Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017195.1 Corchorus olitorius cultivar O-4 contig17228, 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: 2705
ACGTcount: A:0.32, C:0.22, G:0.18, T:0.28
Found at i:203 original size:51 final size:50
Alignment explanation
Indices: 102--203 Score: 127
Period size: 51 Copynumber: 2.0 Consensus size: 50
92 GTTCTTCATA
* **
102 TTTTCCTTGTTTAGATCTTGTCTCCGGACAAACAAACACTCTTTTAGTGT
1 TTTTCCTTGTTTAGATCTTGTCTCCGGACAAACAAACACTCGTACAGTGT
*
152 TTTTCTCTTGTTTCA-ATCTTGTCTCCGGACATACAAACACT-GTACACGTGT
1 TTTTC-CTTGTTT-AGATCTTGTCTCCGGACAAACAAACACTCGTACA-GTGT
203 T
1 T
204 CTTCATTCAG
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
50 7 0.16
51 37 0.82
52 1 0.02
ACGTcount: A:0.22, C:0.24, G:0.14, T:0.41
Consensus pattern (50 bp):
TTTTCCTTGTTTAGATCTTGTCTCCGGACAAACAAACACTCGTACAGTGT
Found at i:565 original size:33 final size:33
Alignment explanation
Indices: 518--589 Score: 117
Period size: 33 Copynumber: 2.2 Consensus size: 33
508 TTTTGGCGCA
* * *
518 ACATCTCTTTTTGGCATGCCCTGTGGGACAAGC
1 ACATTTCTTTTTGGCACGCCCGGTGGGACAAGC
551 ACATTTCTTTTTGGCACGCCCGGTGGGACAAGC
1 ACATTTCTTTTTGGCACGCCCGGTGGGACAAGC
584 ACATTT
1 ACATTT
590 GCTCTCCCTC
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.19, C:0.26, G:0.24, T:0.31
Consensus pattern (33 bp):
ACATTTCTTTTTGGCACGCCCGGTGGGACAAGC
Done.