#!/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 -
[download]

Output:

$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'
  ]
];
[download]

_($_=" "x(1<<5)."?\n".q·/)Oo.  G°\        /
                              /\_¯/(q    /
----------------------------  \__(m.====·.(_("always off the crowd"))."·
");sub _{s./.($e="'Itrs `mnsgdq Gdbj O`qkdq")=~y/"-y/#-z/;$e.e && print}