Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010581.1 Corchorus capsularis cultivar CVL-1 contig10602, 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: 30289
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.31
Found at i:72 original size:25 final size:24
Alignment explanation
Indices: 9--72 Score: 74
Period size: 25 Copynumber: 2.6 Consensus size: 24
1 TAGGTTGG
*
9 GGGAGTCTCTCCTAGCGCACAGCA
1 GGGAGTCTCACCTAGCGCACAGCA
*
33 GGTGAGTCTCACCTAGCGCATAGCAA
1 GG-GAGTCTCACCTAGCGCACAGC-A
* *
59 GGGAGGCTCCCCTA
1 GGGAGTCTCACCTA
73 AGGGAGTCTC
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
24 2 0.06
25 29 0.85
26 3 0.09
ACGTcount: A:0.22, C:0.31, G:0.30, T:0.17
Consensus pattern (24 bp):
GGGAGTCTCACCTAGCGCACAGCA
Found at i:131 original size:33 final size:33
Alignment explanation
Indices: 49--172 Score: 158
Period size: 33 Copynumber: 3.7 Consensus size: 33
39 TCTCACCTAG
*
49 CGCATAGCAAGGGAGGCTCCCCTAAGGGAGTCT
1 CGCATAGCAAGGGAGTCTCCCCTAAGGGAGTCT
* * * * * *
82 CTCGTAGTAAAGGGAGTCTCCTCTGAGGAAGTCT
1 CGCATAG-CAAGGGAGTCTCCCCTAAGGGAGTCT
*
116 CGCATAGCAAGGGAGTCTCCCCTTAGGGAGTCT
1 CGCATAGCAAGGGAGTCTCCCCTAAGGGAGTCT
*
149 CGCGTAGCAAGGGAGTCTCCCCTA
1 CGCATAGCAAGGGAGTCTCCCCTA
173 GCGCACAACA
Statistics
Matches: 75, Mismatches: 15, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
33 49 0.65
34 26 0.35
ACGTcount: A:0.23, C:0.27, G:0.31, T:0.20
Consensus pattern (33 bp):
CGCATAGCAAGGGAGTCTCCCCTAAGGGAGTCT
Found at i:134 original size:18 final size:18
Alignment explanation
Indices: 111--167 Score: 57
Period size: 18 Copynumber: 3.3 Consensus size: 18
101 CCTCTGAGGA
111 AGTCTCGCATAGCAAGGG
1 AGTCTCGCATAGCAAGGG
* * *
129 AGTCTCCCCT---TAGGG
1 AGTCTCGCATAGCAAGGG
*
144 AGTCTCGCGTAGCAAGGG
1 AGTCTCGCATAGCAAGGG
162 AGTCTC
1 AGTCTC
168 CCCTAGCGCA
Statistics
Matches: 30, Mismatches: 6, Indels: 6
0.71 0.14 0.14
Matches are distributed among these distances:
15 12 0.40
18 18 0.60
ACGTcount: A:0.21, C:0.26, G:0.32, T:0.21
Consensus pattern (18 bp):
AGTCTCGCATAGCAAGGG
Found at i:419 original size:37 final size:36
Alignment explanation
Indices: 312--420 Score: 112
Period size: 37 Copynumber: 3.0 Consensus size: 36
302 ATACTTAGAG
** * * *
312 AAGGGGGTATGACGCCTCCCCACATGATATTGTTATT
1 AAGGGGGCGTGACGCCTCCCCACATTAAATTG-TAAT
* * *
349 AAGGGGGCGTAAAGCCTCCCC-CATTAATTTTGTAAT
1 AAGGGGGCGTGACGCCTCCCCACATTAA-ATTGTAAT
385 AAGGGGGGCGTGACGCCTCCCCACATTAAATTGTAA
1 AA-GGGGGCGTGACGCCTCCCCACATTAAATTGTAA
421 GGGAGGCGTG
Statistics
Matches: 58, Mismatches: 11, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
36 9 0.16
37 43 0.74
38 6 0.10
ACGTcount: A:0.27, C:0.23, G:0.25, T:0.26
Consensus pattern (36 bp):
AAGGGGGCGTGACGCCTCCCCACATTAAATTGTAAT
Found at i:1692 original size:36 final size:36
Alignment explanation
Indices: 1642--1730 Score: 135
Period size: 36 Copynumber: 2.5 Consensus size: 36
1632 TTATGTATTA
* *
1642 GGCGACTTAGGCCAGCGGCGTTATAG-CAAACATTG
1 GGCGACTAAGGCCAGCGGCGTTATAGCCAAACATCG
*
1677 GGCGACTAAAGGCCAGCGGCGTTATAGCCAAGCATCG
1 GGCGACT-AAGGCCAGCGGCGTTATAGCCAAACATCG
1714 GGCGACTAAGGCCAGCG
1 GGCGACTAAGGCCAGCG
1731 ACATTACAAC
Statistics
Matches: 49, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
35 7 0.14
36 28 0.57
37 14 0.29
ACGTcount: A:0.26, C:0.26, G:0.34, T:0.15
Consensus pattern (36 bp):
GGCGACTAAGGCCAGCGGCGTTATAGCCAAACATCG
Found at i:3594 original size:16 final size:16
Alignment explanation
Indices: 3554--3682 Score: 134
Period size: 16 Copynumber: 7.9 Consensus size: 16
3544 TTGGTGACCT
3554 CACCAGGTGAGTATTG
1 CACCAGGTGAGTATTG
* **
3570 TACTGGGTGAGTATCT-
1 CACCAGGTGAGTAT-TG
3586 CACCAGGTGAGTATTG
1 CACCAGGTGAGTATTG
* *
3602 CACCAGGTAAGTGTTG
1 CACCAGGTGAGTATTG
*
3618 CACCAGGTGAGTGTTG
1 CACCAGGTGAGTATTG
* *
3634 CACCAAGTGAGTGTTTG
1 CACCAGGTGAGT-ATTG
*
3651 TACCAGGTGAGTATTTG
1 CACCAGGTGAGTA-TTG
*
3668 TACCAGGTGAGTATT
1 CACCAGGTGAGTATT
3683 TGTATTGGGT
Statistics
Matches: 95, Mismatches: 14, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
15 1 0.01
16 64 0.67
17 30 0.32
ACGTcount: A:0.23, C:0.16, G:0.31, T:0.29
Consensus pattern (16 bp):
CACCAGGTGAGTATTG
Found at i:9846 original size:29 final size:30
Alignment explanation
Indices: 9814--9879 Score: 98
Period size: 30 Copynumber: 2.2 Consensus size: 30
9804 TTTTGCCTTA
9814 TGAACTTCAATCTTGG-ACATTTTGCCCCC
1 TGAACTTCAATCTTGGTACATTTTGCCCCC
* *
9843 TGAACTTCAATTTTGGTACGTTTTGCCCCC
1 TGAACTTCAATCTTGGTACATTTTGCCCCC
*
9873 TCAACTT
1 TGAACTT
9880 AACGGCTCCG
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
29 15 0.45
30 18 0.55
ACGTcount: A:0.20, C:0.29, G:0.14, T:0.38
Consensus pattern (30 bp):
TGAACTTCAATCTTGGTACATTTTGCCCCC
Done.