Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006391.1 Corchorus capsularis cultivar CVL-1 contig06412, 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: 65897
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Found at i:2084 original size:21 final size:21
Alignment explanation
Indices: 2060--2109 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
2050 GGCCTTGTTC
* *
2060 CTGCCTCATTTCTTCTTGCGA
1 CTGCCTCATTTCTCCCTGCGA
2081 CTGCCTCATTTCTCCCTGCGA
1 CTGCCTCATTTCTCCCTGCGA
2102 CTGCCTCA
1 CTGCCTCA
2110 ACTGTTGGAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.10, C:0.40, G:0.14, T:0.36
Consensus pattern (21 bp):
CTGCCTCATTTCTCCCTGCGA
Found at i:5860 original size:15 final size:14
Alignment explanation
Indices: 5837--5878 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
5827 AAAAATTCGG
5837 AAAAAA-AAAAA-C
1 AAAAAACAAAAATC
5849 AAAAATACAAAAATC
1 AAAAA-ACAAAAATC
*
5864 AAAAATCAAAAATC
1 AAAAAACAAAAATC
5878 A
1 A
5879 GGAAAAATGC
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
12 5 0.19
13 1 0.04
14 14 0.54
15 6 0.23
ACGTcount: A:0.79, C:0.12, G:0.00, T:0.10
Consensus pattern (14 bp):
AAAAAACAAAAATC
Found at i:5866 original size:7 final size:7
Alignment explanation
Indices: 5842--5878 Score: 56
Period size: 7 Copynumber: 5.1 Consensus size: 7
5832 TTCGGAAAAA
*
5842 AAAAAAC
1 AAAAATC
5849 AAAAATAC
1 AAAAAT-C
5857 AAAAATC
1 AAAAATC
5864 AAAAATC
1 AAAAATC
5871 AAAAATC
1 AAAAATC
5878 A
1 A
5879 GGAAAAATGC
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
7 21 0.75
8 7 0.25
ACGTcount: A:0.76, C:0.14, G:0.00, T:0.11
Consensus pattern (7 bp):
AAAAATC
Found at i:5876 original size:14 final size:15
Alignment explanation
Indices: 5842--5878 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
5832 TTCGGAAAAA
*
5842 AAAAAACAAAAATAC
1 AAAAATCAAAAATAC
5857 AAAAATCAAAAAT-C
1 AAAAATCAAAAATAC
5871 AAAAATCA
1 AAAAATCA
5879 GGAAAAATGC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 9 0.43
15 12 0.57
ACGTcount: A:0.76, C:0.14, G:0.00, T:0.11
Consensus pattern (15 bp):
AAAAATCAAAAATAC
Found at i:11528 original size:19 final size:19
Alignment explanation
Indices: 11504--11541 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
11494 CAATTTTCTC
*
11504 CAATTAGGACTAATTGCAA
1 CAATTAAGACTAATTGCAA
*
11523 CAATTAAGATTAATTGCAA
1 CAATTAAGACTAATTGCAA
11542 AATCACAAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.45, C:0.13, G:0.13, T:0.29
Consensus pattern (19 bp):
CAATTAAGACTAATTGCAA
Found at i:18837 original size:21 final size:21
Alignment explanation
Indices: 18794--18851 Score: 59
Period size: 21 Copynumber: 2.8 Consensus size: 21
18784 AAAATAATGG
*
18794 GAAGAGGAAAGGAAAAG--GAA
1 GAAGATGAAA-GAAAAGATGAA
18814 GAA-ATGAACAGAAAAGATGAA
1 GAAGATGAA-AGAAAAGATGAA
*
18835 GAAGATGAAAGCAAAGA
1 GAAGATGAAAGAAAAGA
18852 GAGAGCGGCT
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
19 10 0.31
20 4 0.12
21 13 0.41
22 5 0.16
ACGTcount: A:0.60, C:0.03, G:0.31, T:0.05
Consensus pattern (21 bp):
GAAGATGAAAGAAAAGATGAA
Found at i:20628 original size:17 final size:17
Alignment explanation
Indices: 20606--20642 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
20596 GTTATCCAGC
20606 ACCTCATGCTACCTAGT
1 ACCTCATGCTACCTAGT
*
20623 ACCTCATGCTACCTGGT
1 ACCTCATGCTACCTAGT
20640 ACC
1 ACC
20643 ATGAGGGGGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.22, C:0.38, G:0.14, T:0.27
Consensus pattern (17 bp):
ACCTCATGCTACCTAGT
Found at i:22587 original size:41 final size:41
Alignment explanation
Indices: 22530--22613 Score: 168
Period size: 41 Copynumber: 2.0 Consensus size: 41
22520 CAAACGTTGC
22530 ACATAGCTCTAAAAACCCATAATTGAAAGCTGCATTCAGGT
1 ACATAGCTCTAAAAACCCATAATTGAAAGCTGCATTCAGGT
22571 ACATAGCTCTAAAAACCCATAATTGAAAGCTGCATTCAGGT
1 ACATAGCTCTAAAAACCCATAATTGAAAGCTGCATTCAGGT
22612 AC
1 AC
22614 CATTCTTTTT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 43 1.00
ACGTcount: A:0.39, C:0.23, G:0.14, T:0.24
Consensus pattern (41 bp):
ACATAGCTCTAAAAACCCATAATTGAAAGCTGCATTCAGGT
Found at i:26682 original size:6 final size:6
Alignment explanation
Indices: 26671--26712 Score: 75
Period size: 6 Copynumber: 7.0 Consensus size: 6
26661 TTAATGAGAG
*
26671 AATGCT AATGCT AATGCT AATGCT AATGCT AATGCT ATTGCT
1 AATGCT AATGCT AATGCT AATGCT AATGCT AATGCT AATGCT
26713 GCTATTAAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.36
Consensus pattern (6 bp):
AATGCT
Found at i:31831 original size:3 final size:3
Alignment explanation
Indices: 31823--31863 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
31813 CAATAATGAA
31823 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
31864 CATGTCCATG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:42611 original size:14 final size:14
Alignment explanation
Indices: 42592--42624 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
42582 AAAACAGATG
42592 TTTTCCAAAAACCA
1 TTTTCCAAAAACCA
*
42606 TTTTCCAAAGACCA
1 TTTTCCAAAAACCA
42620 TTTTC
1 TTTTC
42625 ATCAAATCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.33, C:0.27, G:0.03, T:0.36
Consensus pattern (14 bp):
TTTTCCAAAAACCA
Found at i:47715 original size:14 final size:14
Alignment explanation
Indices: 47696--47722 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
47686 AGTTTTGTGA
47696 ATTGTCATTAACAG
1 ATTGTCATTAACAG
47710 ATTGTCATTAACA
1 ATTGTCATTAACA
47723 AATTCTGAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.15, G:0.11, T:0.37
Consensus pattern (14 bp):
ATTGTCATTAACAG
Found at i:55054 original size:16 final size:16
Alignment explanation
Indices: 55029--55059 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
55019 TTACTTAATT
*
55029 CAGAATTAAAATAACA
1 CAGAAATAAAATAACA
55045 CAGAAATAAAATAAC
1 CAGAAATAAAATAAC
55060 TATCATAGAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.65, C:0.13, G:0.06, T:0.16
Consensus pattern (16 bp):
CAGAAATAAAATAACA
Found at i:56133 original size:31 final size:32
Alignment explanation
Indices: 56097--56157 Score: 97
Period size: 31 Copynumber: 1.9 Consensus size: 32
56087 GAGAATAAAC
56097 TCAGAGGGAAATCGATGAAAGCG-AAAATGAG
1 TCAGAGGGAAATCGATGAAAGCGCAAAATGAG
* *
56128 TCAGAGGGAAATCGATTAAGGCGCAAAATG
1 TCAGAGGGAAATCGATGAAAGCGCAAAATG
56158 GGAGCAAAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
31 21 0.78
32 6 0.22
ACGTcount: A:0.43, C:0.11, G:0.31, T:0.15
Consensus pattern (32 bp):
TCAGAGGGAAATCGATGAAAGCGCAAAATGAG
Found at i:56687 original size:19 final size:20
Alignment explanation
Indices: 56663--56702 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
56653 TTAATTATTG
56663 ATATG-TTAATGGGTTTTTA
1 ATATGTTTAATGGGTTTTTA
*
56682 ATATGTTTAGTGGGTTTTTA
1 ATATGTTTAATGGGTTTTTA
56702 A
1 A
56703 GACATCTCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.25, C:0.00, G:0.23, T:0.53
Consensus pattern (20 bp):
ATATGTTTAATGGGTTTTTA
Done.