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Sb! ab@ j b #6-b$,b$,.//%0~%0~%0612&c23b&i3b3b&sym3b&r3b4b&mis4b555&pf6b'6b6b(AS7F\%8F9:b;bb?b@) b*+o+x, -.++/ 0ib0s/8 1/ 0A%2&--/ ++3++3+%+1+=4I{*4V}+b+m+x+4~++/* 0bp1W/ 57kT70pl859*0sK5L6 'b-'b-6 'U-'U-6'V-'V-6B'W-'W-6n'X-'X-6'\-'\-'\s'\b6'-'-6'e-'e-6n'-'-'s'b6'-'-6'-'-/5_0cp`N 5a1b0enc5c7z-0-$-. -/+<+F+P+Z+d+p+|+++/++*++7[.-.y-m*3+++++3+++4 ~7 :-#8}*4/|3;*+ /3@ / 0meak5k1k'-'- F W9 m %  ] b  %   [ %  b  % %  , 6:;  P P% e  @;;;; b; b; b; b; b; b; b; ;*; ; "T ; &; 'b; (b; )b;;<b8 ./../H/usr/include/usr/include/bits/usr/lib/gcc/x86_64-redhat-linux/4.1.2/includeRNAalifold.cpair_mat.halifold.hPS_dot.hstdio.hlibio.htypes.hstddef.hfold_vars.h vl`J{M zW=/ 6xMti<kxmtx;=.XXJXiXf}.!}%-u-<}$Ws-UwY;=;gI=wJ t~kvLX-/&;1-;~.-KeYK%(xmҫ=WKIKe=Ixf fvJ #Y3u";YChUwYWYWYWYv$IwE;X(:K#}O7EJJj:uuY!@Y.##X(tX+J~t~.=~Jg%u[rv!}<}J=e  }$Ws-L;t~!wJ8&'ɟ%rf  u Ju Xf~X=ӅO!g)%zXBYyʟ;Y=u_N$~0ԇ0҉yɃבuJs(K0CtM+$+q); C  ])e.K. 3K/(~~ o0ԇ)d>8KM!;i-\FYZ]s/;$heGVYL2|.x0;!=$<`=/ufXɃg'.~X;K~.~J~~~<$~T<wIg+h ~J<~KL~<*u;/suguK{.I=YI/g~.J,jKe*mJ%㻻p~J gI/9vr/>r~~u~"~#~&)ZHY~ ~B Ws|X {Gz???fffffq@%zr?@@-C6J?Y@@usage: RNAalifold [-cv float] [-nc float] [-E] [-old] [-r] [-R ribosum] [-mis] [-aln] [-color] [-circ] [-s num] [-se num] [-p[0]] [-C] [-T temp] [-4] [-d] [-noGU] [-noCloseGU] [-noLP] [-e e_set] [-P paramfile] [-nsp pairs] [-S scale]What energy_set are YOU using??warning, depending on the origin of the circular sequence, some structures may be missed when using -noLP Try rotating your sequence a few times Input constraints using the following notation:< : base i is paired with a base j : base i is paired with a base j>imatching brackets ( ): base i pairs base j Input aligned sequences in clustalw format minimum free energy = %6.2f kcal/mol (%6.2f + %6.2f) free energy of ensemble = %6.2f kcal/mol frequency of mfe structure in ensemble %g can't open %s skipping output %d sequence; length of alignment %d mfe base pair with very low prob in pf: %d %d %lf%d-noGU-noCloseGU-noLP-nsp-nc-old-mis-MEA-cv-circ-color-alnrcan't open %s | : paired with another base. : no constraint at allx : base must not pairno sequences foundconstraints missing %s %s (%6.2f = %6.2f + %6.2f) out of memory in realloc%d %d %s colorpair %d %d %d gmark %d cmark aln.psscaling factor %f %s %6g %.2f %s [%6.2f] %s %6.2f {%6.2f + %6.2f} %s {%6.2f MEA=%.2f} walifold output CGGCGUUGAUUA--%5d %5d %2d %5.1f%% %7.3f %s:%-4d +%s 0.0 10.0 0.60.0 0.20.16 10.16 0.60.16 0.20.32 10.32 0.60.32 0.20.48 10.48 0.60.48 0.20.65 10.65 0.60.65 0.20.81 10.81 0.60.81 0.2....,....1....,....2....,....3....,....4....,....5....,....6....,....7....,....8_ACGUTXKI?x  MD<$BLE E(A0A8GFzRx 4 LMD4d$BLE E(A0A8GFwwUPUTQQwwww  w(  w0 w8%wU]@]@VUV] ]>]f]?K]jD]dyUy]U]U]U;];WUWl]lvUv]U=]=JUJs]svUv]U]U.].;U;g]gvUv]U]U]]UF]#$]($-$U-$5$]5$E$U$$]c%u%]u%%]%%]%%]T^Y ^ ^^G#b#^#E$^$$^c%%^%%^b к >ккu?кKjккF#к$($кE$$к$c%к%%к{ غ >غغu?غKjغDdغغF#غ$($غE$$غ$c%غ%%غj  >p=f?KjDdF#$($E$$$c%%%% X @@VXVddyXyX+X+;;WXWllXJXJssX;X;NNZXZggvXvXX($($-$X-$5$5$E$XE$$$$X$u%u%z%Xz%%%%X%%%%X%%%%X%%%%X%%<T?KT  >f?KjDdF#$($E$$$c%%%\P@\@EPE\UQP Q%P%7Q6V6L\ V \>\f\fuVwV?K\jD\dN\NPPP\V\F\FVy V~!""V|""Vb##V#$\$($V($($\E$$V$$\$$VE%c%Vc%c%\%%V%%\h  >u?KjDdF#$($E$$$c%%%<X?FX*PluPzP PPPPhsPP\gP%%6  >u?KjF#$($E$$$c%%%?  >u?KjF#$($E$$$c%%%:KKjjFF##$$($($E$E$$$$$c%c%%%%%%%V  >{=f?KjDdF#$($E$$$c%%%A_Y _ ___G#b#_#E$_$$_c%%_%%_%%%%%yv$v$$$$$$$%RUPUAXAFPFXX0<X R R X  P B X} U=fUjXDRFRQQ.TgTT0<T P P B T} Q=fQj{TPPPSQQ)GQGbQffSfpQDdSR R  P GRGbRfpRTPGTGbTfpTV~VY c V' V >VVuwV?VKjVVFVy V~!""V|""VG##V$($VE$$V$$VE%c%V%%Vc]cc  >u?KjF#$($E$$$c%%%  >u?KjF#$($E$$$c%%%  >u?KjF#$($E$$$c%%%  >u?KjF#$($E$$$c%%%  >u?KjF#$($E$$$c%%%VY V V>VuwV?VKjVVFVy V~!""V|""VG##V$($VE$$V$$VE%c%V%%V   >u?KjF#$($E$$$c%%%  >u?KjF#$($E$$$c%%%^R R ^>^u?^Kj^^F^G#b#^$($^2 _2 I P _>_u?_Kj___F_G#b#_$($_  >u?KjF#$($E$$$c%%%Q Q  PE a Q  >u?KjF#$($E$$$c%%% ܻ ܻ>ܻu?ܻKjܻܻF#ܻ$($ܻE$$ܻ$c%ܻ%%ܻ _ S SuSSKjSSFSG#b#S$($Smmaa hG#b##E$$$c%%% KjF#$($E$$$c%%% _ S SSSFS$($S FG#b##$($E$$$c%%% ȻhȻG#Ȼb##Ȼ$c%Ȼ%%Ȼ лhлe &#лb#{#л%%лPTSyS{##SE$$S$$SE%c%Sb hG#b##E$$$c%%% \h\5\5\C!\~!("\|""\b##\$E%\%%\`_C _&#G#_{##_%%_ ļhļ`ļMļ&G#ļb##ļ%%ļ h@G#b##%% hG#b##%% hKG#b##%% h^G#b##%% h\Q6KQb##%E%%% hG#b##3%E%%% h`G#b##%% h(G#b##@%E%%%`_C _&#G#_{##_%%_YRR`S1S&PPP h &#b#{#%% _ S ShSq S""S%%S ܼhܼ| &#ܼb#{#ܼ ؼhؼ& &#ؼb#{#ؼ ]h] &#]b#{#] \h\ ("\|""\b#{#\ !R3!!R,"W"Pp""P""P,""Q""Q  _ _ S Shh_hSC ,"_,"&#Sb#{#_%%_ R!"Rb#{#R ػhػ G#ػb##ػq$$ػ$c%ػ%%ػ$$a}j main,%zFD=f AgzFD=f e \ ` T W  B Ag6?)-#~> e a ~ h  e a a ~ h  a e  a ) . 7 ' e  a k0d  u%%$c%E$$$($!#F~!Kj~!%%$c%E$$b##!G#$E%&#G#y+%3% %%&#G#wy&j y|M(  y|M:y|%%b#{#"&#!|" ~!  %%%%b#{#"&#""!|"3!~!-!1!e V ] @ C  9   &#G#36/\.H" &#G#36/\.H"  b#{#!!3!~!-!1!,"c""&#""k"x"E$$$$make_color_pinfocodealiout_shortbufpair_info_IO_lock_tsfact_IO_buf_endcv_fact__resultcstrucgfnamebase_pair_IO_write_endunsigned intLaw_and_Orderreal_en_flagsscalemake_pair_matrixRibosumFilebondT_markersshort integapdangles_posn_back_IO_write_base__res$Id: RNAalifold.c,v 1.23 2009/02/24 14:21:26 ivo Exp $long long unsigned intdoMEAfilencompduckParamFile_offset_fileno__pad3mark_endgapsbondsize_t_vtable_offsetnonstandards_IO_read_baseenergy_set_IO_save_endnoGUenergystringprobargvnoPSRNAalifold.ctemperaturealias__s1_lencharBP_pair_moderibono_closingGU_IO_read_ptrtetra_loopcompare_pair_infoprint_pieval_energyrtype/projects/remc_bigdata/miR/ViennaRNA-1.8.5/Progs_IO_markerlong long int__s2_len_IO_save_baseMEAgammanofoundptabledoColornc_factnamesisttyclust_filestdout_IO_backup_basens_basesdist__pad1__pad2__pad4__pad5annotemaxlfname__s1centdoAlnPSfold_constraineddo_backtrackunsigned charpairingspairGNU C 4.1.2 20080704 (Red Hat 4.1.2-48)_IO_read_endmea_enlong intCVenlengthcolorMatrixprint_alioutnoLonelyPairsusageplistpfreqoldAliEnn_seqpf_scaleencode_char_locklong unsigned int_old_offsetstdin_IO_FILEfloatargcrcsidtype_sbuf_IO_write_ptrcpairsequencesmax_pendgapsffnamestderr__off_tcircsigned charshort unsigned intmaindouble_chainmin_encolorpsFILEstructure_flags2num_pcomp_cur_columnpname_nextmfe_struceos_debug_unused2_IO_buf_base__off64_tGCC: (GNU) 4.1.2 20080704 (Red Hat 4.1.2-48).symtab.strtab.shstrtab.rela.text.data.bss.debug_abbrev.rela.debug_info.rela.debug_line.rodata.cst8.rodata.str1.8.rodata.str1.1.rela.rodata.rodata.cst16.rodata.cst4.rela.debug_frame.rela.eh_frame.debug_loc.rela.debug_pubnames.rela.debug_aranges.debug_ranges.debug_str.comment.note.GNU-stack @% &@& ,`&$ 1`&Ds)}?P!U=<P(a0DHn2xD}2/HJ0 @ N OOO`XP%B} 0( 0 Ȓ` 0(".+55;X /    &M2    @*F N@S Y c Qi n s y  ( # 6 0 8  @$ $2FLSZar ';BGQYmv#19KXlu{RNAalifold.ccompare_pair_infousageencode_charLaw_and_OrderaliasBP_pairpairrtypeC.75.5732scale.LC0.LC1.LC43.LC44.LC45.LC46.LC12.LC16.LC54.LC59.LC70.LC5.LC75.LC76nrerrorenergy_setstrchrmainstdindo_backtrackdanglesoldAliEnfopenstderrfprintfnoGUnonstandardsnoLonelyPairsread_parameter_filespacestdoutfilenoisattyfold_constrainedread_clustalstrlenfclosestrncpycircalifoldeos_debugenergy_of_circ_structconsens_misprintfstrcpymemcpymake_pair_tablereallocsnprintfstrcatfreePS_rna_plot_abase_pairfree_alifold_arraysfflushputsconsensusalifoldenergy_of_alistructget_line__strduptemperatureexppf_scalealipf_circ_foldputcharalipbacktracklogPS_color_alnalipf_foldfwritesscanfinit_randRibosumFileribono_closingGUnc_facttetra_loop__ctype_b_loccv_factfree_alipf_arrayscentroid_ali__ctype_toupper_locxreallocqsortfputcPS_color_dot_plotMEAenergy_of_struct8 @! 0 1 =3N4i5{6  L7R \8a Nh9|0   @:;1 @= @W t<=>;;;;;3?8@?A]BCD93CE^Dl>rBFGHIYJo tK KL7L MD>>>N @ D D O OG  V Pf Q   P Q 0 P Q 0 P# QU R S R R R T > T U T R' T, R3 ?8 VB RL R` Rm R @  / @ @- P ;u @ ; D  / K5SA3F@MA[B3 pWB  WXYZ*3/[B;ISDg l/{\"]#$%^_? 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