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C5xym؃;4|͍e[^_]ÐUWVShh ju 1I;] E}%h hju(UC;] |1;] }:}u u]Uu}QC;] |1;M}FEE܋Uu]vUu}}܉ωTA;M|ػ;] }eu;M}GE [-%s] [-%s <%s>] %d%cis not an integer. integer at its end. is not a positive integer. point number at its end. PAGERmorers more than once on the command line. does not match any of the legal options. An option in the "exclusive" array does not appear in the "options" array. A required option is mutually exclusive with a non-required option. and "-%s" options are mutually exclusive. One of the following mutually exclusive options is required on the command line: The required option "-%s" is missing The command line is missing an integer at its end. "%s" (from item %d on the command line) The command line is missing a positive The command line is missing a non-negative is not a non-negative integer. The command line is missing a floating is not a floating point number. The command line is missing a positive floating is not a positive floating point number. The command line is missing a non-negative floating is not a non-negative floating point number. The command line is missing a string of characters at its end Copyright 1991--1999 Gerald Z. Hertz May be copied forAuthor: Gerald Z. Hertz Dept. of Molecular, Cellular, and Developmental Biology University of Colorado Campus Box 347 Boulder, CO 80309-0347 This program determines consensus patterns in unaligned sequences. The major difference between "wconsensus" and "consensus" is that this program will determine the width of the pattern being sought. The algorithm is based on a matrix representation of a consensus pattern. Each row corresponds to one of the letters of the relevant alphabet---e.g., 4 rows in the case of DNA. Each column corresponds to one of the positions within the pattern. The elements of the matrix are determined by the number of times that the indicated letter occurs at the indicated position based on the words sumMatrices are constructed by sequentially adding additional words to previously saved matrices. During each cycle, only the most significant matrices are saved. The maximum number of matrices to save is determined by the "-q" option (see section 1 below). In practice, less matrices are ultimately saved because many of the matrices initially saved are identical to each otherThe program can use 3 different criteria for deciding to stop adding additional words to the saved matrices: 1) Each sequence has contributed exactly one word to the saved matrices (the default). 2) The saved matrices contain a maximum allowable number of words (set with the -n and -N options). 3) The program has completed a designated number of cycles since finding the current most significant alignment (set with the -t option). This latter criteria is used in addition to criteria 1 and 2 to terminate the program sooner.The significance of a matrix is initially measured by its information content. A higher information content indicates a rarer pattern and a more desirable matrix. The information content of alignments having different widths are compared after subtracting from each position the average information and a multiple of the standard deviation expected from an arbitrary alignment of random sequences. The program also estimates for each matrix a p-value, which is the probability of observing the particular information content or higher in an arbitrary alignment of random words having a length equal to the matrix's width. The ultimate statistical significance of a matrix is determined by multiplying the p-value by the approximate number of possible alignments, containing the designated number of sequences and having the observed width. We refer to this product as the expected frequency of the matrix alignment. The expected frequency allows the comparison of matrices summarizing differing numbers of sequences and havinTo identify an overall best alignment, it is necessary to determine the alignments using various multiples of the standard-deviation correction to the information content (set with the -s option). As the standard-deviation correction is increased, less positions will tend to be in the resulting alignments. The overall best alignment is the one having the lowest expected frequency. We have found standard-deviation corrections of 0.5, 1, 1.5, and 2 to be useful starting values. The program can print two different lists of matrices. The first list contains the matrices having the highest adjusted information from each cycle, ordered by decreasing statistical significance (i.e., increasing expected frequency). In general, this first list will contain the most interesting alignment. The second list contains the matrices saved after the final cycle of the program, also ordered by decreasing statistical significance. In general, this latter list will be useful when the user wishes each sequence to contribute exactly one word to the final alignment (i.e., when the -n and -N options are not used). In the program's output, the words contained in each matrix are listed in the order of their occurrence in the input sequences. The order is indicated by "integer|integer". The first integer is simply a sequential count of the words, and the second integer indicates during which cycle the word was added to the matrix. The location of a word is indicated by "integer/integer". The first integer indicates which sequence contains the word, and the second integer indicates where in that sequence the word is located. If the first integer is preceded by a minus sign, then the complementary word is the one included in the matrix. The output of the program is sent to the standard output. The input files---those containing the actual sequences and those indicated by the "-f", "-a", and "-i" options---can contain comments according to the following convention. The portion of a line following a ';', '%%', or '#' is considered a comment and is ignored. Comments can begin anywhere in a line and always end at the end of the line. The one minor exception is that, to avoid ambiguity, comments in the list of sequences (see the "-f" option below) must be preceded by a blank space when not occurring at the beginning 0) -h: print these directions. 1) General information -f filename: this file (default: read from the standard input) contains the names of the sequences. The names of the sequences must be less than 512 characters. The corresponding sequence may follow its name if the sequence is enclosed between backslashes (\). Otherwise, the sequence is assumed to be in a separate file having the indicated name. The format of the actual sequences is described at the end of these directions. The following four modifiers can appear in front of the name of the relevant sequence: -c: the sequence is circular. WARNING: circular sequences are not handled completely properly, unless the sequence has a discontinuity; in other words, circular sequences should be modified by the -i or -e modifiers described below. -s integer-integer integer-integer: the positions in the sequence indicated by the integer pairs, inclusive, are seed sequences. If the "-s" modifier is used anywhere in the input file, then the initial set of matrices will only be constructed (i.e., seeded) from the sequences within the marked regions. If this modifier is not used anywhere in the input file, then all the sequences will be used to seed matrices. One or more integer pair can be indicated for a single sequence. However, if no integer pairs are given, the whole sequence will be used for seeding matrices. -i integer-integer integer-integer: the positions in the sequence indicated by the integer pairs, inclusive, are the only positions to be analyzed. -e integer-integer integer-integer: the positions in the sequence indicated by the integer pairs, inclusive, are to be excluded from the analysis. When both the "-i" and "-e" modifiers are used, the intersection of permissible positions is analyzed. When a sequence name is not marked by either the "-i" or "-e" modifier, then the whole sequence is included in the analysis. -q integer: the maximum number of matrices to save between cycles of the program---i.e., the queue size (default: save 200 matrices). This option can also be changed while the program is running: -s number: the number of standard deviations to lower the information content at each position before identifying information peaks (required). A range of values should be tried. For example, try values of 0.5, 1, 1.5, and 2. The overall best alignment is the one having the lowest expected -d: use the designated prior probabilities of the letters to override the observed frequencies. By default, the program uses the frequencies observed in your own sequence data for the prior probabilities of the letters. However, if the "-d" option is set, the prior probabilities designated by one of the next 3 options are used. If the "-d" option is not set, the next 3 options are still used to determine the sequence alphabet, but any prior probability information is ignored. The next three options are mutually exclusive (default: "-a alphabet"). -a filename: file containing the alphabet and normalization information. [Use "-af" when using the VMS operating system] Each line contains a letter (a symbol in the alphabet) followed by an optional normalization number (default: 1.0). The normalization is based on the relative prior probabilities of the letters. For nucleic acids, this might be be the genomic frequency of the bases; however, if the "-d" option is not used, the frequencies observed in your own sequence data are used. In nucleic acid alphabets, a letter and its complement appear on the same line, separated by a colon (a letter can be its own complement, e.g. when using a dimer alphabet). Complementary letters may use the same normalization number. Only the standard 26 letters are permissible; however, when the "-CS" option is used, the alphabet is case sensitive so that a total of 52 different characters are possible. POSSIBLE LINE FORMATS WITHOUT COMPLEMENTARY LETTERS: letter letter normalization POSSIBLE LINE FORMATS WITH COMPLEMENTARY LETTERS: letter:complement letter:complement normalization letter:complement normalization:co -i filename: same as the "-a" option, except that the symbols of the alphabet are represented by integers rather than by letters. Any integer permitted by the machine is a permissible symbol. [Use "-if" when using the VMS operating system] -A alphabet_and_normalization_information: same as "-a" option, except information appears on the command line (e.g., -A a:t 3 c:g 2). [Use "-ac" when using the VMS operating system] 3) Alphabet modifier indicating whether ascii alphabets are case sensitive---the following option is mutually exclusive with the "-i" option (default: ascii alphabets are case insensitive). -CS: ascii alphabets are case sensitive. [Use "-as" when using the VMS operating system] 4) Options for handling the complement of nucleic acid sequences--- the 3 options in this section are mutually exclusive. -c0: ignore the complement (the default option) -c1: include both strands as separate sequences -c2: include both strands as a single sequence (i.e., orientation unknown) [ONLY IMPLEMENTED FOR WHEN THE "-n" and "-N" OPTIONS ARE 5) Algorithm options the "-pr1" and "-pr2" options are mutually exclusive; the "-l" and "-n" options are mutually exclusive; the "-n" and "-N" options are mutually exclusive; the "-m" option can only be used when the "-n" or " -pr1: save the top progeny matrices regardless of parentage. -pr2: try to save the top progeny matrices for each parental matrix (the default). This option prevents a strong pattern found in only a subset of the sequences from overwhelming the algorithm and eliminating other potential patterns. This undesirable situation can occur when a subset of the sequences share an evolutionary relationship not common to the majority of the sequences. This option corresponds to the original "consensus" algorithm (Stormo and Hartzell, 1989, PNAS, 86:1183-1187; Hertz et al., 1990, CABIOS, 6:81-92) -l: (lowercase L) seed with the first sequence and proceed linearly through the list. This option results in a significant speed up in the program, but the algorithm becomes dependent on the order of the sequence-file names. This option corresponds to the original "consensus" algorithm (Stormo and Hartzell, 1989, PNAS, 86:1183-1187; Hertz et al., 1990, CABIOS, 6:81-92). -n integer: repeat the matrix building cycle a maximum of "integer" times and allow each sequence to contribute zero or more words per matrix. [Use "-n1" when using the VMS operating system] -N integer: repeat the matrix building cycle a maximum of "integer" times and allow each sequence to contribute one or more words per matrix. [Use "-n2" when using the VMS operating system] -m integer: the minimum distance between the starting points of words within the same matrix pattern; must be a positive integer; can only be used when the "-n" or "-N" option is also used. If the integer is a 1, then there is no restriction on the overlap. (default: 1). -t integer: terminate the program "integer" cycles after the current most significant alignment is identified (default: terminate only when the maximum number of matrix building cycles is completed) -pg0: do NOT permit terminal gaps (the default). -pg1: permit penalized terminal gaps---i.e. terminal deletions. **** "-pg1" cannot currently be used with the "-n" option. **** The "-q", "-n", and "-t" options can be changed after the program starts by placing the new options in a file called "changes." suffixed with the process identification number---the PID number listed at the beginning of the program's output. For example a file called "changes.10568" might contain "-q10 -n50 -t2". The "-n" option can change the maximum number of words in the alignments even if it was not used at the beginning of the program, although it will not permit a sequence to contribute more than one word to the alignment unless the "-n" or "-N" option was used on the command line. If the "-t" option was not used when the program was started, this option will only keep track of alignments beginning with the cycle during which i 6) Output options -pt integer: the number of matrices to print of the top matrices from each cycle (default: 4). A negative value means print all the top matrices. -pf integer: the number of matrices to print of the matrices saved from the final cycle (default when NOT using "-n" or "-N" option: print 4 matrices; default when using "-n" or "-N" option: print no matrices). Do not explicitly give the complements of nucleic acid sequences. If needed, the complementary sequence is determined by the program. Whitespace, periods, dashes (unless part of an integer when the "-i" option is used), and comments beginning with ';', '%%', or '#' are ignored. When using letter characters (i.e., with the "-a" and "-A" alphabet options), integers are also ignored so that the sequence file can contain positional information. When using integer characters (i.e., with the "-i" alphabet option) the integers must bSequences surrounded by slashes (/) do not contribute to the generation of the patterns; thus, a portion of a sequence can be ignored without disrupting the overall numbering of the sequence. A double slash (//) would indicate a discontinuity in the sequence. A '/' at the beginning or the end of a sequence will cause the sequence to be marked as non-circular even if the sequence's name is marked with a "-c" (see the "-f" option in section 1). The effect of the single slashes can also be created with the "-i" and "-e" modifiers in the file containing the names of the sequences (see the "-f" option in section 1). When slashes and the "-i" and "-e" modifiers are all used, the intersection of permissible positions is analyzed. Sequences that follow their name in the file indicated by the "-f" option must be enclosed between backslashes (\) (i.e., the actual sequence must be preceded and followed by a backslash). However, if the sequence is contained in a separate file, do NOT use a '\'. noncommercial purposes. hertz@colorado.edu WCONSENSUS (version 5c) marized by the pattern. g differing widths. of a line. COMMAND LINE OPTIONS: see section 5 below. frequency. 2) Alphabet options mplement's_normalization NOT USED!!!!] -N" option is used. t is first initiated. FORMAT OF THE SEQUENCES e separated by whitespace. %%%dsCannot open file "%s". read_sequences()STseedSTinclusiveSTexclusive-c-s-i-esequence information. read_string modify sequence %d. %*d-%*d%c%d-%d in sequence "%s", The letter "%c" (ASCII code %d in sequence "%s", is not a slash or the beginning of a comment. read_int_seq()ignore_away_from_NO()truncate_fragmentSTfragmenttruncate_fragment()construct_complementcomp_fraginsert_letter()check_fragmentcheck_seq_end()STcircle_fragadjust_circle()mark_seed_seq()All_Seq_flag[]check_range()(*range)check_seq()All_Seq_infocheck_frag()All_Frag_infoAll_SequenceAll_Seq_flagcheck_gene()Gene_infotruncate_seq_frag()sequence %d: %s Gene Index: %d Ortholog Index: %d CIRCULAR CIRCULAR SEEDS: %d-%d[1-%d] [%d-%d] %d-%d nonefragments: %d-%d none %d-%d[1-%d] %d-%d deter_obs_print_freq()Num_letdeter_obs_print_freq() 1P_odeter_obs_print_freq() 2each letter. ****# print_obs_freq()eliminate_zeros()print_seq_frag()***** Sequence information from the standard input. ***** ***** Sequence information from file "%s". ***** Total number of sequences: %d. Total number of sequence fragments: %d. A "getc" error while reading the Cannot open sequence file "%s". Cannot find the sequence name corresponding to The "%s" modifier is used more than once toThe "%s" modifying sequence %d is not followed by any integers pairs. In the sequence information, the following integer pair contains negative numbers: In the sequence information, the second integer of the following pair is less than the first: ASCII code "%d", following letter is not a slash or an alphanumeric character. "ungetc" error in "read_int_seq()" "%d"), following integer letter The letter "%c" (letter %d in sequence "%s") is not a member of the alphabet. The integer "%d" (letter %d in sequence "%s") An error occurred while reading sequence "%s". PRIOR FREQUENCIES DETERMINED BY OBSERVED FREQUENCIES. #**** Information on observed frequency and occurrence of #Total number of letters in the input sequences = %d %c %#G; observed occurrence = %5d (letter %3d) %3d %#G; observed occurrence = %5d (letter %3d) An "ungetc" error while reading the A "getc" error occurred while reading the seq %2d: begin = %2d; end = %2d; total = %3d; circle = %3d seq frag %2d: number = %2d; start = %3d; length = %3d; adj_length = %3d; max_L = %3d HeapHeap[]Ln_NN_multipleInt_N_ln_NDiff_N_ln_NInfo_factorInt_info_factorDiff_info_factorInfo_factor[]Int_info_factor[]Diff_info_factor[]matrix->matrixmatrix->seq_fragmatrix->positionupdate_matrix()mat_matrixupdate_matrix() 1update_matrix() 2(matrix->matrix[k])->column(matrix->matrix[k])alloc_column()free_seq_flag()free_matrix()free_column()column->columnfree_columnLn_N %d: %f N_multiple letter: %d %d: %12.6f %10ld %10ld %d: %12.6f %10ld %4d: %15f %14f @@Info_factor[][], Int_info_factor[][], and Diff_info_factor[][] index Avg_info_factor Std_info_factor--(BASE 2) DET_scan_sequences_cycle1() 3DET_scan_sequences_cycle() 3DET_init_cycle_flag()DET_score_alignment()DET_init_seq_flag()The alphabet only contains one letter, The alphabet contains no letters, STANDARD DEVIATION ADJUSTMENT HAS BEEN LOWERED TO %.3f deter_background()an uninteresting situation. back_alloc_GLarrays()Avg_info_factorStd_info_factorFactor_backgroundback_alloc_STarrays()Ln_factorialSTln_pSTln_1_pfree_background()?add_word()scan_sequences_cycle_1a scan_sequences_cycle_1b init_seq_flag_2()init_seq_flag_3()scan_sequences_cycle_3b scan_sequences_cycle_4a scan_sequences_cycle_4b scan_sequences_cycle1_1a scan_sequences_cycle1_1b scan_sequences_cycle1_3a()scan_sequences_cycle1_3b scan_sequences_cycle1_3b()scan_fragment_1a scan_fragment_1b scan_fragment_2b scan_fragment_3a scan_fragment_3b scan_fragment_4a scan_fragment_4b add_to_list_1()add_to_list_2()pack_heap()Save top 2 isolate_top_peaks()sum_int_infoadd_to_top()mat_matrix[]->columnmat_matrix[]add_alloc_arrays()STalign_regionSTcycle_flagremove_alloc_arrays() STseq_minus_flagalloc_seq_minus()STseq_minus_flag[]Seq_frag = %d; Sequence = %d init_unlimited_possible_matSTstart_sitesunlimited_possible_mat() 1unlimited_possible_mat() 2unlimited_possible_mat() 3init_one_match_possible_mat()init_1_match_possible_mat()replace_heap_new_matrix()heap[1]new_elementinit_p_value()STln_info_factorSTln_info_factor[i]STp_sumSTln_p_sumSTcomp_pSTcomp_ln_pSTcomp_info_factorSTcomp_ln_info_factorSTcomp_info_factor[]STcomp_ln_info_factor[]STcomp_p_sumSTcomp_ln_p_sumreset_p_value()STln_info_factor[]STtwistinit_n()STln_mom_0STln_mom_1STln_mom_2STln_par_mom_0STln_par_mom_1STln_par_mom_2det_info_factor()det_min_col_ln_like()sum_newsum_oldfind_gamma_twist()STnew_twistdel_twist()find_twist_range()integer log-like %7d %9.4f %10.4f %11.4e ?ư>"@}Ô%IT@9B.?Conversion factor from log-likelihood score to integer: %g score score ln(p-value) p-valuechanges.%d%1schange_q_size()MAXIMUM NUMBER OF CYCLES: %d realloc_variables()back_realloc_GLarrays()realloc_matrix()NUMBER OF CYCLES AFTER SIGNIFICANCE PEAK: %d MAXIMUM NUMBER OF MATRICES TO SAVE: %d print_resultsSTseq_posreset_print_results()STmat_queue_cycleMATRIX %d Print final: %d print_list_cycle() . %3dnumber of sequences = %d width = %d crude information = %.3f %c |%3d |%3d|%-3d : %3d/%-5d cleanup_mat_list() [] MATRICES SAVED FOR NEXT CYCLE [] []---------------------------------------------------------------[] [] total | crude | ln top [] ln expected | [] CYCLE [] number | information | p-value [] frequency | width [] ------[]----------|-------------|-------------[]-------------|---------[] %5d []%9d |%12.4f |%12.4f []%12.4f |%8d [] THE LIST OF TOP MATRICES FROM EACH CYCLE-- sorted by expected frequency (total of %d): THE LIST OF MATRICES FROM FINAL CYCLE-- unadjusted information = %.3f sample size adjusted information = %.3f ln(p-value) = %G p-value = %G ln(expected frequency) = %G expected frequency = %G LIST OF WHOLE MATRICES FROM THE FINAL CYCLE. PROGRAM BUG: ln_chi_square()log-likelihood=%g alpha=%g ln_gamma_prob()det_gamma_prob()integrate_normal_2()ln_geo_series()Cannot determine the chi square probability when the negative log-likelihood ratio is less than 0 or the degrees of freedom is less than 0. log-likelihood=%g degrees of freedom=%g Cannot determine the gamma probability when the alpha parameter is less than 0. The function "ln_gamma()" only works with values > 0 The function "det_psi()" only works with values > 0 ư@% @@@9B.}Ô%I-q=Target value is too large in "root_find()". Target value is too small in "root_find()". ?root_newton_multi()deltasolve_2()mallocreallocrecallocfrePROGRAM BUG: %s Cannot %s space for "%s" in the "%s" function. The memory being %sed for the "%s" variable in the "%s" function has already been freed. The beginning of the memory being %s"%s" function has been overwritten. The end of the memory being %sinit_profile_variables()Init_profilesInit_profile[]Num_init_profileadd_list_cycle()Mat_to_Profile()add_one_profile()int_matrixSTgene_idxSTseq_fragSTpositionGene groups included: crude_infomation = %.3f fill_heap_mat_peak()add_to_mat_queue()mat_queue[]sort_seq_poscompare_profile()init_hspProfilesProfiles[]Num_cycle_profileinit_pairwise_comp()SThspcomp_cycle()comp_2_profiles()max_positionscore_function()STscoreSTscore[]score_energy()f_1f_2score_energy2()H_1H_2score_energy4()colcal_H()STHcal_f()STfDP_functionDPDP_function()DP[]sum_positions()DP_checkDP_check[]find_hsp_peak()trace_back()free_scores()insert_hsp()merge_HSP()free_HSPhsp[i]make_mirror_profile()mirrorseq_orderinitialize_C_LN()C_LN_CC_LN_C()C_LN_N()C_LN_P CYCLE %d: No matrix is saved. MATRIX %d-%d: HSP of matrix %dx%d: %6.2fC_LN_C[%d][%d][%d]: %.3f C_LN_N[%d][%d][%d]: %.3f C_LN_P[%d][%d]: %.3f [] PROFILES SAVED FROM P-CONSENSUS [] [] sequence | HSP | saved [] shortest | longest [] CYCLE [] number | number | matrices [] peak | peak [] score %.2f (%d,%d)--(%d,%d) l=%d ?2@l:VQ$dX0Sl@PpXx0x4cD2 NsD8D0 0@0D((`qst@ )ppD=opH'x `DPPPLT`pX p D0cc)p=o)p=oqs)p mBSv S@+WU8@뒦~4M&S?1!e[־Sv S@+WU8@뒦~4M&S?1!e[־" $ (d o $$0oooTDRbrˆ҈"2BRbr‰҉"2Bdtdt:<Is1-W2W cV&[Nd{ ! "#5%M&c1z234568 9$;D=Z>p?@ABCDEF&G=HVIkNQR S T;UWVoX[^ehl q r7 uR vo y z }  ( B ˔v F  #X [ 4w < C F S Z ^ltOyp6 Nd8ybKN#5NyH:KiLUZ^Aayb^t5 7#8;9U:o dtinit.c/usr/src/build/150971-i386/BUILD/glibc-2.2.5/csu/gcc2_compiled.int:t(0,1)=r(0,1);-2147483648;2147483647;char:t(0,2)=r(0,2);0;127;long int:t(0,3)=r(0,3);-2147483648;2147483647;unsigned int:t(0,4)=r(0,4);0000000000000;0037777777777;long unsigned int:t(0,5)=r(0,5);0000000000000;0037777777777;long long int:t(0,6)=@s64;r(0,6);01000000000000000000000;0777777777777777777777;long long unsigned int:t(0,7)=@s64;r(0,7);0000000000000;01777777777777777777777;short int:t(0,8)=@s16;r(0,8);-32768;32767;short unsigned int:t(0,9)=@s16;r(0,9);0;65535;signed char:t(0,10)=@s8;r(0,10);-128;127;unsigned char:t(0,11)=@s8;r(0,11);0;255;float:t(0,12)=r(0,1);4;0;double:t(0,13)=r(0,1);8;0;long double:t(0,14)=r(0,1);12;0;complex int:t(0,15)=s8real:(0,1),0,32;imag:(0,1),32,32;;complex float:t(0,16)=r(0,16);8;0;complex double:t(0,17)=r(0,17);16;0;complex long double:t(0,18)=r(0,18);24;0;__builtin_va_list:t(0,19)=*(0,20)=(0,20)../include/libc-symbols.h/usr/src/build/150971-i386/BUILD/glibc-2.2.5/build-i386-linux/config.h../sysdeps/gnu/_G_config.h../sysdeps/unix/sysv/linux/bits/types.h../include/features.h../include/sys/cdefs.h../misc/sys/cdefs.h/usr/lib/gcc-lib/i386-redhat-linux/2.96/include/stddef.hsize_t:t(8,1)=(0,4)__u_char:t(4,1)=(0,11)__u_short:t(4,2)=(0,9)__u_int:t(4,3)=(0,4)__u_long:t(4,4)=(0,5)__u_quad_t:t(4,5)=(0,7)__quad_t:t(4,6)=(0,6)__int8_t:t(4,7)=(0,10)__uint8_t:t(4,8)=(0,11)__int16_t:t(4,9)=(0,8)__uint16_t:t(4,10)=(0,9)__int32_t:t(4,11)=(0,1)__uint32_t:t(4,12)=(0,4)__int64_t:t(4,13)=(0,6)__uint64_t:t(4,14)=(0,7)__qaddr_t:t(4,15)=(4,16)=*(4,6)__dev_t:t(4,17)=(4,5)__uid_t:t(4,18)=(4,3)__gid_t:t(4,19)=(4,3)__ino_t:t(4,20)=(4,4)__mode_t:t(4,21)=(4,3)__nlink_t:t(4,22)=(4,3)__off_t:t(4,23)=(0,3)__loff_t:t(4,24)=(4,6)__pid_t:t(4,25)=(0,1)__ssize_t:t(4,26)=(0,1)__rlim_t:t(4,27)=(4,4)__rlim64_t:t(4,28)=(4,5)__id_t:t(4,29)=(4,3)__fsid_t:t(4,30)=(4,31)=s8__val:(4,32)=ar(4,33)=r(4,33);0000000000000;0037777777777;;0;1;(0,1),0,64;;__daddr_t:t(4,34)=(0,1)__caddr_t:t(4,35)=(4,36)=*(0,2)__time_t:t(4,37)=(0,3)__useconds_t:t(4,38)=(0,4)__suseconds_t:t(4,39)=(0,3)__swblk_t:t(4,40)=(0,3)__clock_t:t(4,41)=(0,3)__clockid_t:t(4,42)=(0,1)__timer_t:t(4,43)=(0,1)__key_t:t(4,44)=(0,1)__ipc_pid_t:t(4,45)=(0,9)__blksize_t:t(4,46)=(0,3)__blkcnt_t:t(4,47)=(0,3)__blkcnt64_t:t(4,48)=(4,6)__fsblkcnt_t:t(4,49)=(4,4)__fsblkcnt64_t:t(4,50)=(4,5)__fsfilcnt_t:t(4,51)=(4,4)__fsfilcnt64_t:t(4,52)=(4,5)__ino64_t:t(4,53)=(4,5)__off64_t:t(4,54)=(4,24)__t_scalar_t:t(4,55)=(0,3)__t_uscalar_t:t(4,56)=(0,5)__intptr_t:t(4,57)=(0,1)__socklen_t:t(4,58)=(0,4)../linuxthreads/sysdeps/pthread/bits/pthreadtypes.h../sysdeps/unix/sysv/linux/bits/sched.h__sched_param:T(10,1)=s4__sched_priority:(0,1),0,32;;_pthread_fastlock:T(9,1)=s8__status:(0,3),0,32;__spinlock:(0,1),32,32;;_pthread_descr:t(9,2)=(9,3)=*(9,4)=xs_pthread_descr_struct:__pthread_attr_s:T(9,5)=s36__detachstate:(0,1),0,32;__schedpolicy:(0,1),32,32;__schedparam:(10,1),64,32;__inheritsched:(0,1),96,32;__scope:(0,1),128,32;__guardsize:(8,1),160,32;__stackaddr_set:(0,1),192,32;__stackaddr:(0,19),224,32;__stacksize:(8,1),256,32;;pthread_attr_t:t(9,6)=(9,5)pthread_cond_t:t(9,7)=(9,8)=s12__c_lock:(9,1),0,64;__c_waiting:(9,2),64,32;;pthread_condattr_t:t(9,9)=(9,10)=s4__dummy:(0,1),0,32;;pthread_key_t:t(9,11)=(0,4)pthread_mutex_t:t(9,12)=(9,13)=s24__m_reserved:(0,1),0,32;__m_count:(0,1),32,32;__m_owner:(9,2),64,32;__m_kind:(0,1),96,32;__m_lock:(9,1),128,64;;pthread_mutexattr_t:t(9,14)=(9,15)=s4__mutexkind:(0,1),0,32;;pthread_once_t:t(9,16)=(0,1)_pthread_rwlock_t:T(9,17)=s32__rw_lock:(9,1),0,64;__rw_readers:(0,1),64,32;__rw_writer:(9,2),96,32;__rw_read_waiting:(9,2),128,32;__rw_write_waiting:(9,2),160,32;__rw_kind:(0,1),192,32;__rw_pshared:(0,1),224,32;;pthread_rwlock_t:t(9,18)=(9,17)pthread_rwlockattr_t:t(9,19)=(9,20)=s8__lockkind:(0,1),0,32;__pshared:(0,1),32,32;;pthread_spinlock_t:t(9,21)=(0,1)pthread_barrier_t:t(9,22)=(9,23)=s20__ba_lock:(9,1),0,64;__ba_required:(0,1),64,32;__ba_present:(0,1),96,32;__ba_waiting:(9,2),128,32;;pthread_barrierattr_t:t(9,24)=(9,25)=s4__pshared:(0,1),0,32;;pthread_t:t(9,26)=(0,5)wchar_t:t(11,1)=(0,3)wint_t:t(11,2)=(0,4)../include/wchar.h../wcsmbs/wchar.h../sysdeps/unix/sysv/linux/i386/bits/wchar.h__mbstate_t:t(13,1)=(13,2)=s8__count:(0,1),0,32;__value:(13,3)=u4__wch:(11,2),0,32;__wchb:(13,4)=ar(4,33);0;3;(0,2),0,32;;,32,32;;_G_fpos_t:t(3,1)=(3,2)=s12__pos:(4,23),0,32;__state:(13,1),32,64;;_G_fpos64_t:t(3,3)=(3,4)=s16__pos:(4,54),0,64;__state:(13,1),64,64;;../include/gconv.h../iconv/gconv.h :T(17,1)=e__GCONV_OK:0,__GCONV_NOCONV:1,__GCONV_NODB:2,__GCONV_NOMEM:3,__GCONV_EMPTY_INPUT:4,__GCONV_FULL_OUTPUT:5,__GCONV_ILLEGAL_INPUT:6,__GCONV_INCOMPLETE_INPUT:7,__GCONV_ILLEGAL_DESCRIPTOR:8,__GCONV_INTERNAL_ERROR:9,; :T(17,2)=e__GCONV_IS_LAST:1,__GCONV_IGNORE_ERRORS:2,;__gconv_fct:t(17,3)=(17,4)=*(17,5)=f(0,1)__gconv_init_fct:t(17,6)=(17,7)=*(17,8)=f(0,1)__gconv_end_fct:t(17,9)=(17,10)=*(17,11)=f(0,20)__gconv_trans_fct:t(17,12)=(17,13)=*(17,14)=f(0,1)__gconv_trans_context_fct:t(17,15)=(17,16)=*(17,17)=f(0,1)__gconv_trans_query_fct:t(17,18)=(17,19)=*(17,20)=f(0,1)__gconv_trans_init_fct:t(17,21)=(17,22)=*(17,23)=f(0,1)__gconv_trans_end_fct:t(17,24)=(17,25)=*(17,26)=f(0,20)__gconv_trans_data:T(17,27)=s20__trans_fct:(17,12),0,32;__trans_context_fct:(17,15),32,32;__trans_end_fct:(17,24),64,32;__data:(0,19),96,32;__next:(17,28)=*(17,27),128,32;;__gconv_step:T(17,29)=s56__shlib_handle:(17,30)=*(17,31)=xs__gconv_loaded_object:,0,32;__modname:(17,32)=*(0,2),32,32;__counter:(0,1),64,32;__from_name:(4,36),96,32;__to_name:(4,36),128,32;__fct:(17,3),160,32;__init_fct:(17,6),192,32;__end_fct:(17,9),224,32;__min_needed_from:(0,1),256,32;__max_needed_from:(0,1),288,32;__min_needed_to:(0,1),320,32;__max_needed_to:(0,1),352,32;__stateful:(0,1),384,32;__data:(0,19),416,32;;__gconv_step_data:T(17,33)=s36__outbuf:(17,34)=*(0,11),0,32;__outbufend:(17,34),32,32;__flags:(0,1),64,32;__invocation_counter:(0,1),96,32;__internal_use:(0,1),128,32;__statep:(17,35)=*(13,1),160,32;__state:(13,1),192,64;__trans:(17,28),256,32;;__gconv_info:T(17,36)=s8__nsteps:(8,1),0,32;__steps:(17,37)=*(17,29),32,32;__data:(17,38)=ar(4,33);0;-1;(17,33),64,0;;__gconv_t:t(17,39)=(17,40)=*(17,36)_G_iconv_t:t(3,5)=(3,6)=u44__cd:(17,36),0,64;__combined:(3,7)=s44__cd:(17,36),0,64;__data:(17,33),64,288;;,0,352;;_G_int16_t:t(3,8)=(0,8)_G_int32_t:t(3,9)=(0,1)_G_uint16_t:t(3,10)=(0,9)_G_uint32_t:t(3,11)=(0,4)_IO_stdin_used:G(0,1)GCC: (GNU) 2.96 20000731 (Red Hat Linux 7.3 2.96-110)GCC: (GNU) 2.96 20000731 (Red Hat Linux 7.3 2.96-110)GCC: (GNU) 2.96 20000731 (Red Hat Linux 7.3 2.96-112)GCC: (GNU) 2.96 20000731 (Red Hat Linux 7.3 2.96-112)GCC: (GNU) 2.96 20000731 (Red Hat Linux 7.3 2.96-112)GCC: (GNU) 2.96 20000731 (Red Hat Linux 7.3 2.96-112)GCC: (GNU) 2.96 20000731 (Red Hat Linux 7.3 2.96-112)GCC: (GNU) 2.96 20000731 (Red Hat Linux 7.3 2.96-112)GCC: (GNU) 2.96 20000731 (Red Hat Linux 7.3 2.96-112)GCC: (GNU) 2.96 20000731 (Red Hat Linux 7.3 2.96-112)GCC: (GNU) 2.96 20000731 (Red Hat Linux 7.3 2.96-112)GCC: (GNU) 2.96 20000731 (Red Hat Linux 7.3 2.96-112)GCC: (GNU) 2.96 20000731 (Red Hat Linux 7.3 2.96-112)GCC: (GNU) 2.96 20000731 (Red Hat Linux 7.3 2.96-112)GCC: (GNU) 2.96 20000731 (Red Hat Linux 7.3 2.96-112)GCC: (GNU) 2.96 20000731 (Red Hat Linux 7.3 2.96-112)GCC: (GNU) 2.96 20000731 (Red Hat Linux 7.3 2.96-112)GCC: (GNU) 2.96 20000731 (Red Hat Linux 7.3 2.96-112)GCC: (GNU) 2.96 20000731 (Red Hat Linux 7.3 2.96-112)GCC: (GNU) 2.96 20000731 (Red Hat Linux 7.3 2.96-112)GCC: (GNU) 2.96 20000731 (Red Hat Linux 7.3 2.96-112)GCC: (GNU) 2.96 20000731 (Red Hat Linux 7.3 2.96-112)GCC: (GNU) 2.96 20000731 (Red Hat Linux 7.3 2.96-112)GCC: (GNU) 2.96 20000731 (Red Hat Linux 7.3 2.96-112)GCC: (GNU) 2.96 20000731 (Red Hat Linux 7.3 2.96-112)GCC: (GNU) 2.96 20000731 (Red Hat Linux 7.3 2.96-112)GCC: (GNU) 2.96 20000731 (Red Hat Linux 7.3 2.96-110)01.0101.0101.0101.0101.0101.0101.0101.0101.0101.0101.0101.0101.0101.0101.0101.0101.0101.0101.0101.0101.0101.0101.0101.0101.0101.0101.01.symtab.strtab.shstrtab.interp.note.ABI-tag.hash.dynsym.dynstr.gnu.version.gnu.version_r.rel.dyn.rel.plt.init.text.fini.rodata.data.eh_frame.dynamic.ctors.dtors.got.bss.stab.stabstr.comment.note# 1((<7 dd?oGoTTPToPc 0l $$ u$$p<<{PP `iss @ @@DD$$h  d6<>8D, p$(dT$ $ < P  @D$t "t 2 =AO [ q@ ԕ @ 2p p  @ @ P P  & 5D@̒`Mp U8bp t4 Ȟ |Y ؟t L      8_ G -H :i KH ] n<z@DHL  @LT\D PX-`AdM \ldpw|htxH    D P& %T6FTclyԖؖܖȖ̖\Ė Ж+8XLU am {b h `dhlptx|)8GV_XcTlh\zl`dxp$;KPR^mȗЗؗ (08@Huo ~   k +Xs 2w B(y  VHz nxl  @  ` $ ؆ ; 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init.cinitfini.cgcc2_compiled.call_gmon_startcrtstuff.cp.0__DTOR_LIST__completed.1__do_global_dtors_aux__EH_FRAME_BEGIN__fini_dummyobject.2frame_dummyinit_dummyforce_to_data__CTOR_LIST____do_global_ctors_aux__CTOR_END____DTOR_END____FRAME_END__options.cmain.crun_wcons.ccommand-line.cST_optionsST_exclusivealpha.cSTalpha_flagALPHA_read_letterALPHA_read_numberALPHA_read_colonALPHA_allocALPHA_reallocALPHA_truncateALPHA_get_letterALPHA_get_doubleALPHA_get_colonALPHA_get_intALPHA_repeatALPHA_read_intALPHA_read_asciiparse-line.cprint_directionstext-directions.cread-sequences.cSTseed_sizeSTinclusive_sizeSTexclusive_sizeSTseq_sizeSTfrag_sizeSTformatSTseq_fileGene_counterOrtho_counterSTseedSTinclusiveSTexclusiveSTcircleSTseed_regionsSTinclusive_regionsSTexclusive_regionsSTexcl_rootroot_element.0STstartSTnum_frag_lettersSTfragment_sizeSTfragmentSTexcludeSTignoreSTcircle_fraginitial-mat.cfunctions.cdeter-background.cSTln_pSTln_1_pSTstd_flag.0STprobSTln_probSTln_1_probadd-word.cSTmat_queue_sizeSTmini_heap_posSTmin_progenySTmini_num_matSTmatrixSTmat_matrixSTseq_fragSTpositionSTmax_progenySTrem_progenySTmaxi_heap_posSTbeginSTendSTalign_regionSTcurrent_fragSTcycle_flagSTcurrent_posSTwidthSTprog_int_infoSTseq_minus_flagSTnew_matrixSTseq_minus_width.0deter-possible-mat.cSTmax_indexSTstart_sitesSTcomp_skipSTnum_seqSTorig_max_cyclesheap.cp-value-2.cSTnSTtwistSTtwist_maxSTtwist_memSTparent_twistSTlarger_twistSTsmaller_twistSTln_mom_0STln_mom_1STln_mom_2STln_par_mom_0STln_par_mom_1STln_par_mom_2num_seqsSTpSTa_sizeSTinfo_factorSTln_info_factorSTp_sumSTln_p_sumSTln_num_min_lettSTmax_infoSTcomp_pSTcomp_a_sizeSTcomp_ln_pSTcomp_info_factorSTcomp_ln_info_factorSTcomp_p_sumSTcomp_ln_p_sumSTcomp_ln_num_min_lettSTcomp_max_infoSTln_NSTtwist_varSTln_mom_gammaSTmin_col_ln_likeSTcomp_min_col_ln_likeSTnew_twistavg.0var.1min_ln_like.2max_ln_like.3min_p_value.4ln_mom_0.5alpha.6beta.7init_n_widthinit_widthfind_twist_rangetwisted_avg_varseriesdet_info_factordet_min_col_ln_likedet_min_col_info_factorfind_gamma_twistsingle_gamma_momentstwisted_momentsinit_momentsmultiply_symbolsmultiply_last_symboldel_twisttwisted_avgterminate.cSTmin_ln_exp_freq.0STtop_cycle.1print-results.cSTprint_seqSTseq_posSTmat_queue_cycleSTtotal_num_matgamma-prob.ccoef.0coef.1root-find.calloc-error-debug.cmalloc_checkrealloc_checkdet_sizedet_arraybuild-profiles.cSTprint_fragcomp-profiles.cPrint_topinit_seq_flag_2pl_Int_3scan_fragment_1binitialize_heap_int_infoC_LN_Nadd_one_profileprint_wcons_headinginit_int_infoadd_to_list_2init_p_valueinit_wcons_matinit_seq_flag_3down_heap_new_matrixprint_mat_listAlpha_fileback_alloc_GLarraysopen_seq_fileln_c_in_psiinit_int_info_2pl_Alpha_acadjust_circleroot_newtonMat_to_Profileunlimited_possible_matln_combisum_ln_numdeter_factor_backgroundreplace_heap_new_matrixscan_sequences_cycle1_3bMax_cycle_int_infodet_averageadd_wordscan_fragment_4bA_sizefeof@@GLIBC_2.0init_cycle_flag_1compare_profileschange_q_sizeprint_ascii_fragDET_scan_sequences_cycle_storeNum_init_profileinit_cycle_flagungetc@@GLIBC_2.0gene_separatorgetpid@@GLIBC_2.0_DYNAMICscore_alignment_2amark_comp_flagInit_profilereset_print_resultsDistanceprint_seq_fragSeq_flagalloc_variablesprint_variablesHSP_thresholdcal_HDET_init_int_info__register_frame_info@@GLIBC_2.0comp_cyclefree_matrixInt_N_ln_Nfree_backgroundread_range_pairsprint_alphaisolate_top_peaksstrcmp@@GLIBC_2.0sum_positionscomp_2_profilesaverageusage_fp_hwprint_hspC_LN_Cprint_int_seqPIDsort_heap_int_infoscan_fragment_1aAparse_linefprintf@@GLIBC_2.0scan_sequences_cycle1_1bAll_Frag_infogetenv@@GLIBC_2.0init_profilesscore_alignment_1aignore_towards_NOfflush@@GLIBC_2.0pclose@@GLIBC_2.1DET_scan_sequences_cycleDET_init_seq_flaginitial_matcomp_clear_seq_flagln_chi_squarecheck_optionsread_ascii_seqpeak_foundsave_topscan_sequences_cycle1adj_max_cyclesFactor_background_1bug_reportredeter_N_factorsinit_1_match_possible_matmark_seedP_oavg_prodclear_seq_flagprint_cycle_headingsort_heap_mat_queuealloc_columninit_one_match_possible_matInfo_factorpl_Nn_IntRootComp_flagln_geo_seriesDET_scan_sequences_cycle1print_scoresAsciiinit_wcons_globalback_realloc_GLarraysadd_list_cycledet_psiscan_sequences_cycle_1bprint_mat_introread_sequencesinsert_profiledown_heap_sub_matrixftell@@GLIBC_2.0num_to_ln_numNum_seqdet_in_psisort_heap_new_matrixmatrix_sameln_possible_alignCycle_num_seqscan_fragment_3bscan_fragment_3aread_changesRoot_newA_compdet_true_seq_postruncate_seq_fragadd_to_mat_queuesort_true_seq_pos_initpl_Stringpopen@@GLIBC_2.1pl_Alpha_afinit_profile_variablesdeter_info_factorsread_stringintegrate_normal_1link_heap_new_matrixadd_alloc_arraysprint_pcons_headingduplicate_matmalloc@@GLIBC_2.0Std_adjcleanup_mat_listFactor_backgroundfscanf@@GLIBC_2.0single_match_possible_matpl_Int_2pl_Int_4check_rangedet_mod_in_psimultiply_longcombine_sort_listsnull_functionprint_obs_freqrealloc_matrixscore_energy2realloc_variablesinitialize_heap_sub_matrixscan_fragment_2bscan_sequences_cycle1_3aset_wconsremove@@GLIBC_2.0set_wcons_1__deregister_frame_info@@GLIBC_2.0ignore_away_from_NOSeq_infoinsert_hspLn_2save_top_2find_linefill_heap_mat_peakconsolidate_listpl_Nn_Doublescan_sequences_cycle_4bstdout@@GLIBC_2.0stderr@@GLIBC_2.0print_tablefree_columnHsp_sizesave_top_1Init_profile_sizeMin_ln_probpl_Intmake_initialdeter_obs_print_freqrecalloc_errorQ_sizescan_sequences_cycle_3bmalloc_erroradjust_alphabetadd_to_topprint_seq_infosort_mat_listfseek@@GLIBC_2.0translate_letterlink_heapprint_wcons_cyclecheck_geneObs_freqmake_mirror_profile_startscan_sequences_cycle_storeOrientationfgets@@GLIBC_2.0All_Seq_flagredeter_info_factorsdeter_N_factorsconsolidate_posscore_alignmentFrag_infoscan_sequences_cycle_3aAll_Sequencemult_ln_numAlgo_optionscore_alignment_1bSequenceCase_sensitiveprofile_sizereset_p_valueSeq_filecheck_fragmentprint_final_resultsDET_scan_fragment_storescore_alignment_2bmark_seed_seqinit_cycle_flag_2pl_P_Doublepl_Charsort_position_by_fragprint_mat_seqpack_heappl_Helpcommand_linechange_max_cyclesMat_queue_topC_LN_Proot_find__ctype_toupper@@GLIBC_2.0Ln_exp_freqDiff_N_ln_Nsetup_mat_listconstruct_complementln_gammadown_heap_mat_queueadd_list_topadd_to_list_1alloc_matrixpl_Alpha_ifscan_fragment_storecomplete_profilestrncmp@@GLIBC_2.0calloc_errorscore_functionPost_peak_cyclesStd_info_factorinitialize_variablesEdge_penaltyis_same_profileadd_ascii_seqOrig_max_cyclesfind_hsp_peak__bss_startcal_Ifree_seq_flagfunction_optionsDP_functionmaindet_p_valueone_match_possible_mateliminate_zerosNum_top_matln_gamma_cfunmark_endsLn_probprint_C_LN__libc_start_main@@GLIBC_2.0raise@@GLIBC_2.0argminroot_newton_multiscan_sequences_cycle_1aDET_save_topcheck_profile_spaceln_num_to_numscore_energy3print_list_topAll_Num_fragexp@@GLIBC_2.0fill_heap_int_inforemove_alloc_arraysdown_heap_mat_queue_bakscan_fragmentAll_Seq_infoupdate_matrixrealloc@@GLIBC_2.0initialize_C_LNLN_ln_Ncomp_mark_seq_flaginit_unlimited_possible_matprint_mat_matrixadjust_no_circledata_startmerge_HSPinit_seq_flag_1redeter_diff_factorsHsp_countprintf@@GLIBC_2.0sort_heap_sub_matrixConvergencescan_sequencesDET_ln_possible_alignprint_pcons_cycle_finiWidthinit_seq_flagNum_seq_fragfclose@@GLIBC_2.1construct_mat_listmark_seq_flagis_comparableNum_letfree_errorprint_int_fragscan_fragment_2aerror_repeatintegrate_normal_2free_new_matrixDiff_info_factortext_directionscheck_seq_endpl_P_IntSkipinit_cycle_flag_3free_matrix2print_all_fragreplace_heap_sub_matrixadd_int_seqDET_init_cycle_flagalloc_seq_minusprocess_slashpl_ICharremove_redundanttruncate_fragmentprint_ascii_seqProfilesAll_Num_geneNum_cycle_matinit_comp_variablesreset_add_wordprint_resultsscan_fragment_4aupdate_variablesexit@@GLIBC_2.0N_multiplereset_wconsln_gamma_probTop_progenyinitialize_heap_mat_queuedown_heap_int_infoscan_sequences_cycle1_1asscanf@@GLIBC_2.0_edatadeter_backgroundinit_int_info_1_IO_putc@@GLIBC_2.0_GLOBAL_OFFSET_TABLE_free@@GLIBC_2.0read_int_seq_endAvg_info_factorCycle_profile_sizeDET_score_alignmentComp_status__ctype_b@@GLIBC_2.0incl_to_exclstdin@@GLIBC_2.0scan_sequences_cycle_4aHspexchange_heap_eltback_alloc_STarraysprint_list_cyclerealloc_errorcopy_mat_peaksort_arrayreplace_heap_int_infoSeedsinit_pairwise_compHeapfopen@@GLIBC_2.1replace_heap_mat_queuePrint_finalswap_pointers_IO_stdin_usedscan_sequences_cyclebuild_init_profilesprint_seq_flagmake_initial_seedsprintf@@GLIBC_2.0error_no_pairsinsert_lettersolve_2Int_info_factor__data_startcheck_seqprint_cycle_infodet_gamma_prob_IO_getc@@GLIBC_2.0Num_cycle_profilescore_energy4terminatescore_energy1Min_ln_exp_freqCyclecal_fMax_cyclestrace_back_2mark_noncomp_flaglog@@GLIBC_2.0Max_sequencesPfind_line_2gamma_serAll_Num_seqGene_infoform_matricespl_Doubleprint_profileprint_optionsLn_Nprint_matrixfree_HSPtrace_backpl_NBoolpl_BoolLn_factorialPrint_cycle_numinitialize_heap_new_matrixfree_scorescheck_frag__gmon_start__check_arrayDET_scan_fragment