Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016509.1 Corchorus capsularis cultivar CVL-1 contig16530, 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: 43259
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Found at i:4531 original size:21 final size:21
Alignment explanation
Indices: 4493--4537 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 21
4483 GGCGCCCACA
*
4493 TGGTTGCCTTGAGCACCCATGT
1 TGGTTGCCTGGAGCACCCA-GT
4515 TGGTTGCCTGGAG-ACCCAGT
1 TGGTTGCCTGGAGCACCCAGT
4535 TGG
1 TGG
4538 GTAGTGTCCC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 5 0.23
21 5 0.23
22 12 0.55
ACGTcount: A:0.13, C:0.24, G:0.33, T:0.29
Consensus pattern (21 bp):
TGGTTGCCTGGAGCACCCAGT
Found at i:14491 original size:42 final size:42
Alignment explanation
Indices: 14419--14505 Score: 111
Period size: 42 Copynumber: 2.1 Consensus size: 42
14409 AAAGGGTCGA
* * * *
14419 ATGGCCGGTTGTGGCCGGATGGCCCATGCGACGGCCCGTGTG
1 ATGGCCGATTGTGGCCCGATGGCCCATGCGACAGCCCGTGCG
* * *
14461 ATGGCCGATTGTGGCCCGATGGCTCGTGCGATAGCCCGTGCG
1 ATGGCCGATTGTGGCCCGATGGCCCATGCGACAGCCCGTGCG
14503 ATG
1 ATG
14506 TCCCATGCGT
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.11, C:0.28, G:0.40, T:0.21
Consensus pattern (42 bp):
ATGGCCGATTGTGGCCCGATGGCCCATGCGACAGCCCGTGCG
Found at i:14912 original size:44 final size:42
Alignment explanation
Indices: 14791--14914 Score: 142
Period size: 41 Copynumber: 2.9 Consensus size: 42
14781 TTTGCCATAT
* * * *
14791 AGAAATTGCCCTTGCGTTATAATTGTGTTTAGGGACTTTAGT
1 AGAAATTGCCCCTGTGTTATAATTGTGTTTGGGGACTTTAGA
* * * *
14833 ATAAA-TGCCTCTGTGTTATAAATGTGTTTGAGGACTTTAGAA
1 AGAAATTGCCCCTGTGTTATAATTGTGTTTGGGGACTTTAG-A
*
14875 AGAGAATTGCCCCTGTGTTATAATTGTGCTTGGGGACTTT
1 AGA-AATTGCCCCTGTGTTATAATTGTGTTTGGGGACTTT
14915 GGGGGGAGAG
Statistics
Matches: 66, Mismatches: 13, Indels: 4
0.80 0.16 0.05
Matches are distributed among these distances:
41 29 0.44
42 6 0.09
43 2 0.03
44 29 0.44
ACGTcount: A:0.25, C:0.12, G:0.24, T:0.39
Consensus pattern (42 bp):
AGAAATTGCCCCTGTGTTATAATTGTGTTTGGGGACTTTAGA
Found at i:18104 original size:41 final size:41
Alignment explanation
Indices: 18032--18361 Score: 211
Period size: 41 Copynumber: 8.1 Consensus size: 41
18022 GTTTTATCAC
* * *
18032 CTTTGAGAAATTGCC-CT-TGTGT-TACATGTGCTTAG-GGA
1 CTTTGAGATATTGCCTCTGTGT-TATAAATGTGCTTGGAGGA
* *
18070 CTTTGATATATATTCCTCTGTGTTATAAATGTGCTT-GAGGA
1 CTTTGAGATAT-TGCCTCTGTGTTATAAATGTGCTTGGAGGA
* * * **
18111 CTTTAGAGAGAGTTGCCCCTGTGTTATAATTGTTTTTGG-GGA
1 CTTT-GAGATA-TTGCCTCTGTGTTATAAATGTGCTTGGAGGA
* * * *
18153 TTTTGATATAGATGCCTCTGTGTTATAAATGTG-TTTGAGGA
1 CTTTGAGATA-TTGCCTCTGTGTTATAAATGTGCTTGGAGGA
* * * *
18194 CTTTCGAGAGAGTTGCC-CTATGTTATAATTGTGTTTGG-GGA
1 CTTT-GAGATA-TTGCCTCTGTGTTATAAATGTGCTTGGAGGA
* * *
18235 CTTTGATATAGGTT-TCTCTGTGTTATAAATGTG-TTTGAGGA
1 CTTTGAGATA--TTGCCTCTGTGTTATAAATGTGCTTGGAGGA
* * *
18276 CTTTGAGAGAGTTGCC-CATGTGTTATAATTGTGTTTGG-GGA
1 CTTTGAGATA-TTGCCTC-TGTGTTATAAATGTGCTTGGAGGA
* * *
18317 CTTTGACATAGATGCCTCTATGTTATAAATGTGCTT-GAGGA
1 CTTTGAGATA-TTGCCTCTGTGTTATAAATGTGCTTGGAGGA
18358 CTTT
1 CTTT
18362 TGAAGAGAAT
Statistics
Matches: 230, Mismatches: 43, Indels: 35
0.75 0.14 0.11
Matches are distributed among these distances:
38 9 0.04
39 3 0.01
40 20 0.09
41 151 0.66
42 45 0.20
43 2 0.01
ACGTcount: A:0.22, C:0.12, G:0.25, T:0.41
Consensus pattern (41 bp):
CTTTGAGATATTGCCTCTGTGTTATAAATGTGCTTGGAGGA
Found at i:18262 original size:82 final size:81
Alignment explanation
Indices: 18032--18361 Score: 450
Period size: 82 Copynumber: 4.0 Consensus size: 81
18022 GTTTTATCAC
* * * * * *
18032 CTTTGAGA-AATTGCCCTTGTGTTA-CA-TGTGCTTAGGGACTTTGATATATATTCCTCTGTGTT
1 CTTTGAGAGAGTTGCCC-TGTGTTATAATTGTGTTTGGGGACTTTGATATAGATGCCTCTGTGTT
18094 ATAAATGTGCTTGAGGA
65 ATAAATGTGCTTGAGGA
* *
18111 CTTTAGAGAGAGTTGCCCCTGTGTTATAATTGTTTTTGGGGATTTTGATATAGATGCCTCTGTGT
1 CTTT-GAGAGAGTTG-CCCTGTGTTATAATTGTGTTTGGGGACTTTGATATAGATGCCTCTGTGT
*
18176 TATAAATGTGTTTGAGGA
64 TATAAATGTGCTTGAGGA
* * **
18194 CTTTCGAGAGAGTTGCCCTATGTTATAATTGTGTTTGGGGACTTTGATATAGGTTTCTCTGTGTT
1 CTTT-GAGAGAGTTGCCCTGTGTTATAATTGTGTTTGGGGACTTTGATATAGATGCCTCTGTGTT
*
18259 ATAAATGTGTTTGAGGA
65 ATAAATGTGCTTGAGGA
* *
18276 CTTTGAGAGAGTTGCCCATGTGTTATAATTGTGTTTGGGGACTTTGACATAGATGCCTCTATGTT
1 CTTTGAGAGAGTTGCCC-TGTGTTATAATTGTGTTTGGGGACTTTGATATAGATGCCTCTGTGTT
18341 ATAAATGTGCTTGAGGA
65 ATAAATGTGCTTGAGGA
18358 CTTT
1 CTTT
18362 TGAAGAGAAT
Statistics
Matches: 222, Mismatches: 23, Indels: 9
0.87 0.09 0.04
Matches are distributed among these distances:
79 4 0.02
80 4 0.02
81 24 0.11
82 130 0.59
83 60 0.27
ACGTcount: A:0.22, C:0.12, G:0.25, T:0.41
Consensus pattern (81 bp):
CTTTGAGAGAGTTGCCCTGTGTTATAATTGTGTTTGGGGACTTTGATATAGATGCCTCTGTGTTA
TAAATGTGCTTGAGGA
Found at i:18309 original size:123 final size:123
Alignment explanation
Indices: 18084--18361 Score: 319
Period size: 123 Copynumber: 2.3 Consensus size: 123
18074 GATATATATT
* * * * * * *
18084 CCTCTGTGTTATAAATGTGCTTGAGGACTTT-AGAGAGAGTTGCCCCTGTGTTATAATTGTTTTT
1 CCTCTATGTTATAAATGTGCTTGAGGACTTTGATATAG-GTT-TCTCTGTGTTATAAATGTGTTT
* * * * * *
18148 GGGGATTTTGATATAGATGCCTCTGTGTTATAAATGTGTTTGAGGACTTTCGAGAGAGTTG
64 GAGGACTTTGAGAGAGATGCCTCTGTGTTATAAATGTGTTTGAGGACTTT-GACAGAGATG
* * *
18209 CC-CTATGTTATAATTGTGTTTGGGGACTTTGATATAGGTTTCTCTGTGTTATAAATGTGTTTGA
1 CCTCTATGTTATAAATGTGCTTGAGGACTTTGATATAGGTTTCTCTGTGTTATAAATGTGTTTGA
* * * *
18273 GGACTTTGAGAGAGTTGCC-CATGTGTTATAATTGTGTTTGGGGACTTTGACATAGATG
66 GGACTTTGAGAGAGATGCCTC-TGTGTTATAAATGTGTTTGAGGACTTTGACAGAGATG
18331 CCTCTATGTTATAAATGTGCTTGAGGACTTT
1 CCTCTATGTTATAAATGTGCTTGAGGACTTT
18362 TGAAGAGAAT
Statistics
Matches: 127, Mismatches: 23, Indels: 8
0.80 0.15 0.05
Matches are distributed among these distances:
122 10 0.08
123 84 0.66
124 27 0.21
125 6 0.05
ACGTcount: A:0.22, C:0.11, G:0.26, T:0.41
Consensus pattern (123 bp):
CCTCTATGTTATAAATGTGCTTGAGGACTTTGATATAGGTTTCTCTGTGTTATAAATGTGTTTGA
GGACTTTGAGAGAGATGCCTCTGTGTTATAAATGTGTTTGAGGACTTTGACAGAGATG
Found at i:19076 original size:35 final size:35
Alignment explanation
Indices: 18993--19085 Score: 114
Period size: 35 Copynumber: 2.7 Consensus size: 35
18983 AGCCCTAAGC
* *
18993 GTTGAATGATGAAAGAGTTGGTGGAATACCCAACT
1 GTTGAATGATGAAGGGGTTGGTGGAATACCCAACT
* * ** *
19028 GTTGAATGATGAAGGGGTTGTTGGAGTTTCCAAGT
1 GTTGAATGATGAAGGGGTTGGTGGAATACCCAACT
*
19063 GTTGAATGATGAAGGGGTCGGTG
1 GTTGAATGATGAAGGGGTTGGTG
19086 CAGCCCCTAG
Statistics
Matches: 49, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 49 1.00
ACGTcount: A:0.27, C:0.08, G:0.37, T:0.29
Consensus pattern (35 bp):
GTTGAATGATGAAGGGGTTGGTGGAATACCCAACT
Found at i:19925 original size:209 final size:209
Alignment explanation
Indices: 19565--19990 Score: 843
Period size: 209 Copynumber: 2.0 Consensus size: 209
19555 TTCCTGTCGT
19565 GAGGAGATCAGCATTCTCGCTATAGACTGAAGGTGGAATAGTTAAACTTGTTGTTGTAGGGAGAC
1 GAGGAGATCAGCATTCTCGCTATAGACTGAAGGTGGAATAGTTAAACTTGTTGTTGTAGGGAGAC
19630 CATAAGAGCTGGTCTTAGAAGCAAACGTATGTAGATGCTTTGATTGATGCTTATGAGCTTGAATA
66 CATAAGAGCTGGTCTTAGAAGCAAACGTATGTAGATGCTTTGATTGATGCTTATGAGCTTGAATA
19695 GCGTGGCTGGATGCTTTTTACGTAGCGGGATGCGCTTTACTGCCTTTTCTGCGATAGGATGTTGC
131 GCGTGGCTGGATGCTTTTTACGTAGCGGGATGCGCTTTACTGCCTTTTCTGCGATAGGATGTTGC
19760 TTGACATGCGGTAG
196 TTGACATGCGGTAG
19774 GAGGAGATCAGCATTCTCGCTATAGACTGAAGGTGGAATAGTTAAACTTGTTGTTGTAGGGAGAC
1 GAGGAGATCAGCATTCTCGCTATAGACTGAAGGTGGAATAGTTAAACTTGTTGTTGTAGGGAGAC
19839 CATAAGAGCTGGTCTTAGAAGCAAACGTATGTAGATGCTTTGATTGATGCTTATGAGCTTGAATA
66 CATAAGAGCTGGTCTTAGAAGCAAACGTATGTAGATGCTTTGATTGATGCTTATGAGCTTGAATA
19904 GCGTGGCTGGATGCTTTTTACGTAGCGGGATGCGCTTTACTGCCTTTTCTGCGATAGGATGTTGC
131 GCGTGGCTGGATGCTTTTTACGTAGCGGGATGCGCTTTACTGCCTTTTCTGCGATAGGATGTTGC
19969 TTGACATGCGGTAG
196 TTGACATGCGGTAG
*
19983 GATGAGAT
1 GAGGAGAT
19991 AAGAAAATTT
Statistics
Matches: 216, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
209 216 1.00
ACGTcount: A:0.24, C:0.15, G:0.30, T:0.31
Consensus pattern (209 bp):
GAGGAGATCAGCATTCTCGCTATAGACTGAAGGTGGAATAGTTAAACTTGTTGTTGTAGGGAGAC
CATAAGAGCTGGTCTTAGAAGCAAACGTATGTAGATGCTTTGATTGATGCTTATGAGCTTGAATA
GCGTGGCTGGATGCTTTTTACGTAGCGGGATGCGCTTTACTGCCTTTTCTGCGATAGGATGTTGC
TTGACATGCGGTAG
Found at i:24721 original size:21 final size:21
Alignment explanation
Indices: 24687--24736 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
24677 ACAAGTAACT
*
24687 AAGAAAAATAAAAATAAACAAA
1 AAGAAAAA-GAAAATAAACAAA
* * *
24709 AATAAAAAGAAAATTAACGAA
1 AAGAAAAAGAAAATAAACAAA
24730 AAGAAAA
1 AAGAAAA
24737 GATAAAGGTA
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
21 16 0.70
22 7 0.30
ACGTcount: A:0.78, C:0.04, G:0.08, T:0.10
Consensus pattern (21 bp):
AAGAAAAAGAAAATAAACAAA
Found at i:27392 original size:30 final size:31
Alignment explanation
Indices: 27342--27410 Score: 86
Period size: 30 Copynumber: 2.3 Consensus size: 31
27332 GCCGCTAAAT
*
27342 TCAATTCAGGATACACCGTTA-CCACTTGTG
1 TCAATTCAGGATACAACGTTATCCACTTGTG
* * * *
27372 TTAATTCAGGATATAACGTTATCGATTTGTG
1 TCAATTCAGGATACAACGTTATCCACTTGTG
27403 TCAATTCA
1 TCAATTCA
27411 AGCAAAAACG
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
30 18 0.56
31 14 0.44
ACGTcount: A:0.29, C:0.19, G:0.16, T:0.36
Consensus pattern (31 bp):
TCAATTCAGGATACAACGTTATCCACTTGTG
Found at i:28057 original size:32 final size:32
Alignment explanation
Indices: 27986--28057 Score: 83
Period size: 32 Copynumber: 2.2 Consensus size: 32
27976 AATCACCCTT
* * **
27986 AGAAAGGAAAAAGGGAAGAAAGGTAATCCATT
1 AGAAAGGAAAAAGGGAAGAAAGGAAATACAGA
28018 AGAAAGGAAAAA-GGAAGAAAGGAAATAACAGA
1 AGAAAGGAAAAAGGGAAGAAAGGAAAT-ACAGA
*
28050 AGCAAGGA
1 AGAAAGGA
28058 GATGATTATT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
31 13 0.38
32 21 0.62
ACGTcount: A:0.58, C:0.06, G:0.29, T:0.07
Consensus pattern (32 bp):
AGAAAGGAAAAAGGGAAGAAAGGAAATACAGA
Found at i:29497 original size:3 final size:3
Alignment explanation
Indices: 29489--29528 Score: 71
Period size: 3 Copynumber: 13.3 Consensus size: 3
29479 GTTACTAACC
*
29489 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA CTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
29529 AGAGTGACAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:36855 original size:30 final size:30
Alignment explanation
Indices: 36815--36878 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 30
36805 AGGATCCATC
* *
36815 GGCCGCTTGTGGCCGGTTGCCCCATGCGAT
1 GGCCGCTTGTGGCCAGTTGCCCCATCCGAT
* *
36845 GGCCGGTTGTGGCCAGTTGCTCCATCCGAT
1 GGCCGCTTGTGGCCAGTTGCCCCATCCGAT
36875 GGCC
1 GGCC
36879 CATGCGATGG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.08, C:0.33, G:0.36, T:0.23
Consensus pattern (30 bp):
GGCCGCTTGTGGCCAGTTGCCCCATCCGAT
Found at i:36899 original size:14 final size:14
Alignment explanation
Indices: 36880--36907 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
36870 CCGATGGCCC
36880 ATGCGATGGCCGGT
1 ATGCGATGGCCGGT
36894 ATGCGATGGCCGGT
1 ATGCGATGGCCGGT
36908 TGTGGCCGGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.21, G:0.43, T:0.21
Consensus pattern (14 bp):
ATGCGATGGCCGGT
Done.