------------------------------------------------------------ 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 25 sequences from file CYTOCHROME_B559 PATTERN CONSERVATION: CM: min Nr of Seqs to Match 25 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 CYTOCHROME_B559.pratt2 OP: PROSITE Pattern Format on ON: max number patterns 20 OA: max number Alignments 20 M: Print Patterns in sequences off Sequence lengths: PSBE_CYAPA 73 PSBE_EUGGR 80 PSBE_MARPO 82 PSBE_MESCR 82 PSBE_OENBE 82 PSBE_PEA 82 PSBE_PINTH 82 PSBE_SPIOL 82 PSBE_SYNVU 33 PSBE_SYNY3 80 PSBE_TOBAC 82 PSBE_WHEAT 82 PSBF_BETVU 39 PSBF_CAPAN 10 PSBF_CHLEU 44 PSBF_CHLRE 44 PSBF_CYAPA 42 PSBF_EUGGR 41 PSBF_MARPO 39 PSBF_ORYSA 39 PSBF_PEA 39 PSBF_PINTH 39 PSBF_SYNVU 21 PSBF_SYNY3 43 PSBF_TOBAC 38 Pratt run started at Thu Feb 6 19:15:02 1997 Best Patterns before refinement: fitness hits(seqs) Pattern 1: 7.3401 51( 25) I-x(1,3)-R Best Patterns (after refinement phase): fitness hits(seqs) Pattern A 1: 7.3401 51( 25) I-x(1,3)-R Best patterns with alignements: fitness hits(seqs) Pattern A 1: 7.3401 51( 25) I-x(1,3)-R Occurences: 51(25) PSBE_CYAPA : 65- 69: rqevp IinqR fstn PSBE_CYAPA : 66- 69: qevpi Inq-R fstn PSBE_EUGGR : 13- 17: pfsdi ItsiR ywvih PSBE_EUGGR : 65- 68: qqapl Isd-R fnale PSBE_MARPO : 13- 17: pfadi ItsiR ywvih PSBE_MARPO : 65- 68: qevpl Itg-R fnsle PSBE_MESCR : 13- 17: sfadi ItsiR ywvih PSBE_MESCR : 65- 68: qgipl Itg-R fdsle PSBE_OENBE : 13- 17: sfadi ItsiR ywvih PSBE_OENBE : 65- 68: qgipl Itg-R fdsle PSBE_PEA : 13- 17: sfadi ItsiR ywiih PSBE_PEA : 65- 68: qgipl Itg-R fdsle PSBE_PINTH : 13- 17: sfadi ItsiR ywvih PSBE_SPIOL : 13- 17: sfadi ItsiR ywvih PSBE_SPIOL : 65- 68: qgipl Itg-R fdsle PSBE_SYNVU : 13- 17: pfsdi ItsvR ywvih PSBE_SYNY3 : 64- 68: rqelp IlqeR ydinq PSBE_TOBAC : 13- 17: sfadi ItsiR ywvih PSBE_TOBAC : 65- 68: qgipl Itg-R fdple PSBE_WHEAT : 13- 17: sfadi ItsiR ywvih PSBE_WHEAT : 65- 68: qgipl Itd-R fdsle PSBF_BETVU : 3- 5: mt Id--R typif PSBF_BETVU : 9- 13: drtyp IftvR wlavh PSBF_BETVU : 37- 39: samqf Iq--R PSBF_CAPAN : 8- 10: samqf Iq--R PSBF_CHLEU : 14- 18: vityp IftvR wvsih PSBF_CHLEU : 42- 44: tamqf Iq--R PSBF_CHLRE : 14- 18: vlvyp IftvR wlatt PSBF_CHLRE : 42- 44: tamqf Iq--R PSBF_CYAPA : 12- 16: pvsyp IftvR wlaih PSBF_CYAPA : 40- 42: tamqf Iq--R PSBF_EUGGR : 11- 15: dtryp IftfR wlavh PSBF_EUGGR : 39- 41: samqf Iq--R PSBF_MARPO : 3- 5: mt Id--R typif PSBF_MARPO : 9- 13: drtyp IftvR wlavh PSBF_MARPO : 37- 39: samqf Iq--R PSBF_ORYSA : 3- 5: mt Id--R typif PSBF_ORYSA : 9- 13: drtyp IftvR wlavh PSBF_ORYSA : 37- 39: samqf Iq--R PSBF_PEA : 3- 5: mt Id--R typif PSBF_PEA : 9- 13: drtyp IftvR wlavh PSBF_PEA : 37- 39: samqf Iq--R PSBF_PINTH : 3- 5: mt Id--R typif PSBF_PINTH : 9- 13: drtyp IftvR wlavh PSBF_PINTH : 37- 39: samqf Iq--R PSBF_SYNVU : 14- 18: pvsyp IftvR xva PSBF_SYNY3 : 13- 17: pvtyp IftvR wlavh PSBF_SYNY3 : 41- 43: aamqf Iq--R PSBF_TOBAC : 2- 4: t Id--R typif PSBF_TOBAC : 8- 12: drtyp IftvR wlaih PSBF_TOBAC : 36- 38: samqf Iq--R Number of patterns evaluated by Pratt:1 Total running time: 1 seconds