Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01004961.1 Corchorus capsularis cultivar CVL-1 contig04979, 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: 18990
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.32
Found at i:1336 original size:58 final size:55
Alignment explanation
Indices: 1195--1370 Score: 226
Period size: 55 Copynumber: 3.1 Consensus size: 55
1185 TTCGTTACAT
1195 CATCAGGACCAATTTTTTGGTCCAGATGATCTGAATGATAAATTGAAGGCAACAC
1 CATCAGGACCAATTTTTTGGTCCAGATGATCTGAATGATAAATTGAAGGCAACAC
* * ** * * ** *
1250 CATCAGGATCAATTTATTAATCCCGATGATTTGAGTAATTTTTAATTGAAGGCAACAC
1 CATCAGGACCAATTTTTTGGTCCAGATGATCT--G-AATGATAAATTGAAGGCAACAC
* *
1308 CATCAGGACCAATTTTTTGGTCCAGATGATCTGAATGATAAGTTGAAGGCAACAA
1 CATCAGGACCAATTTTTTGGTCCAGATGATCTGAATGATAAATTGAAGGCAACAC
1363 CATCAGGA
1 CATCAGGA
1371 TCAAGCTATT
Statistics
Matches: 98, Mismatches: 20, Indels: 6
0.79 0.16 0.05
Matches are distributed among these distances:
55 51 0.52
56 1 0.01
57 1 0.01
58 45 0.46
ACGTcount: A:0.35, C:0.17, G:0.19, T:0.29
Consensus pattern (55 bp):
CATCAGGACCAATTTTTTGGTCCAGATGATCTGAATGATAAATTGAAGGCAACAC
Found at i:5233 original size:31 final size:31
Alignment explanation
Indices: 5197--5258 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
5187 AATATTACAA
5197 GTCGGTGGTATTGGTTTCAGGTGAGTCACCG
1 GTCGGTGGTATTGGTTTCAGGTGAGTCACCG
*
5228 GTCGGTGGTGTTGGTTTCAGGTGAGTCACCG
1 GTCGGTGGTATTGGTTTCAGGTGAGTCACCG
5259 ACCGACTACA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.11, C:0.16, G:0.40, T:0.32
Consensus pattern (31 bp):
GTCGGTGGTATTGGTTTCAGGTGAGTCACCG
Found at i:5592 original size:24 final size:24
Alignment explanation
Indices: 5565--5611 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
5555 GAATCTTAAT
5565 TATTTATACCTTTACTATTAAAGC
1 TATTTATACCTTTACTATTAAAGC
5589 TATTTATACCTTTACTATTAAAG
1 TATTTATACCTTTACTATTAAAG
5612 TTATAAGTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.34, C:0.15, G:0.04, T:0.47
Consensus pattern (24 bp):
TATTTATACCTTTACTATTAAAGC
Found at i:5630 original size:36 final size:36
Alignment explanation
Indices: 5583--5651 Score: 138
Period size: 36 Copynumber: 1.9 Consensus size: 36
5573 CCTTTACTAT
5583 TAAAGCTATTTATACCTTTACTATTAAAGTTATAAG
1 TAAAGCTATTTATACCTTTACTATTAAAGTTATAAG
5619 TAAAGCTATTTATACCTTTACTATTAAAGTTAT
1 TAAAGCTATTTATACCTTTACTATTAAAGTTAT
5652 CCCAAATTGC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.38, C:0.12, G:0.07, T:0.43
Consensus pattern (36 bp):
TAAAGCTATTTATACCTTTACTATTAAAGTTATAAG
Found at i:14451 original size:83 final size:83
Alignment explanation
Indices: 14312--14477 Score: 296
Period size: 83 Copynumber: 2.0 Consensus size: 83
14302 ATATTCTATC
*
14312 GTGAAAAAGTGAGAACACACCAAGACAAAAGTTTAAAGCAACAGAACCATTAAATTTTTAAGCCA
1 GTGAAAAAGTGAGAACACACCAAAACAAAAGTTTAAAGCAACAGAACCATTAAATTTTTAAGCCA
*
14377 GGCTTCCATAACAAACTT
66 GACTTCCATAACAAACTT
*
14395 GTGAAAAAGTGAGAACACACCAAAACAAAAGTTTAAAGCAACAGAACCATTGAATTTTTAAGCCA
1 GTGAAAAAGTGAGAACACACCAAAACAAAAGTTTAAAGCAACAGAACCATTAAATTTTTAAGCCA
*
14460 GATTTCCATAACAAACTT
66 GACTTCCATAACAAACTT
14478 ATTTGTATGC
Statistics
Matches: 79, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
83 79 1.00
ACGTcount: A:0.46, C:0.19, G:0.14, T:0.21
Consensus pattern (83 bp):
GTGAAAAAGTGAGAACACACCAAAACAAAAGTTTAAAGCAACAGAACCATTAAATTTTTAAGCCA
GACTTCCATAACAAACTT
Found at i:15914 original size:32 final size:32
Alignment explanation
Indices: 15871--15935 Score: 121
Period size: 32 Copynumber: 2.0 Consensus size: 32
15861 TTCCCTCTTT
15871 TTACATGTTACATAATCATAATTAGTATTAAG
1 TTACATGTTACATAATCATAATTAGTATTAAG
*
15903 TTACATTTTACATAATCATAATTAGTATTAAG
1 TTACATGTTACATAATCATAATTAGTATTAAG
15935 T
1 T
15936 GTTAGTTTCT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.40, C:0.09, G:0.08, T:0.43
Consensus pattern (32 bp):
TTACATGTTACATAATCATAATTAGTATTAAG
Found at i:15961 original size:32 final size:34
Alignment explanation
Indices: 15925--15989 Score: 98
Period size: 32 Copynumber: 2.0 Consensus size: 34
15915 TAATCATAAT
* *
15925 TAGTATTAAGTGTTAGTTTC-TTTTCT-ACTATG
1 TAGTATTAAATGTCAGTTTCTTTTTCTAACTATG
15957 TAGTATTAAATGTCAGTTTCTTTTTCTAACTAT
1 TAGTATTAAATGTCAGTTTCTTTTTCTAACTAT
15990 AAATATAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 18 0.62
33 6 0.21
34 5 0.17
ACGTcount: A:0.25, C:0.11, G:0.12, T:0.52
Consensus pattern (34 bp):
TAGTATTAAATGTCAGTTTCTTTTTCTAACTATG
Done.