Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021584.1 Corchorus olitorius cultivar O-4 contig21617, 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: 5718
ACGTcount: A:0.36, C:0.12, G:0.13, T:0.39
Found at i:324 original size:15 final size:15
Alignment explanation
Indices: 291--333 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
281 TACATACCAC
*
291 TAATAATAATTATTA
1 TAATAATAATAATTA
306 TAATAATAATAAGTT-
1 TAATAATAATAA-TTA
*
321 TAATAATTATAAT
1 TAATAATAATAAT
334 ATTAAGATGT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 1 0.04
15 22 0.88
16 2 0.08
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (15 bp):
TAATAATAATAATTA
Found at i:329 original size:24 final size:24
Alignment explanation
Indices: 297--348 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
287 CCACTAATAA
* *
297 TAATTATTATAATAATAATAAGTT
1 TAATAATTATAATAATAAGAAGTT
* *
321 TAATAATTATAATATTAAGATGTT
1 TAATAATTATAATAATAAGAAGTT
345 TAAT
1 TAAT
349 GTAAAAAAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.46
Consensus pattern (24 bp):
TAATAATTATAATAATAAGAAGTT
Found at i:333 original size:9 final size:9
Alignment explanation
Indices: 293--334 Score: 50
Period size: 9 Copynumber: 4.7 Consensus size: 9
283 CATACCACTA
293 ATAATAATT
1 ATAATAATT
* *
302 ATTATAATA
1 ATAATAATT
311 ATAATAAGTT
1 ATAATAA-TT
321 -TAATAATT
1 ATAATAATT
329 ATAATA
1 ATAATA
335 TTAAGATGTT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
8 2 0.07
9 24 0.89
10 1 0.04
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (9 bp):
ATAATAATT
Found at i:1889 original size:58 final size:58
Alignment explanation
Indices: 1799--1918 Score: 215
Period size: 58 Copynumber: 2.1 Consensus size: 58
1789 GATCTGACAG
1799 AAATATATATATATACTAAATAGTATTTGAAACACCCAATGAAATTACTAAAGGCTCC
1 AAATATATATATATACTAAATAGTATTTGAAACACCCAATGAAATTACTAAAGGCTCC
*
1857 AAATATATACT-TATACTAAATAGTATTTGAAACACCCAATGAAATTACTAAAGGCTTC
1 AAATATATA-TATATACTAAATAGTATTTGAAACACCCAATGAAATTACTAAAGGCTCC
1915 AAAT
1 AAAT
1919 CAGGATTGAT
Statistics
Matches: 60, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
58 59 0.98
59 1 0.02
ACGTcount: A:0.47, C:0.15, G:0.08, T:0.30
Consensus pattern (58 bp):
AAATATATATATATACTAAATAGTATTTGAAACACCCAATGAAATTACTAAAGGCTCC
Found at i:5602 original size:125 final size:129
Alignment explanation
Indices: 5447--5702 Score: 430
Period size: 125 Copynumber: 2.0 Consensus size: 129
5437 GACTAATTAA
* * *
5447 TATATATATATATATATATATCTTACTACTATATAAAATCACGAACTCAAAAATTTTAATTGGGA
1 TATATATATATATATATATATCATACTACTATATAAAATCACGAAATCAAAAATCTTAATTGGGA
* *
5512 AATTTCTAAAATACTCTTAGTGTTATAGTATAATAATTTTTTAATTAATATTCTTATTAGTCAT
66 AATTTCTAAAATACCCTTAGTATTATAGTATAATAATTTTTTAATTAATATTCTTATTAGTCAT
5576 TATAT-TATAT-TATATATAT-ATA-TACTATATAAAATCACGAAATCAAAAATCTTAATTGGGA
1 TATATATATATATATATATATCATACTACTATATAAAATCACGAAATCAAAAATCTTAATTGGGA
*
5637 AATTTCTAAAATACCCTTAGTATTATAGTATAATAATTTTTTAATTAATATTCTTTTTAGTCAT
66 AATTTCTAAAATACCCTTAGTATTATAGTATAATAATTTTTTAATTAATATTCTTATTAGTCAT
5701 TA
1 TA
5703 AATTTTTTTA
Statistics
Matches: 121, Mismatches: 6, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
125 100 0.83
126 2 0.02
127 9 0.07
128 5 0.04
129 5 0.04
ACGTcount: A:0.41, C:0.09, G:0.06, T:0.44
Consensus pattern (129 bp):
TATATATATATATATATATATCATACTACTATATAAAATCACGAAATCAAAAATCTTAATTGGGA
AATTTCTAAAATACCCTTAGTATTATAGTATAATAATTTTTTAATTAATATTCTTATTAGTCAT
Done.