Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012387.1 Corchorus olitorius cultivar O-4 contig12420, 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: 12353
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.31
Found at i:2350 original size:18 final size:18
Alignment explanation
Indices: 2327--2361 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
2317 ACAAAAACTG
2327 AAATTGTTCATAAACAAA
1 AAATTGTTCATAAACAAA
*
2345 AAATTGTTCATGAACAA
1 AAATTGTTCATAAACAA
2362 TGTAATAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.51, C:0.11, G:0.09, T:0.29
Consensus pattern (18 bp):
AAATTGTTCATAAACAAA
Found at i:2489 original size:35 final size:33
Alignment explanation
Indices: 2450--2545 Score: 81
Period size: 35 Copynumber: 2.8 Consensus size: 33
2440 AATAATTAAA
2450 TTTTAATTTAAATATATTAGATAATAGAATATTAT
1 TTTTAATTTAAATATATTA-ATAATA-AATATTAT
* * *
2485 TTTTATATTT--TTTTATTAATAATATATATTAT
1 TTTTA-ATTTAAATATATTAATAATAAATATTAT
*
2517 TATTAATATATAAATA-ATTATATAATAAA
1 TTTTAAT-T-TAAATATATTA-ATAATAAA
2546 CGAACGTTCG
Statistics
Matches: 48, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
31 2 0.04
32 12 0.25
33 7 0.15
34 10 0.21
35 13 0.27
36 4 0.08
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (33 bp):
TTTTAATTTAAATATATTAATAATAAATATTAT
Found at i:2510 original size:19 final size:18
Alignment explanation
Indices: 2497--2543 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 18
2487 TTATATTTTT
2497 TTATTAATAATATATATTA
1 TTATTAAT-ATATATATTA
* *
2516 TTATTAATATATAAATAA
1 TTATTAATATATATATTA
2534 TTATATAATA
1 TTAT-TAATA
2544 AACGAACGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 12 0.48
19 13 0.52
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
TTATTAATATATATATTA
Found at i:2516 original size:16 final size:16
Alignment explanation
Indices: 2497--2528 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
2487 TTATATTTTT
2497 TTATTAATAATATATA
1 TTATTAATAATATATA
*
2513 TTATTATTAATATATA
1 TTATTAATAATATATA
2529 AATAATTATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TTATTAATAATATATA
Found at i:2616 original size:35 final size:35
Alignment explanation
Indices: 2570--2644 Score: 134
Period size: 35 Copynumber: 2.1 Consensus size: 35
2560 TTATATAAAC
2570 GAACACTTAAATGAACAATAAACGAGTC-TGTTCGT
1 GAACACTTAAATGAACAATAAACGAG-CATGTTCGT
2605 GAACACTTAAATGAACAATAAACGAGCATGTTCGT
1 GAACACTTAAATGAACAATAAACGAGCATGTTCGT
2640 GAACA
1 GAACA
2645 TAAACGAACT
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
34 1 0.03
35 38 0.97
ACGTcount: A:0.43, C:0.17, G:0.17, T:0.23
Consensus pattern (35 bp):
GAACACTTAAATGAACAATAAACGAGCATGTTCGT
Found at i:6313 original size:15 final size:15
Alignment explanation
Indices: 6293--6363 Score: 115
Period size: 15 Copynumber: 4.7 Consensus size: 15
6283 CCTTTGAAAC
* *
6293 CTAAAATTCTAAATA
1 CTAAAATGCTGAATA
6308 CTAAAATGCTGAATA
1 CTAAAATGCTGAATA
*
6323 TTAAAATGCTGAATA
1 CTAAAATGCTGAATA
6338 CTAAAATGCTGAATA
1 CTAAAATGCTGAATA
6353 CTAAAATGCTG
1 CTAAAATGCTG
6364 GAAAGTTATC
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 52 1.00
ACGTcount: A:0.46, C:0.13, G:0.11, T:0.30
Consensus pattern (15 bp):
CTAAAATGCTGAATA
Done.