Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018272.1 Corchorus olitorius cultivar O-4 contig18305, 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: 8499
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.33
Found at i:6179 original size:51 final size:50
Alignment explanation
Indices: 6079--6179 Score: 125
Period size: 51 Copynumber: 2.0 Consensus size: 50
6069 GTTCTTCATA
* **
6079 TTTCCTTGTTTAGATCTTGTCTCCGGACAAACAAACACTCTTTTAGTGTT
1 TTTCCTTGTTTAGATCTTGTCTCCGGACAAACAAACACTCGTACAGTGTT
*
6129 TTTCTCTTGTTTCA-ATCTTGTCTCCGGACATACAAACACT-GTACACGTGTT
1 TTTC-CTTGTTT-AGATCTTGTCTCCGGACAAACAAACACTCGTACA-GTGTT
6180 CTTCATTCAG
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
50 6 0.14
51 37 0.84
52 1 0.02
ACGTcount: A:0.22, C:0.24, G:0.14, T:0.41
Consensus pattern (50 bp):
TTTCCTTGTTTAGATCTTGTCTCCGGACAAACAAACACTCGTACAGTGTT
Found at i:7374 original size:31 final size:30
Alignment explanation
Indices: 7339--7445 Score: 105
Period size: 31 Copynumber: 3.5 Consensus size: 30
7329 TCAAAGATCG
7339 GGCCCTTATTTGAGCATTTTCAATAACGTTA
1 GGCCCTTATTTGAGCATTTTCAA-AACGTTA
** **
7370 GGCCCTTATTTG-GCCAAATT-AAAA-GATCG
1 GGCCCTTATTTGAG-CATTTTCAAAACG-TTA
7399 GGCCCTTATTTGAGCATTTTGGC-AAACGTTA
1 GGCCCTTATTTGAGCATTTT--CAAAACGTTA
7430 GGCCCTTATTTGAGCA
1 GGCCCTTATTTGAGCA
7446 ATTAGCCATA
Statistics
Matches: 61, Mismatches: 8, Indels: 14
0.73 0.10 0.17
Matches are distributed among these distances:
28 1 0.02
29 19 0.31
30 4 0.07
31 36 0.59
32 1 0.02
ACGTcount: A:0.25, C:0.21, G:0.21, T:0.34
Consensus pattern (30 bp):
GGCCCTTATTTGAGCATTTTCAAAACGTTA
Done.