------------------------------------------------------------ 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 17 sequences from file RIBOSOMAL_L20 PATTERN CONSERVATION: CM: min Nr of Seqs to Match 17 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_L20.pratt2 OP: PROSITE Pattern Format on ON: max number patterns 20 OA: max number Alignments 20 M: Print Patterns in sequences off Sequence lengths: RL20_ASTLO 117 RL20_BACST 119 RL20_BUCAP 26 RL20_CHLRE 111 RL20_CYAPA 113 RL20_ECOLI 117 RL20_EPIVI 127 RL20_EUGGR 123 RL20_HAEIN 116 RL20_MAIZE 118 RL20_MARPO 115 RL20_MYCFE 116 RL20_ORYSA 118 RL20_PINTH 118 RL20_SOYBN 121 RL20_SPIOL 26 RL20_TOBAC 127 Pratt run started at Thu Feb 6 21:05:50 1997 Best Patterns before refinement: fitness hits(seqs) Pattern 1: 8.3401 43( 17) R-x-K 2: 8.3401 37( 17) K-R 3: 7.8401 47( 17) K-x(3,4)-A Best Patterns (after refinement phase): fitness hits(seqs) Pattern A 1: 11.5883 29( 17) R-x-K-[KR] B 2: 8.3401 37( 17) K-R C 3: 7.8401 47( 17) K-x(3,4)-A Best patterns with alignements: fitness hits(seqs) Pattern A 1: 11.5883 29( 17) R-x-K-[KR] Occurences: 29(17) RL20_ASTLO : 50- 53: fsfsd RkKK krsnk RL20_BACST : 13- 16: pvtrr RrKK vlkla RL20_BUCAP : 2- 5: a RvKR gvtah RL20_BUCAP : 12- 15: vtaha RhKK vlkqa RL20_CHLRE : 2- 5: t RvKR gnvsr RL20_CHLRE : 12- 15: nvsrk RhKK ilnms RL20_CHLRE : 50- 53: syrnr RqKK rdfrr RL20_CYAPA : 2- 5: t RvKR gnvar RL20_CYAPA : 12- 15: nvark RrKK ilkla RL20_CYAPA : 49- 52: yaynd RnKR krdfr RL20_ECOLI : 2- 5: a RvKR gviar RL20_ECOLI : 12- 15: viara RhKK ilkqa RL20_EPIVI : 2- 5: t RiKR gyiar RL20_EPIVI : 12- 15: yiarr RiKK frlfa RL20_EUGGR : 49- 52: yafyd RkKK knlnk RL20_HAEIN : 2- 5: a RvKR gviar RL20_HAEIN : 12- 15: viara RhKK vlkaa RL20_MAIZE : 51- 54: hrdrg RqKR dfrrl RL20_MARPO : 2- 5: t RvKR gyvar RL20_MARPO : 49- 52: sshrd RgKR krnlr RL20_MYCFE : 12- 15: tvtra RrKK wlkla RL20_ORYSA : 51- 54: hrdrv RqKR dfrrl RL20_PINTH : 2- 5: t RvKR gyiar RL20_PINTH : 12- 15: yiark RrKK ilafv RL20_PINTH : 49- 52: sahrd RgKR krdlr RL20_SOYBN : 43- 46: hrdrd RkKR dfrgl RL20_SPIOL : 2- 5: t RvKR gyiar RL20_TOBAC : 2- 5: t RiKR gyiar RL20_TOBAC : 51- 54: hrdrd RkKR dfrrl B 2: 8.3401 37( 17) K-R Occurences: 37(17) RL20_ASTLO : 54- 55: drkkk KR snkki RL20_BACST : 54- 55: drrqr KR dfrkl RL20_BUCAP : 4- 5: arv KR gvtah RL20_CHLRE : 4- 5: trv KR gnvsr RL20_CHLRE : 11- 12: gnvsr KR hkkil RL20_CHLRE : 53- 54: nrrqk KR dfrrm RL20_CYAPA : 4- 5: trv KR gnvar RL20_CYAPA : 11- 12: gnvar KR rkkil RL20_CYAPA : 51- 52: yndrn KR krdfr RL20_CYAPA : 53- 54: drnkr KR dfral RL20_ECOLI : 4- 5: arv KR gviar RL20_ECOLI : 53- 54: drrqr KR qfrql RL20_EPIVI : 4- 5: tri KR gyiar RL20_EPIVI : 53- 54: drnnk KR kfrsl RL20_EUGGR : 12- 13: giskk KR krkis RL20_EUGGR : 14- 15: skkkr KR kiskm RL20_HAEIN : 4- 5: arv KR gviar RL20_HAEIN : 53- 54: drrqr KR qfrql RL20_MAIZE : 53- 54: drgrq KR dfrrl RL20_MARPO : 4- 5: trv KR gyvar RL20_MARPO : 11- 12: gyvar KR rknil RL20_MARPO : 51- 52: hrdrg KR krnlr RL20_MARPO : 53- 54: drgkr KR nlrrl RL20_MYCFE : 53- 54: drkqi KR efrkl RL20_MYCFE : 83- 84: fingl KR anvti RL20_ORYSA : 53- 54: drvrq KR dfrrl RL20_PINTH : 4- 5: trv KR gyiar RL20_PINTH : 11- 12: gyiar KR rkkil RL20_PINTH : 51- 52: hrdrg KR krdlr RL20_PINTH : 53- 54: drgkr KR dlrrl RL20_PINTH : 84- 85: iqyly KR qllpn RL20_SOYBN : 3- 4: ar KR rtkir RL20_SOYBN : 45- 46: drdrk KR dfrgl RL20_SPIOL : 4- 5: trv KR gyiar RL20_TOBAC : 4- 5: tri KR gyiar RL20_TOBAC : 53- 54: drdrk KR dfrrl RL20_TOBAC : 86- 87: ihdly KR qllln C 3: 7.8401 47( 17) K-x(3,4)-A Occurences: 47(17) RL20_ASTLO : 38- 42: kisnq Kimk-A lyfsf RL20_BACST : 16- 21: rrrrk KvlklA kgyfg RL20_BACST : 22- 27: vlkla KgyfgA khaly RL20_BACST : 41- 46: nqqvm KslmyA yrdrr RL20_BUCAP : 4- 9: arv KrgvtA harhk RL20_BUCAP : 15- 20: harhk KvlkqA kgyyg RL20_BUCAP : 21- 26: vlkqa KgyygA RL20_CHLRE : 21- 26: ilnms KgfrgA astlf RL20_CYAPA : 4- 9: trv KrgnvA rkrrk RL20_CYAPA : 15- 20: rkrrk KilklA sgfrg RL20_CYAPA : 40- 45: nqqvm KalryA yndrn RL20_CYAPA : 53- 58: drnkr KrdfrA lwiar RL20_ECOLI : 4- 9: arv KrgviA rarhk RL20_ECOLI : 15- 20: rarhk KilkqA kgyyg RL20_ECOLI : 21- 26: ilkqa KgyygA rsrvy RL20_ECOLI : 40- 45: fqavi KagqyA yrdrr RL20_ECOLI : 102- 107: iavfd KvaftA lveka RL20_ECOLI : 111- 115: talve Kaka-A la RL20_ECOLI : 113- 117: lveka Kaal-A RL20_EPIVI : 4- 9: tri KrgyiA rrrik RL20_EPIVI : 15- 20: rrrik KfrlfA ssfln RL20_EPIVI : 78- 83: vsysy KnfiyA qykiq RL20_EUGGR : 40- 45: nqqlm KarhyA fydrk RL20_HAEIN : 4- 9: arv KrgviA rarhk RL20_HAEIN : 14- 19: ararh KkvlkA akgyy RL20_HAEIN : 15- 19: rarhk Kvlk-A akgyy RL20_HAEIN : 15- 20: rarhk KvlkaA kgyyg RL20_HAEIN : 21- 26: vlkaa KgyygA rsrvy RL20_HAEIN : 40- 45: fqavi KagqyA yrdrr RL20_HAEIN : 102- 106: iavfd Kvaf-A alvek RL20_HAEIN : 102- 107: iavfd KvafaA lveka RL20_HAEIN : 111- 115: aalve Kaks-A l RL20_MAIZE : 15- 20: rrrrt KmrsfA snfrg RL20_MARPO : 4- 9: trv KrgyvA rkrrk RL20_MARPO : 29- 34: qgths KlfrtA nqqgm RL20_MYCFE : 15- 20: rarrk KwlklA kgyfg RL20_MYCFE : 32- 37: ksigy KvakqA vvksw RL20_MYCFE : 40- 45: kqavv KswtyA frdrk RL20_MYCFE : 58- 62: krefr Klwi-A rinaa RL20_MYCFE : 110- 115: famli KiardA k RL20_ORYSA : 15- 20: rrrra KmrsfA snfrg RL20_PINTH : 4- 9: trv KrgyiA rkrrk RL20_PINTH : 14- 18: arkrr Kkil-A fvsgs RL20_PINTH : 29- 34: rgahs KlfrtA nqrka RL20_SOYBN : 7- 12: rkrrt KirlfA ssfrg RL20_SOYBN : 32- 37: tqqki KalvsA hrdrd RL20_SPIOL : 4- 9: trv KrgyiA rxrrk RL20_TOBAC : 4- 9: tri KrgyiA rrrrt RL20_TOBAC : 15- 20: rrrrt KirlfA ssfrg Number of patterns evaluated by Pratt:15 Total running time: 0 seconds