Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009075.1 Corchorus capsularis cultivar CVL-1 contig09096, 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: 55735
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Found at i:4631 original size:22 final size:22
Alignment explanation
Indices: 4584--4636 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
4574 TACCTTTATC
* *
4584 TTTTTCTTTTTCGTTATTCTTC
1 TTTTTATTTTTCGTTATTCTTA
*
4606 TTTTTATTTTTCGTT-TTGTTTA
1 TTTTTATTTTTCGTTATT-CTTA
4628 TTTTTATTT
1 TTTTTATTT
4637 ATTTTTGTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
21 2 0.07
22 25 0.93
ACGTcount: A:0.08, C:0.09, G:0.06, T:0.77
Consensus pattern (22 bp):
TTTTTATTTTTCGTTATTCTTA
Found at i:5776 original size:21 final size:22
Alignment explanation
Indices: 5736--5777 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
5726 GTCAATGCTT
*
5736 TAGGAATGCAAGAGAGATTTCA
1 TAGGAATGCAAGAGACATTTCA
*
5758 TAGGAA-GCAAGAGCCATTTC
1 TAGGAATGCAAGAGACATTTC
5778 CAAGAAGGTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.38, C:0.14, G:0.26, T:0.21
Consensus pattern (22 bp):
TAGGAATGCAAGAGACATTTCA
Found at i:10831 original size:30 final size:30
Alignment explanation
Indices: 10797--10869 Score: 101
Period size: 30 Copynumber: 2.4 Consensus size: 30
10787 AGGAGATGGG
*
10797 ATCGCACCAAAGACATCAAAGGATGGAGGA
1 ATCGCACCAAAGACACCAAAGGATGGAGGA
** **
10827 ATCGCACCAAAGATGCCATTGGATGGAGGA
1 ATCGCACCAAAGACACCAAAGGATGGAGGA
10857 ATCGCACCAAAGA
1 ATCGCACCAAAGA
10870 TGCCATTTGA
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.40, C:0.22, G:0.26, T:0.12
Consensus pattern (30 bp):
ATCGCACCAAAGACACCAAAGGATGGAGGA
Found at i:10870 original size:30 final size:30
Alignment explanation
Indices: 10817--10876 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
10807 AGACATCAAA
10817 GGATGGAGGAATCGCACCAAAGATGCCATT
1 GGATGGAGGAATCGCACCAAAGATGCCATT
10847 GGATGGAGGAATCGCACCAAAGATGCCATT
1 GGATGGAGGAATCGCACCAAAGATGCCATT
10877 TGATCCTTTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.33, C:0.20, G:0.30, T:0.17
Consensus pattern (30 bp):
GGATGGAGGAATCGCACCAAAGATGCCATT
Found at i:19329 original size:15 final size:16
Alignment explanation
Indices: 19309--19338 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
19299 TGTAAGTCAA
19309 TCAAAA-ATCAATTTT
1 TCAAAAGATCAATTTT
19324 TCAAAAGATCAATTT
1 TCAAAAGATCAATTT
19339 GAACTCACAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.47, C:0.13, G:0.03, T:0.37
Consensus pattern (16 bp):
TCAAAAGATCAATTTT
Found at i:20694 original size:19 final size:21
Alignment explanation
Indices: 20648--20696 Score: 57
Period size: 19 Copynumber: 2.4 Consensus size: 21
20638 AAAAAAATAA
*
20648 AATTCTAAATCTAGAAAACAT
1 AATTTTAAATCTAGAAAACAT
* *
20669 AAATTTAAAT-TA-AAAACCT
1 AATTTTAAATCTAGAAAACAT
20688 AATTTTAAA
1 AATTTTAAA
20697 CCTAAATTGG
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
19 14 0.58
20 2 0.08
21 8 0.33
ACGTcount: A:0.55, C:0.10, G:0.02, T:0.33
Consensus pattern (21 bp):
AATTTTAAATCTAGAAAACAT
Found at i:22205 original size:10 final size:10
Alignment explanation
Indices: 22190--22216 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
22180 TGCTTGACAT
22190 GGCATGGAGC
1 GGCATGGAGC
22200 GGCATGGAGC
1 GGCATGGAGC
22210 GGCATGG
1 GGCATGG
22217 CCGGGCTAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.19, C:0.19, G:0.52, T:0.11
Consensus pattern (10 bp):
GGCATGGAGC
Found at i:22474 original size:14 final size:14
Alignment explanation
Indices: 22457--22497 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
22447 GAGAAAATTC
*
22457 ATAAAACCTAAAAA
1 ATAAAAACTAAAAA
22471 ATAAAAACTAAAAA
1 ATAAAAACTAAAAA
* *
22485 TTAAAAATTAAAA
1 ATAAAAACTAAAA
22498 TTGGGTTGCC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.73, C:0.07, G:0.00, T:0.20
Consensus pattern (14 bp):
ATAAAAACTAAAAA
Found at i:22483 original size:21 final size:21
Alignment explanation
Indices: 22458--22497 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
22448 AGAAAATTCA
*
22458 TAAAACCTAAAAAATAAAAAC
1 TAAAAACTAAAAAATAAAAAC
* *
22479 TAAAAATTAAAAATTAAAA
1 TAAAAACTAAAAAATAAAA
22498 TTGGGTTGCC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.72, C:0.07, G:0.00, T:0.20
Consensus pattern (21 bp):
TAAAAACTAAAAAATAAAAAC
Found at i:37121 original size:36 final size:37
Alignment explanation
Indices: 37081--37185 Score: 106
Period size: 39 Copynumber: 2.8 Consensus size: 37
37071 AACATTAGAC
37081 CCAATCATAAAGAGTAAAGCCCAACCA-AAATTAAAA
1 CCAATCATAAAGAGTAAAGCCCAACCAGAAATTAAAA
* **
37117 CCAATCCTAAAAAGAGGTAAAGCCCAA-CAGAAATTAATT
1 CCAAT-C-ATAAAGA-GTAAAGCCCAACCAGAAATTAAAA
* * * *
37156 CCCACCATAAAGAGTAAGGCCCAACAAGAA
1 CCAATCATAAAGAGTAAAGCCCAACCAGAA
37186 TTGAACCCAT
Statistics
Matches: 56, Mismatches: 8, Indels: 9
0.77 0.11 0.12
Matches are distributed among these distances:
36 15 0.27
37 11 0.20
38 9 0.16
39 21 0.38
ACGTcount: A:0.50, C:0.24, G:0.12, T:0.13
Consensus pattern (37 bp):
CCAATCATAAAGAGTAAAGCCCAACCAGAAATTAAAA
Found at i:41694 original size:9 final size:9
Alignment explanation
Indices: 41680--41713 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
41670 TGTGCGCTAT
41680 GCTTAGGTA
1 GCTTAGGTA
*
41689 GCTTAGCTA
1 GCTTAGGTA
*
41698 GCTTAGTTA
1 GCTTAGGTA
41707 GCTTAGG
1 GCTTAGG
41714 GTTTTTCAAC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.21, C:0.15, G:0.29, T:0.35
Consensus pattern (9 bp):
GCTTAGGTA
Found at i:41703 original size:18 final size:19
Alignment explanation
Indices: 41675--41712 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
41665 GGATTTGTGC
41675 GCTATGCTTAGGTAGCTTA
1 GCTATGCTTAGGTAGCTTA
*
41694 GCTA-GCTTAGTTAGCTTA
1 GCTATGCTTAGGTAGCTTA
41712 G
1 G
41713 GGTTTTTCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.21, C:0.16, G:0.26, T:0.37
Consensus pattern (19 bp):
GCTATGCTTAGGTAGCTTA
Found at i:43564 original size:13 final size:13
Alignment explanation
Indices: 43546--43570 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
43536 TAAAAAATTT
43546 AAAAAAACAAAAC
1 AAAAAAACAAAAC
43559 AAAAAAACAAAA
1 AAAAAAACAAAA
43571 AACAGGAAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (13 bp):
AAAAAAACAAAAC
Found at i:45944 original size:19 final size:19
Alignment explanation
Indices: 45922--45959 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
45912 TTAGAATTTA
45922 GAGTA-ATCTTGTAACTTAG
1 GAGTAGATCTT-TAACTTAG
*
45941 GAGTAGCTCTTTAACTTAG
1 GAGTAGATCTTTAACTTAG
45960 CATTTTCCCT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.29, C:0.13, G:0.21, T:0.37
Consensus pattern (19 bp):
GAGTAGATCTTTAACTTAG
Found at i:55677 original size:36 final size:36
Alignment explanation
Indices: 55636--55716 Score: 144
Period size: 36 Copynumber: 2.2 Consensus size: 36
55626 GCCTTGGGGT
* *
55636 GGGTCGCGACCGGGGTCCATGCCCAGGTCACGACAC
1 GGGTCGCGACCCGGGTCCATGCCCAAGTCACGACAC
55672 GGGTCGCGACCCGGGTCCATGCCCAAGTCACGACAC
1 GGGTCGCGACCCGGGTCCATGCCCAAGTCACGACAC
55708 GGGTCGCGA
1 GGGTCGCGA
55717 TCCACCCCAT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
36 43 1.00
ACGTcount: A:0.17, C:0.36, G:0.36, T:0.11
Consensus pattern (36 bp):
GGGTCGCGACCCGGGTCCATGCCCAAGTCACGACAC
Done.