Patch Adams

use strict;
use warnings;
use autodie;    # Handle i/o errors

local $/ = '>'; # Read a '>' delimited record at a time

open my $inFH,  '<', 'test.txt';          # Use lexical file handles
open my $outFH, '>', 'test_output.txt';

while (<$inFH>) {
    chomp;
    my ($string) = /\n(.+)/s or next;
    $string =~ s/\n//g;                   # In case the sequences are multi-line

    my @patches;
    push @patches, substr $string, $_, 11 for 0 .. length($string) - 11;
    print $outFH "@patches\n";
}

close $outFH;
close $inFH;