ch_p_sim is not listed, because a normalization of three weights would be nontrivial.

Archaeal weight = 0.0000  bacterial weight = 1.0000  eukaryotic weight = 1.0000 ++
Group 1: VAD
Group 2: FYCLSW
Group 3: EHQ
Group 4: MITXKRN
Group 5: G
Group 6: P
Chronology: MKVFHYICQTWNAGDPEXRSL
--------------------------------------------------------------------------
Archaeal weight = 0.1000  bacterial weight = 1.0000  eukaryotic weight = 1.0000 ++
Group 1: IMTXKNR
Group 2: VDA
Group 3: QHE
Group 4: CFWYSL
Group 5: G
Group 6: P
Chronology: MKVQFYICHTWNAGDPEXRSL
--------------------------------------------------------------------------
Archaeal weight = 0.2000  bacterial weight = 1.0000  eukaryotic weight = 1.0000 ++
Group 1: IMXNTKR
Group 2: EQH
Group 3: CYWFLS
Group 4: AVD
Group 5: G
Group 6: P
Chronology: MKQYAFICHTWNVGDPEXRSL
--------------------------------------------------------------------------
Archaeal weight = 0.3000  bacterial weight = 1.0000  eukaryotic weight = 1.0000 ++
Group 1: QEH
Group 2: MTKXNRI
Group 3: VAD
Group 4: CFYWLS
Group 5: G
Group 6: P
Chronology: MKQVFYICHTWNAGDPEXRSL
--------------------------------------------------------------------------
Archaeal weight = 0.4000  bacterial weight = 1.0000  eukaryotic weight = 1.0000 ++
Group 1: RINKTMX
Group 2: VAD
Group 3: EQH
Group 4: CYFSLW
Group 5: G
Group 6: P
Chronology: MKVQYFICHTWNAGDPEXRSL
--------------------------------------------------------------------------
Archaeal weight = 0.5000  bacterial weight = 1.0000  eukaryotic weight = 1.0000 ++
Group 1: VDA
Group 2: YFLSCW
Group 3: QEH
Group 4: MTIXKRN
Group 5: G
Group 6: P
Chronology: MKVYQFICHTWNAGDPEXRSL
--------------------------------------------------------------------------
Archaeal weight = 0.6000  bacterial weight = 1.0000  eukaryotic weight = 1.0000 ++
Group 1: RTKNIMX
Group 2: FCSYLW
Group 3: QEH
Group 4: VDA
Group 5: G
Group 6: P
Chronology: MKFQVYICHTWNAGDPEXRSL
--------------------------------------------------------------------------
Archaeal weight = 0.7000  bacterial weight = 1.0000  eukaryotic weight = 1.0000 ++
Group 1: KMXINRT
Group 2: QEH
Group 3: YWFLSC
Group 4: DVA
Group 5: G
Group 6: P
Chronology: MKQYVFICHTWNAGDPEXRSL
--------------------------------------------------------------------------
Archaeal weight = 0.8000  bacterial weight = 1.0000  eukaryotic weight = 1.0000 ++
Group 1: NIMXRKT
Group 2: CSYFLW
Group 3: EQH
Group 4: DVA
Group 5: G
Group 6: P
Chronology: MKYQVFICHTWNAGDPEXRSL
--------------------------------------------------------------------------
Archaeal weight = 0.9000  bacterial weight = 1.0000  eukaryotic weight = 1.0000 ++
Group 1: AVD
Group 2: QEH
Group 3: KITRMXN
Group 4: LFYSWC
Group 5: G
Group 6: P
Chronology: MKAQFYICHTWNVGDPEXRSL
--------------------------------------------------------------------------
Archaeal weight = 1.0000  bacterial weight = 1.0000  eukaryotic weight = 1.0000 ++
Group 1: TNRKIMX
Group 2: ADV
Group 3: QEH
Group 4: FYLSCW
Group 5: G
Group 6: P
Chronology: MKAQFYICHTWNVGDPEXRSL
--------------------------------------------------------------------------
Archaeal weight = 1.1000  bacterial weight = 1.0000  eukaryotic weight = 1.0000 ++
Group 1: VAD
Group 2: CLWSFY
Group 3: QHE
Group 4: KRIMXTN
Group 5: G
Group 6: P
Chronology: MKVFQYICHTWNAGDPEXRSL
--------------------------------------------------------------------------
Archaeal weight = 1.2000  bacterial weight = 1.0000  eukaryotic weight = 1.0000 ++
Group 1: EQH
Group 2: LFSCYW
Group 3: KITMXNR
Group 4: ADV
Group 5: G
Group 6: P
Chronology: MKQFAYICHTWNVGDPEXRSL
--------------------------------------------------------------------------
Archaeal weight = 1.3000  bacterial weight = 1.0000  eukaryotic weight = 1.0000 ++
Group 1: ADV
Group 2: EQH
Group 3: WCYSFL
Group 4: XRNMKIT
Group 5: G
Group 6: P
Chronology: MKAQYFICHTWNVGDPEXRSL
--------------------------------------------------------------------------
Archaeal weight = 1.4000  bacterial weight = 1.0000  eukaryotic weight = 1.0000 ++
Group 1: QEH
Group 2: TMXKRNI
Group 3: YFCWSL
Group 4: AVD
Group 5: G
Group 6: P
Chronology: MKQYAFICHTWNVGDPEXRSL
--------------------------------------------------------------------------
Archaeal weight = 1.5000  bacterial weight = 1.0000  eukaryotic weight = 1.0000 ++
Group 1: WYFCSL
Group 2: IMRXTKN
Group 3: VAD
Group 4: EQH
Group 5: G
Group 6: P
Chronology: MKYVQFICHTWNAGDPEXRSL
--------------------------------------------------------------------------
Archaeal weight = 1.6000  bacterial weight = 1.0000  eukaryotic weight = 1.0000 ++
Group 1: VAD
Group 2: KMNXTIR
Group 3: YCFWSL
Group 4: QHE
Group 5: G
Group 6: P
Chronology: MKVYQFICHTWNAGDPEXRSL
--------------------------------------------------------------------------
Archaeal weight = 1.7000  bacterial weight = 1.0000  eukaryotic weight = 1.0000 ++
Group 1: MINXKTR
Group 2: CFYWSL
Group 3: QHE
Group 4: DVA
Group 5: G
Group 6: P
Chronology: MKFQVYICHTWNAGDPEXRSL
--------------------------------------------------------------------------
Archaeal weight = 1.8000  bacterial weight = 1.0000  eukaryotic weight = 1.0000 ++
Group 1: EQH
Group 2: FYLCWS
Group 3: IMXRTKN
Group 4: AVD
Group 5: G
Group 6: P
Chronology: MKQFAYICHTWNVGDPEXRSL
--------------------------------------------------------------------------
Archaeal weight = 1.9000  bacterial weight = 1.0000  eukaryotic weight = 1.0000 ++
Group 1: EQH
Group 2: RXMTKIN
Group 3: VDA
Group 4: FWCYSL
Group 5: G
Group 6: P
Chronology: MKQVFYICHTWNAGDPEXRSL
--------------------------------------------------------------------------
Archaeal weight = 2.0000  bacterial weight = 1.0000  eukaryotic weight = 1.0000 ++
Group 1: FCYWSL
Group 2: MXKINTR
Group 3: EQH
Group 4: VAD
Group 5: G
Group 6: P
Chronology: MKFQVYICHTWNAGDPEXRSL
--------------------------------------------------------------------------

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
-----------------------------------------------------------
0      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
-----------------------------------------------------------
4      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 
1      BACTERIAL_AND_EUKARYOTIC_WEIGHTS_STAY_EQUAL // only for function = 0
-----------------------if-function=0-----------------------
0.1    domainStep[0]  // archaeal weight
0      domainStart[0]
2      domainStop[0]
1      domainStep[1]  // bacterial weight
1      domainStart[1]
1      domainStop[1]
1      domainStep[2]  // eukaryotic weight
1      domainStart[2]
1      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
-----------------------------------------------------------
THE SIMULATION HAS FINISHED. 
-----------------------------------------------------------