align 230-ribonucleotide fragment 100 times

Question

[natasha.sernova]

Dear all, I have to align 230-ribonucleotide fragment many times (100) to a single reference. Unfortunately there are 80 symbols in any single line. What tool may I use to do it? Is it possible to make it nice somehow? There was a post about that a long time ago, but I lost its number. Thank you very much! Natalia

[natasha.sernova]

I found one probable answer by myself.

Is there a way to get RNAFold output for multifasta in tabular format?

and the tool is RNAFold

But I was looking for a tool to align Stockholm-format fragments...

Then I found another tool:

pytfmpval: Efficient, accurate p-value computation for position weight matrices