An alternative solution.

use strict;
use warnings;
use Data::Dumper;

my %seq_count;

local $/ = '>gb|';
while (my $seq = <DATA>) {
    $seq =~ s/>gb\|//;
    next if ! length($seq);

    # get sequence id
    my ($seq_id) = $seq =~ /\|:(.*)/;

    # remove anything other than sequence characters
    $seq =~ s/^.*\n|\n//g;

    # build hash of sequence count
    $seq_count{$seq_id} = length($seq);
}

print Dumper(\%seq_count);


__DATA__
>gb|AE008689|:2073051-2073458, Atu4895
TTGGTCACATATTTTCGCTATTCGAAACCCAAATATCCCTGCGGAACACGTTTTATTGGAGCCGCCGTTT
TGCAGTTGCTCGGTGCTGGATTCTTGGCGTTCGTCTTTTGTCTGCTGGATGGGCTCACTGCAAAACCAAC
GATAATTCTCGGTCAGTTTGTATCATGCCTAGTGGGGAGCGTCGCCGGCTTTCATTTCGTGGCTTTTCGT
CGCCCAGGCACGGACGGCCAACTTTACCTTATCGCGACGTCGCTCTTGGCATTTGGGACCCATTATTGGC
TGGTGTCATATTCATTACCTGACCTTTTGCTAGCAAGATTGATTTCAGGATTTGGATCGGGTGTGGTTGT
TGCAGGAACTTTCCGACGTCGCTTTCTGGAAAATCCGGTAATTCCCTGCGTTCGATAG
>gb|AE008689|:c2074151-2073549, Atu4896
GTGTTTGGACCATATTTTCTGTGCAAACTAAACGATGACATAGGGCGATTTTTAGTGGCGGACAAATACA
GACTTCCCGAAGAGTTTTTTACCACTCGGTTTCTCGTTAGACGCATCGTACCCACAGACGCTGAAGCTAT
TTTCGAAGGGTGGAACACCGATCCCGAGGTGACGAAGTACCTGACGTGGAAACCCCACTCCGAGCTTGGC
CAGACACAGCGGGCGATTGAAGAAAATTATAGTGCGTGGAATGCAGGTACATCGTTTCCAGCTGTCATCT
GCCATCGCGAACGGCCACATGAACTAATCGGCCGTATTGATGCACGTCCGATGGGCCACAAGGTCTCTTA
CGGGTGGCTTGTCCGAAGAACCTGGTGGGGCCGGGGTGTTGCAAGCGAGGTCGTTCAACTCGCTGTAGAA
CACGCGTTATCGCATCCGCGCATCTTTCGCACCGAAGCATCCTGCGACGTTCTGAACACGGCGTCAGCAA
GAGTGATGGAAAAAGTAGGGATGACAAAGGAGGCCGTGCTTCGACGGTACCTTTTTCACCCCAATTTTTC
GAATATGCCGCGAGACGCCTTCCTGTATTCCAAGGTACGTTAA
>gb|AE008689|:c2074749-2074345, Atu4897
ATGAAACATACCATCGCAGTTCTCGGCCTGATCACCTTCTCCAGCCCGGCCTTCGCAGCATCGTGCGAGA
AAAACTTCACCGTCTCAGGCGTACCGATGGTCACGGCTGTCTCTTACAAATCCTTTCAGGAACTGCCGAA
AGCCAAAGCACCAGCTGTCCTTCAAAAGCTCGCCCAGGCCGTCGCGGCAGAAGGTTTTTCAGGTATCCAG
ATCAACAAGGCACTGTCGTCAATCGATGCCCATCAGGAAACCAGCGGAAGTGGCAGGATTCAGACGCTGC
GGGTTGTCGCCCGCCAGAAAGGCGCCGCTGTCCGGATCGATGCTGTCTTCAATATTCAGGCAGGACAGAT
CGCCGACAAAGACGTCATCCGCAAGGGCATCTGCGACATCATAAAAGGCGCGTAA
[download]

And the output -

$VAR1 = {
          'c2074151-2073549, Atu4896' => 603,
          '2073051-2073458, Atu4895' => 408,
          'c2074749-2074345, Atu4897' => 405
        };
[download]

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