Search sequences for strings of consecutive purines.

 

       beginning of 1st consecutive purines    beginning of 2nd consecutive purines    

       |                                       |    

   NNNNRRRRRRRNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNRRRRRRNNNNNNNNNN

   |

   beginning of leading sequence

 

   R = any purine (AG)

   N = any nucleotide base (ATCG) - actually, any character.

   


   Key to text fields:



   Purines [minimum consecutive] - [maximum consecutive]

   Leading [minimum length] - [maximum length]

   Return top [number of sequences]

   Truncate to [number of bases]



   Purines - indicates the size range of consecutive purines searched for.

   Leading - indicates the size range of leading sequence. The minimum length 

           is also also used to truncate the output sequences leaders.

   Return top - indicates the number of sequences to return as output.

   Truncate to - indicates the number of bases to which each output is shortened. Only the 

                 sequence following the consecutive purines is truncated, until it has 

                 a length of zero if neccessary. The consecutive purines are never 

                 trucated.

   

   Scoring:



   10 points for each consecutive purine (within Purines range)

   1 point for each leading base (within Leading range)

   0.5 points for each leading base (if purines start before minimum leading)