Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018479.1 Corchorus olitorius cultivar O-4 contig18512, 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: 25534
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34
Found at i:1421 original size:96 final size:96
Alignment explanation
Indices: 1257--1433 Score: 336
Period size: 96 Copynumber: 1.8 Consensus size: 96
1247 TCAAACATTA
*
1257 ATATCTCATGGGGACATAAGCAGGAGCGAAATTGAAACTTTTTCTATGGGACCGACGAGTGTGTA
1 ATATCTCATGGGGACATAAGCAGGAGCAAAATTGAAACTTTTTCTATGGGACCGACGAGTGTGTA
*
1322 ATTGTGTGTGTGTGTGTGTCTATATGTATAT
66 ATTGTGTATGTGTGTGTGTCTATATGTATAT
1353 ATATCTCATGGGGACATAAGCAGGAGCAAAATTGAAACTTTTTCTATGGGACCGACGAGTGTGTA
1 ATATCTCATGGGGACATAAGCAGGAGCAAAATTGAAACTTTTTCTATGGGACCGACGAGTGTGTA
1418 ATTGTGTATGTGTGTG
66 ATTGTGTATGTGTGTG
1434 ATACTATATA
Statistics
Matches: 79, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
96 79 1.00
ACGTcount: A:0.27, C:0.12, G:0.28, T:0.33
Consensus pattern (96 bp):
ATATCTCATGGGGACATAAGCAGGAGCAAAATTGAAACTTTTTCTATGGGACCGACGAGTGTGTA
ATTGTGTATGTGTGTGTGTCTATATGTATAT
Found at i:1542 original size:25 final size:25
Alignment explanation
Indices: 1499--1555 Score: 80
Period size: 25 Copynumber: 2.3 Consensus size: 25
1489 TTTTTTTTCA
1499 AATATATTTCTAAATTGTCATTATT
1 AATATATTTCTAAATTGTCATTATT
*
1524 AATATATTT-TAATTATGTCATTATT
1 AATATATTTCTAAAT-TGTCATTATT
*
1549 AAAATAT
1 AATATAT
1556 AATTTTATGT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
24 4 0.14
25 25 0.86
ACGTcount: A:0.40, C:0.05, G:0.04, T:0.51
Consensus pattern (25 bp):
AATATATTTCTAAATTGTCATTATT
Found at i:1631 original size:97 final size:94
Alignment explanation
Indices: 1490--1666 Score: 237
Period size: 97 Copynumber: 1.9 Consensus size: 94
1480 ATTATACCTT
** **
1490 TTTTTTTCAAATATATTTCTAAATTGTCATTATTAATATATTTTAATTATGTCATTATTAAAATA
1 TTTTTTTCAAATATATTTCTAAATTGTCATTATTAATATATTTTAACCATACCATTATTAAAATA
1555 TAATTTTATGTATATTATTCGATTGTACTA
66 TAATTTT-TGTATATTATTCGATTGTACTA
* * * * *
1585 TTTTTTTCAAATATATTTTTTTAATTTTTATTATTAAATATATTTTAACCATACCATTATTATAA
1 TTTTTTTCAAATATA-TTTCTAAATTGTCATTATT-AATATATTTTAACCATACCATTATTAAAA
*
1650 TATAATTTTTGTGTATT
64 TATAATTTTTGTATATT
1667 TTTTTCAAAT
Statistics
Matches: 70, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
95 15 0.21
96 22 0.31
97 33 0.47
ACGTcount: A:0.34, C:0.06, G:0.04, T:0.56
Consensus pattern (94 bp):
TTTTTTTCAAATATATTTCTAAATTGTCATTATTAATATATTTTAACCATACCATTATTAAAATA
TAATTTTTGTATATTATTCGATTGTACTA
Found at i:2561 original size:334 final size:331
Alignment explanation
Indices: 1715--2893 Score: 1352
Period size: 334 Copynumber: 3.6 Consensus size: 331
1705 ATATAAGTTT
* ** * *
1715 TTTAATTAGAAATTAATTCGGAAAAAGGT-AGGAAAAGTGGTATTAGAAGCGTGAGAAGTCC-TT
1 TTTAATTAGAAATTAATTCGGAAAAA-ATAAGGAAAAACGATATTAGAAGCGTGAAAAG-CCTTT
* * * * *
1778 CAGTCTTTTTGGCGTTGAGTTGA-ATATTTTTTATTAGTATTGTGGCCCAAAATTGAGGAGAAAT
64 CAATCTTTTTGGCGTTGAATT-ATATATTTTTTATGAGTATCGTGGCCAAAAATTGAGGAGAAAT
** * * * *
1842 T-TCCCGGATCAAATTCTGCAAAATTTTAACTGAAATCGTGCACTAACCATCACGGTTTTTGACT
128 TCTTTCGGATCAATTTTTGCAAAATTTTAACCGAAATCGTGTACTAACCATCACGGTTTTTGACT
* * * *
1906 AAAAACGCGTTCCGGAGCCCCGACTCATTTTTGCAAGATTTTTGGCGCCAAGTCTCATTGAAATA
193 AAAAACGCATTCCGG-GACCCGACTCAGTTTTGCATGA-TTTTGGCGCCAAGTCTCATTGAAATA
* * * * * ** * *
1971 TATATATGCATCTAACCAAATCTTA-C-C--TGCATTGAATCA--TGTTTCTACGAGCATATGAA
256 TCTATATCCATCTAACCAAATCTCACCACATTGGATTTAAAGATTTGTTTTTACGAGCATCTGAA
2030 TCATGTTTCGA
321 TCATGTTTCGA
* * * * * * *
2041 TTCAATTAGGAATTAATTCAGATAAAAT-AGGAAATACGATATTAGAAGCATGAATAGCCTTTCA
1 TTTAATTAGAAATTAATTCGGAAAAAATAAGGAAAAACGATATTAGAAGCGTGAAAAGCCTTTCA
* * *
2105 ATATTTTTGGTGTTGAATTATATATTTTTTATGAGTATCGTGGCCAAAAATTCAGGA-AAATTCT
66 ATCTTTTTGGCGTTGAATTATATATTTTTTATGAGTATCGTGGCCAAAAATTGAGGAGAAATTCT
* * * *
2169 TTCGGATCAATTTTTACAAAATTTTAGCCGAAATCGTGTACTAACTATCACGGTTTTTGGCTAAA
131 TTCGGATCAATTTTTGCAAAATTTTAACCGAAATCGTGTACTAACCATCACGGTTTTTGACTAAA
*
2234 AACGCATTCCGGGACTCCGACTCAGTTTTGCATGATCTTTGGCGCCAAGACTCATTGAAATATCT
196 AACGCATTCCGGGAC-CCGACTCAGTTTTGCATGAT-TTTGGCGCCAAGTCTCATTGAAATATCT
** * * * * *
2299 ATATTTATCAAACGAAATGTCAGCCACATTGGATTTAAAGATTTGTTTTTACGAGTATCTCAATC
259 ATATCCATCTAACCAAATCTCA-CCACATTGGATTTAAAGATTTGTTTTTACGAGCATCTGAATC
**
2364 CGGTTTCGA
323 ATGTTTCGA
* ** *
2373 TTTAATTAGAAATTAACTCGGAAAAAATTAAAAAAAAAACAATATTAGAAGCGTGAAAAGCC-TT
1 TTTAATTAGAAATTAATTCGGAAAAAA-T-AAGGAAAAACGATATTAGAAGCGTGAAAAGCCTTT
** * * **
2437 CAATCTTTTTGGAATT-AAGTTATATATTTTTTATGAATATGGTGGCCGGAAATTGAGGAGAAA-
64 CAATCTTTTTGGCGTTGAA-TTATATATTTTTTATGAGTATCGTGGCCAAAAATTGAGGAGAAAT
* * *
2500 TGTTTCGTG-TCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACAGTTTTTGAC
128 TCTTTCG-GATCAATTTTTGCAAAATTTTAACCGAAATCGTGTACTAACCATCACGGTTTTTGAC
* * * *
2564 TAAAAACGCGTTTCTGGGTCCCGACTCTGTTTTGCATGAATTTTGGCGCCAAGTCTCATTGAAAT
192 TAAAAACGC-ATTCCGGGACCCGACTCAGTTTTGCATG-ATTTTGGCGCCAAGTCTCATTGAAAT
*
2629 ATCTATATCCATCTAACCAAATCACAACCACATTGGATTTAAAGATTTGTTTTTACGAGCATCTG
255 ATCTATATCCATCTAACCAAATCTC-ACCACATTGGATTTAAAGATTTGTTTTTACGAGCATCTG
2694 AATCATGTTTCGA
319 AATCATGTTTCGA
* *
2707 TTTAATTAGAAATTAATTCGGAAAAAA-ATAGGAAAACCGATATTAGAAGTGTGAAAAGCCTTTC
1 TTTAATTAGAAATTAATTCGGAAAAAATA-AGGAAAAACGATATTAGAAGCGTGAAAAGCCTTTC
* * *
2771 AATCTTTTTGGCGTTGAATTATTTATTTTTTATGAGTATCGTGG-CAAAAATTTA-GAAAAATTC
65 AATCTTTTTGGCGTTGAATTATATATTTTTTATGAGTATCGTGGCCAAAAATTGAGGAGAAATTC
* * * * *
2834 TTTCGGATAAATTTTTGTAAAATTTTAACCAAAATTGTGTATTAACCATCACGGTTTTTG
130 TTTCGGATCAATTTTTGCAAAATTTTAACCGAAATCGTGTACTAACCATCACGGTTTTTG
2894 GTAACAAAGG
Statistics
Matches: 713, Mismatches: 114, Indels: 46
0.82 0.13 0.05
Matches are distributed among these distances:
324 11 0.02
325 200 0.28
326 22 0.03
327 1 0.00
328 1 0.00
330 8 0.01
331 7 0.01
332 132 0.19
333 42 0.06
334 250 0.35
335 39 0.05
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Consensus pattern (331 bp):
TTTAATTAGAAATTAATTCGGAAAAAATAAGGAAAAACGATATTAGAAGCGTGAAAAGCCTTTCA
ATCTTTTTGGCGTTGAATTATATATTTTTTATGAGTATCGTGGCCAAAAATTGAGGAGAAATTCT
TTCGGATCAATTTTTGCAAAATTTTAACCGAAATCGTGTACTAACCATCACGGTTTTTGACTAAA
AACGCATTCCGGGACCCGACTCAGTTTTGCATGATTTTGGCGCCAAGTCTCATTGAAATATCTAT
ATCCATCTAACCAAATCTCACCACATTGGATTTAAAGATTTGTTTTTACGAGCATCTGAATCATG
TTTCGA
Found at i:3168 original size:12 final size:12
Alignment explanation
Indices: 3140--3185 Score: 51
Period size: 12 Copynumber: 3.9 Consensus size: 12
3130 GAAAGTTAAA
3140 ACTAGTATATA-T
1 ACTA-TATATATT
3152 A-TATATATATT
1 ACTATATATATT
3163 ACTATATATATT
1 ACTATATATATT
**
3175 TTTATATATAT
1 ACTATATATAT
3186 GAATAAATGT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
10 6 0.20
11 4 0.13
12 20 0.67
ACGTcount: A:0.41, C:0.04, G:0.02, T:0.52
Consensus pattern (12 bp):
ACTATATATATT
Found at i:9462 original size:78 final size:78
Alignment explanation
Indices: 9370--9532 Score: 254
Period size: 78 Copynumber: 2.1 Consensus size: 78
9360 TTTTCTTAAT
* * * *
9370 TAAAATAGTAAAATGGTAAACTAAAATAGTTATAAGGATATTAGATGTAATTAAATAAAGATAGA
1 TAAAATAGTAAAATGGTAAAATAAAATAATAATAAAGATATTAGATGTAATTAAATAAAGATAGA
*
9435 GTTTTTAGTTGAG
66 ATTTTTAGTTGAG
* * *
9448 TGAAATAGTAAAATGGTAAAATAAAATAATAATAAAGATATTAGATTTAATTAAATAAATATAGA
1 TAAAATAGTAAAATGGTAAAATAAAATAATAATAAAGATATTAGATGTAATTAAATAAAGATAGA
9513 ATTTTTAGTTGAG
66 ATTTTTAGTTGAG
9526 TAAAATA
1 TAAAATA
9533 TATAGATTAT
Statistics
Matches: 76, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
78 76 1.00
ACGTcount: A:0.51, C:0.01, G:0.15, T:0.34
Consensus pattern (78 bp):
TAAAATAGTAAAATGGTAAAATAAAATAATAATAAAGATATTAGATGTAATTAAATAAAGATAGA
ATTTTTAGTTGAG
Found at i:14357 original size:19 final size:19
Alignment explanation
Indices: 14311--14358 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
14301 ACCGACCGAC
*
14311 TATATATATTATATAATTT
1 TATATATATTATATAATTA
* *
14330 TAAAAATATTATAT-ATATA
1 TATATATATTATATAAT-TA
14349 TATATATATT
1 TATATATATT
14359 TTAAAATTCA
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
18 2 0.09
19 21 0.91
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (19 bp):
TATATATATTATATAATTA
Found at i:15637 original size:44 final size:42
Alignment explanation
Indices: 15580--15739 Score: 151
Period size: 50 Copynumber: 3.6 Consensus size: 42
15570 ATTCTATATA
*
15580 AGTGTGGTGATTCTATTTATAACT-TTGTGATATCCATGTCTATT
1 AGTGTGGTGATTCTATTTATAACTGTGGTGAT-T-C-TGTCTATT
* * *
15624 AGTGTGGTGATTCTATTTATAAGTGTGGTGATTCTGTTTCTT
1 AGTGTGGTGATTCTATTTATAACTGTGGTGATTCTGTCTATT
* * *
15666 AGTGTGGTGATTCTATTTATAACTATATAAGTGTGGTGATTCTATTTCTT
1 AGTGTGGTGATTCTATTTATAAC--------TGTGGTGATTCTGTCTATT
15716 AGTGTGGTGATTCTATTTATAACT
1 AGTGTGGTGATTCTATTTATAACT
15740 TTATGATATT
Statistics
Matches: 101, Mismatches: 6, Indels: 20
0.80 0.05 0.16
Matches are distributed among these distances:
42 29 0.29
43 1 0.01
44 24 0.24
45 6 0.06
50 41 0.41
ACGTcount: A:0.22, C:0.09, G:0.21, T:0.48
Consensus pattern (42 bp):
AGTGTGGTGATTCTATTTATAACTGTGGTGATTCTGTCTATT
Found at i:15648 original size:21 final size:21
Alignment explanation
Indices: 15576--15687 Score: 127
Period size: 21 Copynumber: 5.2 Consensus size: 21
15566 TTCTATTCTA
15576 TATAAGTGTGGTGATTCTATT
1 TATAAGTGTGGTGATTCTATT
* * *
15597 TATAACT-TTGTGATATCCATGT
1 TATAAGTGTGGTGAT-TCTAT-T
*
15619 CTATTAGTGTGGTGATTCTATT
1 -TATAAGTGTGGTGATTCTATT
*
15641 TATAAGTGTGGTGATTCTGTT
1 TATAAGTGTGGTGATTCTATT
* *
15662 TCTTAGTGTGGTGATTCTATT
1 TATAAGTGTGGTGATTCTATT
15683 TATAA
1 TATAA
15688 CTATATAAGT
Statistics
Matches: 73, Mismatches: 14, Indels: 8
0.77 0.15 0.08
Matches are distributed among these distances:
20 6 0.08
21 50 0.68
22 2 0.03
23 9 0.12
24 6 0.08
ACGTcount: A:0.22, C:0.08, G:0.21, T:0.48
Consensus pattern (21 bp):
TATAAGTGTGGTGATTCTATT
Found at i:15716 original size:50 final size:50
Alignment explanation
Indices: 15641--15739 Score: 189
Period size: 50 Copynumber: 2.0 Consensus size: 50
15631 TGATTCTATT
*
15641 TATAAGTGTGGTGATTCTGTTTCTTAGTGTGGTGATTCTATTTATAACTA
1 TATAAGTGTGGTGATTCTATTTCTTAGTGTGGTGATTCTATTTATAACTA
15691 TATAAGTGTGGTGATTCTATTTCTTAGTGTGGTGATTCTATTTATAACT
1 TATAAGTGTGGTGATTCTATTTCTTAGTGTGGTGATTCTATTTATAACT
15740 TTATGATATT
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 48 1.00
ACGTcount: A:0.22, C:0.08, G:0.21, T:0.48
Consensus pattern (50 bp):
TATAAGTGTGGTGATTCTATTTCTTAGTGTGGTGATTCTATTTATAACTA
Found at i:18251 original size:7 final size:7
Alignment explanation
Indices: 18241--18273 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
18231 TATAACTTGG
18241 TTTCTGA
1 TTTCTGA
18248 TTTCTGA
1 TTTCTGA
18255 TTTCTGA
1 TTTCTGA
*
18262 TTTCTCA
1 TTTCTGA
18269 TTTCT
1 TTTCT
18274 AACTTCTAAC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.12, C:0.18, G:0.09, T:0.61
Consensus pattern (7 bp):
TTTCTGA
Found at i:18280 original size:21 final size:21
Alignment explanation
Indices: 18241--18280 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
18231 TATAACTTGG
* * *
18241 TTTCTGATTTCTGATTTCTGA
1 TTTCTCATTTCTAACTTCTGA
18262 TTTCTCATTTCTAACTTCT
1 TTTCTCATTTCTAACTTCT
18281 AACTTATAAG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.15, C:0.20, G:0.07, T:0.57
Consensus pattern (21 bp):
TTTCTCATTTCTAACTTCTGA
Found at i:25140 original size:21 final size:21
Alignment explanation
Indices: 25116--25160 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
25106 GTGACACCGC
*
25116 CCACCTGGGTCCTCAAGGAAA
1 CCACATGGGTCCTCAAGGAAA
** *
25137 CCACATGGGTGTTCAAGGCAA
1 CCACATGGGTCCTCAAGGAAA
25158 CCA
1 CCA
25161 TGTGGGCGCC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.29, C:0.31, G:0.24, T:0.16
Consensus pattern (21 bp):
CCACATGGGTCCTCAAGGAAA
Done.