Crunch file for Artemis Comparison Tool

Question

[SushiRoll]

Dear all,

I am meaning to compare a couple of assemblies with a reference. I find ACT great for visualizing this sort of analyses but the online crunch files generator is not working anymore. I have tried doing it manually using blast but somehow every comparison "goes out" from the contig number 1. Is there a way to correctly perform a crunch output. I'm open to other tools other than ACT but I do need to be able to read a feature file on the comparison, a thing that I couldn't achieve using Mauve.

Thanks all!

Edit: The crunch that I produced was following the command in this post:

How to generate Artemis ACT comparison file of multiple sequence alignment