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keeping just the best hit . repeats

Hi. i blasted several short nucleotide sequences that are around 45bp long and very similiar in sequence to each other against a bacterial genome. now i got many overlapping hits for the same region in the bacterial genome. i would like to keep just the best hit for a specific region by bitscore or evalue. so whenever hits share atleast 1bp in positon just keep the best hit remove all others. how can i do that on a big blast output ? i didnt succeed so far

have a nice day

hit best
• 787 views • link
updated by GenoMax GenoMax • written by csag6433 • csag6433

heres a short example of my output . as you can see there are many overlapping hits per subject sequence from different queries . i would like to keep only the best hit per subject region independent of the type of query

rr5 2A  86.486  37  2   3   4   38  15277   15312   0.006   38.1

rr6 2A  86.111  36  3   2   5   38  15279   15314   0.006   38.1

rr6 2A  93.333  30  1   1   5   33  17846   17875   0.000132    43.6

rr9 2A  93.333  30  2   0   1   30* 17847   17876   3.82e-05    45.4

rr4 2A  95.652  23  1   0   1   23* 17851   17873   0.006   38.1

rr5 2A  88.235  34  3   1   5   38* 19903   19935   0.002   39.9

rr9 2A  87.805  41  2   2   1   39* 19905   19944   3.82e-05    45.4

rr6 2A  90.909  44  2   2   1   42* 39077   39120   4.71e-09    58.4

rr2 2A  95.349  43  1   1   1   43* 39078   39119   7.18e-12    67.6

rr9 2A  97.368  38  1   0   1   38  39086   39123   2.93e-11    65.8
• 0 views • link
updated by GenoMax GenoMax • written by csag6433 • csag6433

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