Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01001196.1 Corchorus olitorius cultivar O-4 contig01196, 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, 844
Length: 1407
ACGTcount: A:0.40, C:0.10, G:0.08, T:0.41
Found at i:93 original size:25 final size:24
Alignment explanation
Indices: 61--111 Score: 59
Period size: 25 Copynumber: 2.1 Consensus size: 24
51 AGTTTTTTTA
61 TTTTATATGAT-TTATAAAATTAAT
1 TTTTATATGATATTA-AAAATTAAT
* *
85 TTTTCATATTATATTACAAATTAAT
1 TTTT-ATATGATATTAAAAATTAAT
110 TT
1 TT
112 GATATTTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
24 4 0.17
25 16 0.70
26 3 0.13
ACGTcount: A:0.39, C:0.04, G:0.02, T:0.55
Consensus pattern (24 bp):
TTTTATATGATATTAAAAATTAAT
Found at i:713 original size:135 final size:135
Alignment explanation
Indices: 532--868 Score: 487
Period size: 150 Copynumber: 2.4 Consensus size: 135
522 TTGTTAGTAG
* * *
532 TTTAATATACCAATCTAAAATATATTAAATATAGCAAATA-TCTTTAAAATACCATATAAACTTG
1 TTTAATATATCATTCTAAAATATATTAAATATAGCAAA-AGTATTTAAAATACCATATAAACTTG
*
596 ATCTGAAATATCTAAAATACCTCTTTTAATATTAAACATGAATTTTAAGTTTTAGTAGTTAATAT
65 ATCTGAAATATCTAAAATACCTCTTTTAATATTAAACATGAATTTTAAGCTTTAGTAGTTAATAT
661 ATATAA
130 ATATAA
667 TTTAATATATCATTCTAAAATATATTAAATATAGCAAAAGTATTTAAAATACGTGCCTTTAAAAT
1 TTTAATATATCATTCTAAAATATATTAAATATAGCAAAAG---------TA------TTTAAAAT
732 ACCATATAAACTTGATCTGAAATATCTAAAATACCTCTTTTAATATTAAACATGAATTTTAAGCT
51 ACCATATAAACTTGATCTGAAATATCTAAAATACCTCTTTTAATATTAAACATGAATTTTAAGCT
797 TTAGTAGTTAATATATATAA
116 TTAGTAGTTAATATATATAA
817 TTTAATATATCATTCTAAAATATATTAAATATAGCAAAAGTATTTAAAATAC
1 TTTAATATATCATTCTAAAATATATTAAATATAGCAAAAGTATTTAAAATAC
869 GTGCAACGCA
Statistics
Matches: 182, Mismatches: 4, Indels: 32
0.83 0.02 0.15
Matches are distributed among these distances:
134 1 0.01
135 46 0.25
141 2 0.01
144 1 0.01
150 132 0.73
ACGTcount: A:0.45, C:0.10, G:0.06, T:0.39
Consensus pattern (135 bp):
TTTAATATATCATTCTAAAATATATTAAATATAGCAAAAGTATTTAAAATACCATATAAACTTGA
TCTGAAATATCTAAAATACCTCTTTTAATATTAAACATGAATTTTAAGCTTTAGTAGTTAATATA
TATAA
Found at i:734 original size:150 final size:150
Alignment explanation
Indices: 573--872 Score: 591
Period size: 150 Copynumber: 2.0 Consensus size: 150
563 TAGCAAATAT
573 CTTTAAAATACCATATAAACTTGATCTGAAATATCTAAAATACCTCTTTTAATATTAAACATGAA
1 CTTTAAAATACCATATAAACTTGATCTGAAATATCTAAAATACCTCTTTTAATATTAAACATGAA
*
638 TTTTAAGTTTTAGTAGTTAATATATATAATTTAATATATCATTCTAAAATATATTAAATATAGCA
66 TTTTAAGCTTTAGTAGTTAATATATATAATTTAATATATCATTCTAAAATATATTAAATATAGCA
703 AAAGTATTTAAAATACGTGC
131 AAAGTATTTAAAATACGTGC
723 CTTTAAAATACCATATAAACTTGATCTGAAATATCTAAAATACCTCTTTTAATATTAAACATGAA
1 CTTTAAAATACCATATAAACTTGATCTGAAATATCTAAAATACCTCTTTTAATATTAAACATGAA
788 TTTTAAGCTTTAGTAGTTAATATATATAATTTAATATATCATTCTAAAATATATTAAATATAGCA
66 TTTTAAGCTTTAGTAGTTAATATATATAATTTAATATATCATTCTAAAATATATTAAATATAGCA
853 AAAGTATTTAAAATACGTGC
131 AAAGTATTTAAAATACGTGC
873 AACGCACGTG
Statistics
Matches: 149, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
150 149 1.00
ACGTcount: A:0.44, C:0.10, G:0.07, T:0.39
Consensus pattern (150 bp):
CTTTAAAATACCATATAAACTTGATCTGAAATATCTAAAATACCTCTTTTAATATTAAACATGAA
TTTTAAGCTTTAGTAGTTAATATATATAATTTAATATATCATTCTAAAATATATTAAATATAGCA
AAAGTATTTAAAATACGTGC
Done.