How can one get the correct results of all combinations with bigger input files?

Select or download this

#!/usr/bin/perl  
use strict;
...
close $output;    
exit;  
#############################################

Select or download this

A1T1
A2T3

Select or download this

C1G1
C1G2
C2G1

Select or download this

A1C1

Select or download this

A1R1N1D1C1E1Q1G1H1I1L1K1F1P1S1
A1R1N1D1C1E1Q1G1H1I1L1K1F1P1S1
...
A2R3N1D1C1E1Q1G2H1I1L3K1F1P2S3
A2R3N1D1C1E1Q1G2H1I1L3K1F1P2S3
A2R3N1D1C1E1Q1G2H1I1L3K1F1P2S3

Select or download this

 
T1Y1V1M1W1E1Q1G1H1I1L1K1F1P1S1
T1Y1V1M1W1E1Q1G1H1I1L1K1F1P1S1
...
T2Y3V1M1W1E1Q1G2H1I1L3K1F1P2S3
T2Y3V1M1W1E1Q1G2H1I1L3K1F1P2S3
T2Y3V1M1W1E1Q1G2H1I1L3K1F1P2S3

Select or download this

T1Y1V1M1W1A1R1N1
T1Y1V1M1W1A1R1N1
...
T1Y2V1M1W1A1R1N2
T1Y2V1M1W1A1R1N2
...

Select Code to Download