Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013782.1 Corchorus olitorius cultivar O-4 contig13815, 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: 4343
ACGTcount: A:0.37, C:0.15, G:0.16, T:0.32
Found at i:430 original size:211 final size:211
Alignment explanation
Indices: 66--639 Score: 1094
Period size: 211 Copynumber: 2.7 Consensus size: 211
56 AGATTATGAA
66 TAATATATGGATTAAAACACATTTTAAGGTCATTTTTGGGTATATGGGAAAAAATGTCCAACTCT
1 TAATATATGGATTAAAACACATTTTAAGGTCATTTTTGGGTATATGGGAAAAAATGTCCAACTCT
131 AAAGAATTTGGGGATGGTGCATATGATTATTTGGGGATGATGAGAAAGAATTTGGGTATAAAGTA
66 AAAGAATTTGGGGATGGTGCATATGATTATTTGGGGATGATGAGAAAGAATTTGGGTATAAAGTA
196 TATTACTTTGGGGATACTTAATTTTGCATTTTGTTTAATTAGTAGATGGCACTAAAATCATTTAG
131 TATTACTTTGGGGATACTTAATTTTGCATTTTGTTTAATTAGTAGATGGCACTAAAATCATTTAG
261 ATGGGGTTTATTCAAT
196 ATGGGGTTTATTCAAT
*
277 TAATATATGGATTAAAACACATTTTAAGGTCAATTTTGGGTATATGGGAAAAAATGTCCAACTCT
1 TAATATATGGATTAAAACACATTTTAAGGTCATTTTTGGGTATATGGGAAAAAATGTCCAACTCT
342 AAAGAATTTGGGGATGGTGCATATGATTATTTGGGGATGATGAGAAAGAATTTGGGTATAAAGTA
66 AAAGAATTTGGGGATGGTGCATATGATTATTTGGGGATGATGAGAAAGAATTTGGGTATAAAGTA
407 TATTACTTTGGGGATACTTAATTTTGCATTTTGTTTAATTAGTAGATGGCACTAAAATCATTTAG
131 TATTACTTTGGGGATACTTAATTTTGCATTTTGTTTAATTAGTAGATGGCACTAAAATCATTTAG
472 ATGGGGTTTATTCAAT
196 ATGGGGTTTATTCAAT
* *
488 TAATATATGGATTAAAACACATTTTAAGGTCATTTTTGGGTATATGAGAAAAAATGTCCATCTCT
1 TAATATATGGATTAAAACACATTTTAAGGTCATTTTTGGGTATATGGGAAAAAATGTCCAACTCT
* * *
553 AAAGAATTTGGGGATAGTGCATAAGATTATTTGGGGATGATGAGAAAGAATTTGGGTATAAAATA
66 AAAGAATTTGGGGATGGTGCATATGATTATTTGGGGATGATGAGAAAGAATTTGGGTATAAAGTA
618 TATTACTTTGGGGATACTTAAT
131 TATTACTTTGGGGATACTTAAT
640 ATCACCCCTT
Statistics
Matches: 356, Mismatches: 7, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
211 356 1.00
ACGTcount: A:0.34, C:0.07, G:0.22, T:0.37
Consensus pattern (211 bp):
TAATATATGGATTAAAACACATTTTAAGGTCATTTTTGGGTATATGGGAAAAAATGTCCAACTCT
AAAGAATTTGGGGATGGTGCATATGATTATTTGGGGATGATGAGAAAGAATTTGGGTATAAAGTA
TATTACTTTGGGGATACTTAATTTTGCATTTTGTTTAATTAGTAGATGGCACTAAAATCATTTAG
ATGGGGTTTATTCAAT
Found at i:664 original size:12 final size:12
Alignment explanation
Indices: 647--671 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
637 AATATCACCC
647 CTTTAACAAAAT
1 CTTTAACAAAAT
659 CTTTAACAAAAT
1 CTTTAACAAAAT
671 C
1 C
672 ACACACATTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.20, G:0.00, T:0.32
Consensus pattern (12 bp):
CTTTAACAAAAT
Found at i:1385 original size:47 final size:47
Alignment explanation
Indices: 1316--1411 Score: 174
Period size: 47 Copynumber: 2.0 Consensus size: 47
1306 TGAGGGAATG
1316 GCAAATGGGTACAGAATCTTTGAAAAATTTGAAAGAAAGAACGATTT
1 GCAAATGGGTACAGAATCTTTGAAAAATTTGAAAGAAAGAACGATTT
* *
1363 GCAAATGGGTACAGAATTTTTGAAACATTTGAAAGAAAGAACGATTT
1 GCAAATGGGTACAGAATCTTTGAAAAATTTGAAAGAAAGAACGATTT
1410 GC
1 GC
1412 CCAAAAATTT
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 47 1.00
ACGTcount: A:0.43, C:0.09, G:0.22, T:0.26
Consensus pattern (47 bp):
GCAAATGGGTACAGAATCTTTGAAAAATTTGAAAGAAAGAACGATTT
Found at i:1587 original size:21 final size:24
Alignment explanation
Indices: 1549--1624 Score: 138
Period size: 24 Copynumber: 3.2 Consensus size: 24
1539 AAAACGAAGT
1549 AGAAAACGGAGAAGAAGAGAATAA
1 AGAAAACGGAGAAGAAGAGAATAA
1573 AGAAAACGGAGAAGAAGAGAATAA
1 AGAAAACGGAGAAGAAGAGAATAA
1597 AGAAAACGGAGAAGAAGAGAA-AA
1 AGAAAACGGAGAAGAAGAGAATAA
1620 A-AAAA
1 AGAAAA
1625 TAAATCAAGT
Statistics
Matches: 52, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
22 4 0.08
23 3 0.06
24 45 0.87
ACGTcount: A:0.66, C:0.04, G:0.28, T:0.03
Consensus pattern (24 bp):
AGAAAACGGAGAAGAAGAGAATAA
Done.