__DATA__
Pm 0.2707	Minimum match (10/15)

Top 3 motifs	Wid	Score1	Segment	Con	Deg
Mtf 1	15	1.700	10	CGATATCGATTCGTT	CGATATYGAWTSSTT
Final Motif 1: Wid 15 Score1 1.700 Segment 10
         A     C     G     T     Con  rCon Deg  rDeg 
1        7    81     4     7      C    G    C    G
2       23     4    66     7      G    C    G    C
3       69    19     4     7      A    T    A    T
4        7     4     4    84      T    A    T    A
5       84     4     4     7      A    T    A    T
>2522963-2522975-reverse	St b99	CGATATCGATGGATT
>2522963-2522975-reverse	St f145	CGATATCGAATCGCT
>2522963-2522975-reverse	St b155	CGATATTAATTCCTT
>2522963-2522975-reverse	St f156	CGCTATTGAATGCGT
>2523043-2523055-reverse	St b88	CAATAGCGATTCGAT
Mtf 2	15	1.666	12	AATGAATCAATATCG	AAKSAWTYRATATCG
Final Motif 2: Wid 15 Score1 1.666 Segment 12
         A     C     G     T     Con  rCon Deg  rDeg 
1       73     4    17     6      A    T    A    T
2       60    17    17     6      A    T    A    T
3        6    17    30    46      T    A    K    M
4        6    44    44     6      C    G    S    S
5       46    17    17    20      A    T    A    T
>2522963-2522975-reverse	St b81	ACGCATTCAATAGCG
>2522963-2522975-reverse	St f82	AAGGAATTAATATCG
>2522963-2522975-reverse	St b92	AGCGATTCGATATCG
>2522963-2522975-reverse	St b106	GATGGATTTATATCT
>2522963-2522975-reverse	St f138	AATCCATCGATATCG
Mtf 3	15	1.656	10	TCGATATCGAATGGC	TCGMTATCGAWTSGC
Final Motif 3: Wid 15 Score1 1.656 Segment 10
         A     C     G     T     Con  rCon Deg  rDeg 
1        7     4     4    84      T    A    T    A
2        7    81     4     7      C    G    C    G
3       23     4    66     7      G    C    G    C
4       54    35     4     7      A    T    M    K
5        7     4     4    84      T    A    T    A
6       84     4     4     7      A    T    A    T
7        7     4    19    69      T    A    T    A
8       23    50     4    23      C    G    C    G
9       23     4    66     7      G    C    G    C
10      84     4     4     7      A    T    A    T
11      54     4     4    38      A    T    W    W
12      23     4    19    54      T    A    T    A
13       7    35    50     7      G    C    S    S
14      23    19    50     7      G    C    G    C
15      23    35    19    23      C    G    C    G
>2522963-2522975-reverse	St b87	TCAATAGCGATTCGA
>2522963-2522975-reverse	St b98	TCGATATCGATGGAT
>2522963-2522975-reverse	St f144	TCGATATCGAATCGC
>2522963-2522975-reverse	St f155	TCGCTATTGAATGCG
>2522963-2522975-reverse	St f204	TCGCTATAAAAAGGC
Total time 0:0:0.

##</code><code>##

$VAR = [
['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',]
];

##</code><code>##

Mtf 1	15	1.700	10	CGATATCGATTCGTT	CGATATYGAWTSSTT

##</code><code>##

>2522963-2522975-reverse	St b99	CGATATCGATGGATT

##</code><code>##

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

my @aoa;                 
my @temp;

while (<DATA>) {         
    chomp;               
    if (/^Mtf (\d+) (.*) ([A-Z]+)$/) { # stuck here
        print "$_ \n";            
        push @temp, ($3);
    }
    elsif (/^>(\w+) St (b|f)\d+/) { # not sure how to capture only "f" here
        print "$_\n";             
    }
    push @aoa, [@temp];
}

#print Dumper \@aoa ;