Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016728.1 Corchorus olitorius cultivar O-4 contig16761, 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: 12909
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:4490 original size:24 final size:23
Alignment explanation
Indices: 4430--4496 Score: 107
Period size: 23 Copynumber: 2.9 Consensus size: 23
4420 CACCCTCCGG
* *
4430 GGGCGCCCAGCCAGGGTAGAATA
1 GGGCGCCCAGCCATGGTAGAAGA
4453 GGGCGCCCAGCCATGGTAGAAGA
1 GGGCGCCCAGCCATGGTAGAAGA
4476 GGGCGCCCCAGCCATGGTAGA
1 GGGCG-CCCAGCCATGGTAGA
4497 GGCGCCCTCT
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
23 26 0.63
24 15 0.37
ACGTcount: A:0.24, C:0.28, G:0.39, T:0.09
Consensus pattern (23 bp):
GGGCGCCCAGCCATGGTAGAAGA
Found at i:4524 original size:33 final size:33
Alignment explanation
Indices: 4481--4583 Score: 109
Period size: 33 Copynumber: 3.1 Consensus size: 33
4471 GAAGAGGGCG
4481 CCCCAGCCATGGTAGAGGCGCCCTCTGTGGG-CAC
1 CCCCA-CCATGGTAGAGGCGCCCTCTG-GGGCCAC
* *
4515 CCCCACCATGGTAGAGGCGCCCTTTGGGGCCGC
1 CCCCACCATGGTAGAGGCGCCCTCTGGGGCCAC
* * * * * *
4548 CCCCGCCATGGTAAAGGCTCGCTTTGGGGCCGC
1 CCCCACCATGGTAGAGGCGCCCTCTGGGGCCAC
4581 CCC
1 CCC
4584 TGTTATGGCA
Statistics
Matches: 62, Mismatches: 6, Indels: 3
0.87 0.08 0.04
Matches are distributed among these distances:
32 3 0.05
33 54 0.87
34 5 0.08
ACGTcount: A:0.13, C:0.40, G:0.32, T:0.16
Consensus pattern (33 bp):
CCCCACCATGGTAGAGGCGCCCTCTGGGGCCAC
Found at i:4651 original size:19 final size:20
Alignment explanation
Indices: 4619--4658 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
4609 GGCGCCTCGA
* *
4619 TTTTTTATTTATTATTTATT
1 TTTTTTATTGATTATTAATT
4639 TTTTTTA-TGATTATTAATT
1 TTTTTTATTGATTATTAATT
4658 T
1 T
4659 AAATTTTGGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.75
Consensus pattern (20 bp):
TTTTTTATTGATTATTAATT
Found at i:7025 original size:25 final size:25
Alignment explanation
Indices: 6991--7041 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
6981 ATCTTTTAAC
6991 TTATTATTTA-TTATTTAAAATATAT
1 TTATTATTTATTTA-TTAAAATATAT
* *
7016 TTATTGTTTATTTATTAATATATAT
1 TTATTATTTATTTATTAAAATATAT
7041 T
1 T
7042 ATATCTAAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 20 0.87
26 3 0.13
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (25 bp):
TTATTATTTATTTATTAAAATATAT
Found at i:7628 original size:64 final size:65
Alignment explanation
Indices: 7559--7740 Score: 206
Period size: 74 Copynumber: 2.7 Consensus size: 65
7549 GATTTTATCA
* *
7559 TTTTTCAAATATATTTCTAAATTGCCATTATTAAAATATAAAATATAATTTTATTTAATACGT-T
1 TTTTTCAAATATATTTCTAAATTGTCATTATTAAAATATAAAATATAATTTTATTTAATACATAT
* *
7623 TTTTTCAAAGATACTTT-TAAATTGTCATTATTAAAATATAATTTTTACAGAATATAATTTTCTT
1 TTTTTCAAATATA-TTTCTAAATTGTCATTATT-AAA-AT-A----TA-A-AATATAATTTTATT
*
7687 TAATATATAT
56 TAATACATAT
*
7697 TTTTTCAAATGTATTTCTAAATTGTCATTATTAAAATATAAAAT
1 TTTTTCAAATATATTTCTAAATTGTCATTATTAAAATATAAAAT
7741 TTTTACAAAA
Statistics
Matches: 99, Mismatches: 7, Indels: 23
0.77 0.05 0.18
Matches are distributed among these distances:
64 26 0.26
65 9 0.09
66 3 0.03
67 3 0.03
71 3 0.03
72 3 0.03
73 25 0.25
74 27 0.27
ACGTcount: A:0.40, C:0.07, G:0.04, T:0.49
Consensus pattern (65 bp):
TTTTTCAAATATATTTCTAAATTGTCATTATTAAAATATAAAATATAATTTTATTTAATACATAT
Found at i:7726 original size:74 final size:74
Alignment explanation
Indices: 7598--7762 Score: 237
Period size: 74 Copynumber: 2.2 Consensus size: 74
7588 ATTAAAATAT
*
7598 AAAATATAATTTTATTTAATACGTTTTTTTCAAAGATACTTTTAAATTGTCATTATTAAAATAT-
1 AAAATATAATTTTATTTAATACATTTTTTTCAAAGATACTTTTAAATTGTCATTATTAAAATATA
7662 AATTTTTAC
66 AATTTTTAC
* * *
7671 AGAATATAATTTTCTTTAATATATATTTTTTCAAATG-TA-TTTCTAAATTGTCATTATTAAAAT
1 AAAATATAATTTTATTTAATACAT-TTTTTTCAAA-GATACTTT-TAAATTGTCATTATTAAAAT
7734 ATAAAATTTTTAC
63 AT-AAATTTTTAC
7747 AAAATATAATTTTATT
1 AAAATATAATTTTATT
7763 GGATAAAATT
Statistics
Matches: 81, Mismatches: 6, Indels: 7
0.86 0.06 0.07
Matches are distributed among these distances:
73 23 0.28
74 34 0.42
75 1 0.01
76 23 0.28
ACGTcount: A:0.41, C:0.06, G:0.04, T:0.50
Consensus pattern (74 bp):
AAAATATAATTTTATTTAATACATTTTTTTCAAAGATACTTTTAAATTGTCATTATTAAAATATA
AATTTTTAC
Found at i:7988 original size:5 final size:5
Alignment explanation
Indices: 7924--7973 Score: 86
Period size: 5 Copynumber: 10.4 Consensus size: 5
7914 AATCCCTAAT
7924 AAAT- AAAT- AAATA AAATA AAATA AAATA AAATA AAATA AAATA AAATA
1 AAATA AAATA AAATA AAATA AAATA AAATA AAATA AAATA AAATA AAATA
7972 AA
1 AA
7974 CAGAGTAATA
Statistics
Matches: 45, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
4 8 0.18
5 37 0.82
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
AAATA
Done.