I am running version 1.6.2 under windows7. The problem is that: when I give the amino acid sequence query to 'Find pattern' and ask to perform search with 90% match and include indels, UGENE gives me bench (really long list) of matches starting from the same nucleotide but each next match in list is ending with one nucleotide shift in comparison with previous one. For example:
1165750..1170345
1165750..1170346
1165750..1170347
1165750..1170348
etc.

One more thing. If I tried to perform search of nucleotide sequence (100% similarity) which is located at the beginning of my loaded sequence started from first nucleotide, 'Find pattern' can not see it! It sees only started from second nucleotide of loaded sequence.

Thanks a lot!

P.S. I also wish I could download the manual as pdf or in epub format for my reader :]

The problem with first symbol is fixed now. Please check for the new release next week.

As for the "90% ins-del" results list please use "Remove overlaps" button. It will remove all overlapped results. Maybe it worth to make this option selectable before the search, but not after.

Please note that for ins-del search it's recommended to use smith-waterman version of the find algorithm where you can manually select the weight matrix to use.

Thanks a lot! :)