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
