Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007554.1 Corchorus capsularis cultivar CVL-1 contig07575, 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: 15887
ACGTcount: A:0.35, C:0.14, G:0.15, T:0.36
Found at i:1378 original size:2 final size:2
Alignment explanation
Indices: 1367--1410 Score: 72
Period size: 2 Copynumber: 22.5 Consensus size: 2
1357 TATATATATA
*
1367 TG TG TA TG TG TG TG TG TG TG TG TG T- TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1408 TG T
1 TG T
1411 ATATATATAT
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.02, C:0.00, G:0.45, T:0.52
Consensus pattern (2 bp):
TG
Found at i:1397 original size:17 final size:17
Alignment explanation
Indices: 1375--1408 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
1365 TATGTGTATG
1375 TGTGTGTGTGTGTGTGT
1 TGTGTGTGTGTGTGTGT
1392 TGTGTGTGTGTGTGTGT
1 TGTGTGTGTGTGTGTGT
1409 GTATATATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.00, C:0.00, G:0.47, T:0.53
Consensus pattern (17 bp):
TGTGTGTGTGTGTGTGT
Found at i:1968 original size:15 final size:15
Alignment explanation
Indices: 1948--1980 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
1938 TAGTAAATAT
1948 AATAAAAA-AACACAA
1 AATAAAAATAAC-CAA
1963 AATAAAAATAACCAA
1 AATAAAAATAACCAA
1978 AAT
1 AAT
1981 TTAAAATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 14 0.82
16 3 0.18
ACGTcount: A:0.76, C:0.12, G:0.00, T:0.12
Consensus pattern (15 bp):
AATAAAAATAACCAA
Found at i:5994 original size:6 final size:6
Alignment explanation
Indices: 5983--6026 Score: 81
Period size: 6 Copynumber: 7.5 Consensus size: 6
5973 GTTTAGACTT
5983 ATAAAG ATAAAG A-AAAG ATAAAG ATAAAG ATAAAG ATAAAG ATA
1 ATAAAG ATAAAG ATAAAG ATAAAG ATAAAG ATAAAG ATAAAG ATA
6027 TATATATTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
5 5 0.14
6 32 0.86
ACGTcount: A:0.68, C:0.00, G:0.16, T:0.16
Consensus pattern (6 bp):
ATAAAG
Found at i:6287 original size:23 final size:25
Alignment explanation
Indices: 6242--6292 Score: 77
Period size: 27 Copynumber: 2.0 Consensus size: 25
6232 TGAGAAAGCA
6242 TTGATTGAGATTCCTTATATATATTTT
1 TTGATTGAGATTCC-T-TATATATTTT
6269 TTGATTGAGATTCCTTATAT-TTTT
1 TTGATTGAGATTCCTTATATATTTT
6293 ATTGTCTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
24 4 0.17
25 5 0.21
26 1 0.04
27 14 0.58
ACGTcount: A:0.24, C:0.08, G:0.12, T:0.57
Consensus pattern (25 bp):
TTGATTGAGATTCCTTATATATTTT
Found at i:8728 original size:17 final size:16
Alignment explanation
Indices: 8714--8749 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 16
8704 AGAGTTTTGT
8714 TTTATTTTATTTTTTTC
1 TTTATTTT-TTTTTTTC
8731 TTTATTTTTTTTTCTTC
1 TTTATTTTTTTTT-TTC
8748 TT
1 TT
8750 CTAGATTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 5 0.28
17 13 0.72
ACGTcount: A:0.08, C:0.08, G:0.00, T:0.83
Consensus pattern (16 bp):
TTTATTTTTTTTTTTC
Done.