------------------------------------------------------------ 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 63 sequences from file RNASE_PANCREATIC PATTERN CONSERVATION: CM: min Nr of Seqs to Match 63 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 RNASE_PANCREATIC.pratt2 OP: PROSITE Pattern Format on ON: max number patterns 20 OA: max number Alignments 20 M: Print Patterns in sequences off Sequence lengths: ANGI_BOVIN 125 ANGI_CHICK 139 ANGI_HUMAN 147 ANGI_MOUSE 145 ANGI_PIG 123 ANGI_RABIT 125 ECP_HUMAN 160 LECS_RANJA 111 RN30_RANPI 104 RNBR_BOVIN 167 RNKD_BOVIN 127 RNKD_HUMAN 161 RNL1_PIG 34 RNL3_PIG 119 RNL4_BOVIN 119 RNL4_HUMAN 119 RNPA_CAVPO 124 RNPB_CAVPO 128 RNPL_RANCA 111 RNPO_RANCA 111 RNP_AEPME 124 RNP_ALCAA 124 RNP_ANTAM 124 RNP_BALAC 124 RNP_BOSTR 124 RNP_BOVIN 150 RNP_BUBAR 124 RNP_CAMDR 124 RNP_CAPCA 124 RNP_CAPHI 124 RNP_CEREL 124 RNP_CHESE 119 RNP_CHIBR 124 RNP_CHOHO 128 RNP_CONTA 124 RNP_CRILO 130 RNP_DAMDA 124 RNP_DAMKO 124 RNP_GALMU 124 RNP_GAZTH 124 RNP_GIRCA 124 RNP_HIPAM 124 RNP_HORSE 128 RNP_HUMAN 134 RNP_HYDHY 128 RNP_HYSCR 128 RNP_IGUIG 119 RNP_MACRU 122 RNP_MESAU 124 RNP_MOUSE 149 RNP_MYOCO 128 RNP_ODOVI 30 RNP_ONDZI 124 RNP_PIG 124 RNP_PREEN 128 RNP_PROGU 128 RNP_RANTA 124 RNP_RAT 152 RNP_SHEEP 124 RNP_SPAEH 125 RNP_TAUOR 124 RNS_BOVIN 150 RSFR_CHICK 139 Pratt run started at Thu Feb 6 21:06:50 1997 Best Patterns before refinement: fitness hits(seqs) Pattern 1: 8.3401 67( 63) F-x(3)-H 2: 7.3401 156( 63) K-x(1,3)-T Best Patterns (after refinement phase): fitness hits(seqs) Pattern A 1: 8.3401 67( 63) F-x(3)-H B 2: 7.3401 156( 63) K-x(1,3)-T Best patterns with alignements: fitness hits(seqs) Pattern A 1: 8.3401 67( 63) F-x(3)-H Occurences: 67(63) ANGI_BOVIN : 10- 14: yryih FltqH ydakp ANGI_CHICK : 30- 34: ptyqd FlrtH vdfpk ANGI_HUMAN : 33- 37: sryth FltqH ydakp ANGI_MOUSE : 33- 37: srytk FltqH hdakp ANGI_PIG : 9- 13: dryth FltqH ydakp ANGI_RABIT : 9- 13: srykh FltqH ydakp ECP_HUMAN : 38- 42: traqw FaiqH islnp LECS_RANJA : 6- 10: qnwak FqekH ipnts RN30_RANPI : 6- 10: qdwlt FqkkH itntr RNBR_BOVIN : 34- 38: saaak FrrqH mdsgs RNKD_BOVIN : 11- 15: tkarw FeiqH iqprl RNKD_HUMAN : 38- 42: twaqw FetqH inmts RNL1_PIG : 11- 15: traqw FtiqH iqpsp RNL3_PIG : 8- 12: rmyqr FlrqH vdpda RNL4_BOVIN : 8- 12: rmyqr FlrqH vdpde RNL4_HUMAN : 8- 12: gmyqr FlrqH vhpee RNPA_CAVPO : 8- 12: ssamk FerqH vdsgg RNPB_CAVPO : 8- 12: ssamk FqrqH mdpeg RNPL_RANCA : 6- 10: qnwak FkekH irsts RNPO_RANCA : 6- 10: qnwat FqqkH iintp RNP_AEPME : 8- 12: saaak FerqH mdsst RNP_ALCAA : 8- 12: saaak FerqH mdpsa RNP_ANTAM : 8- 12: taaak FerqH idsnp RNP_BALAC : 8- 12: spamk FqrqH mdsgn RNP_BOSTR : 8- 12: taaak FerqH mdsst RNP_BOVIN : 34- 38: taaak FerqH mdsst RNP_BUBAR : 8- 12: taaak FqrqH mdsst RNP_CAMDR : 8- 12: taaek FerqH mdsys RNP_CAPCA : 8- 12: saaak FerqH mdpsp RNP_CAPHI : 8- 12: saaak FerqH mdsst RNP_CEREL : 8- 12: saaak FerqH mdpst RNP_CHESE : 7- 11: tryek FlrqH vdypk RNP_CHIBR : 8- 12: ssamk FqrqH mdssg RNP_CHOHO : 8- 12: taamk FqrqH mdsgs RNP_CONTA : 8- 12: saaak FerqH mdsst RNP_CRILO : 14- 18: saamk FerqH mdstv RNP_CRILO : 121- 125: cegnp FvpvH fdatv RNP_DAMDA : 8- 12: saaak FerqH mdpsm RNP_DAMKO : 8- 12: saaak FzrzH mbsst RNP_GALMU : 8- 12: ssamk FqrqH mdsdg RNP_GAZTH : 8- 12: saaak FzrzH mbsst RNP_GIRCA : 8- 12: saaak FerqH idsst RNP_HIPAM : 8- 12: taaek FqrqH mdtss RNP_HORSE : 8- 12: spamk FerqH mdsgs RNP_HUMAN : 14- 18: srakk FqrqH mdsds RNP_HYDHY : 8- 12: ssamk FqrqH vdseg RNP_HYSCR : 8- 12: ssamk FerqH mdssg RNP_IGUIG : 6- 10: qdwss FqnkH idype RNP_MACRU : 7- 11: tpaek FqrqH mdteh RNP_MESAU : 8- 12: saamk FerqH mdstv RNP_MESAU : 115- 119: cegnp FvpvH fdasv RNP_MOUSE : 33- 37: saaqk FqrqH mdpdg RNP_MYOCO : 8- 12: ssakk FerqH mdsrg RNP_ODOVI : 8- 12: taaak FerqH mdpap RNP_ONDZI : 8- 12: tsaqk FerqH mdstg RNP_ONDZI : 115- 119: cegsp FvpvH fdasv RNP_PIG : 8- 12: spakk FqrqH mdpds RNP_PREEN : 8- 12: sraek FqrqH mdsgs RNP_PROGU : 8- 12: ssakk FqrqH idssg RNP_RANTA : 8- 12: saaak FerqH mdpsp RNP_RAT : 36- 40: ssadk FkrqH mdteg RNP_SHEEP : 8- 12: saaak FerqH mdsst RNP_SPAEH : 8- 12: ssaek FlrqH vdsid RNP_SPAEH : 116- 120: cegdp FvpvH ydasv RNP_TAUOR : 8- 12: taaak FerqH mdsst RNS_BOVIN : 34- 38: saaak FerqH mdsgn RSFR_CHICK : 30- 34: ptyqd FlykH mdfpk B 2: 7.3401 156( 63) K-x(1,3)-T Occurences: 156(63) ANGI_BOVIN : 41- 45: ltrpc KdrnT fihgn ANGI_CHICK : 65- 69: vhgrc KslnT fvhtd ANGI_HUMAN : 64- 68: ltspc KdinT fihgn ANGI_MOUSE : 32- 35: dsryt Kfl-T qhhda ANGI_MOUSE : 64- 68: ltspc KdvnT fihgn ANGI_MOUSE : 105- 107: qvttc Kh--T ggspr ANGI_PIG : 40- 44: ltrpc KevnT fihgt ANGI_RABIT : 7- 11: ddsry KhflT qhyda ANGI_RABIT : 40- 42: ltspc Kd--T ntfvh ANGI_RABIT : 40- 44: ltspc KdtnT fvhgn ECP_HUMAN : 4- 7: mvp Klf-T sqicl ECP_HUMAN : 65- 69: yrwrc KnqnT flrtt LECS_RANJA : 35- 39: vggqc KernT fiiss RN30_RANPI : 8- 12: wltfq KkhiT ntrdv RN30_RANPI : 9- 12: ltfqk Khi-T ntrdv RN30_RANPI : 31- 35: nlfhc KdknT fiysr RN30_RANPI : 33- 35: fhckd Kn--T fiysr RN30_RANPI : 55- 59: giias KnvlT tsefy RN30_RANPI : 80- 83: ckykl Kks-T nkfcv RN30_RANPI : 81- 83: kyklk Ks--T nkfcv RN30_RANPI : 85- 89: kkstn KfcvT cenqa RNBR_BOVIN : 67- 71: thgrc KpvnT fvhes RNBR_BOVIN : 87- 90: avcsq Kni-T ckngh RNBR_BOVIN : 102- 104: ncyqs Ks--T msitd RNBR_BOVIN : 130- 133: tsqkq Kyi-T vaceg RNKD_BOVIN : 3- 6: vp Kgl-T karwf RNKD_BOVIN : 38- 42: ytqhc KpenT flhnv RNKD_HUMAN : 4- 7: mvp Klf-T sqicl RNKD_HUMAN : 65- 69: yqrrc KnqnT flltt RNL1_PIG : 3- 6: ip Knl-T raqwf RNL3_PIG : 33- 35: mmqrr Km--T shyck RNL3_PIG : 40- 44: tshyc KrfnT fihed RNL3_PIG : 77- 79: hegvv Kv--T dcret RNL4_BOVIN : 33- 35: mmqrr Km--T shqck RNL4_BOVIN : 40- 44: tshqc KrfnT fihed RNL4_BOVIN : 97- 100: cryra Kas-T rrvvi RNL4_HUMAN : 33- 35: mmqrr Km--T lyhck RNL4_HUMAN : 40- 44: tlyhc KrfnT fihed RNL4_HUMAN : 77- 79: hegvv Kv--T dcrdt RNPA_CAVPO : 32- 36: nemmk KremT kdrck RNPA_CAVPO : 41- 45: tkdrc KpvnT fvhep RNPA_CAVPO : 66- 70: rnvsc KngqT ncyqs RNPB_CAVPO : 41- 45: tqgrc KpvnT fvhes RNPB_CAVPO : 66- 70: knvlc KngqT ncyqs RNPL_RANCA : 35- 39: vggkc KernT fiiss RNPL_RANCA : 60- 64: vspdr KelsT tsfkl RNPL_RANCA : 68- 71: sttsf Kln-T cirds RNPO_RANCA : 35- 39: vggqc KrvnT fiiss RNPO_RANCA : 49- 53: sattv KaicT gvinm RNP_AEPME : 41- 45: tqsrc KpvnT fvhes RNP_AEPME : 66- 70: knvac KngqT ncyqs RNP_AEPME : 98- 100: pncay Kt--T qakkh RNP_ALCAA : 41- 45: tqdrc KpvnT fvhes RNP_ALCAA : 98- 100: pncvy Kt--T qaekh RNP_ANTAM : 1- 3: Ke--T aaakf RNP_ANTAM : 41- 45: tqgrc KpvnT fvhes RNP_ANTAM : 66- 70: knvac KngqT ncyqs RNP_ANTAM : 98- 100: pncay Kt--T qakkh RNP_BALAC : 34- 36: mmmrr Km--T qgrck RNP_BALAC : 41- 45: tqgrc KpvnT fvhes RNP_BALAC : 66- 70: knvlc KngrT ncyes RNP_BOSTR : 1- 3: Ke--T aaakf RNP_BOSTR : 41- 45: tqnrc KpvbT fvhzs RNP_BOSTR : 66- 70: kbvac KbgzT bcyzs RNP_BOVIN : 27- 29: qpslg Ke--T aaakf RNP_BOVIN : 67- 71: tkdrc KpvnT fvhes RNP_BOVIN : 92- 96: knvac KngqT ncyqs RNP_BOVIN : 124- 126: pncay Kt--T qankh RNP_BUBAR : 1- 3: Ke--T aaakf RNP_BUBAR : 41- 45: tsdrc KpvnT fvhes RNP_BUBAR : 66- 70: envac KngqT ncyqs RNP_BUBAR : 98- 100: pncay Kt--T qankh RNP_CAMDR : 41- 45: tdgwc KpvnT fihes RNP_CAMDR : 61- 64: avcsq Ksv-T ckngq RNP_CAMDR : 66- 70: ksvtc KngqT nchqs RNP_CAPCA : 41- 45: tqdrc KpvnT fvhes RNP_CAPCA : 98- 100: pncvy Kt--T qaekh RNP_CAPHI : 41- 45: tqdrc KpvnT fvhes RNP_CAPHI : 66- 70: knvac KngzT bcyqs RNP_CAPHI : 98- 100: pncay Kt--T qaekh RNP_CEREL : 34- 36: mmqsr Km--T qdrck RNP_CEREL : 41- 45: tqdrc KpvnT fvhes RNP_CEREL : 98- 100: pncvy Ka--T qaekh RNP_CHESE : 41- 43: tspvc Kf--T ntfvh RNP_CHESE : 41- 45: tspvc KftnT fvhas RNP_CHIBR : 41- 45: tqgyc KpvnT fvhep RNP_CHOHO : 1- 3: Ke--T aamkf RNP_CHOHO : 41- 45: tqesc KpvnT fvhes RNP_CONTA : 41- 45: tqdrc KpvnT fvhep RNP_CONTA : 66- 70: knvac KngqT ncyqs RNP_CONTA : 98- 100: pncay Ka--T qakkh RNP_CRILO : 47- 51: tqgqc KpvnT fvhes RNP_DAMDA : 34- 36: mmqsr Km--T qdrck RNP_DAMDA : 41- 45: tqdrc KpvnT fvhes RNP_DAMDA : 98- 100: pncvy Ka--T qaekh RNP_DAMKO : 41- 45: tqdrc KpvbT fvhzs RNP_DAMKO : 66- 70: kbvac KbgzT bcyzs RNP_DAMKO : 98- 100: pbcay Kt--T qakkh RNP_GALMU : 41- 45: tqgrc KpvnT fvhep RNP_GALMU : 66- 70: knvpc KngqT ncyqs RNP_GAZTH : 41- 45: tqdrc KpvnT fvhes RNP_GAZTH : 66- 70: knvqc KngqT ncyqs RNP_GAZTH : 98- 100: pncay Kt--T qaqkh RNP_GIRCA : 41- 45: tqdrc KpvnT fvhes RNP_GIRCA : 66- 70: knvac KngqT ncyqs RNP_HIPAM : 1- 3: Ke--T aaekf RNP_HIPAM : 41- 45: tqdrc KpvnT fvhes RNP_HIPAM : 61- 64: avcsq Knv-T ckngq RNP_HIPAM : 66- 70: knvtc KngqT ncyqs RNP_HORSE : 41- 45: tqgwc KpvnT fvhep RNP_HORSE : 61- 64: aiclq Kni-T ckngq RNP_HUMAN : 47- 51: tqgrc KpvnT fvhep RNP_HUMAN : 68- 70: vcfqe Kv--T ckngq RNP_HYDHY : 34- 36: mmvrr Km--T qdrck RNP_HYDHY : 41- 45: tqdrc KpvnT fvhep RNP_HYDHY : 66- 70: knvpc KngqT ncyqs RNP_HYSCR : 41- 45: tqdrc KpvnT fvhep RNP_HYSCR : 66- 70: knvac KngqT ncyqs RNP_IGUIG : 38- 41: nlnpt Kck-T rntfv RNP_IGUIG : 40- 44: nptkc KtrnT fvhas RNP_IGUIG : 92- 96: apssc KyngT pgtkr RNP_MACRU : 40- 44: tsgrc KplnT fihep RNP_MACRU : 65- 69: envtc KngrT ncyks RNP_MESAU : 41- 45: tqgyc KpvnT fvhes RNP_MOUSE : 66- 70: tngsc KpvnT fvhep RNP_MOUSE : 123- 125: pncdy Kt--T qyqkh RNP_MYOCO : 41- 45: tqgrc KpvnT fvhep RNP_MYOCO : 66- 70: knvlc KngqT ncyqs RNP_ODOVI : 1- 3: Ke--T aaakf RNP_ONDZI : 1- 3: Ke--T saqkf RNP_ONDZI : 41- 45: tqgyc KpvnT fvhep RNP_PIG : 41- 45: tqgrc KpvnT fvhes RNP_PIG : 66- 70: invnc KngqT ncyqs RNP_PREEN : 41- 45: tqgsc KsvnT fvhep RNP_PREEN : 62- 64: vcfqe Kv--T ckngq RNP_PREEN : 66- 70: ekvtc KngqT ncfks RNP_PROGU : 41- 45: tqerc KpvnT fvhep RNP_RANTA : 41- 45: tqdrc KpvnT fvhes RNP_RANTA : 98- 100: pncvy Kt--T qaekh RNP_RAT : 48- 52: tegps KsspT ycnqm RNP_RAT : 69- 73: tkgsc KpvnT fvhep RNP_RAT : 102- 106: rnnch KsssT lritd RNP_SHEEP : 41- 45: tqdrc KpvnT fvhes RNP_SHEEP : 66- 70: knvac KngqT ncyqs RNP_SHEEP : 98- 100: pncay Kt--T qaekh RNP_SPAEH : 42- 46: tkgsc KpvnT fvhep RNP_TAUOR : 1- 3: Ke--T aaakf RNP_TAUOR : 41- 45: tkdrc KpvnT fvhzs RNP_TAUOR : 66- 70: kbvac KbgzT bcyzs RNP_TAUOR : 98- 100: pbcay Kt--T zazkh RNS_BOVIN : 60- 62: mmccr Km--T qgkck RNS_BOVIN : 67- 71: tqgkc KpvnT fvhes RNS_BOVIN : 87- 90: avcsq Kkv-T ckngq RNS_BOVIN : 88- 90: vcsqk Kv--T ckngq RNS_BOVIN : 92- 96: kkvtc KngqT ncyqs RNS_BOVIN : 102- 104: ncyqs Ks--T mritd RNS_BOVIN : 124- 126: pncay Kt--T qvekh RSFR_CHICK : 65- 69: ahgrc KsfnT fvhtd Number of patterns evaluated by Pratt:2 Total running time: 1 seconds