Fixed the parsing of cmsearch outputs. It had a problem with lines like:

Query = 1 - 124, Target = 31780 - 31836
 Score = 18.96, E = 0.104, P = 1.812e-08, GC =  25

           <<<<<<<<<<___>>>>>>>>>>,,,,<<<<<<___>>>>>>,,,,,,,,,,,,,,,~~~
         1 aaCCcCCaGCuAGGCuGGgGGuuCcGuaaaGCuUucaGCuuugAgaaagUUAuaAAA*[6 57
           ::C::C:A:C   G:U:G::G:: + UAAA::UUU A::UUU+A A A+UUA A AA
     31780 UCCGGCGAUCAUUGAUCGCCGGAUAAUAAAUAUUUUAUAUUUAAUAUAAUUAAAUAA*[  31836

           ~~~
         - 7]* -

         - 0]* -

It was necessary to check if the query AND the target lines end with the end positions recorded in the header (Query = 1 - 124, Target = 31780 - 31836) before to break.