Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014400.1 Corchorus capsularis cultivar CVL-1 contig14421, 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: 17721
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Found at i:1412 original size:15 final size:15
Alignment explanation
Indices: 1392--1422 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
1382 CGATAAGAGG
1392 ACGAAGAGTTTGATA
1 ACGAAGAGTTTGATA
1407 ACGAAGAGTTTGATA
1 ACGAAGAGTTTGATA
1422 A
1 A
1423 AATATATTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.42, C:0.06, G:0.26, T:0.26
Consensus pattern (15 bp):
ACGAAGAGTTTGATA
Found at i:12162 original size:28 final size:28
Alignment explanation
Indices: 12103--12162 Score: 68
Period size: 30 Copynumber: 2.1 Consensus size: 28
12093 GATACGTACC
* *
12103 TATATTTTCTTGTTGTTTTTTTTTGGAATG
1 TATATTTTCTTGTTGTTTTATATT-G-ATG
12133 TATATTTTCTTGTTGTTTTAATATT-ATG
1 TATATTTTCTTGTTGTTTT-ATATTGATG
12161 TA
1 TA
12163 ATTAAAGATC
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
28 5 0.19
30 19 0.70
31 3 0.11
ACGTcount: A:0.18, C:0.03, G:0.13, T:0.65
Consensus pattern (28 bp):
TATATTTTCTTGTTGTTTTATATTGATG
Found at i:13421 original size:33 final size:33
Alignment explanation
Indices: 13377--13443 Score: 91
Period size: 33 Copynumber: 2.0 Consensus size: 33
13367 CTTTTACACT
*
13377 GAGCCTTCCCACTAGGACGGC-TCAGCCACGGCA
1 GAGCCTCCCCACTAGGACGGCTTC-GCCACGGCA
* *
13410 GAGCCTCCCCACTGGGGCGGCTTCGCCACGGCA
1 GAGCCTCCCCACTAGGACGGCTTCGCCACGGCA
13443 G
1 G
13444 GCCGCCCTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
33 28 0.93
34 2 0.07
ACGTcount: A:0.16, C:0.40, G:0.31, T:0.12
Consensus pattern (33 bp):
GAGCCTCCCCACTAGGACGGCTTCGCCACGGCA
Found at i:13470 original size:30 final size:31
Alignment explanation
Indices: 13401--13486 Score: 102
Period size: 30 Copynumber: 2.7 Consensus size: 31
13391 GGACGGCTCA
* * *
13401 GCCACGGCAGAGCCTCCCCACTGGGGCGGCTTC
1 GCCACGGCAG-GCCGCCCTA-TGGCGCGGCTTC
*
13434 GCCACGGCAGGCCGCCCTATGGCGCGG-TTT
1 GCCACGGCAGGCCGCCCTATGGCGCGGCTTC
13464 GCCACGGCAGGCCGCCCTCATGG
1 GCCACGGCAGGCCGCCCT-ATGG
13487 AGTGGCTAGA
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
30 20 0.42
31 11 0.23
32 7 0.15
33 10 0.21
ACGTcount: A:0.12, C:0.41, G:0.35, T:0.13
Consensus pattern (31 bp):
GCCACGGCAGGCCGCCCTATGGCGCGGCTTC
Found at i:13596 original size:32 final size:32
Alignment explanation
Indices: 13560--13667 Score: 164
Period size: 32 Copynumber: 3.3 Consensus size: 32
13550 GCCCCACCGA
13560 GGCGGCCTGCACTGGCTAAGTCGCCCCAGTGG
1 GGCGGCCTGCACTGGCTAAGTCGCCCCAGTGG
13592 GGCGGCCTGCACTGGCTAAGTCGCCCCAGTGG
1 GGCGGCCTGCACTGGCTAAGTCGCCCCAGTGG
* *
13624 GGCGGCCTGCCCATGG-TGAAGCCGCCCCAGTGG
1 GGCGGCCTGCAC-TGGCT-AAGTCGCCCCAGTGG
13657 GGCGGCTCTGC
1 GGCGGC-CTGC
13668 CGTGGTTGAG
Statistics
Matches: 71, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
32 44 0.62
33 23 0.32
34 4 0.06
ACGTcount: A:0.11, C:0.35, G:0.39, T:0.15
Consensus pattern (32 bp):
GGCGGCCTGCACTGGCTAAGTCGCCCCAGTGG
Found at i:13655 original size:33 final size:32
Alignment explanation
Indices: 13546--13695 Score: 160
Period size: 32 Copynumber: 4.6 Consensus size: 32
13536 AAAATAGCCG
** *
13546 AGCCGCCCCACCGAGGCGGCCTGCACTGGCTA
1 AGCCGCCCCAGTGGGGCGGCCTGCACTGGCTA
*
13578 AGTCGCCCCAGTGGGGCGGCCTGCACTGGCTA
1 AGCCGCCCCAGTGGGGCGGCCTGCACTGGCTA
* *
13610 AGTCGCCCCAGTGGGGCGGCCTGCCCATGG-TGA
1 AGCCGCCCCAGTGGGGCGGCCTGCAC-TGGCT-A
* *
13643 AGCCGCCCCAGTGGGGCGGCTCTGC-CGTGGTTG
1 AGCCGCCCCAGTGGGGCGGC-CTGCAC-TGGCTA
* *
13676 AGCCTCCCAAGTGGGGCGGC
1 AGCCGCCCCAGTGGGGCGGC
13696 TTCGCCACGG
Statistics
Matches: 104, Mismatches: 10, Indels: 7
0.86 0.08 0.06
Matches are distributed among these distances:
32 54 0.52
33 45 0.43
34 5 0.05
ACGTcount: A:0.12, C:0.36, G:0.38, T:0.14
Consensus pattern (32 bp):
AGCCGCCCCAGTGGGGCGGCCTGCACTGGCTA
Found at i:13696 original size:33 final size:34
Alignment explanation
Indices: 13581--13696 Score: 109
Period size: 33 Copynumber: 3.5 Consensus size: 34
13571 CTGGCTAAGT
* * *
13581 CGCCCCAGTGGGGCGGC-CTGCAC-TGGCT-AAGT
1 CGCCCAAGTGGGGCGGCTCTGCCCATGG-TGAAGC
*
13613 CGCCCCAGTGGGGCGGC-CTGCCCATGGTGAAGC
1 CGCCCAAGTGGGGCGGCTCTGCCCATGGTGAAGC
* *
13646 CGCCCCAGTGGGGCGGCTCTG-CCGTGGTTG-AGC
1 CGCCCAAGTGGGGCGGCTCTGCCCATGG-TGAAGC
*
13679 CTCCCAAGTGGGGCGGCT
1 CGCCCAAGTGGGGCGGCT
13697 TCGCCACGGT
Statistics
Matches: 75, Mismatches: 5, Indels: 7
0.86 0.06 0.08
Matches are distributed among these distances:
32 23 0.31
33 47 0.63
34 5 0.07
ACGTcount: A:0.10, C:0.34, G:0.40, T:0.16
Consensus pattern (34 bp):
CGCCCAAGTGGGGCGGCTCTGCCCATGGTGAAGC
Found at i:13711 original size:65 final size:64
Alignment explanation
Indices: 13560--13715 Score: 158
Period size: 65 Copynumber: 2.4 Consensus size: 64
13550 GCCCCACCGA
* * *
13560 GGCGGCCTG--CACTGGCTAAGTCGCCCCAGTGGGGCGGCCTGCACTGGCTAAGTCGCCCCAGTG
1 GGCGGCCTGCCCAC-GG-TAAGCCGCCCCAGTGGGGCGGCCTGCACTGGCTAAGCCGCCCAAGTG
13623 G
64 G
* * * *
13624 GGCGGCCTGCCCATGGTGAAGCCGCCCCAGTGGGGCGGCTCTGC-CGTGGTTGAGCCTCCCAAGT
1 GGCGGCCTGCCCACGGT-AAGCCGCCCCAGTGGGGCGGC-CTGCAC-TGGCTAAGCCGCCCAAGT
13688 GG
63 GG
*
13690 GGCGG-CTTCGCCACGGTAAGCCGCCC
1 GGCGGCCTGC-CCACGGTAAGCCGCCC
13716 TCTTGGGACG
Statistics
Matches: 77, Mismatches: 9, Indels: 11
0.79 0.09 0.11
Matches are distributed among these distances:
64 10 0.13
65 35 0.45
66 32 0.42
ACGTcount: A:0.12, C:0.35, G:0.38, T:0.15
Consensus pattern (64 bp):
GGCGGCCTGCCCACGGTAAGCCGCCCCAGTGGGGCGGCCTGCACTGGCTAAGCCGCCCAAGTGG
Found at i:16450 original size:18 final size:18
Alignment explanation
Indices: 16429--16463 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
16419 GTAAATTGAC
16429 ATAAAATATAAA-ATAATA
1 ATAAAA-ATAAATATAATA
16447 ATAAAAATAAATATAAT
1 ATAAAAATAAATATAAT
16464 TACCTCAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (18 bp):
ATAAAAATAAATATAATA
Done.