Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009166.1 Corchorus capsularis cultivar CVL-1 contig09187, 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: 35158
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.33
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--46 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
*
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CG CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
43 CT CT
1 CT CT
47 AAAAAATAGA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.00, C:0.50, G:0.02, T:0.48
Consensus pattern (2 bp):
CT
Found at i:2205 original size:31 final size:31
Alignment explanation
Indices: 2167--2229 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
2157 TTCGATTACC
2167 ACCATAAGACCATGGGTAAAGTCTTGGTCGA
1 ACCATAAGACCATGGGTAAAGTCTTGGTCGA
2198 ACCATAAGACCATGGGTAAAGTCTTGGTCGA
1 ACCATAAGACCATGGGTAAAGTCTTGGTCGA
2229 A
1 A
2230 ATTGAGCTCT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.33, C:0.19, G:0.25, T:0.22
Consensus pattern (31 bp):
ACCATAAGACCATGGGTAAAGTCTTGGTCGA
Found at i:12031 original size:102 final size:102
Alignment explanation
Indices: 11898--12108 Score: 368
Period size: 102 Copynumber: 2.1 Consensus size: 102
11888 AGAAAGTATT
11898 AAGAAAACTAGCCTCTCATGAATTGAAGAAAATCCAGGAGAGAAAAATAAAGAAAAGAAGGATAA
1 AAGAAAACTAGCCTCTCATGAATTGAAGAAAATCCAGGAGAGAAAAATAAAGAAAAGAAGGATAA
* *
11963 CTTACAGAAATTTCCCCACCCTTGGGCAGCTGTCACA
66 CTTACAGAAATTTCCCCACCCTTGGGCAGCTGCCAAA
* *
12000 AAGAAAACTAGCCTCTCATGAATTGAAGAAAATCCATGAGAGAAAAATAAAGAAAAGAATGATAA
1 AAGAAAACTAGCCTCTCATGAATTGAAGAAAATCCAGGAGAGAAAAATAAAGAAAAGAAGGATAA
* *
12065 CTTACAGAAATTTCCCCTCCCTTGGGCGGCTGCCAAA
66 CTTACAGAAATTTCCCCACCCTTGGGCAGCTGCCAAA
12102 AAGAAAA
1 AAGAAAA
12109 GAGAGAAGAA
Statistics
Matches: 103, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
102 103 1.00
ACGTcount: A:0.45, C:0.19, G:0.18, T:0.18
Consensus pattern (102 bp):
AAGAAAACTAGCCTCTCATGAATTGAAGAAAATCCAGGAGAGAAAAATAAAGAAAAGAAGGATAA
CTTACAGAAATTTCCCCACCCTTGGGCAGCTGCCAAA
Found at i:12132 original size:102 final size:102
Alignment explanation
Indices: 11923--12133 Score: 244
Period size: 102 Copynumber: 2.1 Consensus size: 102
11913 TCATGAATTG
11923 AAGAAAATCCAGGAGAGAAAAATAAAGAAAAGAAGGATAACTTACAGAAATTTCCCCACCCTTGG
1 AAGAAAATCCAGGAGAGAAAAATAAAGAAAAGAAGGATAACTTACAGAAATTTCCCCACCCTTGG
* * ** ***** * ***
11988 GCAGCTGTCACAAAGAAAACTAGCCTCTCATGAATTG
66 GCAGCTGCCAAAAAGAAAAAGAGAAGAACATAAAACC
* * *
12025 AAGAAAATCCATGAGAGAAAAATAAAGAAAAGAATGATAACTTACAGAAATTTCCCCTCCCTTGG
1 AAGAAAATCCAGGAGAGAAAAATAAAGAAAAGAAGGATAACTTACAGAAATTTCCCCACCCTTGG
*
12090 GCGGCTGCCAAAAAGAAAAGAGAGAAGAAC-TAAAACC
66 GCAGCTGCCAAAAAGAAAA-AGAGAAGAACATAAAACC
*
12127 TAGAAAA
1 AAGAAAA
12134 ACTAATGTTT
Statistics
Matches: 90, Mismatches: 18, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
102 87 0.97
103 3 0.03
ACGTcount: A:0.47, C:0.18, G:0.18, T:0.16
Consensus pattern (102 bp):
AAGAAAATCCAGGAGAGAAAAATAAAGAAAAGAAGGATAACTTACAGAAATTTCCCCACCCTTGG
GCAGCTGCCAAAAAGAAAAAGAGAAGAACATAAAACC
Found at i:13788 original size:31 final size:30
Alignment explanation
Indices: 13753--13812 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 30
13743 TTGTTTTCTG
13753 ATTGTACCCATATTTTT-AAAATATATTTTCA
1 ATTGTA-CCAT-TTTTTAAAAATATATTTTCA
13784 ATTGTACCATTTTTTAAAAAATATATTTT
1 ATTGTACCATTTTTT-AAAAATATATTTT
13813 TAAATTGCTA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
29 5 0.19
30 4 0.15
31 18 0.67
ACGTcount: A:0.37, C:0.10, G:0.03, T:0.50
Consensus pattern (30 bp):
ATTGTACCATTTTTTAAAAATATATTTTCA
Found at i:14253 original size:22 final size:22
Alignment explanation
Indices: 14225--14334 Score: 102
Period size: 22 Copynumber: 5.0 Consensus size: 22
14215 TGTCTCTATG
*
14225 TGGTTATCAAAATTTTATAAGA
1 TGGTTATCAAAATTTCATAAGA
* * *
14247 TGGTTATTATAATTTCATGAGGA
1 TGGTTATCAAAATTTCAT-AAGA
*
14270 T-GTTACCAAAATTTCAT-AG-
1 TGGTTATCAAAATTTCATAAGA
*
14289 TGTGTTATCAAAATTTCAT-AGTG
1 TG-GTTATCAAAATTTCATAAG-A
*
14312 TGGTTACCAAAATTTCATAAGA
1 TGGTTATCAAAATTTCATAAGA
14334 T
1 T
14335 CAGATTATTA
Statistics
Matches: 71, Mismatches: 11, Indels: 12
0.76 0.12 0.13
Matches are distributed among these distances:
19 1 0.01
20 1 0.01
21 17 0.24
22 44 0.62
23 8 0.11
ACGTcount: A:0.35, C:0.09, G:0.15, T:0.40
Consensus pattern (22 bp):
TGGTTATCAAAATTTCATAAGA
Found at i:14365 original size:22 final size:22
Alignment explanation
Indices: 14224--14385 Score: 58
Period size: 22 Copynumber: 7.3 Consensus size: 22
14214 TTGTCTCTAT
* * * *
14224 GTGGTTATCAAAATTTTATAAG
1 GTGGTTATTAAAATCTCATAGG
* * *
14246 ATGGTTATTATAATTTCATGAGG
1 GTGGTTATTAAAATCTCAT-AGG
* ** * *
14269 AT-GTTACCAAAATTTCATAGT
1 GTGGTTATTAAAATCTCATAGG
* * *
14290 GT-GTTATCAAAATTTCATAGT
1 GTGGTTATTAAAATCTCATAGG
** * *
14311 GTGGTTACCAAAATTTCATAAG
1 GTGGTTATTAAAATCTCATAGG
* * *
14333 ATCAGATTATTAAAATCTCTTAGG
1 GT--GGTTATTAAAATCTCATAGG
* * *
14357 TTGGTTATTGAAATTTCATAGG
1 GTGGTTATTAAAATCTCATAGG
14379 GTGGTTA
1 GTGGTTA
14386 ACTATCACAA
Statistics
Matches: 109, Mismatches: 27, Indels: 8
0.76 0.19 0.06
Matches are distributed among these distances:
21 23 0.21
22 67 0.61
23 4 0.04
24 15 0.14
ACGTcount: A:0.33, C:0.09, G:0.18, T:0.40
Consensus pattern (22 bp):
GTGGTTATTAAAATCTCATAGG
Found at i:14475 original size:22 final size:22
Alignment explanation
Indices: 14450--14554 Score: 74
Period size: 22 Copynumber: 4.8 Consensus size: 22
14440 AAATTATAAG
*
14450 AATTTCATAGTGTGGTTAACAA
1 AATTTCATAGTGAGGTTAACAA
**
14472 AATTTCATTAG-GAGGTT-ATGA
1 AATTTCA-TAGTGAGGTTAACAA
* * * *
14493 TATTTCATGGGGAGGTTATCAA
1 AATTTCATAGTGAGGTTAACAA
* *
14515 AATTTTATAGTGTA-GTTATCAA
1 AATTTCATAGTG-AGGTTAACAA
14537 AATTTCATA-TGAAGGTTA
1 AATTTCATAGTG-AGGTTA
14555 TAAAAGTCTC
Statistics
Matches: 64, Mismatches: 14, Indels: 10
0.73 0.16 0.11
Matches are distributed among these distances:
20 2 0.03
21 17 0.27
22 41 0.64
23 4 0.06
ACGTcount: A:0.34, C:0.07, G:0.20, T:0.39
Consensus pattern (22 bp):
AATTTCATAGTGAGGTTAACAA
Found at i:14555 original size:22 final size:21
Alignment explanation
Indices: 14463--14811 Score: 136
Period size: 22 Copynumber: 15.8 Consensus size: 21
14453 TTCATAGTGT
* *
14463 GGTTAACAAAATTTCATTAGGA
1 GGTTATCAAAATTTCA-TAGAA
* * * *
14485 GGTTAT-GATATTTCATGGGGA
1 GGTTATCAAAATTTCAT-AGAA
* *
14506 GGTTATCAAAATTTTATAG-T
1 GGTTATCAAAATTTCATAGAA
14526 GTAGTTATCAAAATTTCATATGAA
1 G--GTTATCAAAATTTCATA-GAA
* *
14550 GGTTAT-AAAAGTCTCAATTTCATAA
1 GGTTATCAAAA-TTTC-A--T-AGAA
* * *
14575 GGAGTACCAAAATTTGATAGAA
1 GG-TTATCAAAATTTCATAGAA
*
14597 GGTTATC-AAATCTCATAG-A
1 GGTTATCAAAATTTCATAGAA
**
14616 GTGATTATTGAAATTTCATAGACA
1 G-G-TTATCAAAATTTCATAGA-A
14640 TCGGATTATCAAAATTT-ATAGGAA
1 --GG-TTATCAAAATTTCATA-GAA
* *
14664 GATTATCAAAATTTCATAGTAT
1 GGTTATCAAAATTTCATAG-AA
* * *
14686 TGTTATCAAAATTTCAAAGCGA
1 GGTTATCAAAATTTCATAG-AA
* * *
14708 GATTATCAAAATTACATA-AT
1 GGTTATCAAAATTTCATAGAA
* *
14728 GTGATTATCAGAATTTCATAGAGG
1 G-G-TTATCAAAATTTCATAGA-A
* * * *
14752 GGTCAACAAAATTTTATAAAGA
1 GGTTATCAAAATTTCATAGA-A
*
14774 GGTTATCAAAATTTCATAAAGA
1 GGTTATCAAAATTTCATAGA-A
*
14796 GGTTATCAAATTTTCA
1 GGTTATCAAAATTTCA
14812 AAATGTGATT
Statistics
Matches: 246, Mismatches: 54, Indels: 54
0.69 0.15 0.15
Matches are distributed among these distances:
19 2 0.01
20 13 0.05
21 41 0.17
22 148 0.60
23 5 0.02
24 7 0.03
25 20 0.08
26 6 0.02
27 4 0.02
ACGTcount: A:0.40, C:0.09, G:0.16, T:0.35
Consensus pattern (21 bp):
GGTTATCAAAATTTCATAGAA
Found at i:14963 original size:22 final size:22
Alignment explanation
Indices: 14935--15395 Score: 143
Period size: 22 Copynumber: 21.1 Consensus size: 22
14925 TCAGGGAGGA
14935 TATCAAAATTTCATATGAAGGT
1 TATCAAAATTTCATATGAAGGT
**
14957 TATCAAAATTTCATAGTTTA-GT
1 TATCAAAATTTCATA-TGAAGGT
* * *
14979 TTTCAAAATTTCATAAGAGGGT
1 TATCAAAATTTCATATGAAGGT
* * *
15001 TATCAAAATTTTATA-GTATGT
1 TATCAAAATTTCATATGAAGGT
* * * *
15022 AGATCAAAATTTCATAGGGAGAT
1 -TATCAAAATTTCATATGAAGGT
*
15045 TAACAAAATTTCATGATG-AGGT
1 TATCAAAATTTCAT-ATGAAGGT
* *
15067 TATCACAA--T--T-TGTA-GT
1 TATCAAAATTTCATATGAAGGT
* * *
15083 TATCAAGATTTCATAAGAAAGT
1 TATCAAAATTTCATATGAAGGT
* * * *
15105 TATGAAAATTTTATAAGGAGGGT
1 TATCAAAATTTCAT-ATGAAGGT
* ** **
15128 TATCAAAATTTTATGGGAAAATT
1 TATCAAAATTTCATATG-AAGGT
*
15151 TATCAAAATTTCATA-GCGAGGT
1 TATCAAAATTTCATATG-AAGGT
* * *
15173 TATCACAATTTCATAGTG-TGAT
1 TATCAAAATTTCATA-TGAAGGT
* * *
15195 TATCAAAATTTCAGAGTG-TGAT
1 TATCAAAATTTCATA-TGAAGGT
*
15217 TA-CTAATAA-TTCATAT-AGAGAT
1 TATC-AA-AATTTCATATGA-AGGT
* * * * *
15239 TTTTAAATTTTCATAACG-TGGT
1 TATCAAAATTTCAT-ATGAAGGT
* * * *
15261 TATCAATATATCATTTGGAGGT
1 TATCAAAATTTCATATGAAGGT
* * **
15283 TATCAACATCTCATAGTGTTGGT
1 TATCAAAATTTCATA-TGAAGGT
15306 TATCAAAATTTCAT-TGGGAA-GT
1 TATCAAAATTTCATAT--GAAGGT
15328 TATCAAAATTTCATATTG-AGGT
1 TATCAAAATTTCATA-TGAAGGT
* * * *
15350 CT-TCAAAATTCCTTAGGGAGGT
1 -TATCAAAATTTCATATGAAGGT
* *
15372 TAACAAAATTTCATAAGAAGGT
1 TATCAAAATTTCATATGAAGGT
15394 TA
1 TA
15396 AAAAAAATTA
Statistics
Matches: 323, Mismatches: 82, Indels: 68
0.68 0.17 0.14
Matches are distributed among these distances:
16 10 0.03
17 1 0.00
18 2 0.01
20 2 0.01
21 13 0.04
22 231 0.72
23 62 0.19
24 2 0.01
ACGTcount: A:0.37, C:0.10, G:0.16, T:0.37
Consensus pattern (22 bp):
TATCAAAATTTCATATGAAGGT
Found at i:15135 original size:23 final size:22
Alignment explanation
Indices: 15080--15161 Score: 74
Period size: 23 Copynumber: 3.6 Consensus size: 22
15070 CACAATTTGT
* *
15080 AGTTATCAAGATTTCATAAGAA
1 AGTTATCAAAATTTTATAAGAA
* *
15102 AGTTATGAAAATTTTATAAGGAG
1 AGTTATCAAAATTTTATAA-GAA
* **
15125 GGTTATCAAAATTTTATGGGAAA
1 AGTTATCAAAATTTTATAAG-AA
*
15148 ATTTATCAAAATTT
1 AGTTATCAAAATTT
15162 CATAGCGAGG
Statistics
Matches: 47, Mismatches: 11, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
22 17 0.36
23 30 0.64
ACGTcount: A:0.43, C:0.05, G:0.16, T:0.37
Consensus pattern (22 bp):
AGTTATCAAAATTTTATAAGAA
Found at i:15320 original size:45 final size:45
Alignment explanation
Indices: 15257--15342 Score: 118
Period size: 45 Copynumber: 1.9 Consensus size: 45
15247 TTTCATAACG
* * * *
15257 TGGTTATCAATATATCATTTGGAGGTTATCAACATCTCATAGTGT
1 TGGTTATCAAAATATCATTGGGAAGTTATCAAAATCTCATAGTGT
* *
15302 TGGTTATCAAAATTTCATTGGGAAGTTATCAAAATTTCATA
1 TGGTTATCAAAATATCATTGGGAAGTTATCAAAATCTCATA
15343 TTGAGGTCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
45 35 1.00
ACGTcount: A:0.33, C:0.12, G:0.16, T:0.40
Consensus pattern (45 bp):
TGGTTATCAAAATATCATTGGGAAGTTATCAAAATCTCATAGTGT
Found at i:15408 original size:21 final size:22
Alignment explanation
Indices: 15368--15408 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
15358 TTCCTTAGGG
* *
15368 AGGTTAACAAAATTTCATAAGA
1 AGGTTAAAAAAAATTCATAAGA
15390 AGGTTAAAAAAAATT-ATAA
1 AGGTTAAAAAAAATTCATAA
15409 AAAAGGTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 4 0.24
22 13 0.76
ACGTcount: A:0.56, C:0.05, G:0.12, T:0.27
Consensus pattern (22 bp):
AGGTTAAAAAAAATTCATAAGA
Found at i:19722 original size:2 final size:2
Alignment explanation
Indices: 19717--19743 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
19707 AAAGCGTGTG
19717 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
19744 CAAATATAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:20775 original size:3 final size:3
Alignment explanation
Indices: 20767--20815 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
20757 CATTATGTAC
20767 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
20815 A
1 A
20816 CACAAGCTAT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:24235 original size:27 final size:30
Alignment explanation
Indices: 24202--24262 Score: 83
Period size: 27 Copynumber: 2.1 Consensus size: 30
24192 GTCTACTTTC
24202 TTCTTCCTTC-TTCT-TTTCTA-CTTCATT
1 TTCTTCCTTCTTTCTGTTTCTATCTTCATT
24229 TTCTTCCTTCATTTTCTGTTTCTATCTTCATT
1 TTCTTCCTTC--TTTCTGTTTCTATCTTCATT
24261 TT
1 TT
24263 GATAGCATCA
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
27 10 0.34
30 4 0.14
31 6 0.21
32 9 0.31
ACGTcount: A:0.08, C:0.26, G:0.02, T:0.64
Consensus pattern (30 bp):
TTCTTCCTTCTTTCTGTTTCTATCTTCATT
Found at i:35049 original size:2 final size:2
Alignment explanation
Indices: 35042--35070 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
35032 TGTAAACGAG
35042 AT AT AT AT AT AT AT AT AT AT AT -T AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
35071 GATTAAGTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Done.