So you have so many FASTA sequence in a file have translated those multiple nucleotide sequences and now you want to extract the region with the longest gap between two stop codons. I have already shared couple of tool to translate many DNA sequences in a go. So you can translated several DNA sequences easily.

Input

>Seq1
ASKAENM-SRSHFEKLTF-VSVSKFNRMYLRQ-LSAVRISFNIMKPFLYILILHQKLKICSLEVISRNRRFKFLFPNSNGCIFANNCQKLEFLSTL-SPFYIF-FCIKS-KCVVSKSFREIDVLSFCFQIQTDVSSPIIVRS-NFFQHYEALFTYFDPASKAENM-SRSHFEKLEFLSTL-SPFYIF-FCIKS-KYVVSKSFRN-RFKFLFPNSNGCIFANNCQKLEFLSTL-SPFYIF-LCIKS-KYVVSKSFREIDV
>seq2
ASKAENM-SRSHFEKLTF-VSVSKFNRMYLRQ-LSAVRISFNIMKPFLYILILHQKLKICSLEVISRNRRFKFLFPNSNGCIFANNCQKLEFLSTL-SPFYIF-FCIKS-KCVVSKSFREIDVLSFCFQIQTDVSSPIIVRS-NFFQHYEALFTYFDPASKAENM-SRSHFEKLEFLSTL-SPFYIF-FCIKS-KYVVSKSFRN-RFKFLFPNSNGCIFANNCQKLEFLSTL-SPFYIF-LCIKS-KYVVSKSFREIDV

Script 1 : Long1.pl

#!/usr/bin/perl

use strict;
use warnings;

$/ = "\n>";
while (<>) {
    s/>//g;
    my ($id, @seq) = split (/\n/, $_);
    my $seq = join "", @seq;
    my @orfs = split (/\-/, $seq);
    shift @orfs; pop @orfs; 
    my $sel = shift @orfs;
    foreach my $next (@orfs) {
        $sel = $next if ((length $sel) < (length $next))
    }
    print ">$id\n$sel\n";
}

Uses

perl script.pl input.txt result.txt

Result

>Seq1
LSAVRISFNIMKPFLYILILHQKLKICSLEVISRNRRFKFLFPNSNGCIFANNCQKLEFLSTL
>seq2
LSAVRISFNIMKPFLYILILHQKLKICSLEVISRNRRFKFLFPNSNGCIFANNCQKLEFLSTL