Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009829.1 Corchorus capsularis cultivar CVL-1 contig09850, 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: 39486
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.30
Found at i:862 original size:2 final size:2
Alignment explanation
Indices: 855--886 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
845 CTCGAACAAC
855 TA TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
887 GCTCGCATGA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:10602 original size:3 final size:3
Alignment explanation
Indices: 10594--10621 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
10584 CCAACCGTCA
10594 TCT TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT T
10622 TCACTTGGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:30351 original size:2 final size:2
Alignment explanation
Indices: 30344--30374 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
30334 GCTATTCCTA
30344 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
30375 AGAACATCTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:31565 original size:9 final size:9
Alignment explanation
Indices: 31546--31590 Score: 56
Period size: 9 Copynumber: 4.9 Consensus size: 9
31536 CCTTTATTTA
31546 AAAGCAAAAG
1 AAAG-AAAAG
31556 AAAGAAAAG
1 AAAGAAAAG
31565 AAAGAAAAG
1 AAAGAAAAG
*
31574 -AAGAGAAG
1 AAAGAAAAG
31582 AGAAGAAAA
1 A-AAGAAAA
31591 AACCCAGATC
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
8 7 0.23
9 14 0.45
10 10 0.32
ACGTcount: A:0.73, C:0.02, G:0.24, T:0.00
Consensus pattern (9 bp):
AAAGAAAAG
Found at i:32266 original size:6 final size:6
Alignment explanation
Indices: 32257--32297 Score: 64
Period size: 6 Copynumber: 6.5 Consensus size: 6
32247 TTCTCATTCT
32257 ATTAAA ATTAAA ATTAAAAA ATTAAA ATTAAA ATTAAA ATT
1 ATTAAA ATTAAA ATT--AAA ATTAAA ATTAAA ATTAAA ATT
32298 GGTTTAAATA
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
6 27 0.82
8 6 0.18
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (6 bp):
ATTAAA
Found at i:32282 original size:20 final size:20
Alignment explanation
Indices: 32257--32295 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
32247 TTCTCATTCT
32257 ATTAAAATTAAAATTAAAAA
1 ATTAAAATTAAAATTAAAAA
32277 ATTAAAATTAAAATTAAAA
1 ATTAAAATTAAAATTAAAA
32296 TTGGTTTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (20 bp):
ATTAAAATTAAAATTAAAAA
Found at i:32871 original size:2 final size:2
Alignment explanation
Indices: 32864--32905 Score: 54
Period size: 2 Copynumber: 22.0 Consensus size: 2
32854 CACTTCATTC
32864 AT AT AT AT AT AT AT AT AT AT -T AT AT A- AT A- AT AGT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT
32904 AT
1 AT
32906 GCAAATATGA
Statistics
Matches: 36, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
1 3 0.08
2 31 0.86
3 2 0.06
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Done.