t/data/map_hem/HEM1-HEM4.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-HEM4.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_YOR278W         1.0000    635
  38 MIT_Spar_c261_21317      1.0000    635  MIT_Smik_c492_20940      1.0000    635
  39 WashU_Skud_Contig1682.4  1.0000    635  WashU_Sbay_Contig635.57  1.0000    635
  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-HEM4.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=       10    maxsites=       10    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=            5665    N=              10
  59 strands: + -
  60 sample: seed=            0    seqfrac=         1
  61 Letter frequencies in dataset:
  62 A 0.298 C 0.202 G 0.202 T 0.298
  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 =  10   llr = 232   E-value = 3.1e-035
  70 ********************************************************************************
  71 --------------------------------------------------------------------------------
  72         Motif 1 Description
  73 --------------------------------------------------------------------------------
  74 Simplified        A  :5::16:5::55a::a9:1a
  75 pos.-specific     C  a45a::35:a:::aa:::::
  76 probability       G  :15:447:a:55::::1:9:
  77 matrix            T  ::::5::::::::::::a::
  78
  79          bits    2.5 *  *    **   **
  80                  2.3 *  *    **   **
  81                  2.0 *  *    **   **   *
  82                  1.8 *  *    **   **   *
  83 Information      1.5 * **  * **  **** ***
  84 content          1.3 * **  * **  ********
  85 (33.4 bits)      1.0 * ** ***************
  86                  0.8 **** ***************
  87                  0.5 ********************
  88                  0.3 ********************
  89                  0.0 --------------------
  90
  91 Multilevel           CACCTAGAGCAAACCAATGA
  92 consensus             CG GGCC  GG
  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_Skud_Contig2069.5      +    357  6.68e-12 CAAAAAGCGT CCGCGGCCGCAGACCAATGA GCGACGAAGG
 103 MIT_Spar_c117_4603           +    355  6.68e-12 CAAAAAGCGC CCGCGGCCGCAGACCAATGA GCGACGAAGG
 104 SGD_Scer_YDR232W             +    360  6.68e-12 CAAAAAGCGC CCGCGGCCGCAGACCAATGA GCGACGAAGG
 105 WashU_Sbay_Contig461.5       +    354  1.53e-11 AAAAAAACGC CGGCGGGCGCAGACCAATGA GCGACGAAGA
 106 WashU_Skud_Contig1682.4      +    231  1.78e-11 GAGATATGTA CACCTAGAGCGAACCAATGA TAATTTGTTT
 107 MIT_Spar_c261_21317          +    229  1.78e-11 TGAATATGTA CACCTAGAGCGAACCAATGA TAATTTGTTT
 108 SGD_Scer_YOR278W             +    225  1.78e-11 AAGATATGTA CACCTAGAGCGAACCAATGA TAATTTGTTT
 109 MIT_Smik_c228_4055           +    357  3.51e-11 CAAAAAGCGC CCGCAAGCGCAGACCAATGA GCGACGAAAG
 110 WashU_Sbay_Contig635.57      +    237  6.67e-11 AAAACATGTA CACCTAGAGCGAACCAGTGA TAATTTGCTT
 111 MIT_Smik_c492_20940          +    234  1.29e-10 AAGATATGTA CACCTAGAGCGAACCAATAA TAATTTGTTT
 112 --------------------------------------------------------------------------------
 113
 114 --------------------------------------------------------------------------------
 115         Motif 1 block diagrams
 116 --------------------------------------------------------------------------------
 117 SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
 118 -------------            ----------------  -------------
 119 WashU_Skud_Contig2069.5           6.7e-12  356_[+1]_122
 120 MIT_Spar_c117_4603                6.7e-12  354_[+1]_124
 121 SGD_Scer_YDR232W                  6.7e-12  359_[+1]_119
 122 WashU_Sbay_Contig461.5            1.5e-11  353_[+1]_125
 123 WashU_Skud_Contig1682.4           1.8e-11  230_[+1]_385
 124 MIT_Spar_c261_21317               1.8e-11  228_[+1]_387
 125 SGD_Scer_YOR278W                  1.8e-11  224_[+1]_391
 126 MIT_Smik_c228_4055                3.5e-11  356_[+1]_122
 127 WashU_Sbay_Contig635.57           6.7e-11  236_[+1]_379
 128 MIT_Smik_c492_20940               1.3e-10  233_[+1]_382
 129 --------------------------------------------------------------------------------
 130
 131 --------------------------------------------------------------------------------
 132         Motif 1 in BLOCKS format
 133 --------------------------------------------------------------------------------
 134 BL   MOTIF 1 width=20 seqs=10
 135 WashU_Skud_Contig2069.5  (  357) CCGCGGCCGCAGACCAATGA  1
 136 MIT_Spar_c117_4603       (  355) CCGCGGCCGCAGACCAATGA  1
 137 SGD_Scer_YDR232W         (  360) CCGCGGCCGCAGACCAATGA  1
 138 WashU_Sbay_Contig461.5   (  354) CGGCGGGCGCAGACCAATGA  1
 139 WashU_Skud_Contig1682.4  (  231) CACCTAGAGCGAACCAATGA  1
 140 MIT_Spar_c261_21317      (  229) CACCTAGAGCGAACCAATGA  1
 141 SGD_Scer_YOR278W         (  225) CACCTAGAGCGAACCAATGA  1
 142 MIT_Smik_c228_4055       (  357) CCGCAAGCGCAGACCAATGA  1
 143 WashU_Sbay_Contig635.57  (  237) CACCTAGAGCGAACCAGTGA  1
 144 MIT_Smik_c492_20940      (  234) CACCTAGAGCGAACCAATAA  1
 145 //
 146
 147 --------------------------------------------------------------------------------
 148
 149 --------------------------------------------------------------------------------
 150         Motif 1 position-specific scoring matrix
 151 --------------------------------------------------------------------------------
 152 log-odds matrix: alength= 4 w= 20 n= 5475 bayes= 9.09408 E= 3.1e-035
 153   -997    251   -997   -997
 154     62    119    -81   -997
 155   -997    151    151   -997
 156   -997    251   -997   -997
 157   -169   -997    119     62
 158     89   -997    119   -997
 159   -997     77    199   -997
 160     62    151   -997   -997
 161   -997   -997    251   -997
 162   -997    251   -997   -997
 163     62   -997    151   -997
 164     62   -997    151   -997
 165    162   -997   -997   -997
 166   -997    251   -997   -997
 167   -997    251   -997   -997
 168    162   -997   -997   -997
 169    147   -997    -81   -997
 170   -997   -997   -997    162
 171   -169   -997    236   -997
 172    162   -997   -997   -997
 173 --------------------------------------------------------------------------------
 174
 175 --------------------------------------------------------------------------------
 176         Motif 1 position-specific probability matrix
 177 --------------------------------------------------------------------------------
 178 letter-probability matrix: alength= 4 w= 20 nsites= 10 E= 3.1e-035
 179  0.000000  1.000000  0.000000  0.000000
 180  0.500000  0.400000  0.100000  0.000000
 181  0.000000  0.500000  0.500000  0.000000
 182  0.000000  1.000000  0.000000  0.000000
 183  0.100000  0.000000  0.400000  0.500000
 184  0.600000  0.000000  0.400000  0.000000
 185  0.000000  0.300000  0.700000  0.000000
 186  0.500000  0.500000  0.000000  0.000000
 187  0.000000  0.000000  1.000000  0.000000
 188  0.000000  1.000000  0.000000  0.000000
 189  0.500000  0.000000  0.500000  0.000000
 190  0.500000  0.000000  0.500000  0.000000
 191  1.000000  0.000000  0.000000  0.000000
 192  0.000000  1.000000  0.000000  0.000000
 193  0.000000  1.000000  0.000000  0.000000
 194  1.000000  0.000000  0.000000  0.000000
 195  0.900000  0.000000  0.100000  0.000000
 196  0.000000  0.000000  0.000000  1.000000
 197  0.100000  0.000000  0.900000  0.000000
 198  1.000000  0.000000  0.000000  0.000000
 199 --------------------------------------------------------------------------------
 200
 201 --------------------------------------------------------------------------------
 202         Motif 1 regular expression
 203 --------------------------------------------------------------------------------
 204 C[AC][CG]C[TG][AG][GC][AC]GC[AG][AG]ACCAATGA
 205 --------------------------------------------------------------------------------
 206
 207
 208
 209
 210 Time  3.49 secs.
 211
 212 ********************************************************************************
 213
 214
 215 ********************************************************************************
 216 MOTIF  2        width =   20   sites =  10   llr = 215   E-value = 5.3e-029
 217 ********************************************************************************
 218 --------------------------------------------------------------------------------
 219         Motif 2 Description
 220 --------------------------------------------------------------------------------
 221 Simplified        A  53::9a:a5:5::::a14:a
 222 pos.-specific     C  55:11::::a1:::::::::
 223 probability       G  :2a9::a:::4a::5:4:a:
 224 matrix            T  ::::::::5:::aa5:56::
 225
 226          bits    2.5   *   *  * *      *
 227                  2.3   *   *  * *      *
 228                  2.0   **  *  * *      *
 229                  1.8   **  *  * *      *
 230 Information      1.5   ** *** * *** *  **
 231 content          1.3   ****** * *** *  **
 232 (31.1 bits)      1.0 * ****** * *****  **
 233                  0.8 ******** ******* ***
 234                  0.5 ********************
 235                  0.3 ********************
 236                  0.0 --------------------
 237
 238 Multilevel           ACGGAAGAACAGTTGATTGA
 239 consensus            CA      T G   T GA
 240 sequence              G
 241
 242 --------------------------------------------------------------------------------
 243
 244 --------------------------------------------------------------------------------
 245         Motif 2 sites sorted by position p-value
 246 --------------------------------------------------------------------------------
 247 Sequence name            Strand  Start   P-value                    Site
 248 -------------            ------  ----- ---------            --------------------
 249 WashU_Sbay_Contig635.57      +    401  2.33e-11 GCATGGTAAT CCGGAAGATCAGTTTATTGA ATGATGGCTC
 250 WashU_Skud_Contig1682.4      +    394  2.33e-11 GCATGGTAAT CCGGAAGATCAGTTTATTGA ATGATGGTTC
 251 MIT_Smik_c492_20940          +    399  2.33e-11 GCATGGTAAT CCGGAAGATCAGTTTATTGA ATGATGGTTC
 252 MIT_Spar_c261_21317          +    393  2.33e-11 GCATGGTAAT CCGGAAGATCAGTTTATTGA ATGATGGTTC
 253 SGD_Scer_YOR278W             +    390  2.33e-11 GCATGGTAAT CCGGAAGATCAGTTTATTGA ATGATGGTTT
 254 WashU_Skud_Contig2069.5      +    160  7.63e-11 AACCGTGTGG AGGGAAGAACGGTTGAGAGA CAGCAGAGCA
 255 MIT_Spar_c117_4603           +    158  9.24e-11 AAGGCGTGTA AAGGAAGAACGGTTGAGAGA GAGCAGAGCA
 256 SGD_Scer_YDR232W             +    163  9.24e-11 AAGGCGTGTA AAGGAAGAACGGTTGAGAGA CAGCAGAGCA
 257 WashU_Sbay_Contig461.5       +    159  2.91e-10 GAGCGTGTGG AGGGAAGAACCGTTGAGAGA CAACAGAGCA
 258 MIT_Smik_c228_4055           +    159  1.25e-09 AGGACGTGTG AAGCCAGAACGGTTGAATGA CAGTAGAGGA
 259 --------------------------------------------------------------------------------
 260
 261 --------------------------------------------------------------------------------
 262         Motif 2 block diagrams
 263 --------------------------------------------------------------------------------
 264 SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
 265 -------------            ----------------  -------------
 266 WashU_Sbay_Contig635.57           2.3e-11  400_[+2]_215
 267 WashU_Skud_Contig1682.4           2.3e-11  393_[+2]_222
 268 MIT_Smik_c492_20940               2.3e-11  398_[+2]_217
 269 MIT_Spar_c261_21317               2.3e-11  392_[+2]_223
 270 SGD_Scer_YOR278W                  2.3e-11  389_[+2]_226
 271 WashU_Skud_Contig2069.5           7.6e-11  159_[+2]_319
 272 MIT_Spar_c117_4603                9.2e-11  157_[+2]_321
 273 SGD_Scer_YDR232W                  9.2e-11  162_[+2]_316
 274 WashU_Sbay_Contig461.5            2.9e-10  158_[+2]_320
 275 MIT_Smik_c228_4055                1.3e-09  158_[+2]_320
 276 --------------------------------------------------------------------------------
 277
 278 --------------------------------------------------------------------------------
 279         Motif 2 in BLOCKS format
 280 --------------------------------------------------------------------------------
 281 BL   MOTIF 2 width=20 seqs=10
 282 WashU_Sbay_Contig635.57  (  401) CCGGAAGATCAGTTTATTGA  1
 283 WashU_Skud_Contig1682.4  (  394) CCGGAAGATCAGTTTATTGA  1
 284 MIT_Smik_c492_20940      (  399) CCGGAAGATCAGTTTATTGA  1
 285 MIT_Spar_c261_21317      (  393) CCGGAAGATCAGTTTATTGA  1
 286 SGD_Scer_YOR278W         (  390) CCGGAAGATCAGTTTATTGA  1
 287 WashU_Skud_Contig2069.5  (  160) AGGGAAGAACGGTTGAGAGA  1
 288 MIT_Spar_c117_4603       (  158) AAGGAAGAACGGTTGAGAGA  1
 289 SGD_Scer_YDR232W         (  163) AAGGAAGAACGGTTGAGAGA  1
 290 WashU_Sbay_Contig461.5   (  159) AGGGAAGAACCGTTGAGAGA  1
 291 MIT_Smik_c228_4055       (  159) AAGCCAGAACGGTTGAATGA  1
 292 //
 293
 294 --------------------------------------------------------------------------------
 295
 296 --------------------------------------------------------------------------------
 297         Motif 2 position-specific scoring matrix
 298 --------------------------------------------------------------------------------
 299 log-odds matrix: alength= 4 w= 20 n= 5475 bayes= 9.09408 E= 5.3e-029
 300     62    151   -997   -997
 301    -11    151     19   -997
 302   -997   -997    251   -997
 303   -997    -81    236   -997
 304    147    -81   -997   -997
 305    162   -997   -997   -997
 306   -997   -997    251   -997
 307    162   -997   -997   -997
 308     62   -997   -997     62
 309   -997    251   -997   -997
 310     62    -81    119   -997
 311   -997   -997    251   -997
 312   -997   -997   -997    162
 313   -997   -997   -997    162
 314   -997   -997    151     62
 315    162   -997   -997   -997
 316   -169   -997    119     62
 317     30   -997   -997     89
 318   -997   -997    251   -997
 319    162   -997   -997   -997
 320 --------------------------------------------------------------------------------
 321
 322 --------------------------------------------------------------------------------
 323         Motif 2 position-specific probability matrix
 324 --------------------------------------------------------------------------------
 325 letter-probability matrix: alength= 4 w= 20 nsites= 10 E= 5.3e-029
 326  0.500000  0.500000  0.000000  0.000000
 327  0.300000  0.500000  0.200000  0.000000
 328  0.000000  0.000000  1.000000  0.000000
 329  0.000000  0.100000  0.900000  0.000000
 330  0.900000  0.100000  0.000000  0.000000
 331  1.000000  0.000000  0.000000  0.000000
 332  0.000000  0.000000  1.000000  0.000000
 333  1.000000  0.000000  0.000000  0.000000
 334  0.500000  0.000000  0.000000  0.500000
 335  0.000000  1.000000  0.000000  0.000000
 336  0.500000  0.100000  0.400000  0.000000
 337  0.000000  0.000000  1.000000  0.000000
 338  0.000000  0.000000  0.000000  1.000000
 339  0.000000  0.000000  0.000000  1.000000
 340  0.000000  0.000000  0.500000  0.500000
 341  1.000000  0.000000  0.000000  0.000000
 342  0.100000  0.000000  0.400000  0.500000
 343  0.400000  0.000000  0.000000  0.600000
 344  0.000000  0.000000  1.000000  0.000000
 345  1.000000  0.000000  0.000000  0.000000
 346 --------------------------------------------------------------------------------
 347
 348 --------------------------------------------------------------------------------
 349         Motif 2 regular expression
 350 --------------------------------------------------------------------------------
 351 [AC][CAG]GGAAGA[AT]C[AG]GTT[GT]A[TG][TA]GA
 352 --------------------------------------------------------------------------------
 353
 354
 355
 356
 357 Time  6.83 secs.
 358
 359 ********************************************************************************
 360
 361
 362 ********************************************************************************
 363 MOTIF  3        width =   20   sites =  10   llr = 212   E-value = 7.8e-027
 364 ********************************************************************************
 365 --------------------------------------------------------------------------------
 366         Motif 3 Description
 367 --------------------------------------------------------------------------------
 368 Simplified        A  ::::1:::::5:::::::4:
 369 pos.-specific     C  2:64:::aa::555:::a::
 370 probability       G  ::::9:::::55::::2:::
 371 matrix            T  8a46:aa::a::55aa8:6a
 372
 373          bits    2.5        **        *
 374                  2.3        **        *
 375                  2.0     *  **        *
 376                  1.8     *  **        *
 377 Information      1.5  *  ****** *  ** * *
 378 content          1.3  ** ****** *  ** * *
 379 (30.6 bits)      1.0 ****************** *
 380                  0.8 ********************
 381                  0.5 ********************
 382                  0.3 ********************
 383                  0.0 --------------------
 384
 385 Multilevel           TTCTGTTCCTACCCTTTCTT
 386 consensus            C TC      GGTT  G A
 387 sequence
 388
 389 --------------------------------------------------------------------------------
 390
 391 --------------------------------------------------------------------------------
 392         Motif 3 sites sorted by position p-value
 393 --------------------------------------------------------------------------------
 394 Sequence name            Strand  Start   P-value                    Site
 395 -------------            ------  ----- ---------            --------------------
 396 MIT_Smik_c228_4055           +    310  8.08e-12 AGATGAAAAT TTCCGTTCCTGCTCTTTCTT CATATATGAA
 397 SGD_Scer_YDR232W             +    313  8.08e-12 GATGAAAAAT TTCCGTTCCTGCTCTTTCTT CATATATGAA
 398 MIT_Spar_c117_4603           +    308  1.62e-11 GATGAAAAAT TTCTGTTCCTGCTCTTTCTT CATATATGAA
 399 WashU_Skud_Contig2069.5      +    311  6.03e-11 TGTGAAAAAT TTCCGTTCCTGCTCTTGCTT CATATATGAC
 400 MIT_Spar_c261_21317          -    302  1.25e-10 AGACCAATTT TTCTGTTCCTAGCTTTTCAT TATTGAAATC
 401 WashU_Sbay_Contig461.5       +    306  1.76e-10 GATGAAAAAT CTCCGTTCCTGCTCTTGCTT GATATATTAA
 402 MIT_Smik_c492_20940          -    307  3.70e-10 GACAAATTTC TTTTGTTCCTAGCTTTTCAT TATTGAAATC
 403 SGD_Scer_YOR278W             -    298  3.70e-10 GACCAATTTT TTTTGTTCCTAGCTTTTCAT TATTGAAATC
 404 WashU_Sbay_Contig635.57      -    310  4.68e-10 AGACCAATTT CTTTGTTCCTAGCTTTTCTT TAATGAAATC
 405 WashU_Skud_Contig1682.4      -    302  1.32e-09 GACCAATCTC TTTTATTCCTAGCTTTTCAT TATTGAAATC
 406 --------------------------------------------------------------------------------
 407
 408 --------------------------------------------------------------------------------
 409         Motif 3 block diagrams
 410 --------------------------------------------------------------------------------
 411 SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
 412 -------------            ----------------  -------------
 413 MIT_Smik_c228_4055                8.1e-12  309_[+3]_169
 414 SGD_Scer_YDR232W                  8.1e-12  312_[+3]_166
 415 MIT_Spar_c117_4603                1.6e-11  307_[+3]_171
 416 WashU_Skud_Contig2069.5             6e-11  310_[+3]_168
 417 MIT_Spar_c261_21317               1.2e-10  301_[-3]_314
 418 WashU_Sbay_Contig461.5            1.8e-10  305_[+3]_173
 419 MIT_Smik_c492_20940               3.7e-10  306_[-3]_309
 420 SGD_Scer_YOR278W                  3.7e-10  297_[-3]_318
 421 WashU_Sbay_Contig635.57           4.7e-10  309_[-3]_306
 422 WashU_Skud_Contig1682.4           1.3e-09  301_[-3]_314
 423 --------------------------------------------------------------------------------
 424
 425 --------------------------------------------------------------------------------
 426         Motif 3 in BLOCKS format
 427 --------------------------------------------------------------------------------
 428 BL   MOTIF 3 width=20 seqs=10
 429 MIT_Smik_c228_4055       (  310) TTCCGTTCCTGCTCTTTCTT  1
 430 SGD_Scer_YDR232W         (  313) TTCCGTTCCTGCTCTTTCTT  1
 431 MIT_Spar_c117_4603       (  308) TTCTGTTCCTGCTCTTTCTT  1
 432 WashU_Skud_Contig2069.5  (  311) TTCCGTTCCTGCTCTTGCTT  1
 433 MIT_Spar_c261_21317      (  302) TTCTGTTCCTAGCTTTTCAT  1
 434 WashU_Sbay_Contig461.5   (  306) CTCCGTTCCTGCTCTTGCTT  1
 435 MIT_Smik_c492_20940      (  307) TTTTGTTCCTAGCTTTTCAT  1
 436 SGD_Scer_YOR278W         (  298) TTTTGTTCCTAGCTTTTCAT  1
 437 WashU_Sbay_Contig635.57  (  310) CTTTGTTCCTAGCTTTTCTT  1
 438 WashU_Skud_Contig1682.4  (  302) TTTTATTCCTAGCTTTTCAT  1
 439 //
 440
 441 --------------------------------------------------------------------------------
 442
 443 --------------------------------------------------------------------------------
 444         Motif 3 position-specific scoring matrix
 445 --------------------------------------------------------------------------------
 446 log-odds matrix: alength= 4 w= 20 n= 5475 bayes= 9.09408 E= 7.8e-027
 447   -997     19   -997    130
 448   -997   -997   -997    162
 449   -997    177   -997     30
 450   -997    119   -997     89
 451   -169   -997    236   -997
 452   -997   -997   -997    162
 453   -997   -997   -997    162
 454   -997    251   -997   -997
 455   -997    251   -997   -997
 456   -997   -997   -997    162
 457     62   -997    151   -997
 458   -997    151    151   -997
 459   -997    151   -997     62
 460   -997    151   -997     62
 461   -997   -997   -997    162
 462   -997   -997   -997    162
 463   -997   -997     19    130
 464   -997    251   -997   -997
 465     30   -997   -997     89
 466   -997   -997   -997    162
 467 --------------------------------------------------------------------------------
 468
 469 --------------------------------------------------------------------------------
 470         Motif 3 position-specific probability matrix
 471 --------------------------------------------------------------------------------
 472 letter-probability matrix: alength= 4 w= 20 nsites= 10 E= 7.8e-027
 473  0.000000  0.200000  0.000000  0.800000
 474  0.000000  0.000000  0.000000  1.000000
 475  0.000000  0.600000  0.000000  0.400000
 476  0.000000  0.400000  0.000000  0.600000
 477  0.100000  0.000000  0.900000  0.000000
 478  0.000000  0.000000  0.000000  1.000000
 479  0.000000  0.000000  0.000000  1.000000
 480  0.000000  1.000000  0.000000  0.000000
 481  0.000000  1.000000  0.000000  0.000000
 482  0.000000  0.000000  0.000000  1.000000
 483  0.500000  0.000000  0.500000  0.000000
 484  0.000000  0.500000  0.500000  0.000000
 485  0.000000  0.500000  0.000000  0.500000
 486  0.000000  0.500000  0.000000  0.500000
 487  0.000000  0.000000  0.000000  1.000000
 488  0.000000  0.000000  0.000000  1.000000
 489  0.000000  0.000000  0.200000  0.800000
 490  0.000000  1.000000  0.000000  0.000000
 491  0.400000  0.000000  0.000000  0.600000
 492  0.000000  0.000000  0.000000  1.000000
 493 --------------------------------------------------------------------------------
 494
 495 --------------------------------------------------------------------------------
 496         Motif 3 regular expression
 497 --------------------------------------------------------------------------------
 498 [TC]T[CT][TC]GTTCCT[AG][CG][CT][CT]TT[TG]C[TA]T
 499 --------------------------------------------------------------------------------
 500
 501
 502
 503
 504 Time 10.06 secs.
 505
 506 ********************************************************************************
 507
 508
 509 ********************************************************************************
 510 MOTIF  4        width =   20   sites =  10   llr = 206   E-value = 2.2e-024
 511 ********************************************************************************
 512 --------------------------------------------------------------------------------
 513         Motif 4 Description
 514 --------------------------------------------------------------------------------
 515 Simplified        A  :11::::5:::::a5::955
 516 pos.-specific     C  :::::5:2a::aa::aa:::
 517 probability       G  :365::::::::::5:::::
 518 matrix            T  a635a5a3:aa::::::155
 519
 520          bits    2.5         *  **  **
 521                  2.3         *  **  **
 522                  2.0         *  **  **
 523                  1.8         *  **  **
 524 Information      1.5 *   * * ****** **
 525 content          1.3 *   * * ****** ***
 526 (29.7 bits)      1.0 *  **** **********
 527                  0.8 * ***** **********
 528                  0.5 ******* ************
 529                  0.3 ********************
 530                  0.0 --------------------
 531
 532 Multilevel           TTGGTCTACTTCCAACCAAA
 533 consensus             GTT T T      G   TT
 534 sequence                    C
 535
 536 --------------------------------------------------------------------------------
 537
 538 --------------------------------------------------------------------------------
 539         Motif 4 sites sorted by position p-value
 540 --------------------------------------------------------------------------------
 541 Sequence name            Strand  Start   P-value                    Site
 542 -------------            ------  ----- ---------            --------------------
 543 WashU_Sbay_Contig635.57      +    333  2.66e-12 AACAAAGAAA TTGGTCTACTTCCAGCCATT TGCGCTTGAC
 544 WashU_Skud_Contig1682.4      +    326  2.66e-12 ATAAAAGAGA TTGGTCTACTTCCAGCCATT TGCGCTTTAC
 545 MIT_Spar_c261_21317          +    325  2.66e-12 AACAGAAAAA TTGGTCTACTTCCAGCCATT TGCGCTTTAT
 546 SGD_Scer_YOR278W             +    322  2.66e-12 ACAAAAAAAA TTGGTCTACTTCCAGCCATT TGCGCTTTAT
 547 MIT_Smik_c492_20940          +    331  1.15e-10 ACAAAAGAAA TTTGTCTACTTCCAGCCATT TGCGCTTTAT
 548 MIT_Spar_c117_4603           +     56  2.75e-10 CTAGCTCTAT TTGTTTTCCTTCCAACCAAA CTTATATGGG
 549 WashU_Sbay_Contig461.5       +     54  1.18e-09 TAGCTTTATT TGTTTTTTCTTCCAACCAAA CTTATATGGA
 550 SGD_Scer_YDR232W             +     58  1.27e-09 CTAGCTCTAT TAGTTTTCCTTCCAACCAAA CTTATATGGG
 551 WashU_Skud_Contig2069.5      +     59  2.01e-09 TAGCTCTATT TGATTTTTCTTCCAACCAAA CTTATATGGA
 552 MIT_Smik_c228_4055           +     58  2.84e-09 CAGCTTTGTT TGTTTTTTCTTCCAACCTAA CTTATATGGG
 553 --------------------------------------------------------------------------------
 554
 555 --------------------------------------------------------------------------------
 556         Motif 4 block diagrams
 557 --------------------------------------------------------------------------------
 558 SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
 559 -------------            ----------------  -------------
 560 WashU_Sbay_Contig635.57           2.7e-12  332_[+4]_283
 561 WashU_Skud_Contig1682.4           2.7e-12  325_[+4]_290
 562 MIT_Spar_c261_21317               2.7e-12  324_[+4]_291
 563 SGD_Scer_YOR278W                  2.7e-12  321_[+4]_294
 564 MIT_Smik_c492_20940               1.1e-10  330_[+4]_285
 565 MIT_Spar_c117_4603                2.7e-10  55_[+4]_423
 566 WashU_Sbay_Contig461.5            1.2e-09  53_[+4]_425
 567 SGD_Scer_YDR232W                  1.3e-09  57_[+4]_421
 568 WashU_Skud_Contig2069.5             2e-09  58_[+4]_420
 569 MIT_Smik_c228_4055                2.8e-09  57_[+4]_421
 570 --------------------------------------------------------------------------------
 571
 572 --------------------------------------------------------------------------------
 573         Motif 4 in BLOCKS format
 574 --------------------------------------------------------------------------------
 575 BL   MOTIF 4 width=20 seqs=10
 576 WashU_Sbay_Contig635.57  (  333) TTGGTCTACTTCCAGCCATT  1
 577 WashU_Skud_Contig1682.4  (  326) TTGGTCTACTTCCAGCCATT  1
 578 MIT_Spar_c261_21317      (  325) TTGGTCTACTTCCAGCCATT  1
 579 SGD_Scer_YOR278W         (  322) TTGGTCTACTTCCAGCCATT  1
 580 MIT_Smik_c492_20940      (  331) TTTGTCTACTTCCAGCCATT  1
 581 MIT_Spar_c117_4603       (   56) TTGTTTTCCTTCCAACCAAA  1
 582 WashU_Sbay_Contig461.5   (   54) TGTTTTTTCTTCCAACCAAA  1
 583 SGD_Scer_YDR232W         (   58) TAGTTTTCCTTCCAACCAAA  1
 584 WashU_Skud_Contig2069.5  (   59) TGATTTTTCTTCCAACCAAA  1
 585 MIT_Smik_c228_4055       (   58) TGTTTTTTCTTCCAACCTAA  1
 586 //
 587
 588 --------------------------------------------------------------------------------
 589
 590 --------------------------------------------------------------------------------
 591         Motif 4 position-specific scoring matrix
 592 --------------------------------------------------------------------------------
 593 log-odds matrix: alength= 4 w= 20 n= 5475 bayes= 9.09408 E= 2.2e-024
 594   -997   -997   -997    162
 595   -169   -997     77     89
 596   -169   -997    177    -11
 597   -997   -997    151     62
 598   -997   -997   -997    162
 599   -997    151   -997     62
 600   -997   -997   -997    162
 601     62     19   -997    -11
 602   -997    251   -997   -997
 603   -997   -997   -997    162
 604   -997   -997   -997    162
 605   -997    251   -997   -997
 606   -997    251   -997   -997
 607    162   -997   -997   -997
 608     62   -997    151   -997
 609   -997    251   -997   -997
 610   -997    251   -997   -997
 611    147   -997   -997   -169
 612     62   -997   -997     62
 613     62   -997   -997     62
 614 --------------------------------------------------------------------------------
 615
 616 --------------------------------------------------------------------------------
 617         Motif 4 position-specific probability matrix
 618 --------------------------------------------------------------------------------
 619 letter-probability matrix: alength= 4 w= 20 nsites= 10 E= 2.2e-024
 620  0.000000  0.000000  0.000000  1.000000
 621  0.100000  0.000000  0.300000  0.600000
 622  0.100000  0.000000  0.600000  0.300000
 623  0.000000  0.000000  0.500000  0.500000
 624  0.000000  0.000000  0.000000  1.000000
 625  0.000000  0.500000  0.000000  0.500000
 626  0.000000  0.000000  0.000000  1.000000
 627  0.500000  0.200000  0.000000  0.300000
 628  0.000000  1.000000  0.000000  0.000000
 629  0.000000  0.000000  0.000000  1.000000
 630  0.000000  0.000000  0.000000  1.000000
 631  0.000000  1.000000  0.000000  0.000000
 632  0.000000  1.000000  0.000000  0.000000
 633  1.000000  0.000000  0.000000  0.000000
 634  0.500000  0.000000  0.500000  0.000000
 635  0.000000  1.000000  0.000000  0.000000
 636  0.000000  1.000000  0.000000  0.000000
 637  0.900000  0.000000  0.000000  0.100000
 638  0.500000  0.000000  0.000000  0.500000
 639  0.500000  0.000000  0.000000  0.500000
 640 --------------------------------------------------------------------------------
 641
 642 --------------------------------------------------------------------------------
 643         Motif 4 regular expression
 644 --------------------------------------------------------------------------------
 645 T[TG][GT][GT]T[CT]T[ATC]CTTCCA[AG]CCA[AT][AT]
 646 --------------------------------------------------------------------------------
 647
 648
 649
 650
 651 Time 13.18 secs.
 652
 653 ********************************************************************************
 654
 655
 656 ********************************************************************************
 657 MOTIF  5        width =   20   sites =  10   llr = 216   E-value = 2.6e-029
 658 ********************************************************************************
 659 --------------------------------------------------------------------------------
 660         Motif 5 Description
 661 --------------------------------------------------------------------------------
 662 Simplified        A  :5::6::::::56::a::::
 663 pos.-specific     C  9::5::14a::144a:::::
 664 probability       G  :5:5:19::::4:6:::6a:
 665 matrix            T  1:a:49:6:aa:::::a4:a
 666
 667          bits    2.5         *     *   *
 668                  2.3         *     *   *
 669                  2.0 *     * *     *   *
 670                  1.8 *     * *     *   *
 671 Information      1.5 * **  * ***  **** **
 672 content          1.3 * ** ** ***  *******
 673 (31.2 bits)      1.0 **** ****** ********
 674                  0.8 ********************
 675                  0.5 ********************
 676                  0.3 ********************
 677                  0.0 --------------------
 678
 679 Multilevel           CATCATGTCTTAAGCATGGT
 680 consensus             G GT  C   GCC   T
 681 sequence
 682
 683 --------------------------------------------------------------------------------
 684
 685 --------------------------------------------------------------------------------
 686         Motif 5 sites sorted by position p-value
 687 --------------------------------------------------------------------------------
 688 Sequence name            Strand  Start   P-value                    Site
 689 -------------            ------  ----- ---------            --------------------
 690 WashU_Sbay_Contig635.57      +    378  7.23e-12 CATATGGAGG CGTGATGTCTTAAGCATGGT AATCCGGAAG
 691 WashU_Skud_Contig1682.4      +    371  7.23e-12 CATATGGAGG CGTGATGTCTTAAGCATGGT AATCCGGAAG
 692 MIT_Smik_c492_20940          +    376  7.23e-12 CATATGGAGG CGTGATGTCTTAAGCATGGT AATCCGGAAG
 693 MIT_Spar_c261_21317          +    370  7.23e-12 CATATGGAGG CGTGATGTCTTAAGCATGGT AATCCGGAAG
 694 SGD_Scer_YOR278W             +    367  7.23e-12 CATATGGAGG CGTGATGTCTTAAGCATGGT AATCCGGAAG
 695 WashU_Sbay_Contig461.5       -    280  1.38e-10 GGAGATTTTT CATCTTGCCTTGCCCATTGT TCTGTCCCGG
 696 MIT_Smik_c228_4055           -    285  1.38e-10 CGGAAATTTT CATCTTGCCTTGCCCATTGT TCTAATTCAA
 697 MIT_Spar_c117_4603           -    282  1.38e-10 AGAAATTTTT CATCTTGCCTTGCCCATTGT TCTGACCCAT
 698 SGD_Scer_YDR232W             -    287  1.38e-10 GGAAATTTTT CATCTTGCCTTGCCCATTGT TCTGATCCAT
 699 WashU_Skud_Contig2069.5      +    457  2.43e-09 GGCACCACTA TATCAGCTCTTCAGCATGGT AGGCCATTAC
 700 --------------------------------------------------------------------------------
 701
 702 --------------------------------------------------------------------------------
 703         Motif 5 block diagrams
 704 --------------------------------------------------------------------------------
 705 SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
 706 -------------            ----------------  -------------
 707 WashU_Sbay_Contig635.57           7.2e-12  377_[+5]_238
 708 WashU_Skud_Contig1682.4           7.2e-12  370_[+5]_245
 709 MIT_Smik_c492_20940               7.2e-12  375_[+5]_240
 710 MIT_Spar_c261_21317               7.2e-12  369_[+5]_246
 711 SGD_Scer_YOR278W                  7.2e-12  366_[+5]_249
 712 WashU_Sbay_Contig461.5            1.4e-10  279_[-5]_199
 713 MIT_Smik_c228_4055                1.4e-10  284_[-5]_194
 714 MIT_Spar_c117_4603                1.4e-10  281_[-5]_197
 715 SGD_Scer_YDR232W                  1.4e-10  286_[-5]_192
 716 WashU_Skud_Contig2069.5           2.4e-09  456_[+5]_22
 717 --------------------------------------------------------------------------------
 718
 719 --------------------------------------------------------------------------------
 720         Motif 5 in BLOCKS format
 721 --------------------------------------------------------------------------------
 722 BL   MOTIF 5 width=20 seqs=10
 723 WashU_Sbay_Contig635.57  (  378) CGTGATGTCTTAAGCATGGT  1
 724 WashU_Skud_Contig1682.4  (  371) CGTGATGTCTTAAGCATGGT  1
 725 MIT_Smik_c492_20940      (  376) CGTGATGTCTTAAGCATGGT  1
 726 MIT_Spar_c261_21317      (  370) CGTGATGTCTTAAGCATGGT  1
 727 SGD_Scer_YOR278W         (  367) CGTGATGTCTTAAGCATGGT  1
 728 WashU_Sbay_Contig461.5   (  280) CATCTTGCCTTGCCCATTGT  1
 729 MIT_Smik_c228_4055       (  285) CATCTTGCCTTGCCCATTGT  1
 730 MIT_Spar_c117_4603       (  282) CATCTTGCCTTGCCCATTGT  1
 731 SGD_Scer_YDR232W         (  287) CATCTTGCCTTGCCCATTGT  1
 732 WashU_Skud_Contig2069.5  (  457) TATCAGCTCTTCAGCATGGT  1
 733 //
 734
 735 --------------------------------------------------------------------------------
 736
 737 --------------------------------------------------------------------------------
 738         Motif 5 position-specific scoring matrix
 739 --------------------------------------------------------------------------------
 740 log-odds matrix: alength= 4 w= 20 n= 5475 bayes= 9.09408 E= 2.6e-029
 741   -997    236   -997   -169
 742     62   -997    151   -997
 743   -997   -997   -997    162
 744   -997    151    151   -997
 745     89   -997   -997     30
 746   -997   -997    -81    147
 747   -997    -81    236   -997
 748   -997    119   -997     89
 749   -997    251   -997   -997
 750   -997   -997   -997    162
 751   -997   -997   -997    162
 752     62    -81    119   -997
 753     89    119   -997   -997
 754   -997    119    177   -997
 755   -997    251   -997   -997
 756    162   -997   -997   -997
 757   -997   -997   -997    162
 758   -997   -997    177     30
 759   -997   -997    251   -997
 760   -997   -997   -997    162
 761 --------------------------------------------------------------------------------
 762
 763 --------------------------------------------------------------------------------
 764         Motif 5 position-specific probability matrix
 765 --------------------------------------------------------------------------------
 766 letter-probability matrix: alength= 4 w= 20 nsites= 10 E= 2.6e-029
 767  0.000000  0.900000  0.000000  0.100000
 768  0.500000  0.000000  0.500000  0.000000
 769  0.000000  0.000000  0.000000  1.000000
 770  0.000000  0.500000  0.500000  0.000000
 771  0.600000  0.000000  0.000000  0.400000
 772  0.000000  0.000000  0.100000  0.900000
 773  0.000000  0.100000  0.900000  0.000000
 774  0.000000  0.400000  0.000000  0.600000
 775  0.000000  1.000000  0.000000  0.000000
 776  0.000000  0.000000  0.000000  1.000000
 777  0.000000  0.000000  0.000000  1.000000
 778  0.500000  0.100000  0.400000  0.000000
 779  0.600000  0.400000  0.000000  0.000000
 780  0.000000  0.400000  0.600000  0.000000
 781  0.000000  1.000000  0.000000  0.000000
 782  1.000000  0.000000  0.000000  0.000000
 783  0.000000  0.000000  0.000000  1.000000
 784  0.000000  0.000000  0.600000  0.400000
 785  0.000000  0.000000  1.000000  0.000000
 786  0.000000  0.000000  0.000000  1.000000
 787 --------------------------------------------------------------------------------
 788
 789 --------------------------------------------------------------------------------
 790         Motif 5 regular expression
 791 --------------------------------------------------------------------------------
 792 C[AG]T[CG][AT]TG[TC]CTT[AG][AC][GC]CAT[GT]GT
 793 --------------------------------------------------------------------------------
 794
 795
 796
 797
 798 Time 16.24 secs.
 799
 800 ********************************************************************************
 801
 802
 803 ********************************************************************************
 804 SUMMARY OF MOTIFS
 805 ********************************************************************************
 806
 807 --------------------------------------------------------------------------------
 808         Combined block diagrams: non-overlapping sites with p-value < 0.0001
 809 --------------------------------------------------------------------------------
 810 SEQUENCE NAME            COMBINED P-VALUE  MOTIF DIAGRAM
 811 -------------            ----------------  -------------
 812 SGD_Scer_YDR232W                 1.48e-30  57_[+4(1.27e-09)]_29_[-3(6.67e-05)]_36_[+2(9.24e-11)]_104_[-5(1.38e-10)]_6_[+3(8.08e-12)]_27_[+1(6.68e-12)]_119
 813 MIT_Spar_c117_4603               6.70e-31  55_[+4(2.75e-10)]_30_[-3(3.93e-05)]_32_[+2(9.24e-11)]_104_[-5(1.38e-10)]_6_[+3(1.62e-11)]_27_[+1(6.68e-12)]_124
 814 MIT_Smik_c228_4055               1.84e-28  57_[+4(2.84e-09)]_30_[-3(3.93e-05)]_31_[+2(1.25e-09)]_106_[-5(1.38e-10)]_5_[+3(8.08e-12)]_27_[+1(3.51e-11)]_122
 815 WashU_Skud_Contig2069.5          1.98e-28  58_[+4(2.01e-09)]_30_[-3(3.79e-05)]_31_[+2(7.63e-11)]_105_[-5(1.61e-07)]_6_[+3(6.03e-11)]_26_[+1(6.68e-12)]_80_[+5(2.43e-09)]_22
 816 WashU_Sbay_Contig461.5           1.68e-28  53_[+4(1.18e-09)]_10_[-3(5.72e-06)]_3_[-3(3.63e-05)]_32_[+2(2.91e-10)]_6_[+1(9.53e-05)]_75_[-5(1.38e-10)]_6_[+3(1.76e-10)]_28_[+1(1.53e-11)]_125
 817 SGD_Scer_YOR278W                 2.15e-32  224_[+1(1.78e-11)]_53_[-3(3.70e-10)]_4_[+4(2.66e-12)]_25_[+5(7.23e-12)]_3_[+2(2.33e-11)]_226
 818 MIT_Spar_c261_21317              7.63e-33  228_[+1(1.78e-11)]_53_[-3(1.25e-10)]_3_[+4(2.66e-12)]_25_[+5(7.23e-12)]_3_[+2(2.33e-11)]_223
 819 MIT_Smik_c492_20940              5.17e-30  62_[-4(6.56e-06)]_151_[+1(1.29e-10)]_53_[-3(3.70e-10)]_4_[+4(1.15e-10)]_25_[+5(7.23e-12)]_3_[+2(2.33e-11)]_217
 820 WashU_Skud_Contig1682.4          7.25e-32  89_[-4(8.96e-05)]_121_[+1(1.78e-11)]_51_[-3(1.32e-09)]_4_[+4(2.66e-12)]_25_[+5(7.23e-12)]_3_[+2(2.33e-11)]_141_[+1(3.09e-05)]_61
 821 WashU_Sbay_Contig635.57          9.51e-32  188_[-3(5.84e-05)]_28_[+1(6.67e-11)]_53_[-3(4.68e-10)]_3_[+4(2.66e-12)]_25_[+5(7.23e-12)]_3_[+2(2.33e-11)]_215
 822 --------------------------------------------------------------------------------
 823
 824 ********************************************************************************
 825
 826
 827 ********************************************************************************
 828 Stopped because nmotifs = 5 reached.
 829 ********************************************************************************
 830
 831 CPU: dhn02990.mrc-dunn.cam.ac.uk
 832
 833 ********************************************************************************