Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012187.1 Corchorus olitorius cultivar O-4 contig12220, 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: 16589
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Found at i:9886 original size:443 final size:434
Alignment explanation
Indices: 9211--10007 Score: 1109
Period size: 443 Copynumber: 1.8 Consensus size: 434
9201 AAGTGACCAT
9211 TTGATAAATAATCCAAATAAAAAATTGTTTGTTGATGAGACGAAACATAAAAATTTCCTCTTAAG
1 TTGATAAATAATCCAAATAAAAAATTGTTTGTTGATGAGACGAAACATAAAAATTTCCTCTTAAG
* ** * * *
9276 TCTTTCATGAAACTCGTTGATCAAATTCAGCATCGGGTACTTCATGAAAGTTGTAGATTATGCAA
66 GCTTTCATGAAACTCGTCAATCAAATTCAACATCGGGTACTTCATGAAAGTCGTAGATCATGCAA
* * * *
9341 TAACCTTTTAACTGAACTTGAATAACTTCAATCAGATATGTGGATCGAAAGTTATATGATATTAA
131 TAACCTTTTAACCGAACTTCAATAACTTCAATCAGATATGTGGATCGAAAATTATATGAAATTAA
* *
9406 ATAGACCGACAATCGAAACCACCAAATTTCAGAAGCATTTTGTAGAGTTGAAACAAAAAAATTGG
196 ATAGACCGACAATCGAAACCACCAAATTTCAGAAGCATTTTGTAGAGCTGAAACAAAAAAATTAG
*
9471 ATTGTGAGTCCTTAATGAAAGATGTAGTCTTGTAGATCATGAAAATACCTTTTAATAGACATTTA
261 ATTGTGAGTCCTTAATG-AA-A-GTA-----GTAGATCATGAAAATACCTTTTAATAGACACTTA
* * * *
9536 AATCACCTTATTCAGACAAATATAACAAAAAATAAAAATAAAACTGAAGTGTTTAATCGATTAAG
318 AATCACCTTAATCAGAAAAATAGAAAAAAAAATAAAAATAAAACTGAAGTGTTTAATCGATTAAG
9601 ATAGAATTAATAAAGGACTAAGTAGTATGAAATAGAAAAGTATGTGGGTCAA
383 ATAGAATTAATAAAGGACTAAGTAGTATGAAATAGAAAAGTATGTGGGTCAA
**
9653 TTGATAAATAATCCAAATAAAAAA-TGTTTGTTGATGAAGATTAAACAT-AAAATTTCCTCTTGA
1 TTGATAAATAATCCAAATAAAAAATTGTTTGTTGATG-AGACGAAACATAAAAATTTCCTCTT-A
* * * * *
9716 GGGC-TTCATTAAACTCGTCAATCAAGTTCAACTTTCGGGTCCTTCATGAAAGTCGTAGATCATG
64 AGGCTTTCATGAAACTCGTCAATCAAATTCAAC-ATCGGGTACTTCATGAAAGTCGTAGATCATG
9780 CAATAACCTTTTAACCGACACTTCAATAACTTCAAT-AGGATATGTGGATCGAAAATTATATGAA
128 CAATAACCTTTTAACCGA-ACTTCAATAACTTCAATCA-GATATGTGGATCGAAAATTATATGAA
* * * * *
9844 ATTAAATAGACTGGCAATC-AGAACCACCAAATTTCGGAAGCATTTTTTAGAGCTGAAACATAAA
191 ATTAAATAGACCGACAATCGA-AACCACCAAATTTCAGAAGCATTTTGTAGAGCTGAAACAAAAA
* * * * * *
9908 AATTAGCTTTTGAGTCCTTCATGAAAGTAGTAGATCATGAAATTACCTTTTAATGGACACTTGAA
255 AATTAGATTGTGAGTCCTTAATGAAAGTAGTAGATCATGAAAATACCTTTTAATAGACACTTAAA
*
9973 TCACCTTAATCGGAAAAATAGAAAAAAAAATAAAA
320 TCACCTTAATCAGAAAAATAGAAAAAAAAATAAAA
10008 CAATTAAAAT
Statistics
Matches: 313, Mismatches: 36, Indels: 19
0.85 0.10 0.05
Matches are distributed among these distances:
435 62 0.20
440 3 0.01
441 49 0.16
442 84 0.27
443 115 0.37
ACGTcount: A:0.41, C:0.14, G:0.15, T:0.30
Consensus pattern (434 bp):
TTGATAAATAATCCAAATAAAAAATTGTTTGTTGATGAGACGAAACATAAAAATTTCCTCTTAAG
GCTTTCATGAAACTCGTCAATCAAATTCAACATCGGGTACTTCATGAAAGTCGTAGATCATGCAA
TAACCTTTTAACCGAACTTCAATAACTTCAATCAGATATGTGGATCGAAAATTATATGAAATTAA
ATAGACCGACAATCGAAACCACCAAATTTCAGAAGCATTTTGTAGAGCTGAAACAAAAAAATTAG
ATTGTGAGTCCTTAATGAAAGTAGTAGATCATGAAAATACCTTTTAATAGACACTTAAATCACCT
TAATCAGAAAAATAGAAAAAAAAATAAAAATAAAACTGAAGTGTTTAATCGATTAAGATAGAATT
AATAAAGGACTAAGTAGTATGAAATAGAAAAGTATGTGGGTCAA
Found at i:11009 original size:16 final size:15
Alignment explanation
Indices: 10980--11012 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
10970 AAGAAAAACA
10980 TTTTTTTTTATTTTG
1 TTTTTTTTTATTTTG
*
10995 TTTTTTTTTCTTTT-
1 TTTTTTTTTATTTTG
11009 TTTT
1 TTTT
11013 GGACTTTGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 4 0.24
15 13 0.76
ACGTcount: A:0.03, C:0.03, G:0.03, T:0.91
Consensus pattern (15 bp):
TTTTTTTTTATTTTG
Found at i:11762 original size:10 final size:10
Alignment explanation
Indices: 11744--11783 Score: 71
Period size: 10 Copynumber: 4.0 Consensus size: 10
11734 ACCCCCCTTT
*
11744 CTTAAGAACA
1 CTTATGAACA
11754 CTTATGAACA
1 CTTATGAACA
11764 CTTATGAACA
1 CTTATGAACA
11774 CTTATGAACA
1 CTTATGAACA
11784 AAACCCACCC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
10 29 1.00
ACGTcount: A:0.42, C:0.20, G:0.10, T:0.28
Consensus pattern (10 bp):
CTTATGAACA
Found at i:12656 original size:22 final size:22
Alignment explanation
Indices: 12621--12667 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 22
12611 ATGTTCTGAC
12621 TTTTGCTTTTTTTTCTTTTTTT
1 TTTTGCTTTTTTTTCTTTTTTT
*
12643 TTTTG-TTTTGTTTTGTTTTTTT
1 TTTTGCTTTT-TTTTCTTTTTTT
12665 TTT
1 TTT
12668 AAATAATAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 4 0.17
22 19 0.83
ACGTcount: A:0.00, C:0.04, G:0.09, T:0.87
Consensus pattern (22 bp):
TTTTGCTTTTTTTTCTTTTTTT
Found at i:12675 original size:3 final size:3
Alignment explanation
Indices: 12669--12747 Score: 131
Period size: 3 Copynumber: 25.7 Consensus size: 3
12659 TTTTTTTTTA
12669 AAT AAT AAT ACGAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT A--AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
12716 AAT AAT AAT AAT AAT AAT AAT AAT GAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
12748 GAGAAAGCAA
Statistics
Matches: 72, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
3 69 0.96
5 3 0.04
ACGTcount: A:0.65, C:0.01, G:0.03, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:13517 original size:55 final size:54
Alignment explanation
Indices: 13384--13576 Score: 257
Period size: 54 Copynumber: 3.6 Consensus size: 54
13374 ACGAAGATTA
* * * * * * *
13384 ATTGAAAGGCCGCACAAGACCACCAGAATATCAGCAAAGATTTTCTGAAAATTG
1 ATTGAAAGGTCGCCCAGGACCATCAGAAGATCAACATAGATTTTCTGAAAATTG
*
13438 ATTGAAAGGTCGCTCAGGACCATCAGAAGATCAACATAGATTTTCTGAAAATTG
1 ATTGAAAGGTCGCCCAGGACCATCAGAAGATCAACATAGATTTTCTGAAAATTG
13492 ACTTGAAAGGTCGCCCAGGACCATCAGAA-ATCAACATAGA-TTTCTG-AAATTG
1 A-TTGAAAGGTCGCCCAGGACCATCAGAAGATCAACATAGATTTTCTGAAAATTG
* * *
13544 ATTGAAAGGTCACCCGGGACCATCAAAAGATCA
1 ATTGAAAGGTCGCCCAGGACCATCAGAAGATCA
13577 GCTTAGATCT
Statistics
Matches: 126, Mismatches: 11, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
51 24 0.19
52 11 0.09
53 6 0.05
54 59 0.47
55 26 0.21
ACGTcount: A:0.38, C:0.20, G:0.20, T:0.22
Consensus pattern (54 bp):
ATTGAAAGGTCGCCCAGGACCATCAGAAGATCAACATAGATTTTCTGAAAATTG
Done.