note Lotus1 <p><c>tr///</c> can be used to count characters in a string. No need to loop through.</p> <c>use warnings; use strict; print "LATCG-\n"; while(<DATA>) { print $. . tr/A// . tr/T// . tr/C// . tr/G// . tr/-// . "\n"; } __DATA__ ATGAAAAAGAC AGCTATCGCGA TTGCAGTGGCA CTGGCTGGTTT CGCTACCGTAG CGC-A---TAG </c> <p>Output:</p> <c> LATCG- 171120 232330 323240 405240 522430 621224 </c> 1007821 1007821