Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015486.1 Corchorus capsularis cultivar CVL-1 contig15507, 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: 71111
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:567 original size:17 final size:20
Alignment explanation
Indices: 545--595 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 20
535 AAAGCTGAAG
545 TTATAACCTTA-A-TT-TTT
1 TTATAACCTTATAGTTATTT
562 TTATAACCTCTATAGTTATTT
1 TTATAACCT-TATAGTTATTT
583 TTAGTAACCTTAT
1 TTA-TAACCTTAT
596 TAGATGTGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
17 9 0.31
18 2 0.07
19 1 0.03
20 2 0.07
21 9 0.31
22 6 0.21
ACGTcount: A:0.29, C:0.14, G:0.04, T:0.53
Consensus pattern (20 bp):
TTATAACCTTATAGTTATTT
Found at i:13073 original size:29 final size:29
Alignment explanation
Indices: 13012--13092 Score: 92
Period size: 29 Copynumber: 2.8 Consensus size: 29
13002 GCATCCGACG
* * *
13012 TGGCATGCCACGTATACAAAAAAATGTCACA
1 TGGCATGCCACGTGTAC--AAAAAGGACACA
*
13043 TGGCATGCCATGTGTACAAAAAGGACACA
1 TGGCATGCCACGTGTACAAAAAGGACACA
*
13072 TGACATGCCACGTGTA-AAAAA
1 TGGCATGCCACGTGTACAAAAA
13093 TGCCACGTGT
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
28 5 0.11
29 24 0.55
31 15 0.34
ACGTcount: A:0.41, C:0.21, G:0.20, T:0.19
Consensus pattern (29 bp):
TGGCATGCCACGTGTACAAAAAGGACACA
Found at i:24717 original size:18 final size:18
Alignment explanation
Indices: 24694--24729 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
24684 TTTGGATACA
24694 TTTCATTTAAATTCTTTT
1 TTTCATTTAAATTCTTTT
24712 TTTCATTTAAATTCTTTT
1 TTTCATTTAAATTCTTTT
24730 GATTTGCCCC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.22, C:0.11, G:0.00, T:0.67
Consensus pattern (18 bp):
TTTCATTTAAATTCTTTT
Found at i:24719 original size:23 final size:23
Alignment explanation
Indices: 24658--24719 Score: 61
Period size: 27 Copynumber: 2.5 Consensus size: 23
24648 TTGGTAACCA
* * *
24658 TTTTTTGCCTTTCATTTAAATTT
1 TTTTTTTCATTTCATTTAAATTC
24681 TTTTTTGGATACATTTCATTTAAATTC
1 TTTTTT---T-CATTTCATTTAAATTC
24708 TTTTTTTCATTT
1 TTTTTTTCATTT
24720 AAATTCTTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
23 11 0.34
24 1 0.03
27 20 0.62
ACGTcount: A:0.19, C:0.11, G:0.05, T:0.65
Consensus pattern (23 bp):
TTTTTTTCATTTCATTTAAATTC
Found at i:27110 original size:24 final size:24
Alignment explanation
Indices: 27042--27110 Score: 95
Period size: 24 Copynumber: 2.9 Consensus size: 24
27032 ATTTAGACCG
*
27042 ATAAAATTACTTAATTCTAAAGAA
1 ATAAAATTACTTAATTCTTAAGAA
*
27066 ATAAAATTACTTAATTTTTAAGAA
1 ATAAAATTACTTAATTCTTAAGAA
*
27090 ATAAAATTGCTT-ATTACTTAA
1 ATAAAATTACTTAATT-CTTAA
27111 TTCTAAAGCG
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
23 3 0.08
24 37 0.93
ACGTcount: A:0.49, C:0.07, G:0.04, T:0.39
Consensus pattern (24 bp):
ATAAAATTACTTAATTCTTAAGAA
Found at i:53180 original size:1 final size:1
Alignment explanation
Indices: 53174--53211 Score: 76
Period size: 1 Copynumber: 38.0 Consensus size: 1
53164 TTGATCCATC
53174 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
53212 GGAGGGATTC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 37 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:55467 original size:15 final size:16
Alignment explanation
Indices: 55437--55469 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
55427 TTCTCATAAT
55437 TTAATTTCCCCCTTAA
1 TTAATTTCCCCCTTAA
*
55453 TTAATTT-CTCCTTAA
1 TTAATTTCCCCCTTAA
55468 TT
1 TT
55470 TCGATTTTGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.24, C:0.24, G:0.00, T:0.52
Consensus pattern (16 bp):
TTAATTTCCCCCTTAA
Found at i:59195 original size:39 final size:39
Alignment explanation
Indices: 59121--59197 Score: 100
Period size: 39 Copynumber: 2.0 Consensus size: 39
59111 TAGATGTTTG
* *
59121 GGCATATGAAGATTTATTTTGATTGTAACGAGATTTCAT
1 GGCATATGAAGATTTATTCTAATTGTAACGAGATTTCAT
* * * *
59160 GGCATATGGAGATTTATTCTAATTTTAATGCGATTTCA
1 GGCATATGAAGATTTATTCTAATTGTAACGAGATTTCA
59198 CTTGTACAAC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
39 32 1.00
ACGTcount: A:0.30, C:0.09, G:0.19, T:0.42
Consensus pattern (39 bp):
GGCATATGAAGATTTATTCTAATTGTAACGAGATTTCAT
Found at i:69253 original size:69 final size:68
Alignment explanation
Indices: 69141--69278 Score: 258
Period size: 69 Copynumber: 2.0 Consensus size: 68
69131 GGGGAAAAGC
*
69141 TACCCCTCTTCCATCAGCTGGGGGAACACGGAATACTTCATATTCGACATCCAGGTCACAACCCA
1 TACCCCTCTTCCATCAGCTGGGGGAACACAGAATACTTCATATTCGACATCCAGGTCACAACCCA
69206 TCT
66 TCT
69209 TACCCCTCTTCCATCAGCTGGGGGGAACACAGAATACTTCATATTCGACATCCAGGTCACAACCC
1 TACCCCTCTTCCATCAGCT-GGGGGAACACAGAATACTTCATATTCGACATCCAGGTCACAACCC
69274 ATCT
65 ATCT
69278 T
1 T
69279 TGATAATTTG
Statistics
Matches: 68, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
68 19 0.28
69 49 0.72
ACGTcount: A:0.27, C:0.33, G:0.16, T:0.24
Consensus pattern (68 bp):
TACCCCTCTTCCATCAGCTGGGGGAACACAGAATACTTCATATTCGACATCCAGGTCACAACCCA
TCT
Done.