>gb|CP000351.1|:139-891 ParA-like protein [Leptospira borgpetersenii serovar Hardjo-bovis JB197]
ATGATAGTTGTATCCATAGCAAACCAGAAAGGTGGAGAAGGTAAAACTACAACCTCTCTTAATTTATCGA
TGGGGCTTGCGAGAAGAGGAAAAAAAACTCTGCTCGTTGATATAGATCCTCAAGCAAATTCAACCGGTAT
TTTTACAAATCCAGAAGGTATTGAGAAATCAATGCATGGAGTTTTTAACTCAAAAATGACTATCCAAGAA
ATCATGATTGAAACGAGGTTACCTGATCTTTTTTTGGCCCCTTCTAAAATGAATCTTGCGGAAGTAGAAA
CACTTTCCGGAAATTCCGTAGATGCGCCTTATATTCTGAGAGACTCTCTTCAAAGTGTGAGTGGGATCGA
CTTTTGTATCATCGATTGTCCACCTAGCTTATCTATTTTTACGATTAATGCACTCGTCGGATCAAATTAC
GTAATTATTCCACTTCAGGCTGAAAAATTTTCCGTAGATGGAATTGTAGGACTTCAACAAACAATCACAA
GCATCAAAAAAAGAATCAATCCTAACCTTGAAATTTTAGGAGCCCTAGTTACTCAACTCAAGCCTCAAAC
ACTTTTGACGAAAACTATCGTACCCGTTTTAACAAAATACTTTCGAATTTTCGAAACAAGCATCTCTGAT
GGAGTTGCAGTAGGAGAATCCCATCTTGCTAAAAAGTCGGTATTTGAATACAACAAGACGAGTAAACAAG
CCCAGGAATATGAAGGGTTTATAGAGGAGTTTTTAAATGAGCTCAAAAAGTAA
>gb|CP000351.1|:875-1720 ParB-like protein [Leptospira borgpetersenii serovar Hardjo-bovis JB197]
ATGAGCTCAAAAAGTAAACGACTCGGCTCTCTCGCAGATGTATTCCAAGCCGAAAAGTTGGAGGGGACTA
TTCGTAAAATTCGGCTCGATAAAATTCTTCCATCCGAAAACCAGCCCAGACAAGATCGAAAAAAAGGAAT
CGAAGACCTCGCGAGAAGTTTAGACAAAGACGGACTACTCCAACCAATCATTGTCACAAAACAAAATCCG
GAAGATGAGAACTATAAAATTGTAGCCGGAGAAAGAAGATACCACGCAGCGAAACAATTAGGCTGGGCAG
AAATAGAATGTAAAATTTTAGACCGGGACGAAAAAGAAACCTTTCGACTTGCAATTATAGAAAATCTTCA
AAGAGAAAATTTATCCCCTTATGAAGAAGTGGAAGCCATGTCACACTTAAAGAATAGCTTCAAATATACA
GATCAAGAATTAGGAACTCTCTTTGGAAAAAGTAGAAGTTACATGACGGAGCTTCTTGGAATTTCAAATC
TAAGCAAAGAAGAACTTAGATCCTGCAAAGAAGCAGGAATTGAAAGTAAAAATTTATTGATCCAAGCAGT
TGCAGCTTCTCGAAAAGGAACCTTCTCTGAGTTTTTAAATTTATTTCAAACGGGTGCACTTAAAACCGTT
AAAGATGCAAAATCTTTTAACCGGGAAGAGGAAAACTTGTCCACACCTAAAATTACAAGTGCGACAAACC
CAAAAGTTTCAAATTTAAATTCAACGGAATATAAGATCACAAAAAAACAAGGTCTAATTCAAATTAGTTC
TGATAATGAAGAACTGTTAGGTAATATTTTTAAACTAATCAAAAAAGAAATCCGTAAAAAATTCAATTCT
ATATAA

use strict;
use warnings;
use Bio::FASTASequence::File;
use File::Find::Rule;

my @ffns = File::Find::Rule->file->name( '*.ffn' )->in( '.' );

my %result;
my $output = 'org.fasta';

my $bff = Bio::FASTASequence::File->new;
for my $ffn ( @ffns ) {
    my $parsed = $bff->file( $ffn );

    for my $orga ( keys %{$parsed} ) {
        my $subsequence = substr $parsed->{$orga}->getSequence(), 3, 24;
        my ($name)      = $parsed->{$orga}->getDescription() =~ m{ \[ (.*?) \] }x;

        push @{ $result{$name} }, $subsequence;
    }
}

open my $fh, '>', $output;
for my $key ( sort keys %result ) {
    print $fh "> $key\n", join( '', @{ $result{$key} } ),"\n";
}
close $fh;

> Leptospira borgpetersenii serovar Hardjo-bovis JB197
ATAGTTGTATCCATAGCAAACCAGAGCTCAAAAAGTAAACGACTCGGC