Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01002808.1 Corchorus olitorius cultivar O-4 contig02810, 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: 2163
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:1844 original size:31 final size:31
Alignment explanation
Indices: 1773--1857 Score: 90
Period size: 28 Copynumber: 2.8 Consensus size: 31
1763 TGGGCCTTAG
*
1773 TAATTAATTATTGGTTTATTATTCA-CATGAA
1 TAATTAATTATTGGTTTATTA-TCATTATGAA
1804 -AA--AATTATTGGTTTATTATCATTA-GTAA
1 TAATTAATTATTGGTTTATTATCATTATG-AA
**
1832 TAATTAATTATTGGTGCATTATCATT
1 TAATTAATTATTGGTTTATTATCATT
1858 TGATTAGTGT
Statistics
Matches: 46, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
27 4 0.09
28 19 0.41
29 2 0.04
30 2 0.04
31 19 0.41
ACGTcount: A:0.35, C:0.06, G:0.11, T:0.48
Consensus pattern (31 bp):
TAATTAATTATTGGTTTATTATCATTATGAA
Found at i:2046 original size:31 final size:28
Alignment explanation
Indices: 2028--2083 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 28
2018 TGTGTTTTGC
2028 TTTT-GGGACAAAATAATCCCTTATGTT
1 TTTTCGGGACAAAATAATCCCTTATGTT
* *
2055 TTTTCGGGACAAATTAATCCCTTACGTT
1 TTTTCGGGACAAAATAATCCCTTATGTT
2083 T
1 T
2084 CAAATATGAG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
27 4 0.15
28 22 0.85
ACGTcount: A:0.27, C:0.18, G:0.14, T:0.41
Consensus pattern (28 bp):
TTTTCGGGACAAAATAATCCCTTATGTT
Done.