Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020518.1 Corchorus olitorius cultivar O-4 contig20551, 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: 13819
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Found at i:2456 original size:28 final size:28
Alignment explanation
Indices: 2412--2480 Score: 120
Period size: 28 Copynumber: 2.5 Consensus size: 28
2402 GAAATCAAAC
*
2412 ATGGAATATGCACATGTAACTTCTTAAA
1 ATGGAATATGCAAATGTAACTTCTTAAA
*
2440 ATGGGATATGCAAATGTAACTTCTTAAA
1 ATGGAATATGCAAATGTAACTTCTTAAA
2468 ATGGAATATGCAA
1 ATGGAATATGCAA
2481 CTTAAATAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 38 1.00
ACGTcount: A:0.41, C:0.12, G:0.17, T:0.30
Consensus pattern (28 bp):
ATGGAATATGCAAATGTAACTTCTTAAA
Found at i:2645 original size:27 final size:27
Alignment explanation
Indices: 2610--2715 Score: 185
Period size: 27 Copynumber: 3.9 Consensus size: 27
2600 TTATGCCTCC
2610 TATGCAAATGACTAAAATGCCCCTGAA
1 TATGCAAATGACTAAAATGCCCCTGAA
*
2637 TATGCAAATGACTAAAATGCCCCTAAA
1 TATGCAAATGACTAAAATGCCCCTGAA
*
2664 TGTGCAAATGACTAAAATGCCCCTGAA
1 TATGCAAATGACTAAAATGCCCCTGAA
*
2691 TGTGCAAATGACTAAAATGCCCCTG
1 TATGCAAATGACTAAAATGCCCCTG
2716 GTTGACTCTA
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 76 1.00
ACGTcount: A:0.39, C:0.23, G:0.16, T:0.23
Consensus pattern (27 bp):
TATGCAAATGACTAAAATGCCCCTGAA
Found at i:5016 original size:130 final size:130
Alignment explanation
Indices: 4782--5042 Score: 391
Period size: 130 Copynumber: 2.0 Consensus size: 130
4772 CATTGTTTAA
* *
4782 ACTTTTATAGTTTTACCCAACTAAAAACTCTATTTTTATTTAATTCAATCTAATATCCTTATAAC
1 ACTTTTATAGTTTTACCCAACTAAAAACTCTATTTTTATCTAATTAAATCTAATATCCTTATAAC
* * * *
4847 TATTTAATTTTTACCATTATATTATTTTAATTAAAAACTTATATATGTTAGAATGTTTT-AAATA
66 TATTTAATTTTTACCATTATACTAATTTAATTAAAAACTTAGATATATTAGAAT-TTTTAAAATA
4911 T
130 T
* *
4912 ACTTTTATAGTTTTACTCAACTAAAAACTCTATTTTT-TCTAATTAAATCTAATATCCTTATACC
1 ACTTTTATAGTTTTACCCAACTAAAAACTCTATTTTTATCTAATTAAATCTAATATCCTTATAAC
* * *
4976 TATTTTATTTTTATCATTTTACTAATTTAATTAGAAAACTTAGATATATTAGAATTTTTAAAATA
66 TATTTAATTTTTACCATTATACTAATTTAATTA-AAAACTTAGATATATTAGAATTTTTAAAATA
5041 T
130 T
5042 A
1 A
5043 TTTCTTAAAT
Statistics
Matches: 118, Mismatches: 11, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
129 56 0.47
130 62 0.53
ACGTcount: A:0.37, C:0.11, G:0.03, T:0.48
Consensus pattern (130 bp):
ACTTTTATAGTTTTACCCAACTAAAAACTCTATTTTTATCTAATTAAATCTAATATCCTTATAAC
TATTTAATTTTTACCATTATACTAATTTAATTAAAAACTTAGATATATTAGAATTTTTAAAATAT
Found at i:8114 original size:27 final size:27
Alignment explanation
Indices: 8064--8116 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
8054 CAAGACTAAA
* *
8064 AACTCTGATGAATATGTGACTAGATTG
1 AACTCTGATGAATATATCACTAGATTG
* *
8091 AACTTTGATGAATATATCAGTAGATT
1 AACTCTGATGAATATATCACTAGATT
8117 AAGACAAGCG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.36, C:0.09, G:0.19, T:0.36
Consensus pattern (27 bp):
AACTCTGATGAATATATCACTAGATTG
Found at i:9078 original size:29 final size:29
Alignment explanation
Indices: 9039--9117 Score: 149
Period size: 29 Copynumber: 2.7 Consensus size: 29
9029 AAATATAATA
9039 ATAAATAACTGAAAAATTATTTTTTTGAG
1 ATAAATAACTGAAAAATTATTTTTTTGAG
*
9068 ATAAATTACTGAAAAATTATTTTTTTGAG
1 ATAAATAACTGAAAAATTATTTTTTTGAG
9097 ATAAATAACTGAAAAATTATT
1 ATAAATAACTGAAAAATTATT
9118 AGTATAATAA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 48 1.00
ACGTcount: A:0.47, C:0.04, G:0.09, T:0.41
Consensus pattern (29 bp):
ATAAATAACTGAAAAATTATTTTTTTGAG
Found at i:12600 original size:35 final size:35
Alignment explanation
Indices: 12561--12634 Score: 130
Period size: 35 Copynumber: 2.1 Consensus size: 35
12551 TCTCTAACTC
*
12561 TCTGTAGAGATCTATGCTTTCTCTTTCTTGAAGAA
1 TCTGTAGAGATCTATGCTTTCTCTCTCTTGAAGAA
*
12596 TCTGTAGAGATCTATGCTTTCTCTCTGTTGAAGAA
1 TCTGTAGAGATCTATGCTTTCTCTCTCTTGAAGAA
12631 TCTG
1 TCTG
12635 AAAAATTTAA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.22, C:0.18, G:0.19, T:0.42
Consensus pattern (35 bp):
TCTGTAGAGATCTATGCTTTCTCTCTCTTGAAGAA
Found at i:12783 original size:26 final size:27
Alignment explanation
Indices: 12746--12800 Score: 69
Period size: 26 Copynumber: 2.1 Consensus size: 27
12736 TCAATAAAAA
*
12746 AAAACATAAAAGTATAAACAA-AGAAAG
1 AAAACATAAAAG-AGAAACAAGAGAAAG
*
12773 AAAA-ATAAAAGAGAAAGAAGAGAAAG
1 AAAACATAAAAGAGAAACAAGAGAAAG
12799 AA
1 AA
12801 TTGGAGCTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 6 0.24
26 15 0.60
27 4 0.16
ACGTcount: A:0.73, C:0.04, G:0.16, T:0.07
Consensus pattern (27 bp):
AAAACATAAAAGAGAAACAAGAGAAAG
Done.