Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014101.1 Corchorus capsularis cultivar CVL-1 contig14122, 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: 31524
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.31
Found at i:4697 original size:17 final size:17
Alignment explanation
Indices: 4673--4707 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
4663 TCTGGTCGAA
*
4673 ATTTTTTTATTTTATTTT
1 ATTTTTTT-TTATATTTT
4691 ATTTTTTTTTATATTTT
1 ATTTTTTTTTATATTTT
4708 TCGATATAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (17 bp):
ATTTTTTTTTATATTTT
Found at i:5885 original size:33 final size:33
Alignment explanation
Indices: 5792--5885 Score: 80
Period size: 33 Copynumber: 2.8 Consensus size: 33
5782 TGGCCGGTTG
* * * * * *
5792 TGGCCGGACATGTCCATGTCGCGTGGCCGGTGT
1 TGGCCGGGCATCTCCAAGTCACATGGCCAGTGT
** * *
5825 TGGCCGGGCATCTCTGAGTCGCGTGGCCAGTGT
1 TGGCCGGGCATCTCCAAGTCACATGGCCAGTGT
* *
5858 TGGCCGGTCTTCTCCAAGTCACATGGCC
1 TGGCCGGGCATCTCCAAGTCACATGGCC
5886 GGTCACTCGC
Statistics
Matches: 49, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
33 49 1.00
ACGTcount: A:0.11, C:0.30, G:0.35, T:0.24
Consensus pattern (33 bp):
TGGCCGGGCATCTCCAAGTCACATGGCCAGTGT
Found at i:15985 original size:2 final size:2
Alignment explanation
Indices: 15978--16003 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
15968 CTCCTCACAA
15978 GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT
16004 ACACCTTTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
GT
Found at i:20777 original size:16 final size:16
Alignment explanation
Indices: 20758--20792 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
20748 GCCGAGACAA
20758 CCCGAACCCGAACCCG
1 CCCGAACCCGAACCCG
*
20774 CCCGAACCCGTACCCG
1 CCCGAACCCGAACCCG
20790 CCC
1 CCC
20793 CGAGCCCGAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.20, C:0.60, G:0.17, T:0.03
Consensus pattern (16 bp):
CCCGAACCCGAACCCG
Found at i:21614 original size:16 final size:16
Alignment explanation
Indices: 21593--21660 Score: 104
Period size: 16 Copynumber: 4.3 Consensus size: 16
21583 CCGATCCGAG
21593 CCCGAACCCGAAAATA
1 CCCGAACCCGAAAATA
*
21609 CCCGAACCCGACAGA-A
1 CCCGAACCCGA-AAATA
21625 CCCGAACCCGAAAATA
1 CCCGAACCCGAAAATA
21641 CCCGAACCCG-AAATA
1 CCCGAACCCGAAAATA
21656 CCCGA
1 CCCGA
21661 GCCCAAACCC
Statistics
Matches: 48, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
15 12 0.25
16 34 0.71
17 2 0.04
ACGTcount: A:0.40, C:0.41, G:0.15, T:0.04
Consensus pattern (16 bp):
CCCGAACCCGAAAATA
Found at i:21634 original size:32 final size:33
Alignment explanation
Indices: 21561--21651 Score: 129
Period size: 32 Copynumber: 2.9 Consensus size: 33
21551 ACCTGAACCC
*
21561 GAACCCGAACCCG---A-ACCCGAACCCGATCC
1 GAACCCGAACCCGAAAATACCCGAACCCGATCA
*
21590 GAGCCCGAACCCGAAAATACCCGAACCCGA-CA
1 GAACCCGAACCCGAAAATACCCGAACCCGATCA
21622 GAACCCGAACCCGAAAATACCCGAACCCGA
1 GAACCCGAACCCGAAAATACCCGAACCCGA
21652 AATACCCGAG
Statistics
Matches: 55, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
29 12 0.22
32 31 0.56
33 12 0.22
ACGTcount: A:0.36, C:0.43, G:0.18, T:0.03
Consensus pattern (33 bp):
GAACCCGAACCCGAAAATACCCGAACCCGATCA
Found at i:21652 original size:6 final size:6
Alignment explanation
Indices: 21543--21636 Score: 95
Period size: 6 Copynumber: 15.5 Consensus size: 6
21533 TATCGAAAGT
* *
21543 GAACCC GAACCT GAACCC GAACCC GAACCC GAACCC GAACCC G-ATCC
1 GAACCC GAACCC GAACCC GAACCC GAACCC GAACCC GAACCC GAACCC
* *
21590 GAGCCC GAACCC GAAAATACCC GAACCC G-A-CA GAACCC GAACCC GAA
1 GAACCC GAACCC G---A-ACCC GAACCC GAACCC GAACCC GAACCC GAA
21637 AATACCCGAA
Statistics
Matches: 73, Mismatches: 8, Indels: 14
0.77 0.08 0.15
Matches are distributed among these distances:
4 2 0.03
5 6 0.08
6 58 0.79
7 1 0.01
9 1 0.01
10 5 0.07
ACGTcount: A:0.35, C:0.44, G:0.18, T:0.03
Consensus pattern (6 bp):
GAACCC
Found at i:23674 original size:21 final size:20
Alignment explanation
Indices: 23648--23695 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
23638 CTATAAATTT
23648 AAAACAATATATAAGA-CAAC
1 AAAACAATA-ATAAGAGCAAC
* *
23668 ACAAACAGTAATAGGAGCAAC
1 A-AAACAATAATAAGAGCAAC
23689 AAAACAA
1 AAAACAA
23696 AACTTAATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
20 11 0.48
21 12 0.52
ACGTcount: A:0.62, C:0.17, G:0.10, T:0.10
Consensus pattern (20 bp):
AAAACAATAATAAGAGCAAC
Found at i:24658 original size:23 final size:23
Alignment explanation
Indices: 24626--24670 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
24616 AACCCTAAAC
* *
24626 ATAACGTTAAGAATTTAATATAT
1 ATAACCTTAAGAATTAAATATAT
24649 ATAACCTTAAGAATTAAATATA
1 ATAACCTTAAGAATTAAATATA
24671 ACATCATATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.51, C:0.07, G:0.07, T:0.36
Consensus pattern (23 bp):
ATAACCTTAAGAATTAAATATAT
Found at i:28764 original size:35 final size:35
Alignment explanation
Indices: 28725--28822 Score: 151
Period size: 35 Copynumber: 2.8 Consensus size: 35
28715 AACAATAGTA
*
28725 GCTCTTCTGGAGCCTTCAATCAAATTTGAATACTG
1 GCTCTTCTGGAGCCTTCAATCAAATTTGAATAATG
* * *
28760 GCTCTTCTGGAGCCTTTAATCAATTTTAAATAATG
1 GCTCTTCTGGAGCCTTCAATCAAATTTGAATAATG
*
28795 GCTCTTCTGGAGTCTTCAATCAAATTTG
1 GCTCTTCTGGAGCCTTCAATCAAATTTG
28823 TACCATCTGA
Statistics
Matches: 55, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
35 55 1.00
ACGTcount: A:0.26, C:0.20, G:0.16, T:0.38
Consensus pattern (35 bp):
GCTCTTCTGGAGCCTTCAATCAAATTTGAATAATG
Found at i:30181 original size:54 final size:54
Alignment explanation
Indices: 30099--30201 Score: 188
Period size: 54 Copynumber: 1.9 Consensus size: 54
30089 ATATAATTTA
* *
30099 AAGTGGATAGTATGACAACTTCGGGTGTCAAACTTTGGCAACAGTTAAAGTTTC
1 AAGTGGATAGTATGACAACTTCAGGTGTCAAACTTTGGCAACAATTAAAGTTTC
30153 AAGTGGATAGTATGACAACTTCAGGTGTCAAACTTTGGCAACAATTAAA
1 AAGTGGATAGTATGACAACTTCAGGTGTCAAACTTTGGCAACAATTAAA
30202 CAAATATTTC
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 47 1.00
ACGTcount: A:0.35, C:0.15, G:0.22, T:0.28
Consensus pattern (54 bp):
AAGTGGATAGTATGACAACTTCAGGTGTCAAACTTTGGCAACAATTAAAGTTTC
Found at i:30327 original size:33 final size:33
Alignment explanation
Indices: 30252--30408 Score: 224
Period size: 33 Copynumber: 4.7 Consensus size: 33
30242 AATGATACTA
* *
30252 TGACAACTTCAGGCGTCACTAATATGCTTGATAATG
1 TGACAACTTCAGGTGCCACTAATATGCTTG---ATG
30288 TGACAACTTCAGGTGCCACTAATATGCTTGATG
1 TGACAACTTCAGGTGCCACTAATATGCTTGATG
* *
30321 TGACAACTTCAAGTGCCACTGATATGCTTGATG
1 TGACAACTTCAGGTGCCACTAATATGCTTGATG
* *
30354 TGACAACTTCAGGTGCCACTGATATTCTTGATG
1 TGACAACTTCAGGTGCCACTAATATGCTTGATG
*
30387 TGACAACTTCTGGTGCCACTAA
1 TGACAACTTCAGGTGCCACTAA
30409 CATTCAAGGA
Statistics
Matches: 113, Mismatches: 8, Indels: 3
0.91 0.06 0.02
Matches are distributed among these distances:
33 85 0.75
36 28 0.25
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.31
Consensus pattern (33 bp):
TGACAACTTCAGGTGCCACTAATATGCTTGATG
Found at i:30511 original size:32 final size:33
Alignment explanation
Indices: 30446--30518 Score: 112
Period size: 33 Copynumber: 2.2 Consensus size: 33
30436 ATAAATTTTA
* *
30446 ATGATAAAGAAAGGTAGAAGGAGGAGATTATGC
1 ATGATAAAGAAAGGTAGAAGGAAGAGATCATGC
30479 ATGATAAAGAAAGGTAGAA-GAAGAGATCATGC
1 ATGATAAAGAAAGGTAGAAGGAAGAGATCATGC
*
30511 ATGTTAAA
1 ATGATAAA
30519 TAAACTTTGT
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
32 18 0.49
33 19 0.51
ACGTcount: A:0.48, C:0.04, G:0.29, T:0.19
Consensus pattern (33 bp):
ATGATAAAGAAAGGTAGAAGGAAGAGATCATGC
Found at i:30718 original size:17 final size:17
Alignment explanation
Indices: 30685--30736 Score: 70
Period size: 17 Copynumber: 3.1 Consensus size: 17
30675 TATGGAAAAG
*
30685 ACAAGAGAAT-TAAGAGA
1 ACAAGAGAATAT-GGAGA
30702 ACAAGAGAATATGGAGA
1 ACAAGAGAATATGGAGA
*
30719 AGAAGAGAATATGGAGA
1 ACAAGAGAATATGGAGA
30736 A
1 A
30737 TGGGAGAGAC
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
17 31 0.97
18 1 0.03
ACGTcount: A:0.56, C:0.04, G:0.29, T:0.12
Consensus pattern (17 bp):
ACAAGAGAATATGGAGA
Found at i:31404 original size:2 final size:2
Alignment explanation
Indices: 31397--31429 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
31387 GCTATACAGT
31397 TA 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 TA T
31430 GAAAGCTATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.