Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011606.1 Corchorus capsularis cultivar CVL-1 contig11627, 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: 8750
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.29
Found at i:545 original size:33 final size:33
Alignment explanation
Indices: 473--580 Score: 101
Period size: 33 Copynumber: 3.3 Consensus size: 33
463 GCGCCAAGCG
* * * *
473 ATGGCCGGT-TGTGGCCGGACATGTCCATGTCGC
1 ATGGCCGGTGT-TGGCCGGGCATCTCCAAGTCAC
** * *
506 GCGGCCGGTGTTGGCTGGGCATCTCCGAGTCAC
1 ATGGCCGGTGTTGGCCGGGCATCTCCAAGTCAC
* * *
539 GTGGCCGGTGTTGGCCGGGCTTCTCCAAGTCGC
1 ATGGCCGGTGTTGGCCGGGCATCTCCAAGTCAC
572 ATGGCCGGT
1 ATGGCCGGT
581 CACTAGTGCT
Statistics
Matches: 60, Mismatches: 14, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
33 59 0.98
34 1 0.02
ACGTcount: A:0.09, C:0.29, G:0.39, T:0.23
Consensus pattern (33 bp):
ATGGCCGGTGTTGGCCGGGCATCTCCAAGTCAC
Found at i:5000 original size:33 final size:33
Alignment explanation
Indices: 4960--5066 Score: 119
Period size: 33 Copynumber: 3.2 Consensus size: 33
4950 AGCACTTGTG
*
4960 ACCGGCCAAGCGACTTGGAGATGCCCGCGCAAC
1 ACCGGCCAAGCGACATGGAGATGCCCGCGCAAC
* *
4993 ACCGGCCATGCGACATGGAGATGCCCGAC-CATC
1 ACCGGCCAAGCGACATGGAGATGCCCG-CGCAAC
* ** *
5026 ACCGGCCACGCGACATGGCCATGCCCG-GCCAC
1 ACCGGCCAAGCGACATGGAGATGCCCGCGCAAC
5058 ACCAGGCCA
1 ACC-GGCCA
5067 CATGACTCGG
Statistics
Matches: 63, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
32 5 0.08
33 57 0.90
34 1 0.02
ACGTcount: A:0.23, C:0.40, G:0.28, T:0.08
Consensus pattern (33 bp):
ACCGGCCAAGCGACATGGAGATGCCCGCGCAAC
Found at i:5067 original size:33 final size:32
Alignment explanation
Indices: 4960--5096 Score: 114
Period size: 33 Copynumber: 4.2 Consensus size: 32
4950 AGCACTTGTG
* * ** *
4960 ACCGGCCAAGCGACTTGGAGATGCCCGCGCAAC
1 ACCGGCCACGCGACATGGCCATGCCCG-GCCAC
* ** *
4993 ACCGGCCATGCGACATGGAGATGCCCGACCATC
1 ACCGGCCACGCGACATGGCCATGCCCGGCCA-C
5026 ACCGGCCACGCGACATGGCCATGCCCGGCCAC
1 ACCGGCCACGCGACATGGCCATGCCCGGCCAC
** *
5058 ACCAGGCCACATGAC-TCGGCCATGCTCGGCCAC
1 ACC-GGCCACGCGACAT-GGCCATGCCCGGCCAC
5091 AACCGG
1 -ACCGG
5097 TCACATGATC
Statistics
Matches: 89, Mismatches: 11, Indels: 8
0.82 0.10 0.07
Matches are distributed among these distances:
32 7 0.08
33 79 0.89
34 3 0.03
ACGTcount: A:0.23, C:0.40, G:0.28, T:0.09
Consensus pattern (32 bp):
ACCGGCCACGCGACATGGCCATGCCCGGCCAC
Found at i:5102 original size:33 final size:33
Alignment explanation
Indices: 5042--5104 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
5032 CACGCGACAT
5042 GGCCATGCCCGGCCACACCAGGCCACATGACTC
1 GGCCATGCCCGGCCACACCAGGCCACATGACTC
* *
5075 GGCCATGCTCGGCCACAACC-GGTCACATGA
1 GGCCATGCCCGGCCAC-ACCAGGCCACATGA
5105 TCCTTTAACT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
33 24 0.89
34 3 0.11
ACGTcount: A:0.22, C:0.41, G:0.25, T:0.11
Consensus pattern (33 bp):
GGCCATGCCCGGCCACACCAGGCCACATGACTC
Found at i:6187 original size:159 final size:158
Alignment explanation
Indices: 5882--6455 Score: 911
Period size: 159 Copynumber: 3.6 Consensus size: 158
5872 TTCGTATCAC
* * *
5882 TGTTGGACAGCCCTGTGCAAAAACAAAGCTGTCCTTGAAGCCCAAATCCTCTGCATTTCGCGTTT
1 TGTTGGACAGCCCTGTGCAAAAACAAAGCTCTCCTTGAAGCCCAAATCCTCTACATTGCGCGTTT
* *
5947 GTGTGCAAAACATCGTTCTTATCGAAAGGCTTATTCCAGAAGCATTTTTTGTGCAACGATTGCTC
66 GTGTGCAAAACATCGTTCTTATCGAAAGGCTCATTCCAGAAGCA-TTTTTGTGCAACGAGTGCTC
*
6012 AAAAGTCTTGTGTCGGAGTGAGATGAGCT
130 AAAAGTCTTGTATCGGAGTGAGATGAGCT
* * *
6041 TGTTTGATAGCCTTGTGCAAAAACAAAGCTCTCCTTGAAGCCCAAATCCTCTACATTGCGCGTTT
1 TGTTGGACAGCCCTGTGCAAAAACAAAGCTCTCCTTGAAGCCCAAATCCTCTACATTGCGCGTTT
* *
6106 GTGTGCAAAACATCGTTCTTA-CTAAAAGGCTCATTCCAGAAGCATTTTATGTG-AACCAAGTGC
66 GTGTGCAAAACATCGTTCTTATC-GAAAGGCTCATTCCAGAAGCATTTT-TGTGCAA-CGAGTGC
6169 TCAAAAGTCTTGTATCGGAGTGAGATGAGCT
128 TCAAAAGTCTTGTATCGGAGTGAGATGAGCT
6200 TGTTGGACAGCCCTGTGCAAAAACAAAGCTCTCCTTGAAGCCCAAATCCTCTGA-ATTGCGCGTT
1 TGTTGGACAGCCCTGTGCAAAAACAAAGCTCTCCTTGAAGCCCAAATCCTCT-ACATTGCGCGTT
* *
6264 TGTGTGCAAAAAATTGTTCTTATCGAAAGGCTCATTCCAGAAGCATTTTTCGTGCAACGAGTGCT
65 TGTGTGCAAAACATCGTTCTTATCGAAAGGCTCATTCCAGAAGCATTTTT-GTGCAACGAGTGCT
* *
6329 CAAAATTCTTGTATCGGAGTGAGATAAGCT
129 CAAAAGTCTTGTATCGGAGTGAGATGAGCT
* *
6359 TCTTGGACAGCCCTGTGCAAAAACAAAGCTCTCCTTGAAGCCCAAATCCTCTGCATTGCGCGTTT
1 TGTTGGACAGCCCTGTGCAAAAACAAAGCTCTCCTTGAAGCCCAAATCCTCTACATTGCGCGTTT
*
6424 GTGTGCAAAACATTGTTCTTATCGAAAGGCTC
66 GTGTGCAAAACATCGTTCTTATCGAAAGGCTC
6456 TGATACGAAT
Statistics
Matches: 384, Mismatches: 23, Indels: 16
0.91 0.05 0.04
Matches are distributed among these distances:
158 8 0.02
159 372 0.97
160 4 0.01
ACGTcount: A:0.27, C:0.22, G:0.21, T:0.29
Consensus pattern (158 bp):
TGTTGGACAGCCCTGTGCAAAAACAAAGCTCTCCTTGAAGCCCAAATCCTCTACATTGCGCGTTT
GTGTGCAAAACATCGTTCTTATCGAAAGGCTCATTCCAGAAGCATTTTTGTGCAACGAGTGCTCA
AAAGTCTTGTATCGGAGTGAGATGAGCT
Found at i:7274 original size:10 final size:10
Alignment explanation
Indices: 7259--7310 Score: 59
Period size: 10 Copynumber: 4.9 Consensus size: 10
7249 TAAAGGTTCA
7259 TGTGGCCGGT
1 TGTGGCCGGT
*
7269 TGTGGCCGGG
1 TGTGGCCGGT
*
7279 TATGGCCGAGT
1 TGTGGCCG-GT
7290 CATGTGGCCGGT
1 --TGTGGCCGGT
7302 TGTGGCCGG
1 TGTGGCCGG
7311 GCATGTCCTT
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
10 25 0.71
11 1 0.03
12 2 0.06
13 7 0.20
ACGTcount: A:0.06, C:0.21, G:0.48, T:0.25
Consensus pattern (10 bp):
TGTGGCCGGT
Found at i:7330 original size:33 final size:33
Alignment explanation
Indices: 7260--7377 Score: 130
Period size: 33 Copynumber: 3.5 Consensus size: 33
7250 AAAGGTTCAT
* * * **
7260 GTGGCCGGTTGTGGCCGGGTATGGCCGAGTCAT
1 GTGGCCGGTTGTGGCCGGGCATGTCCAAGTCGC
**
7293 GTGGCCGGTTGTGGCCGGGCATGTCCTTGTCGC
1 GTGGCCGGTTGTGGCCGGGCATGTCCAAGTCGC
*
7326 GTGGCCGG-TGATGGCCGGGCATCTCCAAGTCGC
1 GTGGCCGGTTG-TGGCCGGGCATGTCCAAGTCGC
7359 GTGGCCGGTCTTGTGGCCG
1 GTGGCCGG--TTGTGGCCG
7378 ATGTTGCGCG
Statistics
Matches: 72, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
32 2 0.03
33 62 0.86
35 6 0.08
36 2 0.03
ACGTcount: A:0.07, C:0.26, G:0.43, T:0.24
Consensus pattern (33 bp):
GTGGCCGGTTGTGGCCGGGCATGTCCAAGTCGC
Done.