Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01000250.1 Corchorus olitorius cultivar O-4 contig00250, 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, 712
Length: 1188
ACGTcount: A:0.30, C:0.21, G:0.14, T:0.34
Found at i:425 original size:17 final size:15
Alignment explanation
Indices: 403--445 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 15
393 AAAATTCTTA
403 TTTTCTTTATTTATTTT
1 TTTTCTTT-TTT-TTTT
420 TTTTCTTCTTTTTTTT
1 TTTTCTT-TTTTTTTT
436 TTCTTCTTTT
1 TT-TTCTTTT
446 CTTCTTTTGG
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
16 8 0.33
17 15 0.62
18 1 0.04
ACGTcount: A:0.05, C:0.12, G:0.00, T:0.84
Consensus pattern (15 bp):
TTTTCTTTTTTTTTT
Found at i:433 original size:11 final size:11
Alignment explanation
Indices: 417--453 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
407 CTTTATTTAT
417 TTTTTTTCTTC
1 TTTTTTTCTTC
*
428 TTTTTTTTTTC
1 TTTTTTTCTTC
*
439 TTCTTTTCTTC
1 TTTTTTTCTTC
450 TTTT
1 TTTT
454 GGGCCAGGCC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (11 bp):
TTTTTTTCTTC
Found at i:433 original size:14 final size:14
Alignment explanation
Indices: 416--445 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
406 TCTTTATTTA
416 TTTTTTTTCTTCTT
1 TTTTTTTTCTTCTT
430 TTTTTTTTCTTCTT
1 TTTTTTTTCTTCTT
444 TT
1 TT
446 CTTCTTTTGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (14 bp):
TTTTTTTTCTTCTT
Found at i:445 original size:8 final size:8
Alignment explanation
Indices: 420--453 Score: 54
Period size: 8 Copynumber: 4.5 Consensus size: 8
410 TATTTATTTT
420 TTTTCTTC
1 TTTTCTTC
428 TTTT-TT-
1 TTTTCTTC
434 TTTTCTTC
1 TTTTCTTC
442 TTTTCTTC
1 TTTTCTTC
450 TTTT
1 TTTT
454 GGGCCAGGCC
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
6 4 0.17
7 4 0.17
8 16 0.67
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (8 bp):
TTTTCTTC
Found at i:614 original size:39 final size:39
Alignment explanation
Indices: 536--639 Score: 140
Period size: 39 Copynumber: 2.7 Consensus size: 39
526 AGCCAGGCCG
* * * * *
536 CTGGGCCTGCGCT-GGCCCACGCGCTTGGCTTGGCGCGC
1 CTGGGCCTGCGATAGGCCCGCGTGCCTGGCTTGGCACGC
574 CTGGGCCTGCGATAGGCCCGCGTGCCTGGCCTT-GCACGC
1 CTGGGCCTGCGATAGGCCCGCGTGCCTGG-CTTGGCACGC
613 CTGGGCCTGCGATAGGCCCGCGTGCCT
1 CTGGGCCTGCGATAGGCCCGCGTGCCT
640 ATGATTTTTT
Statistics
Matches: 59, Mismatches: 5, Indels: 3
0.88 0.07 0.04
Matches are distributed among these distances:
38 12 0.20
39 44 0.75
40 3 0.05
ACGTcount: A:0.06, C:0.38, G:0.38, T:0.18
Consensus pattern (39 bp):
CTGGGCCTGCGATAGGCCCGCGTGCCTGGCTTGGCACGC
Done.