edit, to expand on Chris' idea:

You can perform a BLAST search on a multi-FASTA file on itself.

blastp -query my.fasta -subject my.fasta -outfmt 7 # or 6

which yields all pairwise scores that you just need to parse from, e.g. tabular file format or XML using BioPython.

-- old answer, which might still be the cleaner way to do it --

I suggest you look at the following resources:

• bl2seq, which comes with the NCBI BLAST tools: how to input sequence 1 and 2, and how to get the score from the output
• How to call bl2seq from Python
• How nested for loops work, with sequence 1 and 2 as the variables

And, most importantly, show us what you have tried already and where you got stuck. We won't write the program for you, you will have to do this yourself.

As for the "score in Matrix format": a score is a scalar (one value) and a matrix consists of n*m values. Are you asking for a matrix of all pairwise scores?

You can also put all sequences in a single file and blast every individual sequence against that file. (Although you will do every comparison twice in that way).

If your data looks like this:

column 1 : seq 1
column 2 : seq 2
column 3 : Score

then, you'll find many examples on the web by searching for "pivot table". For example see: http://www.unix.com/shell-programming-scripting/155448-create-pivot-table.html

To call blast from python: http://stackoverflow.com/search?q=python++call+program+external