Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014221.1 Corchorus capsularis cultivar CVL-1 contig14242, 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: 6564
ACGTcount: A:0.37, C:0.20, G:0.15, T:0.29
Found at i:253 original size:52 final size:52
Alignment explanation
Indices: 138--255 Score: 130
Period size: 52 Copynumber: 2.2 Consensus size: 52
128 TCATTTGCAA
* * ** * * * *
138 CATTACACATTTAATTATGTAATAGGAATGCATCTTATGATTTCAATTTGCAT
1 CATTACACCTTT-ACTATGTAATAGGAATGCATAATATGACTTCAACTGGCAC
191 CATTACACCTTTACTATGTAATAGGAATGCATAATA-GACTTCAACTGGCAC
1 CATTACACCTTTACTATGTAATAGGAATGCATAATATGACTTCAACTGGCAC
*
242 CATTATTACCTTTA
1 CATTA-CACCTTTA
256 GTACAATAGG
Statistics
Matches: 55, Mismatches: 9, Indels: 3
0.82 0.13 0.04
Matches are distributed among these distances:
51 16 0.29
52 28 0.51
53 11 0.20
ACGTcount: A:0.34, C:0.18, G:0.11, T:0.37
Consensus pattern (52 bp):
CATTACACCTTTACTATGTAATAGGAATGCATAATATGACTTCAACTGGCAC
Found at i:783 original size:30 final size:30
Alignment explanation
Indices: 747--814 Score: 75
Period size: 31 Copynumber: 2.2 Consensus size: 30
737 TGGCACATAT
* * *
747 CTTTTTGTGCGCA-TGGCATGCCACGTGTCG
1 CTTTTTG-GCACAGTGGCATGCCACGTATCA
*
777 CTTTTTGGTACATGTGGCATGCCACGTATCA
1 CTTTTTGGCACA-GTGGCATGCCACGTATCA
808 CTTTTTG
1 CTTTTTG
815 ATACATGACA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
29 3 0.09
30 7 0.22
31 22 0.69
ACGTcount: A:0.13, C:0.24, G:0.25, T:0.38
Consensus pattern (30 bp):
CTTTTTGGCACAGTGGCATGCCACGTATCA
Found at i:790 original size:29 final size:29
Alignment explanation
Indices: 758--826 Score: 84
Period size: 31 Copynumber: 2.3 Consensus size: 29
748 TTTTTGTGCG
* * *
758 CATGGCATGCCACGTGTCGCTTTTTGGTA
1 CATGGCATGCCACGTATCACTTTTTGATA
787 CATGTGGCATGCCACGTATCACTTTTTGATA
1 CA--TGGCATGCCACGTATCACTTTTTGATA
*
818 CATGACATG
1 CATGGCATG
827 TCACTTTTTG
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
29 8 0.24
31 26 0.76
ACGTcount: A:0.20, C:0.23, G:0.23, T:0.33
Consensus pattern (29 bp):
CATGGCATGCCACGTATCACTTTTTGATA
Found at i:798 original size:31 final size:31
Alignment explanation
Indices: 760--821 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
750 TTTGTGCGCA
* * *
760 TGGCATGCCACGTGTCGCTTTTTGGTACATG
1 TGGCATGCCACGTATCACTTTTTGATACATG
791 TGGCATGCCACGTATCACTTTTTGATACATG
1 TGGCATGCCACGTATCACTTTTTGATACATG
822 ACATGTCACT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.18, C:0.23, G:0.24, T:0.35
Consensus pattern (31 bp):
TGGCATGCCACGTATCACTTTTTGATACATG
Found at i:875 original size:31 final size:31
Alignment explanation
Indices: 825--918 Score: 91
Period size: 31 Copynumber: 3.0 Consensus size: 31
815 ATACATGACA
* *
825 TGTCACTTTTTG-GCACACGTGACGTGTCACG
1 TGTCACTTTTTGATC-CACGTGACGTGCCACG
**
856 TGTCACTTTTTGATCCACGTGGTGTGCCACG
1 TGTCACTTTTTGATCCACGTGACGTGCCACG
* * * * *
887 TATTACTTTTTTATCCACGTGGCATGCCACG
1 TGTCACTTTTTGATCCACGTGACGTGCCACG
918 T
1 T
919 CGAACACGGT
Statistics
Matches: 53, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
31 52 0.98
32 1 0.02
ACGTcount: A:0.16, C:0.26, G:0.22, T:0.36
Consensus pattern (31 bp):
TGTCACTTTTTGATCCACGTGACGTGCCACG
Found at i:2791 original size:29 final size:29
Alignment explanation
Indices: 2759--2833 Score: 100
Period size: 29 Copynumber: 2.6 Consensus size: 29
2749 ATCACAAATG
* *
2759 TGTGCACCTCCCACACACAGTAATGCTT-T
1 TGTGAACCTCCCACACACAATAATG-TTCT
2788 TGTGAACCTCCCACACACAATAATGTTCGT
1 TGTGAACCTCCCACACACAATAATGTTC-T
2818 T-TGAACCTCCCACACA
1 TGTGAACCTCCCACACA
2834 TATGAGTTAT
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
28 2 0.05
29 38 0.90
30 2 0.05
ACGTcount: A:0.28, C:0.35, G:0.12, T:0.25
Consensus pattern (29 bp):
TGTGAACCTCCCACACACAATAATGTTCT
Found at i:5961 original size:12 final size:12
Alignment explanation
Indices: 5944--5970 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
5934 GTTAAATTGG
5944 AAAAAAAAAACA
1 AAAAAAAAAACA
5956 AAAAAAAAAACA
1 AAAAAAAAAACA
5968 AAA
1 AAA
5971 GTGGAACAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.93, C:0.07, G:0.00, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAACA
Done.