In the Default T-Coffee alignment, the red portions are the most likely to be correct. You can compare this alignment with the reference alignment as provided in prefab (use the command line t_coffee -other_pg aln_compare -al1 aln1 -al2 aln2 if you want a more precise comparison). For your information, 27 % of the positions are correct in this alignment when considering the two structures 1svpA and 1qq4A.
Expresso uses BLAST to find the best structural templates, and reports them in the template_file. Expresso then combines the structure based alignments (sap) with the sequence based alignment methods (slow_pair, lalign_id_pair). Overall, the alignment is better, but this does not show very well in the scoring scheme (*) because the sequence based alignments (slow_pair, lalign_id_pair) are still as unconsistent (and unreliable) as they were before. For your information, 69% of the positions are correct in the alignment of 1svpA with 1qq4A
M-Coffee produces a multiple sequence alignment with the most common methods. Because they tend to use similar algorithm, these methods often produce more consistent output than the default T-Coffee, thus making the consistency output slightly less informative. However, you can safely assume that highly consistent regions (red brick columns) are correctly aligned (*). In this case, the accuracy for the two structures is about the same as the default T-Coffee (27%).
You can run Expresso without using the sequence based methods by going into the advanced mode and unchecking the slow_pair and lalign_id_pair boxes and run your job. As you can see (*) the consistency score is now much higher. This is because the pairwise structural alignment tend to agree very much with one another. This alignment is a whooping 91% correct with respect to the two considered structures. The sequences not colored are those for which a structure was not available.
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