Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011211.1 Corchorus olitorius cultivar O-4 contig11244, 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: 8781
ACGTcount: A:0.33, C:0.22, G:0.22, T:0.24
Found at i:6015 original size:81 final size:82
Alignment explanation
Indices: 5713--6114 Score: 655
Period size: 82 Copynumber: 4.9 Consensus size: 82
5703 TAGCTTAAAT
* *
5713 AACGGTTGAACACCTAAATTGGTGTCCCCGTATAACTAATAAAGAGGACGAACGTCCCCTAATAA
1 AACGGTTGAACACCTAAACTGGTGTCCCCGTATAACTAATAAAGAGGACGAACGTCCCCTAATGA
*
5778 GACGTTTTTCCTCTACA
66 GACGTTTTCCCTCTACA
5795 AACGGTTGAACACCTAAACTGGTGTCCCCGTATAACTAATAAAGAGGACGAACGTCCCCTAATGA
1 AACGGTTGAACACCTAAACTGGTGTCCCCGTATAACTAATAAAGAGGACGAACGTCCCCTAATGA
*
5860 GACATTTTCCCTCTACA
66 GACGTTTTCCCTCTACA
5877 AACGGTTGAACACCTAAACTGGTGTCCCCGTATAACTAATAAAGAGGACGAACGTCCCCTAATGA
1 AACGGTTGAACACCTAAACTGGTGTCCCCGTATAACTAATAAAGAGGACGAACGTCCCCTAATGA
5942 GACGTTTTCCCTCTA-A
66 GACGTTTTCCCTCTACA
* * * *
5958 AATGGTTGAACACCTAAAATGGTGTCCCCGTATAACTAGTAAAGAGGACGAACGTCCCCTACTGA
1 AACGGTTGAACACCTAAACTGGTGTCCCCGTATAACTAATAAAGAGGACGAACGTCCCCTAATGA
*
6023 GACATTTTCCCTCTAC-
66 GACGTTTTCCCTCTACA
* * * *
6039 AACGGTTGAATACCTAAACTGGTATCCCCGTATAACTAATAAAGAGGACGAACATCCCCCCAATG
1 AACGGTTGAACACCTAAACTGGTGTCCCCGTATAACTAATAAAGAGGACGAACGT-CCCCTAATG
*
6104 AGATGTTTTCC
65 AGACGTTTTCC
6115 ATATATAGTC
Statistics
Matches: 298, Mismatches: 20, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
81 125 0.42
82 173 0.58
ACGTcount: A:0.33, C:0.26, G:0.18, T:0.24
Consensus pattern (82 bp):
AACGGTTGAACACCTAAACTGGTGTCCCCGTATAACTAATAAAGAGGACGAACGTCCCCTAATGA
GACGTTTTCCCTCTACA
Found at i:6034 original size:163 final size:163
Alignment explanation
Indices: 5713--6114 Score: 671
Period size: 163 Copynumber: 2.5 Consensus size: 163
5703 TAGCTTAAAT
* *
5713 AACGGTTGAACACCTAAATTGGTGTCCCCGTATAACTAATAAAGAGGACGAACGTCCCCTAATAA
1 AACGGTTGAACACCTAAACTGGTGTCCCCGTATAACTAATAAAGAGGACGAACGTCCCCTAATGA
* *
5778 GACGTTTTTCCTCTACAAACGGTTGAACACCTAAACTGGTGTCCCCGTATAACTAATAAAGAGGA
66 GACGTTTTCCCTCTACAAACGGTTGAACACCTAAAATGGTGTCCCCGTATAACTAATAAAGAGGA
5843 CGAACGTCCCCTAATGAGACATTTTCCCTCTAC
131 CGAACGTCCCCTAATGAGACATTTTCCCTCTAC
5876 AAACGGTTGAACACCTAAACTGGTGTCCCCGTATAACTAATAAAGAGGACGAACGTCCCCTAATG
1 -AACGGTTGAACACCTAAACTGGTGTCCCCGTATAACTAATAAAGAGGACGAACGTCCCCTAATG
* *
5941 AGACGTTTTCCCTCTA-AAATGGTTGAACACCTAAAATGGTGTCCCCGTATAACTAGTAAAGAGG
65 AGACGTTTTCCCTCTACAAACGGTTGAACACCTAAAATGGTGTCCCCGTATAACTAATAAAGAGG
*
6005 ACGAACGTCCCCTACTGAGACATTTTCCCTCTAC
130 ACGAACGTCCCCTAATGAGACATTTTCCCTCTAC
* * * *
6039 AACGGTTGAATACCTAAACTGGTATCCCCGTATAACTAATAAAGAGGACGAACATCCCCCCAATG
1 AACGGTTGAACACCTAAACTGGTGTCCCCGTATAACTAATAAAGAGGACGAACGT-CCCCTAATG
*
6104 AGATGTTTTCC
65 AGACGTTTTCC
6115 ATATATAGTC
Statistics
Matches: 225, Mismatches: 12, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
162 52 0.23
163 96 0.43
164 77 0.34
ACGTcount: A:0.33, C:0.26, G:0.18, T:0.24
Consensus pattern (163 bp):
AACGGTTGAACACCTAAACTGGTGTCCCCGTATAACTAATAAAGAGGACGAACGTCCCCTAATGA
GACGTTTTCCCTCTACAAACGGTTGAACACCTAAAATGGTGTCCCCGTATAACTAATAAAGAGGA
CGAACGTCCCCTAATGAGACATTTTCCCTCTAC
Done.