ELF>{@@HH9 ȃH?HG;A| 1ҋ;ƒH\$Hl$HLd$Lt$ILl$H(L/ILLHBA;$~ *LY,A4$HEH}LH$Hl$Ld$Ll$Lt$ H(H\$Hl$HLt$L|$ILd$Ll$&H8IHHLk)DgHIxD)&ILHt IH1I1LA~0tOD9t H=D1HH\$Hl$Ld$Ll$ Lt$(L|$0H8D%fDHxIIIH1fAWAVAUIATIUHSHDw $G$LD$@AD+w$D$xD$8G0GDL$N;T$tOT$tD$ $ >   I : ;  : ;I8 &I : ; : ; I8 I !I/ & : ; : ;I8 : ;I : ; : ; .: ;' I@ : ;I : ;I.: ;' @: ;I4: ;I4: ;I4: ;I 4: ;I4: ;I4: ;I .: ;' : ;I!: ;I" #.? : ; ' I@$: ; I%4: ; I &4: ; I'4: ; I(4: ; I )4: ; I*4: ; I+1UX Y,1- U.41/ U01UX Y1412!I/34: ; I44: ; I? < 8intiih. b##### #(#0#8#@#H#P#X#`!#h#b#p'b#t)p#x-F#.T#/#3#<{#E#F#G#H#I-#Kb#M#n  # # b#z  s  d(Hd#Id#Md#Ed#b# wb#$j 8 Pi j#Gi j###ib# kb#$jb#(lb#,b#0|ba,i-b#j.b#/#0#1s H' (h# )h# *h# +h# ,b# -h#( .b#0 /h#8 0b#@ 1h#H 2b#P 3h#X 4#` 5#h 6M#p 7M#t 8h#x 9# :# ;h# h# ?b# Ah# Cb# D# Eh# Fb# G# Hh# Ib# Jh# Kb# Lh# M# N# Oh# P# Q# Rh# Sb# Th# Ub# V# Wh# Xb# Yh# Zb# [h# \b# ]h# ^# _# `h# a# b# ch# db# e# fh# hM# iM# jM# kM# lM# mM# nM# oM# pM# qM# rM# sM# tM# uM# vM# wM# xM# yM# zM# {M# |M# }M# ~M# M# M# M# bwp1Up2T bwp1p2To FFFhFlGb TTTTposUcutVbiWb Int s1s2p_c  wbbb~~iblenbl_lbl_sbbbbbbl1bbbbGulGusmfeap/    mi b b b K!p_cK !wKbiLbjLblenLbLbLbMM"U#V7b$7b$7%8ym%9MP&9M%:Vv%:g~%:wz%:Vr%;~%;}%;|&<&<'c<&<&=&='s1=(s2=(s3=&=%=%=&=&=%>]%>~%?b'i@b'j@b&@b&@b)l@b&@b'sym@b)r@b*@b&@b*A*A&B&Cb&Db&Es&Fb&I *I &I &I &I &J 'wNb&Ob&Pb*Qb*Rb&Sb&Tbminbmaxbtmpb+~ I, -. . ." -bwb/lbsf|/b0/ ,I ,= -1S 1] .g .s . 1 . -1 g2 w   O 2  03 %3b (RT4 4444b4b4b46b4;b4@b4Gb4Pb4g4o44b ./../H/usr/include/usr/include/bits/usr/lib/gcc/x86_64-redhat-linux/4.1.2/includeRNAup.cdata_structures.hRNAup_cmdl.hstdio.hlibio.htypes.hstddef.hfold_vars.h i/>#;=YK;u_$TJ@Y;=g2Fg;=V>g=!'gYY>zXz/uXrJ|xXzxf J;wXzJw JOY;Yg@8ɟ;K/  s.\ ",ʟ;=0;YHKY0V\ Y;=:dn@@\8@I:Z9KLLZ#ןs=RX&Ja=-YW= ȓMcxf2NX$tyH`xy<y.Q):v/%y:/;/u;g/gy;/;/;/v%u;g/gx  < "uu;u/ v Jv. 0"""Yu;u/gyYu;u/y wZ:JZ!gPJ|./r0ilfMY;uW:>:>|X>9wvY;=;gI=wJ t|XWxX/=5w9=_$XEt;t3 u 4?Z&u7g X,[h"$!/!g$!&Z?82Y!!!!!!v0~_9Y#ztzt^g~X~P 'X=4vJŽYOȔɠDs=9Ƀ;)NW)hYu82=7k#fwL)w<wJfw<Aoz=|#(>euY|=J= 4'sY}RNfJs=YSKY!uȀ}+u!Mehv&V<|<K<1$Y/#g."Z $)=s|n(h*<⃃-!/!uv  Ju |;gt;=gt;Yg 333333?@O=Q?fffffq@%zr?@@more than one cut-point in inputSequence and Structure have different cut points.%s %3d,%-3d : %3d,%-3d (%.2f = %.2f + %.2f) %s %3d,%-3d : %3d,%-3d (%.2f = %.2f + %.2f + %.2f) RNAduplex structure doesn't match any structure of RNAup structure ensemble constraints for intramolecular folding only:constraints for cofolding (intermolecular folding) only:Use either '&' to connect the 2 sequences or give each sequence on an extra line.Give each sequence on an extra line. The first seq. is stored, every other seq. is compared to the first one.This should never happen (again)Two concatenated sequences given, switching to pairwise interaction mode!After the first sequence (pair): Input a single sequence (no &)! Each input seq. is compared to the very first seq. given. Don't confuse me by mixing concatenated (&) with single sequences! Go, have some sleep and then check your input again...RNAup -C: mixed single/dual sequence or constraint strings or different cut pointsRNAup -C: constraint string and structure have unequal lengthmaximum unpaired region exceeds sequence length# %s # %d %s # %s # %d %s # %s%scut_point = %d cut = %d %s&%s ERRORdiff %.18f -T %f -C -4 -d %d --noLP --noGU --noClosingGU --noconv -e %d -P %s --nsp %s -S %f -w %d --include_both --interaction_pairwise --interaction_first -5 %d -3 %d -c %s -u %d-%d%d%s,%s Enter another sequence.%51s>%s constraints missing%s %s _w%dscaling factor %f %4d,%4d (%.3f) for u=%3d error with prob unpaired# %s # %d %s # %sRNAup output in file: %d.outx "$JML0,NJMV@<yBBB E(D0D8G<f BBB B(D0A8N$zRx 4"LJML0$lNJMV@4yBBB E(D0D8G4f BBB B(D0A8N$ #UPswsw0P|U|VPT^TPQ\QQ w .wUVU.V T ^.^Q_._PS.S-\\02w24w46w6;w ;?w(?Cw0CJw8Jw0UVV0T\0aQaL]0R~0X~0Y~0bb~0bb~N^^SC__!SS@ESTT@JTS@SES$accCrc_cg@+^b^rd\U@\R\wwww w(w0w8'w$USS S ''SOTOW \ ''\ \{\ \\ %\7P\Y\ \ \!$\$&\ '\ .__Q!u!_!!_!$_&&_}Tm!\$&\m!\$&\7!!L!UL!'+VVS  aSaS  Q!SQ!u!u!!S!$$$S$'*!\$&\6!\$&\m!\$&\s  ]$]UQPQPQwQQQQQQQ)Q)AQAvQQQ%]';QQQ]QQ!!]!%"]Y"$]q$$](V-?VVmv\vQ!\$&\m_5PPP _P PQ_E_P& j P$&_A!\$&\oXX%SSSS SS& . S8 &\)&j&\b '\s %"\i"$\q$&\Y $]q$&]s S $]$mSm!]!%"St$}$]}$$S$&]m!]$&]U!]$&]mQVq{VV!V-V(-VVVVVQ!u!V!!Vm^t{^^ U^^-^-^^^^ ^ !^$$^m]w{]]%]A]-]-]PU]G]]Q!!]K &] &] &] '] &]s %"n""""R""""R"""#R####R###$Rq$&s %"n""""P"$q$& > V> N P P P QVVQ!u!V!!V!%"V # R# > PV ] P] i Pl t P R #\\Q!u!\!!\!%"\m>S$S+2P2`S`rPSpS*S(SSQ!u!S!!S$%S%%TDQPm!~$&~m!]$&]Y(hYm]]ZhZ-?]]$&]m!]$&]bya a Yb main,' $ $ m!$& $$ Q!h0?c0?hyCJ(yZccstruc_targetsize_ti_shortunstr_targetulength_argunpaired_values_IO_save_endcstruc_tmpheadermin_jcontributions_orignoLP_given_IO_write_basenoClosingGU_helpfull_help_givenG_min_lockargvextend3_origfname2paramFile_argistty_IO_save_basenonstandardsnix_upversion_help_chaindetailed_help_help_cur_columncompare_unpaired_values_modecmdl_parametersfold_constraineddiffsfactlong intnoTetra_flagpfScale_giventemp_nameulength_numlength1ulength_minpfScale_orig_IO_markermaininteraction_first_givenwindow_argshort unsigned introtateddangles_helpheadfull_help_helpparam_destp_c2energywplushelp_helpsigned chardangles_givenup_mode_IO_FILEinteraction_first_flagconstraint_givenunsigned charargs_info_sbufinput_stringprint_unstruduplexTmax_uunstr_shortparamFile_helpcharread_againmin_i_IO_lock_ttemp_helpdetailed_help_givenwindow_helpnoconvinteraction_pairwise_helpdangles_origpu_contribno_header_helpextend5_arg_IO_read_ptrdoubleulength_given_posstdinnsp_argcontributions_helpinteraction_pairwise_flagmove_useless_unpaired_values_markerswindow_origulength_origextend3_giventemp_givennoGUdefault_uadd_aGNU C 4.1.2 20080704 (Red Hat 4.1.2-48)old_cutmin_guunstr_outi_mininput_typelong unsigned intns_basestemp_arg_flags2energyModel_arg$Id: RNAup.c,v 1.5 2008/07/04 14:27:09 ivo Exp $_IO_read_baseparamFile_givenparameterlength2_unused2no_header_givencontributions_givendanglesnoClosingGU_given_old_offsetinter_outenergyModel_helpno_closingGUdo_backtracktokenizercsidlong long intcontrib2interaction_first_helpadjustUnpairedValuesend3extend5_orig_IO_write_endfname_targetdangles_argstrucoutputenergyModel_origextend5_helpp_c_S_IO_buf_baseend5include_both_given_nextunsigned intinclude_both_helpseq1seq2RNAup.ccstruc1cstruc2ParamFile__pad1__pad2__pad3__pad4__pad5up_outextend5_givenincr3incr5noconv_givenmin_eninclude_both_flagj_min_flagsnoGU_flaglen1cmdl_parameters_lengthextend3_argG_sumlongerSeqFirstconstraint_helpRNAup_args_infonoconv_helpnsp_given_offsetconstraint_flagnoconv_flagno_output_file_helpnoClosingGU_flaglong long unsigned intpf_scalepfScale_helpGi_minlength__off_tGikjlstructureno_output_file_flagGikjl_woversion_givenmy_contribadd_blength_targetulength_helpdG_u_IO_backup_base_shortbuftemperaturecstruc_combinedargccontributions_arg__off64_tenergy_setprint_interactionblubbreal_count_IO_buf_ends_targetnamenoGU_givenstderrshort intwindow_givennoGU_helptetra_loopparam_dest_lengthnoLP_helphelp_given_vtable_offsetcmdl_tmpnoLP_flagpfScale_argi_longunstrnoTetra_help_IO_read_endnsp_origulength_maxextend3_help_filenonsp_helpno_output_file_givencontrib1floatstdoutenergyModel_given_IO_write_ptrnoLonelyPairslast_maxappendCmdlParameterinteraction_pairwise_givencut_pointtemp_orig/projects/remc_bigdata/miR/ViennaRNA-2.0.0/Progslineinteractfname1paramFile_origno_header_flagnoTetra_givenGCC: (GNU) 4.1.2 20080704 (Red Hat 4.1.2-48).symtab.strtab.shstrtab.rela.text.data.bss.debug_abbrev.rela.debug_info.rela.debug_line.rodata.cst8.rodata.str1.8.rodata.str1.1.rodata.cst16.rela.debug_frame.rela.eh_frame.debug_loc.rela.debug_pubnames.rela.debug_aranges.debug_ranges.debug_str.comment.note.GNU-stack @'&X',X'1X'D*?0"U=PaC0n2C}2oH0J0`J  K0LOkjk00kP0m y.yy!H % 7 ! " >P  RN [0ympz      ( #(/f 4AVbj{ &2EJQU^fp)2RNAup.ccompare_unpaired_valuesmove_useless_unpaired_valuesappendCmdlParametertokenizeprint_interactionRTdefault_u.LC0.LC5.LC9.LC10.LC25.LC41.LC42.LC43.LC59strlenxreallocstrcatstrchrspacenrerrorsscanfcut_pointstderrfprintffreestrncpyduplexfoldlogprintffwriteputsstrcpymaindo_backtrackRNAup_cmdline_parsertemperaturesprintffold_constrainedtetra_loopdanglesnoLonelyPairsnoGUno_closingGUenergy_setqsortreallocRNAup_cmdline_parser_freeread_parameter_filenonstandardsstdoutfilenoisattyget_input_linestr_RNA2RNAupdate_fold_paramsfoldfflushexppf_scalepf_foldpf_unstrufree_pf_arraysfree_pu_contrib_structfree_interactfree_arraysstrncatstr_DNA2RNAwarn_userpf_interactUp_plotprint_tty_input_seq_strprint_tty_input_seqstdinprint_tty_constraint__strdupexit}%%&(1)<%G)W(a f*q {+ +,- . (*,% ) (+))00"1<(p%) M22D n3 3- 4/// #"5- )73F)V6~ `38K)u9: 5; <$ <==X @x> D;? K@ S+ AF [ j B t ;+ n x ; % _ ;  ;J )y ) )  C  C / D  C-E3>=>UFh)rGGGGGHIJ E:Y!a"it, P* + 3/KB%W%`,LL<16')M0NH O\0nN#PQ0RS!T(<UV/////%/=/rW' >;XM0]0m0s< `*UUYY& x+Z9,^ e+r y3/K, H*%K! #&*3,: ?*E,e%y- 7. *%- 7. *3[%)  ;( 73G6q ;'5\- C .:)_0t'"}2Z Vd3%) ;1 t6*[+%E)n ; * ]9[6<f 6v 6} < K # *!,! H!*"!,8!,R!^g! l!]! !]!/!_!I!J!<!`! !5"`" H "5"`6" # #;D#)Y# y#+# #+# #;-$0F$ P$; %0%N<%#D%M%Pj%Qs%-x% C%.%0%R%S &T<& I&;s&a& &;&a& {&;'b'//  ' % +) j . 9 @ G N U \  j q |   6     c     !  0 ? 9 N F] Tl !{     ; =  I   A M T [( b8 iH _X t L      *    H q        C R kb  ~  x ( L  I    e    Y! +/ *= iK Y  g ' u t  k    ] u    r   ) 8  G V e t A _     `  W  x     :( U 7 ( F U  d ys     '      "    2  a' 6 E T  c r       w v ;      & 5 ~D  S b qq 7  G   7  B  '  P$ , #1 [< [A L Q  \ j t |  . F   !  & $ m   0   ' 6 F RK fV d i t y  3 k  l    m  ) . 9 >  I DN  Y ^ j z    2     X 6  #  4 t F e 4     '  o   3    | ! 0  ? pN  ]  l {  C s        =  G w           3* ;9 C M H _ R  W L f eu       T        2 - k  & + 5 : D !I 6S pX b g q Rv       8         r   ^ 7   \' 7 P ] 0f o x 7  ; r     S   0 @ p# j, 5 9C sH  $ 2       V % u2  ? L Y f  s    S     4 8 L PPt x 0  8  P Pp  0