t/data/map_hem/HEM1-HEM13.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-HEM13.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_YDR044W         1.0000   1000
  38 MIT_Spar_c130_3912       1.0000   1000  MIT_Sbay_c896_21290      1.0000   1000
  39 WashU_Smik_Contig2283.3  1.0000   1000
  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-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
  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=            6490    N=               9
  59 strands: + -
  60 sample: seed=            0    seqfrac=         1
  61 Letter frequencies in dataset:
  62 A 0.288 C 0.212 G 0.212 T 0.288
  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 = 215   E-value = 3.2e-031
  70 ********************************************************************************
  71 --------------------------------------------------------------------------------
  72         Motif 1 Description
  73 --------------------------------------------------------------------------------
  74 Simplified        A  9:aa:aa:::2:aa4:1aa1
  75 pos.-specific     C  ::::a::::::9::::9:::
  76 probability       G  1a::::::aa7:::67:::8
  77 matrix            T  :::::::a::11:::3:::1
  78
  79          bits    2.5  *  *   **
  80                  2.3  *  *   **
  81                  2.0  *  *   ** *    *
  82                  1.8  *  *   ** *    *
  83 Information      1.5  ********* ***  ***
  84 content          1.3 ********** *** *****
  85 (34.4 bits)      1.0 ********************
  86                  0.8 ********************
  87                  0.5 ********************
  88                  0.3 ********************
  89                  0.0 --------------------
  90
  91 Multilevel           AGAACAATGGGCAAGGCAAG
  92 consensus                      A   AT
  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       +    277  3.60e-13 GCACCGGGAC AGAACAATGGGCAAGGCAAG ATGAAAAATC
 103 MIT_Smik_c228_4055           +    282  3.60e-13 ACATTGAATT AGAACAATGGGCAAGGCAAG ATGAAAATTT
 104 MIT_Spar_c117_4603           +    279  3.60e-13 CGCATGGGTC AGAACAATGGGCAAGGCAAG ATGAAAAATT
 105 SGD_Scer_YDR232W             +    284  3.60e-13 CGCATGGATC AGAACAATGGGCAAGGCAAG ATGAAAAATT
 106 SGD_Scer_YDR044W             +    175  1.02e-12 TTTCGAAACG AGAACAATGGGCAAAGCAAG CTTTATCTTC
 107 MIT_Spar_c130_3912           +    171  2.37e-11 TTTCGAAACG AGAACAATGGACAAATCAAG CTTTATCTAT
 108 WashU_Skud_Contig2069.5      +    282  2.76e-11 ACACTGGATC GGAACAATGGGCAAGGCAAT GTGAAAAATT
 109 WashU_Smik_Contig2283.3      +    167  1.95e-10 TTTCAAAAAG AGAACAATGGTCAAATAAAG GTTTATCTAC
 110 MIT_Sbay_c896_21290          +    177  4.52e-10 TCTCGAAGGG AGAACAATGGATAAATCAAA GCTTATCTAC
 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  276_[+1]_202
 119 MIT_Smik_c228_4055                3.6e-13  281_[+1]_197
 120 MIT_Spar_c117_4603                3.6e-13  278_[+1]_200
 121 SGD_Scer_YDR232W                  3.6e-13  283_[+1]_195
 122 SGD_Scer_YDR044W                    1e-12  174_[+1]_806
 123 MIT_Spar_c130_3912                2.4e-11  170_[+1]_810
 124 WashU_Skud_Contig2069.5           2.8e-11  281_[+1]_197
 125 WashU_Smik_Contig2283.3             2e-10  166_[+1]_814
 126 MIT_Sbay_c896_21290               4.5e-10  176_[+1]_804
 127 --------------------------------------------------------------------------------
 128
 129 --------------------------------------------------------------------------------
 130         Motif 1 in BLOCKS format
 131 --------------------------------------------------------------------------------
 132 BL   MOTIF 1 width=20 seqs=9
 133 WashU_Sbay_Contig461.5   (  277) AGAACAATGGGCAAGGCAAG  1
 134 MIT_Smik_c228_4055       (  282) AGAACAATGGGCAAGGCAAG  1
 135 MIT_Spar_c117_4603       (  279) AGAACAATGGGCAAGGCAAG  1
 136 SGD_Scer_YDR232W         (  284) AGAACAATGGGCAAGGCAAG  1
 137 SGD_Scer_YDR044W         (  175) AGAACAATGGGCAAAGCAAG  1
 138 MIT_Spar_c130_3912       (  171) AGAACAATGGACAAATCAAG  1
 139 WashU_Skud_Contig2069.5  (  282) GGAACAATGGGCAAGGCAAT  1
 140 WashU_Smik_Contig2283.3  (  167) AGAACAATGGTCAAATAAAG  1
 141 MIT_Sbay_c896_21290      (  177) AGAACAATGGATAAATCAAA  1
 142 //
 143
 144 --------------------------------------------------------------------------------
 145
 146 --------------------------------------------------------------------------------
 147         Motif 1 position-specific scoring matrix
 148 --------------------------------------------------------------------------------
 149 log-odds matrix: alength= 4 w= 20 n= 6319 bayes= 9.4535 E= 3.2e-031
 150    145   -982    -66   -982
 151   -982   -982    251   -982
 152    162   -982   -982   -982
 153    162   -982   -982   -982
 154   -982    251   -982   -982
 155    162   -982   -982   -982
 156    162   -982   -982   -982
 157   -982   -982   -982    162
 158   -982   -982    251   -982
 159   -982   -982    251   -982
 160    -55   -982    192   -154
 161   -982    234   -982   -154
 162    162   -982   -982   -982
 163    162   -982   -982   -982
 164     45   -982    166   -982
 165   -982   -982    192      4
 166   -154    234   -982   -982
 167    162   -982   -982   -982
 168    162   -982   -982   -982
 169   -154   -982    215   -154
 170 --------------------------------------------------------------------------------
 171
 172 --------------------------------------------------------------------------------
 173         Motif 1 position-specific probability matrix
 174 --------------------------------------------------------------------------------
 175 letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 3.2e-031
 176  0.888889  0.000000  0.111111  0.000000
 177  0.000000  0.000000  1.000000  0.000000
 178  1.000000  0.000000  0.000000  0.000000
 179  1.000000  0.000000  0.000000  0.000000
 180  0.000000  1.000000  0.000000  0.000000
 181  1.000000  0.000000  0.000000  0.000000
 182  1.000000  0.000000  0.000000  0.000000
 183  0.000000  0.000000  0.000000  1.000000
 184  0.000000  0.000000  1.000000  0.000000
 185  0.000000  0.000000  1.000000  0.000000
 186  0.222222  0.000000  0.666667  0.111111
 187  0.000000  0.888889  0.000000  0.111111
 188  1.000000  0.000000  0.000000  0.000000
 189  1.000000  0.000000  0.000000  0.000000
 190  0.444444  0.000000  0.555556  0.000000
 191  0.000000  0.000000  0.666667  0.333333
 192  0.111111  0.888889  0.000000  0.000000
 193  1.000000  0.000000  0.000000  0.000000
 194  1.000000  0.000000  0.000000  0.000000
 195  0.111111  0.000000  0.777778  0.111111
 196 --------------------------------------------------------------------------------
 197
 198 --------------------------------------------------------------------------------
 199         Motif 1 regular expression
 200 --------------------------------------------------------------------------------
 201 AGAACAATGG[GA]CAA[GA][GT]CAAG
 202 --------------------------------------------------------------------------------
 203
 204
 205
 206
 207 Time  4.41 secs.
 208
 209 ********************************************************************************
 210
 211
 212 ********************************************************************************
 213 MOTIF  2        width =   20   sites =   9   llr = 209   E-value = 1.2e-028
 214 ********************************************************************************
 215 --------------------------------------------------------------------------------
 216         Motif 2 Description
 217 --------------------------------------------------------------------------------
 218 Simplified        A  a99a2:::::::113:::7:
 219 pos.-specific     C  :::::6:8a8:a:1474a:3
 220 probability       G  :11:84a1:1a:98236:27
 221 matrix            T  :::::::1:1::::::::1:
 222
 223          bits    2.5       * * **     *
 224                  2.3       * * **     *
 225                  2.0       * * ***    *
 226                  1.8       * * ***    *
 227 Information      1.5 *  *********** *** *
 228 content          1.3 ************** *** *
 229 (33.5 bits)      1.0 ************** *** *
 230                  0.8 ****************** *
 231                  0.5 ********************
 232                  0.3 ********************
 233                  0.0 --------------------
 234
 235 Multilevel           AAAAGCGCCCGCGGCCGCAG
 236 consensus                AG        AGC GC
 237 sequence                           G
 238
 239 --------------------------------------------------------------------------------
 240
 241 --------------------------------------------------------------------------------
 242         Motif 2 sites sorted by position p-value
 243 --------------------------------------------------------------------------------
 244 Sequence name            Strand  Start   P-value                    Site
 245 -------------            ------  ----- ---------            --------------------
 246 MIT_Spar_c117_4603           +    347  1.67e-14 ACAATGACCA AAAAGCGCCCGCGGCCGCAG ACCAATGAGC
 247 SGD_Scer_YDR232W             +    352  1.67e-14 ACAATGACCA AAAAGCGCCCGCGGCCGCAG ACCAATGAGC
 248 WashU_Smik_Contig2283.3      +    337  6.44e-13 TTTAAAAAAG AAAAGGGCCCGCGGCCCCGC CGTGAAACAC
 249 WashU_Skud_Contig2069.5      +    349  2.55e-12 ACAATGACCA AAAAGCGTCCGCGGCCGCAG ACCAATGAGC
 250 SGD_Scer_YDR044W             +    340  2.62e-11 GTTTAAAAGT AGAAGGGCCCGCGGAGCCGC TGTGAAAGAT
 251 WashU_Sbay_Contig461.5       +    346  2.62e-11 CAATGACCAA AAAAACGCCGGCGGGCGCAG ACCAATGAGC
 252 MIT_Sbay_c896_21290          +    339  6.92e-11 GTTTAAAAAG AAAAGGGCCCGCGCAGCCTG TGTGAAATGT
 253 MIT_Smik_c228_4055           +    349  9.01e-11 ACAATGACCA AAAAGCGCCCGCAAGCGCAG ACCAATGAGC
 254 MIT_Spar_c130_3912           +    332  1.10e-09 CGTTTAAAAG AAGAAGGGCTGCGGAGCCAC TGTGAAAGAC
 255 --------------------------------------------------------------------------------
 256
 257 --------------------------------------------------------------------------------
 258         Motif 2 block diagrams
 259 --------------------------------------------------------------------------------
 260 SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
 261 -------------            ----------------  -------------
 262 MIT_Spar_c117_4603                1.7e-14  346_[+2]_132
 263 SGD_Scer_YDR232W                  1.7e-14  351_[+2]_127
 264 WashU_Smik_Contig2283.3           6.4e-13  336_[+2]_644
 265 WashU_Skud_Contig2069.5           2.5e-12  348_[+2]_130
 266 SGD_Scer_YDR044W                  2.6e-11  339_[+2]_641
 267 WashU_Sbay_Contig461.5            2.6e-11  345_[+2]_133
 268 MIT_Sbay_c896_21290               6.9e-11  338_[+2]_642
 269 MIT_Smik_c228_4055                  9e-11  348_[+2]_130
 270 MIT_Spar_c130_3912                1.1e-09  331_[+2]_649
 271 --------------------------------------------------------------------------------
 272
 273 --------------------------------------------------------------------------------
 274         Motif 2 in BLOCKS format
 275 --------------------------------------------------------------------------------
 276 BL   MOTIF 2 width=20 seqs=9
 277 MIT_Spar_c117_4603       (  347) AAAAGCGCCCGCGGCCGCAG  1
 278 SGD_Scer_YDR232W         (  352) AAAAGCGCCCGCGGCCGCAG  1
 279 WashU_Smik_Contig2283.3  (  337) AAAAGGGCCCGCGGCCCCGC  1
 280 WashU_Skud_Contig2069.5  (  349) AAAAGCGTCCGCGGCCGCAG  1
 281 SGD_Scer_YDR044W         (  340) AGAAGGGCCCGCGGAGCCGC  1
 282 WashU_Sbay_Contig461.5   (  346) AAAAACGCCGGCGGGCGCAG  1
 283 MIT_Sbay_c896_21290      (  339) AAAAGGGCCCGCGCAGCCTG  1
 284 MIT_Smik_c228_4055       (  349) AAAAGCGCCCGCAAGCGCAG  1
 285 MIT_Spar_c130_3912       (  332) AAGAAGGGCTGCGGAGCCAC  1
 286 //
 287
 288 --------------------------------------------------------------------------------
 289
 290 --------------------------------------------------------------------------------
 291         Motif 2 position-specific scoring matrix
 292 --------------------------------------------------------------------------------
 293 log-odds matrix: alength= 4 w= 20 n= 6319 bayes= 9.4535 E= 1.2e-028
 294    162   -982   -982   -982
 295    145   -982    -66   -982
 296    145   -982    -66   -982
 297    162   -982   -982   -982
 298    -55   -982    215   -982
 299   -982    166    134   -982
 300   -982   -982    251   -982
 301   -982    215    -66   -154
 302   -982    251   -982   -982
 303   -982    215    -66   -154
 304   -982   -982    251   -982
 305   -982    251   -982   -982
 306   -154   -982    234   -982
 307   -154    -66    215   -982
 308      4    134     34   -982
 309   -982    192     92   -982
 310   -982    134    166   -982
 311   -982    251   -982   -982
 312    104   -982     34   -154
 313   -982     92    192   -982
 314 --------------------------------------------------------------------------------
 315
 316 --------------------------------------------------------------------------------
 317         Motif 2 position-specific probability matrix
 318 --------------------------------------------------------------------------------
 319 letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 1.2e-028
 320  1.000000  0.000000  0.000000  0.000000
 321  0.888889  0.000000  0.111111  0.000000
 322  0.888889  0.000000  0.111111  0.000000
 323  1.000000  0.000000  0.000000  0.000000
 324  0.222222  0.000000  0.777778  0.000000
 325  0.000000  0.555556  0.444444  0.000000
 326  0.000000  0.000000  1.000000  0.000000
 327  0.000000  0.777778  0.111111  0.111111
 328  0.000000  1.000000  0.000000  0.000000
 329  0.000000  0.777778  0.111111  0.111111
 330  0.000000  0.000000  1.000000  0.000000
 331  0.000000  1.000000  0.000000  0.000000
 332  0.111111  0.000000  0.888889  0.000000
 333  0.111111  0.111111  0.777778  0.000000
 334  0.333333  0.444444  0.222222  0.000000
 335  0.000000  0.666667  0.333333  0.000000
 336  0.000000  0.444444  0.555556  0.000000
 337  0.000000  1.000000  0.000000  0.000000
 338  0.666667  0.000000  0.222222  0.111111
 339  0.000000  0.333333  0.666667  0.000000
 340 --------------------------------------------------------------------------------
 341
 342 --------------------------------------------------------------------------------
 343         Motif 2 regular expression
 344 --------------------------------------------------------------------------------
 345 AAAA[GA][CG]GCCCGCGG[CAG][CG][GC]C[AG][GC]
 346 --------------------------------------------------------------------------------
 347
 348
 349
 350
 351 Time  8.84 secs.
 352
 353 ********************************************************************************
 354
 355
 356 ********************************************************************************
 357 MOTIF  3        width =   20   sites =   9   llr = 205   E-value = 8.3e-027
 358 ********************************************************************************
 359 --------------------------------------------------------------------------------
 360         Motif 3 Description
 361 --------------------------------------------------------------------------------
 362 Simplified        A  :::::::::::::4::::::
 363 pos.-specific     C  1194:::aa::a:64:46::
 364 probability       G  ::12a:::::a:4:::24::
 365 matrix            T  99:3:aa::a::6:6a3:aa
 366
 367          bits    2.5     *  ** **
 368                  2.3     *  ** **
 369                  2.0   * *  ** **
 370                  1.8   * *  ** **
 371 Information      1.5   * ********   * ***
 372 content          1.3 *** ********   * ***
 373 (32.8 bits)      1.0 *** ************ ***
 374                  0.8 ********************
 375                  0.5 ********************
 376                  0.3 ********************
 377                  0.0 --------------------
 378
 379 Multilevel           TTCCGTTCCTGCTCTTCCTT
 380 consensus               T        GAC TG
 381 sequence                G            G
 382
 383 --------------------------------------------------------------------------------
 384
 385 --------------------------------------------------------------------------------
 386         Motif 3 sites sorted by position p-value
 387 --------------------------------------------------------------------------------
 388 Sequence name            Strand  Start   P-value                    Site
 389 -------------            ------  ----- ---------            --------------------
 390 WashU_Skud_Contig2069.5      +    311  1.06e-11 TGTGAAAAAT TTCCGTTCCTGCTCTTGCTT CATATATGAC
 391 MIT_Sbay_c896_21290          +    312  1.49e-11 GAAAAATGGC TTCGGTTCCTGCGACTCGTT TAAAAAGAAA
 392 MIT_Smik_c228_4055           +    310  1.49e-11 AGATGAAAAT TTCCGTTCCTGCTCTTTCTT CATATATGAA
 393 SGD_Scer_YDR232W             +    313  1.49e-11 GATGAAAAAT TTCCGTTCCTGCTCTTTCTT CATATATGAA
 394 MIT_Spar_c130_3912           +    306  1.92e-11 GAAATTTGGA TTCTGTTCCTGCGACTCGTT TAAAAGAAGA
 395 SGD_Scer_YDR044W             +    313  1.92e-11 GAAATTTGGC TTCTGTTCCTGCGACTCGTT TAAAAGTAGA
 396 MIT_Spar_c117_4603           +    308  5.14e-11 GATGAAAAAT TTCTGTTCCTGCTCTTTCTT CATATATGAA
 397 WashU_Sbay_Contig461.5       +    306  6.73e-11 GATGAAAAAT CTCCGTTCCTGCTCTTGCTT GATATATTAA
 398 WashU_Smik_Contig2283.3      +    309  2.36e-10 AATTTTGGTT TCGGGTTCCTGCGACTCGTT TAAAAAAGAA
 399 --------------------------------------------------------------------------------
 400
 401 --------------------------------------------------------------------------------
 402         Motif 3 block diagrams
 403 --------------------------------------------------------------------------------
 404 SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
 405 -------------            ----------------  -------------
 406 WashU_Skud_Contig2069.5           1.1e-11  310_[+3]_168
 407 MIT_Sbay_c896_21290               1.5e-11  311_[+3]_669
 408 MIT_Smik_c228_4055                1.5e-11  309_[+3]_169
 409 SGD_Scer_YDR232W                  1.5e-11  312_[+3]_166
 410 MIT_Spar_c130_3912                1.9e-11  305_[+3]_675
 411 SGD_Scer_YDR044W                  1.9e-11  312_[+3]_668
 412 MIT_Spar_c117_4603                5.1e-11  307_[+3]_171
 413 WashU_Sbay_Contig461.5            6.7e-11  305_[+3]_173
 414 WashU_Smik_Contig2283.3           2.4e-10  308_[+3]_672
 415 --------------------------------------------------------------------------------
 416
 417 --------------------------------------------------------------------------------
 418         Motif 3 in BLOCKS format
 419 --------------------------------------------------------------------------------
 420 BL   MOTIF 3 width=20 seqs=9
 421 WashU_Skud_Contig2069.5  (  311) TTCCGTTCCTGCTCTTGCTT  1
 422 MIT_Sbay_c896_21290      (  312) TTCGGTTCCTGCGACTCGTT  1
 423 MIT_Smik_c228_4055       (  310) TTCCGTTCCTGCTCTTTCTT  1
 424 SGD_Scer_YDR232W         (  313) TTCCGTTCCTGCTCTTTCTT  1
 425 MIT_Spar_c130_3912       (  306) TTCTGTTCCTGCGACTCGTT  1
 426 SGD_Scer_YDR044W         (  313) TTCTGTTCCTGCGACTCGTT  1
 427 MIT_Spar_c117_4603       (  308) TTCTGTTCCTGCTCTTTCTT  1
 428 WashU_Sbay_Contig461.5   (  306) CTCCGTTCCTGCTCTTGCTT  1
 429 WashU_Smik_Contig2283.3  (  309) TCGGGTTCCTGCGACTCGTT  1
 430 //
 431
 432 --------------------------------------------------------------------------------
 433
 434 --------------------------------------------------------------------------------
 435         Motif 3 position-specific scoring matrix
 436 --------------------------------------------------------------------------------
 437 log-odds matrix: alength= 4 w= 20 n= 6319 bayes= 9.4535 E= 8.3e-027
 438   -982    -66   -982    145
 439   -982    -66   -982    145
 440   -982    234    -66   -982
 441   -982    134     34      4
 442   -982   -982    251   -982
 443   -982   -982   -982    162
 444   -982   -982   -982    162
 445   -982    251   -982   -982
 446   -982    251   -982   -982
 447   -982   -982   -982    162
 448   -982   -982    251   -982
 449   -982    251   -982   -982
 450   -982   -982    134     78
 451     45    166   -982   -982
 452   -982    134   -982     78
 453   -982   -982   -982    162
 454   -982    134     34      4
 455   -982    166    134   -982
 456   -982   -982   -982    162
 457   -982   -982   -982    162
 458 --------------------------------------------------------------------------------
 459
 460 --------------------------------------------------------------------------------
 461         Motif 3 position-specific probability matrix
 462 --------------------------------------------------------------------------------
 463 letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 8.3e-027
 464  0.000000  0.111111  0.000000  0.888889
 465  0.000000  0.111111  0.000000  0.888889
 466  0.000000  0.888889  0.111111  0.000000
 467  0.000000  0.444444  0.222222  0.333333
 468  0.000000  0.000000  1.000000  0.000000
 469  0.000000  0.000000  0.000000  1.000000
 470  0.000000  0.000000  0.000000  1.000000
 471  0.000000  1.000000  0.000000  0.000000
 472  0.000000  1.000000  0.000000  0.000000
 473  0.000000  0.000000  0.000000  1.000000
 474  0.000000  0.000000  1.000000  0.000000
 475  0.000000  1.000000  0.000000  0.000000
 476  0.000000  0.000000  0.444444  0.555556
 477  0.444444  0.555556  0.000000  0.000000
 478  0.000000  0.444444  0.000000  0.555556
 479  0.000000  0.000000  0.000000  1.000000
 480  0.000000  0.444444  0.222222  0.333333
 481  0.000000  0.555556  0.444444  0.000000
 482  0.000000  0.000000  0.000000  1.000000
 483  0.000000  0.000000  0.000000  1.000000
 484 --------------------------------------------------------------------------------
 485
 486 --------------------------------------------------------------------------------
 487         Motif 3 regular expression
 488 --------------------------------------------------------------------------------
 489 TTC[CTG]GTTCCTGC[TG][CA][TC]T[CTG][CG]TT
 490 --------------------------------------------------------------------------------
 491
 492
 493
 494
 495 Time 13.06 secs.
 496
 497 ********************************************************************************
 498
 499
 500 ********************************************************************************
 501 MOTIF  4        width =   20   sites =   9   llr = 202   E-value = 5.2e-025
 502 ********************************************************************************
 503 --------------------------------------------------------------------------------
 504         Motif 4 Description
 505 --------------------------------------------------------------------------------
 506 Simplified        A  a1:6a:4a44:7::aa611:
 507 pos.-specific     C  :6a4:::::6::a:::::9:
 508 probability       G  :3:::46:6:93:a::49:a
 509 matrix            T  :::::6::::1:::::::::
 510
 511          bits    2.5   *         **     *
 512                  2.3   *         **     *
 513                  2.0   *       * **   ***
 514                  1.8   *       * **   ***
 515 Information      1.5 * * *  *  * **** ***
 516 content          1.3 * * *  *  * **** ***
 517 (32.4 bits)      1.0 ********************
 518                  0.8 ********************
 519                  0.5 ********************
 520                  0.3 ********************
 521                  0.0 --------------------
 522
 523 Multilevel           ACCAATGAGCGACGAAAGCG
 524 consensus             G C GA AA G    G
 525 sequence
 526
 527 --------------------------------------------------------------------------------
 528
 529 --------------------------------------------------------------------------------
 530         Motif 4 sites sorted by position p-value
 531 --------------------------------------------------------------------------------
 532 Sequence name            Strand  Start   P-value                    Site
 533 -------------            ------  ----- ---------            --------------------
 534 WashU_Skud_Contig2069.5      +    369  8.45e-13 GCGGCCGCAG ACCAATGAGCGACGAAGGCG GCCTTTCGTA
 535 MIT_Spar_c117_4603           +    367  8.45e-13 GCGGCCGCAG ACCAATGAGCGACGAAGGCG GCCTTTCCGA
 536 SGD_Scer_YDR232W             +    372  8.45e-13 GCGGCCGCAG ACCAATGAGCGACGAAGGCG GCCTTTCCGA
 537 MIT_Smik_c228_4055           +    369  2.51e-12 GCAAGCGCAG ACCAATGAGCGACGAAAGCG GCCTTTTGAA
 538 MIT_Spar_c130_3912           +    265  5.38e-11 TGGTGGGAGA AGCCAGAAAAGGCGAAAGCG TAGCGTTCTT
 539 WashU_Sbay_Contig461.5       +    366  5.38e-11 GCGGGCGCAG ACCAATGAGCGACGAAGACG GCTTTTGGGC
 540 SGD_Scer_YDR044W             +    272  1.99e-10 TTGGTGGGAG AACCAGAAAAGGCGAAAGCG TAGCGTTCTT
 541 WashU_Smik_Contig2283.3      +    261  3.58e-10 TGGTGGAAGA AGCCAGAAAAGACGAAAGAG TAGCGTAGCG
 542 MIT_Sbay_c896_21290          +    271  3.78e-10 TGGTGGGAGA AGCCAGAAAATGCGAAAGCG TACCGTTCTG
 543 --------------------------------------------------------------------------------
 544
 545 --------------------------------------------------------------------------------
 546         Motif 4 block diagrams
 547 --------------------------------------------------------------------------------
 548 SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
 549 -------------            ----------------  -------------
 550 WashU_Skud_Contig2069.5           8.5e-13  368_[+4]_110
 551 MIT_Spar_c117_4603                8.5e-13  366_[+4]_112
 552 SGD_Scer_YDR232W                  8.5e-13  371_[+4]_107
 553 MIT_Smik_c228_4055                2.5e-12  368_[+4]_110
 554 MIT_Spar_c130_3912                5.4e-11  264_[+4]_716
 555 WashU_Sbay_Contig461.5            5.4e-11  365_[+4]_113
 556 SGD_Scer_YDR044W                    2e-10  271_[+4]_709
 557 WashU_Smik_Contig2283.3           3.6e-10  260_[+4]_720
 558 MIT_Sbay_c896_21290               3.8e-10  270_[+4]_710
 559 --------------------------------------------------------------------------------
 560
 561 --------------------------------------------------------------------------------
 562         Motif 4 in BLOCKS format
 563 --------------------------------------------------------------------------------
 564 BL   MOTIF 4 width=20 seqs=9
 565 WashU_Skud_Contig2069.5  (  369) ACCAATGAGCGACGAAGGCG  1
 566 MIT_Spar_c117_4603       (  367) ACCAATGAGCGACGAAGGCG  1
 567 SGD_Scer_YDR232W         (  372) ACCAATGAGCGACGAAGGCG  1
 568 MIT_Smik_c228_4055       (  369) ACCAATGAGCGACGAAAGCG  1
 569 MIT_Spar_c130_3912       (  265) AGCCAGAAAAGGCGAAAGCG  1
 570 WashU_Sbay_Contig461.5   (  366) ACCAATGAGCGACGAAGACG  1
 571 SGD_Scer_YDR044W         (  272) AACCAGAAAAGGCGAAAGCG  1
 572 WashU_Smik_Contig2283.3  (  261) AGCCAGAAAAGACGAAAGAG  1
 573 MIT_Sbay_c896_21290      (  271) AGCCAGAAAATGCGAAAGCG  1
 574 //
 575
 576 --------------------------------------------------------------------------------
 577
 578 --------------------------------------------------------------------------------
 579         Motif 4 position-specific scoring matrix
 580 --------------------------------------------------------------------------------
 581 log-odds matrix: alength= 4 w= 20 n= 6319 bayes= 9.4535 E= 5.2e-025
 582    162   -982   -982   -982
 583   -154    166     92   -982
 584   -982    251   -982   -982
 585     78    134   -982   -982
 586    162   -982   -982   -982
 587   -982   -982    134     78
 588     45   -982    166   -982
 589    162   -982   -982   -982
 590     45   -982    166   -982
 591     45    166   -982   -982
 592   -982   -982    234   -154
 593    104   -982     92   -982
 594   -982    251   -982   -982
 595   -982   -982    251   -982
 596    162   -982   -982   -982
 597    162   -982   -982   -982
 598     78   -982    134   -982
 599   -154   -982    234   -982
 600   -154    234   -982   -982
 601   -982   -982    251   -982
 602 --------------------------------------------------------------------------------
 603
 604 --------------------------------------------------------------------------------
 605         Motif 4 position-specific probability matrix
 606 --------------------------------------------------------------------------------
 607 letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 5.2e-025
 608  1.000000  0.000000  0.000000  0.000000
 609  0.111111  0.555556  0.333333  0.000000
 610  0.000000  1.000000  0.000000  0.000000
 611  0.555556  0.444444  0.000000  0.000000
 612  1.000000  0.000000  0.000000  0.000000
 613  0.000000  0.000000  0.444444  0.555556
 614  0.444444  0.000000  0.555556  0.000000
 615  1.000000  0.000000  0.000000  0.000000
 616  0.444444  0.000000  0.555556  0.000000
 617  0.444444  0.555556  0.000000  0.000000
 618  0.000000  0.000000  0.888889  0.111111
 619  0.666667  0.000000  0.333333  0.000000
 620  0.000000  1.000000  0.000000  0.000000
 621  0.000000  0.000000  1.000000  0.000000
 622  1.000000  0.000000  0.000000  0.000000
 623  1.000000  0.000000  0.000000  0.000000
 624  0.555556  0.000000  0.444444  0.000000
 625  0.111111  0.000000  0.888889  0.000000
 626  0.111111  0.888889  0.000000  0.000000
 627  0.000000  0.000000  1.000000  0.000000
 628 --------------------------------------------------------------------------------
 629
 630 --------------------------------------------------------------------------------
 631         Motif 4 regular expression
 632 --------------------------------------------------------------------------------
 633 A[CG]C[AC]A[TG][GA]A[GA][CA]G[AG]CGAA[AG]GCG
 634 --------------------------------------------------------------------------------
 635
 636
 637
 638
 639 Time 17.20 secs.
 640
 641 ********************************************************************************
 642
 643
 644 ********************************************************************************
 645 MOTIF  5        width =   20   sites =   9   llr = 183   E-value = 5.4e-018
 646 ********************************************************************************
 647 --------------------------------------------------------------------------------
 648         Motif 5 Description
 649 --------------------------------------------------------------------------------
 650 Simplified        A  ::96:a26:2a::a:12:a1
 651 pos.-specific     C  94::2::::::86::9:::8
 652 probability       G  :6:32:82a:::4:a:4a::
 653 matrix            T  1:116::2:8:2::::3::1
 654
 655          bits    2.5         *     *  *
 656                  2.3         *     *  *
 657                  2.0 *       *     ** *
 658                  1.8 *       *     ** *
 659 Information      1.5 **   ** * ****** **
 660 content          1.3 **   ** * ****** ***
 661 (29.3 bits)      1.0 ***  ** * ****** ***
 662                  0.8 ***  ** ******** ***
 663                  0.5 ********************
 664                  0.3 ********************
 665                  0.0 --------------------
 666
 667 Multilevel           CGAATAGAGTACCAGCGGAC
 668 consensus             C GC AG A TG   T
 669 sequence                 G  T        A
 670
 671 --------------------------------------------------------------------------------
 672
 673 --------------------------------------------------------------------------------
 674         Motif 5 sites sorted by position p-value
 675 --------------------------------------------------------------------------------
 676 Sequence name            Strand  Start   P-value                    Site
 677 -------------            ------  ----- ---------            --------------------
 678 MIT_Smik_c228_4055           +    203  3.97e-12 GCAACACAAC CGAGTAGAGTACCAGCTGAC GGAATGGAGG
 679 WashU_Skud_Contig2069.5      +    204  8.98e-12 GCAACACAAC CGAGTAGAGTACCAGCAGAC GGAGTGGGTA
 680 MIT_Spar_c130_3912           +    589  1.65e-11 ATTGTTTCTC CCAACAGTGTACGAGCGGAC GAAACTCTAG
 681 MIT_Spar_c117_4603           +    204  7.31e-11 AACACACAAC CGAATAGAGTATCAGCTGAC GGGATGGAGG
 682 SGD_Scer_YDR232W             +    209  7.31e-11 AACACACAAC CGAATAGAGTATCAGCTGAC GGAATGGAGA
 683 WashU_Sbay_Contig461.5       +    199  9.18e-11 GGGTGCAAAC CGATTAGAGTACCAGCAGAC GAGATGGGCG
 684 SGD_Scer_YDR044W             +    595  1.19e-09 ATTGTTTTTC CCAACAGTGAACGAGAGGAC AAACTCCAGA
 685 WashU_Smik_Contig2283.3      +    595  6.61e-09 GTATTGTCTT TCAAGAAGGTACGAGCGGAT GAACTTCTTG
 686 MIT_Sbay_c896_21290          +    597  8.76e-09 ATTGTTTTTT CCTGGAAGGAACGAGCGGAA CTCTTGGGGA
 687 --------------------------------------------------------------------------------
 688
 689 --------------------------------------------------------------------------------
 690         Motif 5 block diagrams
 691 --------------------------------------------------------------------------------
 692 SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
 693 -------------            ----------------  -------------
 694 MIT_Smik_c228_4055                  4e-12  202_[+5]_276
 695 WashU_Skud_Contig2069.5             9e-12  203_[+5]_275
 696 MIT_Spar_c130_3912                1.7e-11  588_[+5]_392
 697 MIT_Spar_c117_4603                7.3e-11  203_[+5]_275
 698 SGD_Scer_YDR232W                  7.3e-11  208_[+5]_270
 699 WashU_Sbay_Contig461.5            9.2e-11  198_[+5]_280
 700 SGD_Scer_YDR044W                  1.2e-09  594_[+5]_386
 701 WashU_Smik_Contig2283.3           6.6e-09  594_[+5]_386
 702 MIT_Sbay_c896_21290               8.8e-09  596_[+5]_384
 703 --------------------------------------------------------------------------------
 704
 705 --------------------------------------------------------------------------------
 706         Motif 5 in BLOCKS format
 707 --------------------------------------------------------------------------------
 708 BL   MOTIF 5 width=20 seqs=9
 709 MIT_Smik_c228_4055       (  203) CGAGTAGAGTACCAGCTGAC  1
 710 WashU_Skud_Contig2069.5  (  204) CGAGTAGAGTACCAGCAGAC  1
 711 MIT_Spar_c130_3912       (  589) CCAACAGTGTACGAGCGGAC  1
 712 MIT_Spar_c117_4603       (  204) CGAATAGAGTATCAGCTGAC  1
 713 SGD_Scer_YDR232W         (  209) CGAATAGAGTATCAGCTGAC  1
 714 WashU_Sbay_Contig461.5   (  199) CGATTAGAGTACCAGCAGAC  1
 715 SGD_Scer_YDR044W         (  595) CCAACAGTGAACGAGAGGAC  1
 716 WashU_Smik_Contig2283.3  (  595) TCAAGAAGGTACGAGCGGAT  1
 717 MIT_Sbay_c896_21290      (  597) CCTGGAAGGAACGAGCGGAA  1
 718 //
 719
 720 --------------------------------------------------------------------------------
 721
 722 --------------------------------------------------------------------------------
 723         Motif 5 position-specific scoring matrix
 724 --------------------------------------------------------------------------------
 725 log-odds matrix: alength= 4 w= 20 n= 6319 bayes= 9.4535 E= 5.4e-018
 726   -982    234   -982   -154
 727   -982    134    166   -982
 728    145   -982   -982   -154
 729     78   -982     92   -154
 730   -982     34     34     78
 731    162   -982   -982   -982
 732    -55   -982    215   -982
 733     78   -982     34    -55
 734   -982   -982    251   -982
 735    -55   -982   -982    126
 736    162   -982   -982   -982
 737   -982    215   -982    -55
 738   -982    166    134   -982
 739    162   -982   -982   -982
 740   -982   -982    251   -982
 741   -154    234   -982   -982
 742    -55   -982    134      4
 743   -982   -982    251   -982
 744    162   -982   -982   -982
 745   -154    215   -982   -154
 746 --------------------------------------------------------------------------------
 747
 748 --------------------------------------------------------------------------------
 749         Motif 5 position-specific probability matrix
 750 --------------------------------------------------------------------------------
 751 letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 5.4e-018
 752  0.000000  0.888889  0.000000  0.111111
 753  0.000000  0.444444  0.555556  0.000000
 754  0.888889  0.000000  0.000000  0.111111
 755  0.555556  0.000000  0.333333  0.111111
 756  0.000000  0.222222  0.222222  0.555556
 757  1.000000  0.000000  0.000000  0.000000
 758  0.222222  0.000000  0.777778  0.000000
 759  0.555556  0.000000  0.222222  0.222222
 760  0.000000  0.000000  1.000000  0.000000
 761  0.222222  0.000000  0.000000  0.777778
 762  1.000000  0.000000  0.000000  0.000000
 763  0.000000  0.777778  0.000000  0.222222
 764  0.000000  0.555556  0.444444  0.000000
 765  1.000000  0.000000  0.000000  0.000000
 766  0.000000  0.000000  1.000000  0.000000
 767  0.111111  0.888889  0.000000  0.000000
 768  0.222222  0.000000  0.444444  0.333333
 769  0.000000  0.000000  1.000000  0.000000
 770  1.000000  0.000000  0.000000  0.000000
 771  0.111111  0.777778  0.000000  0.111111
 772 --------------------------------------------------------------------------------
 773
 774 --------------------------------------------------------------------------------
 775         Motif 5 regular expression
 776 --------------------------------------------------------------------------------
 777 C[GC]A[AG][TCG]A[GA][AGT]G[TA]A[CT][CG]AGC[GTA]GAC
 778 --------------------------------------------------------------------------------
 779
 780
 781
 782
 783 Time 21.26 secs.
 784
 785 ********************************************************************************
 786
 787
 788 ********************************************************************************
 789 SUMMARY OF MOTIFS
 790 ********************************************************************************
 791
 792 --------------------------------------------------------------------------------
 793         Combined block diagrams: non-overlapping sites with p-value < 0.0001
 794 --------------------------------------------------------------------------------
 795 SEQUENCE NAME            COMBINED P-VALUE  MOTIF DIAGRAM
 796 -------------            ----------------  -------------
 797 SGD_Scer_YDR232W                 2.11e-38  208_[+5(7.31e-11)]_55_[+1(3.60e-13)]_9_[+3(1.49e-11)]_19_[+2(1.67e-14)]_[+4(8.45e-13)]_107
 798 MIT_Spar_c117_4603               6.91e-38  203_[+5(7.31e-11)]_55_[+1(3.60e-13)]_9_[+3(5.14e-11)]_19_[+2(1.67e-14)]_[+4(8.45e-13)]_44_[+2(5.31e-05)]_48
 799 MIT_Smik_c228_4055               1.40e-35  202_[+5(3.97e-12)]_59_[+1(3.60e-13)]_8_[+3(1.49e-11)]_19_[+2(9.01e-11)]_[+4(2.51e-12)]_110
 800 WashU_Skud_Contig2069.5          1.63e-35  203_[+5(8.98e-12)]_58_[+1(2.76e-11)]_9_[+3(1.06e-11)]_18_[+2(2.55e-12)]_[+4(8.45e-13)]_110
 801 WashU_Sbay_Contig461.5           6.88e-33  46_[-1(4.97e-05)]_100_[+4(2.76e-05)]_12_[+5(9.18e-11)]_58_[+1(3.60e-13)]_9_[+3(6.73e-11)]_20_[+2(2.62e-11)]_[+4(5.38e-11)]_17_[+1(5.86e-05)]_76
 802 SGD_Scer_YDR044W                 6.91e-30  174_[+1(1.02e-12)]_11_[-2(3.63e-05)]_46_[+4(1.99e-10)]_21_[+3(1.92e-11)]_7_[+2(2.62e-11)]_235_[+5(1.19e-09)]_386
 803 MIT_Spar_c130_3912               2.36e-29  170_[+1(2.37e-11)]_28_[+3(2.57e-05)]_26_[+4(5.38e-11)]_21_[+3(1.92e-11)]_6_[+2(1.10e-09)]_237_[+5(1.65e-11)]_77_[+1(7.05e-05)]_23_[+3(9.81e-05)]_252
 804 MIT_Sbay_c896_21290              5.38e-26  117_[+1(4.54e-05)]_39_[+1(4.52e-10)]_74_[+4(3.78e-10)]_21_[+3(1.49e-11)]_7_[+2(6.92e-11)]_238_[+5(8.76e-09)]_172_[+3(3.90e-05)]_192
 805 WashU_Smik_Contig2283.3          2.87e-27  166_[+1(1.95e-10)]_74_[+4(3.58e-10)]_28_[+3(2.36e-10)]_8_[+2(6.44e-13)]_27_[+4(3.86e-05)]_191_[+5(6.61e-09)]_111_[+5(3.65e-05)]_255
 806 --------------------------------------------------------------------------------
 807
 808 ********************************************************************************
 809
 810
 811 ********************************************************************************
 812 Stopped because nmotifs = 5 reached.
 813 ********************************************************************************
 814
 815 CPU: dhn02990.mrc-dunn.cam.ac.uk
 816
 817 ********************************************************************************