Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018803.1 Corchorus olitorius cultivar O-4 contig18836, 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: 8459
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:1914 original size:54 final size:54
Alignment explanation
Indices: 1832--1941 Score: 220
Period size: 54 Copynumber: 2.0 Consensus size: 54
1822 GCAACTTCCT
1832 CATTGATTTACTTTTTAATATTGCATCTTCAGGATGCAAAACAGTGCCATAAAA
1 CATTGATTTACTTTTTAATATTGCATCTTCAGGATGCAAAACAGTGCCATAAAA
1886 CATTGATTTACTTTTTAATATTGCATCTTCAGGATGCAAAACAGTGCCATAAAA
1 CATTGATTTACTTTTTAATATTGCATCTTCAGGATGCAAAACAGTGCCATAAAA
1940 CA
1 CA
1942 ACTATGTATG
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 56 1.00
ACGTcount: A:0.35, C:0.17, G:0.13, T:0.35
Consensus pattern (54 bp):
CATTGATTTACTTTTTAATATTGCATCTTCAGGATGCAAAACAGTGCCATAAAA
Found at i:2779 original size:122 final size:121
Alignment explanation
Indices: 2385--2985 Score: 823
Period size: 122 Copynumber: 5.0 Consensus size: 121
2375 GAAAGGTAAA
* * * *
2385 ATCA-TGACAACTTCTGGTGTCAATTG-AATTATCATGACAACTTCTAGTGTCAATTGCAAGAGC
1 ATCATTGACAACTTCTGGTGTCAATTGCAA-GACCATGACAACTTCTGGTGTCAATTGCAAGACC
* *
2448 ATGACAACTTCTGGTGTCAATTGCAAGAGCATGACAAGTTCTGGTGTCAATTGCAAG
65 ATGACAACTTCTGGTGTCAATTGCAAGACCATGACAACTTCTGGTGTCAATTGCAAG
* * * * * * * * * * *
2505 AGCA-TAACAAGTTTTGGTGTCAATTGCAGGAGCATGACAAGTTTTGGTGTCAACTGCAGGAGCA
1 ATCATTGACAACTTCTGGTGTCAATTGCAAGACCATGACAACTTCTGGTGTCAATTGCAAGACCA
* * * * * *
2569 TGACAAGTTCTGGTGTCAACTGCAGGAGCATGACAAGTTCTGGTGTCAATTGCACG
66 TGACAACTTCTGGTGTCAATTGCAAGACCATGACAACTTCTGGTGTCAATTGCAAG
2625 ATCATTGACAACTTCTGGTGTCAATTGCAAGACCATGACAACTTCTGGTGTCAATTGCAAGACCA
1 ATCATTGACAACTTCTGGTGTCAATTGCAAGACCATGACAACTTCTGGTGTCAATTGCAAGACCA
2690 TGACAACTTCTGGTGTCAATTGCAAGACCATTGACAACTTCTGGTGTCAATTGCAAG
66 TGACAACTTCTGGTGTCAATTGCAAGACCA-TGACAACTTCTGGTGTCAATTGCAAG
* * ** *
2747 A-CGATTGACAACTTCTGGTGTCAATTGTAAGACCATGACAACTTCTGGTGTCATTTATAAGATC
1 ATC-ATTGACAACTTCTGGTGTCAATTGCAAGACCATGACAACTTCTGGTGTCAATTGCAAGACC
*
2811 ATGACAACTTCTGGTGTCAATTGCAAGACCATTGACAACTTCTGGTGTCAATTGTAAG
65 ATGACAACTTCTGGTGTCAATTGCAAGACCA-TGACAACTTCTGGTGTCAATTGCAAG
* * * *
2869 ATCATTGACAACTTATGGTGTCAATTGTAAGACCATGACAACTTCTGGTGTCATTTGTAAGACCA
1 ATCATTGACAACTTCTGGTGTCAATTGCAAGACCATGACAACTTCTGGTGTCAATTGCAAGACCA
* *
2934 TGACAACTTCTGGTGTCATTTGTAAGACCATGACAACTTCTGGTGTCAATTG
66 TGACAACTTCTGGTGTCAATTGCAAGACCATGACAACTTCTGGTGTCAATTG
2986 TAAGTAGATT
Statistics
Matches: 432, Mismatches: 44, Indels: 9
0.89 0.09 0.02
Matches are distributed among these distances:
120 105 0.24
121 100 0.23
122 226 0.52
123 1 0.00
ACGTcount: A:0.29, C:0.19, G:0.22, T:0.30
Consensus pattern (121 bp):
ATCATTGACAACTTCTGGTGTCAATTGCAAGACCATGACAACTTCTGGTGTCAATTGCAAGACCA
TGACAACTTCTGGTGTCAATTGCAAGACCATGACAACTTCTGGTGTCAATTGCAAG
Found at i:2989 original size:30 final size:30
Alignment explanation
Indices: 2387--2985 Score: 795
Period size: 30 Copynumber: 19.8 Consensus size: 30
2377 AAGGTAAAAT
* *
2387 CATGACAACTTCTGGTGTCAATTG-AATTAT
1 CATGACAACTTCTGGTGTCAATTGCAA-GAC
* *
2417 CATGACAACTTCTAGTGTCAATTGCAAGAG
1 CATGACAACTTCTGGTGTCAATTGCAAGAC
*
2447 CATGACAACTTCTGGTGTCAATTGCAAGAG
1 CATGACAACTTCTGGTGTCAATTGCAAGAC
* *
2477 CATGACAAGTTCTGGTGTCAATTGCAAGAG
1 CATGACAACTTCTGGTGTCAATTGCAAGAC
* * * * *
2507 CATAACAAGTTTTGGTGTCAATTGCAGGAG
1 CATGACAACTTCTGGTGTCAATTGCAAGAC
* * * * *
2537 CATGACAAGTTTTGGTGTCAACTGCAGGAG
1 CATGACAACTTCTGGTGTCAATTGCAAGAC
* * * *
2567 CATGACAAGTTCTGGTGTCAACTGCAGGAG
1 CATGACAACTTCTGGTGTCAATTGCAAGAC
* * *
2597 CATGACAAGTTCTGGTGTCAATTGCACGAT
1 CATGACAACTTCTGGTGTCAATTGCAAGAC
2627 CATTGACAACTTCTGGTGTCAATTGCAAGAC
1 CA-TGACAACTTCTGGTGTCAATTGCAAGAC
2658 CATGACAACTTCTGGTGTCAATTGCAAGAC
1 CATGACAACTTCTGGTGTCAATTGCAAGAC
2688 CATGACAACTTCTGGTGTCAATTGCAAGAC
1 CATGACAACTTCTGGTGTCAATTGCAAGAC
2718 CATTGACAACTTCTGGTGTCAATTGCAAGAC
1 CA-TGACAACTTCTGGTGTCAATTGCAAGAC
* *
2749 GATTGACAACTTCTGGTGTCAATTGTAAGAC
1 CA-TGACAACTTCTGGTGTCAATTGCAAGAC
* ** *
2780 CATGACAACTTCTGGTGTCATTTATAAGAT
1 CATGACAACTTCTGGTGTCAATTGCAAGAC
2810 CATGACAACTTCTGGTGTCAATTGCAAGAC
1 CATGACAACTTCTGGTGTCAATTGCAAGAC
* *
2840 CATTGACAACTTCTGGTGTCAATTGTAAGAT
1 CA-TGACAACTTCTGGTGTCAATTGCAAGAC
* *
2871 CATTGACAACTTATGGTGTCAATTGTAAGAC
1 CA-TGACAACTTCTGGTGTCAATTGCAAGAC
* *
2902 CATGACAACTTCTGGTGTCATTTGTAAGAC
1 CATGACAACTTCTGGTGTCAATTGCAAGAC
* *
2932 CATGACAACTTCTGGTGTCATTTGTAAGAC
1 CATGACAACTTCTGGTGTCAATTGCAAGAC
2962 CATGACAACTTCTGGTGTCAATTG
1 CATGACAACTTCTGGTGTCAATTG
2986 TAAGTAGATT
Statistics
Matches: 531, Mismatches: 34, Indels: 8
0.93 0.06 0.01
Matches are distributed among these distances:
30 387 0.73
31 144 0.27
ACGTcount: A:0.29, C:0.19, G:0.22, T:0.30
Consensus pattern (30 bp):
CATGACAACTTCTGGTGTCAATTGCAAGAC
Found at i:4072 original size:22 final size:24
Alignment explanation
Indices: 4037--4090 Score: 60
Period size: 22 Copynumber: 2.3 Consensus size: 24
4027 ATAAATGTTG
* *
4037 CTGATAA-TCTTCT-CTTTTATCT
1 CTGATAATTCTTCTCCATTTATCA
4059 CTGATAATTC-TCTCCATTTATCA
1 CTGATAATTCTTCTCCATTTATCA
4082 CTTGATAAT
1 C-TGATAAT
4091 ATCTAGCCAG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
22 10 0.37
23 10 0.37
24 7 0.26
ACGTcount: A:0.24, C:0.22, G:0.06, T:0.48
Consensus pattern (24 bp):
CTGATAATTCTTCTCCATTTATCA
Found at i:4559 original size:19 final size:19
Alignment explanation
Indices: 4535--4572 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
4525 TCTTGCTGTG
*
4535 GTTTAAATTTGTTGTTTTA
1 GTTTAAATTTATTGTTTTA
4554 GTTTAAATTTATTGTTTTA
1 GTTTAAATTTATTGTTTTA
4573 CCTTTTATAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.24, C:0.00, G:0.13, T:0.63
Consensus pattern (19 bp):
GTTTAAATTTATTGTTTTA
Done.