ELF>@@LJxLJ|LJLJLJLJLJLJLJLJLJLJLJLJLJLJLJLJLJLJLJfDAWAVAUATUSHH8 HC(HC@HCXHǃHǃHǃHǃ0Hǃ8HǃHHǃPHǃhHH-L=C FCP #Mt9Mt4E1M&%D$D\$hEufD1H\$Hl$ Ld$(Ll$0Lt$8L|$@HHDEA-\H$HHH=AELEξ1H>Ht$11HEH!HD$Ht 8HH=Hپ1-DT$`E:?1}EHEuH}HtHHEHHt$1HZEHtL3I1kH$HHH=ALEƾ12H\$Hl$HLd$HIHHt*HLH߉H$Hl$Ld$HH=H1f1f.HH5>uKH5>u/ H5>u H@1H1f1fSH=Ht1H<HHu[@SZH=Ht1H<HHu[@S*H=Ht1H<HHu[@AWAVAUATUSHHHiHT$pQ $Ht$xHLD$h$$H$1A?[$1HD$$-D%-<:$EEۉ$HDEL%MA<$HT$xHcHH$x-)A,$LIL%DDE{H @:| x: -%HL%-M--=9-O9-A9G;tH|$x-9$H\$xHcʼnH*H;$ tH8-uxt܋-9$ H\$xHcH:/:-EHAE1HD%A-HD%$ Auw D$H|$hAH=LED$hD1-99-A$$MHH MDAD)M)E1HDŽ$DŽ$DŽ$D$dI I]HtsALD$XLLHLD$XuH9D$dLD$XH$`H$BA;EI DŽ$I]HuD$E$ LA?E1IL%-HD%-HD%$.:B:B9 E 9t H$;AʼntI]H9ZBA;E\H|$pL$D$8<=MIA<=uBHJ<-L$L% $ >   I : ;  : ;I8 &I : ; : ; I8 I !I/  : ;  : ; (  : ; : ;I8 .? : ;' I : ;I.: ; ' @ : ; I .: ; ' : ; I.: ; ' .? : ;' @: ;I1UX Y11UX Y .? : ;' @ : ;I !.? : ;' I@ ".: ;' @ #: ;I $4: ;I%4: ;I& U'4: ;I( U): ;I*.? : ;' I@+.: ;' @,.: ;' I@-4: ;I .4: ;I/1X Y01X Y1.? : ; ' @ 2.: ; ' @3.: ;' I 44: ;I 5: ;I6.: ;' 7 8 : ;91UX Y:41;1<41= > ?4: ; I? < @4: ; I?  8intii.s. b##### #(#0#8#@#H#P#X#`!#h#b#p'b#t)p#x-F#.T#/#3#<{#E#F#G#H#I-#Kb#M#y ? ~  # # b#    ' (~# )~# *~# +~# ,b# -#( .~#0 /b#8 0#@ 1~#H 2#P 3#X 4~#` 5b#h 6~#p 7b#x 8# 9~# :b# ;~# b# ?~# @# A# B~# Cb# D~# Eb# F# G~# Hb# I~# Jb# K~# Lb# M~# N# O# P~# Q# R# S~# Tb# U# V~# XM# YM# ZM# [M# \M# ]M# ^M# _M# `M# aM# bM# cM# dM# eM# fM# gM# hM# iM# jM# kM# lM#hr sb# tb# ub# vb# wb#h ~#b##valb#bv0AFb#Gb#Hb#I#Lb#T# [b#(\b#,OiM~MMbIH~H w U ,  E  Ce     "  , #9 E N  (w ' U!D bw  U ~T" w#d T$b$b%topb%tem& 'lenb%ib('lenb%ib"l _w^l )opt^~)arg^~^* kbjl j %ilb+ >)s=+) IH [ w * 5 $6 , )s~$,qbhhiijj k~l mb mbnb nb( o~0op~-r@%vals~.tb.u/Iv/p0M*b~ $l %ib1w2d'ib'ib'ib3 MbKbK K~LL  3<b:b: :~;;.=b4d? 3bb ~5d 'retb.b65d 3bb 5d 7.-.-7.s.b3H&b#b# #~$$%b5d% .''p(.).*b.+b.,b.-b3bb ~b5d 'c.~,5bb  ~%cb.b- {-b{.b.b-b{$$b$b$b8&$b9#NeYMA5(:q9C(::H7~r;fZ(<:-0RF:.(:]:i(:v:95(<:< :<#:/:;=.-.-=.-.-=.-.-=<.-.-=j.-.-=.-.-=.-.-=.-.->.s.b- *bb bbb$b-P!1bwb *bb  $b  -k -|b -b -b -S ???@~ @~  ~ @y  ~ @a  ~ @! @~  /usr/include/usr/include/bits/usr/lib/gcc/x86_64-redhat-linux/4.1.2/includeRNAplfold_cmdl.cstdlib.hRNAplfold_cmdl.hstdio.hlibio.htypes.hstddef.h X~uutwtwrYXutX~uuwruwuuuvvuuutt Xqtuvyzt|ztuwSwvvqvvuuuuwsstuuktrthtyjttjt t׻sztuuyttuuw=\OTKzJK^vsvwtK XuuuttK Xtt JuuYIuVLWK:Lf Js=:L>8}Y"o]E3y<rrVVVVVrrVV)N' =Yv >=~"Ʉ:>5/oW? (vt <v< +LY=c<fkK^w<4#:y<I' Yvyy&Y z9X@:>4;/[xJ~+KZuIS"YWrf"YWrf"YWfYs>tgut~fgut{e f!:.|J^$<tؑ^)=;u zfz.!."~ Ytv?~PyYt"N;$_ X\GRGM|G~G[{Gss#!/u~>.#>:Ivegf\|Gz<(# J&${G. XC{W)FGYxtYxJ=]bYZ_a\":>Z_) %s="%s" %s RNAplfoldhelpdetailed-helpfull-helpversionwinsizespancutoffprint_ontheflyulengthopening_energiesplex_outputnoconvtempnoTetradanglesnoLPnoGUnoClosingGUparamFilenspenergyModelw2.0.0%s %s %s %s --%s: option `%s' is ambiguous hVW:L:c:ou:OT:4d:P:e:%s: invalid option -- %c 700.01312%s: option unknown: %c%s Usage: RNAplfold [OPTIONS]... General Options: Model Details:%s: cannot dump options to stream %s: `--%s' (`-%c') option given more than once%s %s: `--%s' option given more than once%s %s: invalid numeric value: %s %s: cannot open file for writing: %s %s: option `--%s' doesn't allow an argument %s: option `%c%s' doesn't allow an argument %s: option `%s' requires an argument %s: unrecognized option `--%s' %s: option requires an argument -- %c calculate locally stable secondary structure - pair probabilitiesComputes local pair probabilities for base pairs with a maximal span of L. The probabilities are averaged over all windows of size L that contain the base pair. For a sequence of length n and a window size of L the algorithm uses only O(n+L*L) memory and O(n*L*L) CPU time. Thus it is practical to "scan" very large genomes for short stable RNA structures. -h, --help Print help and exit --detailed-help Print help, including all details and hidden options, and exit --full-help Print help, including hidden options, and exit -V, --version Print version and exit Below are command line options which alter the general behavior of this program -W, --winsize=size Average the pair probabilities over windows of given size (default=`70') -L, --span=size Set the maximum allowed separation of a base pair to span. I.e. no pairs (i,j) with j-i > span will be allowed. Defaults to winsize if parameter is omitted -c, --cutoff=FLOAT Report only base pairs with an average probability > cutoff in the dot plot (default=`0.01') -o, --print_onthefly Save memory by printing out everything during computation. NOTE: activated per default for sequences over 1M bp. (default=off) -u, --ulength=length Compute the mean probability that regions of length 1 to a given length are unpaired. Output is saved in a _lunp file. (default=`31') -O, --opening_energies Switch output from probabilities to their logarithms, which are NOT exactly the mean energies needed to the respective stretch of bases! NOTE: This actives -u option. (default=off) --plex_output Create additional output files for RNAplex. (default=off) --noconv Do not automatically substitude nucleotide "T" with "U" (default=off) -T, --temp=DOUBLE Rescale energy parameters to a temperature of temp C. Default is 37C. -4, --noTetra Do not include special tabulated stabilizing energies for tri-, tetra- and hexaloop hairpins. Mostly for testing. (default=off) -d, --dangles=INT How to treat "dangling end" energies for bases adjacent to helices in free ends and multi-loops (default=`2') With -d2 dangling energies will be added for the bases adjacent to a helix on both sides in any case. -d0 ignores dangling ends altogether (mostly for debugging). --noLP Produce structures without lonely pairs (helices of length 1). (default=off) For partition function folding this only disallows pairs that can only occur isolated. Other pairs may still occasionally occur as helices of length 1. --noGU Do not allow GU pairs (default=off) --noClosingGU Do not allow GU pairs at the end of helices (default=off) -P, --paramFile=paramfile Read energy parameters from paramfile, instead of using the default parameter set. A sample parameter file should accompany your distribution. See the RNAlib documentation for details on the file format. --nsp=STRING Allow other pairs in addition to the usual AU,GC,and GU pairs. Its argument is a comma separated list of additionally allowed pairs. If the first character is a "-" then AB will imply that AB and BA are allowed pairs. e.g. RNAfold -nsp -GA will allow GA and AG pairs. Nonstandard pairs are given 0 stacking energy. -e, --energyModel=INT Rarely used option to fold sequences from the artificial ABCD... alphabet, where A pairs B, C-D etc. Use the energy parameters for GC (-e 1) or AU (-e 2) pairs. See also: RNALfold(1) References: S. H. Bernhart, I.L. Hofacker, and P.F. Stadler (2006) "Local Base Pairing Probabilities in Large RNAs", Bioinformatics 22: 614-615 A.F. Bompfuenewerer, R. Backofen, S.H. Bernhart, J. Hertel, I.L. Hofacker, P.F. Stadler, S. Will (2007) "Variations on RNA Folding and Alignment: Lessons from Benasque", J. Math. Biol. Written by: Stephan H Bernhart, Ivo L Hofacker, Peter F Stadler. Report bugs: If in doubt our program is right, nature is at fault. Comments should be sent to rna@tbi.univie.ac.at. x < BBB B(A0A8Gp)$ EHYM&$kADG AAASN ,JMQP$wJL nD,A,A,A<2BBB B(A0A8JOAG0%AzRx 44 BBB B(A0A8Gpl)$ EHYM&kADG AA,DA\SN $tJMQPwJL nD,A,A,A442BBB B(A0A8JlOAG0%Awwww w(w0w8wUS0lUl]U9]f\9\8VP9VlS9SlQQ29QlY29YlY9Y@WUWfU@RTRWQWaTafQ@MQMWRWZQ@HRWfRpqwquwu|w| w pUVV V U V U VpTSS S T SPPP P w w U S  w w  U S U U w w U w  w U V U  V S  S H wH w } U} V % U% V g Tg  ^% ^ J Qu Q Q  Q ' Q0 @ QV f Qx Q Q Q C Ru R R  R ' R0 H RV n Rx R R R p Xp  \% \ Z Yu Y Y  Y ' Y0 H YV n Yx Y Y Y } }  ] % % u ]u P ] P  ]  P 0 ]0 H PH V ]V n Pn ] }  } _ %  % _ } 8} X 8 X % 8% n Xn u 8u X 8  X 0 80 H XH V 8V n Xn 8 X 8 } } T   T % % g Tg n Yn u u T   T 0 0 > T> V V d Td  T X  S S  Su S S w Gw U V%@V@ER T \%G\ P S%GS V@GVptwtww ww<w@AwAlwprwrtwtvwvxw xyw(yzw0zw8!wpU!{pT!{pQ!{pRSRSpX!{]]B]4]4PPP]P] P ]P]P]P&]&+P+]P]PK]KgPg]P]P]P],P,]]q]]X]]" ]P !]S$S(S4S\SSS+?S" SP S)!!SBV;V(V4V\VV?V" VP V)!!V{!{j\\+\(\4\\\\?\" \P \)!!\{^^{^^4^^QPQ\^w^P^q"^X^Pb^^PP ^P m Pm ^)!@!P@!p!^p!u!Pu!!^!!P!!^xUinUV^V^^V^!V!4^\d^dV>V>N^NqV"(V(X^brVr^ )!^VrXX>FT(XXnXX4XXXX&XX\XXXXXrX?NXN]RX" D X{]]{]B]]]q]]X]?b]]" P ]{!{!!w!!w!!w0!!U!!T!!Q!!S!!S!!R!!X!!Y!!P!!P""U""T""Q "!"w!"E"w ","U ","T ","Q,"2"S3"E"S ","R/"2"P3";"PW RNAplfold_cmdline_parser_init RNAplfold_cmdline_parser_params_init RNAplfold_cmdline_parser_requiredr RNAplfold_cmdline_parser_dump) RNAplfold_cmdline_parser_free[ RNAplfold_cmdline_parser_params_createRNAplfold_cmdline_parser_file_saveRNAplfold_cmdline_parser_print_version7RNAplfold_cmdline_parser_print_detailed_helpdRNAplfold_cmdline_parser_print_full_helpRNAplfold_cmdline_parser_print_help5RNAplfold_cmdline_parser2RNAplfold_cmdline_parser1RNAplfold_cmdline_parser_extMRNAplfold_args_info_purposecRNAplfold_args_info_usageRNAplfold_args_info_helpRNAplfold_args_info_full_helpRNAplfold_args_info_detailed_helpRNAplfold_args_info_description,E"f{f{f{gyN`-G- @y`gGN9?!+!)!" P ?+\4(5I-+ '!)!" P ?+\4(5I-+ '!)!" P ?+\4(5I-+ '!)!" P ?\4(3'!)!" P ?\4(3'!)!b"Xq\4!)!b"Xq\4 $0!6B((8(8" P ?bX"qB3" P ?brjmXg"qBWFOopening_energies_givendefault_valuelongind_shortbufoverridecustom_opterr_IO_lock_tRNAplfold_args_infoRNAplfold_args_info_full_helpgetopt_internal_r_IO_buf_endnoTetra_helpRNAplfold_cmdline_parser_releaseoptoptopt_indexexact_IO_write_endunsigned intnoGU_helpprint_errorsnoLP_givenparamFile_orig_flags__nptrfull_help_helpparamFile_helpplex_output_flag_markersvaluesRNAplfold_cmdline_parser_freeshort intlong_optionslast_nonoptnoGU_givenARG_NOcheck_short_optfoundargs_infooptstringwrite_into_filenoClosingGU_givenparamFile_givenstrtod_posstdoutplex_output_helpfloatprint_onthefly_flagfree_string_fieldfieldnameendresultlong long unsigned intparamFile_argulength_origwinsize_helpnsp_argulength_helpRNAplfold_cmdline_parser_internalRNAplfold_cmdline_parser_requiredhelp_givenRNAplfold_cmdline_parser_params_offsetRNAplfold_cmdline_parser_extstrtolcustom_optindcustom_getopt_initializevalue_filenoRNAplfold_cmdl.cupdate_arginit_args_infoinit_full_help_arrayshort_optsize_tinitialize_vtable_offsetprint_onthefly_helpnoconv_givendetailed_help_help_IO_read_baseinitializedRNAplfold_args_info_purposeargcRNAplfold_cmdline_parser_print_detailed_help_IO_save_endenergyModel_argcustom_getopt_internaldangles_origulength_argRNAplfold_args_info_detailed_helpdangles_helpclear_args__s1_lencharflagoutfile_modecutoff_argarg_typeerrorARG_STRINGfilenamecustom_optarglongoptsorig_field_IO_write_base_IO_read_ptrmultiple_optionwinsize_argcustom_getopt_longnsp_orignsp_helpRNAplfold_cmdline_parser_arg_typetemp_given_IO_markerprint_onthefly_givenRNAplfold_cmdline_parser_print_helplong long int__s2_len_IO_save_baseARG_FLAGRNAplfold_cmdline_parser_params_initRNAplfold_cmdline_parserRNAplfold_cmdline_parser_params_createcheck_ambiguityoptindpfoundnsp_givenRNAplfold_cmdline_parser_print_full_help__baselong_optdetailed_help_givenRNAplfold_args_info_helpmiddlespan_orig_IO_backup_baseRNAplfold_cmdline_parser_file_saveARG_INTspan_helphelp_helpdangles_arg__pad1__pad2__pad3__pad4__pad5prev_givenfirst_nonoptnoTetra_givennoconv_flag__result__s1cutoff_givenenergyModel_origversion_givenenergyModel_helpargvwinsize_given__endptrstop_charplex_output_givenunsigned charoptionslocal_args_infoGNU C 4.1.2 20080704 (Red Hat 4.1.2-48)_IO_read_endno_freeopening_energies_helpRNAplfold_args_info_descriptionoptargstdinlong inttemp_argexchangeARG_FLOATRNAplfold_cmdline_parser_dumpnoconv_helpcustom_getopt_dataindfoundpackage_namenoLP_flagtempfield_givendangles_givenoptionnextcharstring_fieldpossible_valuesnameRNAplfold_cmdline_parser_initbottomcheck_requiredfailuretemp_origRNAplfold_cmdline_parser_print_versiontemp_helpgengetopt_strdup_lockfull_help_givenlong unsigned int_old_offsetnoClosingGU_flagoption_index_IO_FILEprint_help_commonopening_energies_flagadditional_errorcutoff_orignoLP_helpcutoff_helpversion_helpRNAplfold_args_info_usage_sbuf_IO_write_ptrcustom_optoptwinsize_origspan_arg/projects/remc_bigdata/TCGA/RNA/ViennaRNA-2.0.0/Progsspan_givenambigstderrnoClosingGU_help__off_tinit_help_arraysigned charshort unsigned intshuffle_argvprog_nameARG_DOUBLEnoTetra_flagenergyModel_givenclear_givendoubleparams_chainFILE_flags2has_argnoGU_flagulength_given_cur_column_nextRNAplfold_cmdline_parser2__off64_t_unused2_IO_buf_baseopterrcheck_long_optGCC: (GNU) 4.1.2 20080704 (Red Hat 4.1.2-48).symtab.strtab.shstrtab.rela.text.rela.data.bss.debug_abbrev.rela.debug_info.rela.debug_line.rodata.str1.1.rodata.str1.8.rela.rodata.rela.debug_frame.rela.eh_frame.debug_loc.rela.debug_pubnames.rela.debug_aranges.debug_ranges.debug_str.comment.note.GNU-stack @E"8"+" &1&X 6&I*Dh1ZD UP f2&Ju2K@ch  f(&PjX*(l$А,0,0 0 K.yyX ' x= 0  '@& 7 I j S{  pnp2P 0   $ * H j  ) pk 8 _fmt wP,4T,,@,!O"  "%RNAplfold_cmdl.cclear_givenexchangewrite_into_filefree_string_fieldRNAplfold_cmdline_parser_releasegengetopt_strdupupdate_argpackage_nameprint_help_commonRNAplfold_cmdline_parser_internalcustom_optargcustom_optindcustom_optoptd.3955custom_opterrlong_options.4072.LC36.LC37.LC24RNAplfold_cmdline_parser_initRNAplfold_args_info_detailed_helpRNAplfold_args_info_full_helpRNAplfold_args_info_helpRNAplfold_cmdline_parser_params_initRNAplfold_cmdline_parser_requiredfprintfRNAplfold_cmdline_parser_dumpstderrfreeRNAplfold_cmdline_parser_freeRNAplfold_cmdline_parser_params_createmallocstrlenstrcpy__strtol_internal__strtod_internalRNAplfold_cmdline_parser_file_savefopenfcloseRNAplfold_cmdline_parser_print_versionprintfRNAplfold_args_info_purposeRNAplfold_args_info_usageputcharRNAplfold_args_info_descriptionRNAplfold_cmdline_parser_print_detailed_helpputsRNAplfold_cmdline_parser_print_full_helpRNAplfold_cmdline_parser_print_helpstrchrabortstrncmpexitRNAplfold_cmdline_parser2RNAplfold_cmdline_parserRNAplfold_cmdline_parser_exti(p(w( )()) )(,#(*($1(<8(D?(LF(TM(dT(t[(|b(i(u(|))$(4(\),(l)<)D)4)L)\)l)T)d)t)|)))( ((*4"*<)*D5)<(C)J*LQ)X)c*Tn)u(|*\)(*** *(*($*$*,(l*d(**l*t*|*(#***1*8*N ]     % ; Z u    x g _ P I7 DO <e 4{ *   / - 0 3 + 4 3 5 F P /V c (j - 6  / - 0D 7j 7 0  / ` - 9. :(/0 5 A-Q V [ u;|=>?@  < <(B ()%B- )I*UB] *'#L  )/ E(V4f<< E8 <0&H,D8H>HGDMHYD_Hmy  H$, ,'$17 >LEb 0n u/  H-FDHDD  BGS44 <,$  L+$;$JDSb  wH}DH'9<f /-<4<$ ,'8d D1H8  F I >D _ C PV < ;;1H {     * x& e  g D@ p$4<, x,4,:A8V/^ !h- /-<,8  D$D,On4<$    ,L!$'G/O `Y-e($ /-<  , /1 8@ -G <R i %y % % % !/! !- !T! q!C~!1!H!A!1!H!1!H7"1A"HS-b-b<<"I  b   `( 0 8 h@ H P X ` h `p x   x      x (  x  X  p     @ ` * 4 < D I P  _@ g` x      @ `     E" ! % !) ! . ! 9 ! @ !G ! N !U !~ \ !j ! q !f | !X ! !V ! !D !: ! !? !^ ! !  ! !k , !; !J !Y !h !ww !  ! !  !  !,  ! !- !  !^ ! ! # !'3 !.C !5S !hc !b  !N !H !8  !  != ! ! !Y !) !K7 !HE ! S !a ! o !} !  ! ! !n !  !  !` !* ! !  ! !_ ( !T 7 !fF !IU !bd ! s !  !  !  !  ! !  ! !5 !  !  !  ! ' !& 6 !U E !T !+c !Wr ! !  ! ! ! ! !3 ! !  ! ! != & !|5 !SD ! S !b !q !> != !T !*  !  ! ! !& != !  !Z !  !>" !70 !> ! L !Z !q !w !} ! ! !  !  ! !8  !e  !  ![ !  !  !@ ! + !: !lI !? X !Gg !| ! !A ! !p !6 !A ! !  ! !B! !1 !: !F !O !n ] !j e m u z !  P 0 !   !  !   #( !6 ! I ! Q 0Y 9e !p  ! C ! y    A  w ! @ f, !`7 G W ?\ !g x ! p   !`  !  H !t     !     !$ J/ !7  ?  K !V a !m  u  }  !  !    I !  !    !  ! p ! ' , !<7  < !G U L !U W  \ !k !yv l { ! !7 !L  ! !w !  !u B !  ! !H &~ . R9 ZH u_ }n  ! G < ! t !  !`  b ! Pf !M #p+3 = !EM U j !Grz<  !h@l @ ! ! ! ! ! !( !6 !B !N !Z !f !%r !  ! ! ! ! ! !% ! !! ! / !; !G !^ !Mj !w !w !n !  ! ! ! ! !% ! !  !6 !$ !H 0 ! < !7 M ![ !g !s ! ! !  !p! x ! ) ! a !  !   !u  -* e/ !; ! K !7[ !g ! s ! !  Z !/ ; !x    ! C !   !7  $ p p: pH pn @  L     @  p # N p W e s   !M ! !M ! !M !$2$ !M0 !AIR !M^ !ow !M !P ^  !M !f   !M !f   !w !n !, ; !> G!O!W !\ !g Q!l !w t!| ! ! !7 ! ! " !  &" ! I" !  !"" !  " ! "! !, "7 !fC "KE"S "X !c  #h !s C#x ! f# !  # ! # !P ! !@ !  ! ' ! 4 !BA !N N !x[=d ! q> !* !m) !( !j @   u 0 (V 08f@fHfPfXf`fhfpfxfffffffffffffffffffff f(f0f8f@fHfPfXf`fhfpfxffffffffffffffffffff f(0f8f@fHfPfXf`fhfpfxfffffKffff&ffffff f(f0f8f@fHPX4`fhfpxfffffffffff  4 8t x   0 @ p   , 0 L P d h        P p4 8T Xt x@ p ! "   " 8 p    0 @ p    0  H  `  x     P p    @8 pp ! "  "