#!/usr/bin/perl

# https://perlmonks.org/?node_id=11102026

use strict;
use warnings;

my $data = do { local $/; <DATA> };
my $sequence = 'JJ22';

$data =~ /^>$sequence\n((?:\w+\n)*)/m or die "$sequence not found";;
my $count = () = $1 =~ s/\W+//gr =~ /(?=[MT].[KA])/g;
print "$sequence motif count: $count\n";

__DATA__
>JJ57
MKIKLVTVGDAKEEYLIQGINEYLKRLNSYAKRETIEVPDEKAPEKLSDAEMLQVKEKEGEYVFVLAI
NGKQLSSEEFSKEIFQTGISGKSNLTFTTCFSLGLSDSVLQRIMKGEPYHKL
>JJ22
MDQNGASGSHPNRASTRKGAHARERGATVSAMSANRSNIIDEMAKICEADRQTFAIARRTRNESQ
FFGFRTASNKAIEITEAMEKRGAMFLTQSKATDQLNGWQPSDEPDKTSAESEPWFRGKQLSSEEFS
KEIFQTGISGKSNLTFTTCFSLGLSDSVLQRIMKGEPYHKL
>JJ41
MWKTVAPIFAAIFAVGLCGTFRTNTRKGEPTTKCFVFVHDTKARIYQCTFKTWSCPWLNNIVSAQF
QFVTGANYKIVVKLVGELFTETALFNWSSPTTIFTGLGTLITADKTLDCDSNML

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In reply to Re: Find a sequence in a multifasta files and motifs by tybalt89
in thread Find a sequence in a multifasta files and motifs by rebkirl

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