Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007321.1 Corchorus capsularis cultivar CVL-1 contig07342, 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: 27703
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:810 original size:402 final size:401
Alignment explanation
Indices: 1--948 Score: 1734
Period size: 402 Copynumber: 2.4 Consensus size: 401
* *
1 GTTTCTCTCTTAGTAATTGACATGGAGGGAGGTGTTATACCTTGTTAGTAACATAAGAAACGTCC
1 GTTTCTCTCTTAGTAATTGATATGGAGGGAGGTATTATACCTTGTTAGTAACATAAGAAACGTCC
66 GAGTTTTAATTTTCAAGGGCGCCCATAACTCTAACTTTCTTATTTTGTTACAGACCCATTTATTC
66 GAGTTTTAATTTTCAAGGGCGCCCATAACTCTAACTTTCTTATTTTGTTACAGACCCATTTATTC
*
131 CCCAGATTCAACATTAAATTTACCATTGAATCATCAAAAATGTCGTCACCCTTGGCTCCAGATGA
131 CCCAGATTCAACATTAAATTTACCATTGAATCATCAAAAATGTCGTCACCCTTGGCTCCAAATGA
*
196 TAAGATATATTTTTTTTGAACCGGTTGGGTAATTAGAGCCATGGTGAATCGCCCGTGCAGAGCTT
196 CAAGATATATTTTTTTTGAACCGGTTGGGTAATTAGAGCCATGGTGAATCGCCCGTGCAGAGCTT
* *
261 GTGCTTTTCTTGATAGAAGGCTTTCTTGCCTCAATTGAAGTTAAAGATGTGATGAATAGAAGAAA
261 GTGCTTTTCTTGACAGAAGGCTTTCTTGCCTCAACTGAAGTTAAAGATGTGATGAATAGAAGAAA
326 CATGATAGTAGTTAGTAGCCATAAAAGCTAGAAGACATAATCTTCCATCTCTCTTCATGTCTAAA
326 CATGATAGTAGTTAGTAGCCATAAAAGCTAGAAGACATAATCTTCCATCTCTCTTCATGTCTAAA
391 AGCTGAATTTC
391 AGCTGAATTTC
402 GTTTCTCTCTTAGTAATTGATATGGAGGGAGGTATTATACCTTGTTAGTAACATAAGAAACGTCC
1 GTTTCTCTCTTAGTAATTGATATGGAGGGAGGTATTATACCTTGTTAGTAACATAAGAAACGTCC
467 GAGTTTTAATTTTCAAGGGCGCCCATAACTCTAACTTTCTTATTTTGTTACAGACCCATTTATTC
66 GAGTTTTAATTTTCAAGGGCGCCCATAACTCTAACTTTCTTATTTTGTTACAGACCCATTTATTC
*
532 CCTAGATTCAACATTAAATTTACCATTGAATCATCAAAAATGTCGTCACCCTTGGCTCCAAATGA
131 CCCAGATTCAACATTAAATTTACCATTGAATCATCAAAAATGTCGTCACCCTTGGCTCCAAATGA
*
597 CAAGATATATATTTTTTTGAACCGGTTGGGTAATTAGAGCCATGGTGCATCGCCCGTGCAGAGCT
196 CAAGATATAT-TTTTTTTGAACCGGTTGGGTAATTAGAGCCATGGTGAATCGCCCGTGCAGAGCT
662 TGTGCTTTTCTTGACAGAAGGCTTTCTTGCCTCAACTGAAGTTAAAGATGTGATGAATAGAAGAA
260 TGTGCTTTTCTTGACAGAAGGCTTTCTTGCCTCAACTGAAGTTAAAGATGTGATGAATAGAAGAA
*
727 ACATGATAGTAGTTGGTAGCCATAAAAGCTAGAAGACATAATCTTCCATCTCTCTTCATGTCTAA
325 ACATGATAGTAGTTAGTAGCCATAAAAGCTAGAAGACATAATCTTCCATCTCTCTTCATGTCTAA
*
792 AAGCTGAATTTT
390 AAGCTGAATTTC
* * * * *
804 GTTTCTCTCTTAGCAACTGATATGGAGGGAGGTATTATACCTTGTTAGAAACGTAAGAAACGTCA
1 GTTTCTCTCTTAGTAATTGATATGGAGGGAGGTATTATACCTTGTTAGTAACATAAGAAACGTCC
* *
869 GAGTTTTAATTTTCAAGGGCGCCCATAACTTTAACTTTCTTATTTTGTCACAGACCCATTTATTC
66 GAGTTTTAATTTTCAAGGGCGCCCATAACTCTAACTTTCTTATTTTGTTACAGACCCATTTATTC
934 CCCAGATTCAACATT
131 CCCAGATTCAACATT
949 TACCATAATA
Statistics
Matches: 528, Mismatches: 18, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
401 200 0.38
402 328 0.62
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.34
Consensus pattern (401 bp):
GTTTCTCTCTTAGTAATTGATATGGAGGGAGGTATTATACCTTGTTAGTAACATAAGAAACGTCC
GAGTTTTAATTTTCAAGGGCGCCCATAACTCTAACTTTCTTATTTTGTTACAGACCCATTTATTC
CCCAGATTCAACATTAAATTTACCATTGAATCATCAAAAATGTCGTCACCCTTGGCTCCAAATGA
CAAGATATATTTTTTTTGAACCGGTTGGGTAATTAGAGCCATGGTGAATCGCCCGTGCAGAGCTT
GTGCTTTTCTTGACAGAAGGCTTTCTTGCCTCAACTGAAGTTAAAGATGTGATGAATAGAAGAAA
CATGATAGTAGTTAGTAGCCATAAAAGCTAGAAGACATAATCTTCCATCTCTCTTCATGTCTAAA
AGCTGAATTTC
Found at i:15698 original size:10 final size:10
Alignment explanation
Indices: 15675--15704 Score: 51
Period size: 10 Copynumber: 2.9 Consensus size: 10
15665 GACTGAAAAC
15675 GAAGAAAGGAA
1 GAAGAAA-GAA
15686 GAAGAAAGAA
1 GAAGAAAGAA
15696 GAAGAAAGA
1 GAAGAAAGA
15705 GGCGGAGGTG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 12 0.63
11 7 0.37
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (10 bp):
GAAGAAAGAA
Found at i:15831 original size:2 final size:2
Alignment explanation
Indices: 15816--15866 Score: 51
Period size: 2 Copynumber: 28.5 Consensus size: 2
15806 AAAAATTATT
*
15816 TA TA T- TA T- TA TA TA TA TA TT TA TA T- TA T- TA T- TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
15853 T- TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA T
15867 TAATCGGTCG
Statistics
Matches: 41, Mismatches: 2, Indels: 12
0.75 0.04 0.22
Matches are distributed among these distances:
1 6 0.15
2 35 0.85
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (2 bp):
TA
Found at i:15837 original size:20 final size:19
Alignment explanation
Indices: 15812--15860 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 19
15802 AAATAAAAAT
15812 TATTTATATTATTATATATA
1 TATTTATATTATTAT-TATA
15832 TATTTATATTATTATTATA
1 TATTTATATTATTATTATA
15851 TATTATATAT
1 TATT-TATAT
15861 ATATATTAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
19 8 0.29
20 20 0.71
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (19 bp):
TATTTATATTATTATTATA
Found at i:15848 original size:26 final size:25
Alignment explanation
Indices: 15811--15868 Score: 75
Period size: 26 Copynumber: 2.3 Consensus size: 25
15801 AAAATAAAAA
15811 TTAT-TTATATTAT-TATATATATAT
1 TTATATTATATTATATAT-TATATAT
15835 TTATATTATTATTATATATTATATAT
1 TTATATTA-TATTATATATTATATAT
*
15861 ATATATTA
1 TTATATTA
15869 ATCGGTCGGT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
24 4 0.13
25 3 0.10
26 20 0.67
27 3 0.10
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (25 bp):
TTATATTATATTATATATTATATAT
Found at i:15867 original size:20 final size:20
Alignment explanation
Indices: 15810--15868 Score: 75
Period size: 20 Copynumber: 2.9 Consensus size: 20
15800 AAAAATAAAA
15810 ATTATTTATAT-TATTATAT
1 ATTATTTATATATATTATAT
15829 ATATATTTATATTATTATTATAT
1 AT-TATTTATA-TA-TATTATAT
*
15852 ATTATATATATATATTA
1 ATTATTTATATATATTA
15869 ATCGGTCGGT
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
19 2 0.06
20 13 0.37
21 3 0.09
22 7 0.20
23 10 0.29
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (20 bp):
ATTATTTATATATATTATAT
Found at i:16728 original size:27 final size:26
Alignment explanation
Indices: 16705--16753 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
16695 CACTTTTTAG
*
16705 TTTGAG-TAATTTATAACCCATTTTT
1 TTTGAGATAATTTATAAACCATTTTT
*
16730 TTTTAGATAATTTATAAACCATTT
1 TTTGAGATAATTTATAAACCATTT
16754 AAATGTTTGT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 5 0.24
26 16 0.76
ACGTcount: A:0.33, C:0.10, G:0.06, T:0.51
Consensus pattern (26 bp):
TTTGAGATAATTTATAAACCATTTTT
Done.