Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015852.1 Corchorus capsularis cultivar CVL-1 contig15873, 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: 10135
ACGTcount: A:0.30, C:0.16, G:0.20, T:0.34
Found at i:37 original size:10 final size:10
Alignment explanation
Indices: 22--46 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
12 TAACTCCAAT
22 TATGGACTTA
1 TATGGACTTA
32 TATGGACTTA
1 TATGGACTTA
42 TATGG
1 TATGG
47 GCTGAGTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.28, C:0.08, G:0.24, T:0.40
Consensus pattern (10 bp):
TATGGACTTA
Found at i:3927 original size:11 final size:11
Alignment explanation
Indices: 3910--3941 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
3900 ATGGTCTTCA
3910 AATCTTCAAAT
1 AATCTTCAAAT
*
3921 TATCTTCAAAT
1 AATCTTCAAAT
3932 AATCTTCAAA
1 AATCTTCAAA
3942 CACGAACTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.44, C:0.19, G:0.00, T:0.38
Consensus pattern (11 bp):
AATCTTCAAAT
Found at i:5431 original size:331 final size:331
Alignment explanation
Indices: 4829--5493 Score: 1231
Period size: 331 Copynumber: 2.0 Consensus size: 331
4819 AGATTAACAT
*
4829 TGATAAGTCTGCAATCATGTTTAGTAGAAATACACTCGATAGTCTTTGAGATTTGATCATGCAAA
1 TGATAAGTCTGCAATCATGTTTAGTAGAAATACACCCGATAGTCTTTGAGATTTGATCATGCAAA
4894 ATGTAAATGTGCAGAAGACTTTGGCTAGAGATAAATATTTGGGTATGCCGATTATGATAGGCAAG
66 ATGTAAATGTGCAGAAGACTTTGGCTAGAGATAAATATTTGGGTATGCCGATTATGATAGGCAAG
4959 TCCAAGAGAGTGGAATTGGAAATTATTAAAGATAGATTATGGAAGAGAATTCAAGGTTGGCATGG
131 TCCAAGAGAGTGGAATTGGAAATTATTAAAGATAGATTATGGAAGAGAATTCAAGGTTGGCATGG
* * * *
5024 AAAATTACTATCTGTAGTTGGGAAAGCTGTGATGATTCAATCAGTGGCACATGCAATCCCTGCGT
196 AAAATTACTATCTGTAGCTGGGAAAGCTATGATGATTCAATCAGTGGCACAGGCAATCCCTACGT
*
5089 ATCTGATGAGCTGTTTTAAATTCCCTAAGACTTTTTTACAGGAATTGAACATGTTAATTGCTAAA
261 ATCTGATGAGCTGTTTTAAATTCCCTAAGACTTTTTTACAGGAATTGAACATGTTAATTGCAAAA
5154 TTCTGG
326 TTCTGG
* * *
5160 TGATAAGTCTGCAGTTATGTTTAGTAGCAATACACCCGATAGTCTTTGAGATTTGATCATGCAAA
1 TGATAAGTCTGCAATCATGTTTAGTAGAAATACACCCGATAGTCTTTGAGATTTGATCATGCAAA
* *
5225 ATTTAAATGTGTAGAAGACTTTGGCTAGAGATAAATATTTGGGTATGCCGATTATGATAGGCAAG
66 ATGTAAATGTGCAGAAGACTTTGGCTAGAGATAAATATTTGGGTATGCCGATTATGATAGGCAAG
5290 TCCAAGAGAGTGGAATTGGAAATTATTAAAGATAGATTATGGAAGAGAATTCAAGGTTGGCATGG
131 TCCAAGAGAGTGGAATTGGAAATTATTAAAGATAGATTATGGAAGAGAATTCAAGGTTGGCATGG
5355 AAAATTACTATCTGTAGCTGGGAAAGCTATGATGATTCAATCAGTGGCACAGGCAATCCCTACGT
196 AAAATTACTATCTGTAGCTGGGAAAGCTATGATGATTCAATCAGTGGCACAGGCAATCCCTACGT
5420 ATCTGATGAGCTGTTTTAAATTCCCTAAGACTTTTTTACAGGAATTGAACATGTTAATTGCAAAA
261 ATCTGATGAGCTGTTTTAAATTCCCTAAGACTTTTTTACAGGAATTGAACATGTTAATTGCAAAA
5485 TTCTGG
326 TTCTGG
5491 TGA
1 TGA
5494 GGAAGTACCG
Statistics
Matches: 323, Mismatches: 11, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
331 323 1.00
ACGTcount: A:0.33, C:0.12, G:0.23, T:0.32
Consensus pattern (331 bp):
TGATAAGTCTGCAATCATGTTTAGTAGAAATACACCCGATAGTCTTTGAGATTTGATCATGCAAA
ATGTAAATGTGCAGAAGACTTTGGCTAGAGATAAATATTTGGGTATGCCGATTATGATAGGCAAG
TCCAAGAGAGTGGAATTGGAAATTATTAAAGATAGATTATGGAAGAGAATTCAAGGTTGGCATGG
AAAATTACTATCTGTAGCTGGGAAAGCTATGATGATTCAATCAGTGGCACAGGCAATCCCTACGT
ATCTGATGAGCTGTTTTAAATTCCCTAAGACTTTTTTACAGGAATTGAACATGTTAATTGCAAAA
TTCTGG
Done.