Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010292.1 Corchorus capsularis cultivar CVL-1 contig10313, 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: 72318
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:12860 original size:22 final size:22
Alignment explanation
Indices: 12835--12897 Score: 81
Period size: 22 Copynumber: 2.9 Consensus size: 22
12825 TTATGCTATT
**
12835 TATCAACGTGTCATGATAACTA
1 TATCAACGTGTCATGATAAAGA
* *
12857 TATCATCGTGTCATGATAAAGG
1 TATCAACGTGTCATGATAAAGA
*
12879 TATTAACGTGTCATGATAA
1 TATCAACGTGTCATGATAA
12898 TTCGTAACGT
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.35, C:0.14, G:0.17, T:0.33
Consensus pattern (22 bp):
TATCAACGTGTCATGATAAAGA
Found at i:13997 original size:6 final size:6
Alignment explanation
Indices: 13976--14018 Score: 59
Period size: 6 Copynumber: 6.8 Consensus size: 6
13966 ACACACACAA
*
13976 AAAAAT AAATAAAT AAAAAT AAGAAT AAAAAT AAAAAT AAAAA
1 AAAAAT -AA-AAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAA
14019 ATAATATATA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
6 25 0.76
7 4 0.12
8 4 0.12
ACGTcount: A:0.81, C:0.00, G:0.02, T:0.16
Consensus pattern (6 bp):
AAAAAT
Found at i:21149 original size:2 final size:2
Alignment explanation
Indices: 21137--21185 Score: 91
Period size: 2 Copynumber: 25.0 Consensus size: 2
21127 AATCTACAAT
21137 TC TC TC T- TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
21178 TC TC TC TC
1 TC TC TC TC
21186 CACAAATGTC
Statistics
Matches: 46, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 45 0.98
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:23146 original size:2 final size:2
Alignment explanation
Indices: 23139--23166 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
23129 GCAATTCTTA
23139 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
23167 CAAGAAATCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:57132 original size:24 final size:24
Alignment explanation
Indices: 57100--57146 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
57090 ATGAATGTGG
57100 TGCCACTCTTTC-CCTTCCAGATCA
1 TGCCACTCTTTCTCCTT-CAGATCA
57124 TGCCACTCTTTCTCCTTCAGATC
1 TGCCACTCTTTCTCCTTCAGATC
57147 GTATCCAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 18 0.82
25 4 0.18
ACGTcount: A:0.15, C:0.40, G:0.09, T:0.36
Consensus pattern (24 bp):
TGCCACTCTTTCTCCTTCAGATCA
Found at i:57252 original size:21 final size:22
Alignment explanation
Indices: 57223--57263 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
57213 CCACTCTGCA
*
57223 TAAAGAGGGCAACGAGGGTCAT
1 TAAAGAGGGCAACGACGGTCAT
*
57245 TAAA-AGGGTAACGACGGTC
1 TAAAGAGGGCAACGACGGTC
57264 CAAACCAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.37, C:0.15, G:0.34, T:0.15
Consensus pattern (22 bp):
TAAAGAGGGCAACGACGGTCAT
Found at i:65393 original size:24 final size:24
Alignment explanation
Indices: 65361--65407 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
65351 ATGAATGTGG
65361 TGCCACTCTTTC-CCTTCCAGATCA
1 TGCCACTCTTTCTCCTT-CAGATCA
65385 TGCCACTCTTTCTCCTTCAGATC
1 TGCCACTCTTTCTCCTTCAGATC
65408 GTATCCAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 18 0.82
25 4 0.18
ACGTcount: A:0.15, C:0.40, G:0.09, T:0.36
Consensus pattern (24 bp):
TGCCACTCTTTCTCCTTCAGATCA
Found at i:65998 original size:18 final size:18
Alignment explanation
Indices: 65971--66007 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
65961 CTAGAACCAG
65971 ATCTGAAACCCTCCCTTA
1 ATCTGAAACCCTCCCTTA
* *
65989 ATCTGTAACCCTCTCTTA
1 ATCTGAAACCCTCCCTTA
66007 A
1 A
66008 AAAAGGGAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.27, C:0.35, G:0.05, T:0.32
Consensus pattern (18 bp):
ATCTGAAACCCTCCCTTA
Found at i:70934 original size:25 final size:26
Alignment explanation
Indices: 70880--70934 Score: 85
Period size: 25 Copynumber: 2.2 Consensus size: 26
70870 CTAATGATCA
*
70880 TTTAGACTCTACCTTCACTTTTGTGT
1 TTTAGACTCTACCTTCACTTTTGTGC
*
70906 TTTAGACTCTA-CTTTACTTTTGTGC
1 TTTAGACTCTACCTTCACTTTTGTGC
70931 TTTA
1 TTTA
70935 TTACTACTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
25 16 0.59
26 11 0.41
ACGTcount: A:0.16, C:0.20, G:0.11, T:0.53
Consensus pattern (26 bp):
TTTAGACTCTACCTTCACTTTTGTGC
Done.