Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013889.1 Corchorus capsularis cultivar CVL-1 contig13910, 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: 55160
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Found at i:8975 original size:2 final size:2
Alignment explanation
Indices: 8968--9014 Score: 50
Period size: 2 Copynumber: 26.0 Consensus size: 2
8958 TATTTTATTT
*
8968 TA TA TA TA AA TA TA TA T- TA TA T- TA T- TA TA T- TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
9006 TA T- TA TA TA
1 TA TA TA TA TA
9015 ATAATAAGAA
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
1 5 0.13
2 33 0.87
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:8990 original size:24 final size:24
Alignment explanation
Indices: 8958--9013 Score: 78
Period size: 24 Copynumber: 2.3 Consensus size: 24
8948 TTTTATATTT
*
8958 TATTTTATT-TTATATATAAATATA
1 TATTATATTATTATAT-TAAATATA
*
8982 TATTATATTATTATATTATATATA
1 TATTATATTATTATATTAAATATA
9006 TATTATAT
1 TATTATAT
9014 AATAATAAGA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
24 23 0.79
25 6 0.21
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (24 bp):
TATTATATTATTATATTAAATATA
Found at i:8996 original size:13 final size:12
Alignment explanation
Indices: 8932--9013 Score: 64
Period size: 11 Copynumber: 7.1 Consensus size: 12
8922 AGAGGCCAGC
*
8932 TTATATATTACA
1 TTATATATTATA
* *
8944 GTAT-TTTTATA
1 TTATATATTATA
* * *
8955 TTTTATTTTATT
1 TTATATATTATA
8967 TTATATA-TA-A
1 TTATATATTATA
*
8977 ATATATATTATA
1 TTATATATTATA
8989 TTATTATATTATA
1 TTA-TATATTATA
9002 -TATATATTATA
1 TTATATATTATA
9013 T
1 T
9014 AATAATAAGA
Statistics
Matches: 54, Mismatches: 11, Indels: 10
0.72 0.15 0.13
Matches are distributed among these distances:
10 6 0.11
11 20 0.37
12 19 0.35
13 9 0.17
ACGTcount: A:0.38, C:0.01, G:0.01, T:0.60
Consensus pattern (12 bp):
TTATATATTATA
Found at i:9014 original size:13 final size:13
Alignment explanation
Indices: 8968--9008 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
8958 TATTTTATTT
*
8968 TATA-TATAAATA
1 TATATTATATATA
8980 TATATTATAT-TA
1 TATATTATATATA
8992 TTATATTATATATA
1 -TATATTATATATA
9006 TAT
1 TAT
9009 TATATAATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
12 6 0.24
13 17 0.68
14 2 0.08
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
TATATTATATATA
Found at i:10859 original size:6 final size:6
Alignment explanation
Indices: 10821--10887 Score: 54
Period size: 6 Copynumber: 12.0 Consensus size: 6
10811 AGCTAAGATA
* * * *
10821 GTTTTT G-TTTT G-TTTT GGTTCT GGTTTT -CTTTT GTTTTT GTTTTT
1 GTTTTT GTTTTT GTTTTT GTTTTT GTTTTT GTTTTT GTTTTT GTTTTT
*
10866 GTTTTT -TTGTT -TTTTT GTTTTT
1 GTTTTT GTTTTT GTTTTT GTTTTT
10888 AAAGAAAATG
Statistics
Matches: 52, Mismatches: 6, Indels: 6
0.81 0.09 0.09
Matches are distributed among these distances:
5 22 0.42
6 30 0.58
ACGTcount: A:0.00, C:0.03, G:0.18, T:0.79
Consensus pattern (6 bp):
GTTTTT
Found at i:10869 original size:22 final size:21
Alignment explanation
Indices: 10823--10887 Score: 67
Period size: 22 Copynumber: 3.0 Consensus size: 21
10813 CTAAGATAGT
* * *
10823 TTTTGTTTTGTTTTGGTTCTGG
1 TTTT-TTTTGTTTTTGTTTTTG
10845 TTTTCTTTTGTTTTTGTTTTTG
1 TTTT-TTTTGTTTTTGTTTTTG
*
10867 TTTTTTTGTTTTTTTGTTTTT
1 TTTTTTT-TGTTTTTGTTTTT
10888 AAAGAAAATG
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
21 3 0.08
22 34 0.92
ACGTcount: A:0.00, C:0.03, G:0.17, T:0.80
Consensus pattern (21 bp):
TTTTTTTTGTTTTTGTTTTTG
Found at i:10874 original size:8 final size:8
Alignment explanation
Indices: 10861--10887 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
10851 TTTGTTTTTG
10861 TTTTTGTT
1 TTTTTGTT
10869 TTTTTGTT
1 TTTTTGTT
10877 TTTTTGTT
1 TTTTTGTT
10885 TTT
1 TTT
10888 AAAGAAAATG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.00, C:0.00, G:0.11, T:0.89
Consensus pattern (8 bp):
TTTTTGTT
Found at i:16529 original size:14 final size:14
Alignment explanation
Indices: 16510--16539 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
16500 AAAAGGAAAG
16510 TGCTTATATGGACA
1 TGCTTATATGGACA
16524 TGCTTATATGGACA
1 TGCTTATATGGACA
16538 TG
1 TG
16540 GTTTGGTTGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.27, C:0.13, G:0.23, T:0.37
Consensus pattern (14 bp):
TGCTTATATGGACA
Found at i:24351 original size:53 final size:55
Alignment explanation
Indices: 24252--24358 Score: 164
Period size: 53 Copynumber: 2.0 Consensus size: 55
24242 TAAGAAATAC
* *
24252 TCCTAGTACTAATTAGTAGTATATATGAGTTTTACAAAAAATTCTACTAAAAGTTA
1 TCCTAGTACTAATTAGTAG-ATATATGACTTTCACAAAAAATTCTACTAAAAGTTA
*
24308 TCCTAGTTCTAATTAGTAG-TATATGACTTTCAC-AAAAATTCTACTAAAAGT
1 TCCTAGTACTAATTAGTAGATATATGACTTTCACAAAAAATTCTACTAAAAGT
24359 GCTAAACAAG
Statistics
Matches: 48, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
53 18 0.38
54 12 0.25
56 18 0.38
ACGTcount: A:0.39, C:0.13, G:0.10, T:0.37
Consensus pattern (55 bp):
TCCTAGTACTAATTAGTAGATATATGACTTTCACAAAAAATTCTACTAAAAGTTA
Found at i:24666 original size:14 final size:14
Alignment explanation
Indices: 24638--24676 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
24628 TTCCAAGCCG
*
24638 CTCCTCTCTCCCCTT
1 CTCC-CTCTCTCCTT
24653 CTCCCTCTCTCCTT
1 CTCCCTCTCTCCTT
*
24667 CTTCCTCTCT
1 CTCCCTCTCT
24677 AGTTCTCGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 18 0.82
15 4 0.18
ACGTcount: A:0.00, C:0.56, G:0.00, T:0.44
Consensus pattern (14 bp):
CTCCCTCTCTCCTT
Found at i:26807 original size:6 final size:6
Alignment explanation
Indices: 26789--26820 Score: 55
Period size: 6 Copynumber: 5.2 Consensus size: 6
26779 GAAGATTAGG
26789 TAGGAA CTAGGAA TAGGAA TAGGAA TAGGAA T
1 TAGGAA -TAGGAA TAGGAA TAGGAA TAGGAA T
26821 TATTATAGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 19 0.76
7 6 0.24
ACGTcount: A:0.47, C:0.03, G:0.31, T:0.19
Consensus pattern (6 bp):
TAGGAA
Found at i:31066 original size:13 final size:14
Alignment explanation
Indices: 31037--31074 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
31027 GGGCTGCTCA
*
31037 TTTTTCGGTGTC-GG
1 TTTTTCGGT-TCAGT
31051 TTTTTCGGTTCAGT
1 TTTTTCGGTTCAGT
31065 TTTTTCGGTT
1 TTTTTCGGTT
31075 TTTATTTTGG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 2 0.09
14 20 0.91
ACGTcount: A:0.03, C:0.13, G:0.26, T:0.58
Consensus pattern (14 bp):
TTTTTCGGTTCAGT
Found at i:41821 original size:19 final size:20
Alignment explanation
Indices: 41787--41827 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
41777 TAATTACACT
41787 AAAATATAAAATTTTGTACA
1 AAAATATAAAATTTTGTACA
41807 AAAATATAAAA-TTTGTACA
1 AAAATATAAAATTTTGTACA
41826 AA
1 AA
41828 TAAGGGAGTC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 10 0.48
20 11 0.52
ACGTcount: A:0.59, C:0.05, G:0.05, T:0.32
Consensus pattern (20 bp):
AAAATATAAAATTTTGTACA
Found at i:45935 original size:24 final size:24
Alignment explanation
Indices: 45903--45959 Score: 80
Period size: 24 Copynumber: 2.4 Consensus size: 24
45893 GCTACATTGG
45903 CAGCTGCAGCTGCAGCCT-TTGCAA
1 CAGCTGCAGCTGCAG-CTATTGCAA
* *
45927 CAGCAGCAGCTGCTGCTATTGCAA
1 CAGCTGCAGCTGCAGCTATTGCAA
45951 CAGCTGCAG
1 CAGCTGCAG
45960 AAGTCAATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
23 2 0.07
24 27 0.93
ACGTcount: A:0.23, C:0.32, G:0.26, T:0.19
Consensus pattern (24 bp):
CAGCTGCAGCTGCAGCTATTGCAA
Done.