__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.
[download]

$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',]
];
[download]

• capture last column of this type of line:

  Mtf 1    15    1.700    10    CGATATCGATTCGTT    CGATATYGAWTSSTT
  [download]

• don't capture line that started with "b(\d+)" like this:

  >2522963-2522975-reverse    St b99    CGATATCGATGGATT
  [download]

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 ;
[download]