Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016513.1 Corchorus capsularis cultivar CVL-1 contig16534, 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: 2186
ACGTcount: A:0.30, C:0.21, G:0.15, T:0.35
Found at i:676 original size:6 final size:6
Alignment explanation
Indices: 667--719 Score: 56
Period size: 6 Copynumber: 8.8 Consensus size: 6
657 TTTTTTCCTT
* *
667 TTTTTG TTTTTG TTTTTTG TTTTT- TGTTTTG -TTTTG TTTTTC TTTTTC
1 TTTTTG TTTTTG -TTTTTG TTTTTG T-TTTTG TTTTTG TTTTTG TTTTTG
715 TTTTT
1 TTTTT
720 CTCTTTTTTT
Statistics
Matches: 42, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
5 6 0.14
6 30 0.71
7 6 0.14
ACGTcount: A:0.00, C:0.04, G:0.11, T:0.85
Consensus pattern (6 bp):
TTTTTG
Found at i:691 original size:30 final size:28
Alignment explanation
Indices: 648--729 Score: 85
Period size: 29 Copynumber: 2.9 Consensus size: 28
638 ACCAAATTTA
* *
648 TTTTTTCTCTTTTTTCCTTTTTTTGTTT
1 TTTTTTTTCTTTTTTTCTTTTTTTGTTT
*
676 TTGTTTTTTGTTTTTTGT-TTTGTTTTGTTT
1 TT-TTTTTTCTTTTTT-TCTTT-TTTTGTTT
* *
706 TTCTTTTTCTTTTTCTCTTTTTTT
1 TTTTTTTTCTTTTTTTCTTTTTTT
730 TATTAATATA
Statistics
Matches: 44, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
28 7 0.16
29 27 0.61
30 10 0.23
ACGTcount: A:0.00, C:0.10, G:0.07, T:0.83
Consensus pattern (28 bp):
TTTTTTTTCTTTTTTTCTTTTTTTGTTT
Found at i:726 original size:8 final size:7
Alignment explanation
Indices: 649--728 Score: 56
Period size: 7 Copynumber: 10.9 Consensus size: 7
639 CCAAATTTAT
649 TTTTTCTC
1 TTTTT-TC
657 TTTTTTCC
1 TTTTTT-C
665 TTTTTT-
1 TTTTTTC
*
671 TGTTTTTG
1 T-TTTTTC
*
679 TTTTTTG
1 TTTTTTC
*
686 TTTTTTG
1 TTTTTTC
*
693 TTTTGTTT
1 TTTT-TTC
701 TGTTTTTC
1 T-TTTTTC
709 -TTTTTC
1 TTTTTTC
715 TTTTTCTC
1 TTTTT-TC
723 TTTTTT
1 TTTTTT
729 TTATTAATAT
Statistics
Matches: 63, Mismatches: 2, Indels: 15
0.79 0.03 0.19
Matches are distributed among these distances:
6 7 0.11
7 28 0.44
8 25 0.40
9 3 0.05
ACGTcount: A:0.00, C:0.10, G:0.07, T:0.82
Consensus pattern (7 bp):
TTTTTTC
Found at i:1275 original size:19 final size:18
Alignment explanation
Indices: 1251--1298 Score: 62
Period size: 17 Copynumber: 2.7 Consensus size: 18
1241 AAACTGATCA
*
1251 CCGCCGGCCACCACTTCCG
1 CCGCCGGCCACC-CTACCG
1270 CCGCCGGCCA-CCTACCG
1 CCGCCGGCCACCCTACCG
*
1287 CCGCCGGTCACC
1 CCGCCGGCCACC
1299 GCCACTGCCG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
17 14 0.54
18 2 0.08
19 10 0.38
ACGTcount: A:0.10, C:0.58, G:0.23, T:0.08
Consensus pattern (18 bp):
CCGCCGGCCACCCTACCG
Found at i:1841 original size:52 final size:52
Alignment explanation
Indices: 1763--1897 Score: 220
Period size: 50 Copynumber: 2.6 Consensus size: 52
1753 TGTTAATGCA
1763 TGTATTTGCTTGATCTTCTCTCTGACTTGAAAATCTAGGCTCATCATTTTAC
1 TGTATTTGCTTGATCTTCTCTCTGACTTGAAAATCTAGGCTCATCATTTTAC
* *
1815 TGTATTTGCTTGATCTTCCCTCTGACTTG--AATGTAGGCTCATCATTTTAC
1 TGTATTTGCTTGATCTTCTCTCTGACTTGAAAATCTAGGCTCATCATTTTAC
* *
1865 TTTGTTTGCTTGATCTTCTCTCTGACTTGAAAA
1 TGTATTTGCTTGATCTTCTCTCTGACTTGAAAA
1898 GACTTGAAAA
Statistics
Matches: 76, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
50 46 0.61
52 30 0.39
ACGTcount: A:0.19, C:0.21, G:0.15, T:0.45
Consensus pattern (52 bp):
TGTATTTGCTTGATCTTCTCTCTGACTTGAAAATCTAGGCTCATCATTTTAC
Done.