Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015243.1 Corchorus capsularis cultivar CVL-1 contig15264, 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: 27278
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.32
Found at i:512 original size:6 final size:6
Alignment explanation
Indices: 501--549 Score: 50
Period size: 6 Copynumber: 8.2 Consensus size: 6
491 TTCTTGGAAC
501 TGCTTG TGCTTG TGCTTG TGCTTCCTG TGC-T- TG-TTG TGCTTG TGCTTG
1 TGCTTG TGCTTG TGCTTG TGC-T--TG TGCTTG TGCTTG TGCTTG TGCTTG
549 T
1 T
550 ATCAGGGGAA
Statistics
Matches: 37, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
4 3 0.08
5 3 0.08
6 25 0.68
7 1 0.03
9 5 0.14
ACGTcount: A:0.00, C:0.18, G:0.31, T:0.51
Consensus pattern (6 bp):
TGCTTG
Found at i:544 original size:15 final size:15
Alignment explanation
Indices: 504--549 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
494 TTGGAACTGC
504 TTGTGCTTGTGCTTG
1 TTGTGCTTGTGCTTG
* *
519 -TGCTTCCTGTGCTTG
1 TTG-TGCTTGTGCTTG
534 TTGTGCTTGTGCTTG
1 TTGTGCTTGTGCTTG
549 T
1 T
550 ATCAGGGGAA
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
14 2 0.08
15 21 0.84
16 2 0.08
ACGTcount: A:0.00, C:0.17, G:0.30, T:0.52
Consensus pattern (15 bp):
TTGTGCTTGTGCTTG
Found at i:16853 original size:2 final size:2
Alignment explanation
Indices: 16848--16879 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
16838 TATATATATA
16848 TG TG TG TG TG TG TG TG 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
16880 GATGAAGGAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:23083 original size:17 final size:16
Alignment explanation
Indices: 23031--23079 Score: 62
Period size: 17 Copynumber: 2.9 Consensus size: 16
23021 TCACCCCCAT
23031 ATCACTAGTGATCTAAG
1 ATCACTAGTGATC-AAG
*
23048 ATCACCAGTGATGCAAG
1 ATCACTAGTGAT-CAAG
*
23065 ATCACTGGTGATCAA
1 ATCACTAGTGATCAA
23080 AGATTACATG
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
16 3 0.11
17 24 0.86
18 1 0.04
ACGTcount: A:0.35, C:0.20, G:0.20, T:0.24
Consensus pattern (16 bp):
ATCACTAGTGATCAAG
Found at i:26309 original size:28 final size:30
Alignment explanation
Indices: 26246--26307 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 30
26236 TAAAAGTACA
*
26246 AAATTGGTCCCTTAAGTGGAGCAAAAATAGC
1 AAATTGGTCCCTCAAGTGGA-CAAAAATAGC
26277 AAATTGGTCCCTCAAGT-GA-AAAAATATGC
1 AAATTGGTCCCTCAAGTGGACAAAAATA-GC
26306 AA
1 AA
26308 TTTAATCCCA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
28 7 0.24
29 4 0.14
30 2 0.07
31 16 0.55
ACGTcount: A:0.42, C:0.16, G:0.19, T:0.23
Consensus pattern (30 bp):
AAATTGGTCCCTCAAGTGGACAAAAATAGC
Found at i:26613 original size:15 final size:15
Alignment explanation
Indices: 26590--26628 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
26580 AAATAAAAAA
*
26590 TTTCATTTTTCTTCT
1 TTTCTTTTTTCTTCT
26605 TTTCTTTTTTCTTCT
1 TTTCTTTTTTCTTCT
*
26620 GTT-TTTTTT
1 TTTCTTTTTT
26629 AAATCATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 6 0.27
15 16 0.73
ACGTcount: A:0.03, C:0.15, G:0.03, T:0.79
Consensus pattern (15 bp):
TTTCTTTTTTCTTCT
Done.