Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012697.1 Corchorus olitorius cultivar O-4 contig12730, 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: 2899
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.29
Found at i:1658 original size:30 final size:30
Alignment explanation
Indices: 1612--1716 Score: 201
Period size: 30 Copynumber: 3.5 Consensus size: 30
1602 GAGTCTATTT
1612 CCCTTCCCCTGGCAAAAACCAGAAAAAGTTA
1 CCCTTCCCC-GGCAAAAACCAGAAAAAGTTA
1643 CCCTTCCCCGGCAAAAACCAGAAAAAGTTA
1 CCCTTCCCCGGCAAAAACCAGAAAAAGTTA
1673 CCCTTCCCCGGCAAAAACCAGAAAAAGTTA
1 CCCTTCCCCGGCAAAAACCAGAAAAAGTTA
1703 CCCTTCCCCGGCAA
1 CCCTTCCCCGGCAA
1717 CGGCGCCAAA
Statistics
Matches: 74, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
30 65 0.88
31 9 0.12
ACGTcount: A:0.36, C:0.36, G:0.13, T:0.14
Consensus pattern (30 bp):
CCCTTCCCCGGCAAAAACCAGAAAAAGTTA
Found at i:1927 original size:16 final size:15
Alignment explanation
Indices: 1889--1930 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
1879 ACAGAGATTG
*
1889 ACAGAAAGCAATTAA
1 ACAGAAAACAATTAA
1904 ACAGAAAACAATTAA
1 ACAGAAAACAATTAA
1919 ACTAGAAAACAA
1 AC-AGAAAACAA
1931 AGCAGAGTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 16 0.64
16 9 0.36
ACGTcount: A:0.64, C:0.14, G:0.10, T:0.12
Consensus pattern (15 bp):
ACAGAAAACAATTAA
Done.