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/test-data/meme/meme/meme_output_txt_1.txt

https://bitbucket.org/cistrome/cistrome-harvard/
Plain Text | 325 lines | 288 code | 37 blank | 0 comment | 0 complexity | e10abfb51a2b5c00990e2dd4803152d0 MD5 | raw file
  1********************************************************************************
  2MEME - Motif discovery tool
  3********************************************************************************
  4MEME version 4.6.0 (Release date: Thu Jan 20 14:06:48 PST 2011)
  5
  6For further information on how to interpret these results or to get
  7a copy of the MEME software please access http://meme.nbcr.net.
  8
  9This file may be used as input to the MAST algorithm for searching
 10sequence databases for matches to groups of motifs.  MAST is available
 11for interactive use and downloading at http://meme.nbcr.net.
 12********************************************************************************
 13
 14
 15********************************************************************************
 16REFERENCE
 17********************************************************************************
 18If you use this program in your research, please cite:
 19
 20Timothy L. Bailey and Charles Elkan,
 21"Fitting a mixture model by expectation maximization to discover
 22motifs in biopolymers", Proceedings of the Second International
 23Conference on Intelligent Systems for Molecular Biology, pp. 28-36,
 24AAAI Press, Menlo Park, California, 1994.
 25********************************************************************************
 26
 27
 28********************************************************************************
 29TRAINING SET
 30********************************************************************************
 31DATAFILE= dataset_3.dat
 32ALPHABET= ACDEFGHIKLMNPQRSTVWY
 33Sequence name            Weight Length  Sequence name            Weight Length  
 34-------------            ------ ------  -------------            ------ ------  
 35chr21_19617074_19617124_ 1.0000     50  chr21_26934381_26934431_ 1.0000     50  
 36chr21_28217753_28217803_ 1.0000     50  chr21_31710037_31710087_ 1.0000     50  
 37chr21_31744582_31744632_ 1.0000     50  chr21_31768316_31768366_ 1.0000     50  
 38chr21_31914206_31914256_ 1.0000     50  chr21_31933633_31933683_ 1.0000     50  
 39chr21_31962741_31962791_ 1.0000     50  chr21_31964683_31964733_ 1.0000     50  
 40chr21_31973364_31973414_ 1.0000     50  chr21_31992870_31992920_ 1.0000     50  
 41chr21_32185595_32185645_ 1.0000     50  chr21_32202076_32202126_ 1.0000     50  
 42chr21_32253899_32253949_ 1.0000     50  chr21_32410820_32410870_ 1.0000     50  
 43chr21_36411748_36411798_ 1.0000     50  chr21_37838750_37838800_ 1.0000     50  
 44chr21_45705687_45705737_ 1.0000     50  chr21_45971413_45971463_ 1.0000     50  
 45chr21_45978668_45978718_ 1.0000     50  chr21_45993530_45993580_ 1.0000     50  
 46chr21_46020421_46020471_ 1.0000     50  chr21_46031920_46031970_ 1.0000     50  
 47chr21_46046964_46047014_ 1.0000     50  chr21_46057197_46057247_ 1.0000     50  
 48chr21_46086869_46086919_ 1.0000     50  chr21_46102103_46102153_ 1.0000     50  
 49chr21_47517957_47518007_ 1.0000     50  chr21_47575506_47575556_ 1.0000     50  
 50********************************************************************************
 51
 52********************************************************************************
 53COMMAND LINE SUMMARY
 54********************************************************************************
 55This information can also be useful in the event you wish to report a
 56problem with the MEME software.
 57
 58command: meme dataset_3.dat -o dataset_4_files -nostatus 
 59
 60model:  mod=         zoops    nmotifs=         1    evt=           inf
 61object function=  E-value of product of p-values
 62width:  minw=            8    maxw=           50    minic=        0.00
 63width:  wg=             11    ws=              1    endgaps=       yes
 64nsites: minsites=        2    maxsites=       30    wnsites=       0.8
 65theta:  prob=            1    spmap=         pam    spfuzz=        120
 66global: substring=     yes    branching=      no    wbranch=        no
 67em:     prior=       megap    b=            7500    maxiter=        50
 68        distance=    1e-05
 69data:   n=            1500    N=              30
 70
 71sample: seed=            0    seqfrac=         1
 72Dirichlet mixture priors file: prior30.plib
 73Letter frequencies in dataset:
 74A 0.294 C 0.231 D 0.000 E 0.000 F 0.000 G 0.257 H 0.000 I 0.000 K 0.000 
 75L 0.000 M 0.000 N 0.000 P 0.000 Q 0.000 R 0.000 S 0.000 T 0.217 V 0.000 
 76W 0.000 Y 0.000 
 77Background letter frequencies (from dataset with add-one prior applied):
 78A 0.291 C 0.229 D 0.001 E 0.001 F 0.001 G 0.255 H 0.001 I 0.001 K 0.001 
 79L 0.001 M 0.001 N 0.001 P 0.001 Q 0.001 R 0.001 S 0.001 T 0.215 V 0.001 
 80W 0.001 Y 0.001 
 81********************************************************************************
 82
 83
 84********************************************************************************
 85MOTIF  1	width =   11   sites =  25   llr = 239   E-value = 2.4e-011
 86********************************************************************************
 87--------------------------------------------------------------------------------
 88	Motif 1 Description
 89--------------------------------------------------------------------------------
 90Simplified        A  2323:a:a8a8
 91pos.-specific     C  ::3::::::::
 92probability       D  :::::::::::
 93matrix            E  :::::::::::
 94                  F  :::::::::::
 95                  G  7746::::::1
 96                  H  :::::::::::
 97                  I  :::::::::::
 98                  K  :::::::::::
 99                  L  :::::::::::
100                  M  :::::::::::
101                  N  :::::::::::
102                  P  :::::::::::
103                  Q  :::::::::::
104                  R  :::::::::::
105                  S  :::::::::::
106                  T  1:2:a:a:2::
107                  V  :::::::::::
108                  W  :::::::::::
109                  Y  :::::::::::
110
111         bits   10.6            
112                 9.5            
113                 8.5            
114                 7.4            
115Relative         6.3            
116Entropy          5.3            
117(13.8 bits)      4.2            
118                 3.2            
119                 2.1     * **   
120                 1.1 ** ********
121                 0.0 -----------
122
123Multilevel           GGGGTATAAAA
124consensus            AACA    T  
125sequence                        
126                                
127                                
128--------------------------------------------------------------------------------
129
130--------------------------------------------------------------------------------
131	Motif 1 sites sorted by position p-value
132--------------------------------------------------------------------------------
133Sequence name             Start   P-value               Site  
134-------------             ----- ---------            -----------
135chr21_46046964_46047014_     13  1.06e-06 AAGGCCAGGA GGGGTATAAAA GCCTGAGAGC
136chr21_46057197_46057247_     37  3.41e-06 ACAGGCCCTG GGCATATAAAA GCC       
137chr21_45971413_45971463_     10  3.41e-06  CAGGCCCTG GGCATATAAAA GCCCCAGCAG
138chr21_31964683_31964733_     14  3.41e-06 GATTCACTGA GGCATATAAAA GGCCCTCTGC
139chr21_45993530_45993580_      8  4.00e-06    CCAAGGA GGAGTATAAAA GCCCCACAAA
140chr21_32202076_32202126_     14  5.01e-06 CCACCAGCTT GAGGTATAAAA AGCCCTGTAC
141chr21_46031920_46031970_     16  6.06e-06 ATACCCAGGG AGGGTATAAAA CCTCAGCAGC
142chr21_32410820_32410870_     22  8.67e-06 AATCACTGAG GATGTATAAAA GTCCCAGGGA
143chr21_32185595_32185645_     19  8.67e-06 CACCAGAGCT GGGATATATAA AGAAGGTTCT
144chr21_31992870_31992920_     17  8.67e-06 CACTATTGAA GATGTATAAAA TTTCATTTGC
145chr21_46020421_46020471_      3  1.21e-05         GA GACATATAAAA GCCAACATCC
146chr21_47517957_47518007_     33  1.59e-05 CCGGCGGGGC GGGGTATAAAG GGGGCGG   
147chr21_45978668_45978718_      5  1.59e-05       CAGA GGGGTATAAAG GTTCCGACCA
148chr21_31914206_31914256_     16  1.68e-05 CCCACTACTT AGAGTATAAAA TCATTCTGAG
149chr21_32253899_32253949_     20  2.03e-05 CACCAGCAAG GATATATAAAA GCTCAGGAGT
150chr21_31744582_31744632_     13  3.06e-05 CAGGTCTAAG AGCATATATAA CTTGGAGTCC
151chr21_19617074_19617124_     40  3.06e-05 CCTCGGGACG TGGGTATATAA           
152chr21_45705687_45705737_     38  3.82e-05 CGTGGTCGCG GGGGTATAACA GC        
153chr21_31768316_31768366_      1  3.82e-05          . AACGTATATAA ATGGTCCTGT
154chr21_47575506_47575556_     31  4.02e-05 GCTGCCGGTG AGCGTATAAAG GCCCTGGCG 
155chr21_26934381_26934431_     28  5.52e-05 AGTCACAAGT GAGTTATAAAA GGGTCGCACG
156chr21_31710037_31710087_     15  5.94e-05 CCCAGGTTTC TGAGTATATAA TCGCCGCACC
157chr21_36411748_36411798_     23  6.78e-05 AGTTTCAGTT GGCATCTAAAA ATTATATAAC
158chr21_31933633_31933683_      3  2.08e-04         TC AGAGTATATAT AAATGTTCCT
159chr21_31962741_31962791_     14  4.05e-04 TATAACTCAG GTTGGATAAAA TAATTTGTAC
160--------------------------------------------------------------------------------
161
162--------------------------------------------------------------------------------
163	Motif 1 block diagrams
164--------------------------------------------------------------------------------
165SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
166-------------            ----------------  -------------
167chr21_46046964_46047014_          1.1e-06  12_[1]_27
168chr21_46057197_46057247_          3.4e-06  36_[1]_3
169chr21_45971413_45971463_          3.4e-06  9_[1]_30
170chr21_31964683_31964733_          3.4e-06  13_[1]_26
171chr21_45993530_45993580_            4e-06  7_[1]_32
172chr21_32202076_32202126_            5e-06  13_[1]_26
173chr21_46031920_46031970_          6.1e-06  15_[1]_24
174chr21_32410820_32410870_          8.7e-06  21_[1]_18
175chr21_32185595_32185645_          8.7e-06  18_[1]_21
176chr21_31992870_31992920_          8.7e-06  16_[1]_23
177chr21_46020421_46020471_          1.2e-05  2_[1]_37
178chr21_47517957_47518007_          1.6e-05  32_[1]_7
179chr21_45978668_45978718_          1.6e-05  4_[1]_35
180chr21_31914206_31914256_          1.7e-05  15_[1]_24
181chr21_32253899_32253949_            2e-05  19_[1]_20
182chr21_31744582_31744632_          3.1e-05  12_[1]_27
183chr21_19617074_19617124_          3.1e-05  39_[1]
184chr21_45705687_45705737_          3.8e-05  37_[1]_2
185chr21_31768316_31768366_          3.8e-05  [1]_39
186chr21_47575506_47575556_            4e-05  30_[1]_9
187chr21_26934381_26934431_          5.5e-05  27_[1]_12
188chr21_31710037_31710087_          5.9e-05  14_[1]_25
189chr21_36411748_36411798_          6.8e-05  22_[1]_17
190chr21_31933633_31933683_          0.00021  2_[1]_37
191chr21_31962741_31962791_           0.0004  13_[1]_26
192--------------------------------------------------------------------------------
193
194--------------------------------------------------------------------------------
195	Motif 1 in BLOCKS format
196--------------------------------------------------------------------------------
197BL   MOTIF 1 width=11 seqs=25
198chr21_46046964_46047014_ (   13) GGGGTATAAAA  1 
199chr21_46057197_46057247_ (   37) GGCATATAAAA  1 
200chr21_45971413_45971463_ (   10) GGCATATAAAA  1 
201chr21_31964683_31964733_ (   14) GGCATATAAAA  1 
202chr21_45993530_45993580_ (    8) GGAGTATAAAA  1 
203chr21_32202076_32202126_ (   14) GAGGTATAAAA  1 
204chr21_46031920_46031970_ (   16) AGGGTATAAAA  1 
205chr21_32410820_32410870_ (   22) GATGTATAAAA  1 
206chr21_32185595_32185645_ (   19) GGGATATATAA  1 
207chr21_31992870_31992920_ (   17) GATGTATAAAA  1 
208chr21_46020421_46020471_ (    3) GACATATAAAA  1 
209chr21_47517957_47518007_ (   33) GGGGTATAAAG  1 
210chr21_45978668_45978718_ (    5) GGGGTATAAAG  1 
211chr21_31914206_31914256_ (   16) AGAGTATAAAA  1 
212chr21_32253899_32253949_ (   20) GATATATAAAA  1 
213chr21_31744582_31744632_ (   13) AGCATATATAA  1 
214chr21_19617074_19617124_ (   40) TGGGTATATAA  1 
215chr21_45705687_45705737_ (   38) GGGGTATAACA  1 
216chr21_31768316_31768366_ (    1) AACGTATATAA  1 
217chr21_47575506_47575556_ (   31) AGCGTATAAAG  1 
218chr21_26934381_26934431_ (   28) GAGTTATAAAA  1 
219chr21_31710037_31710087_ (   15) TGAGTATATAA  1 
220chr21_36411748_36411798_ (   23) GGCATCTAAAA  1 
221chr21_31933633_31933683_ (    3) AGAGTATATAT  1 
222chr21_31962741_31962791_ (   14) GTTGGATAAAA  1 
223//
224
225--------------------------------------------------------------------------------
226
227--------------------------------------------------------------------------------
228	Motif 1 position-specific scoring matrix
229--------------------------------------------------------------------------------
230log-odds matrix: alength= 20 w= 11 n= 1200 bayes= 5.33554 E= 2.4e-011 
231   -32   -680     91     77      7    138    -20     55     64    107     11    150    142     72     87    396   -148    221   -140    -36 
232   -11   -680     89     76      7    137    -21     55     63    107     10    149    141     71     87    396   -239    220   -140    -36 
233   -79     41      4     21     -7     44    -62     42     -5     99      0     99    138     52     42    399    -46    223   -173    -68 
234    11   -677     48     47     -2    127    -43     46     27    101      3    124    138     60     62    397   -235    220   -160    -55 
235  -596   -820     12    -21    -53   -267    -74     37     16     44    -37     98     31      9     19    319    212    127   -193    -95 
236   165   -261     70    110     77   -521     -4    147     95    201     90    121    124     91    107    425   -527    314    -95      8 
237  -838   -990    -89   -149   -151   -841   -161   -117   -113    -66   -209    -68    -69   -129    -91    111    221    -55   -255   -173 
238   176   -858    -79   -103   -115   -717   -148    -95   -108    -17   -162    -61    -12    -95    -69    193   -737     52   -240   -153 
239   134   -686      0     16    -12   -553    -68     44     -8     96     -9     88    124     41     36    384     11    216   -177    -71 
240   165   -261     70    110     77   -521     -4    147     95    201     90    121    124     91    107    425   -527    314    -95      8 
241   147   -614     89    129     93   -121     12    160    113    217    108    144    144    111    125    447   -241    332    -81     22 
242--------------------------------------------------------------------------------
243
244--------------------------------------------------------------------------------
245	Motif 1 position-specific probability matrix
246--------------------------------------------------------------------------------
247letter-probability matrix: alength= 20 w= 11 nsites= 25 E= 2.4e-011 
248 0.240000  0.000000  0.000000  0.000000  0.000000  0.680000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.080000  0.000000  0.000000  0.000000 
249 0.280000  0.000000  0.000000  0.000000  0.000000  0.680000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.040000  0.000000  0.000000  0.000000 
250 0.160000  0.320000  0.000000  0.000000  0.000000  0.360000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.160000  0.000000  0.000000  0.000000 
251 0.320000  0.000000  0.000000  0.000000  0.000000  0.640000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.040000  0.000000  0.000000  0.000000 
252 0.000000  0.000000  0.000000  0.000000  0.000000  0.040000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.960000  0.000000  0.000000  0.000000 
253 0.960000  0.040000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000 
254 0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  1.000000  0.000000  0.000000  0.000000 
255 1.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000 
256 0.760000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.240000  0.000000  0.000000  0.000000 
257 0.960000  0.040000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000 
258 0.840000  0.000000  0.000000  0.000000  0.000000  0.120000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.040000  0.000000  0.000000  0.000000 
259--------------------------------------------------------------------------------
260
261--------------------------------------------------------------------------------
262	Motif 1 regular expression
263--------------------------------------------------------------------------------
264[GA][GA][GC][GA]TATA[AT]AA
265--------------------------------------------------------------------------------
266
267
268
269
270Time  2.13 secs.
271
272********************************************************************************
273
274
275********************************************************************************
276SUMMARY OF MOTIFS
277********************************************************************************
278
279--------------------------------------------------------------------------------
280	Combined block diagrams: non-overlapping sites with p-value < 0.0001
281--------------------------------------------------------------------------------
282SEQUENCE NAME            COMBINED P-VALUE  MOTIF DIAGRAM
283-------------            ----------------  -------------
284chr21_19617074_19617124_         1.22e-03  39_[1(3.06e-05)]
285chr21_26934381_26934431_         2.21e-03  27_[1(5.52e-05)]_12
286chr21_28217753_28217803_         7.29e-01  50
287chr21_31710037_31710087_         2.37e-03  14_[1(5.94e-05)]_25
288chr21_31744582_31744632_         1.22e-03  12_[1(3.06e-05)]_27
289chr21_31768316_31768366_         1.53e-03  [1(3.82e-05)]_39
290chr21_31914206_31914256_         6.70e-04  15_[1(1.68e-05)]_24
291chr21_31933633_31933683_         1.81e-03  4_[1(4.54e-05)]_35
292chr21_31962741_31962791_         1.61e-02  50
293chr21_31964683_31964733_         1.36e-04  13_[1(3.41e-06)]_26
294chr21_31973364_31973414_         1.99e-01  50
295chr21_31992870_31992920_         3.47e-04  16_[1(8.67e-06)]_23
296chr21_32185595_32185645_         3.47e-04  18_[1(8.67e-06)]_21
297chr21_32202076_32202126_         2.01e-04  13_[1(5.01e-06)]_26
298chr21_32253899_32253949_         8.11e-04  19_[1(2.03e-05)]_20
299chr21_32410820_32410870_         3.47e-04  21_[1(8.67e-06)]_18
300chr21_36411748_36411798_         2.71e-03  22_[1(6.78e-05)]_17
301chr21_37838750_37838800_         8.23e-02  50
302chr21_45705687_45705737_         1.53e-03  37_[1(3.82e-05)]_2
303chr21_45971413_45971463_         1.36e-04  9_[1(3.41e-06)]_30
304chr21_45978668_45978718_         6.37e-04  4_[1(1.59e-05)]_35
305chr21_45993530_45993580_         1.60e-04  7_[1(4.00e-06)]_32
306chr21_46020421_46020471_         4.83e-04  2_[1(1.21e-05)]_37
307chr21_46031920_46031970_         2.43e-04  15_[1(6.06e-06)]_24
308chr21_46046964_46047014_         4.26e-05  12_[1(1.06e-06)]_27
309chr21_46057197_46057247_         1.36e-04  36_[1(3.41e-06)]_3
310chr21_46086869_46086919_         4.30e-02  50
311chr21_46102103_46102153_         4.30e-02  50
312chr21_47517957_47518007_         6.37e-04  32_[1(1.59e-05)]_7
313chr21_47575506_47575556_         1.61e-03  30_[1(4.02e-05)]_9
314--------------------------------------------------------------------------------
315
316********************************************************************************
317
318
319********************************************************************************
320Stopped because nmotifs = 1 reached.
321********************************************************************************
322
323CPU: scofield
324
325********************************************************************************