The hits from the subject sequence are quite close together, so I would like to join the hits from the subject sequences together into one long sequence from 116345 to 114413 bp in the subject sequence together, with the gaps in between the hips marked by n or - characters
Does anyone know of a method to concatenate multiple blast hits into one long sequence?
BLAST is a local aligner (L in its name stands for local) and you seem to need a global aligner. You can find one by going to the BLAST web site and selecting Global Alignment. If you paste your subject and query sequences, it will give you the output you want.
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