATCACCTTTATCAGGCTAACTGAATATT
Found at i:124956 original size:16 final size:17
Alignment explanation
Indices: 124928--124964 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
124918 ATTAAATATT
*
124928 AAATAAATCAAATGAAA
1 AAATAAATCAAATAAAA
124945 AAATAAAT-AAATAAAA
1 AAATAAATCAAATAAAA
124961 AAAT
1 AAAT
124965 TGAATAAAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 11 0.58
17 8 0.42
ACGTcount: A:0.76, C:0.03, G:0.03, T:0.19
Consensus pattern (17 bp):
AAATAAATCAAATAAAA
Found at i:126972 original size:37 final size:34
Alignment explanation
Indices: 126905--126997 Score: 91
Period size: 37 Copynumber: 2.6 Consensus size: 34
126895 CTAAAATTAT
*
126905 AAAAATAATAAAAT-AAAATAGTAAATATATAATTGAAG
1 AAAAATAA-AAAATAAAAAT-GTAAAAATATAA---AAG
126943 -AAAATAAAAAATAAAAATGTAAAAAATATAAAAG
1 AAAAATAAAAAATAAAAATGT-AAAAATATAAAAG
*
126977 AAAAATAACAAATAATAAATG
1 AAAAATAAAAAATAA-AAATG
126998 ATGATAACTA
Statistics
Matches: 49, Mismatches: 2, Indels: 10
0.80 0.03 0.16
Matches are distributed among these distances:
34 3 0.06
35 13 0.27
36 12 0.24
37 21 0.43
ACGTcount: A:0.71, C:0.01, G:0.06, T:0.22
Consensus pattern (34 bp):
AAAAATAAAAAATAAAAATGTAAAAATATAAAAG
Found at i:127039 original size:2 final size:2
Alignment explanation
Indices: 127032--127070 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
127022 GTACATAAAA
127032 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
127071 GAACATCAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:127233 original size:201 final size:197
Alignment explanation
Indices: 126880--127270 Score: 476
Period size: 201 Copynumber: 1.9 Consensus size: 197
126870 AATTTAAAAC
* * *
126880 TAAAATATATGAGTACTAAAATTATAAAAATAATAAAATAAAATAGTAAATATATAATTGAAGAA
1 TAAAATATATGAGTAATAAAATTATAAAAATAATAAAATAAAATAATAAATATATAATAGAAGAA
*
126945 AATAAAAAATAAAAATGTAAAAAATATAAAAGAAAAATAACAAATAATAAATGATGATAACTAAA
66 AATAAAAAATAAAAATGCAAAAAATATAAAAG----A-AACAAATAATAAATGATGATAACTAAA
* *
127010 ACTTAAATACATGTACAT-AAAAAT-ATATATATATATATATATATATATATATATATAATATGA
126 ACTTAAATACATGTAAATAAAAAATAATATAT-TA-AAATATATATATATA-ATATATAATATGA
127073 ACATCAAATT
188 ACATCAAATT
127083 TAAAATTATATGAGTAAT-AAATTACTAAAAATAAT-AAA-AAAATAAT-AATATATAAATGAAG
1 TAAAA-TATATGAGTAATAAAATTA-TAAAAATAATAAAATAAAATAATAAATATAT-AAT--AG
* *
127144 AAGAAAGTAATAAAAAATAAATATGCAAAACAATATAAAAG-AA-AAATAATAAATGATGATATC
61 AAG-AA--AATAAAAAATAAAAATGCAAAA-AATATAAAAGAAACAAATAATAAATGATGATAAC
*
127207 TAAAAAC-TAAATACATGTAAATAAAAAATAATATATTAAAATATGTATATATAATATATAATAT
122 T-AAAACTTAAATACATGTAAATAAAAAATAATATATTAAAATATATATATATAATATATAATAT
127271 AGTATATAAG
Statistics
Matches: 167, Mismatches: 9, Indels: 27
0.82 0.04 0.13
Matches are distributed among these distances:
200 11 0.07
201 54 0.32
202 25 0.15
203 20 0.12
204 25 0.15
205 2 0.01
207 20 0.12
208 10 0.06
ACGTcount: A:0.62, C:0.04, G:0.06, T:0.29
Consensus pattern (197 bp):
TAAAATATATGAGTAATAAAATTATAAAAATAATAAAATAAAATAATAAATATATAATAGAAGAA
AATAAAAAATAAAAATGCAAAAAATATAAAAGAAACAAATAATAAATGATGATAACTAAAACTTA
AATACATGTAAATAAAAAATAATATATTAAAATATATATATATAATATATAATATGAACATCAAA
TT
Found at i:127275 original size:21 final size:23
Alignment explanation
Indices: 127234--127278 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
127224 TAAATAAAAA
127234 ATAATATATTAAAATATGTATAT
1 ATAATATATTAAAATATGTATAT
*
127257 ATAATATA-TAATATA-GTATAT
1 ATAATATATTAAAATATGTATAT
127278 A
1 A
127279 AGATGATATG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 7 0.33
22 6 0.29
23 8 0.38
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.42
Consensus pattern (23 bp):
ATAATATATTAAAATATGTATAT
Found at i:129893 original size:49 final size:49
Alignment explanation
Indices: 129836--129961 Score: 252
Period size: 49 Copynumber: 2.6 Consensus size: 49
129826 AAATTATCAC
129836 ACGTTAAGTATACACTTAGTGAGACAATCTTAGTAATAGTTAATGTAAT
1 ACGTTAAGTATACACTTAGTGAGACAATCTTAGTAATAGTTAATGTAAT
129885 ACGTTAAGTATACACTTAGTGAGACAATCTTAGTAATAGTTAATGTAAT
1 ACGTTAAGTATACACTTAGTGAGACAATCTTAGTAATAGTTAATGTAAT
129934 ACGTTAAGTATACACTTAGTGAGACAAT
1 ACGTTAAGTATACACTTAGTGAGACAAT
129962 TTCACTTTAC
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 77 1.00
ACGTcount: A:0.39, C:0.11, G:0.17, T:0.33
Consensus pattern (49 bp):
ACGTTAAGTATACACTTAGTGAGACAATCTTAGTAATAGTTAATGTAAT
Found at i:130377 original size:70 final size:70
Alignment explanation
Indices: 130168--130377 Score: 305
Period size: 70 Copynumber: 3.0 Consensus size: 70
130158 AAGTACCAAT
* *
130168 ACACATAAGGTTGTGCCCACCATTTGCACTAAGTGTCCTTTATATACACTGTAGTGCTAAA-TAG
1 ACACATAAGGTTGTGCCCACCACTTGCACTAAGTGTCCTTTATATACACTATAGTGCTAAACT-G
130232 AATATG
65 AATATG
* * * * *
130238 ACACATAAGGTTGTGCCCACCACCTACACTAAGTTTCCTTTATATACATTATAGTGCTAAACCGA
1 ACACATAAGGTTGTGCCCACCACTTGCACTAAGTGTCCTTTATATACACTATAGTGCTAAACTGA
130303 ATATG
66 ATATG
* * * *
130308 ACATATAAGGTTGTGCCCACTACTTGCACTAAGTGTCCTTTATATGCACTATAGTGCTAAACTGG
1 ACACATAAGGTTGTGCCCACCACTTGCACTAAGTGTCCTTTATATACACTATAGTGCTAAACTGA
130373 ATATG
66 ATATG
130378 TAGCCTACTG
Statistics
Matches: 123, Mismatches: 16, Indels: 2
0.87 0.11 0.01
Matches are distributed among these distances:
70 123 1.00
ACGTcount: A:0.31, C:0.21, G:0.16, T:0.31
Consensus pattern (70 bp):
ACACATAAGGTTGTGCCCACCACTTGCACTAAGTGTCCTTTATATACACTATAGTGCTAAACTGA
ATATG
Found at i:142634 original size:311 final size:313
Alignment explanation
Indices: 142054--142683 Score: 1096
Period size: 311 Copynumber: 2.0 Consensus size: 313
142044 TTTTCAAGTG
142054 ACTGACAGAATGTTTTGAGCAGATCTGATGCCCCGTTTTCTGACTATCCTCGATAAAAAATTAAT
1 ACTGACAGAATGTTTTGAGCAGATCTGATGCCCCGTTTTCTGACTATCCTCGATAAAAAATTAAT
142119 ATCTTTTGTGTATATATCAAAATCAGTTTCCGTTTATTCTAAAAACAAAATTAAACTGATATACG
66 ATCTTTTGTGTATATATCAAAATCAGTTTCCGTTTATTCT-AAAACAAAATTAAACTGA-ATACG
*
142184 CTCCAACAGTATAAAATTTATCCTCTAATAATATTTTTACAATTTACGGGGATTTTCTAAAACTT
129 ATCCAACAGTATAAAATTTATCCTCTAATAATATTTTTACAATTTACGGGGATTTTCTAAAACTT
*
142249 GTCCAAAACTAAATTCTAAGAAGATTTCACCAATTTACATTTTCAACTTGTTTAATAATTATATT
194 GTCCAAAAATAAATTCTAAGAAGATTTCACCAATTTACATTTTCAACTTGTTTAATAATTATATT
142314 AGCTCACAAATGCACATATATGCATGCATCAC-AAATAATATAACATTTTAGGAGTC
259 AGCTCACAAAT--ACATATATGCATGCATCACAAAATAATATAACATTTTAGGAGTC
142370 ACTGACAGAATTGTTTTGAGCAGAATCTGATGCCCCGTTTTCTGACCTATCC-CGATAAAAAATT
1 ACTGACAGAA-TGTTTTGAGCAG-ATCTGATGCCCCGTTTTCTGA-CTATCCTCGATAAAAAATT
142434 AATATCTTTTGTGTATATATCAAAATCAGTTTCCGTTTATTCT-AAACAAAATTAAACTG-ATAC
63 AATATCTTTTGTGTATATATCAAAATCAGTTTCCGTTTATTCTAAAACAAAATTAAACTGAATAC
*
142497 GAATCCAACAGTATAAAATTTAT-C-CTAATAATA-TTTTACAATTTACGGTGATTTTCT-AAAC
128 G-ATCCAACAGTATAAAATTTATCCTCTAATAATATTTTTACAATTTACGGGGATTTTCTAAAAC
142558 TTGTCCAAAAATAAATTCTAAGAAGATTTCACCAATTTACATTTTCAACTTGTTTAATAATTATA
192 TTGTCCAAAAATAAATTCTAAGAAGATTTCACCAATTTACATTTTCAACTTGTTTAATAATTATA
142623 TTAGCTCACAAATACATATATGCATGCATCACAAAAATAATATAACATTTTAGGAGTC
257 TTAGCTCACAAATACATATATGCATGCATCAC-AAAATAATATAACATTTTAGGAGTC
142681 ACT
1 ACT
142684 TATTACCATA
Statistics
Matches: 305, Mismatches: 3, Indels: 17
0.94 0.01 0.05
Matches are distributed among these distances:
309 19 0.06
311 108 0.35
312 23 0.08
313 9 0.03
314 6 0.02
315 20 0.07
316 26 0.09
317 12 0.04
318 76 0.25
319 6 0.02
ACGTcount: A:0.37, C:0.17, G:0.10, T:0.36
Consensus pattern (313 bp):
ACTGACAGAATGTTTTGAGCAGATCTGATGCCCCGTTTTCTGACTATCCTCGATAAAAAATTAAT
ATCTTTTGTGTATATATCAAAATCAGTTTCCGTTTATTCTAAAACAAAATTAAACTGAATACGAT
CCAACAGTATAAAATTTATCCTCTAATAATATTTTTACAATTTACGGGGATTTTCTAAAACTTGT
CCAAAAATAAATTCTAAGAAGATTTCACCAATTTACATTTTCAACTTGTTTAATAATTATATTAG
CTCACAAATACATATATGCATGCATCACAAAATAATATAACATTTTAGGAGTC
Found at i:147945 original size:14 final size:14
Alignment explanation
Indices: 147925--147963 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
147915 AACCAAATAA
147925 ATTTATAATTTATT
1 ATTTATAATTTATT
* *
147939 TTTTATACTTTATT
1 ATTTATAATTTATT
147953 ATTTATTAATT
1 ATTTA-TAATT
147964 AAATCCTAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
14 16 0.80
15 4 0.20
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.67
Consensus pattern (14 bp):
ATTTATAATTTATT
Found at i:152206 original size:16 final size:15
Alignment explanation
Indices: 152187--152224 Score: 67
Period size: 16 Copynumber: 2.5 Consensus size: 15
152177 ATGAATTCAG
152187 AGCTCCTAAACTCTT
1 AGCTCCTAAACTCTT
152202 CAGCTCCTAAACTCTT
1 -AGCTCCTAAACTCTT
152218 AGCTCCT
1 AGCTCCT
152225 TTGGGATAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 7 0.32
16 15 0.68
ACGTcount: A:0.24, C:0.37, G:0.08, T:0.32
Consensus pattern (15 bp):
AGCTCCTAAACTCTT
Found at i:153239 original size:79 final size:81
Alignment explanation
Indices: 153140--153781 Score: 802
Period size: 80 Copynumber: 8.1 Consensus size: 81
153130 TATTAAGCAT
** * * * *
153140 TTAATCTTTTAGACAAAGGCATTTAGCCTCTCATTTAAC-TGCAATATTGGCATCTTTCTGCAAA
1 TTAATCTTTTACTCAAAGGCATTTAGCCTTTCATCTAACTTGCAATATTGGCACCTTTCTGCCAA
* *
153204 ATGCACAGCTCGACAA
66 ATGCACAGCTAGGCAA
* *
153220 TT-ATCTTTTAGTCAAAGGCATTTAGCC-TTCA--T--CTTGCAATATTGGCACCTTTCTACCAA
1 TTAATCTTTTACTCAAAGGCATTTAGCCTTTCATCTAACTTGCAATATTGGCACCTTTCTGCCAA
* *
153279 ATTCACAGCTAGGTAA
66 ATGCACAGCTAGGCAA
* * * *
153295 TTAATATTTTTACTCAAAGGTA-TTATCCTTTCATCTAACTTGCAAT-TTGACACCTTTCTGCCA
1 TTAAT-CTTTTACTCAAAGGCATTTAGCCTTTCATCTAACTTGCAATATTGGCACCTTTCTGCCA
*
153358 AATGCACAGCTAGAC-A
65 AATGCACAGCTAGGCAA
* * *
153374 TTAATCTTTTACTCAAAGGCATTTAGCCTTTCATCTAAATTGCAATATTGGCACCTTT-AGCTAA
1 TTAATCTTTTACTCAAAGGCATTTAGCCTTTCATCTAACTTGCAATATTGGCACCTTTCTGCCAA
*
153438 ATGCACAGCTAGGAAA
66 ATGCACAGCTAGGCAA
* *
153454 TTAATCTTTTACTCAAAGGCATTTAGCCTTTCATCTAAACTTGCAATATTGACACCTTTCTGCCG
1 TTAATCTTTTACTCAAAGGCATTTAGCCTTTCATCT-AACTTGCAATATTGGCACCTTTCTGCCA
153519 AATGCACAGCTAGGC-A
65 AATGCACAGCTAGGCAA
* * * *
153535 -T-ATCCTTTTACTC-AATG-ATTTAGCATTTCATCTAACTTGCAATATTGGAACCTTTCAGCCA
1 TTAAT-CTTTTACTCAAAGGCATTTAGCCTTTCATCTAACTTGCAATATTGGCACCTTTCTGCCA
*
153596 AATGCAAAGCTAGGCAA
65 AATGCACAGCTAGGCAA
*
153613 TTAATCATTTACTCAAAGGCA-TTAGCCTTTCATCTAACTTGCAATATTGGCACCTTTCTGCCAA
1 TTAATCTTTTACTCAAAGGCATTTAGCCTTTCATCTAACTTGCAATATTGGCACCTTTCTGCCAA
* *
153677 ATTCACAGCTAGGTAA
66 ATGCACAGCTAGGCAA
* *
153693 TTAATC-TTTACTCAAAGGCA--TATCCTTTCATCTAACTTGCAATATTGGCACATTTCTGCCAA
1 TTAATCTTTTACTCAAAGGCATTTAGCCTTTCATCTAACTTGCAATATTGGCACCTTTCTGCCAA
* *
153755 ATGCACAACTAGGTAA
66 ATGCACAGCTAGGCAA
153771 TTAATCTTTTA
1 TTAATCTTTTA
153782 TTTTAAAAAC
Statistics
Matches: 490, Mismatches: 52, Indels: 41
0.84 0.09 0.07
Matches are distributed among these distances:
74 1 0.00
75 36 0.07
76 8 0.02
77 55 0.11
78 93 0.19
79 101 0.21
80 150 0.31
81 30 0.06
82 16 0.03
ACGTcount: A:0.31, C:0.22, G:0.12, T:0.35
Consensus pattern (81 bp):
TTAATCTTTTACTCAAAGGCATTTAGCCTTTCATCTAACTTGCAATATTGGCACCTTTCTGCCAA
ATGCACAGCTAGGCAA
Found at i:153580 original size:158 final size:160
Alignment explanation
Indices: 153140--153781 Score: 807
Period size: 158 Copynumber: 4.1 Consensus size: 160
153130 TATTAAGCAT
** * * * * *
153140 TTAATCTTTTAGACAAAGGCATTTAGCCTCTCATTTAAC-TGCAATATTGGCATCTTTCTGCAAA
1 TTAATCTTTTACTCAAAGGCA-TTAGCCTTTCATCTAACTTGCAATATTGACACCTTTCTGCCAA
* *
153204 ATGCACAGCTCGACAATT-ATCTTTTAGTCAAAGGCATTTAGCC-TTCA--T--CTTGCAATATT
65 ATGCACAGCTAGAC-ATTAATCTTTTACTCAAAGGCATTTAGCCTTTCATCTAACTTGCAATATT
*
153263 GGCACCTTTCTA-CCAAATTCACAGCTAGGTAA
129 GGCACCTTTC-AGCCAAATGCACAGCTAGGTAA
* * *
153295 TTAATATTTTTACTCAAAGGTATTATCCTTTCATCTAACTTGCAAT-TTGACACCTTTCTGCCAA
1 TTAAT-CTTTTACTCAAAGGCATTAGCCTTTCATCTAACTTGCAATATTGACACCTTTCTGCCAA
*
153359 ATGCACAGCTAGACATTAATCTTTTACTCAAAGGCATTTAGCCTTTCATCTAAATTGCAATATTG
65 ATGCACAGCTAGACATTAATCTTTTACTCAAAGGCATTTAGCCTTTCATCTAACTTGCAATATTG
* *
153424 GCACCTTT-AGCTAAATGCACAGCTAGGAAA
130 GCACCTTTCAGCCAAATGCACAGCTAGGTAA
*
153454 TTAATCTTTTACTCAAAGGCATTTAGCCTTTCATCTAAACTTGCAATATTGACACCTTTCTGCCG
1 TTAATCTTTTACTCAAAGGCA-TTAGCCTTTCATCT-AACTTGCAATATTGACACCTTTCTGCCA
* * *
153519 AATGCACAGCTAGGCA-T-ATCCTTTTACTC-AATG-ATTTAGCATTTCATCTAACTTGCAATAT
64 AATGCACAGCTAGACATTAAT-CTTTTACTCAAAGGCATTTAGCCTTTCATCTAACTTGCAATAT
* * *
153580 TGGAACCTTTCAGCCAAATGCAAAGCTAGGCAA
128 TGGCACCTTTCAGCCAAATGCACAGCTAGGTAA
* *
153613 TTAATCATTTACTCAAAGGCATTAGCCTTTCATCTAACTTGCAATATTGGCACCTTTCTGCCAAA
1 TTAATCTTTTACTCAAAGGCATTAGCCTTTCATCTAACTTGCAATATTGACACCTTTCTGCCAAA
* *
153678 TTCACAGCTAGGTA-ATTAATC-TTTACTCAAAGGCA--TATCCTTTCATCTAACTTGCAATATT
66 TGCACAGCTA-G-ACATTAATCTTTTACTCAAAGGCATTTAGCCTTTCATCTAACTTGCAATATT
* * *
153739 GGCACATTTCTGCCAAATGCACAACTAGGTAA
129 GGCACCTTTCAGCCAAATGCACAGCTAGGTAA
153771 TTAATCTTTTA
1 TTAATCTTTTA
153782 TTTTAAAAAC
Statistics
Matches: 424, Mismatches: 43, Indels: 37
0.84 0.09 0.07
Matches are distributed among these distances:
154 3 0.01
155 71 0.17
156 22 0.05
157 37 0.09
158 134 0.32
159 84 0.20
160 42 0.10
161 31 0.07
ACGTcount: A:0.31, C:0.22, G:0.12, T:0.35
Consensus pattern (160 bp):
TTAATCTTTTACTCAAAGGCATTAGCCTTTCATCTAACTTGCAATATTGACACCTTTCTGCCAAA
TGCACAGCTAGACATTAATCTTTTACTCAAAGGCATTTAGCCTTTCATCTAACTTGCAATATTGG
CACCTTTCAGCCAAATGCACAGCTAGGTAA
Found at i:155272 original size:129 final size:129
Alignment explanation
Indices: 155042--155300 Score: 464
Period size: 129 Copynumber: 2.0 Consensus size: 129
155032 TAATTTCAAC
* * *
155042 ACTCAAACTTAATTTACATAATAGTATATCAAATATTGAACAATTACACAACGATCCATAACTTT
1 ACTCAAACATAATTTACAGAATAGTATATCAAATATTGAACAATTACACAACAATCCATAACTTT
*
155107 TTCATAATTATTGAGTAGGTCTCTTAACTTTCATAAAATTATATAATGGCCCCAAATATTTCTA
66 TTCATAATTATTGAGTAGGTCCCTTAACTTTCATAAAATTATATAATGGCCCCAAATATTTCTA
*
155171 ACTCAAACATAATTTACAGAATAGTATATCAAATATTGAATAATTACACAACAATCCATAACTTT
1 ACTCAAACATAATTTACAGAATAGTATATCAAATATTGAACAATTACACAACAATCCATAACTTT
*
155236 TTCATAATTATTGATTAGGTCCCTTAACTTTCATAAAATTATATAATGGCCCCAAATATTTCTA
66 TTCATAATTATTGAGTAGGTCCCTTAACTTTCATAAAATTATATAATGGCCCCAAATATTTCTA
155300 A
1 A
155301 GGCTTGTAAA
Statistics
Matches: 124, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
129 124 1.00
ACGTcount: A:0.41, C:0.17, G:0.07, T:0.36
Consensus pattern (129 bp):
ACTCAAACATAATTTACAGAATAGTATATCAAATATTGAACAATTACACAACAATCCATAACTTT
TTCATAATTATTGAGTAGGTCCCTTAACTTTCATAAAATTATATAATGGCCCCAAATATTTCTA
Found at i:159396 original size:21 final size:21
Alignment explanation
Indices: 159372--159411 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
159362 ATTGAAAAAT
159372 AAATAT-TAAAATAATTATTAA
1 AAATATAT-AAATAATTATTAA
*
159393 AAATATATAAATTATTATT
1 AAATATATAAATAATTATT
159412 TATTATATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 16 0.94
22 1 0.06
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (21 bp):
AAATATATAAATAATTATTAA
Found at i:160303 original size:15 final size:15
Alignment explanation
Indices: 160280--160316 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
160270 CTCGGTAAGC
160280 TTCTCTTCTTTCTTT
1 TTCTCTTCTTTCTTT
*
160295 TTCTTTTCTTTCTTT
1 TTCTCTTCTTTCTTT
*
160310 TTTTCTT
1 TTCTCTT
160317 TTTTGTTTCT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (15 bp):
TTCTCTTCTTTCTTT
Found at i:160328 original size:19 final size:19
Alignment explanation
Indices: 160280--160318 Score: 55
Period size: 17 Copynumber: 2.1 Consensus size: 19
160270 CTCGGTAAGC
160280 TTCTCTTCTTTCTTTTTCTT
1 TTCT-TTCTTTCTTTTTCTT
160300 TTCTTTC-TT-TTTTTCTT
1 TTCTTTCTTTCTTTTTCTT
160317 TT
1 TT
160319 TTGTTTCTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 10 0.53
18 2 0.11
19 3 0.16
20 4 0.21
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (19 bp):
TTCTTTCTTTCTTTTTCTT
Found at i:160807 original size:3 final size:3
Alignment explanation
Indices: 160793--160869 Score: 91
Period size: 3 Copynumber: 25.3 Consensus size: 3
160783 TGTAATATTA
* * * *
160793 AAT AAT ATAT AAT AAT AAT AAT AAT AAT AAT TAT TAT TAT TAT AAT
1 AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* *
160839 TAT AAT AAT AAT AAT TAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
160870 TAAATAACAT
Statistics
Matches: 67, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
3 64 0.96
4 3 0.04
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (3 bp):
AAT
Found at i:161323 original size:113 final size:113
Alignment explanation
Indices: 161099--162107 Score: 1492
Period size: 113 Copynumber: 9.0 Consensus size: 113
161089 TAGAGTCATT
* ** * *
161099 CAAAAGGTTGAATAAGCTCTTCTCATTATGAACTTCTTCTT-C-TC--CTGATGAGGTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* * *
161160 TTATGAAC-TTATCTGGAAAA-ATTGACCCATCAAGTGATGGATTTGAG
66 TTATGAACTTTCTCTGGAAAAGA-TAATCCATCAAGTGATGGATTTGAG
* * *
161207 CAAAAAGCTGAACAAATTCTTCTCATTATGAACTTTTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* * * *
161272 TTATGAACTTTCTCTAGAAAAGTTGATCCATCAAGTTATGGATTTGAG
66 TTATGAACTTTCTCTGGAAAAGATAATCCATCAAGTGATGGATTTGAG
* * * *
161320 CAAAAAGCTGAACAAATTCTTCCCATTATGAACTTCTTCTTCCTTCTTTAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* * *
161385 TTATGAACTTTCTCTAGAAAAGTTGATCCATCAAGTGATGGATTTGAG
66 TTATGAACTTTCTCTGGAAAAGATAATCCATCAAGTGATGGATTTGAG
*** * * *
161433 CAAAAAACTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTTAAATGAGTTCTTTTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* * *
161498 TTATGAAC-TTCTTCTTGAAAGGCTAATCCATCAAGTGATGGATTTGAG
66 TTATGAACTTTC-TCTGGAAAAGATAATCCATCAAGTGATGGATTTGAG
* *
161546 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTTAAATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* *
161611 TTATGAACTTCCTCTGGAAAAGCTAATCCATCAAGTGATGGATTTGAG
66 TTATGAACTTTCTCTGGAAAAGATAATCCATCAAGTGATGGATTTGAG
161659 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
****
161724 TTATGAACTCGAACTGGAAAAGATAATCCATCAAGTGATGGATTTGAG
66 TTATGAACTTTCTCTGGAAAAGATAATCCATCAAGTGATGGATTTGAG
161772 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
****
161837 TTATGAACTCGAACTGGAAAAGATAATCCATCAAGTGATGGATTTGAG
66 TTATGAACTTTCTCTGGAAAAGATAATCCATCAAGTGATGGATTTGAG
161885 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
****
161950 TTATGAACTCGAACTGGAAAAGATAATCCATCAAGTGATGGATTTGAG
66 TTATGAACTTTCTCTGGAAAAGATAATCCATCAAGTGATGGATTTGAG
*
161998 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGACGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* * *
162063 TTATGAACTTCCTCTGGAAAAGCTGATCCATCAAGTGATGGATTT
66 TTATGAACTTTCTCTGGAAAAGATAATCCATCAAGTGATGGATTT
162108 AAATCTTTGC
Statistics
Matches: 847, Mismatches: 46, Indels: 11
0.94 0.05 0.01
Matches are distributed among these distances:
108 35 0.04
109 1 0.00
110 2 0.00
112 26 0.03
113 781 0.92
114 2 0.00
ACGTcount: A:0.30, C:0.19, G:0.15, T:0.36
Consensus pattern (113 bp):
CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
TTATGAACTTTCTCTGGAAAAGATAATCCATCAAGTGATGGATTTGAG
Found at i:163009 original size:83 final size:83
Alignment explanation
Indices: 162835--163307 Score: 797
Period size: 83 Copynumber: 5.7 Consensus size: 83
162825 AAACCAAATT
* * * *
162835 AGATCAGATAATTCAAAGAACACTTCCAGAAGATGCTATTGGGTCTCCTT-ATTTCTTTCAAATT
1 AGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA-TGAG-CACATTCA--TCTTTCAAATT
*
162899 CAATGATTGGTTTTACCAAACC
62 CATTGATTGGTTTTACCAAACC
* *
162921 AGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCCTCTTTCAAATTCAAT
1 AGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTCAAATTCATT
*
162986 GATTAGTTTTACCAAACC
66 GATTGGTTTTACCAAACC
*
163004 AGATCAGATAACTCAAAGGACACTTCCAGAAGATGCTATGAGCACATTCATCTTTCAAATTCATT
1 AGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTCAAATTCATT
163069 GATTGGTTTTACCAAACC
66 GATTGGTTTTACCAAACC
*
163087 AGATCAGATAACTCAAAGAACACTTCCAAAAGATGCTATGAGCACATTCATCTTTCAAATTCATT
1 AGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTCAAATTCATT
163152 GATTGGTTTTACCAAACC
66 GATTGGTTTTACCAAACC
163170 AGATCAGATAACTCAAAG-ACACTTCCAGAAGATGCTATGAGCACATTCATCTTTCAAATTCATT
1 AGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTCAAATTCATT
163234 GATTGGTTTTACCAAACC
66 GATTGGTTTTACCAAACC
*
163252 AGATCAGATAACTCAAAGGACACTTCCAGAAGATGCTATGAGCACATTCATCTTTC
1 AGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTC
163308 CAGCTAATGT
Statistics
Matches: 372, Mismatches: 13, Indels: 7
0.95 0.03 0.02
Matches are distributed among these distances:
82 81 0.22
83 247 0.66
84 4 0.01
85 3 0.01
86 37 0.10
ACGTcount: A:0.36, C:0.22, G:0.14, T:0.29
Consensus pattern (83 bp):
AGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTCAAATTCATT
GATTGGTTTTACCAAACC
Found at i:164447 original size:4 final size:4
Alignment explanation
Indices: 164431--164474 Score: 53
Period size: 4 Copynumber: 12.2 Consensus size: 4
164421 TCTTTTTCTT
164431 TTTC TTT- TTTC TTTC TTTC TTT- TTT- TTTC TTTC TTT- TTT- TTTC
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC
164474 T
1 T
164475 CTTTTTTTTA
Statistics
Matches: 37, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
3 15 0.41
4 22 0.59
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (4 bp):
TTTC
Found at i:164453 original size:14 final size:14
Alignment explanation
Indices: 164421--164474 Score: 67
Period size: 14 Copynumber: 3.9 Consensus size: 14
164411 CCTTGACCCC
164421 TCTTTTTC-TT-TT
1 TCTTTTTCTTTCTT
164433 TCTTTTTTCTTTCTT
1 TC-TTTTTCTTTCTT
*
164448 TCTTTTTTTTTCTT
1 TCTTTTTCTTTCTT
*
164462 TCTTTTTTTTTCT
1 TCTTTTTCTTTCT
164475 CTTTTTTTTA
Statistics
Matches: 38, Mismatches: 1, Indels: 4
0.88 0.02 0.09
Matches are distributed among these distances:
12 2 0.05
13 6 0.16
14 26 0.68
15 4 0.11
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (14 bp):
TCTTTTTCTTTCTT
Found at i:164457 original size:25 final size:24
Alignment explanation
Indices: 164424--164494 Score: 81
Period size: 25 Copynumber: 2.8 Consensus size: 24
164414 TGACCCCTCT
164424 TTTTCTTTTTCTTTTTTCTTTCTTTC
1 TTTT-TTTTTCTTTTTT-TTTCTTTC
164450 TTTTTTTTTCTTTCTTTTTT-TTTC
1 TTTTTTTTTCTTT-TTTTTTCTTTC
*
164474 TCTTTTTTTTATTATTTTTTT
1 T-TTTTTTTTCTT-TTTTTTT
164495 TCATTAAGCA
Statistics
Matches: 41, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
24 5 0.12
25 28 0.68
26 8 0.20
ACGTcount: A:0.03, C:0.13, G:0.00, T:0.85
Consensus pattern (24 bp):
TTTTTTTTTCTTTTTTTTTCTTTC
Found at i:164458 original size:18 final size:17
Alignment explanation
Indices: 164425--164472 Score: 78
Period size: 18 Copynumber: 2.8 Consensus size: 17
164415 GACCCCTCTT
*
164425 TTTCTTTTTCTTTTTTC
1 TTTCTTTTTTTTTTTTC
164442 TTTCTTTCTTTTTTTTTC
1 TTTCTTT-TTTTTTTTTC
164460 TTTCTTTTTTTTT
1 TTTCTTTTTTTTT
164473 CTCTTTTTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
17 13 0.45
18 16 0.55
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (17 bp):
TTTCTTTTTTTTTTTTC
Found at i:164495 original size:14 final size:13
Alignment explanation
Indices: 164423--164483 Score: 70
Period size: 13 Copynumber: 4.5 Consensus size: 13
164413 TTGACCCCTC
*
164423 TTTTTCTTTTTCT
1 TTTTTTTTTTTCT
164436 TTTTTCTTTCTTTCT
1 TTTTT-TTT-TTTCT
164451 TTTTTTTTCTTTC-
1 TTTTTTTT-TTTCT
*
164464 TTTTTTTTTCTCT
1 TTTTTTTTTTTCT
164477 TTTTTTT
1 TTTTTTT
164484 ATTATTTTTT
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
12 3 0.07
13 20 0.47
14 10 0.23
15 10 0.23
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (13 bp):
TTTTTTTTTTTCT
Found at i:174603 original size:9 final size:9
Alignment explanation
Indices: 174589--174613 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
174579 TAAACATTCT
174589 TTTAAATAA
1 TTTAAATAA
174598 TTTAAATAA
1 TTTAAATAA
174607 TTTAAAT
1 TTTAAAT
174614 TTACATGTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (9 bp):
TTTAAATAA
Found at i:176690 original size:15 final size:15
Alignment explanation
Indices: 176667--176714 Score: 57
Period size: 15 Copynumber: 3.4 Consensus size: 15
176657 CTCGGTAAGC
*
176667 TTCTCTTCTTTCTTT
1 TTCTTTTCTTTCTTT
176682 TTCTTTTCTTTC-TT
1 TTCTTTTCTTTCTTT
*
176696 TT-TTTT-TTTCTGT
1 TTCTTTTCTTTCTTT
176709 TTCTTT
1 TTCTTT
176715 GTTGCGTTGT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
12 4 0.14
13 7 0.24
14 7 0.24
15 11 0.38
ACGTcount: A:0.00, C:0.19, G:0.02, T:0.79
Consensus pattern (15 bp):
TTCTTTTCTTTCTTT
Found at i:177196 original size:3 final size:3
Alignment explanation
Indices: 177178--177247 Score: 52
Period size: 3 Copynumber: 23.3 Consensus size: 3
177168 TGTAATATTA
* * * * * *
177178 AAT AAT ATAT ATT AAT AAT AAT -AT TAT TAT TAT TAT TAT AAT AAT
1 AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* *
177223 AAT TAT TAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
177248 TAAATAACAT
Statistics
Matches: 60, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
2 2 0.03
3 55 0.92
4 3 0.05
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (3 bp):
AAT
Found at i:177201 original size:12 final size:12
Alignment explanation
Indices: 177170--177254 Score: 75
Period size: 12 Copynumber: 7.0 Consensus size: 12
177160 TTTGGGCTTG
177170 TAATATTAAATAA
1 TAATATT-AATAA
177183 TATATATTAATAA
1 TA-ATATTAATAA
* *
177196 TAATATTATTAT
1 TAATATTAATAA
*
177208 TATTATT-ATAA
1 TAATATTAATAA
*
177219 TAATAATT-ATTA
1 TAAT-ATTAATAA
*
177231 TAATAATAATAA
1 TAATATTAATAA
*
177243 TAATATAAATAA
1 TAATATTAATAA
177255 CATTAAAATG
Statistics
Matches: 58, Mismatches: 11, Indels: 7
0.76 0.14 0.09
Matches are distributed among these distances:
11 7 0.12
12 37 0.64
13 9 0.16
14 5 0.09
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (12 bp):
TAATATTAATAA
Found at i:177227 original size:18 final size:18
Alignment explanation
Indices: 177178--177243 Score: 71
Period size: 18 Copynumber: 3.5 Consensus size: 18
177168 TGTAATATTA
177178 AATAAT-ATATATTAATAAT
1 AATAATAAT-TATT-ATAAT
* *
177197 AATATTATTATTATTATTAT
1 AATA--ATAATTATTATAAT
177217 AATAATAATTATTATAAT
1 AATAATAATTATTATAAT
177235 AATAATAAT
1 AATAATAAT
177244 AATATAAATA
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
18 21 0.51
19 4 0.10
20 8 0.20
21 6 0.15
22 2 0.05
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
AATAATAATTATTATAAT
Found at i:177229 original size:15 final size:15
Alignment explanation
Indices: 177190--177240 Score: 65
Period size: 15 Copynumber: 3.7 Consensus size: 15
177180 TAATATATAT
177190 TAATAATAA-TATTA
1 TAATAATAATTATTA
*
177204 T--T-ATTATTATTA
1 TAATAATAATTATTA
177216 TAATAATAATTATTA
1 TAATAATAATTATTA
177231 TAATAATAAT
1 TAATAATAAT
177241 AATAATATAA
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
11 3 0.10
12 7 0.23
14 2 0.06
15 19 0.61
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
TAATAATAATTATTA
Found at i:177850 original size:13 final size:13
Alignment explanation
Indices: 177832--177862 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
177822 TAACACCCAT
177832 AACCCGCACACAC
1 AACCCGCACACAC
177845 AACCCGCACACAC
1 AACCCGCACACAC
177858 AACCC
1 AACCC
177863 AATACGAGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.39, C:0.55, G:0.06, T:0.00
Consensus pattern (13 bp):
AACCCGCACACAC
Found at i:178770 original size:59 final size:59
Alignment explanation
Indices: 178651--178772 Score: 147
Period size: 59 Copynumber: 2.1 Consensus size: 59
178641 CTAACCCAAG
* * * *
178651 TATGAAACATAAGGTCATGCCCACCATCTGCACTAATTATACTTTAGTACAGTCCTGAA
1 TATGAAACATAAGGTCATGCCCACCATATACACTAATTATACTTTACTACAATCCTGAA
* * * * *
178710 TATGACACATAAGGTCGTGCCCACCATATATACTAGTTATACTTTACTGCAAT-CTCGAA
1 TATGAAACATAAGGTCATGCCCACCATATACACTAATTATACTTTACTACAATCCT-GAA
178769 TATG
1 TATG
178773 TTGCCTGCTG
Statistics
Matches: 53, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
58 2 0.04
59 51 0.96
ACGTcount: A:0.33, C:0.23, G:0.14, T:0.30
Consensus pattern (59 bp):
TATGAAACATAAGGTCATGCCCACCATATACACTAATTATACTTTACTACAATCCTGAA
Found at i:184312 original size:14 final size:15
Alignment explanation
Indices: 184288--184327 Score: 57
Period size: 14 Copynumber: 2.8 Consensus size: 15
184278 GGGTTGTAAG
184288 TTATCTTCATTTTAT
1 TTATCTTCATTTTAT
184303 TTAT-TTCATTTTAT
1 TTATCTTCATTTTAT
*
184317 TT-TCTTTATTT
1 TTATCTTCATTT
184328 CGTTTCATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
13 1 0.04
14 18 0.78
15 4 0.17
ACGTcount: A:0.17, C:0.10, G:0.00, T:0.72
Consensus pattern (15 bp):
TTATCTTCATTTTAT
Found at i:184324 original size:19 final size:19
Alignment explanation
Indices: 184293--184342 Score: 73
Period size: 19 Copynumber: 2.6 Consensus size: 19
184283 GTAAGTTATC
*
184293 TTCATTTTATTTATTTCAT
1 TTCATTTTCTTTATTTCAT
* *
184312 TTTATTTTCTTTATTTCGT
1 TTCATTTTCTTTATTTCAT
184331 TTCATTTTCTTT
1 TTCATTTTCTTT
184343 CATTCTTTCT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.14, C:0.12, G:0.02, T:0.72
Consensus pattern (19 bp):
TTCATTTTCTTTATTTCAT
Found at i:189473 original size:5 final size:5
Alignment explanation
Indices: 189463--189509 Score: 53
Period size: 5 Copynumber: 9.4 Consensus size: 5
189453 ATTTTATCCC
*
189463 TTTCA TTTCA TATCA TTTCA TTTC- TTTC- TTTCA TTTCTTA TTTCA TT
1 TTTCA TTTCA TTTCA TTTCA TTTCA TTTCA TTTCA TTTC--A TTTCA TT
189510 AATCCATTCC
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
4 8 0.22
5 24 0.65
7 5 0.14
ACGTcount: A:0.17, C:0.19, G:0.00, T:0.64
Consensus pattern (5 bp):
TTTCA
Found at i:190749 original size:69 final size:69
Alignment explanation
Indices: 190604--190779 Score: 232
Period size: 69 Copynumber: 2.5 Consensus size: 69
190594 GCCCACCATA
* * *
190604 TGCACTAAGTGTCCTTTTTATACACTATAGTGCTAAACTGAATATGACACACAAGGTCGTATCCA
1 TGCACTAATTATCCTTTATATACACTATAGTGCTAAACTGAATATGACACACAAGGTC-TATCCA
*
190669 CAATC
65 CAACC
* * *
190674 TGCACTAATTATCCTTTATATACACTACAATGCTAAAC-GAATATGACACATAAGGT-TATGCCC
1 TGCACTAATTATCCTTTATATACACTATAGTGCTAAACTGAATATGACACACAAGGTCTAT--CC
190737 ACAACC
64 ACAACC
190743 TGCACT-ATATATCCTTTATATACACTATAGTGCTAAA
1 TGCACTAAT-TATCCTTTATATACACTATAGTGCTAAA
190780 TCGGGTATAC
Statistics
Matches: 94, Mismatches: 9, Indels: 7
0.85 0.08 0.06
Matches are distributed among these distances:
67 3 0.03
68 2 0.02
69 56 0.60
70 33 0.35
ACGTcount: A:0.35, C:0.23, G:0.11, T:0.31
Consensus pattern (69 bp):
TGCACTAATTATCCTTTATATACACTATAGTGCTAAACTGAATATGACACACAAGGTCTATCCAC
AACC
Found at i:193544 original size:29 final size:31
Alignment explanation
Indices: 193482--193546 Score: 80
Period size: 29 Copynumber: 2.2 Consensus size: 31
193472 AATCACCATA
* * *
193482 TTGGTCCTTAAACTTTTTACAAATTTGTAAT
1 TTGGTCATTAAACATTTTACAAATTTATAAT
*
193513 TTGGTCATTAAA-ATTTTA-AAATTTATATT
1 TTGGTCATTAAACATTTTACAAATTTATAAT
193542 TTGGT
1 TTGGT
193547 TACTAGCCAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 14 0.47
30 5 0.17
31 11 0.37
ACGTcount: A:0.31, C:0.08, G:0.11, T:0.51
Consensus pattern (31 bp):
TTGGTCATTAAACATTTTACAAATTTATAAT
Found at i:195827 original size:21 final size:20
Alignment explanation
Indices: 195802--195840 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
195792 GTAATAATAC
*
195802 GTAAGAGACATTATCGATAAT
1 GTAAG-GACAGTATCGATAAT
*
195823 GTAAGGCCAGTATCGATA
1 GTAAGGACAGTATCGATA
195841 GTATGATATT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.38, C:0.13, G:0.23, T:0.26
Consensus pattern (20 bp):
GTAAGGACAGTATCGATAAT
Found at i:200515 original size:70 final size:70
Alignment explanation
Indices: 200423--200599 Score: 241
Period size: 70 Copynumber: 2.5 Consensus size: 70
200413 ATGCAACATA
* * *
200423 TGCACTAAGTGTCCTTTTTATACACTATAGTGCTGAACTGAATATGACACACAAGG-T-CGCACC
1 TGCACTAAGTGTCCTTTATATACACTATAGTGCTAAACCGAATATGACACACAAGGTTACGC-CC
200486 GACCACC
65 -ACCACC
* * * *
200493 TGCACTAAGTGTCCTTTATATACACTACAGTGCTAAACCGAATATGACACATAAGGTTATGCTCA
1 TGCACTAAGTGTCCTTTATATACACTATAGTGCTAAACCGAATATGACACACAAGGTTACGCCCA
200558 CCACC
66 CCACC
* *
200563 TGCACTAAGTATCCTTTATATACACTTTAGTGCTAAA
1 TGCACTAAGTGTCCTTTATATACACTATAGTGCTAAA
200600 TCGGGTTTGC
Statistics
Matches: 95, Mismatches: 10, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
70 91 0.96
71 2 0.02
72 2 0.02
ACGTcount: A:0.32, C:0.25, G:0.15, T:0.29
Consensus pattern (70 bp):
TGCACTAAGTGTCCTTTATATACACTATAGTGCTAAACCGAATATGACACACAAGGTTACGCCCA
CCACC
Found at i:206740 original size:24 final size:24
Alignment explanation
Indices: 206708--206760 Score: 88
Period size: 24 Copynumber: 2.2 Consensus size: 24
206698 ATATGGATGA
*
206708 TAGGTCATGCCATAGTCATTACGG
1 TAGGCCATGCCATAGTCATTACGG
*
206732 TAGGCCATGCCATAGTCATTGCGG
1 TAGGCCATGCCATAGTCATTACGG
206756 TAGGC
1 TAGGC
206761 AAGAGTGTAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.23, C:0.23, G:0.28, T:0.26
Consensus pattern (24 bp):
TAGGCCATGCCATAGTCATTACGG
Done.