Hi, out of curiosity, as I work with fasta files a bit, why not use the Bio::DB::Fasta module from BioPerl for indexed access to any number of fasta files. Your example is precisely what this module is for, unless you're exercising OO programming. I used your sample data for the code below, if interested.

update: Initially, creating the db may take a moment depending on size of input files, but it works pretty quick every time it's accessed after that. 

#!/usr/bin/perl
use Modern::Perl '2011';
use autodie;
use Bio::DB::Fasta;

die "Usage: $0 <fastaFile> <queryFile>\n" unless my( $fastaFile, $quer
+yFile ) = @ARGV;

open my $fh, '<', $queryFile;
chomp( my @queries  = <$fh> );
close $fh;
# trim header
@queries = map{ local $_ = $_; s/^>(\S+)\s+\d+/$1/; $_ } @queries;

# create indexed database from fasta file
my $db = Bio::DB::Fasta->new( $fastaFile );

open my $fh2, '>', 'querySeqs.fa';
for my $query ( @queries ) {
    my $seqheader = $db->header( $query );
    my $seqdna = $db->seq( $seqheader );
    say {$fh2} ">$seqheader";
    print {$fh2} format_sequence( $seqdna, 60 );
}
close $fh2;


sub format_sequence {
    my($sequence, $length) = @_; # sequence and length of line 
    open my $string_fh, '>', \ my $string; # print sequence to string
    for( my $pos = 0; $pos < length( $sequence ); $pos += $length ) {
        print {$string_fh} substr( $sequence, $pos, $length ), "\n";
    }
    $string;
}


output in file querySeqs.fa

>Chr1.ID=PAC:19650373;Name=AT1G11900.1;pacid=19650373;longest=1;Parent
+=AT1G11900.len361.i1.1_111
GTATGAATTCCAAAAATCCAGAACCGTTTTCGTGATTCATGTTATGCTCTCGTTGTTGTT
TTCTGATTGTTACTGCTCAGCGAGTTTCTTCTATCAATGTTTGATTCGATGAAGATGCGA
AATTTCGAACCATTGCTGTTCTTCTGAGTTTGATCGTTTTTTAGTTTCGGGGCTTTCACG
CTTCAGCTAGTGTTTGATTACGAAGTTTTCTGATTAAATGTGTGAGTTTTTTTGTAGTCA
TCTCGAAAACTGAGAAATCCATTTTTATAGATTTACATTGTTCATAGTTATATGTGGAAG
TTGATGATTGATGGTGATTCTGCAAATTGATGATTTGGTTTTCTGTTTATTGGCATTGCA
G
>Chr1.ID=PAC:19657430;Name=AT1G76660.1;pacid=19657430;longest=1;Parent
+=AT1G76660.len490.i1.2_394
GTTTCTGTTTAATTCTCTCTATTTTCGTTTGATTTCGACTTCTTGAGCTTTTACTTCTCT
CTGTCTCAGTTCTAACTTCTTCAGATTTTAAAGCTTTCGTTTTTTTGGCAAGTTGTTTTT
TTTTCCTACTTAGATCTGACTACTCCGACTCTGTTCACACTAATGTTCGTTAGGGTTTAT
GTTGAATCTCTCCTTTGATCATTATGTTATTGTAAAAATCCCAGCTTTATGCTAAATCGA
GCTAGTGATTCTTGAGAATTGAACAAAAAAGTTTTACATTTTTCTGAATTGCCATTCAAT
TAGAAGAAGAAAAAATTCAACCTTTTACTGGTTATGATCTAGATTCGATGCGTGTAAGCT
ATAAGATCACCATTTCGTGCTTTAGATCCATAATCATTGATTCACTATATGGCAATTATC
TTCTTGCTTCACAGATCTCTTTTACACTTACATGTCAAGTGTCTGAGTGTGTGTGTGTGT
CCTTTTGCAG
>Chr1.ID=PAC:19652608;Name=AT1G31420.1;pacid=19652608;longest=1;Parent
+=AT1G31420.len415.i1.13_217
GTTCTTATAATTCTTACTAATTCTGTTTGCTTTTAAAGCTATAACCTTTGATATTGTTGG
AAAGAGTGGGGTTTTGGGTCTTTTGCTGAATCGTTTTTTGGATTTGTTATATTGTTCGAA
TCTTCAGTTGTTATTGTGTTATAGGATTGGATGGTATCTGGGAATTTCGTAATCTATGTT
AAGCTAGAGCTGTTTTTGAGCTCTTTTGTTGATGATGATTTTGAGATTGTTGGCCGAATT
TAGCTCTCGTTTTCTGATTTTAGCAATTGGAAAGTGTGTATTGGTTCTTGTGAGGCAATT
TCACTGTTTTGAGTACTCAAAATGTAGATGAGAGCATGCATAAGTTGTGTGGAGACTGAG
CTTAATGTGTAGTGTAATTGACAATTAGTTTTGTGGGCTTTCCTTTGTTTTTCAG

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in thread Searching array against hash by drhicks

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