Trimming does not work for tracy align

[sebschulz1]

It was found that although trim_left and trim_right are set to identical values for tracy align and tracy decompose, the trimming does not seem to work for tracy align as judged from Sage visualisation and inspection of .align.fa files from the tracy align process compared to alignments from the tracy decompose process.
Consequently, alignments and visualisations from tracy align and tracy decompose are currently not comparable although identical trimming parameters were set.

It needs to be investigated if this bugs stems from this code base or from the tracy software itself.

[sebschulz1]

For downstream analysis, this might not be that much of an issue (for details see #34 (comment)). However, in general this should be investigated further.