use strict;
use warnings;

my @comp;
# open FH in some suitable way...

while(<FH>) {
    s/^\s+//;
    s/\s+$//;
    my @flds = split( / *\t */ );  # tabs might have spaces around them

    if ( @flds == 5 ) {  # presumably first line of pair
        warn "Input line $. replaces previous first-line data: @comp\n" if ( @comp );
        @comp = @flds;
    }
    elsif ( @flds == 6 and $flds[5] =~ /number=(\d+)/
            and $flds[0].$flds[1] eq $comp[0].$comp[1] ) {
        push @comp, $1;
        print join( "\t", @comp ), "\n";
        @comp = ();
    }
    else {
        warn "Input line $. ignored: $_\n";
    }
}