Chlamydia test data: fragment color bars are not correct

[hoelzer]

Test data:
hctb_26strains_only_type_strains.fasta.gz

Test command:

nextflow run poseidon.nf --fasta hctb_26strains_only_type_strains.fasta --cores 8

Output:
https://www.rna.uni-jena.de/supplements/chlamydia_genome_comparison/poseidon/hctb_26strains_only_type_strains/html/full_aln/

Fragment 2 is too short.

Likely an indexing issue due to the many gaps in the alignment.