Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018611.1 Corchorus olitorius cultivar O-4 contig18644, 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: 9832
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Found at i:2107 original size:33 final size:33
Alignment explanation
Indices: 2065--2132 Score: 127
Period size: 33 Copynumber: 2.1 Consensus size: 33
2055 TGCAGGTTTG
*
2065 ACATGTATCACATAAGGAAAAGCATAACTTAGA
1 ACATGTATCACATAAGGAAAAGCAGAACTTAGA
2098 ACATGTATCACATAAGGAAAAGCAGAACTTAGA
1 ACATGTATCACATAAGGAAAAGCAGAACTTAGA
2131 AC
1 AC
2133 TCGAGAAAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.49, C:0.16, G:0.16, T:0.19
Consensus pattern (33 bp):
ACATGTATCACATAAGGAAAAGCAGAACTTAGA
Found at i:2780 original size:29 final size:29
Alignment explanation
Indices: 2738--2810 Score: 110
Period size: 29 Copynumber: 2.5 Consensus size: 29
2728 GGACTAAAAC
2738 GACCAAAATGCCCCTCTAAATGCACAAAT
1 GACCAAAATGCCCCTCTAAATGCACAAAT
* **
2767 GACCAAAATGCCCCTCTACATGTGCAAAT
1 GACCAAAATGCCCCTCTAAATGCACAAAT
*
2796 GACCAAGATGCCCCT
1 GACCAAAATGCCCCT
2811 TAGGTGAACC
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.36, C:0.33, G:0.14, T:0.18
Consensus pattern (29 bp):
GACCAAAATGCCCCTCTAAATGCACAAAT
Found at i:2960 original size:29 final size:26
Alignment explanation
Indices: 2890--2966 Score: 91
Period size: 27 Copynumber: 2.8 Consensus size: 26
2880 CTACAAGATT
* *
2890 AAAAATGACCAAGATGCCCATGAATGT
1 AAAAATGACCAA-ATGCCCCTGAATGC
2917 AAAAATGACCAAAATGCCCCTGAATACGC
1 AAAAATGACC-AAATGCCCCTGAAT--GC
2946 AAAAATGACCTAAATGCCCCT
1 AAAAATGACC-AAATGCCCCT
2967 ACATGACCCT
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
27 21 0.48
28 2 0.05
29 21 0.48
ACGTcount: A:0.44, C:0.25, G:0.14, T:0.17
Consensus pattern (26 bp):
AAAAATGACCAAATGCCCCTGAATGC
Found at i:3410 original size:11 final size:11
Alignment explanation
Indices: 3394--3423 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
3384 TATTGGTGCT
3394 GAAATCTTTGA
1 GAAATCTTTGA
3405 GAAATCTTTGA
1 GAAATCTTTGA
*
3416 TAAATCTT
1 GAAATCTT
3424 CAGTAGAAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.37, C:0.10, G:0.13, T:0.40
Consensus pattern (11 bp):
GAAATCTTTGA
Found at i:5229 original size:30 final size:30
Alignment explanation
Indices: 5195--5256 Score: 72
Period size: 30 Copynumber: 2.1 Consensus size: 30
5185 CAATTCTTGC
* *
5195 TTCTTGAAATAATTCTTCAAT-GATCTTCAA
1 TTCTTCAAATAA-TCTTCAATAAATCTTCAA
* *
5225 TTCTTCCAATTATCTTCAATAAATCTTCAA
1 TTCTTCAAATAATCTTCAATAAATCTTCAA
5255 TT
1 TT
5257 ACGAACTTCG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 8 0.30
30 19 0.70
ACGTcount: A:0.32, C:0.19, G:0.03, T:0.45
Consensus pattern (30 bp):
TTCTTCAAATAATCTTCAATAAATCTTCAA
Found at i:5239 original size:19 final size:18
Alignment explanation
Indices: 5205--5244 Score: 62
Period size: 19 Copynumber: 2.2 Consensus size: 18
5195 TTCTTGAAAT
5205 AATTCTTCAATGATCTTC
1 AATTCTTCAATGATCTTC
*
5223 AATTCTTCCAATTATCTTC
1 AATTCTT-CAATGATCTTC
5242 AAT
1 AAT
5245 AAATCTTCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 7 0.35
19 13 0.65
ACGTcount: A:0.30, C:0.23, G:0.03, T:0.45
Consensus pattern (18 bp):
AATTCTTCAATGATCTTC
Found at i:5380 original size:16 final size:16
Alignment explanation
Indices: 5359--5390 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
5349 TACAAGTTTC
5359 CACAAATACTTACAAA
1 CACAAATACTTACAAA
5375 CACAAATACTTACAAA
1 CACAAATACTTACAAA
5391 ATAGGGTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.56, C:0.25, G:0.00, T:0.19
Consensus pattern (16 bp):
CACAAATACTTACAAA
Found at i:5407 original size:28 final size:28
Alignment explanation
Indices: 5375--5434 Score: 111
Period size: 28 Copynumber: 2.1 Consensus size: 28
5365 TACTTACAAA
5375 CACAAATACTTACAAAATAGGGTTAAAT
1 CACAAATACTTACAAAATAGGGTTAAAT
*
5403 CACAAATGCTTACAAAATAGGGTTAAAT
1 CACAAATACTTACAAAATAGGGTTAAAT
5431 CACA
1 CACA
5435 CATAAAAATA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.48, C:0.17, G:0.12, T:0.23
Consensus pattern (28 bp):
CACAAATACTTACAAAATAGGGTTAAAT
Found at i:6233 original size:88 final size:87
Alignment explanation
Indices: 6059--6237 Score: 331
Period size: 88 Copynumber: 2.0 Consensus size: 87
6049 TCGATATCAG
6059 CAACAGTCCATCCAATAGCTTCCTTGTATTCCTTCAAGACTCTGAGCAGTTGTTCTTCTTGTAAA
1 CAACAGTCCATCCAATAGCTTCCTTGTATTCCTTCAAGACTCTGAGCAGTTGTTCTTCTTGTAAA
6124 TCATTTAATTTACTTGAAATAA
66 TCATTTAATTTACTTGAAATAA
* *
6146 CAACAGTCCATCCAATAGCTTCCTTGTATTCCTTCAAGACTTTTGATCAGTTGTTCTTCTTGTAA
1 CAACAGTCCATCCAATAGCTTCCTTGTATTCCTTCAAGAC-TCTGAGCAGTTGTTCTTCTTGTAA
6211 ATCATTTAATTTACTTGAAATAA
65 ATCATTTAATTTACTTGAAATAA
6234 CAAC
1 CAAC
6238 GAGCAGAGTT
Statistics
Matches: 89, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
87 40 0.45
88 49 0.55
ACGTcount: A:0.29, C:0.22, G:0.11, T:0.39
Consensus pattern (87 bp):
CAACAGTCCATCCAATAGCTTCCTTGTATTCCTTCAAGACTCTGAGCAGTTGTTCTTCTTGTAAA
TCATTTAATTTACTTGAAATAA
Done.