Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016117.1 Corchorus olitorius cultivar O-4 contig16150, 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: 26290
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:589 original size:14 final size:14
Alignment explanation
Indices: 564--602 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
554 AATTTGTCAT
564 GAGAAA-TAAAAAA
1 GAGAAATTAAAAAA
*
577 GATAAATTAAAAAA
1 GAGAAATTAAAAAA
*
591 GAGAAATGAAAA
1 GAGAAATTAAAA
603 TTTGTTTTCT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
13 5 0.23
14 17 0.77
ACGTcount: A:0.72, C:0.00, G:0.15, T:0.13
Consensus pattern (14 bp):
GAGAAATTAAAAAA
Found at i:5348 original size:86 final size:86
Alignment explanation
Indices: 5203--5374 Score: 335
Period size: 86 Copynumber: 2.0 Consensus size: 86
5193 GAGCAATGTG
5203 GATGAATGAGGTTATTGCAGATTTTGTTTTAATGCCCCTTCTTGGTTTTGCTAATATCAAATTGG
1 GATGAATGAGGTTATTGCAGATTTTGTTTTAATGCCCCTTCTTGGTTTTGCTAATATCAAATTGG
5268 GGTTTGTTCTAATTGGGGTTT
66 GGTTTGTTCTAATTGGGGTTT
*
5289 GATGAATGAGGTTATTGCAGGTTTTGTTTTAATGCCCCTTCTTGGTTTTGCTAATATCAAATTGG
1 GATGAATGAGGTTATTGCAGATTTTGTTTTAATGCCCCTTCTTGGTTTTGCTAATATCAAATTGG
5354 GGTTTGTTCTAATTGGGGTTT
66 GGTTTGTTCTAATTGGGGTTT
5375 AACAGTGAAT
Statistics
Matches: 85, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
86 85 1.00
ACGTcount: A:0.19, C:0.10, G:0.25, T:0.45
Consensus pattern (86 bp):
GATGAATGAGGTTATTGCAGATTTTGTTTTAATGCCCCTTCTTGGTTTTGCTAATATCAAATTGG
GGTTTGTTCTAATTGGGGTTT
Found at i:7689 original size:24 final size:24
Alignment explanation
Indices: 7636--7689 Score: 74
Period size: 24 Copynumber: 2.2 Consensus size: 24
7626 CCAAAGCCAG
7636 TCAGGCACGAGGGCCTAAGCTGGC
1 TCAGGCACGAGGGCCTAAGCTGGC
* *
7660 -CTAGGCACGCGGGCCTGAGCTGGC
1 TC-AGGCACGAGGGCCTAAGCTGGC
7684 TCAGGC
1 TCAGGC
7690 GTGCCAAGCC
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
23 1 0.04
24 24 0.92
25 1 0.04
ACGTcount: A:0.17, C:0.31, G:0.39, T:0.13
Consensus pattern (24 bp):
TCAGGCACGAGGGCCTAAGCTGGC
Found at i:16279 original size:16 final size:16
Alignment explanation
Indices: 16258--16291 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
16248 AGTGTGTTTT
16258 CATATATGGTTTTATG
1 CATATATGGTTTTATG
16274 CATATATGGTTTTATG
1 CATATATGGTTTTATG
16290 CA
1 CA
16292 GGTCAAACTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.26, C:0.09, G:0.18, T:0.47
Consensus pattern (16 bp):
CATATATGGTTTTATG
Found at i:24439 original size:22 final size:24
Alignment explanation
Indices: 24378--24439 Score: 65
Period size: 24 Copynumber: 2.7 Consensus size: 24
24368 TGAATATTTT
* *
24378 TATGAAATTTTGATAACTACCCTC
1 TATGAAATTTTGATAACCACACTC
* *
24402 TATTAAATTCTGATAACCA-AC-C
1 TATGAAATTTTGATAACCACACTC
*
24424 TATGAAATTTTAATAA
1 TATGAAATTTTGATAA
24440 TTTGATAATT
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
22 14 0.45
23 1 0.03
24 16 0.52
ACGTcount: A:0.40, C:0.16, G:0.06, T:0.37
Consensus pattern (24 bp):
TATGAAATTTTGATAACCACACTC
Found at i:24545 original size:44 final size:44
Alignment explanation
Indices: 24440--24531 Score: 114
Period size: 44 Copynumber: 2.1 Consensus size: 44
24430 ATTTTAATAA
* *
24440 TTTGATAA-TTACCTATGAAATTGTGATAAACTCCATATGAAAC
1 TTTGATAACATACCTATGAAATTGTAATAAACTCCATATGAAAC
* * * *
24483 TTTGATAACATAACTATGAAATTTTAATAAACCTTCTTATGAAAC
1 TTTGATAACATACCTATGAAATTGTAATAAA-CTCCATATGAAAC
24528 TTTG
1 TTTG
24532 TAATTTTCCT
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
43 8 0.20
44 18 0.44
45 15 0.37
ACGTcount: A:0.39, C:0.13, G:0.10, T:0.38
Consensus pattern (44 bp):
TTTGATAACATACCTATGAAATTGTAATAAACTCCATATGAAAC
Found at i:24924 original size:46 final size:45
Alignment explanation
Indices: 24831--24925 Score: 109
Period size: 46 Copynumber: 2.1 Consensus size: 45
24821 GTTATCACAC
* * * * *
24831 TGAGTTCCTTCATTCAACATTCCTCCACATAGTATATTATCAATT
1 TGAGCTCCTTCATTCAACATTACTCCAAATAGTACATTACCAATT
* * *
24876 TGAGCTCCATTCATTCAACATTATTCCAAATGGTACATTACCAGTT
1 TGAGCTCC-TTCATTCAACATTACTCCAAATAGTACATTACCAATT
24922 TGAG
1 TGAG
24926 TGCTCTCATA
Statistics
Matches: 41, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
45 7 0.17
46 34 0.83
ACGTcount: A:0.29, C:0.23, G:0.11, T:0.37
Consensus pattern (45 bp):
TGAGCTCCTTCATTCAACATTACTCCAAATAGTACATTACCAATT
Found at i:26010 original size:20 final size:20
Alignment explanation
Indices: 25977--26024 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 20
25967 CAACATAAAA
25977 AAAAAAGAAAA---AAAAGC
1 AAAAAAGAAAATTGAAAAGC
*
25994 AAAAAA-AAAATTGAAAAGG
1 AAAAAAGAAAATTGAAAAGC
26013 AAAAAAGAAAAT
1 AAAAAAGAAAAT
26025 AAAATAAAAG
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
16 4 0.15
17 6 0.23
19 11 0.42
20 5 0.19
ACGTcount: A:0.79, C:0.02, G:0.12, T:0.06
Consensus pattern (20 bp):
AAAAAAGAAAATTGAAAAGC
Done.