--- EXPERIMENT NOTES




 --- EXPERIMENT PROPERTIES

#Mon Nov 14 15:23:45 WET 2016
codeml.models=0 1 2 3 7 8
mrbayes.mpich=
mrbayes.ngen=1000000
tcoffee.alignMethod=CLUSTALW2
tcoffee.params=
tcoffee.maxSeqs=0
codeml.bin=codeml
mrbayes.tburnin=2500
codeml.dir=
input.sequences=
mrbayes.pburnin=2500
mrbayes.bin=mb_adops
tcoffee.bin=t_coffee_ADOPS
mrbayes.dir=/usr/bin/
tcoffee.dir=
tcoffee.minScore=3
input.fasta=/opt/ADOPS/216/Crtc-PC/input.fasta
input.names=
mrbayes.params=
codeml.params=



 --- PSRF SUMMARY

      Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS/216/Crtc-PC/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/216/Crtc-PC/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run2.p":
(Use the harmonic mean for Bayes factor comparisons of models)

(Values are saved to the file /opt/ADOPS/216/Crtc-PC/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)

Run   Arithmetic mean   Harmonic mean
--------------------------------------
1      -8317.33         -8336.49
2      -8317.09         -8333.25
--------------------------------------
TOTAL    -8317.21         -8335.83
--------------------------------------


Model parameter summaries over the runs sampled in files
"/opt/ADOPS/216/Crtc-PC/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/216/Crtc-PC/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run2.p":
Summaries are based on a total of 3002 samples from 2 runs.
Each run produced 2001 samples of which 1501 samples were included.
Parameter summaries saved to file "/opt/ADOPS/216/Crtc-PC/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat".

95% HPD Interval
--------------------
Parameter         Mean      Variance     Lower       Upper       Median    min ESS*  avg ESS    PSRF+
------------------------------------------------------------------------------------------------------
TL{all}         1.039726    0.003197    0.933180    1.150670    1.038607   1473.64   1474.72    1.000
r(A<->C){all}   0.062827    0.000086    0.046185    0.081957    0.062696    911.28   1017.79    1.002
r(A<->G){all}   0.305638    0.000465    0.261799    0.345928    0.305819    890.35    964.76    1.000
r(A<->T){all}   0.137089    0.000314    0.102896    0.170957    0.136548    830.08    925.83    1.000
r(C<->G){all}   0.041803    0.000043    0.030428    0.055768    0.041555   1128.78   1149.98    1.000
r(C<->T){all}   0.377456    0.000577    0.331298    0.423177    0.376858    861.98    988.76    1.000
r(G<->T){all}   0.075186    0.000143    0.051504    0.097981    0.074462    995.44   1202.42    1.000
pi(A){all}      0.247182    0.000066    0.231400    0.262640    0.247175    949.85   1050.19    1.000
pi(C){all}      0.322332    0.000073    0.305216    0.338929    0.322234    944.44    969.77    1.000
pi(G){all}      0.275083    0.000068    0.259260    0.291533    0.274921   1113.20   1177.56    1.000
pi(T){all}      0.155403    0.000040    0.144077    0.168545    0.155206   1063.14   1102.54    1.000
alpha{1,2}      0.127778    0.000104    0.109023    0.149438    0.127319   1440.39   1470.69    1.000
alpha{3}        4.906624    1.136628    2.907462    6.897088    4.784663   1501.00   1501.00    1.000
pinvar{all}     0.354967    0.000779    0.298718    0.407152    0.355908   1371.95   1394.22    1.000
------------------------------------------------------------------------------------------------------
* Convergence diagnostic (ESS = Estimated Sample Size); min and avg values
correspond to minimal and average ESS among runs.
ESS value below 100 may indicate that the parameter is undersampled.
+ Convergence diagnostic (PSRF = Potential Scale Reduction Factor; Gelman
and Rubin, 1992) should approach 1.0 as runs converge.


Setting sumt conformat to Simple



 --- CODEML SUMMARY

Model 1: NearlyNeutral	-6969.568605
Model 2: PositiveSelection	-6969.568606
Model 0: one-ratio	-7061.250838
Model 3: discrete	-6964.560527
Model 7: beta	-6968.380219
Model 8: beta&w>1	-6964.383596


Model 0 vs 1	183.36446599999908

Model 2 vs 1	1.999998858082108E-6

Model 8 vs 7	7.993245999999999

Additional information for M7 vs M8:
Naive Empirical Bayes (NEB) analysis
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: D_melanogaster_Crtc-PC)

            Pr(w>1)     post mean +- SE for w

   175 A      0.973*        1.331
   176 N      0.747         1.099
   183 P      0.676         1.022
   210 L      0.971*        1.329
   232 L      0.900         1.256
   293 Q      0.695         1.044
   425 A      0.968*        1.326
   435 Q      0.911         1.267
   486 P      0.743         1.092
   600 Q      0.549         0.893

Bayes Empirical Bayes (BEB) analysis (Yang, Wong & Nielsen 2005. Mol. Biol. Evol. 22:1107-1118)
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: D_melanogaster_Crtc-PC)

            Pr(w>1)     post mean +- SE for w

   172 S      0.554         1.047 +- 0.527
   175 A      0.945         1.457 +- 0.191
   176 N      0.758         1.283 +- 0.397
   183 P      0.775         1.284 +- 0.418
   186 P      0.529         0.974 +- 0.584
   210 L      0.957*        1.466 +- 0.174
   232 L      0.903         1.416 +- 0.267
   286 G      0.516         0.959 +- 0.587
   293 Q      0.758         1.276 +- 0.411
   425 A      0.949         1.460 +- 0.187
   435 Q      0.909         1.422 +- 0.257
   486 P      0.821         1.331 +- 0.377
   500 P      0.535         1.019 +- 0.539
   592 S      0.584         1.080 +- 0.519
   600 Q      0.639         1.156 +- 0.474

>C1
MANPRKFSEKIALQKQKQAEGTAEFERIMKEVYATKRDEPPANQKILDGL
VGGQEVSQSSPGAGNGTGGGGSGSGSGASGGGASPDGLGGGGGSPTAYRE
SRGRSVGVGPMRRPSERKQDRSPYGSSSTQQTLDNGQLNPHLLGPPTAES
LWRRSSSDSALHQSALVAGFNSDVNSMGANYQQQQHQQQQQPGQPRSHSP
HHGINRTMSPQAQRRKSPLLQPHQLQLQQLQQQQQQMQHQHQLHQQLQMQ
QLQQHQQQHQQQQQQQNTPYNNAKFTNPVFRPLQDQVNFANTGSLPDLTA
LQNYGPQQQQQQSQQQPSQQQQQLQQTLSPVMSPHNHRRERDQSPSPFSP
AGGGGGAGPGSPYQQQQHSPTGNTQQQQQQHQQPSNSPHLSFTNLATTQA
AVTTFNPLPTLGPHNATDYRQPPNPPSPRSSPGLLSSVSATDLHSSAPAS
PIRQQQQAHQQQQQQQQAQQQQQQFDNSYNSLNTSFHNQFEIFSLGDSNS
SPEQQGFANNFVALDFDDLSGGGGGGPSGGGGSNGGGLTNGYNKPEMLDF
SELSGSPEASGNNNHMRRGVSNLNNNGLSNGVVGSTHNGSTNLNGAGNNN
SSSGGGTAQDPLGITTSPVPSPLGCPSSPLPIPIPMSAQSSPQQQHHHHQ
QQQQQHHQQQHHQQQQLSLSLHHSPHHSPMHSPHHGNSPLSSSSPVSHNA
CSNSNVVMNHQQQQQQHHHQQHHHQGSSQSHTPTTANIPSIIFSDYSSNA
DYTREIFDSLDLDLGQMDVAGLQMLSDQNPIMIADPNIEDSFRRDLNooo
ooooooooooooooooooo
>C2
MANPRKFSEKIALQKQKQAEGTAEFERIMKEVYATKRDEPPANQKILDGL
VGGQEVSQSSPGAGNGTGGGGSGSGSGASGGGASPDGLGGGGGSPTAYRE
SRGRSVGVGPMRRPSERKQDRSPYGSSSTQQTLDNGQLNPHLLGPPTAES
LWRRSSSDSALHQSALVAGFNSDVNSMGANYQQQQHQQPGQPRSHSPHHG
INRTMSPQAQRRKSPILQPHQLQLQQLQQQQQQMQHQHQLHQQLQMQQLQ
QHQQQQQQQNTPYNNAKFTNPVFRPLQDQVNFANTGSLPDLTALQNYGPQ
QQQQQSQQQQSQQQQQLQQTLSPVMSPHNHRRERDQSPSPFSPAGGGGGA
GPGSPYQQQQHSPTGNTQQQQHQQPSNSPHLSFTNLATTQAAVTTFNPLP
TLGPHNATDYRQPPNPPSPRSSPGLLSSVSATDLHSSAPASPIRQQQQAH
QQQQQQQQAQQQQQQFDNSYNSLNTSFHNQFEIFSLGDSNSSPEQQGFAN
NFVALDFDDLSGGGGGGPGGGGGSNGGGLTNGYNKPEMLDFSELSGSPEA
SGNNNHMRRGVSNLNNNGLSNGVVGSTHNGSTNLNGAGNNNSSSGGGTAQ
DPLGITTSPVPSPLGCPSSPLPIPIPMSAQSSPQQQHHHHQQQQQQHHQQ
QHHQQQHHQQQQLSLSLHHSPHHSPMHSPHHGNSPLSSSSPVSHNACSNS
NVVMNHQQQQQQQHHHQQHHHQGSSQSHTPTTANIPSIIFSDYSSNADYT
REIFDSLDLDLGQMDVAGLQMLSDQNPIMIADPNIEDSFRRDLNoooooo
ooooooooooooooooooo
>C3
MANPRKFSEKIALQKQKQAEGTAEFERIMKEVYATKRDEPPANQKIIDGL
VGGQEVSQSSPGAGNGTGGGGSGSGSGASGGGASPDGLGGGGGSPTAYRE
SRGRSVGVGPMRRPSERKQDRSPYGSSSTQQTLDNGQLNPHLLGPPTAES
LWRRSSSDSALHQSALVAGFNSDVNAMGASYQQQQHQQPQQGQPRSHSPH
HGINRTMSPQAQRRKSPLLQPHQLQLQQLQQQQQQMQHQHQLHQQLQMQQ
LQQHQQQHQQQQQQQNTPYNNAKFTNPVFRPLQDQVNFANTGSLPDLTAL
QNYGPQQQQQQQQQSQQQPSQQQQQLQQTLSPVMSPHNHRRERDQSPSPF
SPAGGGGGAGPGSPYQQQHSPTGNTQQQQHQQPSNSPHLSFTNLATTQAA
VSTFNPLPTLGPHNATDYRQPPNPPSPRSSPGLLSSVSATDLHSSAPASP
IRQQQQVQQQQQQQQQAQQQQQQFDNSYNSLNTSFHNQFEIFSLGDSNSS
PEQQGFANNFVALDFDDLSGGGGGGPGGGGGSNGGGLTNGYNKSEMLDFS
ELSGSPEASGNNNHMRRGVSNLNNNGLSNGVGSTHNGSTNLNGAGNNNSS
SGGGTAQDPLGITTSPVPSPLGCPSSPLPIPMSAQSSPQQQHHHHQQQQQ
QHHHQQHHQQQQLSLSLHHSPHHSPMHSPHHGNSPLSSSSPVSHNACSNS
NVVMNHQQQQQQHHHQQHHHQGSSQSHTPTTANIPSIIFSDYSSNADFTR
EIFDSLDLDLGQMDVAGLQMLSDQNPIMIADPNIEDSFRRDLNooooooo
ooooooooooooooooooo
>C4
MANPRKFSEKIALQKQKQAEGTAEFERIMKEVYATKRDEPPANQKILDGL
VGGQEVSQSSPGAGNGTGGGGSGSGSGASGGGASPDGLGGGGGSPTAYRE
SRGRSVGVGPMRRPSERKQDRSPYGSSNTQQTLDNGQLNPHLLGPPTAES
LWRRSSSDSALHQSALVAGFNSDVNSMGANYQQQQHQQPQPGQPRSHSPH
HGISRTMSPQAQRRKSPLLQPHQLQLQQLQQQQQQMQHQHQLHQQLQMQQ
LQQHQQQHQQQQQQQNTPYNNAKFTNPVFRPLQDQVNFANTGSLPDLTAL
QNYGPQQPQQQQQQSQQQPSQQQQQLQQTLSPVMSPHNHRRERDQSPSPF
SPAGGGGGAGPGSPYQQQHSPTGNTQQQHQQPSNSPHLSFTNLATTQAAV
STFNPLPTLGPHNATDYRQPPNPPSPRSSPGLLSSVSATDLHSSAPASPI
RQQQQAQQQQQAQQQQQQFDNSYNSLNTSFHNQFEIFSLGDSNSSPEQQG
FANNFVALDFDDLSGGGGGGPGGGGGSNGGGLTNGYNKSEMLDFSELSGS
PEASGNNNHMRRGVSNLNNNGLSNGVGSTHNGSTNLNGAGNNNSNSGGGG
TAQDPLGITTSPVPSPLGCPSSPLPIPMSAQSSPQQHHHHHQQQQQHHQQ
QHHQQQQLSLSLHHSPHHSPLHSPHHGNSPLSSSSPVSHNACSNSNVVMN
HQHQQQQQQQHHHQQHHHQGSSQSHTPTTANIPSIIFSDYSSNADFPREI
FDSLDLDLGQMDVAGLQMLSDQSPIMIADPNIEDSFRRDLNooooooooo
ooooooooooooooooooo
>C5
MANPRKFSEKIALQKQKQAEGTAEFERIMKEVYATKRDEPPVNQNPNQKI
LESLVGGQEVSQSSPGAGNGGGSGSGSGASGGGASPDGLGGGGGSPTAYR
ESRGRSVGVGPMRRPSERKQDRSPYGSSSGTQQTLDNGQLNPHLLGPPTA
ESLWRRSSSDSALHQSALVAGFNADVNSMGGGNYQQQQQHQQQQQSGQTR
SHSPHHGINRTLSPQAQRRKSPLLQPHQLQLQQLQQQQQQMQQQHQHHQL
HQQLQMQQLQQHQQQHQQQQQHQQQQTTPYNNAKFANPVFRPLQDQVNFA
NTGSLPDLTALQNYGPQQQQQQTQQPQQQLQQTLSPVMSPHNHRRDRDQS
PSPFSPAGGGAGPGSPYQQQQHSPTGNTQQQQQQQPSSSPHLSFTNLATT
QAAVSTFNPLPTLGPHNATDYRQPPNPPSPRSSPGLLSSVSATDLHSSAP
ASPIRQQQQQVQQQQQQQQQQQQQQQQGHQQFDNSYNSLNTSFHNQFEIF
SLGDSNSSPEQQGFANNFVALDFDDLSGGGGGGGNGSNGGGALTNGYNNK
QEMLDFSELSGSPEASGNNNHMRRGVSNLNNNNGLSNGVGSTHNGSTNLN
GAGNNNGSSGGGSAQDPLGITASPVPSPLGCPSSPLPIPMSAQASPQHQH
HHQQQQQQQQHHQQQQHHQQQQLSLSLHHSPHHSPMHSPHHGNSPLSSSS
PVSHNACSNSNVVMNHIQQQQQQHQPHLHQGSSQSHTPTTANIPSIIFSD
YSSNADFSREIFDTLDLDLGQMDVAGLQMLSDQNPIMIADPNIEDSFRRD
LNooooooooooooooooo
>C6
MANPRKFSEKIALQKQKQAEGTAEFERIMKEVYATKRDEPPVNQKILESL
VGGPEVSQSSPGAGNGTGGGGGGGSGSGSGASGGGASPDGLGGGGGSPTA
YRESRGRSVGVGPMRRPSERKQDRSPYGSSSTQQTLDNGQLNPHLLGPPT
AESLGRRSNSDSALHHSALVAGFNADVNSMGASYQQQHQQQPGQPRSHSP
HHGINRTLSPQAQRRKSPLLQPHQLQLQQLQQQHQQMQQQHQYQLHQQLQ
MQQLQQQQHQQQQQQQQTTPYNNAKFANPVFRPLQDQVNFANTGSLPDLT
ALQNYGPQQQQQSQQQQQQQQQQQSQQQQQQLQQTLSPVMSPHNHRRDRD
QSPSPFSPAGGGGGGAGPGSPYQQQQHSPTGNTQQQQQQQQQQPSSSPHL
SFTNLATTQAAVSTFNPLPTLGPHNATDYRQPPNPPSPRSSPGLLSSVSA
TDLHSSAPASPIRQQQQAQQQQQQQQQQQQQQGHQQQQQFDNSYNSLNTS
FHNQFEIFSLGDSNSSPEQQGFANNFVALDFDDLSGGGGGGSGSNGGLTN
GYNKQEMLDFSELSGSPEASGNNNHMRRGVSNLNNNGLSNGVGSTHNGST
NLNGAGNNNSSSGGGSAQDPLGIAASPVPSPLGCPSSPLPIPISAQTSPQ
QQQHHHHHQQQQQHHQQQQHHQQQQLSLSLHHSPHHSPMHSPHHGSSPLS
SSSPVSHNACSNSNVVMNHHQQQHQHQPHLHQGSSQSHTPTTANIPSIIF
SDYSSNADFSREIFDTLDLDLGQMDVAGLQMLSDQNPIMIADPNIEDSFR
RDLNooooooooooooooo
>C7
MANPRKFSEKIALQKQKQAEGTAEFERIMKEVYATKRDEPPANQKILECL
GGGQEVSQSSPGAGNGSGGGGGSGSGSGASGGGASPDGLGGGGGSPTAYR
ESRGRSVGVGPMRRPSERKQDRSPYGSSSTQQTLDNGQLNPHLLGPPTTE
NSWRRSSSDSALHQSALVAGFNDVNSMGGNYQQQQHQQQQSGQPRSHSPH
HGINRTLSPQAQRRKSPILQPHQLQLQQLQQQQQHMQQQHQNQLHQQLQM
QQMQQQQQQQQQHQQNTPYNNAKFANPVFRPLQDQVNFANTGSLPDLTAL
HTYGPQQQQQSQQQHTQQQQLQQTLSPVMSPHNHRRDRDQSPSPFSPAGG
GGGAGPGSPYQQQQHSPTGNTQQQQQQPSSSPHLSFTNLATTQAAVSTFN
PLPTLGPHNATDYRQPPNPPSPRSSPGLLSSVSATDLHSSAPASPIRQQQ
QVQQQQQQQQQQQQQQQTHQQQQQFDNSYNSLNTSFHNQFEIFSLGDSNS
SPEQQGFANNFVALDFDDLSGGGGVSGGGNGSNGGGLTNGYNKPDMLDFS
ELSGSPESSGNNNHMRRGVSNLNNNGLSNGVGSTHNGSTNLNGAGNNNSS
SGGGSGQDPLGIAASPVPSPLGCPSSPLPIPMSAQASPQQHHHHHQQQQQ
QHHHQQQHHQQQQLSLSLHHSPHHSPMHSPHHGNSPLSSSSPVSHNACSN
SNVVMNHHQQQQQHQHQHHQHQGSSQSHTPTTANIPSIIFSDYSSNADFS
REIFDTLDLDLGQMDVAGLQMLSDQNPIMIADPNIEDSFRRDLNoooooo
ooooooooooooooooooo
>C8
MANPRKFSEKIALQKQKQAEGTAEFERIMKEVYATKRDDPPANQKILECL
GGGHEVSQSSPGSGNGTGGGGGSGSGSGASGGGASPDGLAGGGGGGSPTT
YRESRGRSVGVGPMRRPSERKQDRSPYGSSGGTQQTLDNGQLNPHLLGPP
TADSLWRRSSSDSALHQTALGAGFDTNVNMMHPNYQPQQHQQQQQQQPGQ
PRSHSPHHGINRTMSPQAQRRKSPGLQPPQLQLQQLQQQHQQMQQQHQMH
QQLQMQQLHQQQHQQQQQQQTTPYNNAKFANPVFRPLQEQANFANTGSLP
DLTALQNYTPQQQQQSQQQQLQQTLSPVMSPHNHRRDRDQSPSPFSPAGG
GGGAGPGSPYQQQQHSPTGNTQQQQQQQQQQQQQPSSSPHLSFTNLATTQ
ATVSTFNPLPTLGPHNATDYRQPPNPPSPRSSPGLLSSVSATDLHSSAPA
SPIRQQQQVQQQQQQQQQQQQQAHQQQQQFDNSYNSLNTSFHNQFEIFSL
GDSNSSPEQQGFANNFVALDFDELSGGGGGGSGGGSNGGGLTNGYNKQEM
LDFSELSGSPEASGNNNHMRRGVSNLNNNGLSNGVGSTHNGSTNLNGAGN
NNSSSGGGSTQDPLGITASPVPSPLGCPSSPLPIPMSAQTSPQQQHHHQH
QQQQQQQHHQQQHHQQQQLSLSLHHSPHHSPLHSPHHGNSPLSSSSPVSH
NACSNSNVVMNHHQQQQQHHHQQQHLQGSSQSHTPTTTNIPSIIFSDYSS
NADFSREIFDTLDLDLGQMDVAGLQMLSDQNSIMIADANIEDSFRRDLNo
ooooooooooooooooooo
>C9
MANPRKFSEKIALQKQKQAEGTAEFERIMKEVYATKRDDPPANQKILECL
GGVQEVSQSSPGSGNGTGGGGGSGSGSGASGGGASPDGLAGGGGGSPTAY
RESRGRSVGVGPMRRPSERKQDRSPYGSSSSTQQTLDNGQLNPHLLGPPT
SDNLWRRSSSDSALHQTALGAGFDTNVNSMYQQQQQQQHHQQQQQQQQQP
GQTRSHSPHHGINRTMSPQAQRRKSPALQHPQLQLQQLQQQQMQQQHQLH
QQLQMQQLQQQQHQQQQQQQQQQQQTTPYNNAKFTNPVFRPLQEQANFAN
TGSLPDLTALQNYAPQQQQQIQQQQQQQLQQTLSPVMSPHNHRRERDQSP
SPFSPAGGGGGAGPGSPYQQQQHSPTGNTQQQQQQQQPSSSPHLSFTNLA
TTQATVATFNPLPTLGPHNATDYRQPPNPPSPRSSPGLLSSVSATDLHSS
APASPIRQQQQAQQQQQQQQQQQQQAAHQQQQQFDNSYNSLNTSFHNQFE
IFSLGDSNSSPEQQGFANNFVALDFDDLSGGGGGGSAGGGGGGGGVGSNG
GGLTNGYNKQEMLDFSELSGSPEASGNNNHMRRGVSNLNNNGLSNGVGST
HNGSTNLNGAGNNNSSSGGGSTQDPLGITTSPVPSPLGCPSSPLPIPMSA
QTSPQQQHNHHHHHHQHQQQQQQHHQQQHHQQQQLSLSLHHSPHHSPMHS
PHHGNSPLSSSSPVSHNACSNSNVVMNHHQQQQQQQQHHHQQQHHLQGSS
QSHTPTTANIPSIIFSDYSSNADFSREIFDTLDLDLGQMDVAGLQMLSDQ
NPIMIADPNIEDSFRRDLN
CLUSTAL FORMAT for T-COFFEE Version_10.00.r1613 [http://www.tcoffee.org] [MODE:  ], CPU=0.00 sec, SCORE=99, Nseq=9, Len=896 

C1              MANPRKFSEKIALQKQKQAEGTAEFERIMKEVYATKRDEPPAN----QKI
C2              MANPRKFSEKIALQKQKQAEGTAEFERIMKEVYATKRDEPPAN----QKI
C3              MANPRKFSEKIALQKQKQAEGTAEFERIMKEVYATKRDEPPAN----QKI
C4              MANPRKFSEKIALQKQKQAEGTAEFERIMKEVYATKRDEPPAN----QKI
C5              MANPRKFSEKIALQKQKQAEGTAEFERIMKEVYATKRDEPPVNQNPNQKI
C6              MANPRKFSEKIALQKQKQAEGTAEFERIMKEVYATKRDEPPVN----QKI
C7              MANPRKFSEKIALQKQKQAEGTAEFERIMKEVYATKRDEPPAN----QKI
C8              MANPRKFSEKIALQKQKQAEGTAEFERIMKEVYATKRDDPPAN----QKI
C9              MANPRKFSEKIALQKQKQAEGTAEFERIMKEVYATKRDDPPAN----QKI
                **************************************:**.*    ***

C1              LDGLVGGQEVSQSSPGAGNGTG---GGGSGSGSGASGGGASPDGLGGGGG
C2              LDGLVGGQEVSQSSPGAGNGTG---GGGSGSGSGASGGGASPDGLGGGGG
C3              IDGLVGGQEVSQSSPGAGNGTG---GGGSGSGSGASGGGASPDGLGGGGG
C4              LDGLVGGQEVSQSSPGAGNGTG---GGGSGSGSGASGGGASPDGLGGGGG
C5              LESLVGGQEVSQSSPGAGN------GGGSGSGSGASGGGASPDGLGGGGG
C6              LESLVGGPEVSQSSPGAGNGTGGGGGGGSGSGSGASGGGASPDGLGGGGG
C7              LECLGGGQEVSQSSPGAGNGSG--GGGGSGSGSGASGGGASPDGLGGGGG
C8              LECLGGGHEVSQSSPGSGNGTG--GGGGSGSGSGASGGGASPDGLAGGGG
C9              LECLGGVQEVSQSSPGSGNGTG--GGGGSGSGSGASGGGASPDGLAGGGG
                :: * *  ********:**      ********************.****

C1              S--PTAYRESRGRSVGVGPMRRPSERKQDRSPYGSSS-TQQTLDNGQLNP
C2              S--PTAYRESRGRSVGVGPMRRPSERKQDRSPYGSSS-TQQTLDNGQLNP
C3              S--PTAYRESRGRSVGVGPMRRPSERKQDRSPYGSSS-TQQTLDNGQLNP
C4              S--PTAYRESRGRSVGVGPMRRPSERKQDRSPYGSSN-TQQTLDNGQLNP
C5              S--PTAYRESRGRSVGVGPMRRPSERKQDRSPYGSSSGTQQTLDNGQLNP
C6              S--PTAYRESRGRSVGVGPMRRPSERKQDRSPYGSSS-TQQTLDNGQLNP
C7              S--PTAYRESRGRSVGVGPMRRPSERKQDRSPYGSSS-TQQTLDNGQLNP
C8              GGSPTTYRESRGRSVGVGPMRRPSERKQDRSPYGSSGGTQQTLDNGQLNP
C9              G-SPTAYRESRGRSVGVGPMRRPSERKQDRSPYGSSSSTQQTLDNGQLNP
                .  **:******************************. ************

C1              HLLGPPTAESLWRRSSSDSALHQSALVAGFNSDVNSMG-ANYQQQQHQQQ
C2              HLLGPPTAESLWRRSSSDSALHQSALVAGFNSDVNSMG-ANYQQQQHQQ-
C3              HLLGPPTAESLWRRSSSDSALHQSALVAGFNSDVNAMG-ASYQQQQHQQP
C4              HLLGPPTAESLWRRSSSDSALHQSALVAGFNSDVNSMG-ANYQQQQHQQP
C5              HLLGPPTAESLWRRSSSDSALHQSALVAGFNADVNSMGGGNYQQQQQHQQ
C6              HLLGPPTAESLGRRSNSDSALHHSALVAGFNADVNSMG-ASYQQQHQ---
C7              HLLGPPTTENSWRRSSSDSALHQSALVAGFN-DVNSMG-GNYQQQQHQQ-
C8              HLLGPPTADSLWRRSSSDSALHQTALGAGFDTNVNMMHPNYQPQQHQQQQ
C9              HLLGPPTSDNLWRRSSSDSALHQTALGAGFDTNVNSMYQQQQQQQHHQQQ
                *******::.  ***.******::** ***: :** *      **::   

C1              -QQ---PGQPRSHSPHHGINRTMSPQAQRRKSPLLQPHQLQLQQLQQQQQ
C2              ------PGQPRSHSPHHGINRTMSPQAQRRKSPILQPHQLQLQQLQQQQQ
C3              -Q----QGQPRSHSPHHGINRTMSPQAQRRKSPLLQPHQLQLQQLQQQQQ
C4              -Q----PGQPRSHSPHHGISRTMSPQAQRRKSPLLQPHQLQLQQLQQQQQ
C5              QQQ---SGQTRSHSPHHGINRTLSPQAQRRKSPLLQPHQLQLQQLQQQQQ
C6              -QQ---PGQPRSHSPHHGINRTLSPQAQRRKSPLLQPHQLQLQQLQQQHQ
C7              -QQ---SGQPRSHSPHHGINRTLSPQAQRRKSPILQPHQLQLQQLQQQQQ
C8              QQQ---PGQPRSHSPHHGINRTMSPQAQRRKSPGLQPPQLQLQQLQQQHQ
C9              QQQQQQPGQTRSHSPHHGINRTMSPQAQRRKSPALQHPQLQLQQLQQQ--
                       **.*********.**:********** **  **********  

C1              QMQHQHQL---HQQLQMQQLQQ---HQQQHQQQQQQQNTPYNNAKFTNPV
C2              QMQHQHQL---HQQLQMQQLQQ---HQQQ----QQQQNTPYNNAKFTNPV
C3              QMQHQHQL---HQQLQMQQLQQ---HQQQHQQQQQQQNTPYNNAKFTNPV
C4              QMQHQHQL---HQQLQMQQLQQ---HQQQHQQQQQQQNTPYNNAKFTNPV
C5              QMQQQHQHHQLHQQLQMQQLQQHQQQHQQQQQHQQQQTTPYNNAKFANPV
C6              QMQQQHQY-QLHQQLQMQQLQQ--QQHQQQQ--QQQQTTPYNNAKFANPV
C7              HMQQQHQN-QLHQQLQMQQMQQ---QQQQQQ--QHQQNTPYNNAKFANPV
C8              QMQQQHQM---HQQLQMQQLHQQQHQQQQQQQ-----TTPYNNAKFANPV
C9              QMQQQHQL---HQQLQMQQLQQQQHQQQQQQQQQQQQTTPYNNAKFTNPV
                :**:***    ********::*   ::**        .********:***

C1              FRPLQDQVNFANTGSLPDLTALQNYGPQQ---QQQQSQQ--------QPS
C2              FRPLQDQVNFANTGSLPDLTALQNYGPQQ---QQQQSQQ--------QQS
C3              FRPLQDQVNFANTGSLPDLTALQNYGPQQQQQQQQQSQQ--------QPS
C4              FRPLQDQVNFANTGSLPDLTALQNYGPQQPQQQQQQSQQ--------QPS
C5              FRPLQDQVNFANTGSLPDLTALQNYGPQQ----QQQ-----------QTQ
C6              FRPLQDQVNFANTGSLPDLTALQNYGPQQ----QQQSQQQQQQQQQQQSQ
C7              FRPLQDQVNFANTGSLPDLTALHTYGPQQ----QQQSQ---------QQH
C8              FRPLQEQANFANTGSLPDLTALQNYTPQQ-----QQ-------------Q
C9              FRPLQEQANFANTGSLPDLTALQNYAPQQ-----QQQI----------QQ
                *****:*.**************:.* ***     **              

C1              QQQQQLQQTLSPVMSPHNHRRERDQSPSPFSPAGGGGG-AGPGSPYQQQQ
C2              QQQQQLQQTLSPVMSPHNHRRERDQSPSPFSPAGGGGG-AGPGSPYQQQQ
C3              QQQQQLQQTLSPVMSPHNHRRERDQSPSPFSPAGGGGG-AGPGSPY-QQQ
C4              QQQQQLQQTLSPVMSPHNHRRERDQSPSPFSPAGGGGG-AGPGSPY-QQQ
C5              QPQQQLQQTLSPVMSPHNHRRDRDQSPSPFSPAGGG---AGPGSPYQQQQ
C6              QQQQQLQQTLSPVMSPHNHRRDRDQSPSPFSPAGGGGGGAGPGSPYQQQQ
C7              TQQQQLQQTLSPVMSPHNHRRDRDQSPSPFSPAGGGGG-AGPGSPYQQQQ
C8              SQQQQLQQTLSPVMSPHNHRRDRDQSPSPFSPAGGGGG-AGPGSPYQQQQ
C9              QQQQQLQQTLSPVMSPHNHRRERDQSPSPFSPAGGGGG-AGPGSPYQQQQ
                  *******************:**************   ******* ***

C1              HSPTGNTQQQQQQHQQ------PSNSPHLSFTNLATTQAAVTTFNPLPTL
C2              HSPTGNTQQQ--QHQQ------PSNSPHLSFTNLATTQAAVTTFNPLPTL
C3              HSPTGNTQQQ--QHQQ------PSNSPHLSFTNLATTQAAVSTFNPLPTL
C4              HSPTGNT-QQ--QHQQ------PSNSPHLSFTNLATTQAAVSTFNPLPTL
C5              HSPTGNTQQQ--QQQQ------PSSSPHLSFTNLATTQAAVSTFNPLPTL
C6              HSPTGNTQQQ--QQQQQQ---QPSSSPHLSFTNLATTQAAVSTFNPLPTL
C7              HSPTGNTQQQ--QQQP-------SSSPHLSFTNLATTQAAVSTFNPLPTL
C8              HSPTGNTQQQ--QQQQQQQQQQPSSSPHLSFTNLATTQATVSTFNPLPTL
C9              HSPTGNTQQQ--QQQQ-----QPSSSPHLSFTNLATTQATVATFNPLPTL
                ******* **  *:*        *.**************:*:********

C1              GPHNATDYRQPPNPPSPRSSPGLLSSVSATDLHSSAPASPIRQQQQAHQQ
C2              GPHNATDYRQPPNPPSPRSSPGLLSSVSATDLHSSAPASPIRQQQQAHQQ
C3              GPHNATDYRQPPNPPSPRSSPGLLSSVSATDLHSSAPASPIRQQQQVQQQ
C4              GPHNATDYRQPPNPPSPRSSPGLLSSVSATDLHSSAPASPIRQQQQAQQQ
C5              GPHNATDYRQPPNPPSPRSSPGLLSSVSATDLHSSAPASPIRQQQQQVQQ
C6              GPHNATDYRQPPNPPSPRSSPGLLSSVSATDLHSSAPASPIRQQQQAQQQ
C7              GPHNATDYRQPPNPPSPRSSPGLLSSVSATDLHSSAPASPIRQQQQVQQQ
C8              GPHNATDYRQPPNPPSPRSSPGLLSSVSATDLHSSAPASPIRQQQQVQQQ
C9              GPHNATDYRQPPNPPSPRSSPGLLSSVSATDLHSSAPASPIRQQQQAQQQ
                **********************************************  **

C1              QQQQQQAQQQQQ------QFDNSYNSLNTSFHNQFEIFSLGDSNSSPEQQ
C2              QQQQQQAQQQQQ------QFDNSYNSLNTSFHNQFEIFSLGDSNSSPEQQ
C3              QQQQQQAQQQQQ------QFDNSYNSLNTSFHNQFEIFSLGDSNSSPEQQ
C4              QQ----AQQQQQ------QFDNSYNSLNTSFHNQFEIFSLGDSNSSPEQQ
C5              QQQQQQQQQQQQ-QQGHQQFDNSYNSLNTSFHNQFEIFSLGDSNSSPEQQ
C6              QQQQQQQQQQQG-HQQQQQFDNSYNSLNTSFHNQFEIFSLGDSNSSPEQQ
C7              QQQQQQQQQQQQTHQQQQQFDNSYNSLNTSFHNQFEIFSLGDSNSSPEQQ
C8              QQQQQQQQQQ-AHQQQ-QQFDNSYNSLNTSFHNQFEIFSLGDSNSSPEQQ
C9              QQQQQQQQQQAAHQQQ-QQFDNSYNSLNTSFHNQFEIFSLGDSNSSPEQQ
                **     ***        ********************************

C1              GFANNFVALDFDDLSGGGGGGPSGG------GGSNGGG-LTNGYN-KPEM
C2              GFANNFVALDFDDLSGGGGGGPGGG------GGSNGGG-LTNGYN-KPEM
C3              GFANNFVALDFDDLSGGGGGGPGGG------GGSNGGG-LTNGYN-KSEM
C4              GFANNFVALDFDDLSGGGGGGPGGG------GGSNGGG-LTNGYN-KSEM
C5              GFANNFVALDFDDLSGGG---GGGG------NGSNGGGALTNGYNNKQEM
C6              GFANNFVALDFDDLSGGG---GGG-------SGSNGG--LTNGYN-KQEM
C7              GFANNFVALDFDDLSGGGGV-SGGG------NGSNGGG-LTNGYN-KPDM
C8              GFANNFVALDFDELSGGGGGGSGGG--------SNGGG-LTNGYN-KQEM
C9              GFANNFVALDFDDLSGGGGGGSAGGGGGGGGVGSNGGG-LTNGYN-KQEM
                ************:*****    .*         ****  ****** * :*

C1              LDFSELSGSPEASGNNNHMRRGVSNLNNN-GLSNGVVGSTHNGSTNLNGA
C2              LDFSELSGSPEASGNNNHMRRGVSNLNNN-GLSNGVVGSTHNGSTNLNGA
C3              LDFSELSGSPEASGNNNHMRRGVSNLNNN-GLSNG-VGSTHNGSTNLNGA
C4              LDFSELSGSPEASGNNNHMRRGVSNLNNN-GLSNG-VGSTHNGSTNLNGA
C5              LDFSELSGSPEASGNNNHMRRGVSNLNNNNGLSNG-VGSTHNGSTNLNGA
C6              LDFSELSGSPEASGNNNHMRRGVSNLNNN-GLSNG-VGSTHNGSTNLNGA
C7              LDFSELSGSPESSGNNNHMRRGVSNLNNN-GLSNG-VGSTHNGSTNLNGA
C8              LDFSELSGSPEASGNNNHMRRGVSNLNNN-GLSNG-VGSTHNGSTNLNGA
C9              LDFSELSGSPEASGNNNHMRRGVSNLNNN-GLSNG-VGSTHNGSTNLNGA
                ***********:***************** ***** **************

C1              GNNNSSSGGG-TAQDPLGITTSPVPSPLGCPSSPLPIPIPMSAQSSPQQQ
C2              GNNNSSSGGG-TAQDPLGITTSPVPSPLGCPSSPLPIPIPMSAQSSPQQQ
C3              GNNNSSSGGG-TAQDPLGITTSPVPSPLGCPSS--PLPIPMSAQSSPQQQ
C4              GNNNSNSGGGGTAQDPLGITTSPVPSPLGCPSS--PLPIPMSAQSSPQQ-
C5              GNNNGSSGGG-SAQDPLGITASPVPSPLGCPSS--PLPIPMSAQASPQHQ
C6              GNNNSSSGGG-SAQDPLGIAASPVPSPLGCPSS--PLPIPISAQTSPQQQ
C7              GNNNSSSGGG-SGQDPLGIAASPVPSPLGCPSS--PLPIPMSAQASPQ-Q
C8              GNNNSSSGGG-STQDPLGITASPVPSPLGCPSS--PLPIPMSAQTSPQQQ
C9              GNNNSSSGGG-STQDPLGITTSPVPSPLGCPSS--PLPIPMSAQTSPQQQ
                ****..**** : ******::************  *:***:***:***  

C1              H----HHHQQQQQ-----QHHQQQHHQQQQLSLSLHHSPHHSPMHSPHHG
C2              H----HHHQQQQQQHHQQQHHQQQHHQQQQLSLSLHHSPHHSPMHSPHHG
C3              H----HHHQQQQQ-----QHHHQQHHQQQQLSLSLHHSPHHSPMHSPHHG
C4              H----HHHHQQQQ-----QHHQQQHHQQQQLSLSLHHSPHHSPLHSPHHG
C5              H----HHQQQQQQQ---QHHQQQQHHQQQQLSLSLHHSPHHSPMHSPHHG
C6              Q----HHHHHQQQQ---QHHQQQQHHQQQQLSLSLHHSPHHSPMHSPHHG
C7              H----HHHHQQQQQ---QHHHQQQHHQQQQLSLSLHHSPHHSPMHSPHHG
C8              H----HHQHQQQQQ---QQHHQQQHHQQQQLSLSLHHSPHHSPLHSPHHG
C9              HNHHHHHHQHQQQQ---QQHHQQQHHQQQQLSLSLHHSPHHSPMHSPHHG
                :    **:::***     :*::*********************:******

C1              NSPLSSSSPVSHNACSNSNVVMNHQ--QQQQQ-----HHHQQHHHQGSSQ
C2              NSPLSSSSPVSHNACSNSNVVMNHQ--QQQQQQ----HHHQQHHHQGSSQ
C3              NSPLSSSSPVSHNACSNSNVVMNHQ---QQQQQ----HHHQQHHHQGSSQ
C4              NSPLSSSSPVSHNACSNSNVVMNHQHQQQQQQQ----HHHQQHHHQGSSQ
C5              NSPLSSSSPVSHNACSNSNVVMNHIQ----QQQ----QQHQPHLHQGSSQ
C6              SSPLSSSSPVSHNACSNSNVVMNHH-----QQQ----HQHQPHLHQGSSQ
C7              NSPLSSSSPVSHNACSNSNVVMNHHQ---QQQQ----HQHQHHQHQGSSQ
C8              NSPLSSSSPVSHNACSNSNVVMNHHQ---QQQQ----HHHQQQHLQGSSQ
C9              NSPLSSSSPVSHNACSNSNVVMNHHQ---QQQQQQQHHHQQQHHLQGSSQ
                .***********************      **     :::* :  *****

C1              SHTPTTANIPSIIFSDYSSNADYTREIFDSLDLDLGQMDVAGLQMLSDQN
C2              SHTPTTANIPSIIFSDYSSNADYTREIFDSLDLDLGQMDVAGLQMLSDQN
C3              SHTPTTANIPSIIFSDYSSNADFTREIFDSLDLDLGQMDVAGLQMLSDQN
C4              SHTPTTANIPSIIFSDYSSNADFPREIFDSLDLDLGQMDVAGLQMLSDQS
C5              SHTPTTANIPSIIFSDYSSNADFSREIFDTLDLDLGQMDVAGLQMLSDQN
C6              SHTPTTANIPSIIFSDYSSNADFSREIFDTLDLDLGQMDVAGLQMLSDQN
C7              SHTPTTANIPSIIFSDYSSNADFSREIFDTLDLDLGQMDVAGLQMLSDQN
C8              SHTPTTTNIPSIIFSDYSSNADFSREIFDTLDLDLGQMDVAGLQMLSDQN
C9              SHTPTTANIPSIIFSDYSSNADFSREIFDTLDLDLGQMDVAGLQMLSDQN
                ******:***************:.*****:*******************.

C1              PIMIADPNIEDSFRRDLNoooooooooooooooooooooo------
C2              PIMIADPNIEDSFRRDLNooooooooooooooooooooooooo---
C3              PIMIADPNIEDSFRRDLNoooooooooooooooooooooooooo--
C4              PIMIADPNIEDSFRRDLNoooooooooooooooooooooooooooo
C5              PIMIADPNIEDSFRRDLNooooooooooooooooo-----------
C6              PIMIADPNIEDSFRRDLNooooooooooooooo-------------
C7              PIMIADPNIEDSFRRDLNooooooooooooooooooooooooo---
C8              SIMIADANIEDSFRRDLNoooooooooooooooooooo--------
C9              PIMIADPNIEDSFRRDLN----------------------------
                .*****.***********                            




PROGRAM: T-COFFEE Version_10.00.r1613 (2013-10-22 15:49:04 - Revision 1613 - Build 427)
-full_log      	S	[0] 
-genepred_score	S	[0] 	nsd
-run_name      	S	[0] 
-mem_mode      	S	[0] 	mem
-extend        	D	[1] 	1 
-extend_mode   	S	[0] 	very_fast_triplet
-max_n_pair    	D	[0] 	10 
-seq_name_for_quadruplet	S	[0] 	all
-compact       	S	[0] 	default
-clean         	S	[0] 	no
-do_self       	FL	[0] 	0
-do_normalise  	D	[0] 	1000 
-template_file 	S	[0] 
-setenv        	S	[0] 	0
-template_mode 	S	[0] 
-flip          	D	[0] 	0 
-remove_template_file	D	[0] 	0 
-profile_template_file	S	[0] 
-in            	S	[0] 
-seq           	S	[0] 
-aln           	S	[0] 
-method_limits 	S	[0] 
-method        	S	[0] 
-lib           	S	[0] 
-profile       	S	[0] 
-profile1      	S	[0] 
-profile2      	S	[0] 
-pdb           	S	[0] 
-relax_lib     	D	[0] 	1 
-filter_lib    	D	[0] 	0 
-shrink_lib    	D	[0] 	0 
-out_lib       	W_F	[0] 	no
-out_lib_mode  	S	[0] 	primary
-lib_only      	D	[0] 	0 
-outseqweight  	W_F	[0] 	no
-dpa           	FL	[0] 	0
-seq_source    	S	[0] 	ANY
-cosmetic_penalty	D	[0] 	0 
-gapopen       	D	[0] 	0 
-gapext        	D	[0] 	0 
-fgapopen      	D	[0] 	0 
-fgapext       	D	[0] 	0 
-nomatch       	D	[0] 	0 
-newtree       	W_F	[0] 	default
-tree          	W_F	[0] 	NO
-usetree       	R_F	[0] 
-tree_mode     	S	[0] 	nj
-distance_matrix_mode	S	[0] 	ktup
-distance_matrix_sim_mode	S	[0] 	idmat_sim1
-quicktree     	FL	[0] 	0
-outfile       	W_F	[0] 	default
-maximise      	FL	[1] 	1
-output        	S	[1] 	score_ascii	html	score_ascii
-len           	D	[0] 	0 
-infile        	R_F	[1] 	/opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln
-matrix        	S	[0] 	default
-tg_mode       	D	[0] 	1 
-profile_mode  	S	[0] 	cw_profile_profile
-profile_comparison	S	[0] 	profile
-dp_mode       	S	[0] 	linked_pair_wise
-ktuple        	D	[0] 	1 
-ndiag         	D	[0] 	0 
-diag_threshold	D	[0] 	0 
-diag_mode     	D	[0] 	0 
-sim_matrix    	S	[0] 	vasiliky
-transform     	S	[0] 
-extend_seq    	FL	[0] 	0
-outorder      	S	[0] 	input
-inorder       	S	[0] 	aligned
-seqnos        	S	[0] 	off
-case          	S	[0] 	keep
-cpu           	D	[0] 	0 
-maxnseq       	D	[0] 	1000 
-maxlen        	D	[0] 	-1 
-sample_dp     	D	[0] 	0 
-weight        	S	[0] 	default
-seq_weight    	S	[0] 	no
-align         	FL	[1] 	1
-mocca         	FL	[0] 	0
-domain        	FL	[0] 	0
-start         	D	[0] 	0 
-len           	D	[0] 	0 
-scale         	D	[0] 	0 
-mocca_interactive	FL	[0] 	0
-method_evaluate_mode	S	[0] 	default
-evaluate_mode 	S	[1] 	t_coffee_fast
-get_type      	FL	[0] 	0
-clean_aln     	D	[0] 	0 
-clean_threshold	D	[1] 	1 
-clean_iteration	D	[1] 	1 
-clean_evaluate_mode	S	[0] 	t_coffee_fast
-extend_matrix 	FL	[0] 	0
-prot_min_sim  	D	[40] 	40 
-prot_max_sim  	D	[90] 	90 
-prot_min_cov  	D	[40] 	40 
-pdb_type      	S	[0] 	d
-pdb_min_sim   	D	[35] 	35 
-pdb_max_sim   	D	[100] 	100 
-pdb_min_cov   	D	[50] 	50 
-pdb_blast_server	W_F	[0] 	EBI
-blast         	W_F	[0] 
-blast_server  	W_F	[0] 	EBI
-pdb_db        	W_F	[0] 	pdb
-protein_db    	W_F	[0] 	uniprot
-method_log    	W_F	[0] 	no
-struc_to_use  	S	[0] 
-cache         	W_F	[0] 	use
-align_pdb_param_file	W_F	[0] 	no
-align_pdb_hasch_mode	W_F	[0] 	hasch_ca_trace_bubble
-external_aligner	S	[0] 	NO
-msa_mode      	S	[0] 	tree
-master        	S	[0] 	no
-blast_nseq    	D	[0] 	0 
-lalign_n_top  	D	[0] 	10 
-iterate       	D	[1] 	0 
-trim          	D	[0] 	0 
-split         	D	[0] 	0 
-trimfile      	S	[0] 	default
-split         	D	[0] 	0 
-split_nseq_thres	D	[0] 	0 
-split_score_thres	D	[0] 	0 
-check_pdb_status	D	[0] 	0 
-clean_seq_name	D	[0] 	0 
-seq_to_keep   	S	[0] 
-dpa_master_aln	S	[0] 
-dpa_maxnseq   	D	[0] 	0 
-dpa_min_score1	D	[0] 
-dpa_min_score2	D	[0] 
-dpa_keep_tmpfile	FL	[0] 	0
-dpa_debug     	D	[0] 	0 
-multi_core    	S	[0] 	templates_jobs_relax_msa_evaluate
-n_core        	D	[0] 	0 
-max_n_proc    	D	[0] 	0 
-lib_list      	S	[0] 
-prune_lib_mode	S	[0] 	5
-tip           	S	[0] 	none
-rna_lib       	S	[0] 
-no_warning    	D	[0] 	0 
-run_local_script	D	[0] 	0 
-plugins       	S	[0] 	default
-proxy         	S	[0] 	unset
-email         	S	[0] 
-clean_overaln 	D	[0] 	0 
-overaln_param 	S	[0] 
-overaln_mode  	S	[0] 
-overaln_model 	S	[0] 
-overaln_threshold	D	[0] 	0 
-overaln_target	D	[0] 	0 
-overaln_P1    	D	[0] 	0 
-overaln_P2    	D	[0] 	0 
-overaln_P3    	D	[0] 	0 
-overaln_P4    	D	[0] 	0 
-exon_boundaries	S	[0] 
-dump          	S	[0] 	no
-display       	D	[0] 	100 

INPUT FILES
	Input File (S) /opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln  Format clustal_aln
	Input File (M) proba_pair 

Identify Master Sequences [no]:

Master Sequences Identified
INPUT SEQUENCES: 9 SEQUENCES  [PROTEIN]
  Input File /opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C1 Length  819 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C2 Length  819 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C3 Length  819 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C4 Length  819 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C5 Length  819 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C6 Length  819 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C7 Length  819 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C8 Length  819 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C9 Length  819 type PROTEIN Struct Unchecked

	Multi Core Mode: 72 processors:
gins       	S	[0] 	default
-proxy         	S	[0] 	unset
-email         	S	[0] 
-clean_overaln 	D	[0] 	0 
-overaln_param 	S	[0] 
-overaln_mode  	S	[0] 
-overaln_model 	S	[0] 
-overaln_threshold	D	[0] 	0 
-overaln_target	D	[0] 	0 
-overaln_P1    	D	[0] 	0 
-overaln_P2    	D	[0] 	0 
-overaln_P3    	D	[0] 	0 
-overaln_P4    	D	[0] 	0 
-exon_boundaries	S	[0] 
-dump          	S	[0] 	no
-display       	D	[0] 	100 

INPUT FILES
	Input File (S) /opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln  Format clustal_aln
	Input File (M) proba_pair 

Identify Master Sequences [no]:

Master Sequences Identified
INPUT SEQUENCES: 9 SEQUENCES  [PROTEIN]
  Input File /opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C1 Length  819 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C2 Length  819 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C3 Length  819 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C4 Length  819 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C5 Length  819 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C6 Length  819 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C7 Length  819 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C8 Length  819 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C9 Length  819 type PROTEIN Struct Unchecked

	Multi Core Mode: 72 processors:

	--- Process Method/Library/Aln S/opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.alngins       	S	[0] 	default
-proxy         	S	[0] 	unset
-email         	S	[0] 
-clean_overaln 	D	[0] 	0 
-overaln_param 	S	[0] 
-overaln_mode  	S	[0] 
-overaln_model 	S	[0] 
-overaln_threshold	D	[0] 	0 
-overaln_target	D	[0] 	0 
-overaln_P1    	D	[0] 	0 
-overaln_P2    	D	[0] 	0 
-overaln_P3    	D	[0] 	0 
-overaln_P4    	D	[0] 	0 
-exon_boundaries	S	[0] 
-dump          	S	[0] 	no
-display       	D	[0] 	100 

INPUT FILES
	Input File (S) /opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln  Format clustal_aln
	Input File (M) proba_pair 

Identify Master Sequences [no]:

Master Sequences Identified
INPUT SEQUENCES: 9 SEQUENCES  [PROTEIN]
  Input File /opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C1 Length  819 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C2 Length  819 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C3 Length  819 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C4 Length  819 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C5 Length  819 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C6 Length  819 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C7 Length  819 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C8 Length  819 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C9 Length  819 type PROTEIN Struct Unchecked

	Multi Core Mode: 72 processors:

	--- Process Method/Library/Aln S/opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.alngins       	S	[0] 	default
-proxy         	S	[0] 	unset
-email         	S	[0] 
-clean_overaln 	D	[0] 	0 
-overaln_param 	S	[0] 
-overaln_mode  	S	[0] 
-overaln_model 	S	[0] 
-overaln_threshold	D	[0] 	0 
-overaln_target	D	[0] 	0 
-overaln_P1    	D	[0] 	0 
-overaln_P2    	D	[0] 	0 
-overaln_P3    	D	[0] 	0 
-overaln_P4    	D	[0] 	0 
-exon_boundaries	S	[0] 
-dump          	S	[0] 	no
-display       	D	[0] 	100 

INPUT FILES
	Input File (S) /opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln  Format clustal_aln
	Input File (M) proba_pair 

Identify Master Sequences [no]:

Master Sequences Identified
INPUT SEQUENCES: 9 SEQUENCES  [PROTEIN]
  Input File /opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C1 Length  819 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C2 Length  819 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C3 Length  819 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C4 Length  819 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C5 Length  819 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C6 Length  819 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C7 Length  819 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C8 Length  819 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C9 Length  819 type PROTEIN Struct Unchecked

	Multi Core Mode: 72 processors:

	--- Process Method/Library/Aln S/opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.alngins       	S	[0] 	default
-proxy         	S	[0] 	unset
-email         	S	[0] 
-clean_overaln 	D	[0] 	0 
-overaln_param 	S	[0] 
-overaln_mode  	S	[0] 
-overaln_model 	S	[0] 
-overaln_threshold	D	[0] 	0 
-overaln_target	D	[0] 	0 
-overaln_P1    	D	[0] 	0 
-overaln_P2    	D	[0] 	0 
-overaln_P3    	D	[0] 	0 
-overaln_P4    	D	[0] 	0 
-exon_boundaries	S	[0] 
-dump          	S	[0] 	no
-display       	D	[0] 	100 

INPUT FILES
	Input File (S) /opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln  Format clustal_aln
	Input File (M) proba_pair 

Identify Master Sequences [no]:

Master Sequences Identified
INPUT SEQUENCES: 9 SEQUENCES  [PROTEIN]
  Input File /opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C1 Length  819 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C2 Length  819 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C3 Length  819 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C4 Length  819 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C5 Length  819 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C6 Length  819 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C7 Length  819 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C8 Length  819 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C9 Length  819 type PROTEIN Struct Unchecked

	Multi Core Mode: 72 processors:

	--- Process Method/Library/Aln S/opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.alngins       	S	[0] 	default
-proxy         	S	[0] 	unset
-email         	S	[0] 
-clean_overaln 	D	[0] 	0 
-overaln_param 	S	[0] 
-overaln_mode  	S	[0] 
-overaln_model 	S	[0] 
-overaln_threshold	D	[0] 	0 
-overaln_target	D	[0] 	0 
-overaln_P1    	D	[0] 	0 
-overaln_P2    	D	[0] 	0 
-overaln_P3    	D	[0] 	0 
-overaln_P4    	D	[0] 	0 
-exon_boundaries	S	[0] 
-dump          	S	[0] 	no
-display       	D	[0] 	100 

INPUT FILES
	Input File (S) /opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln  Format clustal_aln
	Input File (M) proba_pair 

Identify Master Sequences [no]:

Master Sequences Identified
INPUT SEQUENCES: 9 SEQUENCES  [PROTEIN]
  Input File /opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C1 Length  819 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C2 Length  819 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C3 Length  819 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C4 Length  819 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C5 Length  819 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C6 Length  819 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C7 Length  819 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C8 Length  819 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C9 Length  819 type PROTEIN Struct Unchecked

	Multi Core Mode: 72 processors:

	--- Process Method/Library/Aln S/opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.alngins       	S	[0] 	default
-proxy         	S	[0] 	unset
-email         	S	[0] 
-clean_overaln 	D	[0] 	0 
-overaln_param 	S	[0] 
-overaln_mode  	S	[0] 
-overaln_model 	S	[0] 
-overaln_threshold	D	[0] 	0 
-overaln_target	D	[0] 	0 
-overaln_P1    	D	[0] 	0 
-overaln_P2    	D	[0] 	0 
-overaln_P3    	D	[0] 	0 
-overaln_P4    	D	[0] 	0 
-exon_boundaries	S	[0] 
-dump          	S	[0] 	no
-display       	D	[0] 	100 

INPUT FILES
	Input File (S) /opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln  Format clustal_aln
	Input File (M) proba_pair 

Identify Master Sequences [no]:

Master Sequences Identified
INPUT SEQUENCES: 9 SEQUENCES  [PROTEIN]
  Input File /opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C1 Length  819 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C2 Length  819 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C3 Length  819 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C4 Length  819 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C5 Length  819 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C6 Length  819 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C7 Length  819 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C8 Length  819 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C9 Length  819 type PROTEIN Struct Unchecked

	Multi Core Mode: 72 processors:

	--- Process Method/Library/Aln S/opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.alngins       	S	[0] 	default
-proxy         	S	[0] 	unset
-email         	S	[0] 
-clean_overaln 	D	[0] 	0 
-overaln_param 	S	[0] 
-overaln_mode  	S	[0] 
-overaln_model 	S	[0] 
-overaln_threshold	D	[0] 	0 
-overaln_target	D	[0] 	0 
-overaln_P1    	D	[0] 	0 
-overaln_P2    	D	[0] 	0 
-overaln_P3    	D	[0] 	0 
-overaln_P4    	D	[0] 	0 
-exon_boundaries	S	[0] 
-dump          	S	[0] 	no
-display       	D	[0] 	100 

INPUT FILES
	Input File (S) /opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln  Format clustal_aln
	Input File (M) proba_pair 

Identify Master Sequences [no]:

Master Sequences Identified
INPUT SEQUENCES: 9 SEQUENCES  [PROTEIN]
  Input File /opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C1 Length  819 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C2 Length  819 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C3 Length  819 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C4 Length  819 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C5 Length  819 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C6 Length  819 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C7 Length  819 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C8 Length  819 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C9 Length  819 type PROTEIN Struct Unchecked

	Multi Core Mode: 72 processors:

	--- Process Method/Library/Aln S/opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.alngins       	S	[0] 	default
-proxy         	S	[0] 	unset
-email         	S	[0] 
-clean_overaln 	D	[0] 	0 
-overaln_param 	S	[0] 
-overaln_mode  	S	[0] 
-overaln_model 	S	[0] 
-overaln_threshold	D	[0] 	0 
-overaln_target	D	[0] 	0 
-overaln_P1    	D	[0] 	0 
-overaln_P2    	D	[0] 	0 
-overaln_P3    	D	[0] 	0 
-overaln_P4    	D	[0] 	0 
-exon_boundaries	S	[0] 
-dump          	S	[0] 	no
-display       	D	[0] 	100 

INPUT FILES
	Input File (S) /opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln  Format clustal_aln
	Input File (M) proba_pair 

Identify Master Sequences [no]:

Master Sequences Identified
INPUT SEQUENCES: 9 SEQUENCES  [PROTEIN]
  Input File /opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C1 Length  819 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C2 Length  819 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C3 Length  819 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C4 Length  819 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C5 Length  819 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C6 Length  819 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C7 Length  819 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C8 Length  819 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C9 Length  819 type PROTEIN Struct Unchecked

	Multi Core Mode: 72 processors:

	--- Process Method/Library/Aln S/opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.alngins       	S	[0] 	default
-proxy         	S	[0] 	unset
-email         	S	[0] 
-clean_overaln 	D	[0] 	0 
-overaln_param 	S	[0] 
-overaln_mode  	S	[0] 
-overaln_model 	S	[0] 
-overaln_threshold	D	[0] 	0 
-overaln_target	D	[0] 	0 
-overaln_P1    	D	[0] 	0 
-overaln_P2    	D	[0] 	0 
-overaln_P3    	D	[0] 	0 
-overaln_P4    	D	[0] 	0 
-exon_boundaries	S	[0] 
-dump          	S	[0] 	no
-display       	D	[0] 	100 

INPUT FILES
	Input File (S) /opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln  Format clustal_aln
	Input File (M) proba_pair 

Identify Master Sequences [no]:

Master Sequences Identified
INPUT SEQUENCES: 9 SEQUENCES  [PROTEIN]
  Input File /opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C1 Length  819 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C2 Length  819 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C3 Length  819 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C4 Length  819 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C5 Length  819 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C6 Length  819 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C7 Length  819 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C8 Length  819 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C9 Length  819 type PROTEIN Struct Unchecked

	Multi Core Mode: 72 processors:

	--- Process Method/Library/Aln S/opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.alngins       	S	[0] 	default
-proxy         	S	[0] 	unset
-email         	S	[0] 
-clean_overaln 	D	[0] 	0 
-overaln_param 	S	[0] 
-overaln_mode  	S	[0] 
-overaln_model 	S	[0] 
-overaln_threshold	D	[0] 	0 
-overaln_target	D	[0] 	0 
-overaln_P1    	D	[0] 	0 
-overaln_P2    	D	[0] 	0 
-overaln_P3    	D	[0] 	0 
-overaln_P4    	D	[0] 	0 
-exon_boundaries	S	[0] 
-dump          	S	[0] 	no
-display       	D	[0] 	100 

INPUT FILES
	Input File (S) /opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln  Format clustal_aln
	Input File (M) proba_pair 

Identify Master Sequences [no]:

Master Sequences Identified
INPUT SEQUENCES: 9 SEQUENCES  [PROTEIN]
  Input File /opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C1 Length  819 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C2 Length  819 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C3 Length  819 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C4 Length  819 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C5 Length  819 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C6 Length  819 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C7 Length  819 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C8 Length  819 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C9 Length  819 type PROTEIN Struct Unchecked

	Multi Core Mode: 72 processors:

	--- Process Method/Library/Aln S/opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.alngins       	S	[0] 	default
-proxy         	S	[0] 	unset
-email         	S	[0] 
-clean_overaln 	D	[0] 	0 
-overaln_param 	S	[0] 
-overaln_mode  	S	[0] 
-overaln_model 	S	[0] 
-overaln_threshold	D	[0] 	0 
-overaln_target	D	[0] 	0 
-overaln_P1    	D	[0] 	0 
-overaln_P2    	D	[0] 	0 
-overaln_P3    	D	[0] 	0 
-overaln_P4    	D	[0] 	0 
-exon_boundaries	S	[0] 
-dump          	S	[0] 	no
-display       	D	[0] 	100 

INPUT FILES
	Input File (S) /opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln  Format clustal_aln
	Input File (M) proba_pair 

Identify Master Sequences [no]:

Master Sequences Identified
INPUT SEQUENCES: 9 SEQUENCES  [PROTEIN]
  Input File /opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C1 Length  819 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C2 Length  819 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C3 Length  819 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C4 Length  819 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C5 Length  819 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C6 Length  819 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C7 Length  819 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C8 Length  819 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C9 Length  819 type PROTEIN Struct Unchecked

	Multi Core Mode: 72 processors:

	--- Process Method/Library/Aln S/opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.alngins       	S	[0] 	default
-proxy         	S	[0] 	unset
-email         	S	[0] 
-clean_overaln 	D	[0] 	0 
-overaln_param 	S	[0] 
-overaln_mode  	S	[0] 
-overaln_model 	S	[0] 
-overaln_threshold	D	[0] 	0 
-overaln_target	D	[0] 	0 
-overaln_P1    	D	[0] 	0 
-overaln_P2    	D	[0] 	0 
-overaln_P3    	D	[0] 	0 
-overaln_P4    	D	[0] 	0 
-exon_boundaries	S	[0] 
-dump          	S	[0] 	no
-display       	D	[0] 	100 

INPUT FILES
	Input File (S) /opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln  Format clustal_aln
	Input File (M) proba_pair 

Identify Master Sequences [no]:

Master Sequences Identified
INPUT SEQUENCES: 9 SEQUENCES  [PROTEIN]
  Input File /opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C1 Length  819 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C2 Length  819 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C3 Length  819 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C4 Length  819 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C5 Length  819 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C6 Length  819 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C7 Length  819 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C8 Length  819 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C9 Length  819 type PROTEIN Struct Unchecked

	Multi Core Mode: 72 processors:

	--- Process Method/Library/Aln S/opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.alngins       	S	[0] 	default
-proxy         	S	[0] 	unset
-email         	S	[0] 
-clean_overaln 	D	[0] 	0 
-overaln_param 	S	[0] 
-overaln_mode  	S	[0] 
-overaln_model 	S	[0] 
-overaln_threshold	D	[0] 	0 
-overaln_target	D	[0] 	0 
-overaln_P1    	D	[0] 	0 
-overaln_P2    	D	[0] 	0 
-overaln_P3    	D	[0] 	0 
-overaln_P4    	D	[0] 	0 
-exon_boundaries	S	[0] 
-dump          	S	[0] 	no
-display       	D	[0] 	100 

INPUT FILES
	Input File (S) /opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln  Format clustal_aln
	Input File (M) proba_pair 

Identify Master Sequences [no]:

Master Sequences Identified
INPUT SEQUENCES: 9 SEQUENCES  [PROTEIN]
  Input File /opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C1 Length  819 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C2 Length  819 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C3 Length  819 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C4 Length  819 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C5 Length  819 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C6 Length  819 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C7 Length  819 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C8 Length  819 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C9 Length  819 type PROTEIN Struct Unchecked

	Multi Core Mode: 72 processors:

	--- Process Method/Library/Aln S/opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.alngins       	S	[0] 	default
-proxy         	S	[0] 	unset
-email         	S	[0] 
-clean_overaln 	D	[0] 	0 
-overaln_param 	S	[0] 
-overaln_mode  	S	[0] 
-overaln_model 	S	[0] 
-overaln_threshold	D	[0] 	0 
-overaln_target	D	[0] 	0 
-overaln_P1    	D	[0] 	0 
-overaln_P2    	D	[0] 	0 
-overaln_P3    	D	[0] 	0 
-overaln_P4    	D	[0] 	0 
-exon_boundaries	S	[0] 
-dump          	S	[0] 	no
-display       	D	[0] 	100 

INPUT FILES
	Input File (S) /opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln  Format clustal_aln
	Input File (M) proba_pair 

Identify Master Sequences [no]:

Master Sequences Identified
INPUT SEQUENCES: 9 SEQUENCES  [PROTEIN]
  Input File /opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C1 Length  819 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C2 Length  819 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C3 Length  819 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C4 Length  819 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C5 Length  819 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C6 Length  819 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C7 Length  819 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C8 Length  819 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C9 Length  819 type PROTEIN Struct Unchecked

	Multi Core Mode: 72 processors:

	--- Process Method/Library/Aln S/opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.alngins       	S	[0] 	default
-proxy         	S	[0] 	unset
-email         	S	[0] 
-clean_overaln 	D	[0] 	0 
-overaln_param 	S	[0] 
-overaln_mode  	S	[0] 
-overaln_model 	S	[0] 
-overaln_threshold	D	[0] 	0 
-overaln_target	D	[0] 	0 
-overaln_P1    	D	[0] 	0 
-overaln_P2    	D	[0] 	0 
-overaln_P3    	D	[0] 	0 
-overaln_P4    	D	[0] 	0 
-exon_boundaries	S	[0] 
-dump          	S	[0] 	no
-display       	D	[0] 	100 

INPUT FILES
	Input File (S) /opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln  Format clustal_aln
	Input File (M) proba_pair 

Identify Master Sequences [no]:

Master Sequences Identified
INPUT SEQUENCES: 9 SEQUENCES  [PROTEIN]
  Input File /opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C1 Length  819 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C2 Length  819 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C3 Length  819 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C4 Length  819 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C5 Length  819 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C6 Length  819 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C7 Length  819 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C8 Length  819 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C9 Length  819 type PROTEIN Struct Unchecked

	Multi Core Mode: 72 processors:

	--- Process Method/Library/Aln S/opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.alngins       	S	[0] 	default
-proxy         	S	[0] 	unset
-email         	S	[0] 
-clean_overaln 	D	[0] 	0 
-overaln_param 	S	[0] 
-overaln_mode  	S	[0] 
-overaln_model 	S	[0] 
-overaln_threshold	D	[0] 	0 
-overaln_target	D	[0] 	0 
-overaln_P1    	D	[0] 	0 
-overaln_P2    	D	[0] 	0 
-overaln_P3    	D	[0] 	0 
-overaln_P4    	D	[0] 	0 
-exon_boundaries	S	[0] 
-dump          	S	[0] 	no
-display       	D	[0] 	100 

INPUT FILES
	Input File (S) /opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln  Format clustal_aln
	Input File (M) proba_pair 

Identify Master Sequences [no]:

Master Sequences Identified
INPUT SEQUENCES: 9 SEQUENCES  [PROTEIN]
  Input File /opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C1 Length  819 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C2 Length  819 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C3 Length  819 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C4 Length  819 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C5 Length  819 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C6 Length  819 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C7 Length  819 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C8 Length  819 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C9 Length  819 type PROTEIN Struct Unchecked

	Multi Core Mode: 72 processors:

	--- Process Method/Library/Aln S/opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.alngins       	S	[0] 	default
-proxy         	S	[0] 	unset
-email         	S	[0] 
-clean_overaln 	D	[0] 	0 
-overaln_param 	S	[0] 
-overaln_mode  	S	[0] 
-overaln_model 	S	[0] 
-overaln_threshold	D	[0] 	0 
-overaln_target	D	[0] 	0 
-overaln_P1    	D	[0] 	0 
-overaln_P2    	D	[0] 	0 
-overaln_P3    	D	[0] 	0 
-overaln_P4    	D	[0] 	0 
-exon_boundaries	S	[0] 
-dump          	S	[0] 	no
-display       	D	[0] 	100 

INPUT FILES
	Input File (S) /opt/ADOPS/216/Crtc-PC/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln  Format clustal_aln
	Input File (M) proba_pair 

Identify Master Sequences [no]:

Master Sequences Identified
INPUT SEQUENCES: 9 SEQUENCES  [P