bp_process_wormbase: move program to new Bio-DB-Ace distribution
[bioperl-live.git] / t / data / map_hem / HEM12-HEM13.meme.txt
blobc8fbfe9cdf0e737690ce4dce45880cae7cd29c5f
1 ********************************************************************************
2 MEME - Motif discovery tool
3 ********************************************************************************
4 MEME version 3.5.4 (Release date:    )
6 For further information on how to interpret these results or to get
7 a copy of the MEME software please access http://meme.nbcr.net.
9 This file may be used as input to the MAST algorithm for searching
10 sequence databases for matches to groups of motifs.  MAST is available
11 for interactive use and downloading at http://meme.nbcr.net.
12 ********************************************************************************
15 ********************************************************************************
16 REFERENCE
17 ********************************************************************************
18 If you use this program in your research, please cite:
20 Timothy L. Bailey and Charles Elkan,
21 "Fitting a mixture model by expectation maximization to discover
22 motifs in biopolymers", Proceedings of the Second International
23 Conference on Intelligent Systems for Molecular Biology, pp. 28-36,
24 AAAI Press, Menlo Park, California, 1994.
25 ********************************************************************************
28 ********************************************************************************
29 TRAINING SET
30 ********************************************************************************
31 DATAFILE= HEM12-HEM13.fa
32 ALPHABET= ACGT
33 Sequence name            Weight Length  Sequence name            Weight Length  
34 -------------            ------ ------  -------------            ------ ------  
35 SGD_Scer_YDR047W         1.0000   1000  MIT_Spar_c130_3923       1.0000   1000  
36 MIT_Sbay_c896_21277      1.0000   1000  WashU_Skud_Contig1362.1  1.0000    761  
37 SGD_Scer_YDR044W         1.0000   1000  MIT_Spar_c130_3912       1.0000   1000  
38 MIT_Sbay_c896_21290      1.0000   1000  WashU_Smik_Contig2283.3  1.0000   1000  
39 ********************************************************************************
41 ********************************************************************************
42 COMMAND LINE SUMMARY
43 ********************************************************************************
44 This information can also be useful in the event you wish to report a
45 problem with the MEME software.
47 command: meme HEM12-HEM13.fa -nostatus -dna -revcomp -nmotifs 5 -bfile yeast.nc.1.freq -maxw 20 -mod oops -dir /Volumes/DATA/Home/ajr/sw/powerpc/meme-3.5.4 
49 model:  mod=          oops    nmotifs=         5    evt=           inf
50 object function=  E-value of product of p-values
51 width:  minw=            6    maxw=           20    minic=        0.00
52 width:  wg=             11    ws=              1    endgaps=       yes
53 nsites: minsites=        8    maxsites=        8    wnsites=       0.8
54 theta:  prob=            1    spmap=         uni    spfuzz=        0.5
55 em:     prior=   dirichlet    b=            0.01    maxiter=        50
56         distance=    1e-05
57 data:   n=            7761    N=               8
58 strands: + -
59 sample: seed=            0    seqfrac=         1
60 Letter frequencies in dataset:
61 A 0.291 C 0.209 G 0.209 T 0.291 
62 Background letter frequencies (from yeast.nc.1.freq):
63 A 0.324 C 0.176 G 0.176 T 0.324 
64 ********************************************************************************
67 ********************************************************************************
68 MOTIF  1        width =   20   sites =   8   llr = 167   E-value = 1.0e-013
69 ********************************************************************************
70 --------------------------------------------------------------------------------
71         Motif 1 Description
72 --------------------------------------------------------------------------------
73 Simplified        A  :1165:9:1a::11:::1a:
74 pos.-specific     C  :::::a::4:3::11:5:::
75 probability       G  :9945:1:::1:98:559:a
76 matrix            T  a::::::a5:6a::95::::
78          bits    2.5      *             *
79                  2.3      *             *
80                  2.0      *             *
81                  1.8  **  *      *    * *
82 Information      1.5 ***  * * * **   ****
83 content          1.3 ***  *** * **** ****
84 (30.1 bits)      1.0 ******** * *********
85                  0.8 ******** ***********
86                  0.5 ********************
87                  0.3 ********************
88                  0.0 --------------------
90 Multilevel           TGGAACATTATTGGTGCGAG
91 consensus               GG   C C    TG   
92 sequence                                 
93                                          
94 --------------------------------------------------------------------------------
96 --------------------------------------------------------------------------------
97         Motif 1 sites sorted by position p-value
98 --------------------------------------------------------------------------------
99 Sequence name            Strand  Start   P-value                    Site      
100 -------------            ------  ----- ---------            --------------------
101 MIT_Spar_c130_3912           +    244  1.31e-12 TGGTTCAAGC TGGGGCATTATTGGTGGGAG AAGCCAGAAA
102 MIT_Sbay_c896_21290          +    250  2.00e-11 AGGTCCAAGC TGGGGCATAATTGGTGGGAG AAGCCAGAAA
103 SGD_Scer_YDR044W             +    252  2.47e-11 TTGTTCAAGC TGGAGCGTTATTGGTGGGAG AACCAGAAAA
104 WashU_Smik_Contig2283.3      +    240  7.53e-11 TGGTTGAAGC TGGGGCATTATTGGTGGAAG AAGCCAGAAA
105 WashU_Skud_Contig1362.1      +    101  2.45e-10 TTCTTTCGTT TGGAACATTACTGCTTCGAG CAATAAACAT
106 MIT_Spar_c130_3923           +    134  5.96e-10 CCACTTCGTT TGAAACATCAGTGGTTCGAG CAGTAATGAC
107 MIT_Sbay_c896_21277          +    107  7.56e-10 CTAAGTTCTT TAGAACATCATTGGCTCGAG CATTAGTGAC
108 SGD_Scer_YDR047W             +    137  1.93e-09 TACCTTCGTC TGGAACATCACTAATTCGAG CGGTAAAGAT
109 --------------------------------------------------------------------------------
111 --------------------------------------------------------------------------------
112         Motif 1 block diagrams
113 --------------------------------------------------------------------------------
114 SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
115 -------------            ----------------  -------------
116 MIT_Spar_c130_3912                1.3e-12  243_[+1]_737
117 MIT_Sbay_c896_21290                 2e-11  249_[+1]_731
118 SGD_Scer_YDR044W                  2.5e-11  251_[+1]_729
119 WashU_Smik_Contig2283.3           7.5e-11  239_[+1]_741
120 WashU_Skud_Contig1362.1           2.5e-10  100_[+1]_641
121 MIT_Spar_c130_3923                  6e-10  133_[+1]_847
122 MIT_Sbay_c896_21277               7.6e-10  106_[+1]_874
123 SGD_Scer_YDR047W                  1.9e-09  136_[+1]_844
124 --------------------------------------------------------------------------------
126 --------------------------------------------------------------------------------
127         Motif 1 in BLOCKS format
128 --------------------------------------------------------------------------------
129 BL   MOTIF 1 width=20 seqs=8
130 MIT_Spar_c130_3912       (  244) TGGGGCATTATTGGTGGGAG  1 
131 MIT_Sbay_c896_21290      (  250) TGGGGCATAATTGGTGGGAG  1 
132 SGD_Scer_YDR044W         (  252) TGGAGCGTTATTGGTGGGAG  1 
133 WashU_Smik_Contig2283.3  (  240) TGGGGCATTATTGGTGGAAG  1 
134 WashU_Skud_Contig1362.1  (  101) TGGAACATTACTGCTTCGAG  1 
135 MIT_Spar_c130_3923       (  134) TGAAACATCAGTGGTTCGAG  1 
136 MIT_Sbay_c896_21277      (  107) TAGAACATCATTGGCTCGAG  1 
137 SGD_Scer_YDR047W         (  137) TGGAACATCACTAATTCGAG  1 
140 --------------------------------------------------------------------------------
142 --------------------------------------------------------------------------------
143         Motif 1 position-specific scoring matrix
144 --------------------------------------------------------------------------------
145 log-odds matrix: alength= 4 w= 20 n= 7609 bayes= 9.89197 E= 1.0e-013 
146   -965   -965   -965    162 
147   -137   -965    232   -965 
148   -137   -965    232   -965 
149     95   -965    109   -965 
150     62   -965    151   -965 
151   -965    251   -965   -965 
152    143   -965    -49   -965 
153   -965   -965   -965    162 
154   -137    109   -965     62 
155    162   -965   -965   -965 
156   -965     51    -49     95 
157   -965   -965   -965    162 
158   -137   -965    232   -965 
159   -137    -49    209   -965 
160   -965    -49   -965    143 
161   -965   -965    151     62 
162   -965    151    151   -965 
163   -137   -965    232   -965 
164    162   -965   -965   -965 
165   -965   -965    251   -965 
166 --------------------------------------------------------------------------------
168 --------------------------------------------------------------------------------
169         Motif 1 position-specific probability matrix
170 --------------------------------------------------------------------------------
171 letter-probability matrix: alength= 4 w= 20 nsites= 8 E= 1.0e-013 
172  0.000000  0.000000  0.000000  1.000000 
173  0.125000  0.000000  0.875000  0.000000 
174  0.125000  0.000000  0.875000  0.000000 
175  0.625000  0.000000  0.375000  0.000000 
176  0.500000  0.000000  0.500000  0.000000 
177  0.000000  1.000000  0.000000  0.000000 
178  0.875000  0.000000  0.125000  0.000000 
179  0.000000  0.000000  0.000000  1.000000 
180  0.125000  0.375000  0.000000  0.500000 
181  1.000000  0.000000  0.000000  0.000000 
182  0.000000  0.250000  0.125000  0.625000 
183  0.000000  0.000000  0.000000  1.000000 
184  0.125000  0.000000  0.875000  0.000000 
185  0.125000  0.125000  0.750000  0.000000 
186  0.000000  0.125000  0.000000  0.875000 
187  0.000000  0.000000  0.500000  0.500000 
188  0.000000  0.500000  0.500000  0.000000 
189  0.125000  0.000000  0.875000  0.000000 
190  1.000000  0.000000  0.000000  0.000000 
191  0.000000  0.000000  1.000000  0.000000 
192 --------------------------------------------------------------------------------
194 --------------------------------------------------------------------------------
195         Motif 1 regular expression
196 --------------------------------------------------------------------------------
197 TGG[AG][AG]CAT[TC]A[TC]TGGT[GT][CG]GAG
198 --------------------------------------------------------------------------------
203 Time  6.16 secs.
205 ********************************************************************************
208 ********************************************************************************
209 MOTIF  2        width =   20   sites =   8   llr = 161   E-value = 5.1e-011
210 ********************************************************************************
211 --------------------------------------------------------------------------------
212         Motif 2 Description
213 --------------------------------------------------------------------------------
214 Simplified        A  ::1:1::1:6:1:::1:98a
215 pos.-specific     C  1::951:9::a:85:3::::
216 probability       G  9:4:4:a:a4::154:513:
217 matrix            T  :a51:9:::::91:665:::
219          bits    2.5       * * *         
220                  2.3       * * *         
221                  2.0 *     * * *         
222                  1.8 *  *  *** *         
223 Information      1.5 ** *  *** *  *     *
224 content          1.3 ** * **** * **   * *
225 (29.0 bits)      1.0 ** ************ ****
226                  0.8 ** ************ ****
227                  0.5 ********************
228                  0.3 ********************
229                  0.0 --------------------
231 Multilevel           GTTCCTGCGACTCCTTGAAA
232 consensus              G G    G   GGCT G 
233 sequence                                 
234                                          
235 --------------------------------------------------------------------------------
237 --------------------------------------------------------------------------------
238         Motif 2 sites sorted by position p-value
239 --------------------------------------------------------------------------------
240 Sequence name            Strand  Start   P-value                    Site      
241 -------------            ------  ----- ---------            --------------------
242 WashU_Smik_Contig2283.3      +    313  1.96e-11 TTGGTTTCGG GTTCCTGCGACTCGTTTAAA AAAGAAAAGG
243 MIT_Sbay_c896_21290          +    316  1.96e-11 AATGGCTTCG GTTCCTGCGACTCGTTTAAA AAGAAAAGGG
244 MIT_Spar_c130_3912           +    310  1.96e-11 TTTGGATTCT GTTCCTGCGACTCGTTTAAA AGAAGAAGGG
245 SGD_Scer_YDR044W             +    317  1.96e-11 TTTGGCTTCT GTTCCTGCGACTCGTTTAAA AGTAGAAGGG
246 SGD_Scer_YDR047W             +    871  6.56e-11 TAATGTAGCC GTGCATGCGGCTCCGCGAAA AGAGCTCTGC
247 MIT_Spar_c130_3923           +    880  1.43e-10 TTATATAGCC GTACGTGCGGCTCCTCGAGA AAGGCCCTGC
248 WashU_Skud_Contig1362.1      -    420  9.20e-09 GAAGGTGGCA CTGCGTGAGACTGCGTGGAA AGTATAAATA
249 MIT_Sbay_c896_21277          +    841  2.90e-08 TTTTATAGCC GTGTGCGCGGCATCGAGAGA CAGGTTCAGC
250 --------------------------------------------------------------------------------
252 --------------------------------------------------------------------------------
253         Motif 2 block diagrams
254 --------------------------------------------------------------------------------
255 SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
256 -------------            ----------------  -------------
257 WashU_Smik_Contig2283.3             2e-11  312_[+2]_668
258 MIT_Sbay_c896_21290                 2e-11  315_[+2]_665
259 MIT_Spar_c130_3912                  2e-11  309_[+2]_671
260 SGD_Scer_YDR044W                    2e-11  316_[+2]_664
261 SGD_Scer_YDR047W                  6.6e-11  870_[+2]_110
262 MIT_Spar_c130_3923                1.4e-10  879_[+2]_101
263 WashU_Skud_Contig1362.1           9.2e-09  419_[-2]_322
264 MIT_Sbay_c896_21277               2.9e-08  840_[+2]_140
265 --------------------------------------------------------------------------------
267 --------------------------------------------------------------------------------
268         Motif 2 in BLOCKS format
269 --------------------------------------------------------------------------------
270 BL   MOTIF 2 width=20 seqs=8
271 WashU_Smik_Contig2283.3  (  313) GTTCCTGCGACTCGTTTAAA  1 
272 MIT_Sbay_c896_21290      (  316) GTTCCTGCGACTCGTTTAAA  1 
273 MIT_Spar_c130_3912       (  310) GTTCCTGCGACTCGTTTAAA  1 
274 SGD_Scer_YDR044W         (  317) GTTCCTGCGACTCGTTTAAA  1 
275 SGD_Scer_YDR047W         (  871) GTGCATGCGGCTCCGCGAAA  1 
276 MIT_Spar_c130_3923       (  880) GTACGTGCGGCTCCTCGAGA  1 
277 WashU_Skud_Contig1362.1  (  420) CTGCGTGAGACTGCGTGGAA  1 
278 MIT_Sbay_c896_21277      (  841) GTGTGCGCGGCATCGAGAGA  1 
281 --------------------------------------------------------------------------------
283 --------------------------------------------------------------------------------
284         Motif 2 position-specific scoring matrix
285 --------------------------------------------------------------------------------
286 log-odds matrix: alength= 4 w= 20 n= 7609 bayes= 9.89197 E= 5.1e-011 
287   -965    -49    232   -965 
288   -965   -965   -965    162 
289   -137   -965    109     62 
290   -965    232   -965   -137 
291   -137    151    109   -965 
292   -965    -49   -965    143 
293   -965   -965    251   -965 
294   -137    232   -965   -965 
295   -965   -965    251   -965 
296     95   -965    109   -965 
297   -965    251   -965   -965 
298   -137   -965   -965    143 
299   -965    209    -49   -137 
300   -965    151    151   -965 
301   -965   -965    109     95 
302   -137     51   -965     95 
303   -965   -965    151     62 
304    143   -965    -49   -965 
305    121   -965     51   -965 
306    162   -965   -965   -965 
307 --------------------------------------------------------------------------------
309 --------------------------------------------------------------------------------
310         Motif 2 position-specific probability matrix
311 --------------------------------------------------------------------------------
312 letter-probability matrix: alength= 4 w= 20 nsites= 8 E= 5.1e-011 
313  0.000000  0.125000  0.875000  0.000000 
314  0.000000  0.000000  0.000000  1.000000 
315  0.125000  0.000000  0.375000  0.500000 
316  0.000000  0.875000  0.000000  0.125000 
317  0.125000  0.500000  0.375000  0.000000 
318  0.000000  0.125000  0.000000  0.875000 
319  0.000000  0.000000  1.000000  0.000000 
320  0.125000  0.875000  0.000000  0.000000 
321  0.000000  0.000000  1.000000  0.000000 
322  0.625000  0.000000  0.375000  0.000000 
323  0.000000  1.000000  0.000000  0.000000 
324  0.125000  0.000000  0.000000  0.875000 
325  0.000000  0.750000  0.125000  0.125000 
326  0.000000  0.500000  0.500000  0.000000 
327  0.000000  0.000000  0.375000  0.625000 
328  0.125000  0.250000  0.000000  0.625000 
329  0.000000  0.000000  0.500000  0.500000 
330  0.875000  0.000000  0.125000  0.000000 
331  0.750000  0.000000  0.250000  0.000000 
332  1.000000  0.000000  0.000000  0.000000 
333 --------------------------------------------------------------------------------
335 --------------------------------------------------------------------------------
336         Motif 2 regular expression
337 --------------------------------------------------------------------------------
338 GT[TG]C[CG]TGCG[AG]CTC[CG][TG][TC][GT]A[AG]A
339 --------------------------------------------------------------------------------
344 Time 12.22 secs.
346 ********************************************************************************
349 ********************************************************************************
350 MOTIF  3        width =   15   sites =   8   llr = 136   E-value = 3.8e-008
351 ********************************************************************************
352 --------------------------------------------------------------------------------
353         Motif 3 Description
354 --------------------------------------------------------------------------------
355 Simplified        A  :9::6:::::1::::
356 pos.-specific     C  5::::::5:5:::4:
357 probability       G  519a4:::a59a5::
358 matrix            T  ::1::aa5::::56a
360          bits    2.5    *    *  *   
361                  2.3    *    *  *   
362                  2.0    *    *  *   
363                  1.8   **    * **   
364 Information      1.5 * ** ** ****  *
365 content          1.3 **** ** ****  *
366 (24.5 bits)      1.0 ***************
367                  0.8 ***************
368                  0.5 ***************
369                  0.3 ***************
370                  0.0 ---------------
372 Multilevel           CAGGATTCGCGGGTT
373 consensus            G   G  T G  TC 
374 sequence                            
375                                     
376 --------------------------------------------------------------------------------
378 --------------------------------------------------------------------------------
379         Motif 3 sites sorted by position p-value
380 --------------------------------------------------------------------------------
381 Sequence name            Strand  Start   P-value                 Site    
382 -------------            ------  ----- ---------            ---------------
383 SGD_Scer_YDR044W             +    623  5.51e-09 ACAAACTCCA GAGGATTTGCGGGCT TGATGATAAA
384 MIT_Sbay_c896_21277          -    211  5.51e-09 CTCGTTTATA CAGGGTTCGGGGTTT TTTGACGCCA
385 MIT_Spar_c130_3923           -    240  5.51e-09 ATATACGGGA CAGGGTTCGGGGTTT TGGTGGCAGG
386 SGD_Scer_YDR047W             -    243  5.51e-09 ATATACAGGA CAGGGTTCGGGGTTT TTGGCGGCAG
387 WashU_Smik_Contig2283.3      +    624  8.25e-09 TGAACTTCTT GAGGATTTGCGGGTT CGGTGATAAA
388 MIT_Sbay_c896_21290          +    622  1.72e-08 CGGAACTCTT GGGGATTTGCGGGCT CGCTAATAAA
389 MIT_Spar_c130_3912           +    618  4.23e-08 CGAAACTCTA GAGGATTTGCAGGCT CGGTGATAAA
390 WashU_Skud_Contig1362.1      -    206  5.24e-08 CTCGCTTCTA CATGATTCGGGGTTT TTTGGCAGCA
391 --------------------------------------------------------------------------------
393 --------------------------------------------------------------------------------
394         Motif 3 block diagrams
395 --------------------------------------------------------------------------------
396 SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
397 -------------            ----------------  -------------
398 SGD_Scer_YDR044W                  5.5e-09  622_[+3]_363
399 MIT_Sbay_c896_21277               5.5e-09  210_[-3]_775
400 MIT_Spar_c130_3923                5.5e-09  239_[-3]_746
401 SGD_Scer_YDR047W                  5.5e-09  242_[-3]_743
402 WashU_Smik_Contig2283.3           8.2e-09  623_[+3]_362
403 MIT_Sbay_c896_21290               1.7e-08  621_[+3]_364
404 MIT_Spar_c130_3912                4.2e-08  617_[+3]_368
405 WashU_Skud_Contig1362.1           5.2e-08  205_[-3]_541
406 --------------------------------------------------------------------------------
408 --------------------------------------------------------------------------------
409         Motif 3 in BLOCKS format
410 --------------------------------------------------------------------------------
411 BL   MOTIF 3 width=15 seqs=8
412 SGD_Scer_YDR044W         (  623) GAGGATTTGCGGGCT  1 
413 MIT_Sbay_c896_21277      (  211) CAGGGTTCGGGGTTT  1 
414 MIT_Spar_c130_3923       (  240) CAGGGTTCGGGGTTT  1 
415 SGD_Scer_YDR047W         (  243) CAGGGTTCGGGGTTT  1 
416 WashU_Smik_Contig2283.3  (  624) GAGGATTTGCGGGTT  1 
417 MIT_Sbay_c896_21290      (  622) GGGGATTTGCGGGCT  1 
418 MIT_Spar_c130_3912       (  618) GAGGATTTGCAGGCT  1 
419 WashU_Skud_Contig1362.1  (  206) CATGATTCGGGGTTT  1 
422 --------------------------------------------------------------------------------
424 --------------------------------------------------------------------------------
425         Motif 3 position-specific scoring matrix
426 --------------------------------------------------------------------------------
427 log-odds matrix: alength= 4 w= 15 n= 7649 bayes= 9.89955 E= 3.8e-008 
428   -965    151    151   -965 
429    143   -965    -49   -965 
430   -965   -965    232   -137 
431   -965   -965    251   -965 
432     95   -965    109   -965 
433   -965   -965   -965    162 
434   -965   -965   -965    162 
435   -965    151   -965     62 
436   -965   -965    251   -965 
437   -965    151    151   -965 
438   -137   -965    232   -965 
439   -965   -965    251   -965 
440   -965   -965    151     62 
441   -965    109   -965     95 
442   -965   -965   -965    162 
443 --------------------------------------------------------------------------------
445 --------------------------------------------------------------------------------
446         Motif 3 position-specific probability matrix
447 --------------------------------------------------------------------------------
448 letter-probability matrix: alength= 4 w= 15 nsites= 8 E= 3.8e-008 
449  0.000000  0.500000  0.500000  0.000000 
450  0.875000  0.000000  0.125000  0.000000 
451  0.000000  0.000000  0.875000  0.125000 
452  0.000000  0.000000  1.000000  0.000000 
453  0.625000  0.000000  0.375000  0.000000 
454  0.000000  0.000000  0.000000  1.000000 
455  0.000000  0.000000  0.000000  1.000000 
456  0.000000  0.500000  0.000000  0.500000 
457  0.000000  0.000000  1.000000  0.000000 
458  0.000000  0.500000  0.500000  0.000000 
459  0.125000  0.000000  0.875000  0.000000 
460  0.000000  0.000000  1.000000  0.000000 
461  0.000000  0.000000  0.500000  0.500000 
462  0.000000  0.375000  0.000000  0.625000 
463  0.000000  0.000000  0.000000  1.000000 
464 --------------------------------------------------------------------------------
466 --------------------------------------------------------------------------------
467         Motif 3 regular expression
468 --------------------------------------------------------------------------------
469 [CG]AGG[AG]TT[CT]G[CG]GG[GT][TC]T
470 --------------------------------------------------------------------------------
475 Time 18.15 secs.
477 ********************************************************************************
480 ********************************************************************************
481 MOTIF  4        width =   20   sites =   8   llr = 155   E-value = 1.1e-008
482 ********************************************************************************
483 --------------------------------------------------------------------------------
484         Motif 4 Description
485 --------------------------------------------------------------------------------
486 Simplified        A  aa13::a6a415:5::::1:
487 pos.-specific     C  ::::54::::9:111a:1:4
488 probability       G  ::5856:4:6:5::4:a::6
489 matrix            T  ::4:::::::::945::99:
491          bits    2.5                **   
492                  2.3                **   
493                  2.0                **   
494                  1.8           *    **   
495 Information      1.5 ** **** * *    **  *
496 content          1.3 ** **** *** *  *** *
497 (27.9 bits)      1.0 ** **********  *****
498                  0.8 ************* ******
499                  0.5 ************* ******
500                  0.3 ********************
501                  0.0 --------------------
503 Multilevel           AAGGCGAAAGCATATCGTTG
504 consensus              TAGC G A G TG    C
505 sequence                                 
506                                          
507 --------------------------------------------------------------------------------
509 --------------------------------------------------------------------------------
510         Motif 4 sites sorted by position p-value
511 --------------------------------------------------------------------------------
512 Sequence name            Strand  Start   P-value                    Site      
513 -------------            ------  ----- ---------            --------------------
514 MIT_Spar_c130_3912           +    273  3.90e-12 GAAGCCAGAA AAGGCGAAAGCGTAGCGTTC TTTGAAATTT
515 SGD_Scer_YDR044W             +    280  3.90e-12 AGAACCAGAA AAGGCGAAAGCGTAGCGTTC TTTGAAATTT
516 MIT_Sbay_c896_21290          +    279  2.45e-10 GAAGCCAGAA AATGCGAAAGCGTACCGTTC TGTGAAAAAT
517 MIT_Spar_c130_3923           +    167  3.43e-10 TAATGACAAA AAGGGCAGAACATTTCGTTG GCAAAATTTA
518 MIT_Sbay_c896_21277          +    140  1.28e-09 TAGTGACACG AATAGGAAAGCATTTCGTTG ACAAAAATAA
519 SGD_Scer_YDR047W             +    170  3.28e-09 TAAAGATGAA AATGGCAGAACATTTCGCTG GCAAAATTAA
520 WashU_Smik_Contig2283.3      +    269  7.13e-09 GAAGCCAGAA AAGACGAAAGAGTAGCGTAG CGTTCTTTCA
521 WashU_Skud_Contig1362.1      +    134  8.94e-09 TAAACATACG AAAGGCAGAACACCTCGTTG ACAAAACTGA
522 --------------------------------------------------------------------------------
524 --------------------------------------------------------------------------------
525         Motif 4 block diagrams
526 --------------------------------------------------------------------------------
527 SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
528 -------------            ----------------  -------------
529 MIT_Spar_c130_3912                3.9e-12  272_[+4]_708
530 SGD_Scer_YDR044W                  3.9e-12  279_[+4]_701
531 MIT_Sbay_c896_21290               2.4e-10  278_[+4]_702
532 MIT_Spar_c130_3923                3.4e-10  166_[+4]_814
533 MIT_Sbay_c896_21277               1.3e-09  139_[+4]_841
534 SGD_Scer_YDR047W                  3.3e-09  169_[+4]_811
535 WashU_Smik_Contig2283.3           7.1e-09  268_[+4]_712
536 WashU_Skud_Contig1362.1           8.9e-09  133_[+4]_608
537 --------------------------------------------------------------------------------
539 --------------------------------------------------------------------------------
540         Motif 4 in BLOCKS format
541 --------------------------------------------------------------------------------
542 BL   MOTIF 4 width=20 seqs=8
543 MIT_Spar_c130_3912       (  273) AAGGCGAAAGCGTAGCGTTC  1 
544 SGD_Scer_YDR044W         (  280) AAGGCGAAAGCGTAGCGTTC  1 
545 MIT_Sbay_c896_21290      (  279) AATGCGAAAGCGTACCGTTC  1 
546 MIT_Spar_c130_3923       (  167) AAGGGCAGAACATTTCGTTG  1 
547 MIT_Sbay_c896_21277      (  140) AATAGGAAAGCATTTCGTTG  1 
548 SGD_Scer_YDR047W         (  170) AATGGCAGAACATTTCGCTG  1 
549 WashU_Smik_Contig2283.3  (  269) AAGACGAAAGAGTAGCGTAG  1 
550 WashU_Skud_Contig1362.1  (  134) AAAGGCAGAACACCTCGTTG  1 
553 --------------------------------------------------------------------------------
555 --------------------------------------------------------------------------------
556         Motif 4 position-specific scoring matrix
557 --------------------------------------------------------------------------------
558 log-odds matrix: alength= 4 w= 20 n= 7609 bayes= 9.89197 E= 1.1e-008 
559    162   -965   -965   -965 
560    162   -965   -965   -965 
561   -137   -965    151     21 
562    -38   -965    209   -965 
563   -965    151    151   -965 
564   -965    109    183   -965 
565    162   -965   -965   -965 
566     95   -965    109   -965 
567    162   -965   -965   -965 
568     21   -965    183   -965 
569   -137    232   -965   -965 
570     62   -965    151   -965 
571   -965    -49   -965    143 
572     62    -49   -965     21 
573   -965    -49    109     62 
574   -965    251   -965   -965 
575   -965   -965    251   -965 
576   -965    -49   -965    143 
577   -137   -965   -965    143 
578   -965    109    183   -965 
579 --------------------------------------------------------------------------------
581 --------------------------------------------------------------------------------
582         Motif 4 position-specific probability matrix
583 --------------------------------------------------------------------------------
584 letter-probability matrix: alength= 4 w= 20 nsites= 8 E= 1.1e-008 
585  1.000000  0.000000  0.000000  0.000000 
586  1.000000  0.000000  0.000000  0.000000 
587  0.125000  0.000000  0.500000  0.375000 
588  0.250000  0.000000  0.750000  0.000000 
589  0.000000  0.500000  0.500000  0.000000 
590  0.000000  0.375000  0.625000  0.000000 
591  1.000000  0.000000  0.000000  0.000000 
592  0.625000  0.000000  0.375000  0.000000 
593  1.000000  0.000000  0.000000  0.000000 
594  0.375000  0.000000  0.625000  0.000000 
595  0.125000  0.875000  0.000000  0.000000 
596  0.500000  0.000000  0.500000  0.000000 
597  0.000000  0.125000  0.000000  0.875000 
598  0.500000  0.125000  0.000000  0.375000 
599  0.000000  0.125000  0.375000  0.500000 
600  0.000000  1.000000  0.000000  0.000000 
601  0.000000  0.000000  1.000000  0.000000 
602  0.000000  0.125000  0.000000  0.875000 
603  0.125000  0.000000  0.000000  0.875000 
604  0.000000  0.375000  0.625000  0.000000 
605 --------------------------------------------------------------------------------
607 --------------------------------------------------------------------------------
608         Motif 4 regular expression
609 --------------------------------------------------------------------------------
610 AA[GT][GA][CG][GC]A[AG]A[GA]C[AG]T[AT][TG]CGTT[GC]
611 --------------------------------------------------------------------------------
616 Time 24.05 secs.
618 ********************************************************************************
621 ********************************************************************************
622 MOTIF  5        width =   20   sites =   8   llr = 150   E-value = 3.2e-007
623 ********************************************************************************
624 --------------------------------------------------------------------------------
625         Motif 5 Description
626 --------------------------------------------------------------------------------
627 Simplified        A  1::::1a643:6:85:aa::
628 pos.-specific     C  135:a:::44:4:11a::31
629 probability       G  :1:::9:431a:91:::::9
630 matrix            T  865a:::::3::1:4:::8:
632          bits    2.5     *     *    *    
633                  2.3     *     *    *    
634                  2.0     *     *    *   *
635                  1.8     **    * *  *   *
636 Information      1.5    ****   * *  *** *
637 content          1.3    ****   * *  *** *
638 (27.0 bits)      1.0   ******  ***  *****
639                  0.8 ********  **** *****
640                  0.5 ********* **** *****
641                  0.3 ********************
642                  0.0 --------------------
644 Multilevel           TTCTCGAAACGAGAACAATG
645 consensus             CT    GCA C  T   C 
646 sequence                     GT          
647                                          
648 --------------------------------------------------------------------------------
650 --------------------------------------------------------------------------------
651         Motif 5 sites sorted by position p-value
652 --------------------------------------------------------------------------------
653 Sequence name            Strand  Start   P-value                    Site      
654 -------------            ------  ----- ---------            --------------------
655 MIT_Spar_c130_3912           +    160  8.41e-11 TTATATAGCC TTTTCGAAACGAGAACAATG GACAAATCAA
656 MIT_Sbay_c896_21290          +    166  1.14e-10 TTATATAGCT TTCTCGAAGGGAGAACAATG GATAAATCAA
657 MIT_Spar_c130_3923           +    927  2.25e-10 CACTAGCTGA TCCTCGAGCTGCGATCAACG AAAGCCCCAT
658 SGD_Scer_YDR044W             +    164  6.26e-10 CTTATATAGC CTTTCGAAACGAGAACAATG GGCAAAGCAA
659 MIT_Sbay_c896_21277          +    888  1.02e-09 ATTTGCCTAA TTCTCGAGCTGAGGCCAATG AAGGCAGCTT
660 SGD_Scer_YDR047W             +    918  1.45e-09 CTCTACCTGA ACTTCGAGCCGCGATCAACG AAAGCTCTCA
661 WashU_Smik_Contig2283.3      +    156  6.02e-09 TTATATAGCC TTTTCAAAAAGAGAACAATG GTCAAATAAA
662 WashU_Skud_Contig1362.1      +    363  3.46e-08 AATTTGCTAA TGCTCGAAGAGCTCTCAATC AATCACCCAC
663 --------------------------------------------------------------------------------
665 --------------------------------------------------------------------------------
666         Motif 5 block diagrams
667 --------------------------------------------------------------------------------
668 SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
669 -------------            ----------------  -------------
670 MIT_Spar_c130_3912                8.4e-11  159_[+5]_821
671 MIT_Sbay_c896_21290               1.1e-10  165_[+5]_815
672 MIT_Spar_c130_3923                2.2e-10  926_[+5]_54
673 SGD_Scer_YDR044W                  6.3e-10  163_[+5]_817
674 MIT_Sbay_c896_21277                 1e-09  887_[+5]_93
675 SGD_Scer_YDR047W                  1.4e-09  917_[+5]_63
676 WashU_Smik_Contig2283.3             6e-09  155_[+5]_825
677 WashU_Skud_Contig1362.1           3.5e-08  362_[+5]_379
678 --------------------------------------------------------------------------------
680 --------------------------------------------------------------------------------
681         Motif 5 in BLOCKS format
682 --------------------------------------------------------------------------------
683 BL   MOTIF 5 width=20 seqs=8
684 MIT_Spar_c130_3912       (  160) TTTTCGAAACGAGAACAATG  1 
685 MIT_Sbay_c896_21290      (  166) TTCTCGAAGGGAGAACAATG  1 
686 MIT_Spar_c130_3923       (  927) TCCTCGAGCTGCGATCAACG  1 
687 SGD_Scer_YDR044W         (  164) CTTTCGAAACGAGAACAATG  1 
688 MIT_Sbay_c896_21277      (  888) TTCTCGAGCTGAGGCCAATG  1 
689 SGD_Scer_YDR047W         (  918) ACTTCGAGCCGCGATCAACG  1 
690 WashU_Smik_Contig2283.3  (  156) TTTTCAAAAAGAGAACAATG  1 
691 WashU_Skud_Contig1362.1  (  363) TGCTCGAAGAGCTCTCAATC  1 
694 --------------------------------------------------------------------------------
696 --------------------------------------------------------------------------------
697         Motif 5 position-specific scoring matrix
698 --------------------------------------------------------------------------------
699 log-odds matrix: alength= 4 w= 20 n= 7609 bayes= 9.89197 E= 3.2e-007 
700   -137    -49   -965    121 
701   -965     51    -49     95 
702   -965    151   -965     62 
703   -965   -965   -965    162 
704   -965    251   -965   -965 
705   -137   -965    232   -965 
706    162   -965   -965   -965 
707     95   -965    109   -965 
708     21    109     51   -965 
709    -38    109    -49    -38 
710   -965   -965    251   -965 
711     95    109   -965   -965 
712   -965   -965    232   -137 
713    121    -49    -49   -965 
714     62    -49   -965     21 
715   -965    251   -965   -965 
716    162   -965   -965   -965 
717    162   -965   -965   -965 
718   -965     51   -965    121 
719   -965    -49    232   -965 
720 --------------------------------------------------------------------------------
722 --------------------------------------------------------------------------------
723         Motif 5 position-specific probability matrix
724 --------------------------------------------------------------------------------
725 letter-probability matrix: alength= 4 w= 20 nsites= 8 E= 3.2e-007 
726  0.125000  0.125000  0.000000  0.750000 
727  0.000000  0.250000  0.125000  0.625000 
728  0.000000  0.500000  0.000000  0.500000 
729  0.000000  0.000000  0.000000  1.000000 
730  0.000000  1.000000  0.000000  0.000000 
731  0.125000  0.000000  0.875000  0.000000 
732  1.000000  0.000000  0.000000  0.000000 
733  0.625000  0.000000  0.375000  0.000000 
734  0.375000  0.375000  0.250000  0.000000 
735  0.250000  0.375000  0.125000  0.250000 
736  0.000000  0.000000  1.000000  0.000000 
737  0.625000  0.375000  0.000000  0.000000 
738  0.000000  0.000000  0.875000  0.125000 
739  0.750000  0.125000  0.125000  0.000000 
740  0.500000  0.125000  0.000000  0.375000 
741  0.000000  1.000000  0.000000  0.000000 
742  1.000000  0.000000  0.000000  0.000000 
743  1.000000  0.000000  0.000000  0.000000 
744  0.000000  0.250000  0.000000  0.750000 
745  0.000000  0.125000  0.875000  0.000000 
746 --------------------------------------------------------------------------------
748 --------------------------------------------------------------------------------
749         Motif 5 regular expression
750 --------------------------------------------------------------------------------
751 T[TC][CT]TCGA[AG][ACG][CAT]G[AC]GA[AT]CAA[TC]G
752 --------------------------------------------------------------------------------
757 Time 29.84 secs.
759 ********************************************************************************
762 ********************************************************************************
763 SUMMARY OF MOTIFS
764 ********************************************************************************
766 --------------------------------------------------------------------------------
767         Combined block diagrams: non-overlapping sites with p-value < 0.0001
768 --------------------------------------------------------------------------------
769 SEQUENCE NAME            COMBINED P-VALUE  MOTIF DIAGRAM
770 -------------            ----------------  -------------
771 SGD_Scer_YDR047W                 7.45e-23  50_[+5(5.03e-05)]_66_[+1(1.93e-09)]_13_[+4(3.28e-09)]_53_[-3(5.51e-09)]_613_[+2(6.56e-11)]_27_[+5(1.45e-09)]_63
772 MIT_Spar_c130_3923               1.06e-24  133_[+1(5.96e-10)]_13_[+4(3.43e-10)]_53_[-3(5.51e-09)]_110_[-4(7.03e-05)]_238_[+1(6.23e-05)]_237_[+2(1.43e-10)]_27_[+5(2.25e-10)]_54
773 MIT_Sbay_c896_21277              2.78e-21  5_[-4(5.78e-05)]_81_[+1(7.56e-10)]_13_[+4(1.28e-09)]_51_[-3(5.51e-09)]_615_[+2(2.90e-08)]_27_[+5(1.02e-09)]_93
774 WashU_Skud_Contig1362.1          1.22e-19  100_[+1(2.45e-10)]_13_[+4(8.94e-09)]_52_[-3(5.24e-08)]_142_[+5(3.46e-08)]_37_[-2(9.20e-09)]_322
775 SGD_Scer_YDR044W                 3.05e-28  163_[+5(6.26e-10)]_68_[+1(2.47e-11)]_8_[+4(3.90e-12)]_17_[+2(1.96e-11)]_286_[+3(5.51e-09)]_363
776 MIT_Spar_c130_3912               1.93e-29  159_[+5(8.41e-11)]_64_[+1(1.31e-12)]_9_[+4(3.90e-12)]_17_[+2(1.96e-11)]_288_[+3(4.23e-08)]_69_[-4(1.60e-05)]_279
777 MIT_Sbay_c896_21290              7.41e-27  165_[+5(1.14e-10)]_64_[+1(2.00e-11)]_9_[+4(2.45e-10)]_17_[+2(1.96e-11)]_8_[-3(7.60e-05)]_3_[-4(2.55e-05)]_240_[+3(1.72e-08)]_66_[-4(1.70e-05)]_278
778 WashU_Smik_Contig2283.3          1.31e-23  7_[+3(8.33e-05)]_39_[-5(9.82e-05)]_74_[+5(6.02e-09)]_64_[+1(7.53e-11)]_9_[+4(7.13e-09)]_24_[+2(1.96e-11)]_61_[-2(3.93e-05)]_88_[+2(7.74e-05)]_102_[+3(8.25e-09)]_362
779 --------------------------------------------------------------------------------
781 ********************************************************************************
784 ********************************************************************************
785 Stopped because nmotifs = 5 reached.
786 ********************************************************************************
788 CPU: dhn02990.mrc-dunn.cam.ac.uk
790 ********************************************************************************