Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014490.1 Corchorus capsularis cultivar CVL-1 contig14511, 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: 29010
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:2856 original size:31 final size:31
Alignment explanation
Indices: 2821--2888 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 31
2811 CACATGCCAT
** *
2821 TTTTTGAAACATGTGGCATGCCACGTGTCAC
1 TTTTTGAAACACATGGCATGACACGTGTCAC
** *
2852 TTTTTGGTACACATGGCATGACATGTGTCAC
1 TTTTTGAAACACATGGCATGACACGTGTCAC
2883 TTTTTG
1 TTTTTG
2889 GTATATGTGG
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.21, C:0.19, G:0.22, T:0.38
Consensus pattern (31 bp):
TTTTTGAAACACATGGCATGACACGTGTCAC
Found at i:2900 original size:31 final size:31
Alignment explanation
Indices: 2829--2961 Score: 104
Period size: 31 Copynumber: 4.6 Consensus size: 31
2819 ATTTTTTGAA
*
2829 ACATGTGGCATGCCACGTGTCACTTTTTGGT
1 ACATGTGGCATGACACGTGTCACTTTTTGGT
** *
2860 ACACATGGCATGACATGTGTCACTTTTTGGT
1 ACATGTGGCATGACACGTGTCACTTTTTGGT
*
2891 ATATGT-G---G-CAC--G--ACTTTTTGGT
1 ACATGTGGCATGACACGTGTCACTTTTTGGT
* * * *
2913 ACATGTGGCGTGCCACATGTCACTTTTTAGT
1 ACATGTGGCATGACACGTGTCACTTTTTGGT
* *
2944 ACACGTGGCATGCCACGT
1 ACATGTGGCATGACACGT
2962 CGGGCACCGT
Statistics
Matches: 80, Mismatches: 13, Indels: 18
0.72 0.12 0.16
Matches are distributed among these distances:
22 15 0.19
23 1 0.01
24 1 0.01
26 3 0.04
27 4 0.05
29 1 0.01
30 1 0.01
31 54 0.68
ACGTcount: A:0.20, C:0.22, G:0.25, T:0.34
Consensus pattern (31 bp):
ACATGTGGCATGACACGTGTCACTTTTTGGT
Found at i:2952 original size:53 final size:53
Alignment explanation
Indices: 2850--2953 Score: 127
Period size: 53 Copynumber: 2.0 Consensus size: 53
2840 GCCACGTGTC
** * * *
2850 ACTTTTTGGTACACATGGCATGACATGTGTCACTTTTTGGTATATGTGGCACG
1 ACTTTTTGGTACACATGGCATGACACATGTCACTTTTTAGTACACGTGGCACG
** * *
2903 ACTTTTTGGTACATGTGGCGTGCCACATGTCACTTTTTAGTACACGTGGCA
1 ACTTTTTGGTACACATGGCATGACACATGTCACTTTTTAGTACACGTGGCA
2954 TGCCACGTCG
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
53 42 1.00
ACGTcount: A:0.20, C:0.19, G:0.24, T:0.37
Consensus pattern (53 bp):
ACTTTTTGGTACACATGGCATGACACATGTCACTTTTTAGTACACGTGGCACG
Found at i:4081 original size:30 final size:30
Alignment explanation
Indices: 4037--4105 Score: 117
Period size: 30 Copynumber: 2.4 Consensus size: 30
4027 TAGTTTATAA
4037 TAGTTTTC-TTTTTGACACATTTAAATTGG
1 TAGTTTTCTTTTTTGACACATTTAAATTGG
4066 TAGTTTTCTTTTTTGACACATTTAAATTGG
1 TAGTTTTCTTTTTTGACACATTTAAATTGG
4096 TA-TTTT-TTTT
1 TAGTTTTCTTTT
4106 AAGTGATATA
Statistics
Matches: 39, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
28 4 0.10
29 12 0.31
30 23 0.59
ACGTcount: A:0.22, C:0.09, G:0.12, T:0.58
Consensus pattern (30 bp):
TAGTTTTCTTTTTTGACACATTTAAATTGG
Found at i:5165 original size:20 final size:21
Alignment explanation
Indices: 5140--5181 Score: 77
Period size: 20 Copynumber: 2.0 Consensus size: 21
5130 TTTTGGGTTC
5140 TACTCTCACGGAA-TGTGAGT
1 TACTCTCACGGAATTGTGAGT
5160 TACTCTCACGGAATTGTGAGT
1 TACTCTCACGGAATTGTGAGT
5181 T
1 T
5182 TTCTTTGTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 13 0.62
21 8 0.38
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.33
Consensus pattern (21 bp):
TACTCTCACGGAATTGTGAGT
Found at i:5863 original size:6 final size:6
Alignment explanation
Indices: 5852--5878 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
5842 AACACAATAC
5852 AAAAAT AAAAAT AAAAAT AAAAAT AAA
1 AAAAAT AAAAAT AAAAAT AAAAAT AAA
5879 TAACCTCAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (6 bp):
AAAAAT
Found at i:8299 original size:2 final size:2
Alignment explanation
Indices: 8294--8318 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
8284 GAGAGAAAAT
8294 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
8319 TTAAGCTTGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:28691 original size:2 final size:2
Alignment explanation
Indices: 28684--28710 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
28674 TTAATTCATC
28684 TA TA 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 T
28711 GTTGAAATCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.