#!/usr/bin/perl -w
                                                                
open (IN, "one.seq.one.line");
open (OUT, ">out.index.pl");
                                                                
                                                                
                                                                
while(<IN>){
                                                                
print OUT $_;
print OUT "The first occurance of little a is: ", index($_,"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";
}


##</code><code>##

ATGGACTGCACCTGGAGGATCCTCTTCTTGGTGGCAGCAGCTACAGgcaagagaatcctgagttccagggctgatgaggg
The first occurance of little a is: 48
The first occurance of little c is: 47
The first occurance of little g is: 46
The first occurance of little t is: 49