Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007161.1 Corchorus capsularis cultivar CVL-1 contig07182, 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: 31831
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:5551 original size:19 final size:19
Alignment explanation
Indices: 5527--5573 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 19
5517 AGGATAAGTG
5527 GAAAAAATGAAAAAAAAAAA
1 GAAAAAA-GAAAAAAAAAAA
* *
5547 GAAAAAAGAAAGAAAAAGA
1 GAAAAAAGAAAAAAAAAAA
5566 GAAAAAAG
1 GAAAAAAG
5574 CAACGATGGT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 18 0.72
20 7 0.28
ACGTcount: A:0.81, C:0.00, G:0.17, T:0.02
Consensus pattern (19 bp):
GAAAAAAGAAAAAAAAAAA
Found at i:5634 original size:44 final size:44
Alignment explanation
Indices: 5581--5680 Score: 166
Period size: 44 Copynumber: 2.3 Consensus size: 44
5571 AAGCAACGAT
5581 GGTTTTCAAAAAGAGTCAT-GGTTTTCAAAAGGTTTTGATAAAAA
1 GGTTTTCAAAAAGAGTC-TCGGTTTTCAAAAGGTTTTGATAAAAA
*
5625 GGTTTTCAAAAAGAGTCTCGGTTTTCAAAAGGTTTTGATAAAAT
1 GGTTTTCAAAAAGAGTCTCGGTTTTCAAAAGGTTTTGATAAAAA
*
5669 GGTTTTAAAAAA
1 GGTTTTCAAAAA
5681 AAAGAGTGAG
Statistics
Matches: 53, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
43 1 0.02
44 52 0.98
ACGTcount: A:0.38, C:0.07, G:0.20, T:0.35
Consensus pattern (44 bp):
GGTTTTCAAAAAGAGTCTCGGTTTTCAAAAGGTTTTGATAAAAA
Found at i:6578 original size:36 final size:36
Alignment explanation
Indices: 6546--6647 Score: 116
Period size: 35 Copynumber: 2.9 Consensus size: 36
6536 GTTGACCTAA
* *
6546 GGTGGTTTTTCTTCAGTTTATGTCGGAATGACCGAG
1 GGTGGTCTTTCTTCAGTTTATGTCGGAATGACCCAG
** * *
6582 GGTGGTCTTTCTTTGGTTTATTTCGG-TTGACCCAG
1 GGTGGTCTTTCTTCAGTTTATGTCGGAATGACCCAG
* * *
6617 GGAGGCCTTTCTTCAGTTTATGTCAGAATGA
1 GGTGGTCTTTCTTCAGTTTATGTCGGAATGA
6648 TCGATTCAGT
Statistics
Matches: 52, Mismatches: 13, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
35 27 0.52
36 25 0.48
ACGTcount: A:0.16, C:0.16, G:0.28, T:0.40
Consensus pattern (36 bp):
GGTGGTCTTTCTTCAGTTTATGTCGGAATGACCCAG
Found at i:6773 original size:189 final size:191
Alignment explanation
Indices: 6532--6943 Score: 668
Period size: 189 Copynumber: 2.2 Consensus size: 191
6522 TTCAATGCGT
* * * *
6532 TTCAGTTGACCTAAGGTGGTTTTTCTTCAGTTTATGTCGGAATGACCGAGGGTGGTCTTTCTTTG
1 TTCAGTTGACCTAGGGTGGTTTTTCTTCAGTTTATATCGGAAGGACCGAGGGTGGTCTTTCTTTA
*
6597 GTTTATTTCGGTTGACCCAGGGA-GGCCTTTCTTCAGTTTATGTCAGAATGATCGATTCAGTCGA
66 GTTTATTTCGGTTGACCC-GGGACGGCCTTTCTTCAGTTTATGTCAGAATAATCGATTCAGTCGA
*
6661 CCCAGGGTGGTCTTTCTTCAGTTG-TTTCAAGTTTA-TCCAAGTTTATGTCAGAATGATCGA
130 CCCAGGGCGGTCTTTCTTCAGTTGTTTTCAAGTTTATTCCAAGTTTATGTCAGAATGATCGA
* *
6721 TTCAGTTGACCCAGGGTGGTTTTTCTTCAGTTTATATCGGAAGGATCGAGGGTGGTCTTTCTTTA
1 TTCAGTTGACCTAGGGTGGTTTTTCTTCAGTTTATATCGGAAGGACCGAGGGTGGTCTTTCTTTA
* *
6786 GTTTATTTCGGTTGACCCGGGACGGTCTTTCTTCAGTTTATGTCAGAATAATCGATTCAGTCGGC
66 GTTTATTTCGGTTGACCCGGGACGGCCTTTCTTCAGTTTATGTCAGAATAATCGATTCAGTCGAC
*
6851 CCAGGGCGGTCTTTCTTCAGTTGTTTTCAAGTTTATTCGAAGTTTATGTCAGAATGATCGA
131 CCAGGGCGGTCTTTCTTCAGTTGTTTTCAAGTTTATTCCAAGTTTATGTCAGAATGATCGA
* * *
6912 TTCAGTCGACCTAGGGCGGTCTTTCTTCAGTT
1 TTCAGTTGACCTAGGGTGGTTTTTCTTCAGTT
6944 ATTTCCAGGT
Statistics
Matches: 205, Mismatches: 15, Indels: 4
0.92 0.07 0.02
Matches are distributed among these distances:
188 4 0.02
189 138 0.67
190 11 0.05
191 52 0.25
ACGTcount: A:0.18, C:0.18, G:0.25, T:0.39
Consensus pattern (191 bp):
TTCAGTTGACCTAGGGTGGTTTTTCTTCAGTTTATATCGGAAGGACCGAGGGTGGTCTTTCTTTA
GTTTATTTCGGTTGACCCGGGACGGCCTTTCTTCAGTTTATGTCAGAATAATCGATTCAGTCGAC
CCAGGGCGGTCTTTCTTCAGTTGTTTTCAAGTTTATTCCAAGTTTATGTCAGAATGATCGA
Found at i:6991 original size:70 final size:70
Alignment explanation
Indices: 6820--7381 Score: 770
Period size: 70 Copynumber: 8.0 Consensus size: 70
6810 GTCTTTCTTC
* * * *
6820 AGTTTATGTCAGAATAATCGATTCAGTCGGCCCAGGGCGGTCTTTCTTCAGTTGTTTTCAAGTTT
1 AGTTTATGTCAGAATGATCGATTCAGTCGACCCAGGGCGGTCTTTCTTCAGTTATTTCCAAGTTT
*
6885 ATTCGA
66 A-TCCA
* *
6891 AGTTTATGTCAGAATGATCGATTCAGTCGACCTAGGGCGGTCTTTCTTCAGTTATTTCCAGGTTT
1 AGTTTATGTCAGAATGATCGATTCAGTCGACCCAGGGCGGTCTTTCTTCAGTTATTTCCAAGTTT
6956 ATCCA
66 ATCCA
* * * * * *
6961 AGTTTGTGTTAGAATGATCGATTCGGTCGACCCAGGGTGGTCTTTTTTCAG-TAGTTTCCACGTT
1 AGTTTATGTCAGAATGATCGATTCAGTCGACCCAGGGCGGTCTTTCTTCAGTTA-TTTCCAAGTT
7025 TATCCA
65 TATCCA
7031 AGTTTATGTCAGAATGATCGATTCAGTCGACCCAGGGCGGTCTTTCTTCAGTTATTTCCAAGTTT
1 AGTTTATGTCAGAATGATCGATTCAGTCGACCCAGGGCGGTCTTTCTTCAGTTATTTCCAAGTTT
7096 ATCCA
66 ATCCA
* * * * * *
7101 AGTTTGTGTCAGAATGATCGATTCGGTCGAGCCAAGGTGGTCTTTCTTCAG-TAGTTTCCACGTT
1 AGTTTATGTCAGAATGATCGATTCAGTCGACCCAGGGCGGTCTTTCTTCAGTTA-TTTCCAAGTT
7165 TATCCA
65 TATCCA
* * *
7171 AGTTTATGTCAGAATGATCGATTCAATCGACCCAGGGCGGTCTTTCTTCAGTTGTTTTCAAGTTT
1 AGTTTATGTCAGAATGATCGATTCAGTCGACCCAGGGCGGTCTTTCTTCAGTTATTTCCAAGTTT
7236 ATTCCA
66 A-TCCA
* * * *
7242 AGTTTATGTCAGAATGATCGATTCAGTCGACCTAGGGTGGTCATTCTTCAG-TAGTTTCCATGTT
1 AGTTTATGTCAGAATGATCGATTCAGTCGACCCAGGGCGGTCTTTCTTCAGTTA-TTTCCAAGTT
7306 TATCCA
65 TATCCA
* * * * * *
7312 AGTTTATGTCAGAATGATCGATTCAGTCGACCTAGGGAGGTTTTTCATCAGTTGTTTCCAAGTTG
1 AGTTTATGTCAGAATGATCGATTCAGTCGACCCAGGGCGGTCTTTCTTCAGTTATTTCCAAGTTT
7377 ATCCA
66 ATCCA
7382 GGGTGGTCTT
Statistics
Matches: 435, Mismatches: 49, Indels: 15
0.87 0.10 0.03
Matches are distributed among these distances:
69 4 0.01
70 306 0.70
71 125 0.29
ACGTcount: A:0.22, C:0.19, G:0.22, T:0.37
Consensus pattern (70 bp):
AGTTTATGTCAGAATGATCGATTCAGTCGACCCAGGGCGGTCTTTCTTCAGTTATTTCCAAGTTT
ATCCA
Found at i:7244 original size:211 final size:210
Alignment explanation
Indices: 6820--7381 Score: 797
Period size: 211 Copynumber: 2.7 Consensus size: 210
6810 GTCTTTCTTC
* * * *
6820 AGTTTATGTCAGAATAATCGATTCAGTCGGCCCAGGGCGGTCTTTCTTCAGTTGTTTTCAAGTTT
1 AGTTTATGTCAGAATGATCGATTCAGTCGACCCAGGGCGGTCTTTCTTCAGTTATTTCCAAGTTT
* *
6885 ATTCGAAGTTTATGTCAGAATGATCGATTCAGTCGACCTAGGGCGGTCTTTCTTCAGTTA-TTTC
66 A-TCCAAGTTTATGTCAGAATGATCGATTCAGTCGACCTAGGGAGGTCTTTCTTCAG-TAGTTTC
* * * ** * *
6949 CAGGTTTATCCAAGTTTGTGTTAGAATGATCGATTCGGTCGACCCAGGGTGGTCTTTTTTCAGTA
129 CAAGTTTATCCAAGTTTATGTCAGAATGATCGATTCAATCGACCCAGGGCGGTCTTTCTTCAGTA
*
7014 GTTTCCACGTTTATCCA
194 GTTTCCAAGTTTATCCA
7031 AGTTTATGTCAGAATGATCGATTCAGTCGACCCAGGGCGGTCTTTCTTCAGTTATTTCCAAGTTT
1 AGTTTATGTCAGAATGATCGATTCAGTCGACCCAGGGCGGTCTTTCTTCAGTTATTTCCAAGTTT
* * * *
7096 ATCCAAGTTTGTGTCAGAATGATCGATTCGGTCGAGCC-AAGGTGGTCTTTCTTCAGTAGTTTCC
66 ATCCAAGTTTATGTCAGAATGATCGATTCAGTCGA-CCTAGGGAGGTCTTTCTTCAGTAGTTTCC
* *
7160 ACGTTTATCCAAGTTTATGTCAGAATGATCGATTCAATCGACCCAGGGCGGTCTTTCTTCAGTTG
130 AAGTTTATCCAAGTTTATGTCAGAATGATCGATTCAATCGACCCAGGGCGGTCTTTCTTCAGTAG
*
7225 TTTTCAAGTTTATTCCA
195 TTTCCAAGTTTA-TCCA
* * * *
7242 AGTTTATGTCAGAATGATCGATTCAGTCGACCTAGGGTGGTCATTCTTCAG-TAGTTTCCATGTT
1 AGTTTATGTCAGAATGATCGATTCAGTCGACCCAGGGCGGTCTTTCTTCAGTTA-TTTCCAAGTT
* * *
7306 TATCCAAGTTTATGTCAGAATGATCGATTCAGTCGACCTAGGGAGGTTTTTCATCAGTTGTTTCC
65 TATCCAAGTTTATGTCAGAATGATCGATTCAGTCGACCTAGGGAGGTCTTTCTTCAGTAGTTTCC
*
7371 AAGTTGATCCA
130 AAGTTTATCCA
7382 GGGTGGTCTT
Statistics
Matches: 314, Mismatches: 32, Indels: 10
0.88 0.09 0.03
Matches are distributed among these distances:
209 2 0.01
210 123 0.39
211 189 0.60
ACGTcount: A:0.22, C:0.19, G:0.22, T:0.37
Consensus pattern (210 bp):
AGTTTATGTCAGAATGATCGATTCAGTCGACCCAGGGCGGTCTTTCTTCAGTTATTTCCAAGTTT
ATCCAAGTTTATGTCAGAATGATCGATTCAGTCGACCTAGGGAGGTCTTTCTTCAGTAGTTTCCA
AGTTTATCCAAGTTTATGTCAGAATGATCGATTCAATCGACCCAGGGCGGTCTTTCTTCAGTAGT
TTCCAAGTTTATCCA
Found at i:11144 original size:11 final size:10
Alignment explanation
Indices: 11120--11146 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
11110 CAATTTGTCG
11120 AAAAATTTTC
1 AAAAATTTTC
11130 AAAAATTTTC
1 AAAAATTTTC
11140 AAAAATT
1 AAAAATT
11147 GGGGAAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.56, C:0.07, G:0.00, T:0.37
Consensus pattern (10 bp):
AAAAATTTTC
Found at i:11258 original size:22 final size:22
Alignment explanation
Indices: 11230--11275 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
11220 CAATAATCAA
11230 ACAATAATCCTATTAAGTATTC
1 ACAATAATCCTATTAAGTATTC
11252 ACAATAATCCTATTAAGTATTC
1 ACAATAATCCTATTAAGTATTC
11274 AC
1 AC
11276 CCCCCACACT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.41, C:0.20, G:0.04, T:0.35
Consensus pattern (22 bp):
ACAATAATCCTATTAAGTATTC
Found at i:19928 original size:19 final size:18
Alignment explanation
Indices: 19895--19930 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
19885 TTGAAATAAT
19895 TCTTCAATGATCTTCAAA
1 TCTTCAATGATCTTCAAA
*
19913 TCTTCAAATTATCTTCAA
1 TCTTC-AATGATCTTCAA
19931 GAAATCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.33, C:0.22, G:0.03, T:0.42
Consensus pattern (18 bp):
TCTTCAATGATCTTCAAA
Found at i:29843 original size:2 final size:2
Alignment explanation
Indices: 29838--29880 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
29828 AGAAACAACT
*
29838 AC AC AC AA AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
29880 A
1 A
29881 TATATATATA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.53, C:0.47, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Done.