Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006704.1 Corchorus capsularis cultivar CVL-1 contig06725, 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: 27696
ACGTcount: A:0.29, C:0.17, G:0.22, T:0.32
Found at i:45 original size:2 final size:2
Alignment explanation
Indices: 38--77 Score: 59
Period size: 2 Copynumber: 21.5 Consensus size: 2
28 AGCAAAGTAA
38 AT AT AT AT AT AT AT AT AT AT AT AT -T AT A- AT AT A- 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
77 A
1 A
78 ATACTCCCTC
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
1 3 0.09
2 32 0.91
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1414 original size:2 final size:2
Alignment explanation
Indices: 1366--1394 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1356 ACATCTCTAC
1366 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1395 GACACACATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2599 original size:42 final size:42
Alignment explanation
Indices: 2553--2647 Score: 147
Period size: 42 Copynumber: 2.3 Consensus size: 42
2543 ATCAGAATAA
*
2553 TCAGCAGCAGCAACAGCCGCAGCCATTCCCACAACAGCAGTT
1 TCAGCAGCAGCAACAGCCGCAGCCATTCCCACAACAACAGTT
*
2595 TCAGCCA-CAACAACAGCCGCAGCCATTCCCACAACAACAGTT
1 TCAG-CAGCAGCAACAGCCGCAGCCATTCCCACAACAACAGTT
*
2637 TCAGCCGCAGC
1 TCAGCAGCAGC
2648 CAGCACAATA
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
41 1 0.02
42 44 0.94
43 2 0.04
ACGTcount: A:0.32, C:0.40, G:0.17, T:0.12
Consensus pattern (42 bp):
TCAGCAGCAGCAACAGCCGCAGCCATTCCCACAACAACAGTT
Found at i:2641 original size:24 final size:24
Alignment explanation
Indices: 2572--2642 Score: 64
Period size: 24 Copynumber: 3.2 Consensus size: 24
2562 GCAACAGCCG
*
2572 CAGCCATTCCCACAACAGCAGTTT
1 CAGCCATTCCCACAACAACAGTTT
***
2596 CAG------CCACAACAACAGCCG
1 CAGCCATTCCCACAACAACAGTTT
2614 CAGCCATTCCCACAACAACAGTTT
1 CAGCCATTCCCACAACAACAGTTT
2638 CAGCC
1 CAGCC
2643 GCAGCCAGCA
Statistics
Matches: 34, Mismatches: 7, Indels: 12
0.64 0.13 0.23
Matches are distributed among these distances:
18 14 0.41
24 20 0.59
ACGTcount: A:0.32, C:0.41, G:0.13, T:0.14
Consensus pattern (24 bp):
CAGCCATTCCCACAACAACAGTTT
Found at i:2748 original size:24 final size:24
Alignment explanation
Indices: 2683--2767 Score: 89
Period size: 24 Copynumber: 3.5 Consensus size: 24
2673 TAACCAAGCC
* * * *
2683 TATCCACCACAGCAGCCCGCACCA
1 TATCCACCGCAACAGCCTGCAGCA
* *
2707 TACCCACCGCAACAGCCTGCAGCG
1 TATCCACCGCAACAGCCTGCAGCA
** *
2731 TATCCACCGCAACAGCCTGGTGCT
1 TATCCACCGCAACAGCCTGCAGCA
2755 TATCCACCGCAAC
1 TATCCACCGCAAC
2768 CAGTGCAATT
Statistics
Matches: 51, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 51 1.00
ACGTcount: A:0.26, C:0.45, G:0.16, T:0.13
Consensus pattern (24 bp):
TATCCACCGCAACAGCCTGCAGCA
Found at i:9503 original size:15 final size:15
Alignment explanation
Indices: 9485--9515 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
9475 TTTAAGTTTC
9485 AGGGACTTAATTGAA
1 AGGGACTTAATTGAA
*
9500 AGGGACTTATTTGAA
1 AGGGACTTAATTGAA
9515 A
1 A
9516 AGAAATAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.39, C:0.06, G:0.26, T:0.29
Consensus pattern (15 bp):
AGGGACTTAATTGAA
Found at i:16287 original size:71 final size:71
Alignment explanation
Indices: 16197--16339 Score: 259
Period size: 71 Copynumber: 2.0 Consensus size: 71
16187 AAACAAGAAA
16197 AAGAATAAAGATTTCATATGCATAAAAGATTTATTGGTATTTATATTCAAGGGTTTTTTTAAGTT
1 AAGAATAAAGATTTCATATGCATAAAAGATTTATTGGTATTTATATTCAAGGGTTTTTTTAAGTT
16262 CACTCC
66 CACTCC
* * *
16268 AAGATTAAAGATTTCATATGCATAAAAGATTTATTGGTATTTATTTTCCAGGGTTTTTTTAAGTT
1 AAGAATAAAGATTTCATATGCATAAAAGATTTATTGGTATTTATATTCAAGGGTTTTTTTAAGTT
16333 CACTCC
66 CACTCC
16339 A
1 A
16340 TAAGTAACCA
Statistics
Matches: 69, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
71 69 1.00
ACGTcount: A:0.34, C:0.10, G:0.14, T:0.42
Consensus pattern (71 bp):
AAGAATAAAGATTTCATATGCATAAAAGATTTATTGGTATTTATATTCAAGGGTTTTTTTAAGTT
CACTCC
Found at i:21615 original size:20 final size:20
Alignment explanation
Indices: 21590--21628 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
21580 TGCATGCTTC
21590 TGTCTCTACCGCAACTATGT
1 TGTCTCTACCGCAACTATGT
*
21610 TGTCTCTACCGCAGCTATG
1 TGTCTCTACCGCAACTATG
21629 ACACTTCAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.18, C:0.31, G:0.18, T:0.33
Consensus pattern (20 bp):
TGTCTCTACCGCAACTATGT
Found at i:22586 original size:41 final size:41
Alignment explanation
Indices: 22539--22844 Score: 319
Period size: 41 Copynumber: 7.4 Consensus size: 41
22529 CTTGTGTTAC
* *
22539 ATGTGCTT-AGGGACTTTCATATAGATGCCTCTGTGTTATAA
1 ATGTGCTTGA-GGACTTTGAGATAGATGCCTCTGTGTTATAA
* * *
22580 ATGTGCTTGAGGACTTTAGAGAGAGTTGCCCCTGTGTTATAA
1 ATGTGCTTGAGGACTTT-GAGATAGATGCCTCTGTGTTATAA
* * * * *
22622 TTATGTTTGGGGACTTTGATATAGATGCCTCTGTGTTATAA
1 ATGTGCTTGAGGACTTTGAGATAGATGCCTCTGTGTTATAA
* * * *
22663 ATGTGTTTGAGGACTTTAGAGAGAGTTGCCCCTGTGTTATAA
1 ATGTGCTTGAGGACTTT-GAGATAGATGCCTCTGTGTTATAA
* * * * * *
22705 TTGTGTTTGGGGACTTTGATATAGGTGCCTCTATGTTATAA
1 ATGTGCTTGAGGACTTTGAGATAGATGCCTCTGTGTTATAA
* *
22746 ATGTGCTTGAGGACTTTGAGAGAGTTGCAC-CTGTGTTATAA
1 ATGTGCTTGAGGACTTTGAGATAGATGC-CTCTGTGTTATAA
* * * * *
22787 TTGTGTTTGGGGACTTTGACATAGATGTCTCTGTGTTATAA
1 ATGTGCTTGAGGACTTTGAGATAGATGCCTCTGTGTTATAA
22828 ATGTGCTTGAGGACTTT
1 ATGTGCTTGAGGACTTT
22845 TGAAGAGAAT
Statistics
Matches: 216, Mismatches: 44, Indels: 10
0.80 0.16 0.04
Matches are distributed among these distances:
40 1 0.00
41 146 0.68
42 69 0.32
ACGTcount: A:0.22, C:0.12, G:0.27, T:0.39
Consensus pattern (41 bp):
ATGTGCTTGAGGACTTTGAGATAGATGCCTCTGTGTTATAA
Found at i:22824 original size:82 final size:83
Alignment explanation
Indices: 22548--22844 Score: 515
Period size: 83 Copynumber: 3.6 Consensus size: 83
22538 CATGTGCTTA
*
22548 GGGACTTTCATATAGATGCCTCTGTGTTATAAATGTGCTTGAGGACTTTAGAGAGAGTTGCCCCT
1 GGGACTTTGATATAGATGCCTCTGTGTTATAAATGTGCTTGAGGACTTTAGAGAGAGTTGCCCCT
*
22613 GTGTTATAATTATGTTTG
66 GTGTTATAATTGTGTTTG
*
22631 GGGACTTTGATATAGATGCCTCTGTGTTATAAATGTGTTTGAGGACTTTAGAGAGAGTTGCCCCT
1 GGGACTTTGATATAGATGCCTCTGTGTTATAAATGTGCTTGAGGACTTTAGAGAGAGTTGCCCCT
22696 GTGTTATAATTGTGTTTG
66 GTGTTATAATTGTGTTTG
* * *
22714 GGGACTTTGATATAGGTGCCTCTATGTTATAAATGTGCTTGAGGACTTT-GAGAGAGTTGCACCT
1 GGGACTTTGATATAGATGCCTCTGTGTTATAAATGTGCTTGAGGACTTTAGAGAGAGTTGCCCCT
22778 GTGTTATAATTGTGTTTG
66 GTGTTATAATTGTGTTTG
* *
22796 GGGACTTTGACATAGATGTCTCTGTGTTATAAATGTGCTTGAGGACTTT
1 GGGACTTTGATATAGATGCCTCTGTGTTATAAATGTGCTTGAGGACTTT
22845 TGAAGAGAAT
Statistics
Matches: 203, Mismatches: 11, Indels: 1
0.94 0.05 0.00
Matches are distributed among these distances:
82 77 0.38
83 126 0.62
ACGTcount: A:0.22, C:0.12, G:0.27, T:0.39
Consensus pattern (83 bp):
GGGACTTTGATATAGATGCCTCTGTGTTATAAATGTGCTTGAGGACTTTAGAGAGAGTTGCCCCT
GTGTTATAATTGTGTTTG
Found at i:23634 original size:35 final size:34
Alignment explanation
Indices: 23595--23721 Score: 139
Period size: 35 Copynumber: 3.6 Consensus size: 34
23585 TGTTGAAGCC
* * * *
23595 CCCAAGTATTGAATGAAGAATGAGTTGCTGGAGT
1 CCCAAGTGTTGAATGAAGAAGGGGTTGTTGGAGT
*
23629 ACCCAATTGTTGAAT-AATGAAGGGGTTGTTGGAGT
1 -CCCAAGTGTTGAATGAA-GAAGGGGTTGTTGGAGT
* *
23664 CCCCAAGTGTTGAAAGATGAAGGGGTTGTTGGAGT
1 -CCCAAGTGTTGAATGAAGAAGGGGTTGTTGGAGT
*
23699 CTCCAAGTGTTGAATGAGGAAGG
1 C-CCAAGTGTTGAATGAAGAAGG
23722 AGCTTTAATT
Statistics
Matches: 78, Mismatches: 11, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
34 3 0.04
35 74 0.95
36 1 0.01
ACGTcount: A:0.29, C:0.11, G:0.33, T:0.27
Consensus pattern (34 bp):
CCCAAGTGTTGAATGAAGAAGGGGTTGTTGGAGT
Found at i:23668 original size:70 final size:70
Alignment explanation
Indices: 23583--23713 Score: 165
Period size: 70 Copynumber: 1.9 Consensus size: 70
23573 TGAAGTTTTC
* * *
23583 GTTGTTGAAGCCCCCAAGTATTGAATGAAGAATGAGTTGCTGGAGTAC-CCAATTGTTGAATAAT
1 GTTGTTGAAGCCCCCAAGTATTGAAAGAAGAAGGAGTTGCTGGAGT-CTCCAAGTGTTGAATAAT
23647 GAAGGG
65 GAAGGG
* * * * * *
23653 GTTGTTGGAGTCCCCAAGTGTTGAAAGATGAAGGGGTTGTTGGAGTCTCCAAGTGTTGAAT
1 GTTGTTGAAGCCCCCAAGTATTGAAAGAAGAAGGAGTTGCTGGAGTCTCCAAGTGTTGAAT
23714 GAGGAAGGAG
Statistics
Matches: 51, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
69 1 0.02
70 50 0.98
ACGTcount: A:0.27, C:0.12, G:0.31, T:0.29
Consensus pattern (70 bp):
GTTGTTGAAGCCCCCAAGTATTGAAAGAAGAAGGAGTTGCTGGAGTCTCCAAGTGTTGAATAATG
AAGGG
Found at i:25661 original size:60 final size:60
Alignment explanation
Indices: 25594--25713 Score: 222
Period size: 60 Copynumber: 2.0 Consensus size: 60
25584 TGTAAGATCG
*
25594 AAGAGAGTCGCATAGCCTTGATGAGGTTCATTTTGCTACTGCTTCTCAGTGGAGTTCTTT
1 AAGAGAGTCGCATAGCCTTGATGAGGCTCATTTTGCTACTGCTTCTCAGTGGAGTTCTTT
*
25654 AAGAGAGTCGCATAGCCTTGATGAGGCTCATTTTGCTACTGCTTCTCAGTGGTGTTCTTT
1 AAGAGAGTCGCATAGCCTTGATGAGGCTCATTTTGCTACTGCTTCTCAGTGGAGTTCTTT
25714 GTTGAAATCG
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
60 58 1.00
ACGTcount: A:0.19, C:0.19, G:0.25, T:0.37
Consensus pattern (60 bp):
AAGAGAGTCGCATAGCCTTGATGAGGCTCATTTTGCTACTGCTTCTCAGTGGAGTTCTTT
Found at i:26772 original size:60 final size:60
Alignment explanation
Indices: 26705--26824 Score: 240
Period size: 60 Copynumber: 2.0 Consensus size: 60
26695 TGTAAGATCA
26705 AAGAGAGTCGCATAGCCTTGATGAGGCTCATTTTGCTACTGCTTCTCAGTGGTGTTCTTT
1 AAGAGAGTCGCATAGCCTTGATGAGGCTCATTTTGCTACTGCTTCTCAGTGGTGTTCTTT
26765 AAGAGAGTCGCATAGCCTTGATGAGGCTCATTTTGCTACTGCTTCTCAGTGGTGTTCTTT
1 AAGAGAGTCGCATAGCCTTGATGAGGCTCATTTTGCTACTGCTTCTCAGTGGTGTTCTTT
26825 GTTGAAATCG
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
60 60 1.00
ACGTcount: A:0.18, C:0.20, G:0.25, T:0.37
Consensus pattern (60 bp):
AAGAGAGTCGCATAGCCTTGATGAGGCTCATTTTGCTACTGCTTCTCAGTGGTGTTCTTT
Done.