Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017240.1 Corchorus olitorius cultivar O-4 contig17273, 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: 27982
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:9325 original size:27 final size:27
Alignment explanation
Indices: 9295--9355 Score: 113
Period size: 27 Copynumber: 2.3 Consensus size: 27
9285 TAGTGGCAGC
*
9295 CGTGTCCCACTGTGTCCAAGGTGTCGT
1 CGTGTCCCACTGTGTCCAAGGTGCCGT
9322 CGTGTCCCACTGTGTCCAAGGTGCCGT
1 CGTGTCCCACTGTGTCCAAGGTGCCGT
9349 CGTGTCC
1 CGTGTCC
9356 GACACGGATA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.10, C:0.33, G:0.30, T:0.28
Consensus pattern (27 bp):
CGTGTCCCACTGTGTCCAAGGTGCCGT
Found at i:10780 original size:56 final size:56
Alignment explanation
Indices: 10691--10797 Score: 155
Period size: 56 Copynumber: 1.9 Consensus size: 56
10681 GCTTCGTGAA
* * *
10691 TATAAAAATTGGGCCATGTTGAGTTTTTTTTATTTG-AGATCTGACATGACTTGACT
1 TATAAAAATTGGGCCATGTTGAGCTTTTCTTATTTGAAG-CCTGACATGACTTGACT
10747 TATAAAAATT-GGCCGATGTTGAGCTTTTCTTATTTGAAGCCTGACATGACT
1 TATAAAAATTGGGCC-ATGTTGAGCTTTTCTTATTTGAAGCCTGACATGACT
10798 CGATTTAAGA
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
55 4 0.09
56 40 0.87
57 2 0.04
ACGTcount: A:0.27, C:0.13, G:0.20, T:0.40
Consensus pattern (56 bp):
TATAAAAATTGGGCCATGTTGAGCTTTTCTTATTTGAAGCCTGACATGACTTGACT
Found at i:10930 original size:54 final size:54
Alignment explanation
Indices: 10825--10954 Score: 127
Period size: 54 Copynumber: 2.4 Consensus size: 54
10815 TGGTTCAATG
* * * ** * *
10825 TCACAAATTAGTCGAAGTTTGACTCAACTTCAAATTGGTCCAGGTTTAATGTAA
1 TCACAAATTAGTCAAAATTTAACTCAACTTCAAATTGAACCAGATTCAATGTAA
* **
10879 TCACAAATTAGTCAAAATTTAACTTAACTTCAAATT-AACCAAGATTCAATGTGG
1 TCACAAATTAGTCAAAATTTAACTCAACTTCAAATTGAACC-AGATTCAATGTAA
* * *
10933 GCACAAATTAATCCAAATTTAA
1 TCACAAATTAGTCAAAATTTAA
10955 TGTGATCACT
Statistics
Matches: 62, Mismatches: 13, Indels: 2
0.81 0.17 0.03
Matches are distributed among these distances:
53 2 0.03
54 60 0.97
ACGTcount: A:0.40, C:0.17, G:0.12, T:0.32
Consensus pattern (54 bp):
TCACAAATTAGTCAAAATTTAACTCAACTTCAAATTGAACCAGATTCAATGTAA
Found at i:11155 original size:16 final size:16
Alignment explanation
Indices: 11136--11177 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
11126 AGAAAGAAAG
11136 AAAGAAAAGGGAAAAA
1 AAAGAAAAGGGAAAAA
*
11152 AAAGGAAAA-CGAAAAA
1 AAA-GAAAAGGGAAAAA
*
11168 AAAAAAAAGG
1 AAAGAAAAGG
11178 AAACAATGGA
Statistics
Matches: 21, Mismatches: 3, Indels: 4
0.75 0.11 0.14
Matches are distributed among these distances:
15 4 0.19
16 12 0.57
17 5 0.24
ACGTcount: A:0.76, C:0.02, G:0.21, T:0.00
Consensus pattern (16 bp):
AAAGAAAAGGGAAAAA
Found at i:12507 original size:111 final size:111
Alignment explanation
Indices: 12313--12528 Score: 369
Period size: 111 Copynumber: 1.9 Consensus size: 111
12303 ACTGGAAGAA
* * **
12313 AACATGACCAATTTACACAATATGGGGCAAGATTCACAGAGCTTGAGTGCTAATGGTGTTAAGGA
1 AACATGACCAATTTACACAATATGGGGCAAGAATCACAGAGCGTGAGTGCTAATGGTAATAAGGA
12378 AATTAAACTTGAGGAGCCAACTGAAAAAAGTAATGAACCAGTTGTT
66 AATTAAACTTGAGGAGCCAACTGAAAAAAGTAATGAACCAGTTGTT
*
12424 AACATGACCAATTTACACAATATGGGGCAAGAATCACAGATCGTGAGTGCTAATGGTAATAAGGA
1 AACATGACCAATTTACACAATATGGGGCAAGAATCACAGAGCGTGAGTGCTAATGGTAATAAGGA
* *
12489 AATTACACTTGAGGAGCCAACTGAGAAAAGTAATGAACCA
66 AATTAAACTTGAGGAGCCAACTGAAAAAAGTAATGAACCA
12529 ATTCAAACAA
Statistics
Matches: 98, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
111 98 1.00
ACGTcount: A:0.40, C:0.15, G:0.22, T:0.22
Consensus pattern (111 bp):
AACATGACCAATTTACACAATATGGGGCAAGAATCACAGAGCGTGAGTGCTAATGGTAATAAGGA
AATTAAACTTGAGGAGCCAACTGAAAAAAGTAATGAACCAGTTGTT
Found at i:13861 original size:2 final size:2
Alignment explanation
Indices: 13854--13894 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
13844 ATAAGAGTCA
13854 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
13895 TAGGTAGTCT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:24291 original size:18 final size:18
Alignment explanation
Indices: 24270--24304 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
24260 AAAAAAAGGG
24270 AGAAAAAAAAAGAAAGAA
1 AGAAAAAAAAAGAAAGAA
*
24288 AGAAAGAAAAAGAAAGA
1 AGAAAAAAAAAGAAAGA
24305 GAAAATGAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (18 bp):
AGAAAAAAAAAGAAAGAA
Found at i:27959 original size:2 final size:2
Alignment explanation
Indices: 27954--27982 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
27944 CTCTCTCTCT
27954 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.