Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011872.1 Corchorus olitorius cultivar O-4 contig11905, 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: 68035
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Found at i:1534 original size:69 final size:68
Alignment explanation
Indices: 1459--1678 Score: 153
Period size: 69 Copynumber: 3.2 Consensus size: 68
1449 TCCAAGTAAG
* *
1459 AGGATAATAAAGCCAAATAGAAAAGAAAATCTGTCCAAAAGGAAAAGACCAATTAGGAAATAAGA
1 AGGATAAAAAAG-CAAATAGAAAAGAAAATCTGACCAAAAGGAAAAGACCAATTAGGAAATAAGA
1524 TGAA
65 TGAA
* ** * *** ** * * ** **
1528 AGGATAAAAAAGAAAAGT-GCCTAACAAAAGAAGAAGAAGAA-GAAAACA-CAACCTAACCATTT
1 AGGATAAAAAAGCAAA-TAG-AAAAGAAAATCTGACCAA-AAGGAAAAGACCAA--TTAGGAAAT
1590 CAAG-T-AA
61 -AAGATGAA
* *
1597 GAGGATAATAAAGGCAAATAGAAAAGAAAATCTGCCCAAAAGGAAAAGACCAATTAGGAAATAAG
1 -AGGATAA-AAAAGCAAATAGAAAAGAAAATCTGACCAAAAGGAAAAGACCAATTAGGAAATAAG
1662 ATGAA
64 ATGAA
1667 AGGATAAAAAAG
1 AGGATAAAAAAG
1679 AAAAGTGCCT
Statistics
Matches: 103, Mismatches: 35, Indels: 27
0.62 0.21 0.16
Matches are distributed among these distances:
68 14 0.14
69 43 0.42
70 32 0.31
71 14 0.14
ACGTcount: A:0.57, C:0.11, G:0.19, T:0.13
Consensus pattern (68 bp):
AGGATAAAAAAGCAAATAGAAAAGAAAATCTGACCAAAAGGAAAAGACCAATTAGGAAATAAGAT
GAA
Found at i:1582 original size:139 final size:140
Alignment explanation
Indices: 1413--1696 Score: 525
Period size: 139 Copynumber: 2.0 Consensus size: 140
1403 GAAAAAATTT
1413 AAAAGAAGAAAGAAGAAGAAAACACAACCTAACCATTCCAAGTAAGAGGATAATAAAGCCAAATA
1 AAAAGAAGAAAGAAGAAGAAAACACAACCTAACCATTCCAAGTAAGAGGATAATAAAGCCAAATA
*
1478 GAAAAGAAAATCTGTCCAAAAGGAAAAGACCAATTAGGAAATAAGATGAAAGGATAAAAAAGAAA
66 GAAAAGAAAATCTGCCCAAAAGGAAAAGACCAATTAGGAAATAAGATGAAAGGATAAAAAAGAAA
1543 AGTGCCTAAC
131 AGTGCCTAAC
* *
1553 AAAAGAAG-AAGAAGAAGAAAACACAACCTAACCATTTCAAGTAAGAGGATAATAAAGGCAAATA
1 AAAAGAAGAAAGAAGAAGAAAACACAACCTAACCATTCCAAGTAAGAGGATAATAAAGCCAAATA
1617 GAAAAGAAAATCTGCCCAAAAGGAAAAGACCAATTAGGAAATAAGATGAAAGGATAAAAAAGAAA
66 GAAAAGAAAATCTGCCCAAAAGGAAAAGACCAATTAGGAAATAAGATGAAAGGATAAAAAAGAAA
*
1682 AGTGCCTAAT
131 AGTGCCTAAC
1692 AAAAG
1 AAAAG
1697 TCCAAAGTTA
Statistics
Matches: 140, Mismatches: 4, Indels: 1
0.97 0.03 0.01
Matches are distributed among these distances:
139 132 0.94
140 8 0.06
ACGTcount: A:0.57, C:0.12, G:0.18, T:0.12
Consensus pattern (140 bp):
AAAAGAAGAAAGAAGAAGAAAACACAACCTAACCATTCCAAGTAAGAGGATAATAAAGCCAAATA
GAAAAGAAAATCTGCCCAAAAGGAAAAGACCAATTAGGAAATAAGATGAAAGGATAAAAAAGAAA
AGTGCCTAAC
Found at i:4978 original size:7 final size:7
Alignment explanation
Indices: 4966--4999 Score: 68
Period size: 7 Copynumber: 4.9 Consensus size: 7
4956 AAAAGCATAT
4966 GCATTGG
1 GCATTGG
4973 GCATTGG
1 GCATTGG
4980 GCATTGG
1 GCATTGG
4987 GCATTGG
1 GCATTGG
4994 GCATTG
1 GCATTG
5000 TATTTGGTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.15, C:0.15, G:0.41, T:0.29
Consensus pattern (7 bp):
GCATTGG
Found at i:10060 original size:6 final size:6
Alignment explanation
Indices: 10044--10102 Score: 86
Period size: 6 Copynumber: 10.0 Consensus size: 6
10034 AAACTAAAGG
*
10044 ACAAAA A-AAAA ACAAAA AC-AAA ACAAAA CAAAAAA ACAAAA ACAAAA
1 ACAAAA ACAAAA ACAAAA ACAAAA ACAAAA -ACAAAA ACAAAA ACAAAA
10091 ACAAAA ACAAAA
1 ACAAAA ACAAAA
10103 GAGAAAGAGA
Statistics
Matches: 48, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
5 10 0.21
6 33 0.69
7 5 0.10
ACGTcount: A:0.85, C:0.15, G:0.00, T:0.00
Consensus pattern (6 bp):
ACAAAA
Found at i:10067 original size:30 final size:30
Alignment explanation
Indices: 10046--10102 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
10036 ACTAAAGGAC
10046 AAAAA-AAAAACAAAAACAAAACAAAACAA
1 AAAAACAAAAACAAAAACAAAACAAAACAA
10075 AAAAACAAAAACAAAAACAAAAACAAAA
1 AAAAACAAAAACAAAAAC-AAAACAAAA
10103 GAGAAAGAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
29 5 0.19
30 12 0.46
31 9 0.35
ACGTcount: A:0.86, C:0.14, G:0.00, T:0.00
Consensus pattern (30 bp):
AAAAACAAAAACAAAAACAAAACAAAACAA
Found at i:16603 original size:22 final size:22
Alignment explanation
Indices: 16575--16621 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
16565 TTGAATTAAT
16575 ATTATTGCTTTTATTTCAGAAA
1 ATTATTGCTTTTATTTCAGAAA
*
16597 ATTATTGCTTTTATTTTAGAAA
1 ATTATTGCTTTTATTTCAGAAA
16619 ATT
1 ATT
16622 CATGATGCAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.32, C:0.06, G:0.09, T:0.53
Consensus pattern (22 bp):
ATTATTGCTTTTATTTCAGAAA
Found at i:25796 original size:3 final size:3
Alignment explanation
Indices: 25788--25865 Score: 156
Period size: 3 Copynumber: 26.0 Consensus size: 3
25778 TTTATTTTAT
25788 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
25836 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
25866 TTTTATGATA
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 75 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:32898 original size:49 final size:49
Alignment explanation
Indices: 32810--32927 Score: 141
Period size: 49 Copynumber: 2.4 Consensus size: 49
32800 TTTTGTCTAG
* *
32810 AAATTGA-TAAAAGGATGCGAGGAAAAGTAAATATTCAATTTTGATGCAA
1 AAATTGAGAAAAAGG-TGCAAGGAAAAGTAAATATTCAATTTTGATGCAA
* * * *
32859 AATTTGAGAAAAAGGTGCAAGGAAAATTAAA-AGTTCAATTTTGTTGTAA
1 AAATTGAGAAAAAGGTGCAAGGAAAAGTAAATA-TTCAATTTTGATGCAA
32908 AAATTGAGAAAAAGAGTGCA
1 AAATTGAGAAAAAG-GTGCA
32928 GTAAAAATGA
Statistics
Matches: 59, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
48 1 0.02
49 47 0.80
50 11 0.19
ACGTcount: A:0.47, C:0.05, G:0.21, T:0.26
Consensus pattern (49 bp):
AAATTGAGAAAAAGGTGCAAGGAAAAGTAAATATTCAATTTTGATGCAA
Found at i:35525 original size:15 final size:15
Alignment explanation
Indices: 35505--35552 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 15
35495 AGTAAACACT
35505 TTCGGTGCCATCATC
1 TTCGGTGCCATCATC
* *
35520 TTCGGTGCCGTTGAT-
1 TTCGGTGCC-ATCATC
*
35535 TTTGGTGCCATCATC
1 TTCGGTGCCATCATC
35550 TTC
1 TTC
35553 TTCCATGACA
Statistics
Matches: 25, Mismatches: 6, Indels: 4
0.71 0.17 0.11
Matches are distributed among these distances:
14 3 0.12
15 19 0.76
16 3 0.12
ACGTcount: A:0.10, C:0.27, G:0.23, T:0.40
Consensus pattern (15 bp):
TTCGGTGCCATCATC
Found at i:36623 original size:15 final size:15
Alignment explanation
Indices: 36603--36641 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
36593 GCATCCTTCC
* *
36603 GCACCGGGTTTTTCT
1 GCACCGGATGTTTCT
36618 GCACCGGATGTTTCT
1 GCACCGGATGTTTCT
*
36633 GCACTGGAT
1 GCACCGGAT
36642 CTCTCAGCAC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.13, C:0.26, G:0.28, T:0.33
Consensus pattern (15 bp):
GCACCGGATGTTTCT
Found at i:37459 original size:49 final size:49
Alignment explanation
Indices: 37377--37500 Score: 155
Period size: 49 Copynumber: 2.5 Consensus size: 49
37367 AGCGTGCTAA
* * *
37377 TCAATTTTGTCCAGAAATTGA-TAAAAGGATGCGAGGAAAAGTAAATA-T
1 TCAATTTTGTGCAAAAATTGAGAAAAAGGATGCGAGGAAAAGTAAA-AGT
*
37425 TCAATTTTGATGCAAAAATTGAGAAAAAGG-TGCGAGGAAAATTAAAAGT
1 TCAATTTTG-TGCAAAAATTGAGAAAAAGGATGCGAGGAAAAGTAAAAGT
*
37474 TCAATTTTGTTGTAAAAATTGAGAAAA
1 TCAATTTTG-TGCAAAAATTGAGAAAA
37501 GGAGTGCAGT
Statistics
Matches: 67, Mismatches: 6, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
48 10 0.15
49 51 0.76
50 6 0.09
ACGTcount: A:0.45, C:0.06, G:0.20, T:0.28
Consensus pattern (49 bp):
TCAATTTTGTGCAAAAATTGAGAAAAAGGATGCGAGGAAAAGTAAAAGT
Found at i:40091 original size:28 final size:29
Alignment explanation
Indices: 40059--40122 Score: 78
Period size: 28 Copynumber: 2.3 Consensus size: 29
40049 GTGTTTGTAG
*
40059 AAGAAAAAAACTATTTCAAT-TTTTTTTA
1 AAGAAAAAAACAATTTCAATATTTTTTTA
* **
40087 AAGAAAATAACAATTTTTATATTTTTTTA
1 AAGAAAAAAACAATTTCAATATTTTTTTA
40116 AA-AAAAA
1 AAGAAAAA
40123 TTTCTGATTT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
28 20 0.67
29 10 0.33
ACGTcount: A:0.52, C:0.05, G:0.03, T:0.41
Consensus pattern (29 bp):
AAGAAAAAAACAATTTCAATATTTTTTTA
Found at i:41537 original size:14 final size:16
Alignment explanation
Indices: 41512--41544 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
41502 CCAAAATGCC
41512 TCTCCTCTCTCCT-GT
1 TCTCCTCTCTCCTAGT
41527 TCTCC-CTCTCCTAGT
1 TCTCCTCTCTCCTAGT
41542 TCT
1 TCT
41545 TTTAGTTCTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.41
15 10 0.59
ACGTcount: A:0.03, C:0.45, G:0.06, T:0.45
Consensus pattern (16 bp):
TCTCCTCTCTCCTAGT
Found at i:45365 original size:19 final size:19
Alignment explanation
Indices: 45327--45377 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
45317 TAGGTCGTGT
45327 ATCTGTACAGTATCTAATCTA
1 ATCTGTACAG--TCTAATCTA
* *
45348 ATCTGTACAGTGTAATCTC
1 ATCTGTACAGTCTAATCTA
*
45367 ATATGTACAGT
1 ATCTGTACAGT
45378 TGCTAAACAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
19 17 0.63
21 10 0.37
ACGTcount: A:0.31, C:0.18, G:0.14, T:0.37
Consensus pattern (19 bp):
ATCTGTACAGTCTAATCTA
Found at i:49858 original size:6 final size:6
Alignment explanation
Indices: 49841--49871 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
49831 TGAACCTTTG
*
49841 GAAGGT GGAGGT GAAGGT GAAGGT GAAGGT G
1 GAAGGT GAAGGT GAAGGT GAAGGT GAAGGT G
49872 GCAACAAACT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.29, C:0.00, G:0.55, T:0.16
Consensus pattern (6 bp):
GAAGGT
Found at i:54305 original size:131 final size:133
Alignment explanation
Indices: 54155--54409 Score: 387
Period size: 133 Copynumber: 1.9 Consensus size: 133
54145 AAAATATTTT
*
54155 AAATTCTAATATATCTAAG-TTTTTTAATTAAAAT-GATAAAATGGT-AAAAATAAAATAG-GTA
1 AAATTCTAATATATATAAGTTTTTTTAATTAAAATAG-TAAAATGGTAAAAAATAAAAT-GTGTA
* *
54216 TAA-GATATCATATTTAATTAAATAAAAAATAGAGTTTTTAGTT-ATGTAAAACTATAAAAGTAT
64 TAAGGATATCAGATTTAATTAAAT-AAAAATAGAATTTTTAGTTGA-GTAAAACTATAAAAGTAT
54279 ATTTAAA
127 ATTTAAA
*
54286 AAATTCTAATATATATAAGTTTTTTTAATTAAAATAGTAAAATGGTAAAAAATAAAATGTTTATA
1 AAATTCTAATATATATAAGTTTTTTTAATTAAAATAGTAAAATGGTAAAAAATAAAATGTGTATA
*
54351 AGGATATTAGATTTAATTAAATAAAAATAGAATTTTTAGTTGAGTAAAACTATAAAAGT
66 AGGATATCAGATTTAATTAAATAAAAATAGAATTTTTAGTTGAGTAAAACTATAAAAGT
54410 TTAAACAATG
Statistics
Matches: 113, Mismatches: 5, Indels: 10
0.88 0.04 0.08
Matches are distributed among these distances:
131 18 0.16
132 25 0.22
133 51 0.45
134 19 0.17
ACGTcount: A:0.50, C:0.02, G:0.10, T:0.38
Consensus pattern (133 bp):
AAATTCTAATATATATAAGTTTTTTTAATTAAAATAGTAAAATGGTAAAAAATAAAATGTGTATA
AGGATATCAGATTTAATTAAATAAAAATAGAATTTTTAGTTGAGTAAAACTATAAAAGTATATTT
AAA
Found at i:64959 original size:13 final size:13
Alignment explanation
Indices: 64940--64994 Score: 67
Period size: 13 Copynumber: 4.2 Consensus size: 13
64930 CATGATAGCT
*
64940 GAAAAAAACAAAA
1 GAAAAAAAAAAAA
*
64953 -AAAAAAAGAAAA
1 GAAAAAAAAAAAA
*
64965 GAAAGAAAAAAAA
1 GAAAAAAAAAAAA
64978 GAAAGAAAAAAAAA
1 GAAA-AAAAAAAAA
64992 GAA
1 GAA
64995 GCTTTGGGAA
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
12 11 0.31
13 14 0.39
14 11 0.31
ACGTcount: A:0.85, C:0.02, G:0.13, T:0.00
Consensus pattern (13 bp):
GAAAAAAAAAAAA
Done.