bad alignment

[Sabine Reißer]

Hi,

I'm trying to align two sequences, where the first aligns perfectly to
the end of the second. T-Coffee, however, insists in aligning the first
two nucleotides (CC) of seq 1 to the beginning of the seq2 (AA). I
checked this both in the online version and the installed linux version,
with T-COFFEE_installer_Version_13.41.0.28bdc39_linux_x64.

I'm running

t_coffee test.fa -type rna  -output fasta

I'm playing around with the gapopen and gapext but this doesn't fix the
problem and I feel like I should not need to do that at all - the
correct alignment should be absolutely clear.

Am I missing something?

It would be great if someone could help.

Cheers

Sabine