Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009323.1 Corchorus capsularis cultivar CVL-1 contig09344, 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: 29311
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.34
Found at i:4032 original size:21 final size:22
Alignment explanation
Indices: 3994--4037 Score: 81
Period size: 21 Copynumber: 2.0 Consensus size: 22
3984 TATTTGATCT
3994 AATTGTTCTAACCCCCGATATG
1 AATTGTTCTAACCCCCGATATG
4016 AATTGTTCTAA-CCCCGATATG
1 AATTGTTCTAACCCCCGATATG
4037 A
1 A
4038 CTCTTTGATT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 11 0.50
22 11 0.50
ACGTcount: A:0.30, C:0.25, G:0.14, T:0.32
Consensus pattern (22 bp):
AATTGTTCTAACCCCCGATATG
Found at i:10360 original size:22 final size:22
Alignment explanation
Indices: 10335--10963 Score: 200
Period size: 22 Copynumber: 29.0 Consensus size: 22
10325 ATGATCCCAT
10335 TATGAAATTTTGATAACCTTCC
1 TATGAAATTTTGATAACCTTCC
* ** *
10357 TATGAAATTTTAATAACAATAC
1 TATGAAATTTTGATAACCTTCC
* * * *
10379 TATGGAATTTCGAGAACCCTT-T
1 TATGAAATTTTGATAA-CCTTCC
** *
10401 TAT-AAATTTTTTTAACCTTCT
1 TATGAAATTTTGATAACCTTCC
* *
10422 TATGAAATTTGGTTAA-CTTCCC
1 TATGAAATTTTGATAACCTT-CC
* * * *
10444 AAAGGAATTTTGA-AGACC-TCAA
1 TATGAAATTTTGATA-ACCTTC-C
10466 TATGAAATTTTGATAA-CTTCCC
1 TATGAAATTTTGATAACCTT-CC
* * ** *
10488 AATGAAATTTTGATGACCAACAA
1 TATGAAATTTTGATAACCTTC-C
* *
10511 TATGAGATGTTGATAACC-TCC
1 TATGAAATTTTGATAACCTTCC
* * * * *
10532 ATATGATATATTGAAAACC-ACGT
1 -TATGAAATTTTGATAACCTTC-C
* * *
10555 TATGAAAATTTAAAAACC-TCC
1 TATGAAATTTTGATAACCTTCC
* *
10576 ATATG-AATTGTT-AGTAATC-ACAC
1 -TATGAAATT-TTGA-TAACCTTC-C
* * *
10599 TCTGAAATTTTGATAATC-ACAC
1 TATGAAATTTTGATAACCTTC-C
*
10621 TATGAAATTGTGATAACC-TCGC
1 TATGAAATTTTGATAACCTTC-C
**
10643 TATGAAATTTTGATAATTTTCC
1 TATGAAATTTTGATAACCTTCC
* *
10665 TATAAAATTTTGATAAACCTCCC
1 TATGAAATTTTGAT-AACCTTCC
* * *
10688 TATAAAATTTTGATAACTTTCT
1 TATGAAATTTTGATAACCTTCC
*
10710 TATGAAATCTTGATAA-----C
1 TATGAAATTTTGATAACCTTCC
* *
10727 TA-CAAATTTTGATAACCTCCC
1 TATGAAATTTTGATAACCTTCC
** * *
10748 TATGATTTTTTGATAATC-TCAT
1 TATGAAATTTTGATAACCTTC-C
* *
10770 TATGAAATTTTGTTAATCTTCC
1 TATGAAATTTTGATAACCTTCC
* * *
10792 TATGAAATTTTGATCTA-CATAC
1 TATGAAATTTTGAT-AACCTTCC
* * *
10814 TGTGAAATTTTGATAACCCTCT
1 TATGAAATTTTGATAACCTTCC
* * * **
10836 TGTAAAATTTTGA-AAACTAAAC
1 TATGAAATTTTGATAACCT-TCC
* *
10858 TATGAAATTTTTATAACCTTCA
1 TATGAAATTTTGATAACCTTCC
* *
10880 TATGAAATTTTGAGATCC-TCC
1 TATGAAATTTTGATAACCTTCC
* *
10901 -CTG-AATTTTGATATCC-TCC
1 TATGAAATTTTGATAACCTTCC
* *
10920 T-TGAAATTTTGATTA-CTTCA
1 TATGAAATTTTGATAACCTTCC
* * *
10940 TAATAAAAGTTTAATAACCTTCC
1 T-ATGAAATTTTGATAACCTTCC
10963 T
1 T
10964 TGGTAACCAT
Statistics
Matches: 445, Mismatches: 122, Indels: 79
0.69 0.19 0.12
Matches are distributed among these distances:
16 11 0.02
17 2 0.00
19 18 0.04
20 18 0.04
21 31 0.07
22 306 0.69
23 59 0.13
ACGTcount: A:0.35, C:0.16, G:0.10, T:0.39
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTTCC
Found at i:10699 original size:45 final size:44
Alignment explanation
Indices: 10603--10725 Score: 140
Period size: 45 Copynumber: 2.8 Consensus size: 44
10593 TCACACTCTG
** * * *
10603 AAATTTTGATAATCACACTATGAAATTGTGAT-AACCTCGCTATG
1 AAATTTTGATAATTTC-CTATGAAATTTTGATAAACCTCCCTATA
*
10647 AAATTTTGATAATTTTCCTATAAAATTTTGATAAACCTCCCTATA
1 AAATTTTGATAA-TTTCCTATGAAATTTTGATAAACCTCCCTATA
* *
10692 AAATTTTGATAACTTTCTTATGAAATCTTGATAA
1 AAATTTTGATAA-TTTCCTATGAAATTTTGATAA
10726 CTACAAATTT
Statistics
Matches: 67, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
44 25 0.37
45 42 0.63
ACGTcount: A:0.37, C:0.14, G:0.09, T:0.40
Consensus pattern (44 bp):
AAATTTTGATAATTTCCTATGAAATTTTGATAAACCTCCCTATA
Found at i:10929 original size:20 final size:20
Alignment explanation
Indices: 10882--10932 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
10872 AACCTTCATA
*
10882 TGAAATTTTGAGATCCTCCC
1 TGAAATTTTGATATCCTCCC
*
10902 TG-AATTTTGATATCCTCCT
1 TGAAATTTTGATATCCTCCC
10921 TGAAATTTTGAT
1 TGAAATTTTGAT
10933 TACTTCATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 17 0.61
20 11 0.39
ACGTcount: A:0.25, C:0.18, G:0.14, T:0.43
Consensus pattern (20 bp):
TGAAATTTTGATATCCTCCC
Found at i:11360 original size:22 final size:22
Alignment explanation
Indices: 11009--11361 Score: 204
Period size: 22 Copynumber: 15.9 Consensus size: 22
10999 AGAAATACCA
*
11009 CTATGAAATTTTTG-TAATCACAT
1 CTATGAAA-TTTTGATAACCAC-T
* * *
11032 -TTTGAAAATTTGATAACCTCT
1 CTATGAAATTTTGATAACCACT
* * *
11053 TTATAAAATTTTGATAACCTCT
1 CTATGAAATTTTGATAACCACT
* * * * *
11075 TTATAAAATTTTGTTGACCCCT
1 CTATGAAATTTTGATAACCACT
* *
11097 CTATGAAATTCTGATAATCACAT
1 CTATGAAATTTTGATAACCAC-T
* * *
11120 -TATGTAATTTTGATAACCTCG
1 CTATGAAATTTTGATAACCACT
* * *
11141 CTTTGAAATTTTGATAACAACA
1 CTATGAAATTTTGATAACCACT
* **
11163 CTATGAAATTTTGATAATCTTT
1 CTATGAAATTTTGATAACCACT
11185 CTAT-AAATTTTGATAATCCGATCT
1 CTATGAAATTTTGATAA-CC-A-CT
* *
11209 CTATGAAATTTCGATAATCACT
1 CTATGAAATTTTGATAACCACT
* *
11231 CTATGAGA-TTTGATAACC-TT
1 CTATGAAATTTTGATAACCACT
* *
11251 CTATCAAATTTTGGT-ACTC-C-
1 CTATGAAATTTTGATAAC-CACT
* *
11271 CTATGAAATTTAGACTTTTATAACC-TT
1 CTATGAAA--T----TTTGATAACCACT
*
11298 CATATGAAATTTTGATAACCACA
1 C-TATGAAATTTTGATAACCACT
*
11321 CTATGAAATTTTGATAACCACA
1 CTATGAAATTTTGATAACCACT
*
11343 CTATAAAATTTTGATAACC
1 CTATGAAATTTTGATAACC
11362 TCCCCATTAA
Statistics
Matches: 256, Mismatches: 54, Indels: 41
0.73 0.15 0.12
Matches are distributed among these distances:
20 16 0.06
21 31 0.12
22 173 0.68
23 3 0.01
24 6 0.02
25 11 0.04
26 6 0.02
27 3 0.01
28 7 0.03
ACGTcount: A:0.35, C:0.16, G:0.09, T:0.40
Consensus pattern (22 bp):
CTATGAAATTTTGATAACCACT
Found at i:11404 original size:22 final size:23
Alignment explanation
Indices: 11379--11439 Score: 63
Period size: 24 Copynumber: 2.7 Consensus size: 23
11369 TAAATATTTA
11379 ATGAAATTTTGT-TAACCACACT
1 ATGAAATTTTGTATAACCACACT
* * *
11401 ATGAAATTCTTATATAACCTCGCT
1 ATGAAATT-TTGTATAACCACACT
*
11425 ATGACATTTTG-ATAA
1 ATGAAATTTTGTATAA
11440 TCTCTTTGAT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
22 12 0.38
23 5 0.16
24 15 0.47
ACGTcount: A:0.36, C:0.16, G:0.10, T:0.38
Consensus pattern (23 bp):
ATGAAATTTTGTATAACCACACT
Found at i:11582 original size:22 final size:21
Alignment explanation
Indices: 11527--11613 Score: 84
Period size: 22 Copynumber: 4.0 Consensus size: 21
11517 AATAACTTGA
* *
11527 TCCTATGAAATTTTGGTAACG
1 TCCTATGAAATTTTGATAACC
* *
11548 ACACTATGGAATTTTGATAACC
1 TC-CTATGAAATTTTGATAACC
* *
11570 TCCTCATGAAATTATAATAACC
1 TCCT-ATGAAATTTTGATAACC
*
11592 ATCTTATGAAATTTTGATAACC
1 -TCCTATGAAATTTTGATAACC
11614 ACTTAGAGAC
Statistics
Matches: 52, Mismatches: 11, Indels: 5
0.76 0.16 0.07
Matches are distributed among these distances:
21 3 0.06
22 46 0.88
23 3 0.06
ACGTcount: A:0.36, C:0.17, G:0.11, T:0.36
Consensus pattern (21 bp):
TCCTATGAAATTTTGATAACC
Found at i:11802 original size:19 final size:20
Alignment explanation
Indices: 11771--11813 Score: 54
Period size: 19 Copynumber: 2.1 Consensus size: 20
11761 TATTGACATT
11771 TAAAAATTGAAATT-AAAAG
1 TAAAAATTGAAATTAAAAAG
11790 TAAAATATT-AAATTCAAAAAG
1 TAAAA-ATTGAAATT-AAAAAG
11811 TAA
1 TAA
11814 TAGTAAAGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
19 10 0.48
20 3 0.14
21 8 0.38
ACGTcount: A:0.63, C:0.02, G:0.07, T:0.28
Consensus pattern (20 bp):
TAAAAATTGAAATTAAAAAG
Found at i:12150 original size:32 final size:32
Alignment explanation
Indices: 12114--12180 Score: 75
Period size: 31 Copynumber: 2.1 Consensus size: 32
12104 TTAGTAATGG
* * *
12114 CAATTTAGTAATATGTTTTAAAGAA-AATGGTA
1 CAATTTAGAAATATATTTTAAA-AATAAGGGTA
*
12146 CAA-TTGGAAATATATTTTAAAAATAAGGGTA
1 CAATTTAGAAATATATTTTAAAAATAAGGGTA
12177 CAAT
1 CAAT
12181 CGGAAAACAT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
30 2 0.07
31 24 0.83
32 3 0.10
ACGTcount: A:0.46, C:0.04, G:0.15, T:0.34
Consensus pattern (32 bp):
CAATTTAGAAATATATTTTAAAAATAAGGGTA
Found at i:12158 original size:31 final size:31
Alignment explanation
Indices: 12123--12186 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 31
12113 GCAATTTAGT
* * *
12123 AATATGTTTTAAAGAA-AATGGTACAATTGGA
1 AATATATTTTAAA-AATAAGGGTACAATCGGA
12154 AATATATTTTAAAAATAAGGGTACAATCGGA
1 AATATATTTTAAAAATAAGGGTACAATCGGA
12185 AA
1 AA
12187 ACATAAAGTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
30 2 0.07
31 27 0.93
ACGTcount: A:0.48, C:0.05, G:0.17, T:0.30
Consensus pattern (31 bp):
AATATATTTTAAAAATAAGGGTACAATCGGA
Found at i:12590 original size:31 final size:31
Alignment explanation
Indices: 12549--12609 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
12539 GTATCCGACG
* *
12549 TGGCATGCCACGTGGATTAAAAAGTAACACA
1 TGGCAGGCCACGTGGATCAAAAAGTAACACA
*
12580 TGGCAGGCCACGTGGATCAAAAAGTGACAC
1 TGGCAGGCCACGTGGATCAAAAAGTAACAC
12610 GTCACATGTA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.36, C:0.21, G:0.26, T:0.16
Consensus pattern (31 bp):
TGGCAGGCCACGTGGATCAAAAAGTAACACA
Found at i:12668 original size:29 final size:30
Alignment explanation
Indices: 12616--12673 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 30
12606 ACACGTCACA
*
12616 TGTACCAAAAAGTGATACGTGGCACGCCATG
1 TGTACCAAAAAGTGA-ACGCGGCACGCCATG
*
12647 TGTACCAAAAAGTG-ACGCGGCATGCCA
1 TGTACCAAAAAGTGAACGCGGCACGCCA
12674 CGTTCACAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 11 0.44
31 14 0.56
ACGTcount: A:0.33, C:0.24, G:0.26, T:0.17
Consensus pattern (30 bp):
TGTACCAAAAAGTGAACGCGGCACGCCATG
Found at i:12986 original size:22 final size:22
Alignment explanation
Indices: 12958--13004 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
12948 TCGTATTTTT
12958 ATATATAGTATAGATAAAAATA
1 ATATATAGTATAGATAAAAATA
12980 ATATATAGTATAGATAAAAATA
1 ATATATAGTATAGATAAAAATA
13002 ATA
1 ATA
13005 AGGTTTTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.60, C:0.00, G:0.09, T:0.32
Consensus pattern (22 bp):
ATATATAGTATAGATAAAAATA
Found at i:13827 original size:20 final size:19
Alignment explanation
Indices: 13798--13841 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
13788 TTGGGTTTAG
13798 TCAG-TTTTTTGAGTTCAGT
1 TCAGTTTTTTTGAG-TCAGT
13817 TCAGTTTTTTTGAGTCAGT
1 TCAGTTTTTTTGAGTCAGT
13836 T-AGTTT
1 TCAGTTT
13842 GAGTCTAAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
18 5 0.21
19 10 0.42
20 9 0.38
ACGTcount: A:0.16, C:0.09, G:0.20, T:0.55
Consensus pattern (19 bp):
TCAGTTTTTTTGAGTCAGT
Found at i:26400 original size:10 final size:10
Alignment explanation
Indices: 26362--26400 Score: 53
Period size: 10 Copynumber: 4.0 Consensus size: 10
26352 TATATGTGTG
26362 TATAT-TATT
1 TATATATATT
*
26371 TATATATATA
1 TATATATATT
26381 TATATATATT
1 TATATATATT
*
26391 TATTTATATT
1 TATATATATT
26401 AAAATAAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
9 5 0.19
10 21 0.81
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (10 bp):
TATATATATT
Found at i:27567 original size:22 final size:22
Alignment explanation
Indices: 27542--27594 Score: 106
Period size: 22 Copynumber: 2.4 Consensus size: 22
27532 TTGGTCGGAG
27542 GAAACTTCCAGGAAGTTGCAGT
1 GAAACTTCCAGGAAGTTGCAGT
27564 GAAACTTCCAGGAAGTTGCAGT
1 GAAACTTCCAGGAAGTTGCAGT
27586 GAAACTTCC
1 GAAACTTCC
27595 CTCTCCTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.32, C:0.21, G:0.25, T:0.23
Consensus pattern (22 bp):
GAAACTTCCAGGAAGTTGCAGT
Found at i:28375 original size:156 final size:151
Alignment explanation
Indices: 28052--28403 Score: 381
Period size: 156 Copynumber: 2.3 Consensus size: 151
28042 ACGAACCTCT
***
28052 CACCTCAAATTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTTTGAATGAGCTTT
1 CACCTCAAATTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTCCAAATGAGCTTT
* *
28117 TTCCAAGGGACTTAGATTATCTCCATGAGACTATGGAAAAAATTCTAATTAAAACCGAGCTCCCC
66 TTCCAAGGGACTTAGATTATCTCCATGAGACTATGGAAAAAATTCTAAGTAAAACCGAACTCCCC
* * * *
28182 TTGATGGTGAACTAGGTTTCT
131 TAGATAGAGAACTAGGTTTCA
* * * *
28203 CTCC-CTGAGTTATCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTCCAACATG-GCT
1 CACCTC-AAATTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTCCAA-ATGAGCT
*
28266 AATTTTCCACCAGTAGG-CTTATATTATCTCCATGA-AGCTATGGAAAAAATTCTAAGTAAAACC
64 --TTTTCCA--AG--GGACTTAGATTATCTCCATGAGA-CTATGGAAAAAATTCTAAGTAAAACC
* * * *
28329 GAACT-CTCTAGCATAGAGAAGTTGGTTTGA
122 GAACTCCCCTAG-ATAGAGAACTAGGTTTCA
** * *
28359 CACCTCAAACCGTCCTTAACTGAAAAACTTGCATAAGTTTTTCAT
1 CACCTCAAATTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCAT
28404 ACGAAGTCTG
Statistics
Matches: 164, Mismatches: 26, Indels: 17
0.79 0.13 0.08
Matches are distributed among these distances:
150 1 0.01
151 50 0.30
152 3 0.02
153 7 0.04
155 7 0.04
156 93 0.57
157 3 0.02
ACGTcount: A:0.33, C:0.20, G:0.15, T:0.32
Consensus pattern (151 bp):
CACCTCAAATTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTCCAAATGAGCTTT
TTCCAAGGGACTTAGATTATCTCCATGAGACTATGGAAAAAATTCTAAGTAAAACCGAACTCCCC
TAGATAGAGAACTAGGTTTCA
Done.