I need to search for a specific string1 "TTGACA" in another string that is very long and there are no spaces between characters. The occurance of string1 is multiple times. The searching string needs to be in that exact order. This is what I have so far but its not giving me the correct values. 
#/usr/bin/perl
@ARGV = ('test.txt');
open FILE, $ARGV[0] or die "can't open file\n";

$string = '';
@file = <FILE>;
foreach $line(@file){
        if ($line =~ /^>/){next;}
        else {$string .= $line;}
} #the first line is useless so need to skip in

close FILE;
my $search = 'TTGACA';
$string =~ s/\s//g; #getting rid of whitespaces

$n = ($string =~ tr/$search//); 
print "String $search occured $n times\n\n";

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In reply to search for a sequence of chars in a string by imlou

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