Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006841.1 Corchorus capsularis cultivar CVL-1 contig06862, 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: 15656
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.31
Found at i:1257 original size:6 final size:6
Alignment explanation
Indices: 1248--1275 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
1238 TTTTTTTTGG
1248 CTATGC CTATGC CTATGC CTATGC CTAT
1 CTATGC CTATGC CTATGC CTATGC CTAT
1276 ACGAAGAGTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.18, C:0.32, G:0.14, T:0.36
Consensus pattern (6 bp):
CTATGC
Found at i:5592 original size:19 final size:18
Alignment explanation
Indices: 5559--5594 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
5549 TTGAAATAAT
5559 TCTTCAATGATCTTCAAA
1 TCTTCAATGATCTTCAAA
*
5577 TCTTCAAATTATCTTCAA
1 TCTTC-AATGATCTTCAA
5595 GAAATCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.33, C:0.22, G:0.03, T:0.42
Consensus pattern (18 bp):
TCTTCAATGATCTTCAAA
Found at i:7202 original size:21 final size:19
Alignment explanation
Indices: 7169--7215 Score: 51
Period size: 21 Copynumber: 2.4 Consensus size: 19
7159 CCTAAGATGC
*
7169 TTAAAAATA-AAACCTAAA
1 TTAAAAACATAAACCTAAA
*
7187 TCTAGAAAACATAAACTTAAA
1 T-TA-AAAACATAAACCTAAA
7208 TTAAAAAC
1 TTAAAAAC
7216 CCAATTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
18 1 0.04
19 7 0.29
20 7 0.29
21 9 0.38
ACGTcount: A:0.62, C:0.13, G:0.02, T:0.23
Consensus pattern (19 bp):
TTAAAAACATAAACCTAAA
Found at i:7930 original size:25 final size:25
Alignment explanation
Indices: 7864--7921 Score: 107
Period size: 25 Copynumber: 2.3 Consensus size: 25
7854 CTGGTGCTGC
*
7864 GCGGCATGGCCTGACTGTACCGGCT
1 GCGGCATGGCCTGGCTGTACCGGCT
7889 GCGGCATGGCCTGGCTGTACCGGCT
1 GCGGCATGGCCTGGCTGTACCGGCT
7914 GCGGCATG
1 GCGGCATG
7922 CTAGTGCTGC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.10, C:0.31, G:0.40, T:0.19
Consensus pattern (25 bp):
GCGGCATGGCCTGGCTGTACCGGCT
Found at i:9258 original size:16 final size:16
Alignment explanation
Indices: 9118--9266 Score: 180
Period size: 16 Copynumber: 9.4 Consensus size: 16
9108 TGCAGTTTTT
9118 TCGGGTCATTCGGGT-
1 TCGGGTCATTCGGGTC
9133 TACGGGTCA-TCTGGGT-
1 T-CGGGTCATTC-GGGTC
*
9149 TCGGGTTATTCGGGTC
1 TCGGGTCATTCGGGTC
*
9165 TCGGGTCATTCGGATC
1 TCGGGTCATTCGGGTC
* *
9181 TCGGGTCATACGGGTT
1 TCGGGTCATTCGGGTC
9197 TCGGGTCATTCGGGTC
1 TCGGGTCATTCGGGTC
* *
9213 TCAGGTCATTCGGGTT
1 TCGGGTCATTCGGGTC
9229 TCGGGTCATTCGGGTC
1 TCGGGTCATTCGGGTC
*
9245 TCGGGTC-TACCGGGTC
1 TCGGGTCAT-TCGGGTC
9261 TCGGGT
1 TCGGGT
9267 TGGGCGGGTT
Statistics
Matches: 116, Mismatches: 13, Indels: 9
0.84 0.09 0.07
Matches are distributed among these distances:
15 14 0.12
16 102 0.88
ACGTcount: A:0.09, C:0.22, G:0.37, T:0.32
Consensus pattern (16 bp):
TCGGGTCATTCGGGTC
Found at i:9738 original size:21 final size:21
Alignment explanation
Indices: 9713--9760 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
9703 TAGCCAATTT
9713 ATAATAGGTAAAATCATAACA
1 ATAATAGGTAAAATCATAACA
* *
9734 ATAATTGGTAAAATTATAACA
1 ATAATAGGTAAAATCATAACA
9755 ATAATA
1 ATAATA
9761 TAAATTGGAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.56, C:0.06, G:0.08, T:0.29
Consensus pattern (21 bp):
ATAATAGGTAAAATCATAACA
Found at i:9903 original size:32 final size:32
Alignment explanation
Indices: 9865--9978 Score: 126
Period size: 32 Copynumber: 3.6 Consensus size: 32
9855 TCGGGTTAAT
*
9865 GTCTCGGGTTATTCGGGTTTCGGGTCATAC-GG
1 GTCTCGGGTCATTCGGGTTTCGGGTCAT-CTGG
*
9897 GTCTCGGGTCATTCGAGTTTCGGGTCATCTGG
1 GTCTCGGGTCATTCGGGTTTCGGGTCATCTGG
* * *
9929 GT-TACTGGTCATTCGGGTCTCGGGTCAGCT-G
1 GTCT-CGGGTCATTCGGGTTTCGGGTCATCTGG
*
9960 GTTTGCGGGTCATTCGGGT
1 GTCT-CGGGTCATTCGGGT
9979 CACGGGTTAG
Statistics
Matches: 71, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
31 5 0.07
32 66 0.93
ACGTcount: A:0.09, C:0.20, G:0.37, T:0.34
Consensus pattern (32 bp):
GTCTCGGGTCATTCGGGTTTCGGGTCATCTGG
Found at i:9984 original size:16 final size:16
Alignment explanation
Indices: 9865--10002 Score: 111
Period size: 16 Copynumber: 8.6 Consensus size: 16
9855 TCGGGTTAAT
*
9865 GTCTCGGGTTATTCGG
1 GTCTCGGGTCATTCGG
* *
9881 GTTTCGGGTCATACGG
1 GTCTCGGGTCATTCGG
*
9897 GTCTCGGGTCATTCGA
1 GTCTCGGGTCATTCGG
*
9913 GTTTCGGGTCA-TCTGG
1 GTCTCGGGTCATTC-GG
*
9929 GT-TACTGGTCATTCGG
1 GTCT-CGGGTCATTCGG
* *
9945 GTCTCGGGTCA-GCTG
1 GTCTCGGGTCATTCGG
*
9960 GTTTGCGGGTCATTCGG
1 GTCT-CGGGTCATTCGG
* * *
9977 GTCACGGGTTAGTCGG
1 GTCTCGGGTCATTCGG
*
9993 GTCTCTGGTC
1 GTCTCGGGTC
10003 GGGCGGGTTC
Statistics
Matches: 94, Mismatches: 22, Indels: 12
0.73 0.17 0.09
Matches are distributed among these distances:
15 8 0.09
16 79 0.84
17 7 0.07
ACGTcount: A:0.09, C:0.21, G:0.37, T:0.33
Consensus pattern (16 bp):
GTCTCGGGTCATTCGG
Found at i:12680 original size:28 final size:27
Alignment explanation
Indices: 12626--12680 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 27
12616 ATGACTACTT
*
12626 AAGTAACTACAAGGATGTGTTGAAAAAA
1 AAGTAACTACAAGGATGAGTT-AAAAAA
12654 AAGTAACTACAAGGATGAAGATTAAAA
1 AAGTAACTACAAGGATG-AG-TTAAAA
12681 CAGTTCTACC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
28 17 0.71
29 5 0.21
30 2 0.08
ACGTcount: A:0.53, C:0.07, G:0.20, T:0.20
Consensus pattern (27 bp):
AAGTAACTACAAGGATGAGTTAAAAAA
Done.