------------------------------------------------------------
                Pratt version 2.1, Sept. 1996
                 Written by Inge Jonassen, 
                   University of Bergen
                           Norway
                   email: inge@ii.uib.no
                 For more information, see 
            http://www.ii.uib.no/~inge/Pratt.html
------------------------------------------------------------
                        Please quote:
             I.Jonassen, J.F.Collins, D.G.Higgins.
             Protein Science 1995;4(8):1587-1595.
------------------------------------------------------------



                Pratt version 2.1 

        Analysing 45 sequences from file TACHYKININ

PATTERN CONSERVATION:
   CM: min Nr of Seqs to Match                 45
   C%: min Percentage Seqs to Match         100.0

PATTERN RESTRICTIONS :
   PP: pos in seq [off,complete,start]        off
   PL: max Pattern Length                      50
   PN: max Nr of Pattern Symbols               50
   PX: max Nr of consecutive x's                5
   FN: max Nr of flexible spacers               2
   FL: max Flexibility                          2
   FP: max Flex.Product                        10
   BI: Input Pattern Symbol File              off
   BN: Nr of Pattern Symbols Initial Search    20

PATTERN SCORING:
   S: Scoring [info,mdl,tree,dist,ppv]       info

SEARCH PARAMETERS:
   G: Pattern Graph from [seq,al,query]       seq
   E: Search Greediness                         3
   R: Pattern Refinement                       on
   RG: Generalise ambiguous symbols           off

OUTPUT:
   OF: Output Filename          TACHYKININ.pratt2
   OP: PROSITE Pattern Format                  on
   ON: max number patterns                     20
   OA: max number Alignments                   20
   M: Print Patterns in sequences             off




Sequence lengths:
    TKN1_KASMA     12
    TKN1_PSEGU     11
    TKN1_SCYCA     10
    TKN1_UPERU     11
    TKN2_KASMA     12
    TKN2_PSEGU     11
    TKN2_SCYCA     18
    TKN2_UPERU     11
    TKN3_PSEGU     11
    TKN4_PSEGU     11
    TKN5_PSEGU     11
    TKNA_BOVIN    112
    TKNA_CHICK     11
    TKNA_GADMO     11
    TKNA_HORSE     11
    TKNA_ONCMY     11
    TKNA_RANCA     11
    TKNA_RANRI     11
      TKNA_RAT    112
    TKNA_SCYCA     11
    TKNB_BOVIN    130
    TKNB_CHICK     10
    TKNB_HUMAN    129
    TKNB_MOUSE    130
    TKNB_ONCMY     10
    TKNB_RANCA     10
    TKNB_RANRI     10
      TKNB_RAT    130
    TKNC_CARAU     21
    TKNC_RANCA     10
    TKND_RANCA     11
      TKND_RAT     97
    TKNG_BOVIN    115
    TKNG_HUMAN     72
    TKNG_MOUSE     72
    TKNG_RABIT    115
      TKNG_RAT    115
    TKNK_BOVIN    126
      TKNK_PIG     10
      TKNK_RAT    116
    TKNM_RANMA     14
     TKN_ELEMO     11
     TKN_KASSE     12
     TKN_PHYBI     10
     TKN_PHYFU     11

Pratt run started at Thu Feb  6 21:21:31 1997



Best Patterns before refinement:
         fitness     hits(seqs)    Pattern
    1:    8.3401     54(  45)   F-x(3)-M


Best Patterns (after refinement phase):
         fitness     hits(seqs)    Pattern
A   1:   11.5102     54(  45)   F-x-[AG]-x-M


Best patterns with alignements:
         fitness     hits(seqs)    Pattern
A   1:   11.5102     54(  45)   F-x-[AG]-x-M
Occurences: 54(45)
    TKN1_KASMA :     8-    12: pkpdq FvGlM      
    TKN1_PSEGU :     7-    11: phpde FvGlM      
    TKN1_SCYCA :     6-    10: akfdk FyGlM      
    TKN1_UPERU :     7-    11: pdpna FyGlM      
    TKN2_KASMA :     8-    12: pdpdr FyGmM      
    TKN2_PSEGU :     7-    11: pnpde FvGlM      
    TKN2_SCYCA :    14-    18: dgpdc FvGlM      
    TKN2_UPERU :     7-    11: adpkt FyGlM      
    TKN3_PSEGU :     7-    11: phpne FvGlM      
    TKN4_PSEGU :     7-    11: pnpde FfGlM      
    TKN5_PSEGU :     7-    11: pnpne FfGlM      
    TKNA_BOVIN :    64-    68: pkpqq FfGlM gkrda
    TKNA_CHICK :     7-    11: prpqq FfGlM      
    TKNA_GADMO :     7-    11: prpqq FiGlM      
    TKNA_HORSE :     7-    11: pkpqq FfGlM      
    TKNA_ONCMY :     7-    11: prphq FfGlM      
    TKNA_RANCA :     7-    11: pspdr FyGlM      
    TKNA_RANRI :     7-    11: pnper FyGlM      
      TKNA_RAT :    64-    68: pkpqq FfGlM gkrda
    TKNA_SCYCA :     7-    11: prpgq FfGlM      
    TKNB_BOVIN :    64-    68: pkpqq FfGlM gkrda
    TKNB_BOVIN :   103-   107: hktds FvGlM gkral
    TKNB_CHICK :     6-    10: hktds FvGlM      
    TKNB_HUMAN :    64-    68: pkpqq FfGlM gkrda
    TKNB_HUMAN :   103-   107: hktds FvGlM gkral
    TKNB_MOUSE :    64-    68: pkpqq FfGlM gkrda
    TKNB_MOUSE :   103-   107: hktds FvGlM gkral
    TKNB_ONCMY :     6-    10: hkins FvGlM      
    TKNB_RANCA :     6-    10: yksds FyGlM      
    TKNB_RANRI :     6-    10: hklds FiGlM      
      TKNB_RAT :    64-    68: pkpqq FfGlM gkrda
      TKNB_RAT :   103-   107: hktds FvGlM gkral
    TKNC_CARAU :    17-    21: hkins FvGlM      
    TKNC_RANCA :     6-    10: hnpas FiGlM      
    TKND_RANCA :     7-    11: pnper FyApM      
      TKND_RAT :    64-    68: pkpqq FfGlM gkrda
    TKNG_BOVIN :    64-    68: pkpqq FfGlM gkrda
    TKNG_BOVIN :    88-    92: hktds FvGlM gkral
    TKNG_HUMAN :    29-    33: pkpqq FfGlM gkrda
    TKNG_HUMAN :    53-    57: hktds FvGlM gkral
    TKNG_MOUSE :    29-    33: pkpqq FfGlM gkrda
    TKNG_MOUSE :    53-    57: hktds FvGlM gkral
    TKNG_RABIT :    64-    68: pkpqq FfGlM gkrda
    TKNG_RABIT :    88-    92: hktds FvGlM gkral
      TKNG_RAT :    64-    68: pkpqq FfGlM gkrda
      TKNG_RAT :    88-    92: hktds FvGlM gkral
    TKNK_BOVIN :    91-    95: dmhdf FvGlM gkrnl
      TKNK_PIG :     6-    10: dmhdf FvGlM      
      TKNK_RAT :    87-    91: dmhdf FvGlM gkrns
    TKNM_RANMA :    10-    14: drakk FyGlM      
     TKN_ELEMO :     7-    11: pskda FiGlM      
     TKN_KASSE :     8-    12: pksdq FvGlM      
     TKN_PHYBI :     6-    10: qnpnr FiGlM      
     TKN_PHYFU :     7-    11: adpnk FyGlM      

Number of patterns evaluated by Pratt:1
Total running time:    1 seconds