Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009868.1 Corchorus capsularis cultivar CVL-1 contig09889, 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: 42399
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:15229 original size:1 final size:1
Alignment explanation
Indices: 15223--15265 Score: 86
Period size: 1 Copynumber: 43.0 Consensus size: 1
15213 GAGAAACTTT
15223 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
15266 CAGTTTTCAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 42 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:16351 original size:2 final size:2
Alignment explanation
Indices: 16346--16378 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
16336 TACATATATT
16346 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
16379 ATTTGAGCTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:18316 original size:21 final size:21
Alignment explanation
Indices: 18292--18337 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
18282 GAGAGGCTGT
*
18292 TGGAACAGATGCGCCCATCTG
1 TGGAACAGATGCACCCATCTG
* * *
18313 TGGAGCAGATGTACCGATCTG
1 TGGAACAGATGCACCCATCTG
18334 TGGA
1 TGGA
18338 GTAGATATGG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.24, C:0.22, G:0.33, T:0.22
Consensus pattern (21 bp):
TGGAACAGATGCACCCATCTG
Found at i:32187 original size:42 final size:42
Alignment explanation
Indices: 32128--32209 Score: 146
Period size: 42 Copynumber: 2.0 Consensus size: 42
32118 AAGATGATCC
* *
32128 CATATCTCACCTAGTGGGTCAGTTCCACTTAATAATTTTTCG
1 CATATCTCACCTAGTGGGGCAGTTCCACCTAATAATTTTTCG
32170 CATATCTCACCTAGTGGGGCAGTTCCACCTAATAATTTTT
1 CATATCTCACCTAGTGGGGCAGTTCCACCTAATAATTTTT
32210 AGGAGATGAT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.24, C:0.24, G:0.15, T:0.37
Consensus pattern (42 bp):
CATATCTCACCTAGTGGGGCAGTTCCACCTAATAATTTTTCG
Found at i:32462 original size:7 final size:7
Alignment explanation
Indices: 32445--32486 Score: 77
Period size: 7 Copynumber: 6.1 Consensus size: 7
32435 ATCAATAGTT
32445 TTAAA-A
1 TTAAACA
32451 TTAAACA
1 TTAAACA
32458 TTAAACA
1 TTAAACA
32465 TTAAACA
1 TTAAACA
32472 TTAAACA
1 TTAAACA
32479 TTAAACA
1 TTAAACA
32486 T
1 T
32487 ACTCTTATTT
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 5 0.14
7 30 0.86
ACGTcount: A:0.57, C:0.12, G:0.00, T:0.31
Consensus pattern (7 bp):
TTAAACA
Found at i:35446 original size:16 final size:16
Alignment explanation
Indices: 35421--35458 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
35411 TAATCAAGCC
35421 AAAA-AAAGAAAAAGA
1 AAAAGAAAGAAAAAGA
35436 AAAAGAAAGAAAAAGA
1 AAAAGAAAGAAAAAGA
35452 ACAAAGA
1 A-AAAGA
35459 TTTTGCCTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 4 0.19
16 12 0.57
17 5 0.24
ACGTcount: A:0.82, C:0.03, G:0.16, T:0.00
Consensus pattern (16 bp):
AAAAGAAAGAAAAAGA
Found at i:39312 original size:20 final size:21
Alignment explanation
Indices: 39276--39316 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
39266 AGTGGGTAAA
*
39276 ATTAACGGTGTTAAGTAATTT
1 ATTAACGGTGCTAAGTAATTT
39297 ATTAACGG-GCTAAGTAATTT
1 ATTAACGGTGCTAAGTAATTT
39317 GCTAATGGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.34, C:0.07, G:0.20, T:0.39
Consensus pattern (21 bp):
ATTAACGGTGCTAAGTAATTT
Done.