Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011779.1 Corchorus capsularis cultivar CVL-1 contig11800, 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: 7733
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Found at i:126 original size:19 final size:19
Alignment explanation
Indices: 102--145 Score: 88
Period size: 19 Copynumber: 2.3 Consensus size: 19
92 AGTTGGATTG
102 TGGGTTGAAATTCAAGCAA
1 TGGGTTGAAATTCAAGCAA
121 TGGGTTGAAATTCAAGCAA
1 TGGGTTGAAATTCAAGCAA
140 TGGGTT
1 TGGGTT
146 TTTTTTTACC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.32, C:0.09, G:0.30, T:0.30
Consensus pattern (19 bp):
TGGGTTGAAATTCAAGCAA
Found at i:5647 original size:5 final size:5
Alignment explanation
Indices: 5637--5664 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
5627 ATTCAACAAA
5637 AAAAG AAAAG AAAAG AAAAG AAAAG AAA
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAA
5665 CTCAATTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:6186 original size:21 final size:23
Alignment explanation
Indices: 6146--6188 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
6136 TTATTTTTCG
6146 ATTATAATATATTCAATTATGAT
1 ATTATAATATATTCAATTATGAT
*
6169 ATTATAATTTA-T-AATTATGA
1 ATTATAATATATTCAATTATGA
6189 AACTTTTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 8 0.42
22 1 0.05
23 10 0.53
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.49
Consensus pattern (23 bp):
ATTATAATATATTCAATTATGAT
Found at i:7526 original size:323 final size:315
Alignment explanation
Indices: 6831--7703 Score: 1082
Period size: 323 Copynumber: 2.8 Consensus size: 315
6821 AGGTTTGCAT
* * * ** *
6831 GACTCCTTGATATACTTATATTCATCGAACCAAATTCCAATCACA-TCGGATAT-AACGATTTGT
1 GACTCCTTGAAATATTTATATTCATCGAACCAAAATCCAGCCA-ATTCGG-TTTGAACGATTTGT
* * * * * *
6894 TTTTACGAGCATCTGAATGTTATTTCGATTTAATTAGAAATTAATTCGGAAAAAATTGCAAACAC
64 GTTTACGAGTATCTAAATGTTATTTCGATTTAATTAGAAATTAATTCGGAAAAAAATGGAAAAAC
* * *
6959 GATATTAGAAGCGTGAAAAATCCTTTAATCTTTTTGGAGTTGAATTTTATATTTTTTATGAGTAT
129 GATATTAGAAACGTGAAAAACCCTTTAATCTTTTTGGAGTTGAATTATATA-TTTTTATGA-TAT
** * *** * *
7024 TGTGGCAAAAAATTGAG-AAAAAATTTTTCCGGGCAGTTTTTA--G---TC----ACG--A---T
192 TAAGGAAAAAAATTGAGAAAAAAAAAATTCCGGTCAGTTTTAACCGAAATCGTGTACGTTACGGT
* *
7074 TTTGTGCTAAAAACGCATTTTGGGGCGCCGGCTTAGGTTTGCATGATTTTTTGCGTATA
257 TTTGGGCTAAAAACGCATTTTGGGGCGCCGGCTCAGGTTTGCATGATTTTTTGCGTATA
7133 GACTCCTTGAAATATTTATATTCATCGAACCAAAATCCAGCCAATTCGGTTTGAACGATTTGTGT
1 GACTCCTTGAAATATTTATATTCATCGAACCAAAATCCAGCCAATTCGGTTTGAACGATTTGTGT
* * *
7198 TTACGAGTATCTGAATGTTTTTTCGATTTAATAATTAGAAATTAATTGGGAAAAAAAATGGAAAA
66 TTACGAGTATCTAAATGTTATTTCGA-TT--TAATTAGAAATTAATTCGG-AAAAAAATGGAAAA
* * *
7263 ACGATATTAGAAGCGTGAAAACCCCTTTAATCTTTTTGGAGTTGAGTTATATATTATTTTATGAA
127 ACGATATTAGAAACGTGAAAAACCCTTTAATCTTTTTGGAGTTGAATTATATA-T-TTTTATG-A
*
7328 TATTAAGGAAAAAAATTGAGAAAAAAAAAATT-CGGTCAGTTTTTAGCCGAAATCGTGTACGTTA
189 TATTAAGGAAAAAAATTGAGAAAAAAAAAATTCCGGTCAG-TTTTAACCGAAATCGTGTACGTTA
*
7392 CGGTTTTGGGCTAAAAACGCATTTTGGGGCGCCGGCTCAGGTTTGCATGATTTTTTTGCGTATG
253 CGGTTTTGGGCTAAAAACGCATTTTGGGGCGCCGGCTCAGGTTTGCATGA-TTTTTTGCGTATA
* * * * *
7456 GACTCCTTGAAATATTTATATTCATTGAACCAAATTCCATCCAATTTGGATTT-AACGATTTGTT
1 GACTCCTTGAAATATTTATATTCATCGAACCAAAATCCAGCCAATTCGG-TTTGAACGATTTGTG
7520 TTTACGAGTATCTAAATGTTATTTCGATTTAATTAGAAATTAATTCGGAAAAAAATGGAAAAACG
65 TTTACGAGTATCTAAATGTTATTTCGATTTAATTAGAAATTAATTCGGAAAAAAATGGAAAAACG
* * * **
7585 ATATTAGAAACGTGAAAAATCCTTTAATCTTTTTGGATTTGAATTATATATTTTTATGGTATTGT
130 ATATTAGAAACGTGAAAAACCCTTTAATCTTTTTGGAGTTGAATTATATATTTTTATGATATTAA
* *
7650 GGCAAAAAATTGAGAAAAAAAAATTTCCGGTCAGTTTTAACCGAAATCGTGTAC
195 GGAAAAAAATTGAGAAAAAAAAAATTCCGGTCAGTTTTAACCGAAATCGTGTAC
7704 TAACCATTAC
Statistics
Matches: 496, Mismatches: 48, Indels: 40
0.85 0.08 0.07
Matches are distributed among these distances:
301 3 0.01
302 77 0.16
303 2 0.00
305 18 0.04
306 62 0.12
307 30 0.06
308 13 0.03
310 1 0.00
313 2 0.00
316 47 0.09
317 17 0.03
318 1 0.00
319 63 0.13
320 18 0.04
322 47 0.09
323 92 0.19
324 3 0.01
ACGTcount: A:0.34, C:0.12, G:0.18, T:0.36
Consensus pattern (315 bp):
GACTCCTTGAAATATTTATATTCATCGAACCAAAATCCAGCCAATTCGGTTTGAACGATTTGTGT
TTACGAGTATCTAAATGTTATTTCGATTTAATTAGAAATTAATTCGGAAAAAAATGGAAAAACGA
TATTAGAAACGTGAAAAACCCTTTAATCTTTTTGGAGTTGAATTATATATTTTTATGATATTAAG
GAAAAAAATTGAGAAAAAAAAAATTCCGGTCAGTTTTAACCGAAATCGTGTACGTTACGGTTTTG
GGCTAAAAACGCATTTTGGGGCGCCGGCTCAGGTTTGCATGATTTTTTGCGTATA
Done.