A sample of the input file

>gi|269849759|sp|P04637.4|P53_HUMAN
MEEPQSDPSVEPPLSQETFSDLWKLLPENNVLSPLPSQAMDDLMLSPDDIEQWFTEDPGPDEAPRMPEAA....
>gi|143235535|dbj|46784|P53_MUS
----MEEPQSDPSVEPPL---SQETFSDLWKLL---PENNV---LSPLPSQAMDDLMLS....

##</code><code>##

A sample of the second input file

P82L
R112S
A116V
A116T
[...]

##</code><code>##

>gi|269849759|sp|P04637.4|P53_HUMAN
MEEPQSAQWCCTV
>gi|143235535|dbj|46784|P53_MUS
--FKQSARTYC-V
>gi|343556|emb|3432384|P53_EQUUS
--LKQSAPTY--S

and the variant list contains:

E3P
Q8R
T12C

##</code><code>##

Variant    Deviations               Pathogenic_Deviations 
E3P          F (143235535),                 None
                 L (343556)                                    
Q8R         P(343556)                R (143235535)
T12C        None                                  None