The amino acids that are forbidden to represent classes: G P 
Group 1: HYSL
Group 2: VA
Group 3: EDQ
Group 4: WCF
Group 5: ITNKMXR
Group 6: G
Group 7: P
Chronology: MIHVQWTCKYGNFAPXDESRL
ch_p_sim: 18.5737
--------------------------------------------------------------------------
The amino acids that are forbidden to represent classes: G P H 
Group 1: FCW
Group 2: AV
Group 3: TKMXINR
Group 4: EDQ
Group 5: HYLS
Group 6: G
Group 7: P
Chronology: MICAQYTKHWGNFVPXDESRL
ch_p_sim: 18.5721
--------------------------------------------------------------------------
The amino acids that are forbidden to represent classes: G P H C 
Group 1: IMKXNTR
Group 2: VA
Group 3: EQD
Group 4: YHSL
Group 5: CWF
Group 6: G
Group 7: P
Chronology: MIVQYWTKCHGNFAPXDESRL
ch_p_sim: 18.501
--------------------------------------------------------------------------
The amino acids that are forbidden to represent classes: G P H C Q 
Group 1: YLHS
Group 2: NITMXKR
Group 3: VA
Group 4: EQD
Group 5: WCF
Group 6: G
Group 7: P
Chronology: MIYVEWTKCHGNFAQXDPSRL
ch_p_sim: 18.4988
--------------------------------------------------------------------------
The amino acids that are forbidden to represent classes: G P H C Q E 
Group 1: TMXKINR
Group 2: DVA
Group 3: FCHY
Group 4: SL
Group 5: QEW
Group 6: G
Group 7: P
Chronology: MIVYSWTKHQNFAPXCDEGRL
ch_p_sim: 18.4053
--------------------------------------------------------------------------
The amino acids that are forbidden to represent classes: G P H C Q W 
Group 1: EDQ
Group 2: ITNKRMXF
Group 3: AV
Group 4: YSHL
Group 5: CW
Group 6: G
Group 7: P
Chronology: MIEAYTKHWCGNVFQXDPSRL
ch_p_sim: 18.4956
--------------------------------------------------------------------------
The amino acids that are forbidden to represent classes: G P H C W 
Group 1: SLHY
Group 2: TNIRKMXF
Group 3: CW
Group 4: VA
Group 5: EDQ
Group 6: G
Group 7: P
Chronology: MIYVQTKHWCGNAFPXDESRL
ch_p_sim: 18.4976
--------------------------------------------------------------------------
The amino acids that are forbidden to represent classes: G P H C W Y 
Group 1: HYW
Group 2: EQD
Group 3: IKTRNMX
Group 4: CFLS
Group 5: VA
Group 6: G
Group 7: P
Chronology: MIQFVTKCYHGNWAPXDESRL
ch_p_sim: 18.4924
--------------------------------------------------------------------------
The amino acids that are forbidden to represent classes: G P H C W T 
Group 1: KNTIRMXF
Group 2: VA
Group 3: CW
Group 4: QED
Group 5: YLHS
Group 6: G
Group 7: P
Chronology: MIVQYKTHWCGNAFPXDESRL
ch_p_sim: 18.4956
--------------------------------------------------------------------------
The amino acids that are forbidden to represent classes: G P H Q 
Group 1: VA
Group 2: YLSH
Group 3: KNTIMXR
Group 4: DQE
Group 5: CFW
Group 6: G
Group 7: P
Chronology: MIVYECTKHWGNFAQXDPSRL
ch_p_sim: 18.5699
--------------------------------------------------------------------------
The amino acids that are forbidden to represent classes: G P H Q Y 
Group 1: YWSL
Group 2: AV
Group 3: HCF
Group 4: EQD
Group 5: TKIRNMX
Group 6: G
Group 7: P
Chronology: MIWACETKHYGNFVQXDPSRL
ch_p_sim: 18.5493
--------------------------------------------------------------------------
The amino acids that are forbidden to represent classes: G P H Q Y W 
Group 1: TMXNKRI
Group 2: VA
Group 3: EQD
Group 4: CSLW
Group 5: FHY
Group 6: G
Group 7: P
Chronology: MIVECFTKHWGNYAQXDPSRL
ch_p_sim: 18.5387
--------------------------------------------------------------------------
The amino acids that are forbidden to represent classes: G P H Q Y E 
Group 1: WQ
Group 2: FCSL
Group 3: AVD
Group 4: TKINRMX
Group 5: EYH
Group 6: G
Group 7: P
Chronology: MIWCATKYHQFNGVPXDESRL
ch_p_sim: 18.4714
--------------------------------------------------------------------------
The amino acids that are forbidden to represent classes: G P H Q E 
Group 1: VDA
Group 2: YQHE
Group 3: R
Group 4: TIMXKN
Group 5: LWCSF
Group 6: G
Group 7: P
Chronology: MIVYRCTKHWGNFAXDQEPSL
ch_p_sim: 18.4735
--------------------------------------------------------------------------
The amino acids that are forbidden to represent classes: G P H Q E R 
Group 1: DVA
Group 2: WEQ
Group 3: CF
Group 4: IMXTRKN
Group 5: YSHL
Group 6: G
Group 7: P
Chronology: MIVWCYTKHQFNGAPXDESRL
ch_p_sim: 18.4565
--------------------------------------------------------------------------
The amino acids that are forbidden to represent classes: G P H Y 
Group 1: INRTMXK
Group 2: WYLS
Group 3: VA
Group 4: EQD
Group 5: HFC
Group 6: G
Group 7: P
Chronology: MIWVQCTKHYGNFAPXDESRL
ch_p_sim: 18.5515
--------------------------------------------------------------------------
The amino acids that are forbidden to represent classes: G P H Y W 
Group 1: ITMXNRK
Group 2: WSCL
Group 3: EDQ
Group 4: VA
Group 5: HYF
Group 6: G
Group 7: P
Chronology: MICQVFTKHWGNYAPXDESRL
ch_p_sim: 18.541
--------------------------------------------------------------------------
The amino acids that are forbidden to represent classes: G P H Y W F 
Group 1: ITKRNMX
Group 2: VA
Group 3: HYF
Group 4: QED
Group 5: CSLW
Group 6: G
Group 7: P
Chronology: MIVQCTWKYHGNFAPXDESRL
ch_p_sim: 18.5086
--------------------------------------------------------------------------
The amino acids that are forbidden to represent classes: G P Q 
Group 1: TIKNRMX
Group 2: YHSL
Group 3: EQD
Group 4: WFC
Group 5: VA
Group 6: G
Group 7: P
Chronology: MIHEWVTCKYGNFAQXDPSRL
ch_p_sim: 18.5715
--------------------------------------------------------------------------
The amino acids that are forbidden to represent classes: G P Q E 
Group 1: SLY
Group 2: FCW
Group 3: IKTMXNR
Group 4: HQED
Group 5: VA
Group 6: G
Group 7: P
Chronology: MIYCHVTKWQGNFAPXDESRL
ch_p_sim: 18.5429
--------------------------------------------------------------------------
The amino acids that are forbidden to represent classes: G P Q E Y 
Group 1: TIMKXNR
Group 2: WSLY
Group 3: HQED
Group 4: FC
Group 5: VA
Group 6: G
Group 7: P
Chronology: MIWHCVTKYQFNGAPXDESRL
ch_p_sim: 18.5272
--------------------------------------------------------------------------
The amino acids that are forbidden to represent classes: G P Q E Y W 
Group 1: FY
Group 2: HEQD
Group 3: VA
Group 4: TIMXKRN
Group 5: WCSL
Group 6: G
Group 7: P
Chronology: MIFHVCTKWQYNGAPXDESRL
ch_p_sim: 18.5212
--------------------------------------------------------------------------
The amino acids that are forbidden to represent classes: G P Q E Y C 
Group 1: WFC
Group 2: TNRKIMX
Group 3: HSL
Group 4: EYQ
Group 5: VAD
Group 6: G
Group 7: P
Chronology: MIWHVTCKYQNGFAPXDESRL
ch_p_sim: 18.4853
--------------------------------------------------------------------------
The amino acids that are forbidden to represent classes: G P Q E C ++
Group 1: HEQ
Group 2: FWYC
Group 3: KMXTNIR
Group 4: VAD
Group 5: LS
Group 6: G
Group 7: P
Chronology: MIHWVSTKYQNFAPXCDEGRL
ch_p_sim: 18.4816
--------------------------------------------------------------------------
The amino acids that are forbidden to represent classes: G P Q E C S 
Group 1: FCW
Group 2: VA
Group 3: XKTMRIN
Group 4: HQED
Group 5: SLY
Group 6: G
Group 7: P
Chronology: MIWVHYTKCQGNFAPXDESRL
ch_p_sim: 18.4754
--------------------------------------------------------------------------

1      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
-----------------------------------------------------------
3      function // 0=FindLUCA,1=FindScores,2=FindNonStartAAs,3=FindNonGlobAAs,4=GlobOptimizeGroups,5=TestData
0      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
1      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
-----------------------------------------------------------
5      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
10     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
3      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:   01111100   D-arm:00110101000001000
              00011111100           1101
Anticodon arm:0000000011111 Variable loop:1111111111111 T-arm:000000000000
              100000                      1111111111          00000
-----------------------------------------------------------
THE SIMULATION HAS FINISHED. 
-------------------------------------------------