Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012340.1 Corchorus capsularis cultivar CVL-1 contig12361, 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: 19530
ACGTcount: A:0.28, C:0.16, G:0.20, T:0.36
Found at i:5648 original size:17 final size:17
Alignment explanation
Indices: 5600--5654 Score: 65
Period size: 17 Copynumber: 3.1 Consensus size: 17
5590 GAAACGATGG
5600 CCTTCTCTTTTTCTTCT
1 CCTTCTCTTTTTCTTCT
*
5617 TCTTCGTCCTCTTTTCTTCT
1 CCTTC-T-CT-TTTTCTTCT
*
5637 CCTTCTCTTTTTCCTCT
1 CCTTCTCTTTTTCTTCT
5654 C
1 C
5655 ATGTGTTTCT
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
17 13 0.41
18 3 0.09
19 3 0.09
20 13 0.41
ACGTcount: A:0.00, C:0.38, G:0.02, T:0.60
Consensus pattern (17 bp):
CCTTCTCTTTTTCTTCT
Found at i:13453 original size:12 final size:12
Alignment explanation
Indices: 13435--13464 Score: 51
Period size: 12 Copynumber: 2.4 Consensus size: 12
13425 TATACCGAAA
13435 AAAAAAAATAAAT
1 AAAAAAAA-AAAT
13448 AAAAAAAAAAAT
1 AAAAAAAAAAAT
13460 AAAAA
1 AAAAA
13465 GAAGAAGAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 9 0.53
13 8 0.47
ACGTcount: A:0.90, C:0.00, G:0.00, T:0.10
Consensus pattern (12 bp):
AAAAAAAAAAAT
Found at i:13453 original size:16 final size:16
Alignment explanation
Indices: 13432--13462 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
13422 TCTTATACCG
13432 AAAAAAAAAAATAAAT
1 AAAAAAAAAAATAAAT
13448 AAAAAAAAAAATAAA
1 AAAAAAAAAAATAAA
13463 AAGAAGAAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.90, C:0.00, G:0.00, T:0.10
Consensus pattern (16 bp):
AAAAAAAAAAATAAAT
Found at i:13469 original size:3 final size:3
Alignment explanation
Indices: 13463--13494 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
13453 AAAAAATAAA
13463 AAG AAG AAG AAG AAG AAG AAG AAG AA- AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
13495 TTGACTGTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 26 0.93
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:15361 original size:11 final size:11
Alignment explanation
Indices: 15345--15388 Score: 52
Period size: 11 Copynumber: 3.9 Consensus size: 11
15335 AAGATGGGGG
15345 TGAAGGAAAAA
1 TGAAGGAAAAA
15356 TGAAGGAAAAA
1 TGAAGGAAAAA
** *
15367 AAAATGAAAAA
1 TGAAGGAAAAA
15378 TGGAAGGAAAA
1 T-GAAGGAAAA
15389 TTGTGCAAAT
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
11 19 0.73
12 7 0.27
ACGTcount: A:0.66, C:0.00, G:0.25, T:0.09
Consensus pattern (11 bp):
TGAAGGAAAAA
Found at i:19501 original size:55 final size:55
Alignment explanation
Indices: 19417--19525 Score: 218
Period size: 55 Copynumber: 2.0 Consensus size: 55
19407 TTGTTGGCAC
19417 TTCCTGTTGATTATTGAGAATAGTTATAAAATATTAAATACTTGACTGAGGGGAT
1 TTCCTGTTGATTATTGAGAATAGTTATAAAATATTAAATACTTGACTGAGGGGAT
19472 TTCCTGTTGATTATTGAGAATAGTTATAAAATATTAAATACTTGACTGAGGGGA
1 TTCCTGTTGATTATTGAGAATAGTTATAAAATATTAAATACTTGACTGAGGGGA
19526 GGGGG
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 54 1.00
ACGTcount: A:0.35, C:0.07, G:0.20, T:0.38
Consensus pattern (55 bp):
TTCCTGTTGATTATTGAGAATAGTTATAAAATATTAAATACTTGACTGAGGGGAT
Done.