Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021938.1 Corchorus olitorius cultivar O-4 contig21971, 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: 47176
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.31
Found at i:4649 original size:167 final size:167
Alignment explanation
Indices: 4373--4686 Score: 601
Period size: 167 Copynumber: 1.9 Consensus size: 167
4363 CAAAAATAGG
4373 TTTCATGTTCACATGTAGCAAACAAAAAGTATAAGTGATACGTACATAATGGCAATTGTAACAAG
1 TTTCATGTTCACATGTAGCAAACAAAAAGTATAAGTGATACGTACATAATGGCAATTGTAACAAG
* *
4438 TGTAATTGTAGTTATCATTAAGTATATGCTCTGCCATTAGGACTTTTATTTTTTTAGCAAAATAA
66 TGTAATTGTAGTTATCATTAAGCATATGCTCTGCCATCAGGACTTTTATTTTTTTAGCAAAATAA
4503 TCAAATACTTTCATTGAAATTAAGTGTGAACATTTAA
131 TCAAATACTTTCATTGAAATTAAGTGTGAACATTTAA
4540 TTTCATGTTCACATGTAGCAAACAAAAAGTATAAGTGATACGTACATAATGGCAATTGTAACAAG
1 TTTCATGTTCACATGTAGCAAACAAAAAGTATAAGTGATACGTACATAATGGCAATTGTAACAAG
*
4605 TGTAATTGTAGTTATCATTAAGCATATGCTCTGCCATCAGGACTTTTTTTTTTTTAGCAAAATAA
66 TGTAATTGTAGTTATCATTAAGCATATGCTCTGCCATCAGGACTTTTATTTTTTTAGCAAAATAA
4670 TCAAATACTTTCATTGA
131 TCAAATACTTTCATTGA
4687 TTAGAAATAT
Statistics
Matches: 144, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
167 144 1.00
ACGTcount: A:0.36, C:0.13, G:0.14, T:0.36
Consensus pattern (167 bp):
TTTCATGTTCACATGTAGCAAACAAAAAGTATAAGTGATACGTACATAATGGCAATTGTAACAAG
TGTAATTGTAGTTATCATTAAGCATATGCTCTGCCATCAGGACTTTTATTTTTTTAGCAAAATAA
TCAAATACTTTCATTGAAATTAAGTGTGAACATTTAA
Found at i:5300 original size:20 final size:21
Alignment explanation
Indices: 5272--5310 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
5262 ATCTAATCAA
5272 ATTTAATTAATA-AAATTACT
1 ATTTAATTAATATAAATTACT
* *
5292 ATTTTATTATTATAAATTA
1 ATTTAATTAATATAAATTA
5311 TAAAACTAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 10 0.62
21 6 0.38
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (21 bp):
ATTTAATTAATATAAATTACT
Found at i:14286 original size:15 final size:15
Alignment explanation
Indices: 14266--14295 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
14256 AGAAATCATG
14266 TTTTTATTTTAGTTT
1 TTTTTATTTTAGTTT
14281 TTTTTATTTTAGTTT
1 TTTTTATTTTAGTTT
14296 AGTTTATTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.00, G:0.07, T:0.80
Consensus pattern (15 bp):
TTTTTATTTTAGTTT
Found at i:14301 original size:15 final size:15
Alignment explanation
Indices: 14268--14304 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
14258 AAATCATGTT
**
14268 TTTATTTTAGTTTTT
1 TTTATTTTAGTTTAG
14283 TTTATTTTAGTTTAG
1 TTTATTTTAGTTTAG
14298 TTTATTT
1 TTTATTT
14305 ATAAATTTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.16, C:0.00, G:0.08, T:0.76
Consensus pattern (15 bp):
TTTATTTTAGTTTAG
Found at i:18121 original size:21 final size:22
Alignment explanation
Indices: 18081--18121 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
18071 GACAAACTTG
18081 TAATAAATTATTTGTTTAAATT
1 TAATAAATTATTTGTTTAAATT
18103 TAAT-AATATATTT-TTTAAA
1 TAATAAAT-TATTTGTTTAAA
18122 ACTTTTGAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (22 bp):
TAATAAATTATTTGTTTAAATT
Found at i:21836 original size:12 final size:12
Alignment explanation
Indices: 21819--21848 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
21809 TAGAGTTTTG
21819 GAGGATATTGAA
1 GAGGATATTGAA
*
21831 GAGGATATTGAG
1 GAGGATATTGAA
21843 GAGGAT
1 GAGGAT
21849 TGGTTTAGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.37, C:0.00, G:0.40, T:0.23
Consensus pattern (12 bp):
GAGGATATTGAA
Found at i:25097 original size:21 final size:21
Alignment explanation
Indices: 25049--25097 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
25039 AGTAACAATA
*
25049 AAATAAA-TAAGCAAGAAAAT
1 AAATAAATTAAGCAACAAAAT
*
25069 -AATAAAATTAAGCAACAAGAT
1 AAAT-AAATTAAGCAACAAAAT
25090 AAATAAAT
1 AAATAAAT
25098 ACTCCAATCC
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
19 3 0.12
20 3 0.12
21 15 0.62
22 3 0.12
ACGTcount: A:0.67, C:0.06, G:0.08, T:0.18
Consensus pattern (21 bp):
AAATAAATTAAGCAACAAAAT
Found at i:25558 original size:7 final size:7
Alignment explanation
Indices: 25526--25564 Score: 51
Period size: 7 Copynumber: 5.4 Consensus size: 7
25516 AATCAATTAG
25526 AAATCAT
1 AAATCAT
25533 AAATACAT
1 AAAT-CAT
*
25541 AAATAAT
1 AAATCAT
*
25548 AAATCAG
1 AAATCAT
25555 AAATCAT
1 AAATCAT
25562 AAA
1 AAA
25565 ATACCAAGAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 20 0.74
8 7 0.26
ACGTcount: A:0.64, C:0.10, G:0.03, T:0.23
Consensus pattern (7 bp):
AAATCAT
Found at i:27106 original size:124 final size:123
Alignment explanation
Indices: 26951--27300 Score: 497
Period size: 124 Copynumber: 2.8 Consensus size: 123
26941 AGTTACGCTA
* ** * * *
26951 CTGACCTCCTTTATTGACCAAGAATAGGACTTCGGTTGAAA-TGCCTAGCAACAC-TTCTCGGCA
1 CTGACCTCCTTTGTTGATGAAGAATAAGACTTTGG-TGAAAGTGCC-AGCAACACTTTC-CAGCA
*
27014 GTGGAACCTCCTCCTCGGCAGAGTGACACGTCAGCAAGGTTGCACTAGGTTAGCCATGCTG
63 GTGGAACCTCCTCCTCGGCAGAGTGACACGTCAGCAAGGTTGCACCAGGTTAGCCATGCTG
* * * * *
27075 CTGACCTCATTTGTTGATGAAGAATACGACTTTGGTGAAAGTGCCCAACAACACTTTCCATCAGC
1 CTGACCTCCTTTGTTGATGAAGAATAAGACTTTGGTGAAAGTG-CCAGCAACACTTTCCAGCAGT
* * *
27140 GGAACCTCCTCCTCGGCAAAGTGACACGTCAGTAAGGTTGCACCAGGTTAGCCATGTTG
65 GGAACCTCCTCCTCGGCAGAGTGACACGTCAGCAAGGTTGCACCAGGTTAGCCATGCTG
*
27199 CTGACCTCCTTTGTTGATGAAGGATAAGACTTTGGTGAAAGTGCACAGCAACACTTTCCAGCAGT
1 CTGACCTCCTTTGTTGATGAAGAATAAGACTTTGGTGAAAGTGC-CAGCAACACTTTCCAGCAGT
27264 GGAACCTCCTCCTCGGCAGAGTGACACGTCAGCAAGG
65 GGAACCTCCTCCTCGGCAGAGTGACACGTCAGCAAGG
27301 CAGTCCCACA
Statistics
Matches: 200, Mismatches: 22, Indels: 8
0.87 0.10 0.03
Matches are distributed among these distances:
123 6 0.03
124 189 0.94
125 5 0.03
ACGTcount: A:0.26, C:0.26, G:0.24, T:0.24
Consensus pattern (123 bp):
CTGACCTCCTTTGTTGATGAAGAATAAGACTTTGGTGAAAGTGCCAGCAACACTTTCCAGCAGTG
GAACCTCCTCCTCGGCAGAGTGACACGTCAGCAAGGTTGCACCAGGTTAGCCATGCTG
Found at i:29033 original size:25 final size:25
Alignment explanation
Indices: 28999--29052 Score: 99
Period size: 25 Copynumber: 2.2 Consensus size: 25
28989 TTCTGAAATC
28999 ATTGCCACGTAGGTGTGAGCTTTAT
1 ATTGCCACGTAGGTGTGAGCTTTAT
*
29024 ATTGCCACGTAGGTGTGGGCTTTAT
1 ATTGCCACGTAGGTGTGAGCTTTAT
29049 ATTG
1 ATTG
29053 TGGGAAGGCT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.19, C:0.15, G:0.30, T:0.37
Consensus pattern (25 bp):
ATTGCCACGTAGGTGTGAGCTTTAT
Found at i:29114 original size:53 final size:53
Alignment explanation
Indices: 29051--29151 Score: 193
Period size: 53 Copynumber: 1.9 Consensus size: 53
29041 GGCTTTATAT
*
29051 TGTGGGAAGGCTAGGTAAGAAACTCTTAGCTCCCTTGACCACTCCCTTCGGGC
1 TGTGGGAAGGCTAGATAAGAAACTCTTAGCTCCCTTGACCACTCCCTTCGGGC
29104 TGTGGGAAGGCTAGATAAGAAACTCTTAGCTCCCTTGACCACTCCCTT
1 TGTGGGAAGGCTAGATAAGAAACTCTTAGCTCCCTTGACCACTCCCTT
29152 AATCATGATT
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 47 1.00
ACGTcount: A:0.23, C:0.28, G:0.24, T:0.26
Consensus pattern (53 bp):
TGTGGGAAGGCTAGATAAGAAACTCTTAGCTCCCTTGACCACTCCCTTCGGGC
Found at i:32876 original size:3 final size:3
Alignment explanation
Indices: 32863--32895 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
32853 TGGTCAAGGG
*
32863 AAT AGT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
32896 GAAAATGATA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:34560 original size:650 final size:655
Alignment explanation
Indices: 33246--35142 Score: 2941
Period size: 650 Copynumber: 2.9 Consensus size: 655
33236 TTTATTTTAA
33246 TTGTGTATATGTAAAAATTGAAGCATATTTAATGACTATTGATCACCAACTTTCATTGAGATGTA
1 TTGTGTATATGTAAAAATTGAAGCATATTTAATGACTATTGATCACCAACTTTCATT-AGATG--
* *
33311 TATGTTACTATTAGTAACGGCTAGTAGGAAATTACTAGTATTTAAATGCTATGACAGACATAGTT
63 TATG-T--TATTAGTAACGGCTAGTAGGAAATTACTAGTGTTTAAACGCTATGACAGACATAGTT
* * *
33376 AAGCA-TTTTTTAAAAGTAAATTGCAACAGATATTATCAAGTCATGAAAACTTGACTACAAACCT
125 AAGCATTTTTTTAAAGGAAAATTGCAACAGATATTATTAAGTCATGAAAACTTGACTACAAACCT
*
33440 CAACATAACCTATTGGTAAGTCCAAACACAAGACCAAACAAGAAACAAAAAGAACACAAAACATA
190 CAACATAACCTACTGGTAAGTCCAAACACAAGACCAAACAAGAAACAAAAAGAACACAAAACATA
* * *
33505 CACTTTCCTGCAAGAACCCCAAATTATCAACCAAACAAATGAGAACAAAGCCAACATCCAAGACA
255 CCCTTTCCTACAAGAACCCCAAACTATCAACCAAACAAATGAGAACAAAGCCAACATCCAAGACA
**
33570 AGGGATCGACAGTAACCAAGAAAAACTCATCCAAGACAAGGCCGGTCAAAAACACCACAGAAAAA
320 AGGGATCGACACAAACCAAGAAAAACTCATCCAAGACAAGGCCGGTCAAAAACACCACAGAAAAA
33635 AAGAGTCCACCCACTAATTCTTTTGCTTTGACAAAATCAAACTACTAAACACCCTCTAAAAAAAC
385 AAGAGTCCACCCACTAATTCTTTTGCTTTGACAAAATCAAACTACTAAACACCCTCTAAAAAAAC
*
33700 TTACGTACCTTGAAGATCAGCATCCAAATCATGCTTGAACAATCTTTCCAAACTCCTTACTTTTA
450 TTACGTACCATGAAGATCAGCATCCAAATCATGCTTGAACAATCTTTCCAAACTCCTTACTTTTA
*
33765 AAAATCCACATTCCTCCAAAGTTTCAAGTAATACCTTCGTTGCAACAAAAAATAACCACCAAGCT
515 AAAATCCACATTCCTCCAAAGTTCCAAGTAATACCTTCGTTGCAACAAAAAATAACCACCAAGCT
33830 AACCAAACTTTAAGATTTATCCCAATCTCCCCCTTCGGTATCAACCAAGGGTTGAATCACCTATT
580 AACCAAACTTTAAGATTTATCCCAATCTCCCCCTTCGGTATCAACCAAGGGTTGAATCACCTATT
33895 GACTGGCAAAT
645 GACTGGCAAAT
33906 TTGTGTATATGTAAAAATTGAAGCATATTTAATGACTATTGATCACCAACTTTCATT-GA-G-AT
1 TTGTGTATATGTAAAAATTGAAGCATATTTAATGACTATTGATCACCAACTTTCATTAGATGTAT
*
33968 G-TATTAGT-ACGGCTAGTAGGAAATTACTAGTGTTTAAACGCTATGACAGACACAGTTAAGCAT
66 GTTATTAGTAACGGCTAGTAGGAAATTACTAGTGTTTAAACGCTATGACAGACATAGTTAAGCAT
* * *
34031 TTTTTTAAAGGCAAATTGGAACAAATATTATTAAGTCATGAAAACTTGACTACAAACCTCAACAT
131 TTTTTTAAAGGAAAATTGCAACAGATATTATTAAGTCATGAAAACTTGACTACAAACCTCAACAT
*
34096 AACCTACTGGTAAGTCCAAACACAAGACCAAACAAGAAACAGAAAGAACACAAAACATACCCTTT
196 AACCTACTGGTAAGTCCAAACACAAGACCAAACAAGAAACAAAAAGAACACAAAACATACCCTTT
34161 CCTACAAGAACCCCAAACTATCAACCAAACAAATGAGAACAAAGCCAACATCCAAGACAAGGGAT
261 CCTACAAGAACCCCAAACTATCAACCAAACAAATGAGAACAAAGCCAACATCCAAGACAAGGGAT
34226 CGACACAAACCAAGAAAAACTCATCCAAGACAAGGCCGGTCAAAAACACCACAGAAAAAAAGAGT
326 CGACACAAACCAAGAAAAACTCATCCAAGACAAGGCCGGTCAAAAACACCACAGAAAAAAAGAGT
* *
34291 TCACCCACTAATTCTTTTGCTTTGACAAAATCAAACTACTAAACACCCTCTAAAAAAATTTACGT
391 CCACCCACTAATTCTTTTGCTTTGACAAAATCAAACTACTAAACACCCTCTAAAAAAACTTACGT
* *
34356 ATCATGAAGATCAGCATCCAAATCATGCTTGAACAATATTTCCAAACTCCTTACTTTTAAAAATC
456 ACCATGAAGATCAGCATCCAAATCATGCTTGAACAATCTTTCCAAACTCCTTACTTTTAAAAATC
* * *
34421 CACATTCCTCCAAAGTTCCAAGTAATACCTTCGTTGCAACACAAAATAACCTCCAAGGTAACCAA
521 CACATTCCTCCAAAGTTCCAAGTAATACCTTCGTTGCAACAAAAAATAACCACCAAGCTAACCAA
*
34486 ACTTTAAGATTTATCCCAATCTTCCCCTTCGGTATCAACCAAGGGTTGAATCACCTATTGACTGG
586 ACTTTAAGATTTATCCCAATCTCCCCCTTCGGTATCAACCAAGGGTTGAATCACCTATTGACTGG
34551 CAAAT
651 CAAAT
* *
34556 TTGTGTATATGTAAAACTTGAAGCATATTTAATGACTATTGATCAACAACTTTCATTGAGATGTA
1 TTGTGTATATGTAAAAATTGAAGCATATTTAATGACTATTGATCACCAACTTTCATT-AGATG--
* * * *
34621 TATGTTACTATTAGTAATGGCTAGTAGGAAATTAATAGTGTTTAAACGGTATGACAGACATAATT
63 TATG-T--TATTAGTAACGGCTAGTAGGAAATTACTAGTGTTTAAACGCTATGACAGACATAGTT
* *
34686 AAACATTTTTTTAAAGGAAAATTGCAATAGATATTATTAAGTCATGAAAACTTGACTACAAACCT
125 AAGCATTTTTTTAAAGGAAAATTGCAACAGATATTATTAAGTCATGAAAACTTGACTACAAACCT
* * *
34751 CAACATAACCTACTAGTAAAGTCCAAATAC----CCAAACAAGAAACATAAAGAACACAAAACAT
190 CAACATAACCTACTGGT-AAGTCCAAACACAAGACCAAACAAGAAACAAAAAGAACACAAAACAT
* * *
34812 ATCCTTTCCTACAAGAACCCCAAACTATCAACCAAACAAATGAGAAAAAAACCAACATCCAAGAC
254 ACCCTTTCCTACAAGAACCCCAAACTATCAACCAAACAAATGAGAACAAAGCCAACATCCAAGAC
* *
34877 AAGGGATCAACACAAACCAAGAAAAAATCATCCAAGACAAGGCCATCCAATGGATCCGGTCAAAA
319 AAGGGATCGACACAAACCAAGAAAAACTCAT-C----CAA-G--A--CAA-GG--CCGGTCAAAA
* * * * *
34942 ACACCACAGAAAAAAAAAGAGTCCACCCACCAATCCTTTTGCTCTGAAAAAATCGAACTACTAAA
371 ACACCACAG--AAAAAAAGAGTCCACCCACTAATTCTTTTGCTTTGACAAAATCAAACTACTAAA
*
35007 CACCCTCTAAAAAAACTTATGTACCATGAAGATCAGCATCCAAATTCCATATGACACTCTTGAAC
434 CACCCTCTAAAAAAACTTACGTACCATGAAGATCAGCATCCAAA-T-C--ATG-----CTTGAAC
* *
35072 AATCTTTCCAAACTCCTTACTTTTTAAAATCCACATTCCTCCAAAGTTCCAAGTAATACCTACGT
490 AATCTTTCCAAACTCCTTACTTTTAAAAATCCACATTCCTCCAAAGTTCCAAGTAATACCTTCGT
35137 TGCAAC
555 TGCAAC
35143 TAGGGGTGTA
Statistics
Matches: 1143, Mismatches: 57, Indels: 52
0.91 0.05 0.04
Matches are distributed among these distances:
649 51 0.04
650 565 0.49
652 2 0.00
653 1 0.00
654 3 0.00
656 3 0.00
657 1 0.00
658 123 0.11
659 1 0.00
660 64 0.06
661 120 0.10
662 11 0.01
663 3 0.00
664 1 0.00
666 1 0.00
668 3 0.00
669 2 0.00
671 19 0.02
673 89 0.08
674 1 0.00
675 1 0.00
677 3 0.00
682 75 0.07
ACGTcount: A:0.42, C:0.22, G:0.12, T:0.24
Consensus pattern (655 bp):
TTGTGTATATGTAAAAATTGAAGCATATTTAATGACTATTGATCACCAACTTTCATTAGATGTAT
GTTATTAGTAACGGCTAGTAGGAAATTACTAGTGTTTAAACGCTATGACAGACATAGTTAAGCAT
TTTTTTAAAGGAAAATTGCAACAGATATTATTAAGTCATGAAAACTTGACTACAAACCTCAACAT
AACCTACTGGTAAGTCCAAACACAAGACCAAACAAGAAACAAAAAGAACACAAAACATACCCTTT
CCTACAAGAACCCCAAACTATCAACCAAACAAATGAGAACAAAGCCAACATCCAAGACAAGGGAT
CGACACAAACCAAGAAAAACTCATCCAAGACAAGGCCGGTCAAAAACACCACAGAAAAAAAGAGT
CCACCCACTAATTCTTTTGCTTTGACAAAATCAAACTACTAAACACCCTCTAAAAAAACTTACGT
ACCATGAAGATCAGCATCCAAATCATGCTTGAACAATCTTTCCAAACTCCTTACTTTTAAAAATC
CACATTCCTCCAAAGTTCCAAGTAATACCTTCGTTGCAACAAAAAATAACCACCAAGCTAACCAA
ACTTTAAGATTTATCCCAATCTCCCCCTTCGGTATCAACCAAGGGTTGAATCACCTATTGACTGG
CAAAT
Found at i:37356 original size:22 final size:22
Alignment explanation
Indices: 37331--37382 Score: 88
Period size: 22 Copynumber: 2.4 Consensus size: 22
37321 AAAAGCAACT
37331 AAGAAAAATAAACAAAAAT-AAA
1 AAGAAAAATAAAC-AAAATGAAA
37353 AAGAAAAATAAACAAAATGAAA
1 AAGAAAAATAAACAAAATGAAA
37375 AAGAAAAA
1 AAGAAAAA
37383 GATAAGGGTA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
21 5 0.17
22 24 0.83
ACGTcount: A:0.81, C:0.04, G:0.08, T:0.08
Consensus pattern (22 bp):
AAGAAAAATAAACAAAATGAAA
Found at i:39700 original size:37 final size:37
Alignment explanation
Indices: 39657--39766 Score: 159
Period size: 37 Copynumber: 3.0 Consensus size: 37
39647 AAAATGATTT
*
39657 CAAAGTTTTCAAATTGGAAAAGTTCCTATCAAGTTTC
1 CAAAGTTTTCAAATTGGAAAAGTTCCCATCAAGTTTC
* * *
39694 CAAAGTTTTCAAATTGGGAAAGTTCCCATCTAGTTTT
1 CAAAGTTTTCAAATTGGAAAAGTTCCCATCAAGTTTC
*
39731 CAAAGTTTTCAAATTGGGAAAA-TTCCCATCAGGTTT
1 CAAAGTTTTCAAATT-GGAAAAGTTCCCATCAAGTTT
39767 TAGTTTTCAA
Statistics
Matches: 65, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
37 60 0.92
38 5 0.08
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.35
Consensus pattern (37 bp):
CAAAGTTTTCAAATTGGAAAAGTTCCCATCAAGTTTC
Found at i:46481 original size:7 final size:6
Alignment explanation
Indices: 46465--46495 Score: 53
Period size: 6 Copynumber: 5.0 Consensus size: 6
46455 TATATAAGAT
46465 AAATAA AAATAAA AAATAA AAATAA AAATAA
1 AAATAA AAAT-AA AAATAA AAATAA AAATAA
46496 TTTATTTTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 18 0.75
7 6 0.25
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
AAATAA
Found at i:46483 original size:13 final size:13
Alignment explanation
Indices: 46465--46492 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
46455 TATATAAGAT
46465 AAATAAAAATAAA
1 AAATAAAAATAAA
46478 AAATAAAAATAAA
1 AAATAAAAATAAA
46491 AA
1 AA
46493 TAATTTATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (13 bp):
AAATAAAAATAAA
Done.