Perl scipt not working, can anyone help?

[CaptainRAVE]

I wrote a script that basically finds a "start" coordinate in File 1, goes to the correct position in file 2 (then either jumps forward 1 or 2 positions), then counts the number of positions (in groups of 3) until either TAG, TAA or TGA are located; the number of positions are recorded in a new file. The problem is, it is either stoping at random groups of 3 or completely missing TAG, TAA or TGA. I really don't understand why. Can anyone help?


File 1 - http://www.mediafire.com/?jsduwfifoyg8k58

File 2 - http://www.mediafire.com/?6lbpaig84u6to4o

Script - http://www.mediafire.com/?n8ma75imku6iyoc