First of all, your first regex, /SEQ+/, matches: SEQ, SEQQ, SEQQQ, SEQQQQ etc. Is that what you want?

In your second regex, \d matches a digit which are characters 0-9. I think you want \w in order to match the word characters.

if ($csv_line =~ /SEQ/) { # If the line contains 'SEQ' anywhere in it 
+this will be true
    print "header\n";
} elsif ($csv_line =~ /^(\w)\t(\w)\t/) { # This will match a word char
+acter at the beginning of a line followed by a tab, another word char
+acter, and another tab
    print "Amino Acid:$1\nPrediction:$2\n";
}
[download]