#!/usr/bin/perl

# https://perlmonks.org/?node_id=1217240

use strict;
use warnings;

open my $patterns, '<', \<<END;
ATCCCACCGCTGCCACCA
ACCCTGCTCGCTGCGCCA
TCCCCGGCACCTCCACCA
TCCCCGGCATCTCCACCA
ATCCTGCCGACTACGCCA
TCGATTCCCGGCCCATGCACCA
TCGATTCCCGGCCAACGCACCA
GTCCCACCAGAGTCGCCA
ACCCCACTCCTGGTACCA
GTCCCTTCGTGGTCGCCA
END

open my $fh, '<', \<<END;
AACCCCATCCCACCGCTGCCACCA  1
AACCCCATCCTCGTCGCC  1
AACCCCATGAAATAAGAG  2
AACCCCATGATCAGGACAAG  1
AACCCCATTAAAAAATGG  1
AACTGGATTCTCTGAAATCCCACCGCTGCCACCA  1
AACTGGATTGTCTGTTTGT 1
AACTGGCAAGTTCAGGCATG  1
AACTGGCACACACAACC 1
AACTGGCACACACAACCT  1
END

my $seqs = join '|', map tr/ACGT//cdr, <$patterns>;
my $match = qr/^\w*($seqs)/;
/$match/ and print "$1\t$_" while <$fh>;

[download]

Outputs: 

ATCCCACCGCTGCCACCA      AACCCCATCCCACCGCTGCCACCA        1
ATCCCACCGCTGCCACCA      AACTGGATTCTCTGAAATCCCACCGCTGCCACCA      1

[download]

In reply to Re: finding sequence by tybalt89
in thread finding sequence by yueli711

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