file1
>Chr1.ID=PAC:19650373;Name=AT1G11900.1;pacid=19650373;longest=1;Parent=AT1G11900.len361.i1.1_111
GTATGAATTCCAAAAATCCAGAACCGTTTTCGTGATTCATGTTATGCTCTCGTTGTTGTTTTCTGATTGTTACTGCTCAGCGAGTTTCTTCTATCAATGTTTGATTCGATGAAGATGCGAAATTTCGAACCATTGCTGTTCTTCTGAGTTTGATCGTTTTTTAGTTTCGGGGCTTTCACGCTTCAGCTAGTGTTTGATTACGAAGTTTTCTGATTAAATGTGTGAGTTTTTTTGTAGTCATCTCGAAAACTGAGAAATCCATTTTTATAGATTTACATTGTTCATAGTTATATGTGGAAGTTGATGATTGATGGTGATTCTGCAAATTGATGATTTGGTTTTCTGTTTATTGGCATTGCAG
>Chr1.ID=PAC:19657430;Name=AT1G76660.1;pacid=19657430;longest=1;Parent=AT1G76660.len490.i1.2_394
GTTTCTGTTTAATTCTCTCTATTTTCGTTTGATTTCGACTTCTTGAGCTTTTACTTCTCTCTGTCTCAGTTCTAACTTCTTCAGATTTTAAAGCTTTCGTTTTTTTGGCAAGTTGTTTTTTTTTCCTACTTAGATCTGACTACTCCGACTCTGTTCACACTAATGTTCGTTAGGGTTTATGTTGAATCTCTCCTTTGATCATTATGTTATTGTAAAAATCCCAGCTTTATGCTAAATCGAGCTAGTGATTCTTGAGAATTGAACAAAAAAGTTTTACATTTTTCTGAATTGCCATTCAATTAGAAGAAGAAAAAATTCAACCTTTTACTGGTTATGATCTAGATTCGATGCGTGTAAGCTATAAGATCACCATTTCGTGCTTTAGATCCATAATCATTGATTCACTATATGGCAATTATCTTCTTGCTTCACAGATCTCTTTTACACTTACATGTCAAGTGTCTGAGTGTGTGTGTGTGTCCTTTTGCAG
>Chr1.ID=PAC:19657550;Name=AT1G53750.1;pacid=19657550;longest=1;Parent=AT1G53750.len344.i1.9_229
GTAAGCCTTCCCCTTTTAGAACCCTAAGTTTTATTGGGGTTTTCGATTTTTACTCTTCTGATTCATCGGAGAATTCGGATCTACACTAGATTTTAGTTACTCGAATGTGAGGGTTTCGTCTCTTTGCAAACCAATTTGATGTTTCCTCCTGAGCTAGATATGTTCTTGATGAGCTTGATTTTTCTACTTGGTTCAGTTTTTTTTGCTAATTACTACTTATATGAGTGAATCTGCCTCACTGTTTGAATTTATTCCAAGTGGAAATATTCATAGTCATGCTTTGTTGTATCTGTTATCTCTCCATATGTTGTGTTGCTGACCTTGTTAAATCTCATTCTCTGCAG
>Chr1.ID=PAC:19650963;Name=AT1G47740.1;pacid=19650963;longest=1;Parent=AT1G47740.len1091.i1.4_277
GTAAGTTAATCTTCTCTTCTGAAAATTGAATTTGGTGTATCAATTCTTACATTATCTTGAAGATTCATCTCTGAATTTCTCAAATTTATGGGGGTTTTTTGTTTGTCGGAATTGCCGGAGAAATTGGAAAAAACGAGATCTTTGAGTAAAGGGTTTGTTTAATCTTTAGTCTTTATTGCTTTCCTTAAGCTAATTTTGGCAGATCTGGAACATAAACCCTAGAACAAGACCAAATCAGTGTCTCCTTACTCTTAGGGATTTTAGTCTCTGTGATACCTTAAATGTGTTTATAAATTGACTGTGCTTAATGGGTCACATTTGATTTGCAATAAAAGTTTCACAATTCTTCCATTTTCAGTAATGTAAGCTCCAGTTTTCAAGATTTACTATTTTGGGGAACTAGTTAGGTTTGTAGGTTTATTAGATCTTAGAAACACTAATGTAATGCTGTTTGTTTGGTACTCTTTAATATTCACTATTCATCTTAATGTGGAATCAAATTTGCTTTTTTTGGTCAGACTCAATTAGTTGGAATGAGTTGTTGAACCATTGACTTGTCTCCTAAGCTCTTACTTAATCTATCTGTATCATCTTCTCCTGTCTATTTCTCTTTATTTAATACATAACTCGTTCATGATTGCATCTGACATGGTAGCAACTCTTTGTGAACAAGACTTGATTTTATAACACTGTAACATGACCACACTTTTTCCTTTTGATCTCTGTATATTTGGGGAAGTAAGGATTTGGTTTAACAATGATACAAAATCACAGTTTAGATGACTCAGTCTTGTCTTTTATCATTAAGATGGAAAAAATGAGACCAATCTTGTCTTGCTTTATTCTAAGATGCATGCTCTATTATATTTTATGCTTTTGTATATATAACTGATTGAAGCCGGCCAATGGAGATTGGTGCTGACTTTTTAAATGAGCTGTTGTTGTATTTCAGCCAACTAGCATAAGATAAAATAAAATAGGAAAATTTTTCATTTCAGTCTCTTAAGTTCAATGAAAACATAATGTGGCACAGAGGTCTTTGCTTTTGTACCTTTCAGAATCTTTTATTGATTGATGATGTTTACATACAG
>Chr1.ID=PAC:19652608;Name=AT1G31420.1;pacid=19652608;longest=1;Parent=AT1G31420.len415.i1.13_217
GTTCTTATAATTCTTACTAATTCTGTTTGCTTTTAAAGCTATAACCTTTGATATTGTTGGAAAGAGTGGGGTTTTGGGTCTTTTGCTGAATCGTTTTTTGGATTTGTTATATTGTTCGAATCTTCAGTTGTTATTGTGTTATAGGATTGGATGGTATCTGGGAATTTCGTAATCTATGTTAAGCTAGAGCTGTTTTTGAGCTCTTTTGTTGATGATGATTTTGAGATTGTTGGCCGAATTTAGCTCTCGTTTTCTGATTTTAGCAATTGGAAAGTGTGTATTGGTTCTTGTGAGGCAATTTCACTGTTTTGAGTACTCAAAATGTAGATGAGAGCATGCATAAGTTGTGTGGAGACTGAGCTTAATGTGTAGTGTAATTGACAATTAGTTTTGTGGGCTTTCCTTTGTTTTTCAG

##</code><code>##

file2
>Chr1.ID=PAC:19650373;Name=AT1G11900.1;pacid=19650373;longest=1;Parent=AT1G11900.len361.i1.1_111		100
>Chr1.ID=PAC:19657430;Name=AT1G76660.1;pacid=19657430;longest=1;Parent=AT1G76660.len490.i1.2_394		34
>Chr1.ID=PAC:19652608;Name=AT1G31420.1;pacid=19652608;longest=1;Parent=AT1G31420.len415.i1.13_217	76

##</code><code>##

#!/usr/bin/perl

use strict; 
use warnings;
use diagnostics;
use FAlite;

die "usage: $0 <fasta> <list>\n" unless @ARGV == 2;

open(FASTA, $ARGV[0]) or die;
my $fasta = new FAlite(\*FASTA);
while (my $entry = $fasta->nextEntry) {
	my $gseq = $entry->seq;
	my ($chrom) = $entry->def =~ /(^\S+)/;
	my @a1 = $chrom;
	my %hash;
	$hash{$_}++ for @a1;
	
	my $header;
	open(LIST, $ARGV[1]) or die;
	while (<LIST>) {
		next if /^#/;
		my ($header, $score) = split;
		my @a2 = $header;
		
			for my $item (@a2) {
    		if ($hash{$item}) {print "$chrom\n$gseq\n"};
        }
    }
}

close FASTA;
close LIST;
__END__

##</code><code>##

package FAlite;
use strict;
sub new {
	my ($class, $fh) = @_;
	if (ref $fh !~ /GLOB/)
		{die ref $fh, "\n", "FAlite ERROR: expect a GLOB reference\n"}
	my $this = bless {};
	$this->{FH} = $fh;
	while(<$fh>) {last if $_ =~ /\S/} # not supposed to have blanks, but...
	my $firstline = $_;
	if (not defined $firstline) {warn "FAlite: Empty\n"; return $this}
	if ($firstline !~ /^>/) {warn "FAlite: Not FASTA formatted\n"; return $this}
	$this->{LASTLINE} = $firstline;
	chomp $this->{LASTLINE};
	return $this;
}
sub nextEntry {
	my ($this) = @_;
	return 0 if not defined $this->{LASTLINE};
	my $fh = $this->{FH};
	my $def = $this->{LASTLINE};
	my @seq;
	my $lines_read = 0;
	while(<$fh>) {
		$lines_read++;
		if ($_ =~ /^>/) {
			$this->{LASTLINE} = $_;
			chomp $this->{LASTLINE};
			last;
		}
		push @seq, $_;
	}
	return 0 if $lines_read == 0;
	chomp @seq;
	my $entry = FAlite::Entry::new($def, \@seq);
	return $entry;
}

package FAlite::Entry;
use overload '""' => 'all';
sub new {
	my ($def, $seqarry) = @_;
	my $this = bless {};
	$this->{DEF} = $def;
	$this->{SEQ} = join("", @$seqarry);
	$this->{SEQ} =~ s/\s//g; # just in case more spaces
	return $this;
}
sub def {shift->{DEF}}
sub seq {shift->{SEQ}}
sub all {my $e = shift; return $e->{DEF}."\n".$e->{SEQ}."\n"}

1;