------------------------------------------------------------ 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 ANTENNA_COMP_ALPHA 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 ANTENNA_COMP_ALPHA.pratt2 OP: PROSITE Pattern Format on ON: max number patterns 20 OA: max number Alignments 20 M: Print Patterns in sequences off Sequence lengths: LHA1_ECTHA 46 LHA1_ECTHL 52 LHA1_RHOAC 53 LHA1_RHOCA 58 LHA1_RHOPA 59 LHA1_RHOSH 58 LHA2_ECTHA 47 LHA2_ECTHL 65 LHA2_RHOAC 53 LHA2_RHOCA 60 LHA2_RHOPA 66 LHA2_RHOSH 54 LHA3_ECTHA 49 LHA3_RHOAC 53 LHA3_RHOPA 65 LHA4_RHOAC 53 LHA4_RHOPA 59 LHA5_RHOPA 53 LHA6_RHOAC 50 LHA7_RHOAC 49 LHA_CHLAU 57 LHA_ERYSP 52 LHA_RHOMA 52 LHA_RHORU 62 LHA_RHOVI 68 Pratt run started at Thu Feb 6 18:52:01 1997 Best Patterns before refinement: fitness hits(seqs) Pattern 1: 7.3401 25( 25) H-x(2,4)-L 2: 7.3401 50( 25) L-x(1,3)-V Best Patterns (after refinement phase): fitness hits(seqs) Pattern A 1: 7.3401 25( 25) H-x(2,4)-L B 2: 7.3401 50( 25) L-x(1,3)-V Best patterns with alignements: fitness hits(seqs) Pattern A 1: 7.3401 25( 25) H-x(2,4)-L Occurences: 25(25) LHA1_ECTHA : 29- 32: lalvi Hfi--L lstdr LHA1_ECTHA : 29- 33: lalvi Hfil-L stdrf LHA1_ECTHL : 29- 32: ialti Hvi--L mtter LHA1_RHOAC : 31- 35: tallv Haav-L thttw LHA1_RHOCA : 32- 35: lavli Hli--L lstpa LHA1_RHOCA : 32- 36: lavli Hlil-L stpaf LHA1_RHOPA : 31- 35: iailv Hfav-L shttw LHA1_RHOSH : 32- 35: lavmi Hli--L lstps LHA1_RHOSH : 32- 36: lavmi Hlil-L stpsy LHA2_ECTHA : 29- 32: lalli Hfi--L lstes LHA2_ECTHA : 29- 33: lalli Hfil-L stesf LHA2_ECTHL : 18- 23: tavgf HiffaL iafav LHA2_RHOAC : 31- 35: tallv Hlav-L thttw LHA2_RHOCA : 31- 34: aaliv Hag--L ltntt LHA2_RHOCA : 31- 35: aaliv Hagl-L tnttw LHA2_RHOPA : 31- 35: iailv Hyav-L snttw LHA2_RHOSH : 31- 35: asvvi Haav-L ttttw LHA3_ECTHA : 31- 35: iallv Hgai-L tntsw LHA3_RHOAC : 31- 35: iailv Haav-L shttw LHA3_RHOPA : 31- 35: iafav Hfav-L entsw LHA4_RHOAC : 31- 35: iailv Hlai-L shttw LHA4_RHOPA : 31- 35: mvflv Hfav-L thttw LHA5_RHOPA : 31- 35: iailv Hfav-L snttw LHA6_RHOAC : 29- 33: lalii Hfia-L stdrf LHA7_RHOAC : 29- 33: lglii Hfis-L stdrf LHA_CHLAU : 26- 30: valli Hfiv-L sspey LHA_ERYSP : 32- 36: laami Hlvv-L ssgln LHA_RHOMA : 29- 32: lalli Hfi--L lstdr LHA_RHOMA : 29- 33: lalli Hfil-L stdrf LHA_RHORU : 29- 32: lalli Hfi--L lster LHA_RHORU : 29- 33: lalli Hfil-L sterf LHA_RHOVI : 36- 39: ialli Hfg--L lstdr LHA_RHOVI : 36- 40: ialli Hfgl-L stdrl B 2: 7.3401 50( 25) L-x(1,3)-V Occurences: 50(25) LHA1_ECTHA : 21- 23: gifsw La--V lalvi LHA1_ECTHA : 24- 27: swlav Lal-V ihfil LHA1_ECTHL : 26- 30: liiia LtihV ilmtt LHA1_RHOAC : 20- 23: glplm Lga-V aital LHA1_RHOAC : 28- 30: vaita Ll--V haavl LHA1_RHOAC : 45- 49: wyaaf LqggV kkaa LHA1_RHOCA : 26- 29: gvflf Lla-V lihli LHA1_RHOCA : 27- 29: vflfl La--V lihli LHA1_RHOCA : 44- 46: pafnw Lt--V atakh LHA1_RHOPA : 19- 23: vglpl LlgsV tviai LHA1_RHOPA : 20- 23: glpll Lgs-V tviai LHA1_RHOSH : 26- 29: gvflf Lla-V mihli LHA1_RHOSH : 27- 29: vflfl La--V mihli LHA2_ECTHA : 16- 19: rrtvv Lah-V gmavl LHA2_ECTHL : 4- 8: mwk LwkfV dfrmt LHA2_RHOAC : 19- 23: vglpl LlgsV aital LHA2_RHOAC : 20- 23: glpll Lgs-V aital LHA2_RHOAC : 28- 30: vaita Ll--V hlavl LHA2_RHOAC : 32- 34: allvh La--V lthtt LHA2_RHOCA : 20- 23: gipli Lga-V avaal LHA2_RHOCA : 28- 30: vavaa Li--V hagll LHA2_RHOPA : 19- 23: vglpl LlgsV tviai LHA2_RHOPA : 20- 23: glpll Lgs-V tviai LHA2_RHOSH : 8- 10: ngkiw Lv--V kptvg LHA2_RHOSH : 20- 24: gvplf LsaaV iasvv LHA3_ECTHA : 8- 10: qariw Lv--V kpsvg LHA3_ECTHA : 18- 22: svglp LllgV vllia LHA3_ECTHA : 19- 22: vglpl Llg-V vllia LHA3_ECTHA : 19- 23: vglpl LlgvV llial LHA3_ECTHA : 20- 22: glpll Lg--V vllia LHA3_ECTHA : 20- 23: glpll Lgv-V llial LHA3_ECTHA : 28- 30: vllia Ll--V hgail LHA3_RHOAC : 19- 23: vglpl LlgsV tviai LHA3_RHOAC : 20- 23: glpll Lgs-V tviai LHA3_RHOPA : 19- 23: vglpl LlgsV aaiaf LHA3_RHOPA : 20- 23: glpll Lgs-V aaiaf LHA4_RHOAC : 19- 23: igipa LlgsV tviai LHA4_RHOAC : 20- 23: gipal Lgs-V tviai LHA4_RHOPA : 19- 23: vglpl LlgsV aimvf LHA4_RHOPA : 20- 23: glpll Lgs-V aimvf LHA5_RHOPA : 19- 23: vglpl LlgsV tviai LHA5_RHOPA : 20- 23: glpll Lgs-V tviai LHA6_RHOAC : 21- 23: alsaf Lf--V lalii LHA7_RHOAC : 21- 23: alsaf Lf--V lglii LHA_CHLAU : 17- 20: vifti Lgf-V valli LHA_CHLAU : 17- 21: vifti LgfvV allih LHA_ERYSP : 33- 35: aamih Lv--V lssgl LHA_RHOMA : 21- 23: alftf Lf--V lalli LHA_RHORU : 21- 23: glatf Lf--V lalli LHA_RHORU : 60- 62: mpssd La--V LHA_RHOVI : 24- 26: rvlta Lf--V yltvi LHA_RHOVI : 28- 30: alfvy Lt--V ialli LHA_RHOVI : 60- 62: pkaas Lv--V vppav LHA_RHOVI : 60- 63: pkaas Lvv-V ppavg Number of patterns evaluated by Pratt:3 Total running time: 0 seconds