Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024884.1 Corchorus olitorius cultivar O-4 contig24917, 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: 49900
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:3169 original size:24 final size:25
Alignment explanation
Indices: 3137--3183 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
3127 GGCTGGCCAG
3137 GCGCGGCCCA-GCGCGCAAGCCTAT
1 GCGCGGCCCAGGCGCGCAAGCCTAT
*
3161 GCGCGGCCCAGGCGCGCAGGCCT
1 GCGCGGCCCAGGCGCGCAAGCCT
3184 GTGCCAGGCC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 10 0.48
25 11 0.52
ACGTcount: A:0.13, C:0.43, G:0.38, T:0.06
Consensus pattern (25 bp):
GCGCGGCCCAGGCGCGCAAGCCTAT
Found at i:4566 original size:12 final size:11
Alignment explanation
Indices: 4509--4565 Score: 51
Period size: 12 Copynumber: 4.8 Consensus size: 11
4499 TCCGTTGACG
4509 AAATGTTTTAT
1 AAATGTTTTAT
* *
4520 TACTGTTTTACAT
1 AAATGTTTT--AT
*
4533 AAATGATTTAT
1 AAATGTTTTAT
4544 AAAATGTTTTGAT
1 -AAATGTTTT-AT
4557 AAATGTTTT
1 AAATGTTTT
4566 GGGTGCATGA
Statistics
Matches: 36, Mismatches: 6, Indels: 7
0.73 0.12 0.14
Matches are distributed among these distances:
11 9 0.25
12 17 0.47
13 10 0.28
ACGTcount: A:0.35, C:0.04, G:0.11, T:0.51
Consensus pattern (11 bp):
AAATGTTTTAT
Found at i:9531 original size:21 final size:21
Alignment explanation
Indices: 9507--9547 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
9497 TAATTGAGGA
9507 TAAACTCT-ACTAAATTATGTC
1 TAAACT-TAACTAAATTATGTC
*
9528 TAAACTTAATTAAATTATGT
1 TAAACTTAACTAAATTATGT
9548 ACTCCTATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.41, C:0.12, G:0.05, T:0.41
Consensus pattern (21 bp):
TAAACTTAACTAAATTATGTC
Found at i:9777 original size:27 final size:27
Alignment explanation
Indices: 9738--9790 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
9728 TATACACAAA
9738 AAAAGTTCATTGTGATTTGTGTCTAAG
1 AAAAGTTCATTGTGATTTGTGTCTAAG
* *
9765 AAAAGTTTC-TTGTGTTTTGTTTCTAA
1 AAAAG-TTCATTGTGATTTGTGTCTAA
9791 AGGGTGCACC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 20 0.87
28 3 0.13
ACGTcount: A:0.26, C:0.08, G:0.19, T:0.47
Consensus pattern (27 bp):
AAAAGTTCATTGTGATTTGTGTCTAAG
Found at i:11279 original size:28 final size:29
Alignment explanation
Indices: 11228--11283 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 29
11218 CTTTCAGTTC
*
11228 GGACAATCAAGTCCTGTGATTCTCAATTA
1 GGACAATCAAGCCCTGTGATTCTCAATTA
11257 GGACAAT-AAGCCCT-TCGATTCTCAATT
1 GGACAATCAAGCCCTGT-GATTCTCAATT
11284 TTTGGACAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
27 1 0.04
28 17 0.68
29 7 0.28
ACGTcount: A:0.30, C:0.23, G:0.16, T:0.30
Consensus pattern (29 bp):
GGACAATCAAGCCCTGTGATTCTCAATTA
Found at i:12057 original size:137 final size:132
Alignment explanation
Indices: 11730--12001 Score: 337
Period size: 134 Copynumber: 2.0 Consensus size: 132
11720 AAGTAAGAAA
* * ** * * **
11730 ATTGTATAACTTTACATTAGTAAACTTTTATAAATAATGAATGTTATCAACTTTCATATCTAAAG
1 ATTGTATAACTTTACAATAGTAAACTATTATAAAT-AT-AACCTAACCAAAATTCATATCTAAAG
* *
11795 TTACTATAAAAGTTATAAAGGTTTAAAAAAACTATAAGGGTTATTAACAAATTCAGTAACTTACT
64 TTACTATAAAAGTTATAAAGGTTGAAAAAAACTATAAGGGTTATAAACAAATTCAGTAACTTACT
11860 GAGT
129 GAGT
* * ** * *
11864 ATTGTATAACTTTACATTAGTAAACTTTTATAAATAATGAAGGTTACCAAATTTCATATCTAAAG
1 ATTGTATAACTTTACAATAGTAAACTATTATAAAT-AT-AACCTAACCAAAATTCATATCTAAAG
11929 TTACTATAAAAGTTATAAAGGTTGGAAACAAAACTATAAGGGGTTATAAACAAATTCAGTAACTT
64 TTACTATAAAAGTTATAAAGGTT-GAAA-AAAACTATAA-GGGTTATAAACAAATTCAGTAACTT
11994 ACTGAGT
126 ACTGAGT
12001 A
1 A
12002 ATTTTTGTAA
Statistics
Matches: 130, Mismatches: 5, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
134 85 0.65
135 3 0.02
136 10 0.08
137 32 0.25
ACGTcount: A:0.43, C:0.10, G:0.12, T:0.35
Consensus pattern (132 bp):
ATTGTATAACTTTACAATAGTAAACTATTATAAATATAACCTAACCAAAATTCATATCTAAAGTT
ACTATAAAAGTTATAAAGGTTGAAAAAAACTATAAGGGTTATAAACAAATTCAGTAACTTACTGA
GT
Found at i:13724 original size:21 final size:21
Alignment explanation
Indices: 13694--13742 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
13684 TTAATTGAGG
*
13694 GGTGAATACACGAATGTACCC
1 GGTGAGTACACGAATGTACCC
13715 GGTGAGTACACGAATGTACCC
1 GGTGAGTACACGAATGTACCC
*
13736 AGTGAGT
1 GGTGAGT
13743 GAGCCACCCT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.31, C:0.20, G:0.29, T:0.20
Consensus pattern (21 bp):
GGTGAGTACACGAATGTACCC
Found at i:14861 original size:28 final size:29
Alignment explanation
Indices: 14825--14902 Score: 79
Period size: 28 Copynumber: 2.8 Consensus size: 29
14815 TTCAAAGTAC
* * *
14825 AAGGTTAAAACTGTAAATTTA-ACCTTCT
1 AAGGGTAAAACAGTAAATTTATACATTCT
* *
14853 AAGGGTAAAACGGT-AATTTATTCATTCT
1 AAGGGTAAAACAGTAAATTTATACATTCT
* *
14881 TAGGGTAAAACAGTAATTTTAT
1 AAGGGTAAAACAGTAAATTTAT
14903 GTCCATACAG
Statistics
Matches: 41, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
27 6 0.15
28 29 0.71
29 6 0.15
ACGTcount: A:0.38, C:0.10, G:0.15, T:0.36
Consensus pattern (29 bp):
AAGGGTAAAACAGTAAATTTATACATTCT
Found at i:15686 original size:18 final size:19
Alignment explanation
Indices: 15665--15733 Score: 72
Period size: 18 Copynumber: 3.7 Consensus size: 19
15655 TTCAAAATTT
15665 CTTT-TTTTCTTCTTTTCC
1 CTTTCTTTTCTTCTTTTCC
*
15683 CTTTCTTTT-TTCTCTTCC
1 CTTTCTTTTCTTCTTTTCC
* *
15701 CTTT-TTATATATTCTTTTTC
1 CTTTCTT-T-TCTTCTTTTCC
15721 CTTTCTTTTCTTC
1 CTTTCTTTTCTTC
15734 CATTTTGGGC
Statistics
Matches: 42, Mismatches: 4, Indels: 9
0.76 0.07 0.16
Matches are distributed among these distances:
17 2 0.05
18 17 0.40
19 9 0.21
20 12 0.29
21 2 0.05
ACGTcount: A:0.04, C:0.26, G:0.00, T:0.70
Consensus pattern (19 bp):
CTTTCTTTTCTTCTTTTCC
Found at i:16150 original size:2 final size:2
Alignment explanation
Indices: 16143--16174 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
16133 ATTAGTACAG
16143 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
16175 TAAACTTTTT
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:33553 original size:22 final size:22
Alignment explanation
Indices: 33528--33574 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
33518 TTTTTAGTTG
*
33528 AGTAAAACT-ATAAAAGTAAAAT
1 AGTAAAA-TGATAAAAATAAAAT
*
33550 AGTAAAATGGTAAAAATAAAAT
1 AGTAAAATGATAAAAATAAAAT
33572 AGT
1 AGT
33575 TATAAGGATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 1 0.05
22 21 0.95
ACGTcount: A:0.62, C:0.02, G:0.13, T:0.23
Consensus pattern (22 bp):
AGTAAAATGATAAAAATAAAAT
Found at i:33570 original size:93 final size:93
Alignment explanation
Indices: 33467--33635 Score: 320
Period size: 93 Copynumber: 1.8 Consensus size: 93
33457 AGTAATATCA
* *
33467 TAAAAATAAAATAGTTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTA
1 TAAAAATAAAATAGTTATAAGGATATTAAATTTAATTAAATAAAAATAGAGTTTTTAGTTGACTA
33532 AAACTATAAAAGTAAAATAGTAAAATGG
66 AAACTATAAAAGTAAAATAGTAAAATGG
33560 TAAAAATAAAATAGTTATAAGGATATTAAATTTAATTAAATAAAAATAGAGTTTTTAGTTGACTA
1 TAAAAATAAAATAGTTATAAGGATATTAAATTTAATTAAATAAAAATAGAGTTTTTAGTTGACTA
33625 AAACTATAAAA
66 AAACTATAAAA
33636 ATTTAAATAA
Statistics
Matches: 74, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
93 74 1.00
ACGTcount: A:0.53, C:0.02, G:0.12, T:0.33
Consensus pattern (93 bp):
TAAAAATAAAATAGTTATAAGGATATTAAATTTAATTAAATAAAAATAGAGTTTTTAGTTGACTA
AAACTATAAAAGTAAAATAGTAAAATGG
Found at i:33728 original size:30 final size:31
Alignment explanation
Indices: 33673--33731 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 31
33663 ATTCAAAAAT
*
33673 TAAGGGTATAATAGGCGATTCAAAAGTTTAA
1 TAAGAGTATAATAGGCGATTCAAAAGTTTAA
* *
33704 TAAGAGTAT-ATAGGTGATTTAAAAGTTT
1 TAAGAGTATAATAGGCGATTCAAAAGTTT
33732 TACAAAACTC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 17 0.68
31 8 0.32
ACGTcount: A:0.41, C:0.03, G:0.22, T:0.34
Consensus pattern (31 bp):
TAAGAGTATAATAGGCGATTCAAAAGTTTAA
Found at i:34288 original size:31 final size:31
Alignment explanation
Indices: 34253--34311 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
34243 TTGTATTGGA
* *
34253 TTCTCATTAGATGTTTAAGTATAAAAGGGAG
1 TTCTCACTAGATGTTTAAATATAAAAGGGAG
*
34284 TTCTCACTAGATGTTTAAATATATAAGG
1 TTCTCACTAGATGTTTAAATATAAAAGG
34312 AATTATTCTA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.36, C:0.08, G:0.19, T:0.37
Consensus pattern (31 bp):
TTCTCACTAGATGTTTAAATATAAAAGGGAG
Found at i:34388 original size:2 final size:2
Alignment explanation
Indices: 34381--34405 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
34371 TGTTAGTGTA
34381 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
34406 AACAGCTTGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:39572 original size:15 final size:16
Alignment explanation
Indices: 39552--39587 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
39542 GATCTTCCAC
39552 ATTTTATTAT-TTTAT
1 ATTTTATTATGTTTAT
*
39567 ATTTTATTATGTTTTT
1 ATTTTATTATGTTTAT
39583 ATTTT
1 ATTTT
39588 TTTTGGGTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 10 0.53
16 9 0.47
ACGTcount: A:0.22, C:0.00, G:0.03, T:0.75
Consensus pattern (16 bp):
ATTTTATTATGTTTAT
Found at i:40110 original size:20 final size:20
Alignment explanation
Indices: 40086--40131 Score: 67
Period size: 20 Copynumber: 2.3 Consensus size: 20
40076 AGAAATTTGA
*
40086 GTTTTTCTTCTTTTATTTTCT
1 GTTTTTCTTCCTTT-TTTTCT
40107 -TTTTTCTTCCTTTTTTTCT
1 GTTTTTCTTCCTTTTTTTCT
40126 GTTTTT
1 GTTTTT
40132 TCGAAGAAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 6 0.26
20 17 0.74
ACGTcount: A:0.02, C:0.15, G:0.04, T:0.78
Consensus pattern (20 bp):
GTTTTTCTTCCTTTTTTTCT
Found at i:40119 original size:21 final size:20
Alignment explanation
Indices: 40087--40133 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 20
40077 GAAATTTGAG
40087 TTTTTCTTCTTTTATTT-TCT
1 TTTTTCTTCTTTT-TTTCTCT
*
40107 TTTTTCTTCCTTTTTTTCTGT
1 TTTTTCTT-CTTTTTTTCTCT
40128 TTTTTC
1 TTTTTC
40134 GAAGAAGAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 11 0.46
21 13 0.54
ACGTcount: A:0.02, C:0.17, G:0.02, T:0.79
Consensus pattern (20 bp):
TTTTTCTTCTTTTTTTCTCT
Found at i:40359 original size:14 final size:14
Alignment explanation
Indices: 40337--40367 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
40327 ATAATTTTTC
40337 AAATTTTTTT-AAA
1 AAATTTTTTTGAAA
40350 AAATTTTTTTGAAA
1 AAATTTTTTTGAAA
40364 AAAT
1 AAAT
40368 AATAATAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.59
14 7 0.41
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (14 bp):
AAATTTTTTTGAAA
Found at i:43985 original size:33 final size:34
Alignment explanation
Indices: 43880--43988 Score: 119
Period size: 33 Copynumber: 3.5 Consensus size: 34
43870 TGAGAGATCG
*
43880 CCCTCGATCATTCTAAGACTGAAGAAAAGATCAC
1 CCCTCGATCATTCTGAGACTGAAGAAAAGATCAC
*
43914 CCCTCGATCA-TC-----CTGAAGAAAA-ACCAC
1 CCCTCGATCATTCTGAGACTGAAGAAAAGATCAC
* *
43941 CCC-CGACCATTCTGAGATTGAAGAAAAGATCAC
1 CCCTCGATCATTCTGAGACTGAAGAAAAGATCAC
43974 CCCT-GATCATTCTGA
1 CCCTCGATCATTCTGA
43989 TTTTAACTTG
Statistics
Matches: 62, Mismatches: 5, Indels: 17
0.74 0.06 0.20
Matches are distributed among these distances:
26 5 0.08
27 9 0.15
28 10 0.16
32 9 0.15
33 19 0.31
34 10 0.16
ACGTcount: A:0.35, C:0.30, G:0.15, T:0.20
Consensus pattern (34 bp):
CCCTCGATCATTCTGAGACTGAAGAAAAGATCAC
Found at i:44495 original size:2 final size:2
Alignment explanation
Indices: 44490--44528 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
44480 ACACACACAC
44490 AT AT AT AT AT AT -T AT AT AT AT AT AT AT AT 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 AT A
44529 GATTTTCTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 2 0.06
2 33 0.94
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:44514 original size:19 final size:19
Alignment explanation
Indices: 44490--44528 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
44480 ACACACACAC
44490 ATATATATATATTATATAT
1 ATATATATATATTATATAT
44509 ATATATATATATTATATAT
1 ATATATATATATTATATAT
44528 A
1 A
44529 GATTTTCTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
ATATATATATATTATATAT
Found at i:46634 original size:2 final size:2
Alignment explanation
Indices: 46629--46654 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
46619 TATATATATA
46629 AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG
46655 GCATGCATGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:48593 original size:2 final size:2
Alignment explanation
Indices: 48586--48628 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
48576 TGCTGCTTGA
48586 AT AT AT AT AT 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 AT AT AT AT AT
48628 A
1 A
48629 CTAAATATTA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Done.