in reply to Re^4: String Compression Optimization (repeated concatenated subsequences)
in thread String Compression Optimization (repeated concatenated subsequences)

For comparison purposes: 

u:  1 wallclock secs ( 0.53 usr +  0.00 sys =  0.53 CPU) @ 112.78/s (n
+=60)

[download]

The length and complexity of the real data elements are the cause of all your back tracking woe's. So, do away with them:)

What I did was to extract an array of the significant bits of the data ("L 1 0 0 0 L 0 L L H 0 L 0 L 0 L 1 L 1 0 1 0" etc.), then uniq those using a hash and build a substitution or placeholder table using 'aa;', 'ab;', 'ac;' etc. I then concatenate these into a single string and use my findRuns() (with appropriately modified regexes).

Once the placeholder string has been compressed, I use a reverse lookup table to put back the original data elements into the compressed string. 

#! perl -slw
use strict;
use Data::Dumper;

sub findRuns {
    use constant { 
        BASESEQ => 0, SAVED => 1, 
        OFFSET => 2, LENGTH => 3, REPEATS => 4 
};

    my $s = shift;
    
    my @rls;
    
    push @rls, [ 
        $1,
        length $2,
        pos($s) - length( $1 ),
        length( $1 ) + length( $2 ),
        length( $2 ) / length( $1 ) + 1,
    ] while $s =~ m[
        .*?
        ( (?: [a-z]{2} ; )+ ) 
        (?= ( \1{1,254} ) [^>]* (?: < | $ ) )
    ]gx;

    for my $p ( 0 .. $#rls ) { 
        next unless defined $rls[ $p ];
        for my $q ( $p+1 ..  $#rls ) {
            next unless defined $rls[ $p ] and defined $rls[ $q ];
            last if $rls[ $q ][ OFFSET ] > $rls[ $p ][ OFFSET ] + $rls
+[ $p ][ LENGTH ];

            while( 
                $rls[ $q ][ OFFSET ] >= $rls[ $p ][ OFFSET ] 
                && 
                $rls[ $q ][ OFFSET ] <  $rls[ $p ][ OFFSET ] + $rls[ $
+p ][ LENGTH ]
            ) {
                if( $rls[ $p ][ SAVED ] < $rls[ $q ][ SAVED ] ) {
                    last unless $rls[ $p ][ REPEATS ]-- > 2;
                    $rls[ $p ][ REPEATS ] -= length $rls[ $p ][ BASESE
+Q ];
                }
                else {
                    last unless $rls[ $q ][ REPEATS ]-- > 2;
                    $rls[ $q ][ REPEATS ] -= length $rls[ $q ][ BASESE
+Q ];
                    $rls[ $q ][ OFFSET  ] += length $rls[ $q ][ BASESE
+Q ];
                }            
            }
            
            $rls[ $q ][ OFFSET ] >= $rls[ $p ][ OFFSET ] 
            && 
            $rls[ $q ][ OFFSET ] <  $rls[ $p ][ OFFSET ] + $rls[ $p ][
+ LENGTH ]
                and delete $rls[ $rls[ $p ][ SAVED ] < $rls[ $q ][ SAV
+ED ] ? $p : $q ];
        }
    }

    @rls = grep defined, @rls;

    for ( @rls ) {
        my $re = qr[(?:$_->[ BASESEQ ]){$_->[ &REPEATS ]}];
        $s =~ s[( (?: ^ | > ) [^<]*? ) $re]{ ($1||'') . '<' . $_->[ RE
+PEATS ] . ":$_->[ BASESEQ ]>" }ex;
    }

    $s = findRuns( $s ) if $s =~ m[ (?: ^ | > ) [^<]*? ( (?: [a-z]{2} 
+; )+ ) \1 [^>]*? (?: < | $ ) ]x;
    return $s;
}

## Main program

## Extract the significant data
my @seqs = map{ 
    m[^> lst2flex_tset\s+([^;]+);] 
} grep{ m[^>] } <DATA>;
#print Dumper \@seqs;

## Build a placeholder lookup table 
## Using 'aa;', 'ab;' etc. allows for 676 individual elements
## Using 'aaa;' etc. 18525 and so on.
## The semicolon separator allows use to limit backtracking in the reg
+ex
my $placeholder = 'aa';
my %seqs; @seqs{ @seqs } = ();
@seqs{ keys %seqs } = map{ $placeholder++ . ';' } 1 .. keys %seqs;

## Build a reverse lookup table for re-substitution once the 
## compression has been performed.
my %r_seqs; @r_seqs{ values %seqs } = keys %seqs;
#print "Reverse substitution table\n", Dumper \%r_seqs;

## Build the string of placeholders.
my $seq = join'', @seqs{ @seqs };
print "Placeholder sequence\n", $seq;

## Do the compression
my $compressed = findRuns $seq;
print "Compressed placeholder sequence\n", $compressed;

## Substitute back the original data into the compressed sequence
## Add som tabs and newlines in strategic places to aid verification.
$compressed =~ s[( [a-z]{2} ; )][ "\t" . $r_seqs{ $1 } . "\n" ]xge;
$compressed =~ s[(?=<)|(?<=:|>)][\n]g;
print $compressed;




__DATA__
// header
opcode_mode=normal;
import tset lst2flex_tset;
vector ($tset,dbg0,dbg1,dclk,dfrm,dmiso,dmosi,dpin,dpout,dsclk,dscsn,g
+pio0,gpio1,gpio2,gpio3,gpio4,gpio5,gpio6,gpio7,rst_n,vstate0,vstate1,
+vstate2)
{
start_label start_vector:
> lst2flex_tset  L 0 0 0 0 L 0 L L H 0 0 0 0 0 0 0 0 0 0 1 1; //      
+    1
> lst2flex_tset  L 0 1 0 0 L 0 L L H 0 0 0 0 0 0 0 0 0 0 1 1; //      
+    2
> lst2flex_tset  L 0 0 0 0 L 0 L L H 0 0 0 0 0 0 0 0 0 0 1 1; //      
+    3
> lst2flex_tset  L 0 1 0 0 L 0 L L H 0 0 0 0 0 0 0 0 0 0 1 1; //      
+    4
> lst2flex_tset  L 0 0 0 0 L 0 L L H 0 0 0 0 0 0 0 0 0 0 1 1; //      
+    5
> lst2flex_tset  L 0 1 0 0 L 0 L L H 0 0 0 0 0 0 0 0 0 0 1 1; //      
+    6
> lst2flex_tset  L 0 0 0 0 L 0 L L H 0 0 0 0 0 0 0 0 0 0 1 1; //      
+    7
> lst2flex_tset  L 0 1 0 0 L 0 L L H 0 0 0 0 0 0 0 0 0 0 1 1; //      
+    8
> lst2flex_tset  L 0 0 0 0 L 0 L L H 0 0 0 0 0 0 0 0 0 0 1 1; //      
+    9
> lst2flex_tset  L 0 1 0 0 L 0 L L H 0 0 0 0 0 0 0 0 0 0 1 1; //      
+   10
> lst2flex_tset  L 0 0 0 0 L 0 L L H 0 0 0 0 0 0 0 0 0 0 1 1; //      
+   11
> lst2flex_tset  L 0 1 0 0 L 0 L L H 0 0 0 0 0 0 0 0 0 0 1 1; //      
+   12
> lst2flex_tset  L 0 0 0 0 L 0 L L H 0 0 0 0 0 0 0 0 0 0 1 1; //      
+   13
> lst2flex_tset  L 0 1 0 0 L 0 L L H 0 0 0 0 0 0 0 0 0 0 1 1; //      
+   14
> lst2flex_tset  L 0 0 0 0 L 0 L L H 0 0 0 0 0 0 0 0 0 0 1 1; //      
+   15
> lst2flex_tset  L 0 1 0 0 L 0 L L H 0 0 0 0 0 0 0 0 0 0 1 1; //      
+   16
> lst2flex_tset  L 0 0 0 0 L 0 L L H 0 0 0 0 0 0 0 0 0 0 1 1; //      
+   17
> lst2flex_tset  L 0 1 0 0 L 0 L L H 0 0 0 0 0 0 0 0 0 0 1 1; //      
+   18
> lst2flex_tset  L 0 0 0 0 L 0 L L H 0 0 0 0 0 0 0 0 0 0 1 1; //      
+   19
> lst2flex_tset  L 0 1 0 0 L 0 L L H 0 0 0 0 0 0 0 0 0 0 1 1; //      
+   20
> lst2flex_tset  L 0 0 0 0 L 0 L L H 0 0 0 0 0 0 0 0 1 0 1 1; //      
+   21
> lst2flex_tset  L 0 1 0 0 L 0 L L H 0 0 0 0 0 0 0 0 1 0 1 1; //      
+   22
> lst2flex_tset  L 0 0 0 0 L 0 L L H 0 0 0 0 0 0 0 0 1 0 1 1; //      
+   23
> lst2flex_tset  L 0 1 0 0 L 0 L L H 0 0 0 0 0 0 0 0 1 0 1 1; //      
+   24
> lst2flex_tset  L 0 0 0 0 L 0 L L H 0 0 0 0 0 0 0 0 1 0 1 1; //      
+   25
> lst2flex_tset  L 0 1 0 0 L 0 L L H 0 0 0 0 0 0 0 0 1 0 1 1; //      
+   26
> lst2flex_tset  L 0 0 0 0 L 0 L L H 0 0 0 0 0 0 0 0 1 0 1 1; //      
+   27
> lst2flex_tset  L 0 1 0 0 L 0 L L H 0 0 0 0 0 0 0 0 1 0 1 1; //      
+   28
> lst2flex_tset  L 0 0 0 0 L 0 L L H 0 0 0 0 0 0 0 0 1 0 1 1; //      
+   29
> lst2flex_tset  L 0 1 0 0 L 0 L L H 0 0 0 0 0 0 0 0 1 0 1 1; //      
+   30
> lst2flex_tset  L 1 0 0 0 L 0 L L H 0 L 0 L 0 L 0 H 1 0 1 0; //      
+   31
> lst2flex_tset  L 1 1 0 0 L 0 L L H 0 L 0 L 0 L 1 L 1 0 1 0; //      
+   32
> lst2flex_tset  L 1 0 0 0 L 0 L L H 0 L 0 L 0 L 1 L 1 0 1 0; //      
+   33
> lst2flex_tset  L 1 1 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0; //      
+   34
> lst2flex_tset  L 1 0 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0; //      
+   35
> lst2flex_tset  L 1 1 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0; //      
+   36
> lst2flex_tset  L 1 0 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0; //      
+   37
> lst2flex_tset  L 1 1 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0; //      
+   38
> lst2flex_tset  L 1 0 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0; //      
+   39
> lst2flex_tset  L 1 1 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0; //      
+   40
> lst2flex_tset  L 1 0 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0; //      
+   41
> lst2flex_tset  L 1 1 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0; //      
+   42
> lst2flex_tset  L 1 0 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0; //      
+   43
> lst2flex_tset  L 1 1 0 0 L 0 L L H 0 L 0 L 0 L 1 L 1 0 1 0; //      
+   44
> lst2flex_tset  L 1 0 0 0 L 0 L L H 0 L 0 L 0 L 1 L 1 0 1 0; //      
+   45
> lst2flex_tset  L 1 1 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0; //      
+   46
> lst2flex_tset  L 1 0 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0; //      
+   47
> lst2flex_tset  L 1 1 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0; //      
+   48
> lst2flex_tset  L 1 0 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0; //      
+   49
> lst2flex_tset  L 1 1 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0; //      
+   50
> lst2flex_tset  L 1 0 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0; //      
+   51
> lst2flex_tset  L 1 1 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0; //      
+   52
> lst2flex_tset  L 1 0 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0; //      
+   53
> lst2flex_tset  L 1 1 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0; //      
+   54
> lst2flex_tset  L 1 0 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0; //      
+   55
> lst2flex_tset  L 1 1 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0; //      
+   56
> lst2flex_tset  L 1 0 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0; //      
+   57
> lst2flex_tset  L 1 1 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0; //      
+   58
> lst2flex_tset  L 1 0 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0; //      
+   59
> lst2flex_tset  L 1 1 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0; //      
+   60
> lst2flex_tset  L 1 0 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0; //      
+   61
> lst2flex_tset  L 1 1 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0; //      
+   62
> lst2flex_tset  L 1 0 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0; //      
+   63
> lst2flex_tset  L 1 1 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0; //      
+   64
> lst2flex_tset  L 1 0 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0; //      
+   65
> lst2flex_tset  L 1 1 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0; //      
+   66
> lst2flex_tset  L 1 0 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0; //      
+   67
> lst2flex_tset  L 1 1 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0; //      
+   68
> lst2flex_tset  L 1 0 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0; //      
+   69
> lst2flex_tset  L 1 1 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0; //      
+   70
> lst2flex_tset  L 1 0 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0; //      
+   71
> lst2flex_tset  L 1 1 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0; //      
+   72
> lst2flex_tset  L 1 0 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0; //      
+   73
> lst2flex_tset  L 1 1 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0; //      
+   74
> lst2flex_tset  L 1 0 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0; //      
+   75
> lst2flex_tset  L 1 1 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0; //      
+   76
> lst2flex_tset  L 1 0 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0; //      
+   77
> lst2flex_tset  L 1 1 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0; //      
+   78
> lst2flex_tset  L 1 0 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0; //      
+   79
> lst2flex_tset  L 1 1 0 0 L 0 L L H 0 L 0 L 0 L 1 L 1 0 1 0; //      
+   80
> lst2flex_tset  L 1 0 0 0 L 0 L L H 0 L 0 L 0 L 1 L 1 0 1 0; //      
+   81
> lst2flex_tset  L 1 1 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0; //      
+   82
> lst2flex_tset  L 1 0 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0; //      
+   83
> lst2flex_tset  L 1 1 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0; //      
+   84
> lst2flex_tset  L 1 0 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0; //      
+   85
> lst2flex_tset  L 1 1 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0; //      
+   86
> lst2flex_tset  L 1 0 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0; //      
+   87
> lst2flex_tset  L 1 1 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0; //      
+   88
> lst2flex_tset  L 1 0 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0; //      
+   89
> lst2flex_tset  L 1 1 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0; //      
+   90
> lst2flex_tset  L 1 0 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0; //      
+   91
> lst2flex_tset  L 1 1 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0; //      
+   92
> lst2flex_tset  L 1 0 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0; //      
+   93
> lst2flex_tset  L 1 1 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0; //      
+   94
> lst2flex_tset  L 1 0 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0; //      
+   95
> lst2flex_tset  L 1 1 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0; //      
+   96
> lst2flex_tset  L 1 0 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0; //      
+   97
> lst2flex_tset  L 1 1 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0; //      
+   98
> lst2flex_tset  L 1 0 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0; //      
+   99
> lst2flex_tset  L 1 1 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0; //      
+  100
> lst2flex_tset  L 1 0 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0; //      
+  101
> lst2flex_tset  L 1 1 0 0 L 0 L L H 0 L 0 L 0 L 1 L 1 0 1 0; //      
+  102
> lst2flex_tset  L 1 0 0 0 L 0 L L H 0 L 0 L 0 L 1 L 1 0 1 0; //      
+  103
> lst2flex_tset  L 1 1 0 0 L 0 L L H 0 L 0 L 0 L 1 L 1 0 1 0; //      
+  104
> lst2flex_tset  L 1 0 0 0 L 0 L L H 0 L 0 L 0 L 1 L 1 0 1 0; //      
+  105
> lst2flex_tset  L 1 1 0 0 L 0 L L H 0 L 0 L 0 L 0 H 1 0 1 0; //      
+  106
> lst2flex_tset  L 1 0 0 0 L 0 L L H 0 L 0 L 0 L 0 H 1 0 1 0; //      
+  107
> lst2flex_tset  L 1 1 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0; //      
+  108
> lst2flex_tset  L 1 0 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0; //      
+  109
> lst2flex_tset  L 1 1 0 0 L 0 L L H 0 L 0 L 0 L 0 H 1 0 1 0; //      
+  110
> lst2flex_tset  L 0 0 0 0 L 0 L L H 0 0 0 0 0 0 0 0 1 0 1 1; //      
+  111
> lst2flex_tset  L 0 1 0 0 L 0 L L H 0 0 0 0 0 0 0 0 1 1 1 1; //      
+  112
> lst2flex_tset  L 0 0 0 0 L 0 L L H 0 0 0 0 0 0 0 0 1 1 1 1; //      
+  113
> lst2flex_tset  L 0 1 0 0 L 0 L L H 0 0 0 0 0 0 0 0 1 0 1 1; //      
+  114
> lst2flex_tset  L 0 0 0 0 L 0 L L H 0 0 0 0 0 0 0 0 1 0 1 1; //      
+  115
> lst2flex_tset  L 0 1 0 0 L 0 L L H 0 0 0 0 0 0 0 0 1 0 1 1; //      
+  116
> lst2flex_tset  L 0 0 0 0 L 0 L L H 0 0 0 0 0 0 0 0 1 0 1 1; //      
+  117
> lst2flex_tset  L 0 1 0 0 L 0 L L H 0 0 0 0 0 0 0 0 1 0 1 1; //      
+  118
> lst2flex_tset  L 1 0 0 0 L 0 L L H 0 L 0 L 0 L 0 H 1 0 1 0; //      
+  119
> lst2flex_tset  L 1 1 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0; //      
+  120
> lst2flex_tset  L 1 0 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0; //      
+  121
> lst2flex_tset  L 1 1 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0; //      
+  122
> lst2flex_tset  L 1 0 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0; //      
+  123
> lst2flex_tset  L 1 1 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0; //      
+  124
> lst2flex_tset  L 1 0 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0; //      
+  125
> lst2flex_tset  L 1 1 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0; //      
+  126
> lst2flex_tset  L 1 0 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0; //      
+  127
> lst2flex_tset  L 1 1 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0; //      
+  128
> lst2flex_tset  L 1 0 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0; //      
+  129
> lst2flex_tset  L 1 1 0 0 L 0 L L H 0 L 0 L 0 L 0 H 1 0 1 0; //      
+  130
> lst2flex_tset  L 1 0 0 0 L 0 L L H 0 L 0 L 0 L 0 H 1 0 1 0; //      
+  131
> lst2flex_tset  L 1 1 0 0 L 0 L L H 0 L 0 L 0 L 1 L 1 0 1 0; //      
+  132
> lst2flex_tset  L 1 0 0 0 L 0 L L H 0 L 0 L 0 L 1 L 1 0 1 0; //      
+  133
> lst2flex_tset  L 1 1 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0; //      
+  134
> lst2flex_tset  L 1 0 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0; //      
+  135
> lst2flex_tset  L 1 1 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0; //      
+  136
> lst2flex_tset  L 1 0 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0; //      
+  137
> lst2flex_tset  L 1 1 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0; //      
+  138
> lst2flex_tset  L 1 0 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0; //      
+  139
> lst2flex_tset  L 1 1 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0; //      
+  140
> lst2flex_tset  L 1 0 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0; //      
+  141
> lst2flex_tset  L 1 1 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0; //      
+  142
> lst2flex_tset  L 1 0 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0; //      
+  143
> lst2flex_tset  L 1 1 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0; //      
+  144
> lst2flex_tset  L 1 0 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0; //      
+  145
> lst2flex_tset  L 1 1 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0; //      
+  146
> lst2flex_tset  L 1 0 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0; //      
+  147
> lst2flex_tset  L 1 1 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0; //      
+  148
> lst2flex_tset  L 1 0 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0; //      
+  149
> lst2flex_tset  L 1 1 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0; //      
+  150
> lst2flex_tset  L 1 0 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0; //      
+  151
> lst2flex_tset  L 1 1 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0; //      
+  152
> lst2flex_tset  L 1 0 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0; //      
+  153
> lst2flex_tset  L 1 1 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0; //      
+  154
> lst2flex_tset  L 1 0 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0; //      
+  155
> lst2flex_tset  L 1 1 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0; //      
+  156
> lst2flex_tset  L 1 0 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0; //      
+  157
> lst2flex_tset  L 1 1 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0; //      
+  158
> lst2flex_tset  L 1 0 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0; //      
+  159
> lst2flex_tset  L 1 1 0 0 L 0 L L H 0 L 0 L 0 L 1 L 1 0 1 0; //      
+  160
> lst2flex_tset  L 1 0 0 0 L 0 L L H 0 L 0 L 0 L 1 L 1 0 1 0; //      
+  161
> lst2flex_tset  L 1 1 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0; //      
+  162
> lst2flex_tset  L 1 0 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0; //      
+  163
> lst2flex_tset  L 1 1 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0; //      
+  164
> lst2flex_tset  L 1 0 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0; //      
+  165
> lst2flex_tset  L 1 1 0 0 L 0 L L H 0 L 0 L 0 L 0 H 1 0 1 0; //      
+  166
> lst2flex_tset  L 1 0 0 0 L 0 L L H 0 L 0 L 0 L 0 H 1 0 1 0; //      
+  167
> lst2flex_tset  L 1 1 0 0 L 0 L L H 0 L 0 L 0 L 1 L 1 0 1 0; //      
+  168
> lst2flex_tset  L 1 0 0 0 L 0 L L H 0 L 0 L 0 L 1 L 1 0 1 0; //      
+  169
> lst2flex_tset  L 1 1 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0; //      
+  170
> lst2flex_tset  L 1 0 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0; //      
+  171
> lst2flex_tset  L 1 1 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0; //      
+  172
> lst2flex_tset  L 1 0 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0; //      
+  173
> lst2flex_tset  L 1 1 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0; //      
+  174
> lst2flex_tset  L 1 0 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0; //      
+  175
> lst2flex_tset  L 1 1 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0; //      
+  176
> lst2flex_tset  L 1 0 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0; //      
+  177
> lst2flex_tset  L 1 1 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0; //      
+  178
> lst2flex_tset  L 1 0 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0; //      
+  179
> lst2flex_tset  L 1 1 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0; //      
+  180
> lst2flex_tset  L 1 0 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0; //      
+  181
> lst2flex_tset  L 1 1 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0; //      
+  182
> lst2flex_tset  L 1 0 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0; //      
+  183
> lst2flex_tset  L 1 1 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0; //      
+  184
> lst2flex_tset  L 1 0 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0; //      
+  185
> lst2flex_tset  L 1 1 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0; //      
+  186
> lst2flex_tset  L 1 0 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0; //      
+  187
> lst2flex_tset  L 1 1 0 0 L 0 L L H 0 L 0 L 0 L 0 H 1 0 1 0; //      
+  188
> lst2flex_tset  L 1 0 0 0 L 0 L L H 0 L 0 L 0 L 0 H 1 0 1 0; //      
+  189
> lst2flex_tset  L 1 1 0 0 L 0 L L H 0 L 0 L 0 L 1 H 1 0 1 0; //      
+  190
> lst2flex_tset  L 1 0 0 0 L 0 L L H 0 L 0 L 0 L 1 H 1 0 1 0; //      
+  191
> lst2flex_tset  L 1 1 0 0 L 0 L L H 0 L 0 L 0 L 1 L 1 0 1 0; //      
+  192
> lst2flex_tset  L 1 0 0 0 L 0 L L H 0 L 0 L 0 L 1 L 1 0 1 0; //      
+  193
halt > lst2flex_tset  H 0 0 0 0 L 0 L L H L H L H L H L H 1 0 0 0; // 
+   194
}

[download]

As you can see below, the placeholder sequence is much shorter , and the regular nature of the placeholders means the regex engine has a much simpler task finding the sequences.

I haven't bothered to re-integrate the compressed sequences with the header and trailer information, as you haven't said what format would be used for the repeat sequences.

I've also injected some newlines and tabs to make visual verification easier. 

P:\test>390718
Placeholder sequence
ag;ac;ag;ac;ag;ac;ag;ac;ag;ac;ag;ac;ag;ac;ag;ac;ag;ac;ag;ac;aj;af;aj;a
+f;aj;af;aj;af;aj;af;aa;ab;ak;ah;an;ah;an;ah;an;ah;an;ah;an;ab;ak;ah;a
+n;ah;an;ah;an;ah;an;ah;an;ah;an;ah;an;ah;an;ah;an;ah;an;ah;an;ah;an;a
+h;an;ah;an;ah;an;ah;an;ah;an;ab;ak;ah;an;ah;an;ah;an;ah;an;ah;an;ah;a
+n;ah;an;ah;an;ah;an;ah;an;ab;ak;ab;ak;am;aa;ah;an;am;aj;ae;al;af;aj;a
+f;aj;af;aa;ah;an;ah;an;ah;an;ah;an;ah;an;am;aa;ab;ak;ah;an;ah;an;ah;a
+n;ah;an;ah;an;ah;an;ah;an;ah;an;ah;an;ah;an;ah;an;ah;an;ah;an;ab;ak;a
+h;an;ah;an;am;aa;ab;ak;ah;an;ah;an;ah;an;ah;an;ah;an;ah;an;ah;an;ah;a
+n;ah;an;am;aa;ad;ai;ab;ak;
Compressed placeholder sequence
<2:ag;ac;ag;ac;ag;ac;ag;ac;ag;ac;><2:aj;af;aj;af;>aj;af;aa;ab;ak;<2:ah
+;an;ah;an;>ah;an;ab;ak;<2:ah;an;ah;an;ah;an;ah;an;ah;an;ah;an;ah;an;a
+h;an;>ah;an;ab;ak;<2:ah;an;ah;an;ah;an;ah;an;ah;an;><2:ab;ak;>am;aa;a
+h;an;am;aj;ae;al;<2:af;aj;>af;aa;<2:ah;an;><3:ah;an;>am;aa;ab;ak;<2:a
+h;an;ah;an;ah;an;ah;an;ah;an;ah;an;>ah;an;ab;ak;<2:ah;an;>am;aa;ab;ak
+;<2:ah;an;ah;an;ah;an;ah;an;>ah;an;am;aa;ad;ai;ab;ak;

<2:
        L 0 0 0 0 L 0 L L H 0 0 0 0 0 0 0 0 0 0 1 1
        L 0 1 0 0 L 0 L L H 0 0 0 0 0 0 0 0 0 0 1 1
        L 0 0 0 0 L 0 L L H 0 0 0 0 0 0 0 0 0 0 1 1
        L 0 1 0 0 L 0 L L H 0 0 0 0 0 0 0 0 0 0 1 1
        L 0 0 0 0 L 0 L L H 0 0 0 0 0 0 0 0 0 0 1 1
        L 0 1 0 0 L 0 L L H 0 0 0 0 0 0 0 0 0 0 1 1
        L 0 0 0 0 L 0 L L H 0 0 0 0 0 0 0 0 0 0 1 1
        L 0 1 0 0 L 0 L L H 0 0 0 0 0 0 0 0 0 0 1 1
        L 0 0 0 0 L 0 L L H 0 0 0 0 0 0 0 0 0 0 1 1
        L 0 1 0 0 L 0 L L H 0 0 0 0 0 0 0 0 0 0 1 1
>
<2:
        L 0 0 0 0 L 0 L L H 0 0 0 0 0 0 0 0 1 0 1 1
        L 0 1 0 0 L 0 L L H 0 0 0 0 0 0 0 0 1 0 1 1
        L 0 0 0 0 L 0 L L H 0 0 0 0 0 0 0 0 1 0 1 1
        L 0 1 0 0 L 0 L L H 0 0 0 0 0 0 0 0 1 0 1 1
>
        L 0 0 0 0 L 0 L L H 0 0 0 0 0 0 0 0 1 0 1 1
        L 0 1 0 0 L 0 L L H 0 0 0 0 0 0 0 0 1 0 1 1
        L 1 0 0 0 L 0 L L H 0 L 0 L 0 L 0 H 1 0 1 0
        L 1 1 0 0 L 0 L L H 0 L 0 L 0 L 1 L 1 0 1 0
        L 1 0 0 0 L 0 L L H 0 L 0 L 0 L 1 L 1 0 1 0

<2:
        L 1 1 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0
        L 1 0 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0
        L 1 1 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0
        L 1 0 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0
>
        L 1 1 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0
        L 1 0 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0
        L 1 1 0 0 L 0 L L H 0 L 0 L 0 L 1 L 1 0 1 0
        L 1 0 0 0 L 0 L L H 0 L 0 L 0 L 1 L 1 0 1 0

<2:
        L 1 1 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0
        L 1 0 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0
        L 1 1 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0
        L 1 0 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0
        L 1 1 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0
        L 1 0 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0
        L 1 1 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0
        L 1 0 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0
        L 1 1 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0
        L 1 0 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0
        L 1 1 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0
        L 1 0 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0
        L 1 1 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0
        L 1 0 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0
        L 1 1 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0
        L 1 0 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0
>
        L 1 1 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0
        L 1 0 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0
        L 1 1 0 0 L 0 L L H 0 L 0 L 0 L 1 L 1 0 1 0
        L 1 0 0 0 L 0 L L H 0 L 0 L 0 L 1 L 1 0 1 0

<2:
        L 1 1 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0
        L 1 0 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0
        L 1 1 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0
        L 1 0 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0
        L 1 1 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0
        L 1 0 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0
        L 1 1 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0
        L 1 0 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0
        L 1 1 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0
        L 1 0 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0
>
<2:
        L 1 1 0 0 L 0 L L H 0 L 0 L 0 L 1 L 1 0 1 0
        L 1 0 0 0 L 0 L L H 0 L 0 L 0 L 1 L 1 0 1 0
>
        L 1 1 0 0 L 0 L L H 0 L 0 L 0 L 0 H 1 0 1 0
        L 1 0 0 0 L 0 L L H 0 L 0 L 0 L 0 H 1 0 1 0
        L 1 1 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0
        L 1 0 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0
        L 1 1 0 0 L 0 L L H 0 L 0 L 0 L 0 H 1 0 1 0
        L 0 0 0 0 L 0 L L H 0 0 0 0 0 0 0 0 1 0 1 1
        L 0 1 0 0 L 0 L L H 0 0 0 0 0 0 0 0 1 1 1 1
        L 0 0 0 0 L 0 L L H 0 0 0 0 0 0 0 0 1 1 1 1

<2:
        L 0 1 0 0 L 0 L L H 0 0 0 0 0 0 0 0 1 0 1 1
        L 0 0 0 0 L 0 L L H 0 0 0 0 0 0 0 0 1 0 1 1
>
        L 0 1 0 0 L 0 L L H 0 0 0 0 0 0 0 0 1 0 1 1
        L 1 0 0 0 L 0 L L H 0 L 0 L 0 L 0 H 1 0 1 0

<2:
        L 1 1 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0
        L 1 0 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0
>
<3:
        L 1 1 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0
        L 1 0 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0
>
        L 1 1 0 0 L 0 L L H 0 L 0 L 0 L 0 H 1 0 1 0
        L 1 0 0 0 L 0 L L H 0 L 0 L 0 L 0 H 1 0 1 0
        L 1 1 0 0 L 0 L L H 0 L 0 L 0 L 1 L 1 0 1 0
        L 1 0 0 0 L 0 L L H 0 L 0 L 0 L 1 L 1 0 1 0

<2:
        L 1 1 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0
        L 1 0 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0
        L 1 1 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0
        L 1 0 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0
        L 1 1 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0
        L 1 0 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0
        L 1 1 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0
        L 1 0 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0
        L 1 1 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0
        L 1 0 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0
        L 1 1 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0
        L 1 0 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0
>
        L 1 1 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0
        L 1 0 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0
        L 1 1 0 0 L 0 L L H 0 L 0 L 0 L 1 L 1 0 1 0
        L 1 0 0 0 L 0 L L H 0 L 0 L 0 L 1 L 1 0 1 0

<2:
        L 1 1 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0
        L 1 0 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0
>
        L 1 1 0 0 L 0 L L H 0 L 0 L 0 L 0 H 1 0 1 0
        L 1 0 0 0 L 0 L L H 0 L 0 L 0 L 0 H 1 0 1 0
        L 1 1 0 0 L 0 L L H 0 L 0 L 0 L 1 L 1 0 1 0
        L 1 0 0 0 L 0 L L H 0 L 0 L 0 L 1 L 1 0 1 0

<2:
        L 1 1 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0
        L 1 0 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0
        L 1 1 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0
        L 1 0 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0
        L 1 1 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0
        L 1 0 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0
        L 1 1 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0
        L 1 0 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0
>
        L 1 1 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0
        L 1 0 0 0 L 0 L L H 0 L 0 L 0 L 0 L 1 0 1 0
        L 1 1 0 0 L 0 L L H 0 L 0 L 0 L 0 H 1 0 1 0
        L 1 0 0 0 L 0 L L H 0 L 0 L 0 L 0 H 1 0 1 0
        L 1 1 0 0 L 0 L L H 0 L 0 L 0 L 1 H 1 0 1 0
        L 1 0 0 0 L 0 L L H 0 L 0 L 0 L 1 H 1 0 1 0
        L 1 1 0 0 L 0 L L H 0 L 0 L 0 L 1 L 1 0 1 0
        L 1 0 0 0 L 0 L L H 0 L 0 L 0 L 1 L 1 0 1 0

[download]
Examine what is said, not who speaks.
"Efficiency is intelligent laziness." -David Dunham
"Think for yourself!" - Abigail
"Memory, processor, disk in that order on the hardware side. Algorithm, algorithm, algorithm on the code side." - tachyon

In Section Seekers of Perl Wisdom