Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005258.1 Corchorus capsularis cultivar CVL-1 contig05276, 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: 11331
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Found at i:1710 original size:436 final size:432
Alignment explanation
Indices: 790--1820 Score: 1184
Period size: 436 Copynumber: 2.4 Consensus size: 432
780 AATAGATTGT
* * * * *
790 CAATCGAAATCACAAAATTTCAAAAGTATTTTTTAGAATTGAAACATGAAAATTAACTTTTGAGT
1 CAATCGAAA-CACAAAATTTCAGAAG-CTTTTTTAGAATTAAAACATAAAAATTAGCTTTTGAGT
* * * * * **
855 ATTTCATGAAAATTCTAAATCATAAAATTACCTTTTAATAAACACATGAATTACCTTAATTTGAC
64 ACTTCATGAAAATTGTAGATCATGAAATTACCTTTTAATAAACACATGAATCACCTTAATCCGAC
*
920 AAATAGAATAAAGAAAATAAAAAAAAATAAAGCGTTAAATCGAATAAGATAGAATTTGTAAAAGA
129 AAATAG-A-AAA-AAAAT-TAAAAAAATAAAGCGTTAAATCGAATAAGATAGAATTTGTAAAAGA
* * *
985 CTAAGTAGCATAAAATAGAAAAGTATGAGGGTCATTTGATAAGTAATTCAAATAAAAAAAAACTT
190 CTAAGTAGCATAAAATAGAAAAATATGA-GGTCATTTGATAAATAATCCAAATAAAAAAAAACTT
* *
1050 TTTAATGGATATCTTGAAACATAAAAATTTACTTTTGAATCCTTCATGAAACTCGTAGATAAAAT
254 TTTAATGGAGATCTTGAAACATAAAAATTTACTTTTGAACCCTTCATGAAACTCGTAGATAAAAT
* * * *
1115 AAACTTTCGGGTTCTTCATGAAAGTCAAAGATTATACAGTAACCTTTTAACCGACACTTGAATAA
319 AAACATTCGGGTTCTTCATGAAAGTCAAAGATCATACAATAACCTTTTAACCGACACTTCAATAA
* * * *
1180 TTTTAATCGGACATGTGGATCAAAAATTATATGGTATTAAATAGACCAA
384 CTTCAATCGGACATGTGGATCAAAAATTATACGATATTAAATAGACCAA
* * *
1229 CAATCGAAAGATC-AAATTT-AGGAAGCAGTTTTTT-GAATTAAAACATAAAAATTTGTTTTTGA
1 CAATCGAAACA-CAAAATTTCA-GAAGC--TTTTTTAGAATTAAAACATAAAAATTAGCTTTTGA
* * * * * *
1291 GTCCTTCATGAAAGTTGTAGATAATGAAATTACCTTTTAACAAACACATGAATCAACTTAATCGG
62 GTACTTCATGAAAATTGTAGATCATGAAATTACCTTTTAATAAACACATGAATCACCTTAATCCG
* *
1356 ACAAATAGAACAAATAATTAAAAAAATAAATC-TTAAA-CGTTAGATTAAGATAGAATTTGTAAA
127 ACAAATAGAA-AAAAAATTAAAAAAATAAAGCGTTAAATCG--A-A-TAAGATAGAATTTGTAAA
* * * * *
1419 GGACTAAGTAGTATAAAGTAGAAAAATATGA-GTCATTTGATAAATAAATCCAAAT-AAGAAAAT
187 AGACTAAGTAGCATAAAATAGAAAAATATGAGGTCATTTGATAAAT-AATCCAAATAAAAAAAAA
* *
1482 GTTTGTTAATGGAGATCTTGAAGCATAAAAATTCT-CTTTTGAACCCTTCATGAAACTCGTAGAT
251 CTTT-TTAATGGAGATCTTGAAACATAAAAATT-TACTTTTGAACCCTTCATGAAACTCGTAGAT
* * ** * ** *
1546 CAAATTTAACATTCGGG-TCTTTCATGAAAGTTGTAA-ATCATGCAATAACCTTTTAATTGACAT
314 -AAAATAAACATTCGGGTTC-TTCATGAAAG-TCAAAGATCATACAATAACCTTTTAACCGACAC
* * * **
1609 TTCAATAACTTCAATTGGACATGTGGA-GAAAAATTATACGATATTAAATTGACCGG
376 TTCAATAACTTCAATCGGACATGTGGATCAAAAATTATACGATATTAAATAGACCAA
* * * * *
1665 CAATCAAAACCACAAAATTTCAGAAGCTTTTTTAGAATCAAAACATTAAAATTGGCTTTTGAGTT
1 CAATCGAAA-CACAAAATTTCAGAAGCTTTTTTAGAATTAAAACATAAAAATTAGCTTTTGAGTA
* *
1730 CTTCATGAAAATTGTAGATCATGAAATTACCTTTTAATAGACACTTGAATCACCTTAATCCGACA
65 CTTCATGAAAATTGTAGATCATGAAATTACCTTTTAATAAACACATGAATCACCTTAATCCGACA
* *
1795 AATAGAAAAAAAAATACAAAAATAAA
130 AATAGAAAAAAAATTAAAAAAATAAA
1821 AGGCAACATG
Statistics
Matches: 500, Mismatches: 73, Indels: 42
0.81 0.12 0.07
Matches are distributed among these distances:
433 2 0.00
434 5 0.01
435 57 0.11
436 193 0.39
437 129 0.26
438 98 0.20
439 16 0.03
ACGTcount: A:0.44, C:0.12, G:0.13, T:0.31
Consensus pattern (432 bp):
CAATCGAAACACAAAATTTCAGAAGCTTTTTTAGAATTAAAACATAAAAATTAGCTTTTGAGTAC
TTCATGAAAATTGTAGATCATGAAATTACCTTTTAATAAACACATGAATCACCTTAATCCGACAA
ATAGAAAAAAAATTAAAAAAATAAAGCGTTAAATCGAATAAGATAGAATTTGTAAAAGACTAAGT
AGCATAAAATAGAAAAATATGAGGTCATTTGATAAATAATCCAAATAAAAAAAAACTTTTTAATG
GAGATCTTGAAACATAAAAATTTACTTTTGAACCCTTCATGAAACTCGTAGATAAAATAAACATT
CGGGTTCTTCATGAAAGTCAAAGATCATACAATAACCTTTTAACCGACACTTCAATAACTTCAAT
CGGACATGTGGATCAAAAATTATACGATATTAAATAGACCAA
Found at i:3143 original size:21 final size:21
Alignment explanation
Indices: 3117--3156 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
3107 TCTTCGATTA
*
3117 ATCTCCTCAGGTCTGTTCCTT
1 ATCTCCTCACGTCTGTTCCTT
3138 ATCTCCTCACGTCTGTTCC
1 ATCTCCTCACGTCTGTTCC
3157 GCCGTCGCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.10, C:0.38, G:0.12, T:0.40
Consensus pattern (21 bp):
ATCTCCTCACGTCTGTTCCTT
Found at i:3680 original size:35 final size:34
Alignment explanation
Indices: 3628--3698 Score: 108
Period size: 35 Copynumber: 2.1 Consensus size: 34
3618 TGTACCGTAG
3628 GATAATTCAGAATTGCAT-TTTGATTTGTTTTGTA
1 GATAATTCAGAATTGCATATTT-ATTTGTTTTGTA
*
3662 GATAATTCTGAAATTGCATATTTATTTGTTTTGTA
1 GATAATTCAG-AATTGCATATTTATTTGTTTTGTA
3697 GA
1 GA
3699 ATCTTTGGTT
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
34 9 0.26
35 22 0.65
36 3 0.09
ACGTcount: A:0.28, C:0.06, G:0.17, T:0.49
Consensus pattern (34 bp):
GATAATTCAGAATTGCATATTTATTTGTTTTGTA
Found at i:4311 original size:24 final size:24
Alignment explanation
Indices: 4267--4314 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
4257 TCTTTTTTTT
*
4267 TTTTTCTCATGATCTTATGATATA
1 TTTTTCTCATAATCTTATGATATA
*
4291 TTTTTCTCATCAAT-TTCTGATATA
1 TTTTTCTCAT-AATCTTATGATATA
4315 AAAGTTTTGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 19 0.90
25 2 0.10
ACGTcount: A:0.25, C:0.15, G:0.06, T:0.54
Consensus pattern (24 bp):
TTTTTCTCATAATCTTATGATATA
Found at i:5483 original size:228 final size:227
Alignment explanation
Indices: 5083--5668 Score: 958
Period size: 228 Copynumber: 2.6 Consensus size: 227
5073 ATCATCAAAT
* *
5083 GGAAGAAGTTAATGGGAGATTTAAGTACCATTTATGTAAGGATATA-AGGGCAGCTTTTTAACTT
1 GGAACAAGTTAATGGGAGATTTAAGTACCATTTATGTAAGGATATAGATGGCAGCTTTTTAACTT
* * * *
5147 AGGAATGCCTCTCAACAGTAAGTTTTTAACATTTTTCCAAGCATGTCAATTCTTCAATCATTCAT
66 AGGAATGCCTCTCAACAGTCAGTTTTTAACTTTTTTCCAAGCATTTCATTTCTTCAATCATTCAT
5212 TTTTTGGCCTCATCATTCTGAATTAAAACTCCTTTATTACCCTTTAATGAAAAACGAAAGAAAAC
131 TTTTTGGCCTCATCATTCTGAATTAAAACTCCTTTATTACCCTTTAATGAAAAACGAAAGAAAAC
5277 TGTAACAAAACAACGTCCTTTAACAATTAAAA
196 TGTAACAAAACAACGTCCTTTAACAATTAAAA
* *
5309 GGAACAAGTTAATAGGAGATTTAAGTACCATTTATGTAAAGATATAGGATGGCAGCTTTTTAACT
1 GGAACAAGTTAATGGGAGATTTAAGTACCATTTATGTAAGGATATA-GATGGCAGCTTTTTAACT
5374 TAGGAATGCCTCTCAACAGTCAGTTTTTAACTTTTTTCCAAGCATTTCATTTCTTCAATCATTCA
65 TAGGAATGCCTCTCAACAGTCAGTTTTTAACTTTTTTCCAAGCATTTCATTTCTTCAATCATTCA
* *
5439 TTTTTTTGCCTCATCATTCTGAATTAAAACTCCTTTATTACCCTTTATTGAAAAACGAAAGAAAA
130 TTTTTTGGCCTCATCATTCTGAATTAAAACTCCTTTATTACCCTTTAATGAAAAACGAAAGAAAA
* * **
5504 CTGTAACAAAAGAATGTTTTTTAACAATTAAAA
195 CTGTAACAAAACAACGTCCTTTAACAATTAAAA
* *
5537 GGAACAAGTTAATGGGAGATTTAAGTACCATTAATGTAAGGATATATGATGACAGCTTTTTAACT
1 GGAACAAGTTAATGGGAGATTTAAGTACCATTTATGTAAGGATATA-GATGGCAGCTTTTTAACT
* * * *
5602 TAGGAATGCCTCTCAACAGTCAGTTTTAAACTTTTTACCAACCATTTGATTTCTATCAATCATTC
65 TAGGAATGCCTCTCAACAGTCAGTTTTTAACTTTTTTCCAAGCATTTCATTTCT-TCAATCATTC
5667 AT
129 AT
5669 ACGTTTTTAA
Statistics
Matches: 334, Mismatches: 23, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
226 43 0.13
228 279 0.84
229 12 0.04
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.35
Consensus pattern (227 bp):
GGAACAAGTTAATGGGAGATTTAAGTACCATTTATGTAAGGATATAGATGGCAGCTTTTTAACTT
AGGAATGCCTCTCAACAGTCAGTTTTTAACTTTTTTCCAAGCATTTCATTTCTTCAATCATTCAT
TTTTTGGCCTCATCATTCTGAATTAAAACTCCTTTATTACCCTTTAATGAAAAACGAAAGAAAAC
TGTAACAAAACAACGTCCTTTAACAATTAAAA
Found at i:5986 original size:10 final size:9
Alignment explanation
Indices: 5973--6022 Score: 59
Period size: 8 Copynumber: 5.6 Consensus size: 9
5963 CAAAATGATG
5973 ATTATATATT
1 ATTATATA-T
5983 ATTATCATAT
1 ATTAT-ATAT
*
5993 ATTTTATAT
1 ATTATATAT
6002 A-TATATAT
1 ATTATATAT
6010 A-TATATAT
1 ATTATATAT
6018 ATTAT
1 ATTAT
6023 TACAACAAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
8 15 0.42
9 8 0.22
10 10 0.28
11 3 0.08
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (9 bp):
ATTATATAT
Found at i:5994 original size:2 final size:2
Alignment explanation
Indices: 5975--6019 Score: 51
Period size: 2 Copynumber: 23.5 Consensus size: 2
5965 AAATGATGAT
*
5975 TA TA TA T- TA T- TA TCA TA TA T- TT TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA
6015 TA TA T
1 TA TA T
6020 TATTACAACA
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
1 3 0.08
2 33 0.87
3 2 0.05
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (2 bp):
TA
Found at i:5999 original size:15 final size:15
Alignment explanation
Indices: 5975--6019 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
5965 AAATGATGAT
5975 TATATATTAT-TATCA
1 TATATATTATATAT-A
*
5990 TATATTTTATATATA
1 TATATATTATATATA
6005 TATATA-TATATATA
1 TATATATTATATATA
6019 T
1 T
6020 TATTACAACA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
14 9 0.33
15 15 0.56
16 3 0.11
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (15 bp):
TATATATTATATATA
Found at i:7367 original size:21 final size:21
Alignment explanation
Indices: 7343--7383 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
7333 ACTGGCCAGC
*
7343 TTTACTTGCTGAGGAAGGCGT
1 TTTACTTGCTGAAGAAGGCGT
7364 TTTACTTGCTGAAGAAGGCG
1 TTTACTTGCTGAAGAAGGCG
7384 AACTCTTCTG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.22, C:0.15, G:0.32, T:0.32
Consensus pattern (21 bp):
TTTACTTGCTGAAGAAGGCGT
Found at i:7569 original size:17 final size:17
Alignment explanation
Indices: 7531--7563 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
7521 CTCATAGTAC
7531 CTAGGTAGTATGAGGTA
1 CTAGGTAGTATGAGGTA
7548 CTAGGTAGTATGAGGT
1 CTAGGTAGTATGAGGT
7564 GATAGGCTGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.27, C:0.06, G:0.36, T:0.30
Consensus pattern (17 bp):
CTAGGTAGTATGAGGTA
Found at i:11187 original size:20 final size:21
Alignment explanation
Indices: 11159--11213 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
11149 CTTGATCTTG
*
11159 AGTCATTTG-CTCTTTAAGTA
1 AGTCATTTGACTCCTTAAGTA
* *
11179 AGTCGTTTGACTCCTTAAGTTG
1 AGTCATTTGACTCCTTAAG-TA
11201 AG-CATTTGACTCC
1 AGTCATTTGACTCC
11214 ATTACTCGAG
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
20 8 0.28
21 18 0.62
22 3 0.10
ACGTcount: A:0.22, C:0.20, G:0.18, T:0.40
Consensus pattern (21 bp):
AGTCATTTGACTCCTTAAGTA
Done.