test_MEME Testing MEME Scanner noevent : *************************************************************** noevent : MEME - Motif discovery tool noevent : *************************************************************** _version : MEME version 3.0 (Release date: 2004/08/18 09:07:01) noevent : noevent : For further information on how to interpret these results or to noevent : a copy of the MEME software please access http://meme.sdsc.edu. noevent : noevent : This file may be used as input to the MAST algorithm for search noevent : sequence databases for matches to groups of motifs. MAST is av noevent : for interactive use and downloading at http://meme.sdsc.edu. noevent : *************************************************************** noevent : noevent : noevent : *************************************************************** noevent : REFERENCE noevent : *************************************************************** noevent : If you use this program in your research, please cite: noevent : noevent : Timothy L. Bailey and Charles Elkan, noevent : "Fitting a mixture model by expectation maximization to discove noevent : motifs in biopolymers", Proceedings of the Second International noevent : Conference on Intelligent Systems for Molecular Biology, pp. 28 noevent : AAAI Press, Menlo Park, California, 1994. noevent : *************************************************************** noevent : noevent : noevent : *************************************************************** noevent : TRAINING SET noevent : *************************************************************** _datafile : DATAFILE= INO_up800.s _alphabet : ALPHABET= ACGT noevent : Sequence name Weight Length Sequence name noevent : ------------- ------ ------ ------------- _sequence_name : CHO1 1.0000 800 CHO2 _sequence_name : FAS1 1.0000 800 FAS2 _sequence_name : ACC1 1.0000 800 INO1 _sequence_name : OPI3 1.0000 800 noevent : *************************************************************** noevent : noevent : *************************************************************** noevent : COMMAND LINE SUMMARY noevent : *************************************************************** noevent : This information can also be useful in the event you wish to re noevent : problem with the MEME software. noevent : _commandline : command: meme -mod oops -dna -revcomp -nmotifs 2 -bfile yeast.n noevent : noevent : model: mod= oops nmotifs= 2 evt= noevent : object function= E-value of product of p-values noevent : width: minw= 8 maxw= 50 minic= noevent : width: wg= 11 ws= 1 endgaps= noevent : nsites: minsites= 7 maxsites= 7 wnsites= noevent : theta: prob= 1 spmap= uni spfuzz= noevent : em: prior= dirichlet b= 0.01 maxiter= noevent : distance= 1e-05 noevent : data: n= 5600 N= 7 noevent : strands: + - noevent : sample: seed= 0 seqfrac= 1 noevent : Letter frequencies in dataset: noevent : A 0.304 C 0.196 G 0.196 T 0.304 noevent : Background letter frequencies (from yeast.nc.6.freq): noevent : A 0.324 C 0.176 G 0.176 T 0.324 noevent : *************************************************************** noevent : noevent : noevent : *************************************************************** _add_motif_with: MOTIF 1 width = 12 sites = 7 llr = 95 E-value = 2.0e noevent : *************************************************************** noevent : --------------------------------------------------------------- noevent : Motif 1 Description noevent : --------------------------------------------------------------- noevent : Simplified A :::9:a::::3: noevent : pos.-specific C ::a:9:11691a noevent : probability G ::::1::94:4: noevent : matrix T aa:1::9::11: noevent : noevent : bits 2.5 * * noevent : 2.3 * * noevent : 2.0 * * * * noevent : 1.8 * * * * * noevent : Information 1.5 *** ** *** * noevent : content 1.3 *** ****** * noevent : (19.5 bits) 1.0 ********** * noevent : 0.8 ********** * noevent : 0.5 ********** * noevent : 0.3 ************ noevent : 0.0 ------------ noevent : noevent : Multilevel TTCACATGCCGC noevent : consensus G A noevent : sequence noevent : noevent : --------------------------------------------------------------- noevent : noevent : --------------------------------------------------------------- motif_name : Motif 1 sites sorted by position p-value noevent : --------------------------------------------------------------- noevent : Sequence name Strand Start P-value noevent : ------------- ------ ----- --------- --- add_instance : INO1 - 620 1.85e-08 GACAATACTT TTCA add_instance : FAS1 + 95 1.85e-08 GGCCAAAAAC TTCA add_instance : ACC1 + 83 1.52e-07 CGTTAAAATC TTCA add_instance : CHO2 + 354 2.52e-07 TGCCACACTT TTCT add_instance : CHO1 + 611 4.23e-07 ACTTTGAACG TTCA add_instance : FAS2 + 567 9.43e-07 CTCCCGCGTT TTCA add_instance : OPI3 + 340 3.32e-06 CCAAGCCTCC TTCA noevent : --------------------------------------------------------------- noevent : noevent : --------------------------------------------------------------- noevent : Motif 1 block diagrams noevent : --------------------------------------------------------------- noevent : SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM noevent : ------------- ---------------- ------------- noevent : INO1 1.8e-08 619_[-1]_169 noevent : FAS1 1.8e-08 94_[+1]_694 noevent : ACC1 1.5e-07 82_[+1]_706 noevent : CHO2 2.5e-07 353_[+1]_435 noevent : CHO1 4.2e-07 610_[+1]_178 noevent : FAS2 9.4e-07 566_[+1]_222 noevent : OPI3 3.3e-06 339_[+1]_449 noevent : --------------------------------------------------------------- noevent : noevent : --------------------------------------------------------------- noevent : Motif 1 in BLOCKS format noevent : --------------------------------------------------------------- noevent : BL MOTIF 1 width=12 seqs=7 noevent : INO1 ( 620) TTCACATGCCGC 1 noevent : FAS1 ( 95) TTCACATGCCGC 1 noevent : ACC1 ( 83) TTCACATGGCCC 1 noevent : CHO2 ( 354) TTCTCATGCCGC 1 noevent : CHO1 ( 611) TTCACACGGCAC 1 noevent : FAS2 ( 567) TTCACATGCTAC 1 noevent : OPI3 ( 340) TTCAGATCGCTC 1 noevent : // noevent : noevent : --------------------------------------------------------------- noevent : noevent : --------------------------------------------------------------- noevent : Motif 1 position-specific scoring matrix noevent : --------------------------------------------------------------- noevent : log-odds matrix: alength= 4 w= 12 n= 5523 bayes= 9.62205 E= 2.0 add_to_logodds : -945 -945 -945 162 add_to_logodds : -945 -945 -945 162 add_to_logodds : -945 251 -945 -945 add_to_logodds : 140 -945 -945 -118 add_to_logodds : -945 229 -30 -945 add_to_logodds : 162 -945 -945 -945 add_to_logodds : -945 -30 -945 140 add_to_logodds : -945 -30 229 -945 add_to_logodds : -945 170 129 -945 add_to_logodds : -945 229 -945 -118 add_to_logodds : -18 -30 129 -118 add_to_logodds : -945 251 -945 -945 noevent : --------------------------------------------------------------- noevent : noevent : --------------------------------------------------------------- noevent : Motif 1 position-specific probability matrix noevent : --------------------------------------------------------------- noevent : letter-probability matrix: alength= 4 w= 12 nsites= 7 E= 2.0e-0 add_to_pssm : 0.000000 0.000000 0.000000 1.000000 add_to_pssm : 0.000000 0.000000 0.000000 1.000000 add_to_pssm : 0.000000 1.000000 0.000000 0.000000 add_to_pssm : 0.857143 0.000000 0.000000 0.142857 add_to_pssm : 0.000000 0.857143 0.142857 0.000000 add_to_pssm : 1.000000 0.000000 0.000000 0.000000 add_to_pssm : 0.000000 0.142857 0.000000 0.857143 add_to_pssm : 0.000000 0.142857 0.857143 0.000000 add_to_pssm : 0.000000 0.571429 0.428571 0.000000 add_to_pssm : 0.000000 0.857143 0.000000 0.142857 add_to_pssm : 0.285714 0.142857 0.428571 0.142857 add_to_pssm : 0.000000 1.000000 0.000000 0.000000 noevent : --------------------------------------------------------------- noevent : noevent : noevent : noevent : noevent : noevent : Time 20.91 secs. noevent : noevent : *************************************************************** noevent : noevent : noevent : *************************************************************** _add_motif_with: MOTIF 2 width = 10 sites = 7 llr = 81 E-value = 1.1e noevent : *************************************************************** noevent : --------------------------------------------------------------- noevent : Motif 2 Description noevent : --------------------------------------------------------------- noevent : Simplified A ::1:::9:6: noevent : pos.-specific C :a:::a:911 noevent : probability G 3:1aa:1:19 noevent : matrix T 7:7::::11: noevent : noevent : bits 2.5 * *** noevent : 2.3 * *** noevent : 2.0 * *** * noevent : 1.8 * *** * * noevent : Information 1.5 * *** * * noevent : content 1.3 * ***** * noevent : (16.7 bits) 1.0 ** ***** * noevent : 0.8 ** ***** * noevent : 0.5 ******** * noevent : 0.3 ********** noevent : 0.0 ---------- noevent : noevent : Multilevel TCTGGCACAG noevent : consensus G noevent : sequence noevent : noevent : --------------------------------------------------------------- noevent : noevent : --------------------------------------------------------------- motif_name : Motif 2 sites sorted by position p-value noevent : --------------------------------------------------------------- noevent : Sequence name Strand Start P-value noevent : ------------- ------ ----- --------- --- add_instance : OPI3 - 186 3.24e-07 GAAAACCAGA TCTG add_instance : ACC1 + 232 3.24e-07 CCAGTCGTAT TCTG add_instance : CHO1 - 559 3.24e-07 ATATTCAGTG TCTG add_instance : INO1 - 283 5.29e-06 ACGGTCTACG GCGG add_instance : FAS1 + 44 6.25e-06 TACACGAGGT GCAG add_instance : FAS2 - 185 8.48e-06 TTCTTGCTTT TCTG add_instance : CHO2 - 413 8.48e-06 TTTTGCCGTT TCTG noevent : --------------------------------------------------------------- noevent : noevent : --------------------------------------------------------------- noevent : Motif 2 block diagrams noevent : --------------------------------------------------------------- noevent : SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM noevent : ------------- ---------------- ------------- noevent : OPI3 3.2e-07 185_[-2]_605 noevent : ACC1 3.2e-07 231_[+2]_559 noevent : CHO1 3.2e-07 558_[-2]_232 noevent : INO1 5.3e-06 282_[-2]_508 noevent : FAS1 6.3e-06 43_[+2]_747 noevent : FAS2 8.5e-06 184_[-2]_606 noevent : CHO2 8.5e-06 412_[-2]_378 noevent : --------------------------------------------------------------- noevent : noevent : --------------------------------------------------------------- noevent : Motif 2 in BLOCKS format noevent : --------------------------------------------------------------- noevent : BL MOTIF 2 width=10 seqs=7 noevent : OPI3 ( 186) TCTGGCACAG 1 noevent : ACC1 ( 232) TCTGGCACAG 1 noevent : CHO1 ( 559) TCTGGCACAG 1 noevent : INO1 ( 283) GCGGGCGCAG 1 noevent : FAS1 ( 44) GCAGGCACGG 1 noevent : FAS2 ( 185) TCTGGCACTC 1 noevent : CHO2 ( 413) TCTGGCATCG 1 noevent : // noevent : noevent : --------------------------------------------------------------- noevent : noevent : --------------------------------------------------------------- noevent : Motif 2 position-specific scoring matrix noevent : --------------------------------------------------------------- noevent : log-odds matrix: alength= 4 w= 10 n= 5537 bayes= 9.62571 E= 1.1 add_to_logodds : -945 -945 70 114 add_to_logodds : -945 251 -945 -945 add_to_logodds : -118 -945 -30 114 add_to_logodds : -945 -945 251 -945 add_to_logodds : -945 -945 251 -945 add_to_logodds : -945 251 -945 -945 add_to_logodds : 140 -945 -30 -945 add_to_logodds : -945 229 -945 -118 add_to_logodds : 82 -30 -30 -118 add_to_logodds : -945 -30 229 -945 noevent : --------------------------------------------------------------- noevent : noevent : --------------------------------------------------------------- noevent : Motif 2 position-specific probability matrix noevent : --------------------------------------------------------------- noevent : letter-probability matrix: alength= 4 w= 10 nsites= 7 E= 1.1e+0 add_to_pssm : 0.000000 0.000000 0.285714 0.714286 add_to_pssm : 0.000000 1.000000 0.000000 0.000000 add_to_pssm : 0.142857 0.000000 0.142857 0.714286 add_to_pssm : 0.000000 0.000000 1.000000 0.000000 add_to_pssm : 0.000000 0.000000 1.000000 0.000000 add_to_pssm : 0.000000 1.000000 0.000000 0.000000 add_to_pssm : 0.857143 0.000000 0.142857 0.000000 add_to_pssm : 0.000000 0.857143 0.000000 0.142857 add_to_pssm : 0.571429 0.142857 0.142857 0.142857 add_to_pssm : 0.000000 0.142857 0.857143 0.000000 noevent : --------------------------------------------------------------- noevent : noevent : noevent : noevent : noevent : noevent : Time 41.19 secs. noevent : noevent : *************************************************************** noevent : noevent : noevent : *************************************************************** Running tests on MEME parser ************************************************** TESTING meme.dna.oops.txt ************************************************** TESTING meme.protein.oops.txt ************************************************** TESTING meme.protein.tcm.txt Testing MEME Scanner noevent : *************************************************************** noevent : MAST - Motif Alignment and Search Tool noevent : *************************************************************** _version : MAST version 3.0 (Release date: 2004/08/18 09:07:01) noevent : noevent : For further information on how to interpret these results or t noevent : a copy of the MAST software please access http://meme.sdsc.edu noevent : *************************************************************** noevent : noevent : noevent : *************************************************************** noevent : REFERENCE noevent : *************************************************************** noevent : If you use this program in your research, please cite: noevent : noevent : Timothy L. Bailey and Michael Gribskov, noevent : "Combining evidence using p-values: application to sequence ho noevent : searches", Bioinformatics, 14(48-54), 1998. noevent : *************************************************************** noevent : noevent : noevent : *************************************************************** noevent : DATABASE AND MOTIFS noevent : *************************************************************** _database : DATABASE INO_up800.s (nucleotide) noevent : Last updated on Mon Aug 16 21:19:59 2004 noevent : Database contains 7 sequences, 5600 residues noevent : noevent : Scores for positive and reverse complement strands are combine noevent : noevent : MOTIFS meme.INO_up800.oops.txt (nucleotide) noevent : MOTIF WIDTH BEST POSSIBLE MATCH noevent : ----- ----- ------------------- _add_motif : 1 12 TTCACATGCCGC _add_motif : 2 10 TCTGGCACAG noevent : noevent : PAIRWISE MOTIF CORRELATIONS: noevent : MOTIF 1 noevent : ----- ----- noevent : 2 0.32 noevent : No overly similar pairs (correlation > 0.60) found. noevent : noevent : Random model letter frequencies (from non-redundant database): noevent : A 0.281 C 0.222 G 0.229 T 0.267 noevent : *************************************************************** noevent : noevent : noevent : *************************************************************** noevent : SECTION I: HIGH-SCORING SEQUENCES noevent : *************************************************************** noevent : - Each of the following 7 sequences has E-value less than 10. noevent : - The E-value of a sequence is the expected number of sequence noevent : in a random database of the same size that would match the m noevent : well as the sequence does and is equal to the combined p-val noevent : sequence times the number of sequences in the database. noevent : - The combined p-value of a sequence measures the strength of noevent : match of the sequence to all the motifs and is calculated by noevent : o finding the score of the single best match of each motif noevent : to the sequence (best matches may overlap), noevent : o calculating the sequence p-value of each score, noevent : o forming the product of the p-values, noevent : o taking the p-value of the product. noevent : - The sequence p-value of a score is defined as the noevent : probability of a random sequence of the same length containi noevent : some match with as good or better a score. noevent : - The score for the match of a position in a sequence to a mot noevent : is computed by by summing the appropriate entry from each co noevent : the position-dependent scoring matrix that represents the mo noevent : - Sequences shorter than one or more of the motifs are skipped noevent : - The table is sorted by increasing E-value. noevent : *************************************************************** noevent : noevent : SEQUENCE NAME DESCRIPTION noevent : ------------- ----------- noevent : ACC1 sequence of the region up... noevent : CHO1 sequence of the region up... noevent : INO1 sequence of the region up... noevent : FAS1 sequence of the region up... noevent : OPI3 sequence of the region up... noevent : CHO2 sequence of the region up... noevent : FAS2 sequence of the region up... noevent : noevent : *************************************************************** noevent : noevent : noevent : noevent : *************************************************************** noevent : SECTION II: MOTIF DIAGRAMS noevent : *************************************************************** noevent : - The ordering and spacing of all non-overlapping motif occurr noevent : are shown for each high-scoring sequence listed in Section I noevent : - A motif occurrence is defined as a position in the sequence noevent : match to the motif has POSITION p-value less than 0.0001. noevent : - The POSITION p-value of a match is the probability of noevent : a single random subsequence of the length of the motif noevent : scoring at least as well as the observed match. noevent : - For each sequence, all motif occurrences are shown unless th noevent : are overlaps. In that case, a motif occurrence is shown onl noevent : p-value is less than the product of the p-values of the othe noevent : (lower-numbered) motif occurrences that it overlaps. noevent : - The table also shows the E-value of each sequence. noevent : - Spacers and motif occurences are indicated by noevent : o -d- `d' residues separate the end of the preceding mot noevent : occurrence and the start of the following motif occurrenc noevent : o [sn] occurrence of motif `n' with p-value less than 0.00 noevent : A minus sign indicates that the occurrence is on the noevent : reverse complement strand. noevent : *************************************************************** noevent : noevent : SEQUENCE NAME E-VALUE MOTIF DIAGRAM noevent : ------------- -------- ------------- noevent : ACC1 6.1e-05 82_[+1]_137_[+2]_5 noevent : CHO1 0.00016 152_[+2]_396_[-2]_ noevent : [+1]_149 noevent : INO1 0.00019 282_[-2]_327_[-1]_ noevent : FAS1 0.00022 43_[+2]_41_[+1]_69 noevent : OPI3 0.00092 185_[-2]_144_[+1]_ noevent : CHO2 0.0029 353_[+1]_47_[-2]_3 noevent : FAS2 0.0093 184_[-2]_372_[+1]_ noevent : noevent : *************************************************************** noevent : noevent : noevent : noevent : *************************************************************** noevent : SECTION III: ANNOTATED SEQUENCES noevent : *************************************************************** noevent : - The positions and p-values of the non-overlapping motif occu noevent : are shown above the actual sequence for each of the high-sco noevent : sequences from Section I. noevent : - A motif occurrence is defined as a position in the sequence noevent : match to the motif has POSITION p-value less than 0.0001 as noevent : defined in Section II. noevent : - For each sequence, the first line specifies the name of the noevent : - The second (and possibly more) lines give a description of t noevent : sequence. noevent : - Following the description line(s) is a line giving the lengt noevent : combined p-value, and E-value of the sequence as defined in noevent : - The next line reproduces the motif diagram from Section II. noevent : - The entire sequence is printed on the following lines. noevent : - Motif occurrences are indicated directly above their positio noevent : sequence on lines showing noevent : o the motif number of the occurrence (a minus sign indicate noevent : the occurrence is on the reverse complement strand), noevent : o the position p-value of the occurrence, noevent : o the best possible match to the motif (or its reverse comp noevent : o columns whose match to the motif has a positive score (in noevent : by a plus sign). noevent : *************************************************************** noevent : noevent : *************** _parse_buffer *************** _blank_buffer _set_current_se: ACC1 noevent : sequence of the region upstream from YNR016C noevent : LENGTH = 800 COMBINED P-VALUE = 8.78e-06 E-VALUE = 6.1e-05 _add_line_to_bu: DIAGRAM: 82_[+1]_137_[+2]_559 *************** _add_diagram_from_buffer *************** _blank_buffer noevent : noevent : *************** _collapse_buffer _add_line_to_bu: [+1] _add_line_to_bu: 3.1e-07 _add_line_to_bu: TTCACATGCCGC _add_line_to_bu: ++++++++++ + _add_line_to_bu: 76 TAAAATCTTCACATGGCCCGGCCGCGCGCGCGTTGTGCCAACAAGTCGCAGTCGAAAT noevent : *************** _collapse_buffer _add_line_to_bu: [+2] _add_line_to_bu: 7.4e-07 _add_line_to_bu: TCTGGCACAG _add_line_to_bu: ++++++++++ _add_line_to_bu: 226 TCGTATTCTGGCACAGTATAGCCTAGCACAATCACTGTCACAATTGTTATCGGTTCTA noevent : *************** _collapse_buffer noevent : *************** _parse_buffer *************** _blank_buffer _set_current_se: CHO1 noevent : sequence of the region upstream from YER026C noevent : LENGTH = 800 COMBINED P-VALUE = 2.30e-05 E-VALUE = 0.00016 _add_line_to_bu: DIAGRAM: 152_[+2]_396_[-2]_42_[+1]_17_[+1]_149 *************** _add_diagram_from_buffer *************** _blank_buffer noevent : noevent : *************** _collapse_buffer _add_line_to_bu: [+2] _add_line_to_bu: 3.9e-05 _add_line_to_bu: TCTGGCACAG _add_line_to_bu: ++++++ + _add_line_to_bu: 151 CGTCTGGCGCCCTTCCCATTCCGAACCATGTTATATTGAACCATCTGGCGACAAGCAG noevent : *************** _collapse_buffer _add_line_to_bu: [-2] _add_line_to_bu: 7.4e-07 _add_line_to_bu: CTGTGCCAGA _add_line_to_bu: ++++++++++ _add_line_to_bu: 526 CAATCCCCACTCCTTCTCAATGTGTGCAGACTTCTGTGCCAGACACTGAATATATATC noevent : *************** _collapse_buffer _add_line_to_bu: [+1] [+1] _add_line_to_bu: 8.7e-07 2.2e-05 _add_line_to_bu: TTCACATGCCGC TTCACATGCCGC _add_line_to_bu: ++++++ +++ + +++++++++ + _add_line_to_bu: 601 ACTTTGAACGTTCACACGGCACCCTCACGCCTTTGAGCTTTCACATGGACCCATCTAA noevent : *************** _collapse_buffer noevent : *************** _parse_buffer *************** _blank_buffer _set_current_se: INO1 noevent : sequence of the region upstream from YJL153C noevent : LENGTH = 800 COMBINED P-VALUE = 2.71e-05 E-VALUE = 0.00019 _add_line_to_bu: DIAGRAM: 282_[-2]_327_[-1]_55_[+1]_102 *************** _add_diagram_from_buffer *************** _blank_buffer noevent : noevent : *************** _collapse_buffer _add_line_to_bu: [ _add_line_to_bu: 1 _add_line_to_bu: C _add_line_to_bu: + _add_line_to_bu: 226 ACGTTGTATATGAAACGAGTAGTGAACGTTCGTACGATCTTTCACGCAGACATGCGAC noevent : *************** _collapse_buffer _add_line_to_bu: [-1] _add_line_to_bu: 4.2e-08 _add_line_to_bu: GCGGCATGTGAA _add_line_to_bu: ++++++++++++ _add_line_to_bu: 601 TGCGCTTCGGCGGCTAAATGCGGCATGTGAAAAGTATTGTCTATTTTATCTTCATCCT noevent : *************** _collapse_buffer _add_line_to_bu: [+1] _add_line_to_bu: 1.3e-05 _add_line_to_bu: TTCACATGCCGC _add_line_to_bu: +++++++++ ++ _add_line_to_bu: 676 AACTTATTTAATTCACATGGAGCAGAGAAAGCGCACCTCTGCGTTGGCGGCAATGTTA noevent : *************** _collapse_buffer noevent : *************** _parse_buffer *************** _blank_buffer _set_current_se: FAS1 noevent : sequence of the region upstream from YKL182W noevent : LENGTH = 800 COMBINED P-VALUE = 3.19e-05 E-VALUE = 0.00022 _add_line_to_bu: DIAGRAM: 43_[+2]_41_[+1]_694 *************** _add_diagram_from_buffer *************** _blank_buffer noevent : _add_line_to_bu: [+2] _add_line_to_bu: 2.2e-05 _add_line_to_bu: TCTGGCACAG _add_line_to_bu: ++ +++++ + _add_line_to_bu: 1 CCGGGTTATAGCAGCGTCTGCTCCGCATCACGATACACGAGGTGCAGGCACGGTTCAC noevent : *************** _collapse_buffer _add_line_to_bu: [+1] _add_line_to_bu: 4.2e-08 _add_line_to_bu: TTCACATGCCGC _add_line_to_bu: ++++++++++++ _add_line_to_bu: 76 ACAAACGACGGCCAAAAACTTCACATGCCGCCCAGCCAAGCATAATTACGCAACAGCG noevent : *************** _collapse_buffer noevent : *************** _parse_buffer *************** _blank_buffer _set_current_se: OPI3 noevent : sequence of the region upstream from YJR073C noevent : LENGTH = 800 COMBINED P-VALUE = 1.32e-04 E-VALUE = 0.00092 _add_line_to_bu: DIAGRAM: 185_[-2]_144_[+1]_449 *************** _add_diagram_from_buffer *************** _blank_buffer noevent : noevent : *************** _collapse_buffer _add_line_to_bu: [-2] _add_line_to_bu: 7.4e-07 _add_line_to_bu: CTGTGCCAGA _add_line_to_bu: ++++++++++ _add_line_to_bu: 151 GTTAATCTGATCAACGCTACGCCGATGACAACGGTCTGTGCCAGATCTGGTTTTCCCC noevent : *************** _collapse_buffer _add_line_to_bu: [+1] _add_line_to_bu: 5.8e-06 _add_line_to_bu: TTCACATGCCGC _add_line_to_bu: ++++ ++ ++ + _add_line_to_bu: 301 AACTCCGTCAGGTCTTCCACGTGGAACTGCCAAGCCTCCTTCAGATCGCTCTTGTCGA noevent : *************** _collapse_buffer noevent : *************** _parse_buffer *************** _blank_buffer _set_current_se: CHO2 noevent : sequence of the region upstream from YGR157W noevent : LENGTH = 800 COMBINED P-VALUE = 4.18e-04 E-VALUE = 0.0029 _add_line_to_bu: DIAGRAM: 353_[+1]_47_[-2]_378 *************** _add_diagram_from_buffer *************** _blank_buffer noevent : noevent : *************** _collapse_buffer _add_line_to_bu: [+1] _add_line_to_bu: 5.2e- _add_line_to_bu: TTCAC _add_line_to_bu: +++ + _add_line_to_bu: 301 ATATATATTTTTGCCTTGGTTTAAATTGGTCAAGACAGTCAATTGCCACACTTTTCTC noevent : *************** _collapse_buffer _add_line_to_bu: [-2] _add_line_to_bu: 2.9e-05 _add_line_to_bu: CTGTGCCAGA _add_line_to_bu: + +++++++ _add_line_to_bu: 376 CGCGAAGTTTTCCACACAAAACTGTGAAAATGAACGGCGATGCCAGAAACGGCAAAAC noevent : *************** _collapse_buffer noevent : *************** _parse_buffer *************** _blank_buffer _set_current_se: FAS2 noevent : sequence of the region upstream from YPL231W noevent : LENGTH = 800 COMBINED P-VALUE = 1.33e-03 E-VALUE = 0.0093 _add_line_to_bu: DIAGRAM: 184_[-2]_372_[+1]_222 *************** _add_diagram_from_buffer *************** _blank_buffer noevent : noevent : *************** _collapse_buffer _add_line_to_bu: [-2] _add_line_to_bu: 2.9e-05 _add_line_to_bu: CTGTGCCAGA _add_line_to_bu: ++++++++ _add_line_to_bu: 151 AACAGGGTGTCGGTCATACCGATAAAGCCGTCAAGAGTGCCAGAAAAGCAAGAAAGAA noevent : *************** _collapse_buffer _add_line_to_bu: [+1] _add_line_to_bu: 1.9e-06 _add_line_to_bu: TTCACATGCCGC _add_line_to_bu: +++++++++ + _add_line_to_bu: 526 GCTTAGCAAAATCCAACCATTTTTTTTTTATCTCCCGCGTTTTCACATGCTACCTCAT noevent : *************** _collapse_buffer noevent : *************************************************************** *************** _parse_buffer *************** _blank_buffer Running tests on MAST parser ************************************************** TESTING mast.dna.oops.txt ************************************************** TESTING mast.protein.oops.txt ************************************************** TESTING mast.protein.tcm.txt