------------------------------------------------------------ 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 18 sequences from file RIBOSOMAL_L36 PATTERN CONSERVATION: CM: min Nr of Seqs to Match 18 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 RIBOSOMAL_L36.pratt2 OP: PROSITE Pattern Format on ON: max number patterns 20 OA: max number Alignments 20 M: Print Patterns in sequences off Sequence lengths: RL36_ASTLO 37 RL36_BACST 37 RL36_BACSU 37 RL36_CHLTR 37 RL36_CRYPH 13 RL36_ECOLI 38 RL36_EPIVI 37 RL36_EUGGR 37 RL36_HAEIN 37 RL36_LACLA 38 RL36_MARPO 37 RL36_MYCBO 37 RL36_ORYSA 37 RL36_PEA 37 RL36_PINTH 37 RL36_SPIOL 37 RL36_THETH 37 RL36_TOBAC 37 Pratt run started at Thu Feb 6 21:06:01 1997 Best Patterns before refinement: fitness hits(seqs) Pattern 1: 12.0102 18( 18) M-K-x(2,3)-S 2: 8.3401 19( 18) K-x(3)-S 3: 7.8401 19( 18) K-x(2,3)-S 4: 7.3401 60( 18) K-x(1,3)-R Best Patterns (after refinement phase): fitness hits(seqs) Pattern A 1: 20.2978 18( 18) K-[IV]-x-[APS]-S-[IV]-x(2)-[ILM] B 2: 18.1239 18( 18) M-K-x(2,3)-S-[IV]-x(2)-[ILM] C 3: 13.9539 18( 18) K-x(2,3)-S-[IV]-x(2)-[ILM] D 4: 7.3401 60( 18) K-x(1,3)-R Best patterns with alignements: fitness hits(seqs) Pattern A 1: 20.2978 18( 18) K-[IV]-x-[APS]-S-[IV]-x(2)-[ILM] Occurences: 18(18) RL36_ASTLO : 2- 10: m KVySSVrkI ckscg RL36_BACST : 2- 10: m KVrPSVkpI cekck RL36_BACSU : 2- 10: m KVrPSVkpI cekck RL36_CHLTR : 2- 10: m KVrASIkrI ckdck RL36_CRYPH : 2- 10: m KVvSSIgsL knr RL36_ECOLI : 2- 10: m KVrASVkkL crnck RL36_EPIVI : 2- 10: m KIrASIrkI cekcr RL36_EUGGR : 2- 10: m KIrSSVkkI cnkcy RL36_HAEIN : 2- 10: m KVrASVkkM crnck RL36_LACLA : 2- 10: m KVrPSVkpI ceyck RL36_MARPO : 2- 10: m KIrASVrkI cencr RL36_MYCBO : 2- 10: m KVnPSVkpI cdkcr RL36_ORYSA : 2- 10: m KIrASVrkI ctkcr RL36_PEA : 2- 10: m KVaASVrkI cekcr RL36_PINTH : 2- 10: m KIrASIrrI cgkcr RL36_SPIOL : 2- 10: m KIrASVrpI cekcr RL36_THETH : 2- 10: m KVrASVkrI cdkck RL36_TOBAC : 2- 10: m KIrASVrkI cekcr B 2: 18.1239 18( 18) M-K-x(2,3)-S-[IV]-x(2)-[ILM] Occurences: 18(18) RL36_ASTLO : 1- 10: MKvysSVrkI ckscg RL36_BACST : 1- 10: MKvrpSVkpI cekck RL36_BACSU : 1- 10: MKvrpSVkpI cekck RL36_CHLTR : 1- 10: MKvraSIkrI ckdck RL36_CRYPH : 1- 10: MKvvsSIgsL knr RL36_ECOLI : 1- 10: MKvraSVkkL crnck RL36_EPIVI : 1- 10: MKiraSIrkI cekcr RL36_EUGGR : 1- 10: MKirsSVkkI cnkcy RL36_HAEIN : 1- 10: MKvraSVkkM crnck RL36_LACLA : 1- 10: MKvrpSVkpI ceyck RL36_MARPO : 1- 10: MKiraSVrkI cencr RL36_MYCBO : 1- 10: MKvnpSVkpI cdkcr RL36_ORYSA : 1- 10: MKiraSVrkI ctkcr RL36_PEA : 1- 10: MKvaaSVrkI cekcr RL36_PINTH : 1- 10: MKiraSIrrI cgkcr RL36_SPIOL : 1- 10: MKiraSVrpI cekcr RL36_THETH : 1- 10: MKvraSVkrI cdkck RL36_TOBAC : 1- 10: MKiraSVrkI cekcr C 3: 13.9539 18( 18) K-x(2,3)-S-[IV]-x(2)-[ILM] Occurences: 18(18) RL36_ASTLO : 2- 10: m KvysSVrkI ckscg RL36_BACST : 2- 10: m KvrpSVkpI cekck RL36_BACSU : 2- 10: m KvrpSVkpI cekck RL36_CHLTR : 2- 10: m KvraSIkrI ckdck RL36_CRYPH : 2- 10: m KvvsSIgsL knr RL36_ECOLI : 2- 10: m KvraSVkkL crnck RL36_EPIVI : 2- 10: m KiraSIrkI cekcr RL36_EUGGR : 2- 10: m KirsSVkkI cnkcy RL36_HAEIN : 2- 10: m KvraSVkkM crnck RL36_LACLA : 2- 10: m KvrpSVkpI ceyck RL36_MARPO : 2- 10: m KiraSVrkI cencr RL36_MYCBO : 2- 10: m KvnpSVkpI cdkcr RL36_ORYSA : 2- 10: m KiraSVrkI ctkcr RL36_PEA : 2- 10: m KvaaSVrkI cekcr RL36_PINTH : 2- 10: m KiraSIrrI cgkcr RL36_SPIOL : 2- 10: m KiraSVrpI cekcr RL36_THETH : 2- 10: m KvraSVkrI cdkck RL36_TOBAC : 2- 10: m KiraSVrkI cekcr D 4: 7.3401 60( 18) K-x(1,3)-R Occurences: 60(18) RL36_ASTLO : 22- 26: irrhg KlfvR cinsk RL36_ASTLO : 31- 35: rcins KhnqR qn RL36_BACST : 2- 4: m Kv--R psvkp RL36_BACST : 15- 18: icekc Kvi-R rrgkv RL36_BACST : 15- 19: icekc KvirR rgkvm RL36_BACST : 31- 35: icenp KhkqR qg RL36_BACST : 33- 35: enpkh Kq--R qg RL36_BACSU : 2- 4: m Kv--R psvkp RL36_BACSU : 15- 18: icekc Kvi-R rkgkv RL36_BACSU : 15- 19: icekc KvirR kgkvm RL36_CHLTR : 2- 4: m Kv--R asikr RL36_CHLTR : 15- 19: ickdc KiikR hgvnr RL36_CHLTR : 31- 35: icinf KhkqR qg RL36_CHLTR : 33- 35: infkh Kq--R qg RL36_CRYPH : 11- 13: sigsl Kn--R RL36_ECOLI : 2- 4: m Kv--R asvkk RL36_ECOLI : 8- 12: vrasv KklcR nckiv RL36_ECOLI : 9- 12: rasvk Klc-R nckiv RL36_ECOLI : 15- 19: lcrnc KivkR dgvir RL36_ECOLI : 32- 36: csaep KhkqR qg RL36_ECOLI : 34- 36: aepkh Kq--R qg RL36_EPIVI : 2- 4: m Ki--R asirk RL36_EPIVI : 13- 15: rkice Kc--R licrr RL36_EPIVI : 33- 35: snprh Kq--R qg RL36_EUGGR : 2- 4: m Ki--R ssvkk RL36_EUGGR : 31- 35: vcinn KhkqR qg RL36_EUGGR : 33- 35: innkh Kq--R qg RL36_HAEIN : 2- 4: m Kv--R asvkk RL36_HAEIN : 8- 12: vrasv KkmcR nckiv RL36_HAEIN : 9- 12: rasvk Kmc-R nckiv RL36_HAEIN : 15- 19: mcrnc KivkR egvvr RL36_HAEIN : 31- 35: lcsdp KhkqR qg RL36_HAEIN : 33- 35: sdpkh Kq--R qg RL36_LACLA : 2- 4: m Kv--R psvkp RL36_LACLA : 15- 18: iceyc Kvi-R rngrv RL36_LACLA : 15- 19: iceyc KvirR ngrvm RL36_LACLA : 32- 36: cpanp KhkqR qg RL36_LACLA : 34- 36: anpkh Kq--R qg RL36_MARPO : 2- 4: m Ki--R asvrk RL36_MARPO : 31- 35: vcsnp KhkqR qg RL36_MARPO : 33- 35: snpkh Kq--R qg RL36_MYCBO : 13- 15: kpicd Kc--R lirrh RL36_MYCBO : 33- 35: sdprh Kq--R qg RL36_ORYSA : 2- 4: m Ki--R asvrk RL36_ORYSA : 13- 15: rkict Kc--R lirrr RL36_ORYSA : 31- 35: icsnp KhkqR qg RL36_ORYSA : 33- 35: snpkh Kq--R qg RL36_PEA : 13- 15: rkice Kc--R lirrr RL36_PEA : 31- 35: icsnp KhkqR qg RL36_PEA : 33- 35: snpkh Kq--R qg RL36_PINTH : 2- 4: m Ki--R asirr RL36_PINTH : 13- 15: rricg Kc--R pirrr RL36_SPIOL : 2- 4: m Ki--R asvrp RL36_SPIOL : 13- 15: rpice Kc--R lirrr RL36_SPIOL : 31- 35: icsnp KhkqR qg RL36_SPIOL : 33- 35: snpkh Kq--R qg RL36_THETH : 2- 4: m Kv--R asvkr RL36_THETH : 15- 18: icdkc Kvi-R rhgrv RL36_THETH : 15- 19: icdkc KvirR hgrvy RL36_THETH : 31- 35: icenp KhkqR qg RL36_THETH : 33- 35: enpkh Kq--R qg RL36_TOBAC : 2- 4: m Ki--R asvrk RL36_TOBAC : 13- 15: rkice Kc--R lirrr RL36_TOBAC : 33- 35: snprh Kq--R qg Number of patterns evaluated by Pratt:5 Total running time: 0 seconds