Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016809.1 Corchorus olitorius cultivar O-4 contig16842, 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: 6937
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:512 original size:21 final size:21
Alignment explanation
Indices: 487--528 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
477 TTAGAAACAC
487 TAGTACCACTTAG-ATCCAATT
1 TAGTACCACTT-GTATCCAATT
508 TAGTACCACTTGTATCCAATT
1 TAGTACCACTTGTATCCAATT
529 GGGCTTCAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 1 0.05
21 19 0.95
ACGTcount: A:0.31, C:0.24, G:0.10, T:0.36
Consensus pattern (21 bp):
TAGTACCACTTGTATCCAATT
Found at i:2114 original size:30 final size:30
Alignment explanation
Indices: 2080--2141 Score: 97
Period size: 30 Copynumber: 2.1 Consensus size: 30
2070 ATTTTTATCT
2080 TGACTTTCCTCTTATACCCTCAAATTTTAA
1 TGACTTTCCTCTTATACCCTCAAATTTTAA
* * *
2110 TGACTTTTCTCTTATGCTCTCAAATTTTAA
1 TGACTTTCCTCTTATACCCTCAAATTTTAA
2140 TG
1 TG
2142 GCTTATTAAC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.24, C:0.23, G:0.06, T:0.47
Consensus pattern (30 bp):
TGACTTTCCTCTTATACCCTCAAATTTTAA
Found at i:4347 original size:190 final size:190
Alignment explanation
Indices: 4020--4403 Score: 759
Period size: 190 Copynumber: 2.0 Consensus size: 190
4010 AAAAATTAGG
4020 TTTTCCTTATGCAGAAGCCAAATTCTTCCACCTAACCGAATTCATTAATTTAACAATTGCAATCA
1 TTTTCCTTATGCAGAAGCCAAATTCTTCCACCTAACCGAATTCATTAATTTAACAATTGCAATCA
4085 AGATTAAAAAATTACCGCAGCGTACTATGTTTTTTTAGATAATCAGCATACATTTCAAGCAACAA
66 AGATTAAAAAATTACCGCAGCGTACTATGTTTTTTTAGATAATCAGCATACATTTCAAGCAACAA
*
4150 TTAATATTAGCTTTATTTTGATGAATTACCTAGAGATGGAGGAGTAGAATATTAGCTTTA
131 CTAATATTAGCTTTATTTTGATGAATTACCTAGAGATGGAGGAGTAGAATATTAGCTTTA
4210 TTTTCCTTATGCAGAAGCCAAATTCTTCCACCTAACCGAATTCATTAATTTAACAATTGCAATCA
1 TTTTCCTTATGCAGAAGCCAAATTCTTCCACCTAACCGAATTCATTAATTTAACAATTGCAATCA
4275 AGATTAAAAAATTACCGCAGCGTACTATGTTTTTTTAGATAATCAGCATACATTTCAAGCAACAA
66 AGATTAAAAAATTACCGCAGCGTACTATGTTTTTTTAGATAATCAGCATACATTTCAAGCAACAA
4340 CTAATATTAGCTTTATTTTGATGAATTACCTAGAGATGGAGGAGTAGAATATTAGCTTTA
131 CTAATATTAGCTTTATTTTGATGAATTACCTAGAGATGGAGGAGTAGAATATTAGCTTTA
4400 TTTT
1 TTTT
4404 GATGAATTAC
Statistics
Matches: 193, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
190 193 1.00
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.35
Consensus pattern (190 bp):
TTTTCCTTATGCAGAAGCCAAATTCTTCCACCTAACCGAATTCATTAATTTAACAATTGCAATCA
AGATTAAAAAATTACCGCAGCGTACTATGTTTTTTTAGATAATCAGCATACATTTCAAGCAACAA
CTAATATTAGCTTTATTTTGATGAATTACCTAGAGATGGAGGAGTAGAATATTAGCTTTA
Found at i:4406 original size:45 final size:45
Alignment explanation
Indices: 4342--4463 Score: 226
Period size: 45 Copynumber: 2.7 Consensus size: 45
4332 AGCAACAACT
4342 AATATTAGCTTTATTTTGATGAATTACCTAGAGATGGAGGAGTAG
1 AATATTAGCTTTATTTTGATGAATTACCTAGAGATGGAGGAGTAG
* *
4387 AATATTAGCTTTATTTTGATGAATTACCTAGGGATGGAGGAGTAT
1 AATATTAGCTTTATTTTGATGAATTACCTAGAGATGGAGGAGTAG
4432 AATATTAGCTTTATTTTGATGAATTACCTAGA
1 AATATTAGCTTTATTTTGATGAATTACCTAGA
4464 AATGAAGTAG
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 74 1.00
ACGTcount: A:0.33, C:0.07, G:0.21, T:0.39
Consensus pattern (45 bp):
AATATTAGCTTTATTTTGATGAATTACCTAGAGATGGAGGAGTAG
Done.