Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013835.1 Corchorus capsularis cultivar CVL-1 contig13856, 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: 26986
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.31
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:509 original size:15 final size:16
Alignment explanation
Indices: 483--513 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
473 GGGAAAGAAA
483 TAAAATATAAATTATT
1 TAAAATATAAATTATT
499 TAAAA-ATAAATTATT
1 TAAAATATAAATTATT
514 ATATATTCCT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.67
16 5 0.33
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
TAAAATATAAATTATT
Found at i:11826 original size:28 final size:28
Alignment explanation
Indices: 11789--11844 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
11779 TGTCTTTACA
11789 AGTTGAGATTTTTTTTTAATTTCCAAGT
1 AGTTGAGATTTTTTTTTAATTTCCAAGT
*
11817 AGTTGGGATTTTTTTTTAATTTCCAAGT
1 AGTTGAGATTTTTTTTTAATTTCCAAGT
11845 TGGTTTGCAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.23, C:0.07, G:0.16, T:0.54
Consensus pattern (28 bp):
AGTTGAGATTTTTTTTTAATTTCCAAGT
Found at i:11902 original size:23 final size:24
Alignment explanation
Indices: 11871--11927 Score: 73
Period size: 24 Copynumber: 2.4 Consensus size: 24
11861 TTTGTAAAAT
11871 TATTTTTTTGG-TAAT-GGTGTTG
1 TATTTTTTTGGTTAATAGGTGTTG
*
11893 TGATTTTTTTTGGTTCATAGGTGTTG
1 T-A-TTTTTTTGGTTAATAGGTGTTG
11919 TATTTTTTT
1 TATTTTTTT
11928 TTTGTAAATT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
22 1 0.03
23 1 0.03
24 16 0.53
25 4 0.13
26 8 0.27
ACGTcount: A:0.12, C:0.02, G:0.23, T:0.63
Consensus pattern (24 bp):
TATTTTTTTGGTTAATAGGTGTTG
Found at i:11904 original size:24 final size:25
Alignment explanation
Indices: 11873--11928 Score: 80
Period size: 25 Copynumber: 2.3 Consensus size: 25
11863 TGTAAAATTA
11873 TTTTTTTGG-TAAT-GGTGTTGTGAT
1 TTTTTTTGGTTAATAGGTGTTGT-AT
*
11897 TTTTTTTGGTTCATAGGTGTTGTAT
1 TTTTTTTGGTTAATAGGTGTTGTAT
11922 TTTTTTT
1 TTTTTTT
11929 TTGTAAATTT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
24 9 0.31
25 12 0.41
26 8 0.28
ACGTcount: A:0.11, C:0.02, G:0.23, T:0.64
Consensus pattern (25 bp):
TTTTTTTGGTTAATAGGTGTTGTAT
Found at i:12139 original size:20 final size:21
Alignment explanation
Indices: 12114--12155 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
12104 TTATTGTGGA
12114 TTACTAAACACCG-CCCCCTT
1 TTACTAAACACCGTCCCCCTT
**
12134 TTACTAGCCACCGTCCCCCTT
1 TTACTAAACACCGTCCCCCTT
12155 T
1 T
12156 GGACAATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.19, C:0.45, G:0.07, T:0.29
Consensus pattern (21 bp):
TTACTAAACACCGTCCCCCTT
Found at i:12852 original size:130 final size:130
Alignment explanation
Indices: 12670--12926 Score: 514
Period size: 130 Copynumber: 2.0 Consensus size: 130
12660 ACACAACTAC
12670 TTATGCCAAACTTAGCAGCAAAAAAATGTATTTTTCGACCACTATCTTAAGCTTCAATAGCAGCA
1 TTATGCCAAACTTAGCAGCAAAAAAATGTATTTTTCGACCACTATCTTAAGCTTCAATAGCAGCA
12735 CATGATGCAAGAACACTAGTCATTGTGTATCTATCAAATCAAATCACTTTAATCAACAAATCACT
66 CATGATGCAAGAACACTAGTCATTGTGTATCTATCAAATCAAATCACTTTAATCAACAAATCACT
12800 TTATGCCAAACTTAGCAGCAAAAAAATGTATTTTTCGACCACTATCTTAAGCTTCAATAGCAGCA
1 TTATGCCAAACTTAGCAGCAAAAAAATGTATTTTTCGACCACTATCTTAAGCTTCAATAGCAGCA
12865 CATGATGCAAGAACACTAGTCATTGTGTATCTATCAAATCAAATCACTTTAATCAACAAATC
66 CATGATGCAAGAACACTAGTCATTGTGTATCTATCAAATCAAATCACTTTAATCAACAAATC
12927 GCTAATGGTC
Statistics
Matches: 127, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
130 127 1.00
ACGTcount: A:0.39, C:0.21, G:0.11, T:0.29
Consensus pattern (130 bp):
TTATGCCAAACTTAGCAGCAAAAAAATGTATTTTTCGACCACTATCTTAAGCTTCAATAGCAGCA
CATGATGCAAGAACACTAGTCATTGTGTATCTATCAAATCAAATCACTTTAATCAACAAATCACT
Found at i:19649 original size:11 final size:11
Alignment explanation
Indices: 19633--19664 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
19623 GAAGTTCGTG
19633 TTTGAAGATTA
1 TTTGAAGATTA
*
19644 TTTGAAGATAA
1 TTTGAAGATTA
19655 TTTGAAGATT
1 TTTGAAGATT
19665 TGAAGACAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.38, C:0.00, G:0.19, T:0.44
Consensus pattern (11 bp):
TTTGAAGATTA
Found at i:21028 original size:6 final size:6
Alignment explanation
Indices: 21017--21055 Score: 62
Period size: 6 Copynumber: 6.7 Consensus size: 6
21007 ATTAATTTGC
*
21017 TTTAGA TTTAGA TTCAGA TTTAGA TTTAGA TTTA-A TTTA
1 TTTAGA TTTAGA TTTAGA TTTAGA TTTAGA TTTAGA TTTA
21056 CTTTGCTTAG
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
5 5 0.16
6 26 0.84
ACGTcount: A:0.33, C:0.03, G:0.13, T:0.51
Consensus pattern (6 bp):
TTTAGA
Found at i:21093 original size:15 final size:15
Alignment explanation
Indices: 21073--21102 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
21063 TAGTATTTAG
*
21073 TTTAATTGTTTTCTT
1 TTTAATTGCTTTCTT
21088 TTTAATTGCTTTCTT
1 TTTAATTGCTTTCTT
21103 AAAATCCCCT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.13, C:0.10, G:0.07, T:0.70
Consensus pattern (15 bp):
TTTAATTGCTTTCTT
Found at i:21373 original size:17 final size:17
Alignment explanation
Indices: 21351--21387 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
21341 TTTTTCTTAA
21351 AAAAAAAAGTTGCGTCG
1 AAAAAAAAGTTGCGTCG
*
21368 AAAAAAAAGTTGTGTCG
1 AAAAAAAAGTTGCGTCG
21385 AAA
1 AAA
21388 TAAATTTAGG
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:0.51, C:0.08, G:0.22, T:0.19
Consensus pattern (17 bp):
AAAAAAAAGTTGCGTCG
Found at i:25967 original size:11 final size:11
Alignment explanation
Indices: 25951--25982 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
25941 GAAGTTCGTG
25951 TTTGAAGATTA
1 TTTGAAGATTA
*
25962 TTTGAAGATAA
1 TTTGAAGATTA
25973 TTTGAAGATT
1 TTTGAAGATT
25983 TGAAGACAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.38, C:0.00, G:0.19, T:0.44
Consensus pattern (11 bp):
TTTGAAGATTA
Done.