#!/usr/bin/perl
use Data::Dumper;
$Data::Dumper::Indent = 1;

my $ary = [];
my $i   = -1;

while (<DATA>) {
    chomp;
    s/\r//;
    /^Mtf.*\s(\S+)$/ and push @{ $ary->[++$i] }, $1; # next array
    /\s+St f\d+/     and push @{ $ary->[$i]   }, $_;
}
print Dumper($ary);
__DATA__
- your data here -

##</code><code>##

$VAR1 = [
  [
    'CGATATYGAWTSSTT',
    '>2522963-2522975-reverse   St f145 CGATATCGAATCGCT',
    '>2522963-2522975-reverse   St f156 CGCTATTGAATGCGT'
  ],
  [
    'AAKSAWTYRATATCG',
    '>2522963-2522975-reverse   St f82  AAGGAATTAATATCG',
    '>2522963-2522975-reverse   St f138 AATCCATCGATATCG'
  ],
  [
    'TCGMTATCGAWTSGC',
    '>2522963-2522975-reverse   St f144 TCGATATCGAATCGC',
    '>2522963-2522975-reverse   St f155 TCGCTATTGAATGCG',
    '>2522963-2522975-reverse   St f204 TCGCTATAAAAAGGC'
  ]
];