t/data/map_hem/HEM1-HEM14.meme.txt

   1 ********************************************************************************
   2 MEME - Motif discovery tool
   3 ********************************************************************************
   4 MEME version 3.5.4 (Release date:    )
   5
   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.
   8
   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 ********************************************************************************
  13
  14
  15 ********************************************************************************
  16 REFERENCE
  17 ********************************************************************************
  18 If you use this program in your research, please cite:
  19
  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 ********************************************************************************
  26
  27
  28 ********************************************************************************
  29 TRAINING SET
  30 ********************************************************************************
  31 DATAFILE= HEM1-HEM14.fa
  32 ALPHABET= ACGT
  33 Sequence name            Weight Length  Sequence name            Weight Length
  34 -------------            ------ ------  -------------            ------ ------
  35 SGD_Scer_YDR232W         1.0000    498  MIT_Spar_c117_4603       1.0000    498
  36 MIT_Smik_c228_4055       1.0000    498  WashU_Skud_Contig2069.5  1.0000    498
  37 WashU_Sbay_Contig461.5   1.0000    498  SGD_Scer_YER014W         1.0000    322
  38 MIT_Spar_c425_6072       1.0000    322  MIT_Smik_c283_5928       1.0000    322
  39 MIT_Sbay_c84_6418        1.0000    322
  40 ********************************************************************************
  41
  42 ********************************************************************************
  43 COMMAND LINE SUMMARY
  44 ********************************************************************************
  45 This information can also be useful in the event you wish to report a
  46 problem with the MEME software.
  47
  48 command: meme HEM1-HEM14.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
  50 model:  mod=          oops    nmotifs=         5    evt=           inf
  51 object function=  E-value of product of p-values
  52 width:  minw=            6    maxw=           20    minic=        0.00
  53 width:  wg=             11    ws=              1    endgaps=       yes
  54 nsites: minsites=        9    maxsites=        9    wnsites=       0.8
  55 theta:  prob=            1    spmap=         uni    spfuzz=        0.5
  56 em:     prior=   dirichlet    b=            0.01    maxiter=        50
  57         distance=    1e-05
  58 data:   n=            3778    N=               9
  59 strands: + -
  60 sample: seed=            0    seqfrac=         1
  61 Letter frequencies in dataset:
  62 A 0.293 C 0.207 G 0.207 T 0.293
  63 Background letter frequencies (from yeast.nc.1.freq):
  64 A 0.324 C 0.176 G 0.176 T 0.324
  65 ********************************************************************************
  66
  67
  68 ********************************************************************************
  69 MOTIF  1        width =   20   sites =   9   llr = 202   E-value = 1.6e-028
  70 ********************************************************************************
  71 --------------------------------------------------------------------------------
  72         Motif 1 Description
  73 --------------------------------------------------------------------------------
  74 Simplified        A  a3a9:::::aa:::aa:6:1
  75 pos.-specific     C  :7:::1:46::::a:::2:1
  76 probability       G  :::119664::aa:::91:8
  77 matrix            T  ::::9:4:::::::::11a:
  78
  79          bits    2.5            ***
  80                  2.3            ***
  81                  2.0      *     ***  *
  82                  1.8      *     ***  *
  83 Information      1.5 * *  * ********** **
  84 content          1.3 ****** ********** **
  85 (32.4 bits)      1.0 ***************** **
  86                  0.8 ***************** **
  87                  0.5 ***************** **
  88                  0.3 ********************
  89                  0.0 --------------------
  90
  91 Multilevel           ACAATGGGCAAGGCAAGATG
  92 consensus             A    TCG        C
  93 sequence
  94
  95 --------------------------------------------------------------------------------
  96
  97 --------------------------------------------------------------------------------
  98         Motif 1 sites sorted by position p-value
  99 --------------------------------------------------------------------------------
 100 Sequence name            Strand  Start   P-value                    Site
 101 -------------            ------  ----- ---------            --------------------
 102 WashU_Sbay_Contig461.5       +    280  3.60e-13 CCGGGACAGA ACAATGGGCAAGGCAAGATG AAAAATCTCC
 103 MIT_Smik_c228_4055           +    285  3.60e-13 TTGAATTAGA ACAATGGGCAAGGCAAGATG AAAATTTCCG
 104 MIT_Spar_c117_4603           +    282  3.60e-13 ATGGGTCAGA ACAATGGGCAAGGCAAGATG AAAAATTTCT
 105 SGD_Scer_YDR232W             +    287  3.60e-13 ATGGATCAGA ACAATGGGCAAGGCAAGATG AAAAATTTCC
 106 MIT_Spar_c425_6072           +    133  2.98e-11 CCGAAGCAAC AAAATGTCGAAGGCAAGATG AAAGGCGTTT
 107 MIT_Smik_c283_5928           +    128  4.86e-11 CTCCGAAGCA ACAAGGTCGAAGGCAAGCTG AAAGGCATTT
 108 WashU_Skud_Contig2069.5      +    285  9.69e-11 CTGGATCGGA ACAATGGGCAAGGCAATGTG AAAAATTTCC
 109 MIT_Sbay_c84_6418            +    126  8.09e-10 CCGAAACAAC AAAATCTCGAAGGCAAGCTA AGGTAAAAAT
 110 SGD_Scer_YER014W             +    134  8.09e-10 CCGAAGCAAC AAAGTGTCGAAGGCAAGTTC AAAGGCGTTT
 111 --------------------------------------------------------------------------------
 112
 113 --------------------------------------------------------------------------------
 114         Motif 1 block diagrams
 115 --------------------------------------------------------------------------------
 116 SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
 117 -------------            ----------------  -------------
 118 WashU_Sbay_Contig461.5            3.6e-13  279_[+1]_199
 119 MIT_Smik_c228_4055                3.6e-13  284_[+1]_194
 120 MIT_Spar_c117_4603                3.6e-13  281_[+1]_197
 121 SGD_Scer_YDR232W                  3.6e-13  286_[+1]_192
 122 MIT_Spar_c425_6072                  3e-11  132_[+1]_170
 123 MIT_Smik_c283_5928                4.9e-11  127_[+1]_175
 124 WashU_Skud_Contig2069.5           9.7e-11  284_[+1]_194
 125 MIT_Sbay_c84_6418                 8.1e-10  125_[+1]_177
 126 SGD_Scer_YER014W                  8.1e-10  133_[+1]_169
 127 --------------------------------------------------------------------------------
 128
 129 --------------------------------------------------------------------------------
 130         Motif 1 in BLOCKS format
 131 --------------------------------------------------------------------------------
 132 BL   MOTIF 1 width=20 seqs=9
 133 WashU_Sbay_Contig461.5   (  280) ACAATGGGCAAGGCAAGATG  1
 134 MIT_Smik_c228_4055       (  285) ACAATGGGCAAGGCAAGATG  1
 135 MIT_Spar_c117_4603       (  282) ACAATGGGCAAGGCAAGATG  1
 136 SGD_Scer_YDR232W         (  287) ACAATGGGCAAGGCAAGATG  1
 137 MIT_Spar_c425_6072       (  133) AAAATGTCGAAGGCAAGATG  1
 138 MIT_Smik_c283_5928       (  128) ACAAGGTCGAAGGCAAGCTG  1
 139 WashU_Skud_Contig2069.5  (  285) ACAATGGGCAAGGCAATGTG  1
 140 MIT_Sbay_c84_6418        (  126) AAAATCTCGAAGGCAAGCTA  1
 141 SGD_Scer_YER014W         (  134) AAAGTGTCGAAGGCAAGTTC  1
 142 //
 143
 144 --------------------------------------------------------------------------------
 145
 146 --------------------------------------------------------------------------------
 147         Motif 1 position-specific scoring matrix
 148 --------------------------------------------------------------------------------
 149 log-odds matrix: alength= 4 w= 20 n= 3607 bayes= 8.64305 E= 1.6e-028
 150    162   -982   -982   -982
 151      4    192   -982   -982
 152    162   -982   -982   -982
 153    145   -982    -66   -982
 154   -982   -982    -66    145
 155   -982    -66    234   -982
 156   -982   -982    166     45
 157   -982    134    166   -982
 158   -982    166    134   -982
 159    162   -982   -982   -982
 160    162   -982   -982   -982
 161   -982   -982    251   -982
 162   -982   -982    251   -982
 163   -982    251   -982   -982
 164    162   -982   -982   -982
 165    162   -982   -982   -982
 166   -982   -982    234   -154
 167     78     34    -66   -154
 168   -982   -982   -982    162
 169   -154    -66    215   -982
 170 --------------------------------------------------------------------------------
 171
 172 --------------------------------------------------------------------------------
 173         Motif 1 position-specific probability matrix
 174 --------------------------------------------------------------------------------
 175 letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 1.6e-028
 176  1.000000  0.000000  0.000000  0.000000
 177  0.333333  0.666667  0.000000  0.000000
 178  1.000000  0.000000  0.000000  0.000000
 179  0.888889  0.000000  0.111111  0.000000
 180  0.000000  0.000000  0.111111  0.888889
 181  0.000000  0.111111  0.888889  0.000000
 182  0.000000  0.000000  0.555556  0.444444
 183  0.000000  0.444444  0.555556  0.000000
 184  0.000000  0.555556  0.444444  0.000000
 185  1.000000  0.000000  0.000000  0.000000
 186  1.000000  0.000000  0.000000  0.000000
 187  0.000000  0.000000  1.000000  0.000000
 188  0.000000  0.000000  1.000000  0.000000
 189  0.000000  1.000000  0.000000  0.000000
 190  1.000000  0.000000  0.000000  0.000000
 191  1.000000  0.000000  0.000000  0.000000
 192  0.000000  0.000000  0.888889  0.111111
 193  0.555556  0.222222  0.111111  0.111111
 194  0.000000  0.000000  0.000000  1.000000
 195  0.111111  0.111111  0.777778  0.000000
 196 --------------------------------------------------------------------------------
 197
 198 --------------------------------------------------------------------------------
 199         Motif 1 regular expression
 200 --------------------------------------------------------------------------------
 201 A[CA]AATG[GT][GC][CG]AAGGCAAG[AC]TG
 202 --------------------------------------------------------------------------------
 203
 204
 205
 206
 207 Time  1.73 secs.
 208
 209 ********************************************************************************
 210
 211
 212 ********************************************************************************
 213 MOTIF  2        width =   18   sites =   9   llr = 163   E-value = 9.8e-015
 214 ********************************************************************************
 215 --------------------------------------------------------------------------------
 216         Motif 2 Description
 217 --------------------------------------------------------------------------------
 218 Simplified        A  37a:aa:44:4:a27:a:
 219 pos.-specific     C  11::::a1:::::::::4
 220 probability       G  62:a:::46::a:829:1
 221 matrix            T  :::::::::a6:::11:4
 222
 223          bits    2.5    *  *    *
 224                  2.3    *  *    *
 225                  2.0    *  *    *   *
 226                  1.8    *  *    *   *
 227 Information      1.5   *****  * *** **
 228 content          1.3   *****  * *** **
 229 (26.1 bits)      1.0   ***** ** *** **
 230                  0.8 ************** ***
 231                  0.5 ******************
 232                  0.3 ******************
 233                  0.0 ------------------
 234
 235 Multilevel           GAAGAACAGTTGAGAGAC
 236 consensus            AG     GA A  AG  T
 237 sequence
 238
 239 --------------------------------------------------------------------------------
 240
 241 --------------------------------------------------------------------------------
 242         Motif 2 sites sorted by position p-value
 243 --------------------------------------------------------------------------------
 244 Sequence name            Strand  Start   P-value                   Site
 245 -------------            ------  ----- ---------            ------------------
 246 WashU_Skud_Contig2069.5      +    163  6.31e-12 CGTGTGGAGG GAAGAACGGTTGAGAGAC AGCAGAGCAC
 247 SGD_Scer_YDR232W             +    166  6.31e-12 GCGTGTAAAG GAAGAACGGTTGAGAGAC AGCAGAGCAG
 248 WashU_Sbay_Contig461.5       +    162  2.27e-10 CGTGTGGAGG GAAGAACCGTTGAGAGAC AACAGAGCAG
 249 MIT_Spar_c117_4603           +    161  2.27e-10 GCGTGTAAAG GAAGAACGGTTGAGAGAG AGCAGAGCAG
 250 MIT_Smik_c283_5928           -     71  6.85e-09 AGAGTAATGG AAAGAACAATAGAGGGAT TTGCAAAAGA
 251 MIT_Spar_c425_6072           -     69  6.85e-09 AGAATAATAG AGAGAACAATAGAGAGAT CCGCGAAGGA
 252 MIT_Sbay_c84_6418            -     64  1.24e-08 GAACAATAAG GAAGAACAATAGAAGGAT GCGAAAGGAC
 253 MIT_Smik_c228_4055           +    162  3.13e-08 ACGTGTGAAG CCAGAACGGTTGAATGAC AGTAGAGGAG
 254 SGD_Scer_YER014W             -     69  3.60e-08 AGTATAATAG AGAGAACAATAGAGATAT TCGCGAAGAA
 255 --------------------------------------------------------------------------------
 256
 257 --------------------------------------------------------------------------------
 258         Motif 2 block diagrams
 259 --------------------------------------------------------------------------------
 260 SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
 261 -------------            ----------------  -------------
 262 WashU_Skud_Contig2069.5           6.3e-12  162_[+2]_318
 263 SGD_Scer_YDR232W                  6.3e-12  165_[+2]_315
 264 WashU_Sbay_Contig461.5            2.3e-10  161_[+2]_319
 265 MIT_Spar_c117_4603                2.3e-10  160_[+2]_320
 266 MIT_Smik_c283_5928                6.8e-09  70_[-2]_234
 267 MIT_Spar_c425_6072                6.8e-09  68_[-2]_236
 268 MIT_Sbay_c84_6418                 1.2e-08  63_[-2]_241
 269 MIT_Smik_c228_4055                3.1e-08  161_[+2]_319
 270 SGD_Scer_YER014W                  3.6e-08  68_[-2]_236
 271 --------------------------------------------------------------------------------
 272
 273 --------------------------------------------------------------------------------
 274         Motif 2 in BLOCKS format
 275 --------------------------------------------------------------------------------
 276 BL   MOTIF 2 width=18 seqs=9
 277 WashU_Skud_Contig2069.5  (  163) GAAGAACGGTTGAGAGAC  1
 278 SGD_Scer_YDR232W         (  166) GAAGAACGGTTGAGAGAC  1
 279 WashU_Sbay_Contig461.5   (  162) GAAGAACCGTTGAGAGAC  1
 280 MIT_Spar_c117_4603       (  161) GAAGAACGGTTGAGAGAG  1
 281 MIT_Smik_c283_5928       (   71) AAAGAACAATAGAGGGAT  1
 282 MIT_Spar_c425_6072       (   69) AGAGAACAATAGAGAGAT  1
 283 MIT_Sbay_c84_6418        (   64) GAAGAACAATAGAAGGAT  1
 284 MIT_Smik_c228_4055       (  162) CCAGAACGGTTGAATGAC  1
 285 SGD_Scer_YER014W         (   69) AGAGAACAATAGAGATAT  1
 286 //
 287
 288 --------------------------------------------------------------------------------
 289
 290 --------------------------------------------------------------------------------
 291         Motif 2 position-specific scoring matrix
 292 --------------------------------------------------------------------------------
 293 log-odds matrix: alength= 4 w= 18 n= 3625 bayes= 8.65025 E= 9.8e-015
 294      4    -66    166   -982
 295    104    -66     34   -982
 296    162   -982   -982   -982
 297   -982   -982    251   -982
 298    162   -982   -982   -982
 299    162   -982   -982   -982
 300   -982    251   -982   -982
 301     45    -66    134   -982
 302     45   -982    166   -982
 303   -982   -982   -982    162
 304     45   -982   -982     78
 305   -982   -982    251   -982
 306    162   -982   -982   -982
 307    -55   -982    215   -982
 308    104   -982     34   -154
 309   -982   -982    234   -154
 310    162   -982   -982   -982
 311   -982    134    -66     45
 312 --------------------------------------------------------------------------------
 313
 314 --------------------------------------------------------------------------------
 315         Motif 2 position-specific probability matrix
 316 --------------------------------------------------------------------------------
 317 letter-probability matrix: alength= 4 w= 18 nsites= 9 E= 9.8e-015
 318  0.333333  0.111111  0.555556  0.000000
 319  0.666667  0.111111  0.222222  0.000000
 320  1.000000  0.000000  0.000000  0.000000
 321  0.000000  0.000000  1.000000  0.000000
 322  1.000000  0.000000  0.000000  0.000000
 323  1.000000  0.000000  0.000000  0.000000
 324  0.000000  1.000000  0.000000  0.000000
 325  0.444444  0.111111  0.444444  0.000000
 326  0.444444  0.000000  0.555556  0.000000
 327  0.000000  0.000000  0.000000  1.000000
 328  0.444444  0.000000  0.000000  0.555556
 329  0.000000  0.000000  1.000000  0.000000
 330  1.000000  0.000000  0.000000  0.000000
 331  0.222222  0.000000  0.777778  0.000000
 332  0.666667  0.000000  0.222222  0.111111
 333  0.000000  0.000000  0.888889  0.111111
 334  1.000000  0.000000  0.000000  0.000000
 335  0.000000  0.444444  0.111111  0.444444
 336 --------------------------------------------------------------------------------
 337
 338 --------------------------------------------------------------------------------
 339         Motif 2 regular expression
 340 --------------------------------------------------------------------------------
 341 [GA][AG]AGAAC[AG][GA]T[TA]GA[GA][AG]GA[CT]
 342 --------------------------------------------------------------------------------
 343
 344
 345
 346
 347 Time  3.42 secs.
 348
 349 ********************************************************************************
 350
 351
 352 ********************************************************************************
 353 MOTIF  3        width =   20   sites =   9   llr = 185   E-value = 4.5e-020
 354 ********************************************************************************
 355 --------------------------------------------------------------------------------
 356         Motif 3 Description
 357 --------------------------------------------------------------------------------
 358 Simplified        A  :3a6:4a4::a::aa111:4
 359 pos.-specific     C  97:4::::a::63::::63:
 360 probability       G  :::::6:6:a:46::49366
 361 matrix            T  1:::a:::::::1::4::1:
 362
 363          bits    2.5         **
 364                  2.3         **
 365                  2.0 *       **      *
 366                  1.8 *       **      *
 367 Information      1.5 * * * * **** ** *
 368 content          1.3 *** * * **** ** *
 369 (29.6 bits)      1.0 *************** ****
 370                  0.8 *************** ****
 371                  0.5 ********************
 372                  0.3 ********************
 373                  0.0 --------------------
 374
 375 Multilevel           CCAATGAGCGACGAAGGCGG
 376 consensus             A C A A   GC  T GCA
 377 sequence
 378
 379 --------------------------------------------------------------------------------
 380
 381 --------------------------------------------------------------------------------
 382         Motif 3 sites sorted by position p-value
 383 --------------------------------------------------------------------------------
 384 Sequence name            Strand  Start   P-value                    Site
 385 -------------            ------  ----- ---------            --------------------
 386 WashU_Skud_Contig2069.5      +    370  1.19e-13 CGGCCGCAGA CCAATGAGCGACGAAGGCGG CCTTTCGTAG
 387 MIT_Spar_c117_4603           +    368  1.19e-13 CGGCCGCAGA CCAATGAGCGACGAAGGCGG CCTTTCCGAG
 388 SGD_Scer_YDR232W             +    373  1.19e-13 CGGCCGCAGA CCAATGAGCGACGAAGGCGG CCTTTCCGAG
 389 MIT_Smik_c228_4055           +    370  2.41e-11 CAAGCGCAGA CCAATGAGCGACGAAAGCGG CCTTTTGAAG
 390 WashU_Sbay_Contig461.5       +    367  6.46e-11 CGGGCGCAGA CCAATGAGCGACGAAGACGG CTTTTGGGCG
 391 MIT_Sbay_c84_6418            +    161  1.68e-09 AAAATATTCA CCACTAAACGAGCAATGACA GTTATATTCA
 392 MIT_Smik_c283_5928           +    160  3.61e-09 AGGCATTTTA CAACTAAACGAGCAATGGTA GCTTTTGATT
 393 MIT_Spar_c425_6072           +    165  3.61e-09 AGGCGTTTTG CAACTAAACGAGTAATGGCA GCTTTTAATT
 394 SGD_Scer_YER014W             +    166  5.94e-09 AGGCGTTTTG TAACTAAACGAGCAATGGCA GCTTTCAATT
 395 --------------------------------------------------------------------------------
 396
 397 --------------------------------------------------------------------------------
 398         Motif 3 block diagrams
 399 --------------------------------------------------------------------------------
 400 SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
 401 -------------            ----------------  -------------
 402 WashU_Skud_Contig2069.5           1.2e-13  369_[+3]_109
 403 MIT_Spar_c117_4603                1.2e-13  367_[+3]_111
 404 SGD_Scer_YDR232W                  1.2e-13  372_[+3]_106
 405 MIT_Smik_c228_4055                2.4e-11  369_[+3]_109
 406 WashU_Sbay_Contig461.5            6.5e-11  366_[+3]_112
 407 MIT_Sbay_c84_6418                 1.7e-09  160_[+3]_142
 408 MIT_Smik_c283_5928                3.6e-09  159_[+3]_143
 409 MIT_Spar_c425_6072                3.6e-09  164_[+3]_138
 410 SGD_Scer_YER014W                  5.9e-09  165_[+3]_137
 411 --------------------------------------------------------------------------------
 412
 413 --------------------------------------------------------------------------------
 414         Motif 3 in BLOCKS format
 415 --------------------------------------------------------------------------------
 416 BL   MOTIF 3 width=20 seqs=9
 417 WashU_Skud_Contig2069.5  (  370) CCAATGAGCGACGAAGGCGG  1
 418 MIT_Spar_c117_4603       (  368) CCAATGAGCGACGAAGGCGG  1
 419 SGD_Scer_YDR232W         (  373) CCAATGAGCGACGAAGGCGG  1
 420 MIT_Smik_c228_4055       (  370) CCAATGAGCGACGAAAGCGG  1
 421 WashU_Sbay_Contig461.5   (  367) CCAATGAGCGACGAAGACGG  1
 422 MIT_Sbay_c84_6418        (  161) CCACTAAACGAGCAATGACA  1
 423 MIT_Smik_c283_5928       (  160) CAACTAAACGAGCAATGGTA  1
 424 MIT_Spar_c425_6072       (  165) CAACTAAACGAGTAATGGCA  1
 425 SGD_Scer_YER014W         (  166) TAACTAAACGAGCAATGGCA  1
 426 //
 427
 428 --------------------------------------------------------------------------------
 429
 430 --------------------------------------------------------------------------------
 431         Motif 3 position-specific scoring matrix
 432 --------------------------------------------------------------------------------
 433 log-odds matrix: alength= 4 w= 20 n= 3607 bayes= 8.64305 E= 4.5e-020
 434   -982    234   -982   -154
 435      4    192   -982   -982
 436    162   -982   -982   -982
 437     78    134   -982   -982
 438   -982   -982   -982    162
 439     45   -982    166   -982
 440    162   -982   -982   -982
 441     45   -982    166   -982
 442   -982    251   -982   -982
 443   -982   -982    251   -982
 444    162   -982   -982   -982
 445   -982    166    134   -982
 446   -982     92    166   -154
 447    162   -982   -982   -982
 448    162   -982   -982   -982
 449   -154   -982    134     45
 450   -154   -982    234   -982
 451   -154    166     92   -982
 452   -982     92    166   -154
 453     45   -982    166   -982
 454 --------------------------------------------------------------------------------
 455
 456 --------------------------------------------------------------------------------
 457         Motif 3 position-specific probability matrix
 458 --------------------------------------------------------------------------------
 459 letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 4.5e-020
 460  0.000000  0.888889  0.000000  0.111111
 461  0.333333  0.666667  0.000000  0.000000
 462  1.000000  0.000000  0.000000  0.000000
 463  0.555556  0.444444  0.000000  0.000000
 464  0.000000  0.000000  0.000000  1.000000
 465  0.444444  0.000000  0.555556  0.000000
 466  1.000000  0.000000  0.000000  0.000000
 467  0.444444  0.000000  0.555556  0.000000
 468  0.000000  1.000000  0.000000  0.000000
 469  0.000000  0.000000  1.000000  0.000000
 470  1.000000  0.000000  0.000000  0.000000
 471  0.000000  0.555556  0.444444  0.000000
 472  0.000000  0.333333  0.555556  0.111111
 473  1.000000  0.000000  0.000000  0.000000
 474  1.000000  0.000000  0.000000  0.000000
 475  0.111111  0.000000  0.444444  0.444444
 476  0.111111  0.000000  0.888889  0.000000
 477  0.111111  0.555556  0.333333  0.000000
 478  0.000000  0.333333  0.555556  0.111111
 479  0.444444  0.000000  0.555556  0.000000
 480 --------------------------------------------------------------------------------
 481
 482 --------------------------------------------------------------------------------
 483         Motif 3 regular expression
 484 --------------------------------------------------------------------------------
 485 C[CA]A[AC]T[GA]A[GA]CGA[CG][GC]AA[GT]G[CG][GC][GA]
 486 --------------------------------------------------------------------------------
 487
 488
 489
 490
 491 Time  4.97 secs.
 492
 493 ********************************************************************************
 494
 495
 496 ********************************************************************************
 497 MOTIF  4        width =   20   sites =   9   llr = 174   E-value = 3.1e-016
 498 ********************************************************************************
 499 --------------------------------------------------------------------------------
 500         Motif 4 Description
 501 --------------------------------------------------------------------------------
 502 Simplified        A  896a21:1:::411:::4a1
 503 pos.-specific     C  ::::363778:64:8a:6::
 504 probability       G  ::::4:6:32a:442:a::9
 505 matrix            T  214::312:::::4::::::
 506
 507          bits    2.5           *    **
 508                  2.3           *    **
 509                  2.0           *    **  *
 510                  1.8          **   ***  *
 511 Information      1.5    *    ***   *** **
 512 content          1.3    *    ***   *** **
 513 (27.9 bits)      1.0  * *  ******* ******
 514                  0.8 ************* ******
 515                  0.5 ********************
 516                  0.3 ********************
 517                  0.0 --------------------
 518
 519 Multilevel           AAAAGCGCCCGCCGCCGCAG
 520 consensus            T T CTCTGG AGTG  A
 521 sequence                 A
 522
 523 --------------------------------------------------------------------------------
 524
 525 --------------------------------------------------------------------------------
 526         Motif 4 sites sorted by position p-value
 527 --------------------------------------------------------------------------------
 528 Sequence name            Strand  Start   P-value                    Site
 529 -------------            ------  ----- ---------            --------------------
 530 MIT_Spar_c117_4603           +    347  3.34e-14 ACAATGACCA AAAAGCGCCCGCGGCCGCAG ACCAATGAGC
 531 SGD_Scer_YDR232W             +    352  3.34e-14 ACAATGACCA AAAAGCGCCCGCGGCCGCAG ACCAATGAGC
 532 WashU_Skud_Contig2069.5      +    349  3.24e-12 ACAATGACCA AAAAGCGTCCGCGGCCGCAG ACCAATGAGC
 533 WashU_Sbay_Contig461.5       +    346  1.26e-10 CAATGACCAA AAAAACGCCGGCGGGCGCAG ACCAATGAGC
 534 MIT_Spar_c425_6072           +    109  6.37e-10 TTCTTTTTTA AATACTCCGCGACTCCGAAG CAACAAAATG
 535 SGD_Scer_YER014W             +    110  6.37e-10 TCTTTTTTTG AATACTCCGCGACTCCGAAG CAACAAAGTG
 536 MIT_Smik_c228_4055           +    349  6.96e-10 ACAATGACCA AAAAGCGCCCGCAAGCGCAG ACCAATGAGC
 537 MIT_Sbay_c84_6418            +    102  3.58e-08 TCGTTTTTTT TATACTCTGCGACTCCGAAA CAACAAAATC
 538 MIT_Smik_c283_5928           +    106  2.54e-07 TCTTTTCTTT TTTAAATACGGACTCCGAAG CAACAAGGTC
 539 --------------------------------------------------------------------------------
 540
 541 --------------------------------------------------------------------------------
 542         Motif 4 block diagrams
 543 --------------------------------------------------------------------------------
 544 SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
 545 -------------            ----------------  -------------
 546 MIT_Spar_c117_4603                3.3e-14  346_[+4]_132
 547 SGD_Scer_YDR232W                  3.3e-14  351_[+4]_127
 548 WashU_Skud_Contig2069.5           3.2e-12  348_[+4]_130
 549 WashU_Sbay_Contig461.5            1.3e-10  345_[+4]_133
 550 MIT_Spar_c425_6072                6.4e-10  108_[+4]_194
 551 SGD_Scer_YER014W                  6.4e-10  109_[+4]_193
 552 MIT_Smik_c228_4055                  7e-10  348_[+4]_130
 553 MIT_Sbay_c84_6418                 3.6e-08  101_[+4]_201
 554 MIT_Smik_c283_5928                2.5e-07  105_[+4]_197
 555 --------------------------------------------------------------------------------
 556
 557 --------------------------------------------------------------------------------
 558         Motif 4 in BLOCKS format
 559 --------------------------------------------------------------------------------
 560 BL   MOTIF 4 width=20 seqs=9
 561 MIT_Spar_c117_4603       (  347) AAAAGCGCCCGCGGCCGCAG  1
 562 SGD_Scer_YDR232W         (  352) AAAAGCGCCCGCGGCCGCAG  1
 563 WashU_Skud_Contig2069.5  (  349) AAAAGCGTCCGCGGCCGCAG  1
 564 WashU_Sbay_Contig461.5   (  346) AAAAACGCCGGCGGGCGCAG  1
 565 MIT_Spar_c425_6072       (  109) AATACTCCGCGACTCCGAAG  1
 566 SGD_Scer_YER014W         (  110) AATACTCCGCGACTCCGAAG  1
 567 MIT_Smik_c228_4055       (  349) AAAAGCGCCCGCAAGCGCAG  1
 568 MIT_Sbay_c84_6418        (  102) TATACTCTGCGACTCCGAAA  1
 569 MIT_Smik_c283_5928       (  106) TTTAAATACGGACTCCGAAG  1
 570 //
 571
 572 --------------------------------------------------------------------------------
 573
 574 --------------------------------------------------------------------------------
 575         Motif 4 position-specific scoring matrix
 576 --------------------------------------------------------------------------------
 577 log-odds matrix: alength= 4 w= 20 n= 3607 bayes= 8.64305 E= 3.1e-016
 578    126   -982   -982    -55
 579    145   -982   -982   -154
 580     78   -982   -982     45
 581    162   -982   -982   -982
 582    -55     92    134   -982
 583   -154    166   -982      4
 584   -982     92    166   -154
 585   -154    192   -982    -55
 586   -982    192     92   -982
 587   -982    215     34   -982
 588   -982   -982    251   -982
 589     45    166   -982   -982
 590   -154    134    134   -982
 591   -154   -982    134     45
 592   -982    215     34   -982
 593   -982    251   -982   -982
 594   -982   -982    251   -982
 595     45    166   -982   -982
 596    162   -982   -982   -982
 597   -154   -982    234   -982
 598 --------------------------------------------------------------------------------
 599
 600 --------------------------------------------------------------------------------
 601         Motif 4 position-specific probability matrix
 602 --------------------------------------------------------------------------------
 603 letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 3.1e-016
 604  0.777778  0.000000  0.000000  0.222222
 605  0.888889  0.000000  0.000000  0.111111
 606  0.555556  0.000000  0.000000  0.444444
 607  1.000000  0.000000  0.000000  0.000000
 608  0.222222  0.333333  0.444444  0.000000
 609  0.111111  0.555556  0.000000  0.333333
 610  0.000000  0.333333  0.555556  0.111111
 611  0.111111  0.666667  0.000000  0.222222
 612  0.000000  0.666667  0.333333  0.000000
 613  0.000000  0.777778  0.222222  0.000000
 614  0.000000  0.000000  1.000000  0.000000
 615  0.444444  0.555556  0.000000  0.000000
 616  0.111111  0.444444  0.444444  0.000000
 617  0.111111  0.000000  0.444444  0.444444
 618  0.000000  0.777778  0.222222  0.000000
 619  0.000000  1.000000  0.000000  0.000000
 620  0.000000  0.000000  1.000000  0.000000
 621  0.444444  0.555556  0.000000  0.000000
 622  1.000000  0.000000  0.000000  0.000000
 623  0.111111  0.000000  0.888889  0.000000
 624 --------------------------------------------------------------------------------
 625
 626 --------------------------------------------------------------------------------
 627         Motif 4 regular expression
 628 --------------------------------------------------------------------------------
 629 [AT]A[AT]A[GCA][CT][GC][CT][CG][CG]G[CA][CG][GT][CG]CG[CA]AG
 630 --------------------------------------------------------------------------------
 631
 632
 633
 634
 635 Time  6.50 secs.
 636
 637 ********************************************************************************
 638
 639
 640 ********************************************************************************
 641 MOTIF  5        width =   17   sites =   9   llr = 139   E-value = 2.2e-007
 642 ********************************************************************************
 643 --------------------------------------------------------------------------------
 644         Motif 5 Description
 645 --------------------------------------------------------------------------------
 646 Simplified        A  79:::a3:a39::8:3a
 647 pos.-specific     C  ::79::::::::1:76:
 648 probability       G  :1:19:61:61a1211:
 649 matrix            T  3:3:1:19:1::8:2::
 650
 651          bits    2.5            *
 652                  2.3            *
 653                  2.0    **      *
 654                  1.8    **      *
 655 Information      1.5    ***  *  *    *
 656 content          1.3  ***** ** **    *
 657 (22.3 bits)      1.0  ***** ** ** ** *
 658                  0.8 *****************
 659                  0.5 *****************
 660                  0.3 *****************
 661                  0.0 -----------------
 662
 663 Multilevel           AACCGAGTAGAGTACCA
 664 consensus            T T   A  A   GTA
 665 sequence
 666
 667 --------------------------------------------------------------------------------
 668
 669 --------------------------------------------------------------------------------
 670         Motif 5 sites sorted by position p-value
 671 --------------------------------------------------------------------------------
 672 Sequence name            Strand  Start   P-value                  Site
 673 -------------            ------  ----- ---------            -----------------
 674 WashU_Skud_Contig2069.5      +    201  3.60e-11 AGCGCAACAC AACCGAGTAGAGTACCA GCAGACGGAG
 675 MIT_Smik_c228_4055           +    200  3.60e-11 GGTGCAACAC AACCGAGTAGAGTACCA GCTGACGGAA
 676 WashU_Sbay_Contig461.5       +    196  1.71e-09 GCAGGGTGCA AACCGATTAGAGTACCA GCAGACGAGA
 677 MIT_Spar_c117_4603           +    201  3.89e-09 TGCAACACAC AACCGAATAGAGTATCA GCTGACGGGA
 678 SGD_Scer_YDR232W             +    206  3.89e-09 TGCAACACAC AACCGAATAGAGTATCA GCTGACGGAA
 679 SGD_Scer_YER014W             -     28  4.70e-08 AATTCAAACA TATCGAGTAAAGTGCAA TTGAGAACGC
 680 MIT_Spar_c425_6072           -     28  3.05e-07 AATTCAATCC TATCGAGGAAGGTACAA TTGGGAACGC
 681 MIT_Sbay_c84_6418            -      9  1.50e-06 CGTAAGAAAC AGCGGAATAAAGGAGAA CTTCGACA
 682 MIT_Smik_c283_5928           -     30  1.85e-06 AGTTTAACCA TATCTAGTATAGCGCGA TTAAAGAAAT
 683 --------------------------------------------------------------------------------
 684
 685 --------------------------------------------------------------------------------
 686         Motif 5 block diagrams
 687 --------------------------------------------------------------------------------
 688 SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
 689 -------------            ----------------  -------------
 690 WashU_Skud_Contig2069.5           3.6e-11  200_[+5]_281
 691 MIT_Smik_c228_4055                3.6e-11  199_[+5]_282
 692 WashU_Sbay_Contig461.5            1.7e-09  195_[+5]_286
 693 MIT_Spar_c117_4603                3.9e-09  200_[+5]_281
 694 SGD_Scer_YDR232W                  3.9e-09  205_[+5]_276
 695 SGD_Scer_YER014W                  4.7e-08  27_[-5]_278
 696 MIT_Spar_c425_6072                  3e-07  27_[-5]_278
 697 MIT_Sbay_c84_6418                 1.5e-06  8_[-5]_297
 698 MIT_Smik_c283_5928                1.8e-06  29_[-5]_276
 699 --------------------------------------------------------------------------------
 700
 701 --------------------------------------------------------------------------------
 702         Motif 5 in BLOCKS format
 703 --------------------------------------------------------------------------------
 704 BL   MOTIF 5 width=17 seqs=9
 705 WashU_Skud_Contig2069.5  (  201) AACCGAGTAGAGTACCA  1
 706 MIT_Smik_c228_4055       (  200) AACCGAGTAGAGTACCA  1
 707 WashU_Sbay_Contig461.5   (  196) AACCGATTAGAGTACCA  1
 708 MIT_Spar_c117_4603       (  201) AACCGAATAGAGTATCA  1
 709 SGD_Scer_YDR232W         (  206) AACCGAATAGAGTATCA  1
 710 SGD_Scer_YER014W         (   28) TATCGAGTAAAGTGCAA  1
 711 MIT_Spar_c425_6072       (   28) TATCGAGGAAGGTACAA  1
 712 MIT_Sbay_c84_6418        (    9) AGCGGAATAAAGGAGAA  1
 713 MIT_Smik_c283_5928       (   30) TATCTAGTATAGCGCGA  1
 714 //
 715
 716 --------------------------------------------------------------------------------
 717
 718 --------------------------------------------------------------------------------
 719         Motif 5 position-specific scoring matrix
 720 --------------------------------------------------------------------------------
 721 log-odds matrix: alength= 4 w= 17 n= 3634 bayes= 8.65384 E= 2.2e-007
 722    104   -982   -982      4
 723    145   -982    -66   -982
 724   -982    192   -982      4
 725   -982    234    -66   -982
 726   -982   -982    234   -154
 727    162   -982   -982   -982
 728      4   -982    166   -154
 729   -982   -982    -66    145
 730    162   -982   -982   -982
 731      4   -982    166   -154
 732    145   -982    -66   -982
 733   -982   -982    251   -982
 734   -982    -66    -66    126
 735    126   -982     34   -982
 736   -982    192    -66    -55
 737      4    166    -66   -982
 738    162   -982   -982   -982
 739 --------------------------------------------------------------------------------
 740
 741 --------------------------------------------------------------------------------
 742         Motif 5 position-specific probability matrix
 743 --------------------------------------------------------------------------------
 744 letter-probability matrix: alength= 4 w= 17 nsites= 9 E= 2.2e-007
 745  0.666667  0.000000  0.000000  0.333333
 746  0.888889  0.000000  0.111111  0.000000
 747  0.000000  0.666667  0.000000  0.333333
 748  0.000000  0.888889  0.111111  0.000000
 749  0.000000  0.000000  0.888889  0.111111
 750  1.000000  0.000000  0.000000  0.000000
 751  0.333333  0.000000  0.555556  0.111111
 752  0.000000  0.000000  0.111111  0.888889
 753  1.000000  0.000000  0.000000  0.000000
 754  0.333333  0.000000  0.555556  0.111111
 755  0.888889  0.000000  0.111111  0.000000
 756  0.000000  0.000000  1.000000  0.000000
 757  0.000000  0.111111  0.111111  0.777778
 758  0.777778  0.000000  0.222222  0.000000
 759  0.000000  0.666667  0.111111  0.222222
 760  0.333333  0.555556  0.111111  0.000000
 761  1.000000  0.000000  0.000000  0.000000
 762 --------------------------------------------------------------------------------
 763
 764 --------------------------------------------------------------------------------
 765         Motif 5 regular expression
 766 --------------------------------------------------------------------------------
 767 [AT]A[CT]CGA[GA]TA[GA]AGT[AG][CT][CA]A
 768 --------------------------------------------------------------------------------
 769
 770
 771
 772
 773 Time  7.92 secs.
 774
 775 ********************************************************************************
 776
 777
 778 ********************************************************************************
 779 SUMMARY OF MOTIFS
 780 ********************************************************************************
 781
 782 --------------------------------------------------------------------------------
 783         Combined block diagrams: non-overlapping sites with p-value < 0.0001
 784 --------------------------------------------------------------------------------
 785 SEQUENCE NAME            COMBINED P-VALUE  MOTIF DIAGRAM
 786 -------------            ----------------  -------------
 787 SGD_Scer_YDR232W                 1.25e-37  165_[+2(6.31e-12)]_[+5(9.28e-05)]_5_[+5(3.89e-09)]_64_[+1(3.60e-13)]_45_[+4(3.34e-14)]_1_[+3(1.19e-13)]_106
 788 MIT_Spar_c117_4603               3.90e-36  160_[+2(2.27e-10)]_[+5(9.28e-05)]_5_[+5(3.89e-09)]_64_[+1(3.60e-13)]_45_[+4(3.34e-14)]_1_[+3(1.19e-13)]_111
 789 MIT_Smik_c228_4055               1.05e-29  161_[+2(3.13e-08)]_[+5(1.70e-05)]_3_[+5(3.60e-11)]_68_[+1(3.60e-13)]_44_[+4(6.96e-10)]_1_[+3(2.41e-11)]_109
 790 WashU_Skud_Contig2069.5          2.42e-35  162_[+2(6.31e-12)]_20_[+5(3.60e-11)]_67_[+1(9.69e-11)]_44_[+4(3.24e-12)]_1_[+3(1.19e-13)]_109
 791 WashU_Sbay_Contig461.5           1.93e-30  125_[+4(6.68e-05)]_16_[+2(2.27e-10)]_16_[+5(1.71e-09)]_67_[+1(3.60e-13)]_46_[+4(1.26e-10)]_1_[+3(6.46e-11)]_19_[+1(2.50e-06)]_73
 792 SGD_Scer_YER014W                 3.02e-22  27_[-5(4.70e-08)]_24_[-2(3.60e-08)]_23_[+4(6.37e-10)]_4_[+1(8.09e-10)]_12_[+3(5.94e-09)]_137
 793 MIT_Spar_c425_6072               1.04e-23  27_[-5(3.05e-07)]_24_[-2(6.85e-09)]_22_[+4(6.37e-10)]_4_[+1(2.98e-11)]_12_[+3(3.61e-09)]_138
 794 MIT_Smik_c283_5928               2.42e-20  29_[-5(1.85e-06)]_24_[-2(6.85e-09)]_17_[+4(2.54e-07)]_2_[+1(4.86e-11)]_12_[+3(3.61e-09)]_143
 795 MIT_Sbay_c84_6418                3.76e-20  8_[-5(1.50e-06)]_38_[-2(1.24e-08)]_20_[+4(3.58e-08)]_4_[+1(8.09e-10)]_15_[+3(1.68e-09)]_13_[-2(2.04e-05)]_111
 796 --------------------------------------------------------------------------------
 797
 798 ********************************************************************************
 799
 800
 801 ********************************************************************************
 802 Stopped because nmotifs = 5 reached.
 803 ********************************************************************************
 804
 805 CPU: dhn02990.mrc-dunn.cam.ac.uk
 806
 807 ********************************************************************************