------------------------------------------------------------ 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 4 sequences from file RNA_POL_N_8KD PATTERN CONSERVATION: CM: min Nr of Seqs to Match 4 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 RNA_POL_N_8KD.pratt2 OP: PROSITE Pattern Format on ON: max number patterns 20 OA: max number Alignments 20 M: Print Patterns in sequences off Sequence lengths: RPBX_ASFB7 80 RPBX_YEAST 70 RPON_HALMA 66 RPON_SULAC 66 Pratt run started at Thu Feb 6 21:08:42 1997 Best Patterns before refinement: fitness hits(seqs) Pattern 1: 28.1904 4( 4) L-G-x(2,3)-R-x-C-C-R-x(2,3)-L 2: 28.1904 4( 4) L-x(2,3)-L-G-x(2,3)-R-x-C-C-R 3: 25.0203 4( 4) M-x(2)-P-x(2)-C-F-x-C-G 4: 24.5203 5( 4) M-x(1,2)-P-x(2)-C-F-x-C-G 5: 24.0203 4( 4) G-x(2,3)-R-x-C-C-R-x(2,3)-L 6: 24.0203 4( 4) E-x(2,3)-L-x(2,3)-L-G-x(5)-C-x-R 7: 20.8503 4( 4) P-x(2)-C-F-x-C-G 8: 20.3503 4( 4) R-x-C-C-R-x(2,3)-L 9: 16.6802 4( 4) C-F-x-C-G 10: 16.1802 4( 4) C-C-R-x(2,3)-L 11: 15.1802 4( 4) E-x(0,1)-K-x-L-x(2,4)-L 12: 15.1802 4( 4) P-x-R-x(0,1)-C-x(0,2)-C 13: 14.6802 4( 4) K-x-L-x(2,4)-L-x(2,4)-R 14: 12.5102 4( 4) F-x-C-G 15: 12.0102 4( 4) C-R-x(2,3)-L 16: 12.0102 7( 4) C-x(0,1)-R-x(2)-L 17: 12.0102 6( 4) C-x-R-x(1,2)-L 18: 11.5102 4( 4) L-x(1,3)-E-L 19: 11.5102 5( 4) E-x(0,2)-D-x(4)-L 20: 11.0102 4( 4) M-x(0,1)-L-x(0,2)-V Best Patterns (after refinement phase): fitness hits(seqs) Pattern A 1: 56.1117 4( 4) M-[ILM]-[IV]-P-[IV]-x-C-F-[ST]-C-G-x-[PV]-[IV]-[AG]-[DET]-x(2)-[AE]-x-[FY] B 2: 49.4979 5( 4) M-x(1,2)-P-[IV]-x-C-F-[ST]-C-G-x-[PV]-[IV]-[AG]-[DET]-x(2)-[AE]-x-[FY] C 3: 45.8279 4( 4) P-[IV]-x-C-F-[ST]-C-G-x-[PV]-[IV]-[AG]-[DET]-x(2)-[AE]-x-[FY] D 4: 42.7116 4( 4) L-x(2,3)-L-G-x(2,3)-R-x-C-C-R-x(2)-[IL]-[ILV]-[ST]-x(2)-[DN]-x(2)-[DEKR] E 5: 38.4329 4( 4) C-F-[ST]-C-G-x-[PV]-[IV]-[AG]-[DET]-x(2)-[AE]-x-[FY] F 6: 34.2629 4( 4) F-[ST]-C-G-x-[PV]-[IV]-[AG]-[DET]-x(2)-[AE]-x-[FY] G 7: 33.1103 4( 4) E-x(2,3)-L-x(2,3)-L-G-[ILV]-x(3)-[CV]-C-x-R-x(2)-[LV] H 8: 29.6004 4( 4) P-[IMV]-R-x(0,1)-C-x(0,2)-C-x(3)-[LV]-[AGI]-[DET]-x(2)-[DE] I 9: 28.1904 4( 4) L-G-x(2,3)-R-x-C-C-R-x(2,3)-L J 10: 24.0203 4( 4) G-x(2,3)-R-x-C-C-R-x(2,3)-L K 11: 20.3503 4( 4) R-x-C-C-R-x(2,3)-L L 12: 20.1224 5( 4) E-x(0,2)-D-x(3)-[AV]-L-[DGST]-x-[LP] M 13: 18.4088 4( 4) E-x(0,1)-K-x-L-x(2,4)-L-[EG] N 14: 16.1802 4( 4) C-C-R-x(2,3)-L O 15: 15.6802 4( 4) L-x(2,3)-L-G-x(2,3)-R P 16: 14.6802 4( 4) K-x-L-x(2,4)-L-x(2,4)-R Q 17: 13.2150 4( 4) M-x(0,1)-L-x(0,2)-V-[DNSV] R 18: 12.5102 4( 4) F-x-C-G S 19: 12.0102 3( 3) L-G-x(2,3)-R T 20: 12.0102 4( 4) C-R-x(2,3)-L Best patterns with alignements: fitness hits(seqs) Pattern A 1: 56.1117 4( 4) M-[ILM]-[IV]-P-[IV]-x-C-F-[ST]-C-G-x-[PV]-[IV]-[AG]-[DET]-x(2)-[AE]-x-[FY] Occurences: 4(4) RPBX_ASFB7 : 1- 21: MLIPVvCFTCGfPIGTyaAiF dkart RPBX_YEAST : 1- 21: MIVPVrCFSCGkVVGDkwEsY lnllq RPON_HALMA : 1- 21: MMVPVrCFTCGnVVGEhwEeF kartr RPON_SULAC : 1- 21: MIIPIrCFTCGaVVADkwEpF snrvm B 2: 49.4979 5( 4) M-x(1,2)-P-[IV]-x-C-F-[ST]-C-G-x-[PV]-[IV]-[AG]-[DET]-x(2)-[AE]-x-[FY] Occurences: 5(4) RPBX_ASFB7 : 1- 21: MliPVvCFTCGfPIGTyaAiF dkart RPBX_YEAST : 1- 21: MivPVrCFSCGkVVGDkwEsY lnllq RPON_HALMA : 1- 21: MmvPVrCFTCGnVVGEhwEeF kartr RPON_HALMA : 2- 21: m Mv-PVrCFTCGnVVGEhwEeF kartr RPON_SULAC : 1- 21: MiiPIrCFTCGaVVADkwEpF snrvm C 3: 45.8279 4( 4) P-[IV]-x-C-F-[ST]-C-G-x-[PV]-[IV]-[AG]-[DET]-x(2)-[AE]-x-[FY] Occurences: 4(4) RPBX_ASFB7 : 4- 21: mli PVvCFTCGfPIGTyaAiF dkart RPBX_YEAST : 4- 21: miv PVrCFSCGkVVGDkwEsY lnllq RPON_HALMA : 4- 21: mmv PVrCFTCGnVVGEhwEeF kartr RPON_SULAC : 4- 21: mii PIrCFTCGaVVADkwEpF snrvm D 4: 42.7116 4( 4) L-x(2,3)-L-G-x(2,3)-R-x-C-C-R-x(2)-[IL]-[ILV]-[ST]-x(2)-[DN]-x(2)-[DEKR] Occurences: 4(4) RPBX_ASFB7 : 54- 78: ielkd LitaLGipmRvCCRthLITtlDyrK yy RPBX_YEAST : 36- 58: degta Lsr-LGlk-RyCCRrmILThvDliE kflry RPON_HALMA : 38- 60: dpekv Lde-LGve-RhCCRrmLVShkDlvD ivspy RPON_SULAC : 35- 57: dpekv Lte-LGvn-RyCCRrmLLShvNiiR eiihy E 5: 38.4329 4( 4) C-F-[ST]-C-G-x-[PV]-[IV]-[AG]-[DET]-x(2)-[AE]-x-[FY] Occurences: 4(4) RPBX_ASFB7 : 7- 21: lipvv CFTCGfPIGTyaAiF dkart RPBX_YEAST : 7- 21: ivpvr CFSCGkVVGDkwEsY lnllq RPON_HALMA : 7- 21: mvpvr CFTCGnVVGEhwEeF kartr RPON_SULAC : 7- 21: iipir CFTCGaVVADkwEpF snrvm F 6: 34.2629 4( 4) F-[ST]-C-G-x-[PV]-[IV]-[AG]-[DET]-x(2)-[AE]-x-[FY] Occurences: 4(4) RPBX_ASFB7 : 8- 21: ipvvc FTCGfPIGTyaAiF dkart RPBX_YEAST : 8- 21: vpvrc FSCGkVVGDkwEsY lnllq RPON_HALMA : 8- 21: vpvrc FTCGnVVGEhwEeF kartr RPON_SULAC : 8- 21: ipirc FTCGaVVADkwEpF snrvm G 7: 33.1103 4( 4) E-x(2,3)-L-x(2,3)-L-G-[ILV]-x(3)-[CV]-C-x-R-x(2)-[LV] Occurences: 4(4) RPBX_ASFB7 : 50- 70: aslqi ElkdLitaLGIpmrVCcRthL ittld RPBX_YEAST : 32- 51: edeld EgtaLsr-LGLkryCCrRmiL thvdl RPON_HALMA : 35- 53: epedp Ekv-Lde-LGVerhCCrRmlV shkdl RPON_SULAC : 32- 50: ggedp Ekv-Lte-LGVnryCCrRmlL shvni H 8: 29.6004 4( 4) P-[IMV]-R-x(0,1)-C-x(0,2)-C-x(3)-[LV]-[AGI]-[DET]-x(2)-[DE] Occurences: 4(4) RPBX_ASFB7 : 61- 75: talgi PMRvC--CrthLITtlD yrkyy RPBX_YEAST : 4- 19: miv PVR-CfsCgkvVGDkwE sylnl RPON_HALMA : 4- 19: mmv PVR-CftCgnvVGEhwE efkar RPON_SULAC : 4- 19: mii PIR-CftCgavVADkwE pfsnr I 9: 28.1904 4( 4) L-G-x(2,3)-R-x-C-C-R-x(2,3)-L Occurences: 4(4) RPBX_ASFB7 : 58- 70: dlita LGipmRvCCRth-L ittld RPBX_YEAST : 39- 51: talsr LGlk-RyCCRrmiL thvdl RPON_HALMA : 41- 52: kvlde LGve-RhCCRrm-L vshkd RPON_SULAC : 38- 49: kvlte LGvn-RyCCRrm-L lshvn RPON_SULAC : 38- 50: kvlte LGvn-RyCCRrmlL shvni J 10: 24.0203 4( 4) G-x(2,3)-R-x-C-C-R-x(2,3)-L Occurences: 4(4) RPBX_ASFB7 : 59- 70: lital GipmRvCCRth-L ittld RPBX_YEAST : 40- 51: alsrl Glk-RyCCRrmiL thvdl RPON_HALMA : 42- 52: vldel Gve-RhCCRrm-L vshkd RPON_SULAC : 39- 49: vltel Gvn-RyCCRrm-L lshvn RPON_SULAC : 39- 50: vltel Gvn-RyCCRrmlL shvni K 11: 20.3503 4( 4) R-x-C-C-R-x(2,3)-L Occurences: 4(4) RPBX_ASFB7 : 63- 70: lgipm RvCCRth-L ittld RPBX_YEAST : 43- 51: rlglk RyCCRrmiL thvdl RPON_HALMA : 45- 52: elgve RhCCRrm-L vshkd RPON_SULAC : 42- 49: elgvn RyCCRrm-L lshvn RPON_SULAC : 42- 50: elgvn RyCCRrmlL shvni L 12: 20.1224 5( 4) E-x(0,2)-D-x(3)-[AV]-L-[DGST]-x-[LP] Occurences: 5(4) RPBX_ASFB7 : 50- 61: aslqi ElkDlitALGiP mrvcc RPBX_YEAST : 29- 39: llqed El-DegtALSrL glkry RPON_HALMA : 30- 41: treae EpeDpekVLDeL gverh RPON_HALMA : 32- 41: eaeep E--DpekVLDeL gverh RPON_SULAC : 29- 38: rvmgg E--DpekVLTeL gvnry M 13: 18.4088 4( 4) E-x(0,1)-K-x-L-x(2,4)-L-[EG] Occurences: 4(4) RPBX_ASFB7 : 50- 59: aslqi ElKdLita-LG ipmrv RPBX_YEAST : 58- 67: hvdli E-KfLrynpLE krd RPON_HALMA : 35- 42: epedp E-KvLde--LG verhc RPON_SULAC : 32- 39: ggedp E-KvLte--LG vnryc N 14: 16.1802 4( 4) C-C-R-x(2,3)-L Occurences: 4(4) RPBX_ASFB7 : 65- 70: ipmrv CCRth-L ittld RPBX_YEAST : 45- 51: glkry CCRrmiL thvdl RPON_HALMA : 47- 52: gverh CCRrm-L vshkd RPON_SULAC : 44- 49: gvnry CCRrm-L lshvn RPON_SULAC : 44- 50: gvnry CCRrmlL shvni O 15: 15.6802 4( 4) L-x(2,3)-L-G-x(2,3)-R Occurences: 4(4) RPBX_ASFB7 : 54- 63: ielkd LitaLGipmR vccrt RPBX_YEAST : 36- 43: degta Lsr-LGlk-R yccrr RPON_HALMA : 38- 45: dpekv Lde-LGve-R hccrr RPON_SULAC : 35- 42: dpekv Lte-LGvn-R yccrr P 16: 14.6802 4( 4) K-x-L-x(2,4)-L-x(2,4)-R Occurences: 4(4) RPBX_ASFB7 : 52- 63: lqiel KdLita-LgipmR vccrt RPBX_YEAST : 59- 69: vdlie KfLrynpLek--R d RPON_HALMA : 36- 45: pedpe KvLde--Lgve-R hccrr RPON_SULAC : 33- 42: gedpe KvLte--Lgvn-R yccrr Q 17: 13.2150 4( 4) M-x(0,1)-L-x(0,2)-V-[DNSV] Occurences: 4(4) RPBX_ASFB7 : 1- 6: M-LipVV cftcg RPBX_YEAST : 49- 55: yccrr MiLthVD liekf RPON_HALMA : 51- 54: hccrr M-L--VS hkdlv RPON_SULAC : 48- 54: yccrr MlLshVN iirei R 18: 12.5102 4( 4) F-x-C-G Occurences: 4(4) RPBX_ASFB7 : 8- 11: ipvvc FtCG fpigt RPBX_YEAST : 8- 11: vpvrc FsCG kvvgd RPON_HALMA : 8- 11: vpvrc FtCG nvvge RPON_SULAC : 8- 11: ipirc FtCG avvad S 19: 12.0102 3( 3) L-G-x(2,3)-R Occurences: 3(3) RPBX_ASFB7 : 58- 63: dlita LGipmR vccrt RPON_HALMA : 41- 45: kvlde LGve-R hccrr RPON_SULAC : 38- 42: kvlte LGvn-R yccrr T 20: 12.0102 4( 4) C-R-x(2,3)-L Occurences: 4(4) RPBX_ASFB7 : 66- 70: pmrvc CRth-L ittld RPBX_YEAST : 46- 51: lkryc CRrmiL thvdl RPON_HALMA : 48- 52: verhc CRrm-L vshkd RPON_SULAC : 45- 49: vnryc CRrm-L lshvn RPON_SULAC : 45- 50: vnryc CRrmlL shvni Number of patterns evaluated by Pratt:182 Total running time: 0 seconds