The following picture shows 4 gaps inserted into the reference sequence and into the aligned sequence. The reason is that this example was run with the alignment parameter "Minimum number of matches for alignment" set to 4.
To change the alignment parameters, click the Parameters menu option. The defaults are 5 and 15. Increase the first value to 5.
Now the auto-alignment has aligned the sequence with 4 mismatches instead of 4 gaps.
