Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012509.1 Corchorus capsularis cultivar CVL-1 contig12530, 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: 21946
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.33
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:704 original size:22 final size:22
Alignment explanation
Indices: 673--719 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
663 AAGAAGGTTA
* *
673 TACCAATCTTCTTATTCAAGGT
1 TACCAATCTTCTAATCCAAGGT
*
695 TACCATTCTTCTAATCCAAGGT
1 TACCAATCTTCTAATCCAAGGT
717 TAC
1 TAC
720 TAAATAAACT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.28, C:0.26, G:0.09, T:0.38
Consensus pattern (22 bp):
TACCAATCTTCTAATCCAAGGT
Found at i:4851 original size:2 final size:2
Alignment explanation
Indices: 4839--4888 Score: 73
Period size: 2 Copynumber: 24.5 Consensus size: 2
4829 AGTTTAGACT
* *
4839 TA TA TA GTA TA TA TA GA TA TA GA TA TA TA TA TA TA TA 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
4882 TA TA TA T
1 TA TA TA T
4889 TAATCATGTA
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
2 41 0.95
3 2 0.05
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.46
Consensus pattern (2 bp):
TA
Found at i:7379 original size:13 final size:13
Alignment explanation
Indices: 7361--7391 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
7351 TTTTATAATT
*
7361 TTATAAAGGAAAA
1 TTATAAAGAAAAA
7374 TTATAAAGAAAAA
1 TTATAAAGAAAAA
7387 TTATA
1 TTATA
7392 CAATACACTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.61, C:0.00, G:0.10, T:0.29
Consensus pattern (13 bp):
TTATAAAGAAAAA
Found at i:7539 original size:39 final size:39
Alignment explanation
Indices: 7496--7575 Score: 106
Period size: 39 Copynumber: 2.1 Consensus size: 39
7486 TATAAAATTA
* * *
7496 GTTAAGAAAATAAATATGTGTCAACACTTTAATCAGCTT
1 GTTAAGAAAATAAATACGCGTAAACACTTTAATCAGCTT
* **
7535 GTTAAGGAAATGGATACGCGTAAACACTTTAATCAGCTT
1 GTTAAGAAAATAAATACGCGTAAACACTTTAATCAGCTT
7574 GT
1 GT
7576 GAAATCTAAG
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.38, C:0.14, G:0.17, T:0.31
Consensus pattern (39 bp):
GTTAAGAAAATAAATACGCGTAAACACTTTAATCAGCTT
Found at i:19210 original size:51 final size:51
Alignment explanation
Indices: 19114--19214 Score: 139
Period size: 51 Copynumber: 2.0 Consensus size: 51
19104 GTAACATATA
* * *
19114 AAGTAATGACCTGTTGCAGTTTTCAAACAAGAATTACATCATCCAATACTG
1 AAGTAAGGACCTGTCGCAGTTTTCAAACAAAAATTACATCATCCAATACTG
* * * *
19165 AAGTAAGGACCTGTCGCAGTTTTTAAGCAAAAATTGCATCGTCCAATACT
1 AAGTAAGGACCTGTCGCAGTTTTCAAACAAAAATTACATCATCCAATACT
19215 AGGCTCAAAG
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
51 43 1.00
ACGTcount: A:0.36, C:0.20, G:0.16, T:0.29
Consensus pattern (51 bp):
AAGTAAGGACCTGTCGCAGTTTTCAAACAAAAATTACATCATCCAATACTG
Found at i:21006 original size:58 final size:58
Alignment explanation
Indices: 20938--21050 Score: 156
Period size: 58 Copynumber: 1.9 Consensus size: 58
20928 TGAGATAAAT
* *
20938 GACAAAACAAAATAATACT-ACCTTCAAGAAATTTGTCCACTGCATTAATTAATTTTAA
1 GACAAAACAAAATAAT-CTCAACTTCAAGAAATTTGTCCACTGCAGTAATTAATTTTAA
* * * *
20996 GACAACACAAAATACTTTCAACTTCAAGAAATTTGTTCACTGCAGTAATTAATTT
1 GACAAAACAAAATAATCTCAACTTCAAGAAATTTGTCCACTGCAGTAATTAATTT
21051 GAAAGTATTC
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
57 1 0.02
58 47 0.98
ACGTcount: A:0.42, C:0.18, G:0.08, T:0.32
Consensus pattern (58 bp):
GACAAAACAAAATAATCTCAACTTCAAGAAATTTGTCCACTGCAGTAATTAATTTTAA
Found at i:21618 original size:75 final size:75
Alignment explanation
Indices: 21531--21679 Score: 282
Period size: 75 Copynumber: 2.0 Consensus size: 75
21521 CTTTTGGAGG
21531 CTTCCTTTTGTTATGAAGCATGATAAACATGTCAGATTTGGTTGCTTGATACTACATTTTTTTGC
1 CTTCCTTTTGTTATGAAGCATGATAAACATGTCAGATTTGGTTGCTTGATACTAC-TTTTTTTGC
21596 ATTA-TAATTA
65 ATTATTAATTA
21606 CTTCCTTTTGTTATGAAGCATGATAAACATGTCAGATTTGGTTGCTTGATACTACTTTTTTTGCA
1 CTTCCTTTTGTTATGAAGCATGATAAACATGTCAGATTTGGTTGCTTGATACTACTTTTTTTGCA
21671 TTATTAATT
66 TTATTAATT
21680 GAAGTCATGG
Statistics
Matches: 73, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
74 13 0.18
75 60 0.82
ACGTcount: A:0.26, C:0.13, G:0.15, T:0.46
Consensus pattern (75 bp):
CTTCCTTTTGTTATGAAGCATGATAAACATGTCAGATTTGGTTGCTTGATACTACTTTTTTTGCA
TTATTAATTA
Done.