ClustalW alignment - Unexpected result

Question

[pentium3-user]

Hi,
I have two sequences

>seq1
AAAAAAACCCCCCCCCCAAAAAAAAAAAAAAAAAAAAAAAAA
>seq2
TTTTTTTTTTTTTTTTTTTCCCCCCCCCCTTTTTTTTTTTTT

And I want to align them this way using clustalW

AAAAAAA-------------------CCCCCCCCCCAAAAAAAAAAAAAAAAAAAAAAAAA-------------
-------TTTTTTTTTTTTTTTTTTTCCCCCCCCCC-------------------------TTTTTTTTTTTTT

The exact alignment is not important but I want that only the Cs are aligned and the mismatching bases are gapped.

So I set the following scores

• match: 1
• mismatch: -1
• gap opening: 0
• gap extending: 0

But what I get is this alignment

------------AAAAAAACCCCCCCCCCAAAAAAAAAAAAAAAAAAAAAAAAA
TTTTTTTTTTTTTTTTTTTCCCCCCCCCCTTTTTTTTTTTTT------------

I don't understand why this is happening. The score for my expected alignment would be 10 (10 matches) while the score for the alignment I get should be -10 (10 matches and 20 mismatches).

I use the following R code

library (msa)

seqs <- DNAStringSet(c("AAAAAAACCCCCCCCCCAAAAAAAAAAAAAAAAAAAAAAAAA", "TTTTTTTTTTTTTTTTTTTCCCCCCCCCCTTTTTTTTTTTTT"))
smatrix <- matrix(c(1,-1,-1,-1,-1,1,-1,-1,-1,-1,1,-1,-1,-1,-1,1), ncol=4, nrow=4, byrow = T)
colnames(smatrix) <- c("A", "C", "G", "T")
rownames(smatrix) <- c("A", "C", "G", "T")
aln <- msa (seqs, type = "dna", gapOpening=0, gapExtension=0, substitutionMatrix = smatrix)
print(aln, show="complete")

Output:

MsaDNAMultipleAlignment with 2 rows and 54 columns
    aln 
[1] ------------AAAAAAACCCCCCCCCCAAAAAAAAAAAAAAAAAAAAAAAAA
[2] TTTTTTTTTTTTTTTTTTTCCCCCCCCCCTTTTTTTTTTTTT------------
Con ???????????????????CCCCCCCCCC?????????????????????????

Does anyone know why this is happening and what do I have to change to get my expected result?