The amino acids that are forbidden to represent classes: G P 
Group 1: QE
Group 2: KINFMXTR
Group 3: LUSWC
Group 4: VAD
Group 5: HY
Group 6: G
Group 7: P
Chronology: MXQUVHFIKTWNAGEYDCPSRL
ch_p_sim: 17.6824
--------------------------------------------------------------------------
The amino acids that are forbidden to represent classes: G P H 
Group 1: VDA
Group 2: WULS
Group 3: HQE
Group 4: TIKNFMXR
Group 5: YC
Group 6: G
Group 7: P
Chronology: MXVWQCIKFTUNAHYPDGESRL
ch_p_sim: 17.6577
--------------------------------------------------------------------------
The amino acids that are forbidden to represent classes: G P H W 
Group 1: HQE
Group 2: FKMTXNIR
Group 3: YC
Group 4: SWUL
Group 5: VDA
Group 6: G
Group 7: P
Chronology: MXQYUVIKTFWNAHGPDCESRL
ch_p_sim: 17.6513
--------------------------------------------------------------------------
The amino acids that are forbidden to represent classes: G P H W Q 
Group 1: MTKXNIRF
Group 2: ULWSC
Group 3: EQ
Group 4: VAD
Group 5: HY
Group 6: G
Group 7: P
Chronology: MXUEVYIKTFWNAHGQDCPSRL
ch_p_sim: 17.6436
--------------------------------------------------------------------------
The amino acids that are forbidden to represent classes: G P H W Q U 
Group 1: MNKXIRTF
Group 2: YH
Group 3: VAD
Group 4: CLWSU
Group 5: EQ
Group 6: G
Group 7: P
Chronology: MXYVCEIKTFWNAHUQDGPSRL
ch_p_sim: 17.6386
--------------------------------------------------------------------------
The amino acids that are forbidden to represent classes: G P H W Q E 
Group 1: TMKXINF
Group 2: R
Group 3: VDA
Group 4: HYQE
Group 5: UWSLC
Group 6: G
Group 7: P
Chronology: MXRVYUIKTFWNAHGDCPQESL
ch_p_sim: 17.5816
--------------------------------------------------------------------------
The amino acids that are forbidden to represent classes: G P H W Q Y 
Group 1: EQ
Group 2: MXWYC
Group 3: HUSL
Group 4: VDA
Group 5: TKFIRN
Group 6: G
Group 7: P
Chronology: MXEUVFIKTWNHAGQYDCPRSL
ch_p_sim: 17.634
--------------------------------------------------------------------------
The amino acids that are forbidden to represent classes: G P H W Y 
Group 1: KRIFTN
Group 2: MXCW
Group 3: VDA
Group 4: UYLS
Group 5: HQE
Group 6: G
Group 7: P
Chronology: MXFVUQIKTWNHAGYPDCERSL
ch_p_sim: 17.6445
--------------------------------------------------------------------------
The amino acids that are forbidden to represent classes: G P H W Y F 
Group 1: ULSY
Group 2: MXCW
Group 3: ADV
Group 4: HQE
Group 5: IKFRTN
Group 6: G
Group 7: P
Chronology: MXUAQIKFTWNHVGYPDCERSL
ch_p_sim: 17.5551
--------------------------------------------------------------------------
The amino acids that are forbidden to represent classes: G P H W Y U 
Group 1: CSUL
Group 2: TFIKNR
Group 3: MXYW
Group 4: VDA
Group 5: HQE
Group 6: G
Group 7: P
Chronology: MXCFVQIKTWNHAUPYDGESRL
ch_p_sim: 17.6411
--------------------------------------------------------------------------
The amino acids that are forbidden to represent classes: G P H W U 
Group 1: FRTNKIMX
Group 2: CULS
Group 3: HEQ
Group 4: VAD
Group 5: YW
Group 6: G
Group 7: P
Chronology: MXCQVYIKTFHNAUWPDGESRL
ch_p_sim: 17.6418
--------------------------------------------------------------------------
The amino acids that are forbidden to represent classes: G P H W U C +
Group 1: FRKINTMX
Group 2: VDA
Group 3: HQE
Group 4: YWC
Group 5: USL
Group 6: G
Group 7: P
Chronology: MXVQYSIKTFHNAWUPDCEGRL
ch_p_sim: 17.6354
--------------------------------------------------------------------------
The amino acids that are forbidden to represent classes: G P H Q 
Group 1: FNKTRIMX
Group 2: LSUC
Group 3: VAD
Group 4: EQ
Group 5: YHW
Group 6: G
Group 7: P
Chronology: MXUVEWIKFTHNACQDYGPSRL
ch_p_sim: 17.6538
--------------------------------------------------------------------------
The amino acids that are forbidden to represent classes: G P H Q E 
Group 1: KFNITMX
Group 2: VDA
Group 3: SLYU
Group 4: QHWE
Group 5: RC
Group 6: G
Group 7: P
Chronology: MXVUWRIKFTHNAGYDCPQESL
ch_p_sim: 17.596
--------------------------------------------------------------------------
The amino acids that are forbidden to represent classes: G P H Q E U 
Group 1: EQHW
Group 2: MKTXIFN
Group 3: VAD
Group 4: CULYS
Group 5: R
Group 6: G
Group 7: P
Chronology: MXWVCRIKFTHNAUYDGPQESL
ch_p_sim: 17.5895
--------------------------------------------------------------------------
The amino acids that are forbidden to represent classes: G P H Q E R 
Group 1: DAV
Group 2: HULS
Group 3: MXY
Group 4: WQE
Group 5: IKRTCFN
Group 6: G
Group 7: P
Chronology: MXAUWIKFTQNHVGYPDCERSL
ch_p_sim: 17.519
--------------------------------------------------------------------------
The amino acids that are forbidden to represent classes: G P H C 
Group 1: VDA
Group 2: SUCL
Group 3: HYW
Group 4: KMXNIFRT
Group 5: EQ
Group 6: G
Group 7: P
Chronology: MXVUWEIKFTHNACQDYGPSRL
ch_p_sim: 17.6538
--------------------------------------------------------------------------
The amino acids that are forbidden to represent classes: G P H C U +
Group 1: ADV
Group 2: XKMIFNTR
Group 3: YCW
Group 4: EHQ
Group 5: USL
Group 6: G
Group 7: P
Chronology: MXAWQSIKFTHNVYUPDCEGRL
ch_p_sim: 17.6384
--------------------------------------------------------------------------
The amino acids that are forbidden to represent classes: G P H C U Q 
Group 1: ITRFKMXNC
Group 2: WYH
Group 3: VDA
Group 4: LSU
Group 5: EQ
Group 6: G
Group 7: P
Chronology: MXWVSEIKFTHNAUQDYPCGRL
ch_p_sim: 17.6345
--------------------------------------------------------------------------
The amino acids that are forbidden to represent classes: G P H C U S 
Group 1: USLW
Group 2: HQE
Group 3: VDA
Group 4: MXY
Group 5: TIRKFNC
Group 6: G
Group 7: P
Chronology: MXWQVIKUTFNHAGYPDCESRL
ch_p_sim: 17.5489
--------------------------------------------------------------------------
The amino acids that are forbidden to represent classes: G P U 
Group 1: EQ
Group 2: VDA
Group 3: SUCLW
Group 4: IRMXKNTF
Group 5: HY
Group 6: G
Group 7: P
Chronology: MXEVCHFIKTWNAUQYDGPSRL
ch_p_sim: 17.6764
--------------------------------------------------------------------------
The amino acids that are forbidden to represent classes: G P U C 
Group 1: MNFIXTRK
Group 2: QE
Group 3: WUSCL
Group 4: HY
Group 5: AVD
Group 6: G
Group 7: P
Chronology: MXQWHAIKUTFNVGEYDCPSRL
ch_p_sim: 17.6737
--------------------------------------------------------------------------
The amino acids that are forbidden to represent classes: G P U C W 
Group 1: AVD
Group 2: TFNIMXRK
Group 3: SUL
Group 4: EQW
Group 5: YCH
Group 6: G
Group 7: P
Chronology: MXASQHFIKTWNVUPYDCEGRL
ch_p_sim: 17.6547
--------------------------------------------------------------------------
The amino acids that are forbidden to represent classes: G P U C W S 
Group 1: KXMIRTNF
Group 2: UYSL
Group 3: HCW
Group 4: QE
Group 5: ADV
Group 6: G
Group 7: P
Chronology: MXYHQAIKTFUNVGWEDCPSRL
ch_p_sim: 17.6449
--------------------------------------------------------------------------
The amino acids that are forbidden to represent classes: G P U C W Q 
Group 1: DVA
Group 2: SUL
Group 3: TNFMXKIRC
Group 4: EQ
Group 5: WYH
Group 6: G
Group 7: P
Chronology: MXVSEHFIKTWNAUQDYPCGRL
ch_p_sim: 17.6495
--------------------------------------------------------------------------

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
-----------------------------------------------------------
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
1      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
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
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. 
-------------------------------------------------