Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012073.1 Corchorus capsularis cultivar CVL-1 contig12094, 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: 30039
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:524 original size:109 final size:109
Alignment explanation
Indices: 360--651 Score: 448
Period size: 109 Copynumber: 2.7 Consensus size: 109
350 TAAATTAAAA
*
360 TGGT-AAAATAAA--AATTATATAAAATATT-GAATTTAATTAAATGAAAATAGAGTTTTTAGTA
1 TGGTAAAAATAAAGTAATTATA-AAGATATTAG-ATTTAATTAAATGAAAATAGAGTTTTTAGTA
421 GAATAAAATTGTATATTAGAAAAAATTTTAATATATCCAAATTTTT
64 GAATAAAATTGTATATTAGAAAAAATTTTAATATATCCAAATTTTT
*
467 TGGTAAAAATAAAGTAATTATAAAGATATTAGATTTAATTAAATGAAAATTGAGTTTTTAGTAGA
1 TGGTAAAAATAAAGTAATTATAAAGATATTAGATTTAATTAAATGAAAATAGAGTTTTTAGTAGA
*
532 ATAAAATTGTATATTAGAAAAAATTTTAGTATATCCAAATTTTT
66 ATAAAATTGTATATTAGAAAAAATTTTAATATATCCAAATTTTT
* *
576 TGGTAAAAATAAAGTAATTATAAAGATATTAGATTTAATTTAATTGAATAAAAATAGAGTTTCTA
1 TGGTAAAAATAAAGTAATTATAAAGATATTAGATTTAA-TT-A---AATGAAAATAGAGTTTTTA
641 GTAGAATAAAA
61 GTAGAATAAAA
652 CTATAATAGT
Statistics
Matches: 170, Mismatches: 6, Indels: 11
0.91 0.03 0.06
Matches are distributed among these distances:
107 4 0.02
108 8 0.05
109 120 0.71
110 10 0.06
111 1 0.01
114 27 0.16
ACGTcount: A:0.49, C:0.02, G:0.11, T:0.38
Consensus pattern (109 bp):
TGGTAAAAATAAAGTAATTATAAAGATATTAGATTTAATTAAATGAAAATAGAGTTTTTAGTAGA
ATAAAATTGTATATTAGAAAAAATTTTAATATATCCAAATTTTT
Found at i:4005 original size:20 final size:20
Alignment explanation
Indices: 3976--4013 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
3966 CCTCACCAAA
*
3976 AAAAAAAAGAAGGAAAACAG
1 AAAAAAAAGAAAGAAAACAG
*
3996 AAAAAGAAGAAAGAAAAC
1 AAAAAAAAGAAAGAAAAC
4014 TTTTAAGTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.76, C:0.05, G:0.18, T:0.00
Consensus pattern (20 bp):
AAAAAAAAGAAAGAAAACAG
Found at i:6331 original size:31 final size:31
Alignment explanation
Indices: 6295--6454 Score: 149
Period size: 31 Copynumber: 5.5 Consensus size: 31
6285 TTTTGTGCAC
* * **
6295 GTGGCATGCCACGTGCCATTTTTTGAAACAT
1 GTGGCATGCCACGTGTCACTTTTTGGTACAT
6326 GTGGCATGCCACGTGTCACTTTTTGGTACAT
1 GTGGCATGCCACGTGTCACTTTTTGGTACAT
* * *
6357 GTGGCGTGACATGTGTCACTTTTTGGTACAT
1 GTGGCATGCCACGTGTCACTTTTTGGTACAT
6388 GT-G---G-CAC--G--ACTTTTTGGTACAT
1 GTGGCATGCCACGTGTCACTTTTTGGTACAT
* * * *
6410 GTGGCGTGCCACATATCACTTTTTGGTACAC
1 GTGGCATGCCACGTGTCACTTTTTGGTACAT
*
6441 GTGGCGTGCCACGT
1 GTGGCATGCCACGT
6455 CGGATACCGT
Statistics
Matches: 109, Mismatches: 11, Indels: 18
0.79 0.08 0.13
Matches are distributed among these distances:
22 16 0.15
23 1 0.01
24 1 0.01
26 3 0.03
27 4 0.04
30 1 0.01
31 83 0.76
ACGTcount: A:0.17, C:0.22, G:0.27, T:0.34
Consensus pattern (31 bp):
GTGGCATGCCACGTGTCACTTTTTGGTACAT
Found at i:6429 original size:53 final size:53
Alignment explanation
Indices: 6343--6445 Score: 161
Period size: 53 Copynumber: 1.9 Consensus size: 53
6333 GCCACGTGTC
** * *
6343 ACTTTTTGGTACATGTGGCGTGACATGTGTCACTTTTTGGTACATGTGGCACG
1 ACTTTTTGGTACATGTGGCGTGACACATATCACTTTTTGGTACACGTGGCACG
*
6396 ACTTTTTGGTACATGTGGCGTGCCACATATCACTTTTTGGTACACGTGGC
1 ACTTTTTGGTACATGTGGCGTGACACATATCACTTTTTGGTACACGTGGC
6446 GTGCCACGTC
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
53 45 1.00
ACGTcount: A:0.17, C:0.19, G:0.26, T:0.37
Consensus pattern (53 bp):
ACTTTTTGGTACATGTGGCGTGACACATATCACTTTTTGGTACACGTGGCACG
Found at i:10272 original size:12 final size:12
Alignment explanation
Indices: 10255--10285 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
10245 TACTAAACCA
10255 ATCCTCCTCAAT
1 ATCCTCCTCAAT
*
10267 ATCCTCTTCAAT
1 ATCCTCCTCAAT
10279 ATCCTCC
1 ATCCTCC
10286 AAAACTCTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.23, C:0.42, G:0.00, T:0.35
Consensus pattern (12 bp):
ATCCTCCTCAAT
Found at i:24010 original size:22 final size:22
Alignment explanation
Indices: 23985--24156 Score: 73
Period size: 22 Copynumber: 7.8 Consensus size: 22
23975 ATGACCCCAT
23985 TATGAAATTTTGATAACCTTTC
1 TATGAAATTTTGATAACCTTTC
* ****
24007 TATGAAATTTTAATAACGACAC
1 TATGAAATTTTGATAACCTTTC
* * * *
24029 TATGGAATTTCGAGAACCTTTT
1 TATGAAATTTTGATAACCTTTC
** *
24051 TAT-AAATTTTTTTTAACCTTTT
1 TATGAAA-TTTTGATAACCTTTC
** * *
24073 TATGAAATTCGGTTAACC-TCC
1 TATGAAATTTTGATAACCTTTC
* * ***
24094 TTAAGGAATTTTGA-AGACCTCAA
1 -TATGAAATTTTGATA-ACCTTTC
*
24117 TATGAAATTTTGATAA-CTTCCC
1 TATGAAATTTTGATAACCTT-TC
*
24139 AATGAAATTTTGATAACC
1 TATGAAATTTTGATAACC
24157 AACACTATAA
Statistics
Matches: 104, Mismatches: 38, Indels: 15
0.66 0.24 0.10
Matches are distributed among these distances:
21 6 0.06
22 93 0.89
23 5 0.05
ACGTcount: A:0.34, C:0.15, G:0.11, T:0.40
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTTTC
Found at i:24266 original size:22 final size:22
Alignment explanation
Indices: 24241--24547 Score: 120
Period size: 22 Copynumber: 14.1 Consensus size: 22
24231 GAATTGTTAG
*
24241 TAATCACACTCTGAAATTTTGA
1 TAATCACACTATGAAATTTTGA
*
24263 TAATCACACTATGAAATTGTGA
1 TAATCACACTATGAAATTTTGA
* * *
24285 TAACCTCGCTATGAAATTTTGA
1 TAATCACACTATGAAATTTTGA
* *
24307 TAAATCTTC-CTATAAAATTTTGA
1 T-AATC-ACACTATGAAATTTTGA
* * *
24330 TAA-AACCTCCTTATAAAATTTTGA
1 TAATCA-C-AC-TATGAAATTTTGA
** * *
24354 TAAATTTC-TTATGAAATCTTG-
1 T-AATCACACTATGAAATTTTGA
*
24375 --AT-A-ACTA-CAAATTTTGA
1 TAATCACACTATGAAATTTTGA
* * * **
24392 TAACCTCCCTATGATTTTTTGA
1 TAATCACACTATGAAATTTTGA
* *
24414 TAACTTA-ACTATGAAATTTTGT
1 TAA-TCACACTATGAAATTTTGA
* *
24436 TAATCTCCCTATGAAATTTTGA
1 TAATCACACTATGAAATTTTGA
* *
24458 T-CTACATACTATGAAATTTTGA
1 TAAT-CACACTATGAAATTTTGA
* * *
24480 TAA-CCCTCTTGTGAAATTTTGA
1 TAATCACAC-TATGAAATTTTGA
* *
24502 -AAACTAAACTATGAAATTTTGA
1 TAATC-ACACTATGAAATTTTGA
* *
24524 TAACCTTCA-TATGAAATTTTGA
1 TAATC-ACACTATGAAATTTTGA
24546 TA
1 TA
24548 TCCTCCCTGA
Statistics
Matches: 210, Mismatches: 52, Indels: 46
0.68 0.17 0.15
Matches are distributed among these distances:
16 7 0.03
17 2 0.01
18 2 0.01
19 1 0.00
21 10 0.05
22 145 0.69
23 24 0.11
24 16 0.08
25 3 0.01
ACGTcount: A:0.36, C:0.15, G:0.09, T:0.40
Consensus pattern (22 bp):
TAATCACACTATGAAATTTTGA
Found at i:24324 original size:23 final size:23
Alignment explanation
Indices: 24293--24378 Score: 102
Period size: 23 Copynumber: 3.7 Consensus size: 23
24283 GATAACCTCG
*
24293 CTATGAAATTTTGATAAATCTTC
1 CTATAAAATTTTGATAAATCTTC
* *
24316 CTATAAAATTTTGATAAAACCTC
1 CTATAAAATTTTGATAAATCTTC
24339 CTTATAAAATTTTGATAAAT-TTC
1 C-TATAAAATTTTGATAAATCTTC
* * *
24362 TTATGAAATCTTGATAA
1 CTATAAAATTTTGATAA
24379 CTACAAATTT
Statistics
Matches: 54, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
22 14 0.26
23 23 0.43
24 17 0.31
ACGTcount: A:0.40, C:0.12, G:0.07, T:0.42
Consensus pattern (23 bp):
CTATAAAATTTTGATAAATCTTC
Found at i:24444 original size:44 final size:43
Alignment explanation
Indices: 24252--24547 Score: 189
Period size: 44 Copynumber: 6.8 Consensus size: 43
24242 AATCACACTC
* * **
24252 TGAAATTTTGATAA-TCACACTATGAAATTGTGATAACCTCGCTA
1 TGAAATTTTGATAACTC-C-CTATGAAATTTTGATAACTTAACTA
* * * *
24296 TGAAATTTTGATAAATCTTCCTATAAAATTTTGATAAAACCT-CCTTA
1 TGAAATTTTGAT-AA-CTCCCTATGAAATTTTGAT--AACTTAAC-TA
* * * * *
24343 TAAAATTTTGATAAATTTCTTATGAAATCTTGATAAC-T-AC--
1 TGAAATTTTGAT-AACTCCCTATGAAATTTTGATAACTTAACTA
**
24383 --AAATTTTGATAACCTCCCTATGATTTTTTGATAACTTAACTA
1 TGAAATTTTGATAA-CTCCCTATGAAATTTTGATAACTTAACTA
* * *
24425 TGAAATTTTGTTAATCTCCCTATGAAATTTTGATCTACAT-ACTA
1 TGAAATTTTGATAA-CTCCCTATGAAATTTTGAT-AACTTAACTA
* * *
24469 TGAAATTTTGATAAC-CCTCTTGTGAAATTTTGAAAACTAAACTA
1 TGAAATTTTGATAACTCC-C-TATGAAATTTTGATAACTTAACTA
* *
24513 TGAAATTTTGATAACCTTCATATGAAATTTTGATA
1 TGAAATTTTGATAA-CTCCCTATGAAATTTTGATA
24548 TCCTCCCTGA
Statistics
Matches: 201, Mismatches: 32, Indels: 38
0.74 0.12 0.14
Matches are distributed among these distances:
37 2 0.01
38 26 0.13
39 1 0.00
40 2 0.01
42 2 0.01
43 6 0.03
44 103 0.51
45 19 0.09
46 18 0.09
47 22 0.11
ACGTcount: A:0.36, C:0.14, G:0.09, T:0.40
Consensus pattern (43 bp):
TGAAATTTTGATAACTCCCTATGAAATTTTGATAACTTAACTA
Found at i:24742 original size:22 final size:22
Alignment explanation
Indices: 24671--24979 Score: 89
Period size: 22 Copynumber: 13.6 Consensus size: 22
24661 TAATCACATT
* * *
24671 TGAAAATTTGATAACCTCTTTA
1 TGAAATTTTGATAACCCCTCTA
* *
24693 TGAAATTTTGATAACCTCTTTA
1 TGAAATTTTGATAACCCCTCTA
* * *
24715 TAAAATTTTGTTGACCCCTCTA
1 TGAAATTTTGATAACCCCTCTA
* *
24737 TGAAATAAATTTTGATAATCCGATCTTTA
1 TG----AAATTTTGATAA-CC--CCTCTA
* * *
24766 TGAAATTTCGATAATCACTCTA
1 TGAAATTTTGATAACCCCTCTA
* *
24788 TGAGA-TTTGATAA-CCTTCTA
1 TGAAATTTTGATAACCCCTCTA
* * **
24808 TCAAATTTTG-TTACTGCT-TA
1 TGAAATTTTGATAACCCCTCTA
* *
24828 TGAAATTGAGACTTTTATAA-CCTTCATA
1 TGAAA-T-----TTTGATAACCCCTC-TA
* *
24856 TGAAATTTTGATAACCACACTA
1 TGAAATTTTGATAACCCCTCTA
* *
24878 TAAAATTTTGATAACCTCC-CCA
1 TGAAATTTTGATAACC-CCTCTA
* *
24900 TGAAATATT-AGTAACCTCCT-AA
1 TGAAATTTTGA-TAACC-CCTCTA
* *
24922 TGAAATTTT-ATTAACCACACTA
1 TGAAATTTTGA-TAACCCCTCTA
* *
24944 TGAAATTCTT-ATAACCTCGCTA
1 TGAAATT-TTGATAACCCCTCTA
*
24966 TGACATTTTGATAA
1 TGAAATTTTGATAA
24980 TCTCTTTGAT
Statistics
Matches: 213, Mismatches: 49, Indels: 50
0.68 0.16 0.16
Matches are distributed among these distances:
20 16 0.08
21 17 0.08
22 130 0.61
23 6 0.03
24 1 0.00
25 11 0.05
26 14 0.07
27 5 0.02
28 7 0.03
29 6 0.03
ACGTcount: A:0.35, C:0.17, G:0.09, T:0.39
Consensus pattern (22 bp):
TGAAATTTTGATAACCCCTCTA
Found at i:24928 original size:44 final size:44
Alignment explanation
Indices: 24855--24979 Score: 114
Period size: 44 Copynumber: 2.8 Consensus size: 44
24845 TAACCTTCAT
* * * * *
24855 ATGAAATT-TTGATAACCACACTATAAAATTTTGATAACCTCCCC
1 ATGAAATTATT-ATAACCTCGCTATGAAATTTTGATAACCACACC
*
24899 ATGAAA-TATTAGTAACCTC-CTAATGAAATTTT-ATTAACCACACT
1 ATGAAATTATTA-TAACCTCGCT-ATGAAATTTTGA-TAACCACACC
* *
24943 ATGAAATTCTTATAACCTCGCTATGACATTTTGATAA
1 ATGAAATTATTATAACCTCGCTATGAAATTTTGATAA
24980 TCTCTTTGAT
Statistics
Matches: 67, Mismatches: 7, Indels: 14
0.76 0.08 0.16
Matches are distributed among these distances:
43 5 0.07
44 55 0.82
45 7 0.10
ACGTcount: A:0.38, C:0.19, G:0.08, T:0.34
Consensus pattern (44 bp):
ATGAAATTATTATAACCTCGCTATGAAATTTTGATAACCACACC
Found at i:25047 original size:22 final size:21
Alignment explanation
Indices: 25015--25101 Score: 68
Period size: 22 Copynumber: 3.9 Consensus size: 21
25005 TTGTGATAAT
*
25015 TAACCACCCTATGAAATTTCAA
1 TAACCAACCTATGAAATTT-AA
* *
25037 TAACCAACCTAAGAGATATTAA
1 TAACCAACCTATGAAAT-TTAA
* *
25059 TAACCTGATCCTATGAAATTTTGA
1 TAACC--AACCTATGAAA-TTTAA
25083 TAACC-ACGCTATGAAATTT
1 TAACCAAC-CTATGAAATTT
25102 TGAACAAAGT
Statistics
Matches: 52, Mismatches: 8, Indels: 11
0.73 0.11 0.15
Matches are distributed among these distances:
21 4 0.08
22 29 0.56
23 2 0.04
24 16 0.31
25 1 0.02
ACGTcount: A:0.40, C:0.21, G:0.09, T:0.30
Consensus pattern (21 bp):
TAACCAACCTATGAAATTTAA
Found at i:25236 original size:19 final size:20
Alignment explanation
Indices: 25205--25242 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
25195 TATTGACATT
25205 TAAAAATTGAAATT-AAAAG
1 TAAAAATTGAAATTCAAAAG
25224 TAAAATATT-AAATTCAAAA
1 TAAAA-ATTGAAATTCAAAA
25243 AATAATAGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.63, C:0.03, G:0.05, T:0.29
Consensus pattern (20 bp):
TAAAAATTGAAATTCAAAAG
Found at i:25578 original size:32 final size:32
Alignment explanation
Indices: 25541--25608 Score: 95
Period size: 31 Copynumber: 2.2 Consensus size: 32
25531 TTTAGTAATG
* *
25541 ACAATTTAGAAATATGTTTTAAAGAA-AAGGGT
1 ACAATTTAGAAATATATTTTAAA-AATAAGGAT
25573 ACAA-TTAGAAATATATTTTAAAAATAAGGAT
1 ACAATTTAGAAATATATTTTAAAAATAAGGAT
25604 ACAAT
1 ACAAT
25609 CGAAAAACAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
30 2 0.06
31 26 0.81
32 4 0.12
ACGTcount: A:0.51, C:0.04, G:0.13, T:0.31
Consensus pattern (32 bp):
ACAATTTAGAAATATATTTTAAAAATAAGGAT
Done.