Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012084.1 Corchorus capsularis cultivar CVL-1 contig12105, 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: 46415
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Found at i:4394 original size:2 final size:2
Alignment explanation
Indices: 4387--4412 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
4377 TCTTCTACAA
4387 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
4413 TTGCAACACA
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:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4550 original size:9 final size:9
Alignment explanation
Indices: 4538--4568 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
4528 TACGTTTTAC
4538 TTCTTTTCT
1 TTCTTTTCT
4547 TTCTTTTCT
1 TTCTTTTCT
4556 TTCTTTT-T
1 TTCTTTTCT
4564 TTCTT
1 TTCTT
4569 AATAGGGTGA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 6 0.27
9 16 0.73
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (9 bp):
TTCTTTTCT
Found at i:10265 original size:16 final size:17
Alignment explanation
Indices: 10234--10265 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
10224 GTATAGTGAA
10234 GAAAAGGTTTGAGGAAG
1 GAAAAGGTTTGAGGAAG
10251 GAAAAGGTTTG-GGAA
1 GAAAAGGTTTGAGGAA
10266 CAGAATTGCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.41, C:0.00, G:0.41, T:0.19
Consensus pattern (17 bp):
GAAAAGGTTTGAGGAAG
Found at i:10854 original size:6 final size:6
Alignment explanation
Indices: 10830--10868 Score: 51
Period size: 6 Copynumber: 6.2 Consensus size: 6
10820 TTACTTCCTA
*
10830 TTCATTT TTGCATT CTCATT TTCATT TTCATT TTCATT T
1 TTCA-TT TT-CATT TTCATT TTCATT TTCATT TTCATT T
10869 CTTACTCATT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
6 22 0.76
7 5 0.17
8 2 0.07
ACGTcount: A:0.15, C:0.18, G:0.03, T:0.64
Consensus pattern (6 bp):
TTCATT
Found at i:11480 original size:39 final size:40
Alignment explanation
Indices: 11427--11534 Score: 132
Period size: 43 Copynumber: 2.6 Consensus size: 40
11417 ACCAATTTTA
* *
11427 TTATTTTCCAAAAGTCTTCTCTTGGAAATTT-T-AAAGCCT
1 TTATTTTCCAAAAGTCTTCTTTTGG-AATTTCTAAAAACCT
11466 TTATTTTCCAAAAGTCTTCTTTTGG-ATTTGCTAACAAAAACCT
1 TTATTTTCCAAAAGTCTTCTTTTGGAATTT-CT---AAAAACCT
11509 TTATTTTCCAAAAGTCTTCTTTTGGA
1 TTATTTTCCAAAAGTCTTCTTTTGGA
11535 GTTGCTTAAA
Statistics
Matches: 60, Mismatches: 2, Indels: 9
0.85 0.03 0.13
Matches are distributed among these distances:
37 4 0.07
39 25 0.42
43 31 0.52
ACGTcount: A:0.28, C:0.18, G:0.10, T:0.44
Consensus pattern (40 bp):
TTATTTTCCAAAAGTCTTCTTTTGGAATTTCTAAAAACCT
Found at i:11524 original size:43 final size:44
Alignment explanation
Indices: 11463--11550 Score: 151
Period size: 43 Copynumber: 2.0 Consensus size: 44
11453 AATTTTAAAG
* *
11463 CCTTTATTTTCCAAAAGTCTTCTTTTGGATTTGC-TAACAAAAA
1 CCTTTATTTTCCAAAAGTCTTCTTTTGGAGTTGCTTAAAAAAAA
11506 CCTTTATTTTCCAAAAGTCTTCTTTTGGAGTTGCTTAAAAAAAA
1 CCTTTATTTTCCAAAAGTCTTCTTTTGGAGTTGCTTAAAAAAAA
11550 C
1 C
11551 ATTCTTTTTG
Statistics
Matches: 42, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
43 33 0.79
44 9 0.21
ACGTcount: A:0.31, C:0.18, G:0.10, T:0.41
Consensus pattern (44 bp):
CCTTTATTTTCCAAAAGTCTTCTTTTGGAGTTGCTTAAAAAAAA
Found at i:15312 original size:26 final size:26
Alignment explanation
Indices: 15244--15318 Score: 100
Period size: 26 Copynumber: 2.8 Consensus size: 26
15234 AAAGTGGACT
15244 CAAAATGACCAAAATGCCCCTAAGTGTG
1 CAAAATGACCAAAATGCCCCT-A-TGTG
*
15272 C-AAATGACCAGAATGCCCCT-TGTG
1 CAAAATGACCAAAATGCCCCTATGTG
15296 CCAAAATGACCAAAATGCCCCTA
1 -CAAAATGACCAAAATGCCCCTA
15319 GGTGACCCTA
Statistics
Matches: 42, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
24 4 0.10
25 1 0.02
26 18 0.43
27 18 0.43
28 1 0.02
ACGTcount: A:0.37, C:0.29, G:0.16, T:0.17
Consensus pattern (26 bp):
CAAAATGACCAAAATGCCCCTATGTG
Found at i:20039 original size:59 final size:60
Alignment explanation
Indices: 19967--20198 Score: 204
Period size: 59 Copynumber: 3.9 Consensus size: 60
19957 CCTAGAAGAT
*
19967 TTTAAGAATGAGTACGAAGACTGCTCATAGAT-GGTTCTGAAGACAGTTCCTAAAAAGTA
1 TTTAAGAATGAGTACGAAGACAGCTCATAGATGGGTTCTGAAGACAGTTCCTAAAAAGTA
* * * * *
20026 TTTAAGAATGAGTATGAAGATAGCTCA-CGAATGGGTTCTGAAGGCAGATCCTAAAAAGTA
1 TTTAAGAATGAGTACGAAGACAGCTCATAG-ATGGGTTCTGAAGACAGTTCCTAAAAAGTA
* * * * * **
20086 TTT-AGAAGTGAAT-CTGAAGACAGTTCACGAAGGTGGGTTCTGAAGACAGTTCCTCAATGGTA
1 TTTAAGAA-TGAGTAC-GAAGACAGCTCA--TAGATGGGTTCTGAAGACAGTTCCTAAAAAGTA
* * * ** * *
20148 TTTAAGGACGAGTATGAAGACAAATCATAGAT-GGATATGAAGACAGTTCCT
1 TTTAAGAATGAGTACGAAGACAGCTCATAGATGGGTTCTGAAGACAGTTCCT
20199 GAAAGCTTTT
Statistics
Matches: 137, Mismatches: 27, Indels: 18
0.75 0.15 0.10
Matches are distributed among these distances:
58 1 0.01
59 47 0.34
60 45 0.33
62 40 0.29
63 4 0.03
ACGTcount: A:0.36, C:0.13, G:0.25, T:0.26
Consensus pattern (60 bp):
TTTAAGAATGAGTACGAAGACAGCTCATAGATGGGTTCTGAAGACAGTTCCTAAAAAGTA
Found at i:20166 original size:62 final size:60
Alignment explanation
Indices: 19967--20169 Score: 223
Period size: 60 Copynumber: 3.4 Consensus size: 60
19957 CCTAGAAGAT
* * *
19967 TTTAAGAATGAGTACGAAGACTGCTCA-TAGAT-GGTTCTGAAGACAGTTCCTAAAAAGTA
1 TTTAAGAATGAGTATGAAGACAGCTCACGA-ATGGGTTCTGAAGACAGTTCCTAAAAAGTA
* * *
20026 TTTAAGAATGAGTATGAAGATAGCTCACGAATGGGTTCTGAAGGCAGATCCTAAAAAGTA
1 TTTAAGAATGAGTATGAAGACAGCTCACGAATGGGTTCTGAAGACAGTTCCTAAAAAGTA
* * * * **
20086 TTT-AGAAGTGAATCTGAAGACAGTTCACGAAGGTGGGTTCTGAAGACAGTTCCTCAATGGTA
1 TTTAAGAA-TGAGTATGAAGACAGCTCACGAA--TGGGTTCTGAAGACAGTTCCTAAAAAGTA
* *
20148 TTTAAGGACGAGTATGAAGACA
1 TTTAAGAATGAGTATGAAGACA
20170 AATCATAGAT
Statistics
Matches: 119, Mismatches: 19, Indels: 9
0.81 0.13 0.06
Matches are distributed among these distances:
59 30 0.25
60 48 0.40
62 38 0.32
63 3 0.03
ACGTcount: A:0.36, C:0.13, G:0.25, T:0.26
Consensus pattern (60 bp):
TTTAAGAATGAGTATGAAGACAGCTCACGAATGGGTTCTGAAGACAGTTCCTAAAAAGTA
Found at i:20288 original size:56 final size:56
Alignment explanation
Indices: 20221--20344 Score: 178
Period size: 56 Copynumber: 2.2 Consensus size: 56
20211 GATTTAGACT
*
20221 GAAGACGGTCATCCTTTC-CAGTTTTCAGCAGTTTTAAGTAGTTACTCAAGTTGATC
1 GAAGACGGTCAT-CTTTCTCAGTTTCCAGCAGTTTTAAGTAGTTACTCAAGTTGATC
* * * *
20277 GAAGACGGTCATCTTTCTCAGTTTCCAGTAGTTTTTAGTAGTTATTCAAGTTGGTC
1 GAAGACGGTCATCTTTCTCAGTTTCCAGCAGTTTTAAGTAGTTACTCAAGTTGATC
*
20333 GAAGACGATCAT
1 GAAGACGGTCAT
20345 TTTTTTTAGA
Statistics
Matches: 61, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
55 5 0.08
56 56 0.92
ACGTcount: A:0.25, C:0.18, G:0.21, T:0.36
Consensus pattern (56 bp):
GAAGACGGTCATCTTTCTCAGTTTCCAGCAGTTTTAAGTAGTTACTCAAGTTGATC
Found at i:23667 original size:37 final size:39
Alignment explanation
Indices: 23579--23678 Score: 116
Period size: 37 Copynumber: 2.6 Consensus size: 39
23569 TTTAAGCAAT
* *
23579 TCCAAGAGAAAACTTTTGGAAAATAAATGTTTTTTAGCAAAA
1 TCCAAGAGAAGACTTTTGG-GAATAAA-GTTTTTTA-CAAAA
*
23621 -CCAAAAGAAGACTTTTGGGAATAAA-TTTTTTA-AAAA
1 TCCAAGAGAAGACTTTTGGGAATAAAGTTTTTTACAAAA
*
23657 TCCAAGAGAAGACTTTTTGGAA
1 TCCAAGAGAAGACTTTTGGGAA
23679 ATTAATAAAA
Statistics
Matches: 52, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
36 4 0.08
37 19 0.37
38 7 0.13
40 6 0.12
41 16 0.31
ACGTcount: A:0.44, C:0.10, G:0.16, T:0.30
Consensus pattern (39 bp):
TCCAAGAGAAGACTTTTGGGAATAAAGTTTTTTACAAAA
Found at i:35006 original size:14 final size:14
Alignment explanation
Indices: 34958--35007 Score: 57
Period size: 13 Copynumber: 3.6 Consensus size: 14
34948 TTGACTCTTT
34958 AAAATGATAATAATA
1 AAAATGAT-ATAATA
* *
34973 AAAATGTTCTAA-A
1 AAAATGATATAATA
34986 AAAATGATATAATA
1 AAAATGATATAATA
*
35000 AAGATGAT
1 AAAATGAT
35008 GATTGATGAT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
13 11 0.38
14 11 0.38
15 7 0.24
ACGTcount: A:0.60, C:0.02, G:0.10, T:0.28
Consensus pattern (14 bp):
AAAATGATATAATA
Found at i:40959 original size:16 final size:16
Alignment explanation
Indices: 40938--40983 Score: 92
Period size: 16 Copynumber: 2.9 Consensus size: 16
40928 GTTTGGGTAC
40938 TTCGGGTTCGGGTTTT
1 TTCGGGTTCGGGTTTT
40954 TTCGGGTTCGGGTTTT
1 TTCGGGTTCGGGTTTT
40970 TTCGGGTTCGGGTT
1 TTCGGGTTCGGGTT
40984 CGGGCACGGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.00, C:0.13, G:0.39, T:0.48
Consensus pattern (16 bp):
TTCGGGTTCGGGTTTT
Found at i:40979 original size:6 final size:6
Alignment explanation
Indices: 40970--41007 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
40960 TTCGGGTTTT
**
40970 TTCGGG TTCGGG TTCGGG CACGGG -TCGGG TTCGGG TTC
1 TTCGGG TTCGGG TTCGGG TTCGGG TTCGGG TTCGGG TTC
41008 ATTTTCGATA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
5 4 0.14
6 24 0.86
ACGTcount: A:0.03, C:0.21, G:0.47, T:0.29
Consensus pattern (6 bp):
TTCGGG
Found at i:41780 original size:17 final size:18
Alignment explanation
Indices: 41754--41787 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
41744 TATTTTGATC
41754 TCGGGCTCGGG-TCGGGA
1 TCGGGCTCGGGTTCGGGA
*
41771 TCGGGTTCGGGTTCGGG
1 TCGGGCTCGGGTTCGGG
41788 TTGTCTCGGG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.03, C:0.21, G:0.53, T:0.24
Consensus pattern (18 bp):
TCGGGCTCGGGTTCGGGA
Found at i:41798 original size:16 final size:16
Alignment explanation
Indices: 41777--41819 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
41767 GGGATCGGGT
**
41777 TCGGGTTCGGGTTGTC
1 TCGGGTTCGGGTAATC
*
41793 TCGGGTTCGGGTAATT
1 TCGGGTTCGGGTAATC
41809 TCGGGTTCGGG
1 TCGGGTTCGGG
41820 ACGTTGACTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.05, C:0.16, G:0.44, T:0.35
Consensus pattern (16 bp):
TCGGGTTCGGGTAATC
Found at i:44159 original size:13 final size:13
Alignment explanation
Indices: 44141--44165 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
44131 GAGCAAAAAA
44141 AAAAAAAAAGAAG
1 AAAAAAAAAGAAG
44154 AAAAAAAAAGAA
1 AAAAAAAAAGAA
44166 TGCTAAGGAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAGAAG
Found at i:46384 original size:2 final size:2
Alignment explanation
Indices: 46379--46414 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
46369 ATTATATAGA
46379 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
46415 G
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.