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 ********************************************************************************
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 ********************************************************************************
30 ********************************************************************************
31 DATAFILE= HEM12-HEM13.fa
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 ********************************************************************************
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
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 --------------------------------------------------------------------------------
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::::
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
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
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 --------------------------------------------------------------------------------
205 ********************************************************************************
208 ********************************************************************************
209 MOTIF 2 width = 20 sites = 8 llr = 161 E-value = 5.1e-011
210 ********************************************************************************
211 --------------------------------------------------------------------------------
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:::
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
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
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 --------------------------------------------------------------------------------
346 ********************************************************************************
349 ********************************************************************************
350 MOTIF 3 width = 15 sites = 8 llr = 136 E-value = 3.8e-008
351 ********************************************************************************
352 --------------------------------------------------------------------------------
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
364 Information 1.5 * ** ** **** *
365 content 1.3 **** ** **** *
366 (24.5 bits) 1.0 ***************
372 Multilevel CAGGATTCGCGGGTT
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
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 --------------------------------------------------------------------------------
477 ********************************************************************************
480 ********************************************************************************
481 MOTIF 4 width = 20 sites = 8 llr = 155 E-value = 1.1e-008
482 ********************************************************************************
483 --------------------------------------------------------------------------------
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:
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
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
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 --------------------------------------------------------------------------------
618 ********************************************************************************
621 ********************************************************************************
622 MOTIF 5 width = 20 sites = 8 llr = 150 E-value = 3.2e-007
623 ********************************************************************************
624 --------------------------------------------------------------------------------
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:
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
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
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 --------------------------------------------------------------------------------
759 ********************************************************************************
762 ********************************************************************************
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 ********************************************************************************