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copied!<p>I'm not a perl expert but you can use $- and $+ to track index location for last regex match found.<br> Below is code built on top of your code that explains this. </p> <pre><code>use strict; use warnings; my $file="sample.txt"; open(DAT, $file) || die("Could not open file!"); open (OUTPUTFILE, '>data.txt'); my $sequence; my $someVar = 0; my $sequenceNums = 1; my $motif1 = "(HDWFLSFKD)"; my $motif2 = "(HD)"; my $motif3 = "(K)"; my $motif4 = "(DD)"; while (my $line = <DAT>) { $someVar = 0; print "\nSequence $sequenceNums: $line\n"; print OUTPUTFILE "\nSequence $sequenceNums: $line\n"; if ($line=~ /$motif1/g) { &printStuff($sequenceNums, "motif1", $motif1, "$-[0]-$+[0]"); $someVar = 1; } if ($line=~ /$motif2/g and $someVar == 1) { &printStuff($sequenceNums, "motif2", $motif2, "$-[0]-$+[0]"); $someVar = 2; } if ($line=~ /$motif3/g and $someVar == 2) { &printStuff($sequenceNums, "motif3", $motif4, "$-[0]-$+[0]"); $someVar = 3; } if ($line=~ /$motif4/g and $someVar == 3) { &printStuff($sequenceNums, "motif4", $motif4, "$-[0]-$+[0]"); } else { $sequence .= $line; if ($someVar == 0) { &printWrongStuff($sequenceNums, "motif1", $motif1); } elsif ($someVar == 1) { &printWrongStuff($sequenceNums, "motif2", $motif2); } elsif ($someVar == 2) { &printWrongStuff($sequenceNums, "motif3", $motif3); } elsif ($someVar == 3) { &printWrongStuff($sequenceNums, "motif4", $motif4); } } $sequenceNums++; } sub printStuff { print "Sequence: $_[0] $_[1]: $_[2] index location: $_[3] \n"; print OUTPUTFILE "Sequence: $_[0] $_[1]: $_[2] index location: $_[3]\n"; } sub printWrongStuff { print "Sequence: $_[0] $_[1]: $_[2] was not found\n"; print OUTPUTFILE "Sequence: $_[0] $_[1]: $_[2] was not found\n"; } close (OUTPUTFILE); close (DAT); </code></pre> <p>Sample input:</p> <p>MLTSHQKKF<em>HDWFLSFKD</em>SNNYN<em>HD</em>S<em>K</em>QNHSIK<em>DD</em>IFNRFNHYIYNDLGIRTIA MLTSHQKKFSNNYNSKQNHSIKDIFNRFNHYIYNDLGIRTIA MLTSHQKKFSNNYNSK<em>HDWFLSFKD</em>QNHSIKDIFNRFNHYIYNDL</p>

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