Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016648.1 Corchorus olitorius cultivar O-4 contig16681, 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: 8173
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.26
Found at i:2865 original size:51 final size:52
Alignment explanation
Indices: 2764--2865 Score: 129
Period size: 51 Copynumber: 2.0 Consensus size: 52
2754 GTTCTTCATA
* **
2764 TTCTCCTTGTTTAGATCTTGTCTCCGGACAAACAAACACTCTTTTAGTGTTT
1 TTCTCCTTGTTTAGATCTTGTCTCCGGACAAACAAACACTCGTACAGTGTTT
*
2816 TTCT-CTTGTTTCA-ATCTTGTCTCCGGACATACAAACACT-GTACACGTGTT
1 TTCTCCTTGTTT-AGATCTTGTCTCCGGACAAACAAACACTCGTACA-GTGTT
2866 CTTCATTCAG
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
50 2 0.05
51 37 0.84
52 5 0.11
ACGTcount: A:0.22, C:0.25, G:0.14, T:0.40
Consensus pattern (52 bp):
TTCTCCTTGTTTAGATCTTGTCTCCGGACAAACAAACACTCGTACAGTGTTT
Found at i:5333 original size:47 final size:47
Alignment explanation
Indices: 5264--5368 Score: 194
Period size: 47 Copynumber: 2.3 Consensus size: 47
5254 ATGGTCATGT
*
5264 GCAACTTCCCAAATGATGGACAACTGACTAGTAAGGAGAAGAAGGAA
1 GCAACTTCCCAAAGGATGGACAACTGACTAGTAAGGAGAAGAAGGAA
5311 GCAACTTCCCAAAGGATGGACAACTGACTAGTAAGGAGAAGAAGGAA
1 GCAACTTCCCAAAGGATGGACAACTGACTAGTAAGGAGAAGAAGGAA
5358 GCAAC-TCCCAA
1 GCAACTTCCCAA
5369 GAGGTCAAAC
Statistics
Matches: 57, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
46 6 0.11
47 51 0.89
ACGTcount: A:0.42, C:0.20, G:0.25, T:0.13
Consensus pattern (47 bp):
GCAACTTCCCAAAGGATGGACAACTGACTAGTAAGGAGAAGAAGGAA
Done.