Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01006702.1 Corchorus olitorius cultivar O-4 contig06727, 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: 1736
ACGTcount: A:0.34, C:0.17, G:0.20, T:0.29
Found at i:37 original size:30 final size:30
Alignment explanation
Indices: 3--333 Score: 509
Period size: 30 Copynumber: 10.9 Consensus size: 30
1 AG
* * * *
3 CATGACAAGTTCTGGTGTCAATTGCAGGAG
1 CATGACAACTTCTGGTGTCAATTGTAAGAC
* *
33 CATGACAACTTCTGGTGTCAATTGCAAGAT
1 CATGACAACTTCTGGTGTCAATTGTAAGAC
*
63 CATTGACAACTTCTGGTGTCAATTGCAAGAC
1 CA-TGACAACTTCTGGTGTCAATTGTAAGAC
*
94 CATGACAACTTCTGGTGTCAATTGCAAGAC
1 CATGACAACTTCTGGTGTCAATTGTAAGAC
124 CATGACAACTTCTGGTGTCAATTGTAAGAC
1 CATGACAACTTCTGGTGTCAATTGTAAGAC
*
154 CATTGACAACTTCTGGTGTCAATTGTAAGAT
1 CA-TGACAACTTCTGGTGTCAATTGTAAGAC
*
185 CATTGACAACTTATGGTGTCAATTGTAAGAC
1 CA-TGACAACTTCTGGTGTCAATTGTAAGAC
*
216 CATGACAACTTCTGGTGTCATTTGTAAGAC
1 CATGACAACTTCTGGTGTCAATTGTAAGAC
* *
246 CATGACAACTTCTGGTGTCATTTGTAAAAC
1 CATGACAACTTCTGGTGTCAATTGTAAGAC
*
276 CATGACAACTTCTGGTGTCATTTGTAAGAC
1 CATGACAACTTCTGGTGTCAATTGTAAGAC
306 CATGACAACTTCTGGTGTCAATTGTAAG
1 CATGACAACTTCTGGTGTCAATTGTAAG
334 TAGAATAAAT
Statistics
Matches: 286, Mismatches: 13, Indels: 4
0.94 0.04 0.01
Matches are distributed among these distances:
30 199 0.70
31 87 0.30
ACGTcount: A:0.29, C:0.19, G:0.21, T:0.31
Consensus pattern (30 bp):
CATGACAACTTCTGGTGTCAATTGTAAGAC
Found at i:158 original size:91 final size:91
Alignment explanation
Indices: 3--333 Score: 520
Period size: 91 Copynumber: 3.6 Consensus size: 91
1 AG
* * * * *
3 CATGACAAGTTCTGGTGTCAATTGCAGGAGCATGACAACTTCTGGTGTCAATTGCAAGATCATTG
1 CATGACAACTTCTGGTGTCAATTGCAAGACCATGACAACTTCTGGTGTCAATTGTAAGACCATTG
*
68 ACAACTTCTGGTGTCAATTGCAAGAC
66 ACAACTTCTGGTGTCAATTGTAAGAC
94 CATGACAACTTCTGGTGTCAATTGCAAGACCATGACAACTTCTGGTGTCAATTGTAAGACCATTG
1 CATGACAACTTCTGGTGTCAATTGCAAGACCATGACAACTTCTGGTGTCAATTGTAAGACCATTG
*
159 ACAACTTCTGGTGTCAATTGTAAGAT
66 ACAACTTCTGGTGTCAATTGTAAGAC
* * *
185 CATTGACAACTTATGGTGTCAATTGTAAGACCATGACAACTTCTGGTGTCATTTGTAAGACCA-T
1 CA-TGACAACTTCTGGTGTCAATTGCAAGACCATGACAACTTCTGGTGTCAATTGTAAGACCATT
* *
249 GACAACTTCTGGTGTCATTTGTAAAAC
65 GACAACTTCTGGTGTCAATTGTAAGAC
* *
276 CATGACAACTTCTGGTGTCATTTGTAAGACCATGACAACTTCTGGTGTCAATTGTAAG
1 CATGACAACTTCTGGTGTCAATTGCAAGACCATGACAACTTCTGGTGTCAATTGTAAG
334 TAGAATAAAT
Statistics
Matches: 223, Mismatches: 16, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
90 53 0.24
91 113 0.51
92 57 0.26
ACGTcount: A:0.29, C:0.19, G:0.21, T:0.31
Consensus pattern (91 bp):
CATGACAACTTCTGGTGTCAATTGCAAGACCATGACAACTTCTGGTGTCAATTGTAAGACCATTG
ACAACTTCTGGTGTCAATTGTAAGAC
Found at i:219 original size:122 final size:121
Alignment explanation
Indices: 3--333 Score: 529
Period size: 122 Copynumber: 2.7 Consensus size: 121
1 AG
* * * * *
3 CATGACAAGTTCTGGTGTCAATTGCAGGAGCATGACAACTTCTGGTGTCAATTGCAAGATCATTG
1 CATGACAACTTCTGGTGTCAATTGTAAGACCATGACAACTTCTGGTGTCAATTGTAAGATCATTG
*
68 ACAACTTCTGGTGTCAATTGCAAGACCATGACAACTTCTGGTGTCAATTGCAAGAC
66 ACAACTTCTGGTGTCAATTGTAAGACCATGACAACTTCTGGTGTCAATTGCAAGAC
124 CATGACAACTTCTGGTGTCAATTGTAAGACCATTGACAACTTCTGGTGTCAATTGTAAGATCATT
1 CATGACAACTTCTGGTGTCAATTGTAAGACCA-TGACAACTTCTGGTGTCAATTGTAAGATCATT
* * *
189 GACAACTTATGGTGTCAATTGTAAGACCATGACAACTTCTGGTGTCATTTGTAAGAC
65 GACAACTTCTGGTGTCAATTGTAAGACCATGACAACTTCTGGTGTCAATTGCAAGAC
* * * *
246 CATGACAACTTCTGGTGTCATTTGTAAAACCATGACAACTTCTGGTGTCATTTGTAAGACCA-TG
1 CATGACAACTTCTGGTGTCAATTGTAAGACCATGACAACTTCTGGTGTCAATTGTAAGATCATTG
310 ACAACTTCTGGTGTCAATTGTAAG
66 ACAACTTCTGGTGTCAATTGTAAG
334 TAGAATAAAT
Statistics
Matches: 195, Mismatches: 14, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
120 25 0.13
121 56 0.29
122 114 0.58
ACGTcount: A:0.29, C:0.19, G:0.21, T:0.31
Consensus pattern (121 bp):
CATGACAACTTCTGGTGTCAATTGTAAGACCATGACAACTTCTGGTGTCAATTGTAAGATCATTG
ACAACTTCTGGTGTCAATTGTAAGACCATGACAACTTCTGGTGTCAATTGCAAGAC
Found at i:1415 original size:22 final size:24
Alignment explanation
Indices: 1380--1438 Score: 61
Period size: 22 Copynumber: 2.5 Consensus size: 24
1370 ATAAATGTTG
* *
1380 CTGATAA-TCTTCT-CTTTTATCT
1 CTGATAATTCTTCTCCATTTATCA
1402 CTGATAATTC-TCTCCATTTATCA
1 CTGATAATTCTTCTCCATTTATCA
1425 CTTGATAATATCTT
1 C-TGATAAT-TCTT
1439 GCCAGATAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
22 10 0.33
23 10 0.33
24 7 0.23
25 2 0.07
26 1 0.03
ACGTcount: A:0.24, C:0.22, G:0.05, T:0.49
Consensus pattern (24 bp):
CTGATAATTCTTCTCCATTTATCA
Done.