Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017133.1 Corchorus olitorius cultivar O-4 contig17166, 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: 11370
ACGTcount: A:0.28, C:0.17, G:0.21, T:0.34
Found at i:3564 original size:27 final size:27
Alignment explanation
Indices: 3516--3576 Score: 68
Period size: 27 Copynumber: 2.3 Consensus size: 27
3506 TTACCAAAAA
* * *
3516 TACCCGTGATGGACAAATTTACTATGT
1 TACCCCTGATGGACAAAATTACGATGT
* * *
3543 TACCCCTGATTGATAAAATTACGATTT
1 TACCCCTGATGGACAAAATTACGATGT
3570 TACCCCT
1 TACCCCT
3577 ATAATGAAGA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.30, C:0.23, G:0.13, T:0.34
Consensus pattern (27 bp):
TACCCCTGATGGACAAAATTACGATGT
Found at i:5594 original size:6 final size:6
Alignment explanation
Indices: 5583--5607 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
5573 ATAGTTCAAT
5583 TCCAAA TCCAAA TCCAAA TCCAAA T
1 TCCAAA TCCAAA TCCAAA TCCAAA T
5608 ATTAGTGATC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.48, C:0.32, G:0.00, T:0.20
Consensus pattern (6 bp):
TCCAAA
Found at i:8262 original size:33 final size:33
Alignment explanation
Indices: 8210--8298 Score: 90
Period size: 33 Copynumber: 2.6 Consensus size: 33
8200 ATGGCAGTGG
* *
8210 CGCCCCAGGGGGGCACCACCGCCATGCCT-ACGC
1 CGCCCCCGGGGAGCACCACCGCCATG-CTGACGC
* * *
8243 CGCCCCCGGGGAGCGCCACCGCTATGGTGACGC
1 CGCCCCCGGGGAGCACCACCGCCATGCTGACGC
*
8276 CGCCCCCTGGGGCGGCACCACCG
1 CGCCCCC-GGGG-AGCACCACCG
8299 GAAAGTTAAA
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
32 1 0.02
33 33 0.72
34 4 0.09
35 8 0.17
ACGTcount: A:0.12, C:0.47, G:0.34, T:0.07
Consensus pattern (33 bp):
CGCCCCCGGGGAGCACCACCGCCATGCTGACGC
Found at i:8732 original size:33 final size:33
Alignment explanation
Indices: 8685--8766 Score: 137
Period size: 33 Copynumber: 2.5 Consensus size: 33
8675 GCAGTTGCAA
*
8685 AGGGAGAGAGAGGCTGAGGCTGCTCGGATGTAT
1 AGGGAGAGGGAGGCTGAGGCTGCTCGGATGTAT
* *
8718 AGGGTGAGGGAGGCTGAGGTTGCTCGGATGTAT
1 AGGGAGAGGGAGGCTGAGGCTGCTCGGATGTAT
8751 AGGGAGAGGGAGGCTG
1 AGGGAGAGGGAGGCTG
8767 CTGCTGGTGC
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.22, C:0.10, G:0.50, T:0.18
Consensus pattern (33 bp):
AGGGAGAGGGAGGCTGAGGCTGCTCGGATGTAT
Found at i:10778 original size:9 final size:10
Alignment explanation
Indices: 10762--10802 Score: 73
Period size: 10 Copynumber: 4.1 Consensus size: 10
10752 TTATATTTTG
10762 GGATTTTTAT
1 GGATTTTTAT
10772 GGATTTTTAT
1 GGATTTTTAT
*
10782 GTATTTTTAT
1 GGATTTTTAT
10792 GGATTTTTAT
1 GGATTTTTAT
10802 G
1 G
10803 TATATTGGGG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
10 29 1.00
ACGTcount: A:0.20, C:0.00, G:0.20, T:0.61
Consensus pattern (10 bp):
GGATTTTTAT
Found at i:10789 original size:20 final size:20
Alignment explanation
Indices: 10764--10805 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
10754 ATATTTTGGG
10764 ATTTTTATGGATTTTTATGT
1 ATTTTTATGGATTTTTATGT
10784 ATTTTTATGGATTTTTATGT
1 ATTTTTATGGATTTTTATGT
10804 AT
1 AT
10806 ATTGGGGTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.21, C:0.00, G:0.14, T:0.64
Consensus pattern (20 bp):
ATTTTTATGGATTTTTATGT
Done.