Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010876.1 Corchorus capsularis cultivar CVL-1 contig10897, 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: 32611
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Found at i:12500 original size:30 final size:29
Alignment explanation
Indices: 12448--12504 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 29
12438 GTCTACCCGA
* * *
12448 TACTAAACAAAAAACAACCTTATATATTT
1 TACTAAAAAAAAAAAAAACTTATATATTT
12477 TACTCAAAAAAAAAAAAAACTTATATAT
1 TACT-AAAAAAAAAAAAAACTTATATAT
12505 GGTCAAAGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 4 0.17
30 20 0.83
ACGTcount: A:0.58, C:0.14, G:0.00, T:0.28
Consensus pattern (29 bp):
TACTAAAAAAAAAAAAAACTTATATATTT
Found at i:13061 original size:2 final size:2
Alignment explanation
Indices: 13012--13047 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
13002 GTTTACTACA
13012 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
13048 CCTACTATTA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:13940 original size:183 final size:185
Alignment explanation
Indices: 13724--14093 Score: 726
Period size: 183 Copynumber: 2.0 Consensus size: 185
13714 AGACCTTGAA
13724 TTGTTAAAAACATATTCCCTCTGTGCCAAATTATCTAATCCTTTTGAGTCAAAGTAATCTTAATT
1 TTGTTAAAAACATATTCCCTCTGTGCCAAATTATCTAATCCTTTTGAGTCAAAGTAATCTTAATT
13789 TTGACCCTTAATTAT-AAAAAAATTATATAAAATTAAAATTTTAAAAATTATGTTATGATTAAGT
66 TTGACCCTTAATTATAAAAAAAATTATATAAAATTAAAATTTTAAAAATTATGTTATGATTAAGT
13853 TAAATCTTAAACTTTTCAAAATATA-TTTTTTAAAATTTAATTGCATATATATTT
131 TAAATCTTAAACTTTTCAAAATATATTTTTTTAAAATTTAATTGCATATATATTT
13907 TTGTTAAAAACATATTCCCTCTGTGCCAAATTATCTAATCCTTTTGAGTCAAAGTAATCTTAATT
1 TTGTTAAAAACATATTCCCTCTGTGCCAAATTATCTAATCCTTTTGAGTCAAAGTAATCTTAATT
13972 TTGACCCTTAATTATAAAAAAAATTATATAAAATTAAAATTTTAAAAATTATGTTATGATTAAGT
66 TTGACCCTTAATTATAAAAAAAATTATATAAAATTAAAATTTTAAAAATTATGTTATGATTAAGT
14037 TAAATCTTAAACTTTTCAAAATATATTTTTTTAAAATTTAATTGCATATATATTT
131 TAAATCTTAAACTTTTCAAAATATATTTTTTTAAAATTTAATTGCATATATATTT
14092 TT
1 TT
14094 CGTAACTAAA
Statistics
Matches: 185, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
183 80 0.43
184 74 0.40
185 31 0.17
ACGTcount: A:0.40, C:0.10, G:0.06, T:0.44
Consensus pattern (185 bp):
TTGTTAAAAACATATTCCCTCTGTGCCAAATTATCTAATCCTTTTGAGTCAAAGTAATCTTAATT
TTGACCCTTAATTATAAAAAAAATTATATAAAATTAAAATTTTAAAAATTATGTTATGATTAAGT
TAAATCTTAAACTTTTCAAAATATATTTTTTTAAAATTTAATTGCATATATATTT
Found at i:23664 original size:2 final size:2
Alignment explanation
Indices: 23653--23691 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
23643 ATCACATACC
23653 AT AT AT -T AT AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
23692 AATTAAAAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 2 0.06
2 33 0.94
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:32506 original size:2 final size:2
Alignment explanation
Indices: 32501--32549 Score: 57
Period size: 2 Copynumber: 25.0 Consensus size: 2
32491 TATTACATAA
* *
32501 AT AT AT AT ACT AT GT AT AT AT AT AT AT AT AT AT AT TT AT -T A-
1 AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
32542 AT AT AT AT
1 AT AT AT AT
32550 GCTTTTTTTT
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
1 2 0.05
2 36 0.90
3 2 0.05
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (2 bp):
AT
Found at i:32531 original size:27 final size:27
Alignment explanation
Indices: 32472--32535 Score: 76
Period size: 27 Copynumber: 2.4 Consensus size: 27
32462 CCCGGCCCCG
* *
32472 AAATATATATACTATTTTTTATTACAT
1 AAATATATATACTATTATATATTACAT
*
32499 AAATATATATACTATGTATATA-TATAT
1 AAATATATATACTAT-TATATATTACAT
*
32526 ATATATATAT
1 AAATATATAT
32536 TTATTAATAT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
27 28 0.88
28 4 0.12
ACGTcount: A:0.45, C:0.05, G:0.02, T:0.48
Consensus pattern (27 bp):
AAATATATATACTATTATATATTACAT
Done.