Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006286.1 Hibiscus syriacus cultivar Beakdansim tig00015006_pilon, 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: 181793
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
File 2 of 2
Found at i:178057 original size:19 final size:19
Alignment explanation
Indices: 178033--178071 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
178023 TAATATATAT
178033 GATACTTATAGAGTGATGC
1 GATACTTATAGAGTGATGC
178052 GATACTTATAGAGTGATGC
1 GATACTTATAGAGTGATGC
178071 G
1 G
178072 TTGTTGGGTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.31, C:0.10, G:0.28, T:0.31
Consensus pattern (19 bp):
GATACTTATAGAGTGATGC
Found at i:178426 original size:60 final size:61
Alignment explanation
Indices: 178305--178442 Score: 156
Period size: 60 Copynumber: 2.3 Consensus size: 61
178295 AACATACTAA
* *
178305 ATAGTCGG-GTGACCATTTTATAACTTTTAAAAGTCTAGGGACTCAACAAAACAACATCCT
1 ATAGTCGGAGTGACCATTTTATAACTTTTAAAAGTCGAGGGACTCAACAAAACAACACCCT
* * * * * * *
178365 ATAGTCGGAG-GATCATTTTGTAACTTTTGATAGTCGAGGGACTCAACTAAGCATCACCCT
1 ATAGTCGGAGTGACCATTTTATAACTTTTAAAAGTCGAGGGACTCAACAAAACAACACCCT
* *
178425 ATAATCGGA-TGACTATTT
1 ATAGTCGGAGTGACCATTT
178443 GTGTACTTTA
Statistics
Matches: 64, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
60 63 0.98
61 1 0.02
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30
Consensus pattern (61 bp):
ATAGTCGGAGTGACCATTTTATAACTTTTAAAAGTCGAGGGACTCAACAAAACAACACCCT
Done.