Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015648.1 Corchorus capsularis cultivar CVL-1 contig15669, 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: 17567
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.28
Found at i:12434 original size:49 final size:49
Alignment explanation
Indices: 12305--12695 Score: 423
Period size: 50 Copynumber: 8.0 Consensus size: 49
12295 TCAATTTTAG
* * *
12305 GTTTTTATCTGCTATTGCCCAAAATACCCTTCCCGGACGGAGGGCACTT
1 GTTTTTATCTGCTATTTCCCAAAATGCCCTTCCCGGACGGAAGGCACTT
* *
12354 GTTTTTAATCTGCTATTTCTCAAAATCCCCTTCCCGGACGGAAGGCACTT
1 GTTTTT-ATCTGCTATTTCCCAAAATGCCCTTCCCGGACGGAAGGCACTT
* * *
12404 GTTTTTATCTGCTATTGCCCAAAATACCCTTCCTGGACGGAAGGCACTT
1 GTTTTTATCTGCTATTTCCCAAAATGCCCTTCCCGGACGGAAGGCACTT
12453 GTTTTTAATCTGCTATTTCCCAAAATGCCCTTCCCGGACGGAAGGCACTT
1 GTTTTT-ATCTGCTATTTCCCAAAATGCCCTTCCCGGACGGAAGGCACTT
* ** * *
12503 GTTTTTACCTGCTATTTCCCAAAGCGCCCTTCCCAGACGGAAGCCA-TT
1 GTTTTTATCTGCTATTTCCCAAAATGCCCTTCCCGGACGGAAGGCACTT
* * * * ** * *
12551 CATTTTT-GCTAGATATTTCCCTAAAATGCCCATCCTAGATGGAAGGCACTG
1 -GTTTTTATCT-GCTATTTCCC-AAAATGCCCTTCCCGGACGGAAGGCACTT
* * **
12602 GTTTCT-CCTGCT-TTGTCCCAAAATGCCCTTCCCGGACGGAAGGCACCA
1 GTTTTTATCTGCTATT-TCCCAAAATGCCCTTCCCGGACGGAAGGCACTT
* * * **
12650 GTTTTTACCTG-TTTTTCCTAAAACACCCTTCCCGGACGGAAGGCAC
1 GTTTTTATCTGCTATTTCCCAAAATGCCCTTCCCGGACGGAAGGCAC
12696 CATTCTCTTA
Statistics
Matches: 293, Mismatches: 40, Indels: 19
0.83 0.11 0.05
Matches are distributed among these distances:
48 63 0.22
49 112 0.38
50 117 0.40
51 1 0.00
ACGTcount: A:0.22, C:0.29, G:0.18, T:0.31
Consensus pattern (49 bp):
GTTTTTATCTGCTATTTCCCAAAATGCCCTTCCCGGACGGAAGGCACTT
Found at i:12477 original size:99 final size:98
Alignment explanation
Indices: 12305--12695 Score: 425
Period size: 99 Copynumber: 4.0 Consensus size: 98
12295 TCAATTTTAG
* *
12305 GTTTTTATCTGCTATTGCCCAAAATACCCTTCCCGGACGGAGGGCACTTGTTTTTAATCTGCTAT
1 GTTTTTACCTGCTATTGCCCAAAATACCCTTCCCGGACGGAAGGCACTTGTTTTT-ATCTGCTAT
*
12370 TTCTCAAAATCCCCTTCCCGGACGGAAGGCACTT
65 TTCCCAAAATCCCCTTCCCGGACGGAAGGCACTT
* *
12404 GTTTTTATCTGCTATTGCCCAAAATACCCTTCCTGGACGGAAGGCACTTGTTTTTAATCTGCTAT
1 GTTTTTACCTGCTATTGCCCAAAATACCCTTCCCGGACGGAAGGCACTTGTTTTT-ATCTGCTAT
*
12469 TTCCCAAAATGCCCTTCCCGGACGGAAGGCACTT
65 TTCCCAAAATCCCCTTCCCGGACGGAAGGCACTT
* *** * * * * *
12503 GTTTTTACCTGCTATTTCCCAAAGCGCCCTTCCCAGACGGAAGCCA-TTCATTTTT-GCTAGATA
1 GTTTTTACCTGCTATTGCCCAAAATACCCTTCCCGGACGGAAGGCACTT-GTTTTTATCT-GCTA
* * ** * *
12566 TTTCCCTAAAATGCCCATCCTAGATGGAAGGCACTG
64 TTTCCC-AAAATCCCCTTCCCGGACGGAAGGCACTT
* * ** * *
12602 GTTTCT-CCTGCT-TTGTCCCAAAATGCCCTTCCCGGACGGAAGGCACCAGTTTTTACCTG-TTT
1 GTTTTTACCTGCTATTG-CCCAAAATACCCTTCCCGGACGGAAGGCACTTGTTTTTATCTGCTAT
*
12664 TTCCTAAAA-CACCCTTCCCGGACGGAAGGCAC
65 TTCCCAAAATC-CCCTTCCCGGACGGAAGGCAC
12696 CATTCTCTTA
Statistics
Matches: 248, Mismatches: 37, Indels: 17
0.82 0.12 0.06
Matches are distributed among these distances:
96 21 0.08
97 10 0.04
98 48 0.19
99 169 0.68
ACGTcount: A:0.22, C:0.29, G:0.18, T:0.31
Consensus pattern (98 bp):
GTTTTTACCTGCTATTGCCCAAAATACCCTTCCCGGACGGAAGGCACTTGTTTTTATCTGCTATT
TCCCAAAATCCCCTTCCCGGACGGAAGGCACTT
Found at i:16600 original size:33 final size:31
Alignment explanation
Indices: 16522--16617 Score: 99
Period size: 30 Copynumber: 3.1 Consensus size: 31
16512 AAAGGATCAA
* *
16522 ATGGCCGGTTGTGCCCGGAT-GGCCCATGCG
1 ATGGCCGGTTGTGGCCGGTTGGGCCCATGCG
* *
16552 ATGGCTGGTTGTGGCCGGTTGGTGCCTCATGTG
1 ATGGCCGGTTGTGGCCGGTTGG-GCC-CATGCG
*
16585 TTGGCCGGTTGTGGCCGGTT--GCTCCATGCG
1 ATGGCCGGTTGTGGCCGGTTGGGC-CCATGCG
16615 ATG
1 ATG
16618 TCGCATGCGA
Statistics
Matches: 54, Mismatches: 8, Indels: 8
0.77 0.11 0.11
Matches are distributed among these distances:
30 26 0.48
31 2 0.04
32 3 0.06
33 23 0.43
ACGTcount: A:0.07, C:0.24, G:0.41, T:0.28
Consensus pattern (31 bp):
ATGGCCGGTTGTGGCCGGTTGGGCCCATGCG
Done.