Dialign2-2 outputs

[RTK45]

Hi,

i am actually working with dialign2-2 et i have some problems with my alignments. I make pairwise alignment and i try to compare short DNA sequences (between 10 et 4000 nucleotides).

When i use dialign i use -n to specify that i work on DNA sequences, but when i look at my output, i obtain better alignments using no option (in this case dialign considers that i work with proteins sequences).

For example :

input:

GGCGGGCCTCGCCCCGCGCTGTTCTTTCCTC[COLOR="Red"]C[/COLOR]CCC
GGCGGGCCTCGCCCCGCGCTGTTCTTCCCAC[COLOR="Red"]T[/COLOR]CCC

output using dialign2-2 -n file.fa :

GGCGGGCCTCGCCCCGCGCTGTTCTTTCCTC[COLOR="Red"]C[/COLOR]CCC
GGCGGGCCTCGCCCCGCGCTGTTCTTCCCAC[COLOR="Red"]T[/COLOR]CCC

and using this : dialign2-2 file.fa :

GGCGGGCCTCGCCCCGCGCTGTTCTTTCCTC[COLOR="Red"]-[/COLOR]CCC
GGCGGGCCTCGCCCCGCGCTGTTCTTCCCAC[COLOR="Red"]t[/COLOR]CCC

I have underline differences in red.



Moreover, in several cases (always using -n), my output sequences are more longer than my input sequences (between 2 and 5 nucleotides). How can i obtain this difference ?

Thanks

And sorry for my english

[RTK45]

Resolved, my treshold was too low (T=0 per default)