#!/usr/bin/perl -w
                                                                                                                                             
open (IN, "one.seq.one.line.7.19.04") or die "can't open IN: $!";
open (OUT, ">out.index.7.19.04") or die "can't open OUT: $!";
                                                                                                                                             
while(<IN>){
                                                                                                                                             
     print OUT $_; print OUT scalar(localtime), "\n";
     print OUT "The first occurance of little a is: ", index($_,"a"), "\n";
     print OUT "The first occurance of little c is: ", index($_,"c"), "\n";
     print OUT "The first occurance of little g is: ", index($_,"g"), "\n";
     print OUT "The first occurance of little t is: ", index($_,"t"), "\n";
     print OUT "\n\n";
                                                                                                                                             
     print OUT $_;
     print OUT scalar(localtime), "\n";
     print OUT "The first occurance of little a is: ", index($_,"a"), "\n";
     print OUT "The first occurance of little c is: ", index($_,"c"), "\n";
     print OUT "The first occurance of little g is: ", index($_,"g"), "\n";
     print OUT "The first occurance of little t is: ", index($_,"t"), "\n";
     print OUT "\n\n";
                                                                                                                                             
     print  $_;
     print "The first occurance of little a is: ", index($_,"a"), "\n";
     print "The first occurance of little c is: ", index($_,"c"), "\n";
     print "The first occurance of little g is: ", index($_,"g"), "\n";
     print "The first occurance of little t is: ", index($_,"t"), "\n";
     print "\n\n";
                                                                                                                                             
}