Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010311.1 Corchorus capsularis cultivar CVL-1 contig10332, 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: 36518
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:105 original size:26 final size:26
Alignment explanation
Indices: 76--143 Score: 93
Period size: 26 Copynumber: 2.6 Consensus size: 26
66 TACTTAGTTT
76 ATTAGTTTATGTTTAATTAGTATCTA
1 ATTAGTTTATGTTTAATTAGTATCTA
* *
102 ATTAGTTTAT-TATCAATTAGTATTTA
1 ATTAGTTTATGT-TTAATTAGTATCTA
*
128 ATTAGTTTATGATTAA
1 ATTAGTTTATGTTTAA
144 AATGAAGGAA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
25 1 0.03
26 35 0.97
ACGTcount: A:0.34, C:0.03, G:0.10, T:0.53
Consensus pattern (26 bp):
ATTAGTTTATGTTTAATTAGTATCTA
Found at i:191 original size:24 final size:25
Alignment explanation
Indices: 152--211 Score: 79
Period size: 25 Copynumber: 2.5 Consensus size: 25
142 AAAATGAAGG
*
152 AAAATGAA-TTTGAAG-ATTTGTTA
1 AAAATGAAGTTTGAAGAAGTTGTTA
175 AAAATGAAGTTTGAAGAAGTTGTTA
1 AAAATGAAGTTTGAAGAAGTTGTTA
* *
200 GAAATTAAGTTT
1 AAAATGAAGTTT
212 AGGGTTTGAA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
23 8 0.25
24 7 0.22
25 17 0.53
ACGTcount: A:0.43, C:0.00, G:0.20, T:0.37
Consensus pattern (25 bp):
AAAATGAAGTTTGAAGAAGTTGTTA
Found at i:13334 original size:13 final size:13
Alignment explanation
Indices: 13316--13341 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
13306 TAGCCAAGGG
13316 TAATACCATTACC
1 TAATACCATTACC
13329 TAATACCATTACC
1 TAATACCATTACC
13342 ATTACACTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.31, G:0.00, T:0.31
Consensus pattern (13 bp):
TAATACCATTACC
Found at i:17632 original size:10 final size:10
Alignment explanation
Indices: 17599--17652 Score: 51
Period size: 11 Copynumber: 5.5 Consensus size: 10
17589 CCTACGTGGC
17599 TTTTTTAAAT
1 TTTTTTAAAT
*
17609 ATTTTTTATTAT
1 -TTTTTTA-AAT
17621 TTTTTTAAA-
1 TTTTTTAAAT
17630 -TTTTTAAAT
1 TTTTTTAAAT
*
17639 TTTATT-AAT
1 TTTTTTAAAT
17648 TTTTT
1 TTTTT
17653 AATATTTTAA
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
8 8 0.22
9 7 0.19
10 5 0.14
11 14 0.39
12 2 0.06
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (10 bp):
TTTTTTAAAT
Found at i:17633 original size:8 final size:8
Alignment explanation
Indices: 17622--17664 Score: 50
Period size: 8 Copynumber: 5.1 Consensus size: 8
17612 TTTTATTATT
17622 TTTTTAAA
1 TTTTTAAA
17630 TTTTTAAA
1 TTTTTAAA
*
17638 TTTTATTAA
1 TTTT-TAAA
*
17647 TTTTTTAA
1 TTTTTAAA
17655 TATTTTAAA
1 T-TTTTAAA
17664 T
1 T
17665 CGGCTCAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
8 17 0.55
9 14 0.45
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (8 bp):
TTTTTAAA
Found at i:17640 original size:18 final size:19
Alignment explanation
Indices: 17611--17661 Score: 68
Period size: 18 Copynumber: 2.7 Consensus size: 19
17601 TTTTAAATAT
* *
17611 TTTTTATTATTTTTTTAAA
1 TTTTTAATATTTTATTAAA
*
17630 TTTTTAA-ATTTTATTAAT
1 TTTTTAATATTTTATTAAA
17648 TTTTTAATATTTTA
1 TTTTTAATATTTTA
17662 AATCGGCTCA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
18 16 0.57
19 12 0.43
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (19 bp):
TTTTTAATATTTTATTAAA
Found at i:17650 original size:26 final size:26
Alignment explanation
Indices: 17612--17664 Score: 81
Period size: 26 Copynumber: 2.0 Consensus size: 26
17602 TTTAAATATT
*
17612 TTTTATTATTTTTTTAA-ATTTTTAAA
1 TTTTATTAATTTTTTAATA-TTTTAAA
17638 TTTTATTAATTTTTTAATATTTTAAA
1 TTTTATTAATTTTTTAATATTTTAAA
17664 T
1 T
17665 CGGCTCAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 24 0.96
27 1 0.04
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (26 bp):
TTTTATTAATTTTTTAATATTTTAAA
Found at i:17703 original size:31 final size:31
Alignment explanation
Indices: 17657--17734 Score: 122
Period size: 31 Copynumber: 2.5 Consensus size: 31
17647 TTTTTTAATA
*
17657 TTTT-AAATCGGCTCAAATAGGTACTAAACG
1 TTTTAAAATTGGCTCAAATAGGTACTAAACG
17687 TTTTAAAATTGGCTCAAATAGGTACTAAACG
1 TTTTAAAATTGGCTCAAATAGGTACTAAACG
* *
17718 TTTCAAAATTGGATCAA
1 TTTTAAAATTGGCTCAA
17735 TTTAGATTTT
Statistics
Matches: 44, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
30 4 0.09
31 40 0.91
ACGTcount: A:0.38, C:0.14, G:0.15, T:0.32
Consensus pattern (31 bp):
TTTTAAAATTGGCTCAAATAGGTACTAAACG
Found at i:18840 original size:7 final size:7
Alignment explanation
Indices: 18828--18852 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
18818 CTTATCTCCC
18828 CTTCCTT
1 CTTCCTT
18835 CTTCCTT
1 CTTCCTT
18842 CTTCCTT
1 CTTCCTT
18849 CTTC
1 CTTC
18853 TCCATGGCCG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.00, C:0.44, G:0.00, T:0.56
Consensus pattern (7 bp):
CTTCCTT
Found at i:22943 original size:62 final size:62
Alignment explanation
Indices: 22847--22976 Score: 172
Period size: 62 Copynumber: 2.1 Consensus size: 62
22837 TATTAAATTA
* * * *
22847 AAAATTATTATAATTACACTATTTTTGTTGACTTCCTTGTGAAATTTTGATAACATTCCTAT
1 AAAATTATGATAATTACACCATTTTTGTTAACTTCCTTATGAAATTTTGATAACATTCCTAT
* * *
22909 AAAATTATGATTATTACACCATTTTT-TATAACTTCCTTATGAAATTTTGATAACCTTCTTAT
1 AAAATTATGATAATTACACCATTTTTGT-TAACTTCCTTATGAAATTTTGATAACATTCCTAT
*
22971 GAAATT
1 AAAATT
22977 TCAATAACGA
Statistics
Matches: 59, Mismatches: 8, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
61 1 0.02
62 58 0.98
ACGTcount: A:0.34, C:0.13, G:0.07, T:0.46
Consensus pattern (62 bp):
AAAATTATGATAATTACACCATTTTTGTTAACTTCCTTATGAAATTTTGATAACATTCCTAT
Found at i:23262 original size:45 final size:46
Alignment explanation
Indices: 23212--23316 Score: 124
Period size: 45 Copynumber: 2.3 Consensus size: 46
23202 AATCACACTC
*
23212 TGAAATTTTGATAATCATACC-ATGAAAATTGTGAT-AACCTCATTA
1 TGAAATTTTGATAAACATACCTAT-AAAATTGTGATAAACCTCATTA
* * * * *
23257 TGAAATTTTGATAAACCTCCCTATAAAATTTTGATAAATCTCCTTA
1 TGAAATTTTGATAAACATACCTATAAAATTGTGATAAACCTCATTA
*
23303 TAAAATTTTGATAA
1 TGAAATTTTGATAA
23317 CCTCCTTATG
Statistics
Matches: 51, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
45 28 0.55
46 23 0.45
ACGTcount: A:0.40, C:0.13, G:0.09, T:0.38
Consensus pattern (46 bp):
TGAAATTTTGATAAACATACCTATAAAATTGTGATAAACCTCATTA
Found at i:23324 original size:22 final size:22
Alignment explanation
Indices: 22931--23528 Score: 243
Period size: 22 Copynumber: 27.3 Consensus size: 22
22921 ATTACACCAT
* *
22931 TTTTTATAACTTCCTTATGAAA
1 TTTTGATAACCTCCTTATGAAA
*
22953 TTTTGATAACCTTCTTATGAAA
1 TTTTGATAACCTCCTTATGAAA
** * *
22975 TTTCAATAACGATAC-TATGGAAA
1 TTTTGATAAC-CTCCTTAT-GAAA
* * ** *
22998 -TTCGAGAACCTTTTTAT-AAT
1 TTTTGATAACCTCCTTATGAAA
** *
23018 TTTTTTTAACCTTCTTATGAAA
1 TTTTGATAACCTCCTTATGAAA
* * * *
23040 TTTTGTTAATCTCCCTAAGAAA
1 TTTTGATAACCTCCTTATGAAA
23062 TTTTGA-AGACCTCAC-TATGAAA
1 TTTTGATA-ACCTC-CTTATGAAA
* * **
23084 TTTCGATAACTTCCAAATGAAA
1 TTTTGATAACCTCCTTATGAAA
* * *
23106 TTTTGACAACCAACAC-CAT-AAGA
1 TTTTGATAACC-TC-CTTATGAA-A
* * *
23129 TGTTGATAACCTCCATATGATA
1 TTTTGATAACCTCCTTATGAAA
* * * *
23151 TATTGATAACCACGTTATTAAA
1 TTTTGATAACCTCCTTATGAAA
* * * *
23173 ATTTAAAAACCTCCATATG-AA
1 TTTTGATAACCTCCTTATGAAA
* * * * *
23194 TTGTCAGTAATCACAC-TCTGAAA
1 TTTTGA-TAACCTC-CTTATGAAA
*
23217 TTTTGATAATCATACC--ATGAAAA
1 TTTTGATAA-CCT-CCTTATG-AAA
* *
23240 TTGTGATAACCTCATTATGAAA
1 TTTTGATAACCTCCTTATGAAA
* *
23262 TTTTGATAAACCTCCCTATAAAA
1 TTTTGAT-AACCTCCTTATGAAA
* *
23285 TTTTGATAAATCTCCTTATAAAA
1 TTTTGAT-AACCTCCTTATGAAA
23308 TTTTGATAACCTCCTTATGAAAA
1 TTTTGATAACCTCCTTATG-AAA
* *
23331 TCTTGATAA----C-TA-CAAA
1 TTTTGATAACCTCCTTATGAAA
* **
23347 TTTTGATAACCTCCCTATGATT
1 TTTTGATAACCTCCTTATGAAA
*
23369 TTTTGATAACCTCATTATGAAA
1 TTTTGATAACCTCCTTATGAAA
* * *
23391 TTTTGTTAATCTCCCTATGAAA
1 TTTTGATAACCTCCTTATGAAA
* * *
23413 TTTTGATTTACATAC-TATGAAA
1 TTTTGA-TAACCTCCTTATGAAA
23435 TTTTGATAACC-CTCTTATGAAA
1 TTTTGATAACCTC-CTTATGAAA
* *
23457 TTTTGA-AAACTAAAC-TATGAAA
1 TTTTGATAACCT--CCTTATGAAA
* *
23479 TTTTGATAACCCTTCATATGAAA
1 TTTTGATAA-CCTCCTTATGAAA
* * *
23502 TTTCGATATCCTCC--CTGAAA
1 TTTTGATAACCTCCTTATGAAA
23522 TTTTGAT
1 TTTTGAT
23529 TACTCCATAA
Statistics
Matches: 428, Mismatches: 109, Indels: 80
0.69 0.18 0.13
Matches are distributed among these distances:
16 11 0.03
18 2 0.00
19 1 0.00
20 14 0.03
21 31 0.07
22 249 0.58
23 116 0.27
24 4 0.01
ACGTcount: A:0.36, C:0.17, G:0.09, T:0.38
Consensus pattern (22 bp):
TTTTGATAACCTCCTTATGAAA
Found at i:23654 original size:22 final size:22
Alignment explanation
Indices: 23629--23670 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
23619 TTGGTTATCA
*
23629 CTTTTTGAAAATTTGATAACTT
1 CTTTATGAAAATTTGATAACTT
*
23651 CTTTATGAAATTTTGATAAC
1 CTTTATGAAAATTTGATAAC
23671 CTATCTATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.33, C:0.10, G:0.10, T:0.48
Consensus pattern (22 bp):
CTTTATGAAAATTTGATAACTT
Found at i:23683 original size:22 final size:22
Alignment explanation
Indices: 23636--23684 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 22
23626 TCACTTTTTG
* * *
23636 AAAA-TTTGATAACTTCTTTAT
1 AAAATTTTGATAACCTATCTAT
*
23657 GAAATTTTGATAACCTATCTAT
1 AAAATTTTGATAACCTATCTAT
23679 AAAATT
1 AAAATT
23685 GACCCTGACC
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
21 3 0.14
22 19 0.86
ACGTcount: A:0.41, C:0.10, G:0.06, T:0.43
Consensus pattern (22 bp):
AAAATTTTGATAACCTATCTAT
Found at i:26210 original size:91 final size:91
Alignment explanation
Indices: 26055--26278 Score: 344
Period size: 91 Copynumber: 2.5 Consensus size: 91
26045 GCTTAAGAAG
* * *
26055 ATTGAAAGAAGATCCACGTATGTGGAAAATTCTTCTTTCAAAAAAGACTCAATTATTGGAGAATT
1 ATTGAAAGAAGATCCATGTATGTGGAGAATTCTTCTTTCAAAAAAGACTCAATTATTGCAGAATT
*
26120 ACTGAAGACCCAGTTATTTGGG-AGTT
66 ACTGAAGACCCAGTTA-TTGGGAAATT
* *
26146 ATTGAAAGAAGATCCATGTATGTGGAGTATTCTTCTTTCAAAGAAGA-TCCAATTATTGCAGAAT
1 ATTGAAAGAAGATCCATGTATGTGGAGAATTCTTCTTTCAAAAAAGACT-CAATTATTGCAGAAT
26210 TACTGAAGACCCAGTTATTGGGAAATT
65 TACTGAAGACCCAGTTATTGGGAAATT
* *
26237 ATTGAAAGAAAATCCATGTATGTGGAGGATTCTTCTTTCAAA
1 ATTGAAAGAAGATCCATGTATGTGGAGAATTCTTCTTTCAAA
26279 TTATCAAAGA
Statistics
Matches: 123, Mismatches: 8, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
90 6 0.05
91 117 0.95
ACGTcount: A:0.36, C:0.13, G:0.20, T:0.32
Consensus pattern (91 bp):
ATTGAAAGAAGATCCATGTATGTGGAGAATTCTTCTTTCAAAAAAGACTCAATTATTGCAGAATT
ACTGAAGACCCAGTTATTGGGAAATT
Found at i:26450 original size:44 final size:44
Alignment explanation
Indices: 26367--26450 Score: 98
Period size: 45 Copynumber: 1.9 Consensus size: 44
26357 TGTTTGTTCA
* * * * *
26367 AGATCAAGTCGCCAAGACCCTTGAGTCAAATTATCATCAATTCG
1 AGATCAAGTCGCAAAGACCCTCGAATCAAATCATAATCAATTCG
*
26411 AGATCAAGTCATCAAAGACCCTCGAATCAAATCA-AATCAA
1 AGATCAAGTC-GCAAAGACCCTCGAATCAAATCATAATCAA
26451 ATTCCCAAGT
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
44 15 0.45
45 18 0.55
ACGTcount: A:0.40, C:0.25, G:0.13, T:0.21
Consensus pattern (44 bp):
AGATCAAGTCGCAAAGACCCTCGAATCAAATCATAATCAATTCG
Found at i:26487 original size:104 final size:99
Alignment explanation
Indices: 26363--26551 Score: 245
Period size: 104 Copynumber: 1.9 Consensus size: 99
26353 AATTTGTTTG
* * * *
26363 TTCAAGATCAAGTCGCCAAGACCCTTGAGTCAAATTATCATCAATTCGAGATCAAGTCA-TCAAA
1 TTCAAGATCAAGTCGCCAAGAACCTTGAATCAAA-T-T-ATCAATTCAAGACCAAGTCATTC---
*
26427 GACCCTCGAATCAAATCAAATCAAATTCCCAAGTCTTCAA
60 GACCCTCGAATCAAATAAAATCAAATTCCCAAGTCTTCAA
* *
26467 TTCAAGATCAAGTCGTCAAGAACCTTGAATTAAATTATCAATTCAAGACCAAGTCATTCGACCCT
1 TTCAAGATCAAGTCGCCAAGAACCTTGAATCAAATTATCAATTCAAGACCAAGTCATTCGACCCT
*
26532 TGAATCAAATAAAATCAAAT
66 CGAATCAAATAAAATCAAAT
26552 CAAGTTCTCA
Statistics
Matches: 76, Mismatches: 8, Indels: 7
0.84 0.09 0.08
Matches are distributed among these distances:
99 24 0.32
101 18 0.24
102 3 0.04
103 1 0.01
104 30 0.39
ACGTcount: A:0.40, C:0.23, G:0.11, T:0.25
Consensus pattern (99 bp):
TTCAAGATCAAGTCGCCAAGAACCTTGAATCAAATTATCAATTCAAGACCAAGTCATTCGACCCT
CGAATCAAATAAAATCAAATTCCCAAGTCTTCAA
Found at i:36433 original size:2 final size:2
Alignment explanation
Indices: 36428--36518 Score: 182
Period size: 2 Copynumber: 45.5 Consensus size: 2
36418 AAAAAAAAAG
36428 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
36470 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
36512 GA GA GA G
1 GA GA GA G
Statistics
Matches: 89, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 89 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Done.