Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023319.1 Corchorus olitorius cultivar O-4 contig23352, 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: 12303
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.30
Found at i:5043 original size:11 final size:12
Alignment explanation
Indices: 5017--5044 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
5007 GTTTTAGATC
5017 TTTTCTTCTAGT
1 TTTTCTTCTAGT
5029 TTTTCTTCTAGT
1 TTTTCTTCTAGT
5041 TTTT
1 TTTT
5045 AGGCAAGGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.07, C:0.14, G:0.07, T:0.71
Consensus pattern (12 bp):
TTTTCTTCTAGT
Found at i:6954 original size:39 final size:39
Alignment explanation
Indices: 6900--6978 Score: 124
Period size: 39 Copynumber: 2.0 Consensus size: 39
6890 AACATTCGAT
* *
6900 TCCATTTGCATGTGAAAGAAAGA-ACAATTGCAGTAGCTA
1 TCCATTTGCACGTGAAAGAAA-ATACAATTACAGTAGCTA
6939 TCCATTTGCACGTGAAAGAAAATACAATTACAGTAGCTA
1 TCCATTTGCACGTGAAAGAAAATACAATTACAGTAGCTA
6978 T
1 T
6979 AGATTAAATT
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
38 1 0.03
39 36 0.97
ACGTcount: A:0.39, C:0.16, G:0.18, T:0.27
Consensus pattern (39 bp):
TCCATTTGCACGTGAAAGAAAATACAATTACAGTAGCTA
Found at i:11489 original size:15 final size:15
Alignment explanation
Indices: 11412--11505 Score: 62
Period size: 16 Copynumber: 6.0 Consensus size: 15
11402 GGCCTGCCTA
*
11412 GCAGGCCTGGCGCGC
1 GCAGGCCTGGTGCGC
*
11427 GCAGCCCTGGTGCGC
1 GCAGGCCTGGTGCGC
* * *
11442 GCTGGACCAGCTGCGC
1 GCAGG-CCTGGTGCGC
* * *
11458 GCTGGGCCAGCTGGCGC
1 GC-AGGCCTGGT-GCGC
11475 GCAGGCCTGGTGCGC
1 GCAGGCCTGGTGCGC
* *
11490 GCTGGGCCTGGCGCGC
1 GC-AGGCCTGGTGCGC
11506 CTTGGTCCAG
Statistics
Matches: 63, Mismatches: 12, Indels: 7
0.77 0.15 0.09
Matches are distributed among these distances:
15 22 0.35
16 33 0.52
17 8 0.13
ACGTcount: A:0.06, C:0.37, G:0.45, T:0.12
Consensus pattern (15 bp):
GCAGGCCTGGTGCGC
Found at i:11497 original size:16 final size:16
Alignment explanation
Indices: 11432--11505 Score: 69
Period size: 16 Copynumber: 4.6 Consensus size: 16
11422 CGCGCGCAGC
*
11432 CCTGGTGCGCGCTGGA
1 CCTGGTGCGCGCTGGG
* *
11448 CCAGCTGCGCGCTGGG
1 CCTGGTGCGCGCTGGG
* * *
11464 CCAGCTGGCGCGC-AGG
1 CCTGGT-GCGCGCTGGG
11480 CCTGGTGCGCGCTGGG
1 CCTGGTGCGCGCTGGG
*
11496 CCTGGCGCGC
1 CCTGGTGCGC
11506 CTTGGTCCAG
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
15 6 0.12
16 36 0.75
17 6 0.12
ACGTcount: A:0.05, C:0.36, G:0.45, T:0.14
Consensus pattern (16 bp):
CCTGGTGCGCGCTGGG
Found at i:11578 original size:16 final size:17
Alignment explanation
Indices: 11554--11593 Score: 64
Period size: 16 Copynumber: 2.4 Consensus size: 17
11544 CTTGGGCCCA
11554 AATAAAAAAAAATAAAT
1 AATAAAAAAAAATAAAT
*
11571 AA-AAAAAACAATAAAT
1 AATAAAAAAAAATAAAT
11587 AATAAAA
1 AATAAAA
11594 GTGGGCCTGG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 15 0.71
17 6 0.29
ACGTcount: A:0.82, C:0.03, G:0.00, T:0.15
Consensus pattern (17 bp):
AATAAAAAAAAATAAAT
Found at i:11663 original size:18 final size:17
Alignment explanation
Indices: 11633--11674 Score: 57
Period size: 18 Copynumber: 2.4 Consensus size: 17
11623 AAGAAGACAT
11633 AAGGAAAGAAAAAGAGA
1 AAGGAAAGAAAAAGAGA
*
11650 AAGGAAGAGGAAAAGAGA
1 AAGGAA-AGAAAAAGAGA
*
11668 AAAGAAA
1 AAGGAAA
11675 AAGAGAAGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 7 0.32
18 15 0.68
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (17 bp):
AAGGAAAGAAAAAGAGA
Done.