#!/usr/bin/perl
use strict;
use warnings;
use Inline::Files;

my %data;
while (<A>) {
	chomp;
	my (undef, $fragment, undef, $pos) = split /\t/;
	$data{$pos} = $fragment;
}

<B>; # throw away header '300	 dG = -62.54 ...'
while (<B>) {
	my $pos = (split /\t/)[0];
	print "$data{$pos} $pos\n" if $data{$pos};
}

__A__
1-Match:	GGTGTTGTATGCCTTTAAA	5	3545
2-Match:	GGAAAGTCAAGCCCATCTA	9	3254
3-Match:	GTTCTTATTTGCACCTACT	6	180
4-Match:	GATGAGGAACAGCAACCTT	5	844
__B__
300	 dG = -62.54   [initially -70.70] gi178893_M23263_rna_300-1 
1	G	0	2	0	1
2	A	1	3	0	2
3	A	2	4	0	3
4	U	3	5	0	4
5	U	4	6	0	5
6	C	5	7	0	6
7	C	6	8	0	7
8	G	7	9	34	8
9	G	8	10	33	9
........
........
179	A	178	180	231	179
180	G	179	181	230	180
181	U	180	182	229	181
........
........