globStart = 3 globStop = 3 The best result of the first generation: Group 1: WQHYSECUL Group 2: MXVKTINDAFR Group 3: G Group 4: P No Chronology Order ch_p_sim 0 : VAUDWMIKTFYXGQPHNCRESL 13 40.7996 1 : MXUFIKWTYNGQPAVHDCRESL 0 42.0943 2 : IMUKFWXTYNGQPAVHDCRESL 4 41.6668 3 : LSKTIMFNXWRPUYADVCHGQE 15 40.4199 4 : FKUMIWXTYNGQPAVHDCRESL 2 41.6933 5 : ADWUVMIKTFYXGQPHNCRESL 9 41.0307 6 : TKUFMIWYXNGQPAVHDCRESL 5 41.5804 7 : PRUTKIMFWNYXGHAVCDQESL 18 40.1278 8 : EQKTIMFXNWUGAVYPHDCRSL 14 40.6098 9 : DAWUVMIKTFYXGQPHNCRESL 10 41.0307 10: KFUMIWXTYNGQPAVHDCRESL 3 41.6933 11: NKUFMIWXTYGQPAVHDCRESL 6 41.4887 12: QHKTIMFWXNPUAGYVDCRESL 11 40.8059 13: HQKTIMFWXNPUAGYVDCRESL 12 40.8059 14: YFKMIXUTWNGQPAVHDCRESL 20 20.813 15: GSTIKMAFXNWVYRPCHDUQEL 19 39.6443 16: SLKTIMFNXWRPUYADVCHGQE 16 40.4199 17: RKUIMTFWYNXGHAPVCDQESL 8 41.0676 18: WFKMIUXTYNGQPAVHDCRESL 21 20.6765 19: USKTIMFXNWAYVCRPDHQGEL 17 40.3897 20: CWIKMFTYXNUAQPVHGDRESL 7 41.0739 21: XMUFIKWTYNGQPAVHDCRESL 1 42.0943 Max of ch_p_sims: 42.0943 The initial amino acid was found to be: M or X -------------------------------------------------------------------------- The best result after mating: Group 1: WQHYSECUL Group 2: MXVKTINDAFR Group 3: G Group 4: P No Chronology Order ch_p_sim 0 : VAUDWMIKTFYXGQPHNCRESL 13 40.7996 1 : MXUFIKWTYNGQPAVHDCRESL 0 42.0943 2 : IMUKFWXTYNGQPAVHDCRESL 4 41.6668 3 : LSKTIMFNXWRPUYADVCHGQE 15 40.4199 4 : FKUMIWXTYNGQPAVHDCRESL 2 41.6933 5 : ADWUVMIKTFYXGQPHNCRESL 9 41.0307 6 : TKUFMIWYXNGQPAVHDCRESL 5 41.5804 7 : PRUTKIMFWNYXGHAVCDQESL 18 40.1278 8 : EQKTIMFXNWUGAVYPHDCRSL 14 40.6098 9 : DAWUVMIKTFYXGQPHNCRESL 10 41.0307 10: KFUMIWXTYNGQPAVHDCRESL 3 41.6933 11: NKUFMIWXTYGQPAVHDCRESL 6 41.4887 12: QHKTIMFWXNPUAGYVDCRESL 11 40.8059 13: HQKTIMFWXNPUAGYVDCRESL 12 40.8059 14: YFKMIXUTWNGQPAVHDCRESL 20 20.813 15: GSTIKMAFXNWVYRPCHDUQEL 19 39.6443 16: SLKTIMFNXWRPUYADVCHGQE 16 40.4199 17: RKUIMTFWYNXGHAPVCDQESL 8 41.0676 18: WFKMIUXTYNGQPAVHDCRESL 21 20.6765 19: USKTIMFXNWAYVCRPDHQGEL 17 40.3897 20: CWIKMFTYXNUAQPVHGDRESL 7 41.0739 21: XMUFIKWTYNGQPAVHDCRESL 1 42.0943 Max of ch_p_sims: 42.0943 The initial amino acid was found to be: M or X -------------------------------------------------------------------------- The best result after mutations: Group 1: WQHYSECUL Group 2: MXVKTINDAFR Group 3: G Group 4: P No Chronology Order ch_p_sim 0 : VAUDWMIKTFYXGQPHNCRESL 13 40.7996 1 : MXUFIKWTYNGQPAVHDCRESL 0 42.0943 2 : IMUKFWXTYNGQPAVHDCRESL 4 41.6668 3 : LSKTIMFNXWRPUYADVCHGQE 15 40.4199 4 : FKUMIWXTYNGQPAVHDCRESL 2 41.6933 5 : ADWUVMIKTFYXGQPHNCRESL 9 41.0307 6 : TKUFMIWYXNGQPAVHDCRESL 5 41.5804 7 : PRUTKIMFWNYXGHAVCDQESL 18 40.1278 8 : EQKTIMFXNWUGAVYPHDCRSL 14 40.6098 9 : DAWUVMIKTFYXGQPHNCRESL 10 41.0307 10: KFUMIWXTYNGQPAVHDCRESL 3 41.6933 11: NKUFMIWXTYGQPAVHDCRESL 6 41.4887 12: QHKTIMFWXNPUAGYVDCRESL 11 40.8059 13: HQKTIMFWXNPUAGYVDCRESL 12 40.8059 14: YFKMIXUTWNGQPAVHDCRESL 20 20.813 15: GSTIKMAFXNWVYRPCHDUQEL 19 39.6443 16: SLKTIMFNXWRPUYADVCHGQE 16 40.4199 17: RKUIMTFWYNXGHAPVCDQESL 8 41.0676 18: WFKMIUXTYNGQPAVHDCRESL 21 20.6765 19: USKTIMFXNWAYVCRPDHQGEL 17 40.3897 20: CWIKMFTYXNUAQPVHGDRESL 7 41.0739 21: XMUFIKWTYNGQPAVHDCRESL 1 42.0943 Max of ch_p_sims: 42.0943 The initial amino acid was found to be: M or X -------------------------------------------------------------------------- The best result after mating: Group 1: WQHYSECUL Group 2: MXVKTINDAFR Group 3: G Group 4: P No Chronology Order ch_p_sim 0 : VAUDWMIKTFYXGQPHNCRESL 13 40.7996 1 : MXUFIKWTYNGQPAVHDCRESL 0 42.0943 2 : IMUKFWXTYNGQPAVHDCRESL 4 41.6668 3 : LSKTIMFNXWRPUYADVCHGQE 15 40.4199 4 : FKUMIWXTYNGQPAVHDCRESL 2 41.6933 5 : ADWUVMIKTFYXGQPHNCRESL 9 41.0307 6 : TKUFMIWYXNGQPAVHDCRESL 5 41.5804 7 : PRUTKIMFWNYXGHAVCDQESL 18 40.1278 8 : EQKTIMFXNWUGAVYPHDCRSL 14 40.6098 9 : DAWUVMIKTFYXGQPHNCRESL 10 41.0307 10: KFUMIWXTYNGQPAVHDCRESL 3 41.6933 11: NKUFMIWXTYGQPAVHDCRESL 6 41.4887 12: QHKTIMFWXNPUAGYVDCRESL 11 40.8059 13: HQKTIMFWXNPUAGYVDCRESL 12 40.8059 14: YFKMIXUTWNGQPAVHDCRESL 20 20.813 15: GSTIKMAFXNWVYRPCHDUQEL 19 39.6443 16: SLKTIMFNXWRPUYADVCHGQE 16 40.4199 17: RKUIMTFWYNXGHAPVCDQESL 8 41.0676 18: WFKMIUXTYNGQPAVHDCRESL 21 20.6765 19: USKTIMFXNWAYVCRPDHQGEL 17 40.3897 20: CWIKMFTYXNUAQPVHGDRESL 7 41.0739 21: XMUFIKWTYNGQPAVHDCRESL 1 42.0943 Max of ch_p_sims: 42.0943 The initial amino acid was found to be: M or X -------------------------------------------------------------------------- The best result after mutations: Group 1: WQHYSECUL Group 2: MXVKTINDAFR Group 3: G Group 4: P No Chronology Order ch_p_sim 0 : VAUDWMIKTFYXGQPHNCRESL 13 40.7996 1 : MXUFIKWTYNGQPAVHDCRESL 0 42.0943 2 : IMUKFWXTYNGQPAVHDCRESL 4 41.6668 3 : LSKTIMFNXWRPUYADVCHGQE 15 40.4199 4 : FKUMIWXTYNGQPAVHDCRESL 2 41.6933 5 : ADWUVMIKTFYXGQPHNCRESL 9 41.0307 6 : TKUFMIWYXNGQPAVHDCRESL 5 41.5804 7 : PRUTKIMFWNYXGHAVCDQESL 18 40.1278 8 : EQKTIMFXNWUGAVYPHDCRSL 14 40.6098 9 : DAWUVMIKTFYXGQPHNCRESL 10 41.0307 10: KFUMIWXTYNGQPAVHDCRESL 3 41.6933 11: NKUFMIWXTYGQPAVHDCRESL 6 41.4887 12: QHKTIMFWXNPUAGYVDCRESL 11 40.8059 13: HQKTIMFWXNPUAGYVDCRESL 12 40.8059 14: YFKMIXUTWNGQPAVHDCRESL 20 20.813 15: GSTIKMAFXNWVYRPCHDUQEL 19 39.6443 16: SLKTIMFNXWRPUYADVCHGQE 16 40.4199 17: RKUIMTFWYNXGHAPVCDQESL 8 41.0676 18: WFKMIUXTYNGQPAVHDCRESL 21 20.6765 19: USKTIMFXNWAYVCRPDHQGEL 17 40.3897 20: CWIKMFTYXNUAQPVHGDRESL 7 41.0739 21: XMUFIKWTYNGQPAVHDCRESL 1 42.0943 Max of ch_p_sims: 42.0943 The initial amino acid was found to be: M or X -------------------------------------------------------------------------- 0 input database // 0=Leipzig, 1=UCSC, 2=Poznan, 3=testLeipzig, 4=testUCSC D acidType // R means tRNAs, D means tRNA genes (=tDNAs) 1 ARCHAEA_ARE_INCLUDED // 1 = yes, 0 = no 1 BACTERIA_ARE_INCLUDED 1 EUKARYOTES_ARE_INCLUDED 0 VIRUSES_ARE_INCLUDED // only for tRNA genes of database 0 0 SPECIES_ARE_SELECTED 0 numOfSpecies species ----------------------------------------------------------- 4 function // 0=FindLUCA,1=FindScores,2=FindNonStartAAs,3=FindNonGlobAAs,4=GlobOptimizeGroups,5=TestData 1 FIRST_AA_IS_TESTED // 1=all AAs are tested at the 1st position, 0=>see the next row M firstAA // only when FIRST_AA_IS_TESTED = 0 ----------------------------------------------------------- 0 modified_nucleotides // 1=are distinguished (only for tRNAs), 0=not, 2=combined 0 topology // 0 = periodic code 0 aaRS_class // 0 = amino acids of both classes are included, 1 = type I, 2 = type II 1 X_IS_INCLUDED // Ini, i.e., initiation signals 1 O_IS_INCLUDED // Sup, i.e., termination signals 1 U_IS_INCLUDED // Sec, i.e., selenocisteine 0 MX_MOVE_TOGETHER // 1=Met and fMet/Met-ini move together, 0=no 0 NONSTANDARD_ASSIGNMENTS // are 0=ignored or 1=processed according to amino acids ----------------------------------------------------------- 2 numOfOptimizableGroups 2 numOfOneElementGroups G P oneElementGroups 1 groupWeight // vs. familyWeight=1 ----------------------------------------------------------- 0 numOfNonStartAAs nonStartAAs ----------------------------------------------------------- 1 GLOBAL_ADAPTATION 0 numOfNonGlobAAs nonGlobAAs 3 globStart // numbering starts from 1 ----------------------if-database=1------------------------ 1 ISOTYPE_MUST_BE_BEST_MODEL 0 primary ----------------if-database=1-&-function!=1---------------- 67 score cutoff min 150 score cutoff max 0 isoscore cutoff min 150 isoscore cutoff max 0 isoscore_ac cutoff min 150 isoscore_ac cutoff max ----------------if-database=1-&-function=1----------------- 0.5 scoreStep[0] // min score 65 scoreStart[0] 110 scoreStop[0] 1 scoreStep[1] // min isoscore 0 scoreStart[1] 0 scoreStop[1] 1 scoreStep[2] // min isoscore_ac 0 scoreStart[2] 0 scoreStop[2] 1 scoreStep[3] // max score 150 scoreStart[3] 150 scoreStop[3] 1 scoreStep[4] // max isoscore 150 scoreStart[4] 150 scoreStop[4] 1 scoreStep[5] // max isoscore_ac 150 scoreStart[5] 150 scoreStop[5] ----------------------------------------------------------- 2 NumOfMatingsAndMutations 16 numOfTrimmedClassifications 2 4 8 16 32 48 64 0 softwareBruteForce // 0 = basic level, 1,2 = more brute force 0 hardwareBruteForce // 0 = basic level, 1,2 = more brute force ----------------------------------------------------------- 0 ISOACCEPTORS //1=similarities among isoacceptor tRNAs/tDNAs are also computed, 0=no 0 isoWeight // vs. alloacceptorWeight=1 // only when ISOACCEPTORS = 1 16 min number of assignments 15 max number of non-starting AAs 1 SAVE_DATA // save x_tRNA.txt or x_tDNA.txt on a harddisk 0 PRINT_UNRECOMMENDED_DETAILS // if function < 4, the ouput files can get too long -----------------if-DOMAINS_ARE_WEIGHTED=1----------------- 1 archaealWeight // default=1 1 bacterialWeight // default=1 1 eukaryoticWeight // default=1 0 virusesWeight // default=0, when some is not default or function=0, then DOMAINS_ARE_WEIGHTED=1 0 BACTERIAL_AND_EUKARYOTIC_WEIGHTS_STAY_EQUAL // only for function = 0 -----------------------if-function=0----------------------- 1 domainStep[0] // archaeal weight 1 domainStart[0] 3 domainStop[0] 1 domainStep[1] // bacterial weight 1 domainStart[1] 3 domainStop[1] 1 domainStep[2] // eukaryotic weight 1 domainStart[2] 3 domainStop[2] 1 domainStep[3] // viral weight 0 domainStart[3] 0 domainStop[3] -----see-the-bottom-for-a-check-of-included-positions------ 0 included_parts // 0=Giege,1=E.coli,2=S.cerevisiae,3=blocks,4=Lin,5=custom 0 IE cutoff min // only when included_parts < 3 =0(all), =1(identity elements (IEs)), =3(effective IEs), =5(major IEs), =10(most MIEs) --------------------if-included_parts=3-------------------- 1 IS_ACCEPTOR_STEM 3 IECutOffMin3[0] 1 IS_D-ARM 3 IECutOffMin3[1] 1 IS_ANTICODON_ARM 3 IECutOffMin3[2] 1 IS_VARIABLE_LOOP 3 IECutOffMin3[3] 1 IS_T-ARM 3 IECutOffMin3[4] 1 IS_8th_SITE 3 IECutOffMin3[5] 1 IS_9th_SITE 3 IECutOffMin3[6] 1 IS_26th_SITE 3 IECutOffMin3[7] 1 IS_73rd_SITE 3 IECutOffMin3[8] 1 IS_74th_SITE 3 IECutOffMin3[9] 1 IS_75th_SITE 3 IECutOffMin3[10] 1 IS_76th_SITE 3 IECutOffMin3[11] 1 IS_ANTICODON 1 IS_INTERSECTION_WITH_GIEGE 0 IS_INTERSECTION_WITH_E.COLI 0 IS_INTERSECTION_WITH_S.CEREVISIAE --------------------if-included_parts=4-------------------- 0 ARE_SITES_UBIQUITOUS 0 ARE_SITES_NEAR_UBIQUITOUS 1 ARE_SITES_ISOTYPE_DISCRIMINATORS 0 ARE_SITES_CLADE_ISOTYPE_DISCRIMINATORS 0 ARE_SITES_ISOTYPE_SPECIFIC 0 ARE_SITES_TERTIARY_INTERACTING 0 ARE_SITES_A_BOX 0 ARE_SITES_B_BOX --------------------if-included_parts=5-------------------- 11111111 Acceptor stem 5'->3' // 1 = included, 0 = excluded 11111111111 3'->5' 11111111111111111 D-arm 5'->3' 1111 3'->5' 1111111111111 Anticodon arm 5'->3' 111111 3'->5' 1111111111111 Variable loop 5'->3' 1111111111 3'->5' 111111111111 T-arm 5'->3' 11111 3'->5' 333 a check of consistency ---------------a-check-of-included-positions--------------- Included sites of tDNAs (written only after the start of the program): Acceptor stem: 11111111 D-arm:11111111111111111 11111111111 1111 Anticodon arm:1111111111111 Variable loop:1111111111111 T-arm:111111111111 111111 1111111111 11111 -----------------------------------------------------------