Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010924.1 Corchorus capsularis cultivar CVL-1 contig10945, 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: 33362
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.34
Found at i:980 original size:6 final size:6
Alignment explanation
Indices: 952--994 Score: 52
Period size: 6 Copynumber: 7.2 Consensus size: 6
942 GATTGGTTGA
* *
952 TCTGGT T-TGGT TCTGGT TGCTGGT TCTGGT TTTGGT TTTGGT T
1 TCTGGT TCTGGT TCTGGT T-CTGGT TCTGGT TCTGGT TCTGGT T
995 GGGTTCCATG
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
5 5 0.15
6 23 0.68
7 6 0.18
ACGTcount: A:0.00, C:0.09, G:0.35, T:0.56
Consensus pattern (6 bp):
TCTGGT
Found at i:987 original size:19 final size:18
Alignment explanation
Indices: 953--988 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
943 ATTGGTTGAT
953 CTGGTTTGGTTCTGGTTG
1 CTGGTTTGGTTCTGGTTG
*
971 CTGGTTCTGGTTTTGGTT
1 CTGGTT-TGGTTCTGGTT
989 TTGGTTGGGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.00, C:0.11, G:0.36, T:0.53
Consensus pattern (18 bp):
CTGGTTTGGTTCTGGTTG
Found at i:3619 original size:19 final size:19
Alignment explanation
Indices: 3595--3635 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
3585 ATAGGAAAAT
* *
3595 ATGATCAATGTTTGGTGTA
1 ATGATCAATATTTGGCGTA
*
3614 ATGATCATTATTTGGCGTA
1 ATGATCAATATTTGGCGTA
3633 ATG
1 ATG
3636 GCATCAATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.27, C:0.07, G:0.24, T:0.41
Consensus pattern (19 bp):
ATGATCAATATTTGGCGTA
Found at i:4182 original size:31 final size:32
Alignment explanation
Indices: 4147--4214 Score: 104
Period size: 31 Copynumber: 2.2 Consensus size: 32
4137 ATGTTTTCCG
*
4147 ATTGTACTCTTATT-TTTAAAACATATTTCT-A
1 ATTGTACCCTT-TTCTTTAAAACATATTTCTAA
4178 ATTGTACCCTTTTCTTTAAAACATATTTCTAA
1 ATTGTACCCTTTTCTTTAAAACATATTTCTAA
4210 ATTGT
1 ATTGT
4215 CATTACGAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
30 2 0.06
31 26 0.76
32 6 0.18
ACGTcount: A:0.31, C:0.15, G:0.04, T:0.50
Consensus pattern (32 bp):
ATTGTACCCTTTTCTTTAAAACATATTTCTAA
Found at i:4546 original size:19 final size:20
Alignment explanation
Indices: 4519--4556 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
4509 TACTATTATT
4519 TTTTGAATTT-AATATTTTAC
1 TTTTGAATTTCAAT-TTTTAC
4539 TTTT-AATTTCAATTTTTA
1 TTTTGAATTTCAATTTTTA
4557 AATGTCAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.29, C:0.05, G:0.03, T:0.63
Consensus pattern (20 bp):
TTTTGAATTTCAATTTTTAC
Found at i:4881 original size:22 final size:22
Alignment explanation
Indices: 4721--4883 Score: 121
Period size: 22 Copynumber: 7.3 Consensus size: 22
4711 TTGTCTCTAT
* *
4721 GTGGTTATCAAAATTTCATAAG
1 GTGGTTATTAAAATTTCATAGG
* * *
4743 ATGATTATTATAATTTCAT-GAG
1 GTGGTTATTAAAATTTCATAG-G
* * * *
4765 GAGGTTATCAAAATTCCATAGT
1 GTGGTTATTAAAATTTCATAGG
* * *
4787 GTGGTTACTAAAATTTAATAGT
1 GTGGTTATTAAAATTTCATAGG
**
4809 GTGGTTACCAAAATTTCATAGG
1 GTGGTTATTAAAATTTCATAGG
* * *
4831 ATCAGGTTATTAAAATCTCTTAGG
1 GT--GGTTATTAAAATTTCATAGG
* *
4855 TTGGTTATTGAAATTTCATAGG
1 GTGGTTATTAAAATTTCATAGG
4877 GTGGTTA
1 GTGGTTA
4884 ATTATCACAA
Statistics
Matches: 107, Mismatches: 30, Indels: 8
0.74 0.21 0.06
Matches are distributed among these distances:
22 89 0.83
23 1 0.01
24 17 0.16
ACGTcount: A:0.33, C:0.09, G:0.20, T:0.39
Consensus pattern (22 bp):
GTGGTTATTAAAATTTCATAGG
Found at i:5008 original size:22 final size:22
Alignment explanation
Indices: 4974--5278 Score: 135
Period size: 22 Copynumber: 13.6 Consensus size: 22
4964 TAACAAAATT
* *
4974 TTATTAAATATTTCATGGAGAGG
1 TTATCAAA-ATTTCATAGAGAGG
* * *
4997 TTATCAAAATTTTATAGTGTGG
1 TTATCAAAATTTCATAGAGAGG
5019 TTATCAAAATTTCATATGA-AGG
1 TTATCAAAATTTCATA-GAGAGG
*
5041 TTATAAAAGTCTCAATTTCATA-AG-GAG
1 TTAT-CAA-----AATTTCATAGAGAG-G
* * * *
5068 -TACCAAAAATTGATAGA-AGT
1 TTATCAAAATTTCATAGAGAGG
* *
5088 TTATC-AAATCTCATAAAG-GG
1 TTATCAAAATTTCATAGAGAGG
*
5108 ATTATCGAAATTTCATAGAGATTGG
1 -TTATCAAAATTTCATAGAGA--GG
* *
5133 ATTATCAAAATTT-ATAGAAAGA
1 -TTATCAAAATTTCATAGAGAGG
* *
5155 TTATCAAAATTTCAAAGCGAGG
1 TTATCAAAATTTCATAGAGAGG
** * *
5177 TTATCAAAATTAAATA-ATGTGA
1 TTATCAAAATTTCATAGA-GAGG
* *
5199 TTATCAGAATTTCATAGAGGGG
1 TTATCAAAATTTCATAGAGAGG
* * *
5221 TCAACAAAATTTTATA-ATGAGG
1 TTATCAAAATTTCATAGA-GAGG
* * *
5243 TTATCAACATTTTATAAAGAGG
1 TTATCAAAATTTCATAGAGAGG
*
5265 TTATCAAATTTTCA
1 TTATCAAAATTTCA
5279 AAATGTGATT
Statistics
Matches: 208, Mismatches: 51, Indels: 47
0.68 0.17 0.15
Matches are distributed among these distances:
20 16 0.08
21 23 0.11
22 121 0.58
23 12 0.06
24 6 0.03
25 16 0.08
26 4 0.02
27 1 0.00
28 9 0.04
ACGTcount: A:0.41, C:0.09, G:0.15, T:0.35
Consensus pattern (22 bp):
TTATCAAAATTTCATAGAGAGG
Found at i:5419 original size:19 final size:19
Alignment explanation
Indices: 5384--5431 Score: 78
Period size: 19 Copynumber: 2.5 Consensus size: 19
5374 TTATGGATTA
5384 ATCAAAATTTCAAGGAGGAT
1 ATCAAAA-TTCAAGGAGGAT
*
5404 ATCAAAATTCAGGGAGGAT
1 ATCAAAATTCAAGGAGGAT
5423 ATCAAAATT
1 ATCAAAATT
5432 TCATATGAAG
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
19 20 0.74
20 7 0.26
ACGTcount: A:0.46, C:0.10, G:0.19, T:0.25
Consensus pattern (19 bp):
ATCAAAATTCAAGGAGGAT
Found at i:5450 original size:22 final size:22
Alignment explanation
Indices: 5422--5904 Score: 132
Period size: 22 Copynumber: 22.1 Consensus size: 22
5412 TCAGGGAGGA
5422 TATCAAAATTTCATATGAAGGT
1 TATCAAAATTTCATATGAAGGT
**
5444 TATCAAAATTTCATAATTTA-GT
1 TATCAAAATTTCAT-ATGAAGGT
* * * *
5466 TTTCAAAACTTTCACAAGAGGGT
1 TATCAAAA-TTTCATATGAAGGT
* *
5489 TATCAAAATTTCATA-GTATGT
1 TATCAAAATTTCATATGAAGGT
* * *
5510 AGATCAAAATTTCATAGGGAA-AT
1 -TATCAAAATTTCATA-TGAAGGT
*
5533 TA-AAAAATTTCATAATG-AGGT
1 TATCAAAATTTCAT-ATGAAGGT
** * *
5554 TATCAAAAAATCATACGGAGGT
1 TATCAAAATTTCATATGAAGGT
*
5576 TATCAAAA--T--T-TGTA-GT
1 TATCAAAATTTCATATGAAGGT
* * *
5592 TATCAAGATTTCATAAGAAAGT
1 TATCAAAATTTCATATGAAGGT
* * *
5614 TATCAAAATTTTATAGGGAGGTT
1 TATCAAAATTTCATATGAAGG-T
* * * * *
5637 TTTTAAAATTTTATAGGAAGAT
1 TATCAAAATTTCATATGAAGGT
*
5659 ATATCAAAATTTCATA-GCTAGGT
1 -TATCAAAATTTCATATG-AAGGT
* * * *
5682 CATCACAATTTCATAGTG-TGAT
1 TATCAAAATTTCATA-TGAAGGT
* * *
5704 TATCAAAATTTCAGAGTG-TGAT
1 TATCAAAATTTCATA-TGAAGGT
* *
5726 TA-CTAACAA-TTCATATGGAGCT
1 TATC-AA-AATTTCATATGAAGGT
* * * *
5748 TTTTAAATTTTCATA--ACGTGTT
1 TATCAAAATTTCATATGAAG-G-T
* *
5770 TATCAATATATCATAT-AGAGGT
1 TATCAAAATTTCATATGA-AGGT
* * **
5792 TATCAACATCTCATAGTGTTGGT
1 TATCAAAATTTCATA-TGAAGGT
5815 TATCAAAATTTCAT-TGGGAA-GT
1 TATCAAAATTTCATAT--GAAGGT
5837 TATCAAAATTTCATATTG-AGGT
1 TATCAAAATTTCATA-TGAAGGT
* *
5859 CT-TCAAAATTCCTTA-GAGAGGT
1 -TATCAAAATTTCATATGA-AGGT
* * *
5881 TAACCAAATTTCATAAGAAGGT
1 TATCAAAATTTCATATGAAGGT
5903 TA
1 TA
5905 AAAAAAATTA
Statistics
Matches: 340, Mismatches: 79, Indels: 84
0.68 0.16 0.17
Matches are distributed among these distances:
16 9 0.03
17 2 0.01
18 2 0.01
20 5 0.01
21 28 0.08
22 214 0.63
23 75 0.22
24 5 0.01
ACGTcount: A:0.38, C:0.11, G:0.14, T:0.36
Consensus pattern (22 bp):
TATCAAAATTTCATATGAAGGT
Found at i:5517 original size:45 final size:43
Alignment explanation
Indices: 5422--5624 Score: 118
Period size: 45 Copynumber: 4.8 Consensus size: 43
5412 TCAGGGAGGA
* * *
5422 TATCAAAATTTCATATGAAGGTTATCAAAATTTCATAATTTAG
1 TATCAAAATTTCACAAGAAGGTTATCAAAATTTCATAATGTAG
* *
5465 TTTTCAAAACTTTCACAAGAGGGTTATCAAAATTTCATAGTATGTAG
1 -TATCAAAA-TTTCACAAGAAGGTTATCAAAATTTCATA--ATGTAG
* * * *
5512 -ATCAAAATTTCATAGGGAA-ATTA-AAAAATTTCATAATG-AGG
1 TATCAAAATTTCACA-AGAAGGTTATCAAAATTTCATAATGTA-G
** * * * *
5553 TTATCAAAAAATCATACGGAGGTTATCAAAATTT-GT-A-GT--
1 -TATCAAAATTTCACAAGAAGGTTATCAAAATTTCATAATGTAG
* * *
5592 TATCAAGATTTCATAAGAAAGTTATCAAAATTT
1 TATCAAAATTTCACAAGAAGGTTATCAAAATTT
5625 TATAGGGAGG
Statistics
Matches: 125, Mismatches: 24, Indels: 26
0.71 0.14 0.15
Matches are distributed among these distances:
38 27 0.22
40 1 0.01
41 5 0.04
42 3 0.02
43 27 0.22
44 23 0.18
45 34 0.27
47 5 0.04
ACGTcount: A:0.42, C:0.10, G:0.13, T:0.35
Consensus pattern (43 bp):
TATCAAAATTTCACAAGAAGGTTATCAAAATTTCATAATGTAG
Found at i:5667 original size:23 final size:23
Alignment explanation
Indices: 5614--5675 Score: 70
Period size: 23 Copynumber: 2.7 Consensus size: 23
5604 ATAAGAAAGT
* * *
5614 TATCAAAATTTTATAGGGAGGTT
1 TATCAAAATTTTATAGGAAGATA
* *
5637 TTTTAAAATTTTATAGGAAGATA
1 TATCAAAATTTTATAGGAAGATA
*
5660 TATCAAAATTTCATAG
1 TATCAAAATTTTATAG
5676 CTAGGTCATC
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.40, C:0.05, G:0.15, T:0.40
Consensus pattern (23 bp):
TATCAAAATTTTATAGGAAGATA
Found at i:19008 original size:2 final size:2
Alignment explanation
Indices: 19001--19025 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
18991 ACTTTGCTTC
19001 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 A
19026 GATAGAAGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:26299 original size:197 final size:200
Alignment explanation
Indices: 25836--26354 Score: 738
Period size: 197 Copynumber: 2.6 Consensus size: 200
25826 CTTTATAATA
* * *
25836 AGGATTATTATATAAATACACTGTCAATGTAAATTTTGGACTCCATAAGCGGATTAAGAAGTTGA
1 AGGATTATTATA-CAATACACTGTCAGTGTAAATTTTGGACTCCATAAGCGGGTTAAGAAGTTGA
* *
25901 CACATACCCCCATTTCATAATTAATTAGATATTTGATATTAATACATATTCCCTAAGAGGACACA
65 CACATA-CCCCATTTCATAATTAATTAGATATTTAATATTAATACATATTCCCTAAGAGAACACA
* * * * *
25966 TGTCAACCCTTAAACCATGCACGTGCAGTCTACTAAACTCCACTGGCGGTGTACTGTATAATTTT
129 TATAAACCCTTAAACCATGCACATGCAGTCTACTAAACTCCACTGACAGTGTACTGTATAATTTT
26031 GTTTTAT
194 GTTTTAT
* * * *
26038 AGGATTATTATACAATACAATGTCAGTGTAAATTTTGAACTCCATAACCAGGTTAAGAAGTTGAC
1 AGGATTATTATACAATACACTGTCAGTGTAAATTTTGGACTCCATAAGCGGGTTAAGAAGTTGAC
* ** *
26103 ACATACCCTATTTCATAATTAATTAGATATAAAATATTAATACATATTCCCTAAGATAACACATA
66 ACATACCCCATTTCATAATTAATTAGATATTTAATATTAATACATATTCCCTAAGAGAACACATA
* * * * * * *
26168 TAAACCCTTAAACC-TGCGCATGCAGTTTGCTAAATTCTATTGACAGTGTATTGTATAA-TTT-T
131 TAAACCCTTAAACCATGCACATGCAGTCTACTAAACTCCACTGACAGTGTACTGTATAATTTTGT
26230 TTTAT
196 TTTAT
* *
26235 ATGATTATTATACAATACACTGTCAGTGTAAATTTTGGACTCCAAAAGCGGGTTAAGAAGTTGAC
1 AGGATTATTATACAATACACTGTCAGTGTAAATTTTGGACTCCATAAGCGGGTTAAGAAGTTGAC
* *
26300 ACATACCCCATTTCTTAATTAATTAAATATTTAATATTAATACATATTCCCTAAG
66 ACATACCCCATTTCATAATTAATTAGATATTTAATATTAATACATATTCCCTAAG
26355 GAAATATTGG
Statistics
Matches: 281, Mismatches: 36, Indels: 5
0.87 0.11 0.02
Matches are distributed among these distances:
197 115 0.41
198 3 0.01
199 34 0.12
200 66 0.23
201 51 0.18
202 12 0.04
ACGTcount: A:0.36, C:0.17, G:0.13, T:0.34
Consensus pattern (200 bp):
AGGATTATTATACAATACACTGTCAGTGTAAATTTTGGACTCCATAAGCGGGTTAAGAAGTTGAC
ACATACCCCATTTCATAATTAATTAGATATTTAATATTAATACATATTCCCTAAGAGAACACATA
TAAACCCTTAAACCATGCACATGCAGTCTACTAAACTCCACTGACAGTGTACTGTATAATTTTGT
TTTAT
Found at i:30806 original size:14 final size:14
Alignment explanation
Indices: 30789--30832 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
30779 ACTTTAAACT
30789 TTATAATAATAACC
1 TTATAATAATAACC
*
30803 TTATAA-AAT---T
1 TTATAATAATAACC
30813 TTATAATAATAACC
1 TTATAATAATAACC
30827 TTATAA
1 TTATAA
30833 AATTTTTTAC
Statistics
Matches: 24, Mismatches: 2, Indels: 8
0.71 0.06 0.24
Matches are distributed among these distances:
10 6 0.25
11 3 0.12
13 3 0.12
14 12 0.50
ACGTcount: A:0.50, C:0.09, G:0.00, T:0.41
Consensus pattern (14 bp):
TTATAATAATAACC
Found at i:30815 original size:24 final size:24
Alignment explanation
Indices: 30788--30838 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
30778 TACTTTAAAC
30788 TTTATAATAATAACCTTATAAAAT
1 TTTATAATAATAACCTTATAAAAT
30812 TTTATAATAATAACCTTATAAAAT
1 TTTATAATAATAACCTTATAAAAT
30836 TTT
1 TTT
30839 TTACCTTATC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.47, C:0.08, G:0.00, T:0.45
Consensus pattern (24 bp):
TTTATAATAATAACCTTATAAAAT
Done.