I am a perl beginner and need some help with regex Input for this code is : aatgatgataaggtaaggtatgatgatgatgatgatagtagannnnnnnnnatgcatga'/atgca.atgactagca/atgactagcaaggtaaggtaaggtaaggtaaggtatgatgatgannnn./atgatgactagactgacaaggtaaggtaaggtatgatgatgatcgatgacgat... and so on

Here i am trying to assign input file as a scalar variable and trying to find a match of "aaggtaaggt" and then skip some 100 characters whether they are alphabets or symbols or any wildcard characters after skipping exact 100 characters, i am again asking code to start search for match again and every time it finds a match , i am counting and asking to print..

As of my knowledge i have tried using substr of match as pos1 and had set offset for 100 and then assigned that as initial pos for reading second match , but failed to get the correct output, then tried here post match as $' but doubt whether it is correct or not.

#!/usr/bin/perl 
$count1 = 0; 
open (FILE, "INPUT") || die "cannot open $!\n"; 
while ($line = <FILE>){ 

if(($line=~m/(aaggt){2}/ig)&&($'=~m/([atgcn]{100,})/i)) { 
$count1 ++ ; 
print " " ,$1, "\t"; 
print "count1 \t " ,$count1 , "\n" ; 
} 

}

[download]
Please, help me figuring out this task. Thanks

In reply to Need Help with reg ex by Ramya715

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