Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015478.1 Corchorus olitorius cultivar O-4 contig15511, 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: 16228
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:3080 original size:837 final size:838
Alignment explanation
Indices: 1427--3102 Score: 2953
Period size: 837 Copynumber: 2.0 Consensus size: 838
1417 CTCCGACAAT
1427 TATCAGAAGTCCACCCAAGATACTGTGTAGTCAATTTAGGAAAAAAAAAACAAACACAATATGAG
1 TATCAGAAGTCCACCCAAGATACTGTGTAGTCAATTTAGGAAAAAAAAAACAAACACAATATGAG
1492 TGAAATATGCATGATAAGTATAATATCATTGACTAAAAGCTATATTAGAAGTTCAAAGTTTGGTG
66 TGAAATATGCATGATAAGTATAATATCATTGACTAAAAGCTATATTAGAAGTTCAAAGTTTGGTG
*
1557 CTTACTTCCCTAAGTGAAGGTCCTATCGTTGTAAAAGAGGGCTCAGAATTGCTGTAAAGATGAGG
131 CTTACTTCCCTAAGTGAAGGTCCTATCGTTGTAAAAGAGGACTCAGAATTGCTGTAAAGATGAGG
* *
1622 GAAAATGGCGAAAAGGAGGAGACGAAAACTGGACCCCTGTTGCTATGTACATAATGTCACCAGTG
196 GAAAATGGCGAAAAGGAAGAGACGAAAACTGGACCCCTGTTGCTATGTACACAATGTCACCAGTG
**
1687 TTGTTGACATCCTGGATACCAAGATGCCCTATTCAATTTTTATTGAAACATCATTAAGAAAATCA
261 TTGTTGACATCCCAGATACCAAGATGCCCTATTCAATTTTTATTGAAACATCATTAAGAAAATCA
* *
1752 ATAATAATAAGTAAATAAATTCAACATATTTTCAAAGTAGAATCAATCTAAAATTTAAATACGTG
326 ATAATAATAACTAAATAAATTCAACATATTTTCAAAGTAGAATCAATCTAAAATTTAAATACGTA
*
1817 TAATGTAAGGGATATTGACAAGCCTGATAGCTTTCTTCCATGCGCAGCATGCCAAGTCAGGTCTA
391 TAATGTAAGGGATATTGACAAGCCTGATAGCTTTCTTCCATGCGAAGCATGCCAAGTCAGGTCTA
*
1882 TGATCAAAACATATACAGTTGATAACACAAAACTGCTGCCAAACATAAGCAATGTGGACAAGAAA
456 TGATCAAAACATATACAGTTGACAACACAAAACTGCTGCCAAACATAAGCAATGTGGACAAGAAA
*
1947 ACTGGATAGGCGTACGTGACTGTCATCCTCCTCTAATCACAACAAAGAACATTAAATTAAAAAAT
521 ACTGGATAGGCATACGTGACTGTCATCCTCCTCTAATCACAACAAAGAACATTAAATTAAAAAAT
*
2012 TTAGTGAGAAAATAAATGAATATATAGAATCAATCTTATATATATTATATATAGATTCAAGTAGG
586 TTAGTGAGAAAATAAATGAATATATAGAATCAATCTTATATATATTATATATAGATTCAAGTAAG
* * * *
2077 TGTGCTTGGTTACCAGTATAATAAGGAGCATGGCAAAGGAAAAGTAACTGCTGCAAGCTACCAAC
651 TGTGCTTGATTAACAGTACAATAAGAAGCATGGCAAAGGAAAAGTAACTGCTGCAAGCTACCAAC
*
2142 TCGCTCACTACTTGCCTCTGCTGTGTGGTTAGCCTTGACACATTGTTATGATTTAGTAGATATAC
716 TCGCTCACTACTGGCCTCTGCTGTGTGGTTAGCCTTGACACATTGTTATGATTTAGTAGATATAC
*
2207 TGAGGTTTGCCAATGTATGACTGACCCATGATAGAAGGTAATAACCAGTAAGGAGAAA
781 TGAGGTTTGCCAACGTATGACTGACCCATGATAGAAGGTAATAACCAGTAAGGAGAAA
*
2265 TATCAGAAGTCCACCCAAGATACTGTGTAGTTAATTTA-GAAAAAAAAAACAAACACAATATGAG
1 TATCAGAAGTCCACCCAAGATACTGTGTAGTCAATTTAGGAAAAAAAAAACAAACACAATATGAG
* *
2329 TTAAATATGCATGATACGTATAATATCATTGACTAAAAGCTATATTAGAAGTTCAAAGTTTGGTG
66 TGAAATATGCATGATAAGTATAATATCATTGACTAAAAGCTATATTAGAAGTTCAAAGTTTGGTG
*
2394 CTTACTTCCCTAAGTGAAGGTCCTCTCGTTGTAAAAGAGGACTCAGAATTGCTGTAAAGATGAGG
131 CTTACTTCCCTAAGTGAAGGTCCTATCGTTGTAAAAGAGGACTCAGAATTGCTGTAAAGATGAGG
* * ** *
2459 GAAAATGGCGGAAAGGAAGAGATGAGTACTGGACCCCTGTTGCTGTGTACACAATGTCACCAGTG
196 GAAAATGGCGAAAAGGAAGAGACGAAAACTGGACCCCTGTTGCTATGTACACAATGTCACCAGTG
*
2524 TTGTTGACATCCCAGTTACCAAGATGCCCTATTCAATTTTTATTGAAACATCATTAAGAAAATCA
261 TTGTTGACATCCCAGATACCAAGATGCCCTATTCAATTTTTATTGAAACATCATTAAGAAAATCA
*
2589 ATAATAATAACTAAATAAATTCAACATATTTTCAAAGTAGAATCAATCTAAAATTTAACTACGTA
326 ATAATAATAACTAAATAAATTCAACATATTTTCAAAGTAGAATCAATCTAAAATTTAAATACGTA
* * * *
2654 TGATGTAAGGGTTATTGACAAGTCTGATATCTTTCTTCCATGCGAAGCATGCCAAGTGC-GGTCT
391 TAATGTAAGGGATATTGACAAGCCTGATAGCTTTCTTCCATGCGAAGCATGCCAAGT-CAGGTCT
*
2718 ATGATCAAAACATATACAGTTGACAACACAAAACTGCTGCCAAACATAAGCAATGTGGACGAGAA
455 ATGATCAAAACATATACAGTTGACAACACAAAACTGCTGCCAAACATAAGCAATGTGGACAAGAA
* *
2783 AACTGGATAGGCATACGTGACTGTCATCCTCCTCTAATTACAACAAAGAATATTAAATTAAAAAA
520 AACTGGATAGGCATACGTGACTGTCATCCTCCTCTAATCACAACAAAGAACATTAAATTAAAAAA
*
2848 TTTAGTGAGAAAATTAATGAATATATAGAATCAATCTTATATATATTATATATAGATTCAAGTAA
585 TTTAGTGAGAAAATAAATGAATATATAGAATCAATCTTATATATATTATATATAGATTCAAGTAA
*
2913 GTGTGCTTGATTAACAGTACAATAAGAAGCATGTCAAAGGAAAAGTAACTGCTGCAAGCTACCAA
650 GTGTGCTTGATTAACAGTACAATAAGAAGCATGGCAAAGGAAAAGTAACTGCTGCAAGCTACCAA
2978 CTCGCTCACTACTGGCCTCTGCTGTGTGGTTAGCCTTGACACATTGTTATGATTTAGTAGATATA
715 CTCGCTCACTACTGGCCTCTGCTGTGTGGTTAGCCTTGACACATTGTTATGATTTAGTAGATATA
* * *
3043 CTGAGGTGTT-CCAACGTATGGCTGACCCATGATAGAAGGTTATAACCATTAAGGAGAAA
780 CTGAGGT-TTGCCAACGTATGACTGACCCATGATAGAAGGTAATAACCAGTAAGGAGAAA
3102 T
1 T
3103 TTGATACCGT
Statistics
Matches: 796, Mismatches: 40, Indels: 5
0.95 0.05 0.01
Matches are distributed among these distances:
837 756 0.95
838 40 0.05
ACGTcount: A:0.38, C:0.16, G:0.18, T:0.28
Consensus pattern (838 bp):
TATCAGAAGTCCACCCAAGATACTGTGTAGTCAATTTAGGAAAAAAAAAACAAACACAATATGAG
TGAAATATGCATGATAAGTATAATATCATTGACTAAAAGCTATATTAGAAGTTCAAAGTTTGGTG
CTTACTTCCCTAAGTGAAGGTCCTATCGTTGTAAAAGAGGACTCAGAATTGCTGTAAAGATGAGG
GAAAATGGCGAAAAGGAAGAGACGAAAACTGGACCCCTGTTGCTATGTACACAATGTCACCAGTG
TTGTTGACATCCCAGATACCAAGATGCCCTATTCAATTTTTATTGAAACATCATTAAGAAAATCA
ATAATAATAACTAAATAAATTCAACATATTTTCAAAGTAGAATCAATCTAAAATTTAAATACGTA
TAATGTAAGGGATATTGACAAGCCTGATAGCTTTCTTCCATGCGAAGCATGCCAAGTCAGGTCTA
TGATCAAAACATATACAGTTGACAACACAAAACTGCTGCCAAACATAAGCAATGTGGACAAGAAA
ACTGGATAGGCATACGTGACTGTCATCCTCCTCTAATCACAACAAAGAACATTAAATTAAAAAAT
TTAGTGAGAAAATAAATGAATATATAGAATCAATCTTATATATATTATATATAGATTCAAGTAAG
TGTGCTTGATTAACAGTACAATAAGAAGCATGGCAAAGGAAAAGTAACTGCTGCAAGCTACCAAC
TCGCTCACTACTGGCCTCTGCTGTGTGGTTAGCCTTGACACATTGTTATGATTTAGTAGATATAC
TGAGGTTTGCCAACGTATGACTGACCCATGATAGAAGGTAATAACCAGTAAGGAGAAA
Found at i:3527 original size:2 final size:2
Alignment explanation
Indices: 3478--3508 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
3468 TTATCTTAAT
3478 TA TA 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 TA TA T
3509 GTTTCCCGTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:6367 original size:15 final size:16
Alignment explanation
Indices: 6349--6381 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
6339 TATTAAATAA
6349 ATAATAATTATT-TTT
1 ATAATAATTATTATTT
6364 ATAATAATTATTATTT
1 ATAATAATTATTATTT
6380 AT
1 AT
6382 CCCATATATG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
ATAATAATTATTATTT
Found at i:15523 original size:18 final size:19
Alignment explanation
Indices: 15500--15539 Score: 73
Period size: 18 Copynumber: 2.2 Consensus size: 19
15490 AGTCTAGGGC
15500 CAGGGCATGCCATAAA-CT
1 CAGGGCATGCCATAAACCT
15518 CAGGGCATGCCATAAACCT
1 CAGGGCATGCCATAAACCT
15537 CAG
1 CAG
15540 AGAAGACTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 16 0.76
19 5 0.24
ACGTcount: A:0.33, C:0.30, G:0.23, T:0.15
Consensus pattern (19 bp):
CAGGGCATGCCATAAACCT
Found at i:16089 original size:2 final size:2
Alignment explanation
Indices: 16082--16128 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
16072 TGGATATAAC
16082 AT AT AT 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 AT AT AT
16124 AT AT A
1 AT AT A
16129 CTAGTATAAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Done.