Hmmer usage :why the sequence I use to construct hmm model cannot search for themselves
I'm using Hmmer to build hmmer model for the TIR (13bp) of a type of transposon, first truncating its terminal repeats for multiple sequence alignment, and then building its hmm model. But using the contructed model to search the original transposon sequence , can't find TIR in these transposon sequences, can anyone help me?
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