Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012080.1 Corchorus capsularis cultivar CVL-1 contig12101, 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: 8484
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.34
Found at i:717 original size:52 final size:51
Alignment explanation
Indices: 634--731 Score: 133
Period size: 52 Copynumber: 1.9 Consensus size: 51
624 GACGCGACAC
* ** *
634 GCCACGTGTACCAAAAGTGACATGTGGCACGCCACATGTACTAAAAGTCGT
1 GCCACATGTACCAAAAGTGACACATGGCACGCCACATGTACCAAAAGTCGT
* *
685 GCCACATGTACCAAAAAGTGACACATGTCACGCCACGTGTACCAAAA
1 GCCACATGTACC-AAAAGTGACACATGGCACGCCACATGTACCAAAA
732 AGTGACACGT
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
51 11 0.28
52 29 0.73
ACGTcount: A:0.35, C:0.28, G:0.20, T:0.17
Consensus pattern (51 bp):
GCCACATGTACCAAAAGTGACACATGGCACGCCACATGTACCAAAAGTCGT
Found at i:751 original size:31 final size:31
Alignment explanation
Indices: 684--782 Score: 126
Period size: 31 Copynumber: 3.2 Consensus size: 31
674 CTAAAAGTCG
* *
684 TGCCACATGTACCAAAAAGTGACACATGTCA
1 TGCCACATGTACCAAAAAGTGACACGTGGCA
* *
715 CGCCACGTGTACCAAAAAGTGACACGTGGCA
1 TGCCACATGTACCAAAAAGTGACACGTGGCA
** * *
746 TGCCACATGTTTCAAAAAATGGCACGTGGCA
1 TGCCACATGTACCAAAAAGTGACACGTGGCA
777 TGCCAC
1 TGCCAC
783 GTGCACAAAA
Statistics
Matches: 58, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 58 1.00
ACGTcount: A:0.33, C:0.27, G:0.21, T:0.18
Consensus pattern (31 bp):
TGCCACATGTACCAAAAAGTGACACGTGGCA
Found at i:2704 original size:28 final size:27
Alignment explanation
Indices: 2650--2705 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 27
2640 TCTCGTTTTT
* * *
2650 AAAAGTTAATGGACCAATTTGTCCAAA
1 AAAAATTAAAGGACCAATTTATCCAAA
*
2677 AAAAATTAAAGGACCAATTTATCCCAA
1 AAAAATTAAAGGACCAATTTATCCAAA
2704 AA
1 AA
2706 TGGATAGTTA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.50, C:0.16, G:0.11, T:0.23
Consensus pattern (27 bp):
AAAAATTAAAGGACCAATTTATCCAAA
Found at i:3129 original size:5 final size:5
Alignment explanation
Indices: 3119--3162 Score: 52
Period size: 5 Copynumber: 8.2 Consensus size: 5
3109 TGCATTTAAA
*
3119 AATAT AATAT AATAT AATATAT AACAT AATAT ATATAT AATAT A
1 AATAT AATAT AATAT -A-ATAT AATAT AATAT A-ATAT AATAT A
3163 TATGAAAGAA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
5 23 0.68
6 7 0.21
7 4 0.12
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (5 bp):
AATAT
Found at i:4065 original size:29 final size:31
Alignment explanation
Indices: 3996--4070 Score: 100
Period size: 31 Copynumber: 2.5 Consensus size: 31
3986 GCTAAATATC
* *
3996 CAAAAAAATCTCTTATGTTTTTGTTTTGGGA
1 CAAAATAATCCCTTATGTTTTTGTTTTGGGA
4027 CAAAATAATCCCTTATGTTTTT-TTTT-GGA
1 CAAAATAATCCCTTATGTTTTTGTTTTGGGA
* *
4056 TAAATTAATCCCTTA
1 CAAAATAATCCCTTA
4071 CATTTCAAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
29 16 0.40
30 4 0.10
31 20 0.50
ACGTcount: A:0.31, C:0.13, G:0.11, T:0.45
Consensus pattern (31 bp):
CAAAATAATCCCTTATGTTTTTGTTTTGGGA
Found at i:5561 original size:29 final size:31
Alignment explanation
Indices: 5519--5592 Score: 107
Period size: 29 Copynumber: 2.5 Consensus size: 31
5509 CTCACTTTTG
* * *
5519 AAACGTAAGAGATTAATTTGTCCC-AAAC-A
1 AAACATAAGGGATTAATTTATCCCAAAACAA
5548 AAACATAAGGGATTAATTTATCCCAAAACAA
1 AAACATAAGGGATTAATTTATCCCAAAACAA
5579 AAACATAAGGGATT
1 AAACATAAGGGATT
5593 TTTTGGGTAT
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
29 21 0.52
30 4 0.10
31 15 0.38
ACGTcount: A:0.49, C:0.15, G:0.14, T:0.23
Consensus pattern (31 bp):
AAACATAAGGGATTAATTTATCCCAAAACAA
Found at i:7215 original size:440 final size:440
Alignment explanation
Indices: 6684--7533 Score: 1312
Period size: 440 Copynumber: 1.9 Consensus size: 440
6674 CATAAAATGT
* *
6684 TTAATAGAAACTCGTAGATCAAATTTAACTTTCGGGTACTTCATTAAAGTCGTAAATCATGCAAT
1 TTAATAGAAACTAGTAGATCAAATTTAACTTTCGGGTACTTCATGAAAGTCGTAAATCATGCAAT
* * * *
6749 AACCTTTTGACCGACACTTCAATAACTTCAATTGGACATGTGGACAAAAAATTATACGATATT-A
66 AACCTTCTAACCGACACTTCAATAACTTCAATCGGACATATGGACAAAAAATTATACGATATTAA
* *
6813 ATTTGACCGGCAATCAAAACCACAAAATTTCGGAAGCATTTTTTAGAATTAAAACATTAAAATTG
131 ATTT-ACCGGCAATCAAAACCACAAAATTTCGAAAGCATTTTTTAGAATCAAAACATTAAAATTG
6878 GCTTTTGAGTTCTTCAT-AAAAATTGTAGATCATGAAATTACCTTTTAATAGACACTTGAATCAC
195 GCTTTTGAGTTCTTCATGAAAAA-TGTAGATCATGAAATTACCTTTTAATAGACACTTGAATCAC
*
6942 CTTAATCGGACAAATAGGAAAAAATATACAAAAATAAATGCAAACACGTCAAATCGTCTAACCTA
259 CTTAATCGGACAAATAGGAAAAAA-ATACAAAAATAAATGCAAACACGTCAAATCGTCCAACCTA
* * *
7007 TAATCGCAAAGAACTAAATAGCAT-AAAGTATAAAAATATGAAGATCATTAGATAAATAATCCAA
323 TAATCGCAAAGAACTAAATAACATCAAA-CATAAAAATATGAAGATCATTAGATAAATAATCAAA
* *
7071 CAAAAAAATGTTTGTTAATGGAGATCTTGAACATAAAAACTCCCTTTTGAGCCC
387 CAAAAAAATATTAGTTAATGGAGATCTTGAACATAAAAACTCCCTTTTGAGCCC
* * * * *
7125 TTAAT-GAAACTATTAGATTAAATTTAGCTTTCGGGTCCTTCATGAAAGTCGTAAATCATTCAAT
1 TTAATAGAAACTAGTAGATCAAATTTAACTTTCGGGTACTTCATGAAAGTCGTAAATCATGCAAT
*
7189 AACCTTCTAACCGACACTTTAATAACTTCAATCGGACATATGGACAAAAAATTATACGATATTAA
66 AACCTTCTAACCGACACTTCAATAACTTCAATCGGACATATGGACAAAAAATTATACGATATTAA
*
7254 ATTTACCGGCAATCAAAACCACAAAATTTCGAAAGTATTTTTTAGAATCAAAACATTAAAATTGG
131 ATTTACCGGCAATCAAAACCACAAAATTTCGAAAGCATTTTTTAGAATCAAAACATTAAAATTGG
* *
7319 CTTTTGAGTTCTTCATGAAAAATGTAGATGATGAAATTACCTTTTAATAGACACTTGAATTACCT
196 CTTTTGAGTTCTTCATGAAAAATGTAGATCATGAAATTACCTTTTAATAGACACTTGAATCACCT
* * * *
7384 TAATCGGACAAATAGGAAAAAAATACAATAATAAATGCGAACGCGTTAAATCGTCCAACCTATAA
261 TAATCGGACAAATAGGAAAAAAATACAAAAATAAATGCAAACACGTCAAATCGTCCAACCTATAA
* * * * * * *
7449 TTGTAAAGGACTAAATAACATCAAACATAAAAGTATGAGGGTCATTAGATAAATAATCAAACCAA
326 TCGCAAAGAACTAAATAACATCAAACATAAAAATATGAAGATCATTAGATAAATAATCAAACAAA
* *
7514 ATAATATTAGTTTATGGAGA
391 AAAATATTAGTTAATGGAGA
7534 ATGTGACCCA
Statistics
Matches: 370, Mismatches: 36, Indels: 8
0.89 0.09 0.02
Matches are distributed among these distances:
439 105 0.28
440 250 0.68
441 15 0.04
ACGTcount: A:0.42, C:0.15, G:0.13, T:0.29
Consensus pattern (440 bp):
TTAATAGAAACTAGTAGATCAAATTTAACTTTCGGGTACTTCATGAAAGTCGTAAATCATGCAAT
AACCTTCTAACCGACACTTCAATAACTTCAATCGGACATATGGACAAAAAATTATACGATATTAA
ATTTACCGGCAATCAAAACCACAAAATTTCGAAAGCATTTTTTAGAATCAAAACATTAAAATTGG
CTTTTGAGTTCTTCATGAAAAATGTAGATCATGAAATTACCTTTTAATAGACACTTGAATCACCT
TAATCGGACAAATAGGAAAAAAATACAAAAATAAATGCAAACACGTCAAATCGTCCAACCTATAA
TCGCAAAGAACTAAATAACATCAAACATAAAAATATGAAGATCATTAGATAAATAATCAAACAAA
AAAATATTAGTTAATGGAGATCTTGAACATAAAAACTCCCTTTTGAGCCC
Done.