t/data/map_hem/HEM2-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= HEM2-HEM14.fa
  32 ALPHABET= ACGT
  33 Sequence name            Weight Length  Sequence name            Weight Length
  34 -------------            ------ ------  -------------            ------ ------
  35 SGD_Scer_YGL040C         1.0000   1000  MIT_Spar_c19_8512        1.0000   1000
  36 MIT_Smik_c273_7756       1.0000   1000  MIT_Sbay_c77_8808        1.0000   1000
  37 WashU_Skud_Contig2052.17 1.0000   1000  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 HEM2-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=            6288    N=               9
  59 strands: + -
  60 sample: seed=            0    seqfrac=         1
  61 Letter frequencies in dataset:
  62 A 0.328 C 0.172 G 0.172 T 0.328
  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 = 192   E-value = 5.7e-022
  70 ********************************************************************************
  71 --------------------------------------------------------------------------------
  72         Motif 1 Description
  73 --------------------------------------------------------------------------------
  74 Simplified        A  96:42:191:1:::::::a:
  75 pos.-specific     C  :191:34::::a:a:::::6
  76 probability       G  13::8641::9:::a::::4
  77 matrix            T  ::14:1::9a::a::aaa::
  78
  79          bits    2.5            * **
  80                  2.3            * **
  81                  2.0   *       ** **
  82                  1.8   *       ** **
  83 Information      1.5   * *    ***********
  84 content          1.3 * * *  * ***********
  85 (30.8 bits)      1.0 * * ****************
  86                  0.8 *** ****************
  87                  0.5 *** ****************
  88                  0.3 ********************
  89                  0.0 --------------------
  90
  91 Multilevel           AACAGGCATTGCTCGTTTAC
  92 consensus             G TACG            G
  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_Contig2052.17     +    200  4.10e-12 CACCGCACCG AACAGGGATTGCTCGTTTAC CCGTTGCGTT
 103 MIT_Spar_c19_8512            +    201  4.10e-12 CACCGCACCG AACAGGGATTGCTCGTTTAC CCGTAGTTTG
 104 SGD_Scer_YGL040C             +    200  4.10e-12 CACCGCACCG AACAGGGATTGCTCGTTTAC CCGTATTTTG
 105 SGD_Scer_YER014W             -    169  1.37e-11 TTTAATTGAA AGCTGCCATTGCTCGTTTAG TTACAAAACG
 106 MIT_Sbay_c84_6418            -    164  1.01e-10 GTTTGAATAT AACTGTCATTGCTCGTTTAG TGGTGAATAT
 107 MIT_Smik_c283_5928           -    163  1.09e-10 TTCAATCAAA AGCTACCATTGCTCGTTTAG TTGTAAAATG
 108 MIT_Spar_c425_6072           -    168  2.28e-10 TTTAATTAAA AGCTGCCATTACTCGTTTAG TTGCAAAACG
 109 MIT_Smik_c273_7756           +    199  6.00e-10 CACCGCACCG AATAAGGATTGCTCGTTTAC CCGTTGTTCG
 110 MIT_Sbay_c77_8808            +    200  5.23e-09 TCACCGCACC GCCCGGAGATGCTCGTTTAC CGTTGTGCAC
 111 --------------------------------------------------------------------------------
 112
 113 --------------------------------------------------------------------------------
 114         Motif 1 block diagrams
 115 --------------------------------------------------------------------------------
 116 SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
 117 -------------            ----------------  -------------
 118 WashU_Skud_Contig2052.17          4.1e-12  199_[+1]_781
 119 MIT_Spar_c19_8512                 4.1e-12  200_[+1]_780
 120 SGD_Scer_YGL040C                  4.1e-12  199_[+1]_781
 121 SGD_Scer_YER014W                  1.4e-11  168_[-1]_134
 122 MIT_Sbay_c84_6418                   1e-10  163_[-1]_139
 123 MIT_Smik_c283_5928                1.1e-10  162_[-1]_140
 124 MIT_Spar_c425_6072                2.3e-10  167_[-1]_135
 125 MIT_Smik_c273_7756                  6e-10  198_[+1]_782
 126 MIT_Sbay_c77_8808                 5.2e-09  199_[+1]_781
 127 --------------------------------------------------------------------------------
 128
 129 --------------------------------------------------------------------------------
 130         Motif 1 in BLOCKS format
 131 --------------------------------------------------------------------------------
 132 BL   MOTIF 1 width=20 seqs=9
 133 WashU_Skud_Contig2052.17 (  200) AACAGGGATTGCTCGTTTAC  1
 134 MIT_Spar_c19_8512        (  201) AACAGGGATTGCTCGTTTAC  1
 135 SGD_Scer_YGL040C         (  200) AACAGGGATTGCTCGTTTAC  1
 136 SGD_Scer_YER014W         (  169) AGCTGCCATTGCTCGTTTAG  1
 137 MIT_Sbay_c84_6418        (  164) AACTGTCATTGCTCGTTTAG  1
 138 MIT_Smik_c283_5928       (  163) AGCTACCATTGCTCGTTTAG  1
 139 MIT_Spar_c425_6072       (  168) AGCTGCCATTACTCGTTTAG  1
 140 MIT_Smik_c273_7756       (  199) AATAAGGATTGCTCGTTTAC  1
 141 MIT_Sbay_c77_8808        (  200) GCCCGGAGATGCTCGTTTAC  1
 142 //
 143
 144 --------------------------------------------------------------------------------
 145
 146 --------------------------------------------------------------------------------
 147         Motif 1 position-specific scoring matrix
 148 --------------------------------------------------------------------------------
 149 log-odds matrix: alength= 4 w= 20 n= 6117 bayes= 9.40656 E= 5.7e-022
 150    145   -982    -66   -982
 151     78    -66     92   -982
 152   -982    234   -982   -154
 153     45    -66   -982     45
 154    -55   -982    215   -982
 155   -982     92    166   -154
 156   -154    134    134   -982
 157    145   -982    -66   -982
 158   -154   -982   -982    145
 159   -982   -982   -982    162
 160   -154   -982    234   -982
 161   -982    251   -982   -982
 162   -982   -982   -982    162
 163   -982    251   -982   -982
 164   -982   -982    251   -982
 165   -982   -982   -982    162
 166   -982   -982   -982    162
 167   -982   -982   -982    162
 168    162   -982   -982   -982
 169   -982    166    134   -982
 170 --------------------------------------------------------------------------------
 171
 172 --------------------------------------------------------------------------------
 173         Motif 1 position-specific probability matrix
 174 --------------------------------------------------------------------------------
 175 letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 5.7e-022
 176  0.888889  0.000000  0.111111  0.000000
 177  0.555556  0.111111  0.333333  0.000000
 178  0.000000  0.888889  0.000000  0.111111
 179  0.444444  0.111111  0.000000  0.444444
 180  0.222222  0.000000  0.777778  0.000000
 181  0.000000  0.333333  0.555556  0.111111
 182  0.111111  0.444444  0.444444  0.000000
 183  0.888889  0.000000  0.111111  0.000000
 184  0.111111  0.000000  0.000000  0.888889
 185  0.000000  0.000000  0.000000  1.000000
 186  0.111111  0.000000  0.888889  0.000000
 187  0.000000  1.000000  0.000000  0.000000
 188  0.000000  0.000000  0.000000  1.000000
 189  0.000000  1.000000  0.000000  0.000000
 190  0.000000  0.000000  1.000000  0.000000
 191  0.000000  0.000000  0.000000  1.000000
 192  0.000000  0.000000  0.000000  1.000000
 193  0.000000  0.000000  0.000000  1.000000
 194  1.000000  0.000000  0.000000  0.000000
 195  0.000000  0.555556  0.444444  0.000000
 196 --------------------------------------------------------------------------------
 197
 198 --------------------------------------------------------------------------------
 199         Motif 1 regular expression
 200 --------------------------------------------------------------------------------
 201 A[AG]C[AT][GA][GC][CG]ATTGCTCGTTTA[CG]
 202 --------------------------------------------------------------------------------
 203
 204
 205
 206
 207 Time  4.20 secs.
 208
 209 ********************************************************************************
 210
 211
 212 ********************************************************************************
 213 MOTIF  2        width =   15   sites =   9   llr = 154   E-value = 6.2e-015
 214 ********************************************************************************
 215 --------------------------------------------------------------------------------
 216         Motif 2 Description
 217 --------------------------------------------------------------------------------
 218 Simplified        A  :::::49:::a9:2:
 219 pos.-specific     C  :169::1::a::17:
 220 probability       G  79::46:aa::19::
 221 matrix            T  3:416::::::::1a
 222
 223          bits    2.5        ***
 224                  2.3        ***
 225                  2.0  * *   ***  *
 226                  1.8  * *   ***  *
 227 Information      1.5  * *   **** * *
 228 content          1.3 ** *  ******* *
 229 (24.7 bits)      1.0 ***************
 230                  0.8 ***************
 231                  0.5 ***************
 232                  0.3 ***************
 233                  0.0 ---------------
 234
 235 Multilevel           GGCCTGAGGCAAGCT
 236 consensus            T T GA       A
 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_Contig2052.17     -    172  1.54e-10 TGCGGTGATT GGCCTGAGGCAAGCT GCCTGCCCAA
 247 MIT_Spar_c19_8512            -    173  1.54e-10 TGCGGTGATT GGCCTGAGGCAAGCT GCCCGCTTGA
 248 MIT_Smik_c283_5928           +    132  1.35e-09 GAAGCAACAA GGTCGAAGGCAAGCT GAAAGGCATT
 249 SGD_Scer_YGL040C             -    172  7.15e-09 TGCGGTGATT GGCTTGAGGCAAGCT TCCCGCTTGA
 250 MIT_Sbay_c77_8808            -    173  7.55e-09 TGCGGTGATT GGCCTGCGGCAGGCT GCCTGATTTA
 251 MIT_Smik_c273_7756           -    171  2.10e-08 TGCGGTGATT GGCCTGAGGCAACAT ACACTCTTGA
 252 MIT_Spar_c425_6072           +    137  2.87e-08 AGCAACAAAA TGTCGAAGGCAAGAT GAAAGGCGTT
 253 MIT_Sbay_c84_6418            +    130  4.02e-08 AACAACAAAA TCTCGAAGGCAAGCT AAGGTAAAAA
 254 SGD_Scer_YER014W             +    138  4.64e-08 AGCAACAAAG TGTCGAAGGCAAGTT CAAAGGCGTT
 255 --------------------------------------------------------------------------------
 256
 257 --------------------------------------------------------------------------------
 258         Motif 2 block diagrams
 259 --------------------------------------------------------------------------------
 260 SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
 261 -------------            ----------------  -------------
 262 WashU_Skud_Contig2052.17          1.5e-10  171_[-2]_814
 263 MIT_Spar_c19_8512                 1.5e-10  172_[-2]_813
 264 MIT_Smik_c283_5928                1.4e-09  131_[+2]_176
 265 SGD_Scer_YGL040C                  7.1e-09  171_[-2]_814
 266 MIT_Sbay_c77_8808                 7.5e-09  172_[-2]_813
 267 MIT_Smik_c273_7756                2.1e-08  170_[-2]_815
 268 MIT_Spar_c425_6072                2.9e-08  136_[+2]_171
 269 MIT_Sbay_c84_6418                   4e-08  129_[+2]_178
 270 SGD_Scer_YER014W                  4.6e-08  137_[+2]_170
 271 --------------------------------------------------------------------------------
 272
 273 --------------------------------------------------------------------------------
 274         Motif 2 in BLOCKS format
 275 --------------------------------------------------------------------------------
 276 BL   MOTIF 2 width=15 seqs=9
 277 WashU_Skud_Contig2052.17 (  172) GGCCTGAGGCAAGCT  1
 278 MIT_Spar_c19_8512        (  173) GGCCTGAGGCAAGCT  1
 279 MIT_Smik_c283_5928       (  132) GGTCGAAGGCAAGCT  1
 280 SGD_Scer_YGL040C         (  172) GGCTTGAGGCAAGCT  1
 281 MIT_Sbay_c77_8808        (  173) GGCCTGCGGCAGGCT  1
 282 MIT_Smik_c273_7756       (  171) GGCCTGAGGCAACAT  1
 283 MIT_Spar_c425_6072       (  137) TGTCGAAGGCAAGAT  1
 284 MIT_Sbay_c84_6418        (  130) TCTCGAAGGCAAGCT  1
 285 SGD_Scer_YER014W         (  138) TGTCGAAGGCAAGTT  1
 286 //
 287
 288 --------------------------------------------------------------------------------
 289
 290 --------------------------------------------------------------------------------
 291         Motif 2 position-specific scoring matrix
 292 --------------------------------------------------------------------------------
 293 log-odds matrix: alength= 4 w= 15 n= 6162 bayes= 9.41715 E= 6.2e-015
 294   -982   -982    192      4
 295   -982    -66    234   -982
 296   -982    166   -982     45
 297   -982    234   -982   -154
 298   -982   -982    134     78
 299     45   -982    166   -982
 300    145    -66   -982   -982
 301   -982   -982    251   -982
 302   -982   -982    251   -982
 303   -982    251   -982   -982
 304    162   -982   -982   -982
 305    145   -982    -66   -982
 306   -982    -66    234   -982
 307    -55    192   -982   -154
 308   -982   -982   -982    162
 309 --------------------------------------------------------------------------------
 310
 311 --------------------------------------------------------------------------------
 312         Motif 2 position-specific probability matrix
 313 --------------------------------------------------------------------------------
 314 letter-probability matrix: alength= 4 w= 15 nsites= 9 E= 6.2e-015
 315  0.000000  0.000000  0.666667  0.333333
 316  0.000000  0.111111  0.888889  0.000000
 317  0.000000  0.555556  0.000000  0.444444
 318  0.000000  0.888889  0.000000  0.111111
 319  0.000000  0.000000  0.444444  0.555556
 320  0.444444  0.000000  0.555556  0.000000
 321  0.888889  0.111111  0.000000  0.000000
 322  0.000000  0.000000  1.000000  0.000000
 323  0.000000  0.000000  1.000000  0.000000
 324  0.000000  1.000000  0.000000  0.000000
 325  1.000000  0.000000  0.000000  0.000000
 326  0.888889  0.000000  0.111111  0.000000
 327  0.000000  0.111111  0.888889  0.000000
 328  0.222222  0.666667  0.000000  0.111111
 329  0.000000  0.000000  0.000000  1.000000
 330 --------------------------------------------------------------------------------
 331
 332 --------------------------------------------------------------------------------
 333         Motif 2 regular expression
 334 --------------------------------------------------------------------------------
 335 [GT]G[CT]C[TG][GA]AGGCAAG[CA]T
 336 --------------------------------------------------------------------------------
 337
 338
 339
 340
 341 Time  8.46 secs.
 342
 343 ********************************************************************************
 344
 345
 346 ********************************************************************************
 347 MOTIF  3        width =   20   sites =   9   llr = 171   E-value = 1.2e-013
 348 ********************************************************************************
 349 --------------------------------------------------------------------------------
 350         Motif 3 Description
 351 --------------------------------------------------------------------------------
 352 Simplified        A  8718a:aa:a:942:9:1:6
 353 pos.-specific     C  :::::a::::::::::419:
 354 probability       G  2182::::::a16291:6:4
 355 matrix            T  :21:::::a::::61:621:
 356
 357          bits    2.5      *    *
 358                  2.3      *    *
 359                  2.0      *    *   *   *
 360                  1.8      *    *   *   *
 361 Information      1.5     *******   *   *
 362 content          1.3   * ********  **  *
 363 (27.5 bits)      1.0 * *********** *** **
 364                  0.8 * *********** *** **
 365                  0.5 ********************
 366                  0.3 ********************
 367                  0.0 --------------------
 368
 369 Multilevel           AAGAACAATAGAGTGATGCA
 370 consensus            GT G        AA  CT G
 371 sequence                          G
 372
 373 --------------------------------------------------------------------------------
 374
 375 --------------------------------------------------------------------------------
 376         Motif 3 sites sorted by position p-value
 377 --------------------------------------------------------------------------------
 378 Sequence name            Strand  Start   P-value                    Site
 379 -------------            ------  ----- ---------            --------------------
 380 MIT_Sbay_c84_6418            -     61  3.82e-11 AACAATAAGG AAGAACAATAGAAGGATGCG AAAGGACAAC
 381 MIT_Smik_c273_7756           +     99  1.39e-10 CCAATAAATC AGGAACAATAGAATGACGCA CCGAGTTTGC
 382 MIT_Spar_c425_6072           -     66  6.11e-10 GAATAATAGA GAGAACAATAGAGAGATCCG CGAAGGATAC
 383 WashU_Skud_Contig2052.17     +     97  7.49e-10 GCCAGAAATC ATGAACAATAGGATGACGCA TAGACGTCAC
 384 MIT_Spar_c19_8512            +     99  1.07e-09 GCCAAAAAAC AAGGACAATAGAATGACACA TAAAGTTTGC
 385 MIT_Sbay_c77_8808            +    102  1.50e-09 ATGAACTAAC ATTAACAATAGAGTGATGCA TAGACGTCAC
 386 MIT_Smik_c283_5928           -     68  2.37e-09 GAGTAATGGA AAGAACAATAGAGGGATTTG CAAAAGATAG
 387 SGD_Scer_YGL040C             +     98  2.54e-09 CAAGAAAATC AAAGACAATAGAGTGGCGCA TAGATGTTGC
 388 SGD_Scer_YER014W             -     66  6.53e-09 GTATAATAGA GAGAACAATAGAGATATTCG CGAAGAACAC
 389 --------------------------------------------------------------------------------
 390
 391 --------------------------------------------------------------------------------
 392         Motif 3 block diagrams
 393 --------------------------------------------------------------------------------
 394 SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
 395 -------------            ----------------  -------------
 396 MIT_Sbay_c84_6418                 3.8e-11  60_[-3]_242
 397 MIT_Smik_c273_7756                1.4e-10  98_[+3]_882
 398 MIT_Spar_c425_6072                6.1e-10  65_[-3]_237
 399 WashU_Skud_Contig2052.17          7.5e-10  96_[+3]_884
 400 MIT_Spar_c19_8512                 1.1e-09  98_[+3]_882
 401 MIT_Sbay_c77_8808                 1.5e-09  101_[+3]_879
 402 MIT_Smik_c283_5928                2.4e-09  67_[-3]_235
 403 SGD_Scer_YGL040C                  2.5e-09  97_[+3]_883
 404 SGD_Scer_YER014W                  6.5e-09  65_[-3]_237
 405 --------------------------------------------------------------------------------
 406
 407 --------------------------------------------------------------------------------
 408         Motif 3 in BLOCKS format
 409 --------------------------------------------------------------------------------
 410 BL   MOTIF 3 width=20 seqs=9
 411 MIT_Sbay_c84_6418        (   61) AAGAACAATAGAAGGATGCG  1
 412 MIT_Smik_c273_7756       (   99) AGGAACAATAGAATGACGCA  1
 413 MIT_Spar_c425_6072       (   66) GAGAACAATAGAGAGATCCG  1
 414 WashU_Skud_Contig2052.17 (   97) ATGAACAATAGGATGACGCA  1
 415 MIT_Spar_c19_8512        (   99) AAGGACAATAGAATGACACA  1
 416 MIT_Sbay_c77_8808        (  102) ATTAACAATAGAGTGATGCA  1
 417 MIT_Smik_c283_5928       (   68) AAGAACAATAGAGGGATTTG  1
 418 SGD_Scer_YGL040C         (   98) AAAGACAATAGAGTGGCGCA  1
 419 SGD_Scer_YER014W         (   66) GAGAACAATAGAGATATTCG  1
 420 //
 421
 422 --------------------------------------------------------------------------------
 423
 424 --------------------------------------------------------------------------------
 425         Motif 3 position-specific scoring matrix
 426 --------------------------------------------------------------------------------
 427 log-odds matrix: alength= 4 w= 20 n= 6117 bayes= 9.40656 E= 1.2e-013
 428    126   -982     34   -982
 429    104   -982    -66    -55
 430   -154   -982    215   -154
 431    126   -982     34   -982
 432    162   -982   -982   -982
 433   -982    251   -982   -982
 434    162   -982   -982   -982
 435    162   -982   -982   -982
 436   -982   -982   -982    162
 437    162   -982   -982   -982
 438   -982   -982    251   -982
 439    145   -982    -66   -982
 440     45   -982    166   -982
 441    -55   -982     34     78
 442   -982   -982    234   -154
 443    145   -982    -66   -982
 444   -982    134   -982     78
 445   -154    -66    166    -55
 446   -982    234   -982   -154
 447     78   -982    134   -982
 448 --------------------------------------------------------------------------------
 449
 450 --------------------------------------------------------------------------------
 451         Motif 3 position-specific probability matrix
 452 --------------------------------------------------------------------------------
 453 letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 1.2e-013
 454  0.777778  0.000000  0.222222  0.000000
 455  0.666667  0.000000  0.111111  0.222222
 456  0.111111  0.000000  0.777778  0.111111
 457  0.777778  0.000000  0.222222  0.000000
 458  1.000000  0.000000  0.000000  0.000000
 459  0.000000  1.000000  0.000000  0.000000
 460  1.000000  0.000000  0.000000  0.000000
 461  1.000000  0.000000  0.000000  0.000000
 462  0.000000  0.000000  0.000000  1.000000
 463  1.000000  0.000000  0.000000  0.000000
 464  0.000000  0.000000  1.000000  0.000000
 465  0.888889  0.000000  0.111111  0.000000
 466  0.444444  0.000000  0.555556  0.000000
 467  0.222222  0.000000  0.222222  0.555556
 468  0.000000  0.000000  0.888889  0.111111
 469  0.888889  0.000000  0.111111  0.000000
 470  0.000000  0.444444  0.000000  0.555556
 471  0.111111  0.111111  0.555556  0.222222
 472  0.000000  0.888889  0.000000  0.111111
 473  0.555556  0.000000  0.444444  0.000000
 474 --------------------------------------------------------------------------------
 475
 476 --------------------------------------------------------------------------------
 477         Motif 3 regular expression
 478 --------------------------------------------------------------------------------
 479 [AG][AT]G[AG]ACAATAGA[GA][TAG]GA[TC][GT]C[AG]
 480 --------------------------------------------------------------------------------
 481
 482
 483
 484
 485 Time 12.41 secs.
 486
 487 ********************************************************************************
 488
 489
 490 ********************************************************************************
 491 MOTIF  4        width =   20   sites =   9   llr = 148   E-value = 1.9e-005
 492 ********************************************************************************
 493 --------------------------------------------------------------------------------
 494         Motif 4 Description
 495 --------------------------------------------------------------------------------
 496 Simplified        A  :2:::7:11:38a7:a427a
 497 pos.-specific     C  8217119:7412::9:473:
 498 probability       G  :2739:11:16::31::1::
 499 matrix            T  232::2:824::::::1:::
 500
 501          bits    2.5
 502                  2.3
 503                  2.0     * *       *
 504                  1.8     * *       *
 505 Information      1.5 *  ** *     * **   *
 506 content          1.3 *  ** *     * **   *
 507 (23.7 bits)      1.0 * *** * *  ***** ***
 508                  0.8 * *** ********** ***
 509                  0.5 * ******************
 510                  0.3 * ******************
 511                  0.0 --------------------
 512
 513 Multilevel           CTGCGACTCCGAAACAACAA
 514 consensus            TATG T  TTAC G  CAC
 515 sequence              C
 516                       G
 517 --------------------------------------------------------------------------------
 518
 519 --------------------------------------------------------------------------------
 520         Motif 4 sites sorted by position p-value
 521 --------------------------------------------------------------------------------
 522 Sequence name            Strand  Start   P-value                    Site
 523 -------------            ------  ----- ---------            --------------------
 524 MIT_Spar_c425_6072           +    115  3.47e-12 TTTAAATACT CCGCGACTCCGAAGCAACAA AATGTCGAAG
 525 SGD_Scer_YER014W             +    116  3.47e-12 TTTGAATACT CCGCGACTCCGAAGCAACAA AGTGTCGAAG
 526 MIT_Sbay_c84_6418            +    108  4.98e-12 TTTTTATACT CTGCGACTCCGAAACAACAA AATCTCGAAG
 527 SGD_Scer_YGL040C             +    316  8.20e-09 TGATGTATTT CGGCGTCTCTACAAGACCCA ATAAAGTAAT
 528 MIT_Smik_c283_5928           +    112  1.07e-08 CTTTTTTAAA TACGGACTCCGAAGCAACAA GGTCGAAGGC
 529 WashU_Skud_Contig2052.17     -    460  4.18e-08 GAAGAGTCTT CATCGACGCTAAAACACAAA TTCAAGAAGA
 530 MIT_Spar_c19_8512            +    311  5.58e-08 GGGAGTATAC CTGCCTCTTTACAACACCCA ACAAAACACT
 531 MIT_Sbay_c77_8808            +    766  8.32e-07 TGTTGCAATA TGTGGACAAGGAAACACGAA ATATATTGGG
 532 MIT_Smik_c273_7756           -    311  8.97e-07 AATATTGTAA CTGGGCGTTTCAAACATACA AGTGTATATT
 533 --------------------------------------------------------------------------------
 534
 535 --------------------------------------------------------------------------------
 536         Motif 4 block diagrams
 537 --------------------------------------------------------------------------------
 538 SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
 539 -------------            ----------------  -------------
 540 MIT_Spar_c425_6072                3.5e-12  114_[+4]_188
 541 SGD_Scer_YER014W                  3.5e-12  115_[+4]_187
 542 MIT_Sbay_c84_6418                   5e-12  107_[+4]_195
 543 SGD_Scer_YGL040C                  8.2e-09  315_[+4]_665
 544 MIT_Smik_c283_5928                1.1e-08  111_[+4]_191
 545 WashU_Skud_Contig2052.17          4.2e-08  459_[-4]_521
 546 MIT_Spar_c19_8512                 5.6e-08  310_[+4]_670
 547 MIT_Sbay_c77_8808                 8.3e-07  765_[+4]_215
 548 MIT_Smik_c273_7756                  9e-07  310_[-4]_670
 549 --------------------------------------------------------------------------------
 550
 551 --------------------------------------------------------------------------------
 552         Motif 4 in BLOCKS format
 553 --------------------------------------------------------------------------------
 554 BL   MOTIF 4 width=20 seqs=9
 555 MIT_Spar_c425_6072       (  115) CCGCGACTCCGAAGCAACAA  1
 556 SGD_Scer_YER014W         (  116) CCGCGACTCCGAAGCAACAA  1
 557 MIT_Sbay_c84_6418        (  108) CTGCGACTCCGAAACAACAA  1
 558 SGD_Scer_YGL040C         (  316) CGGCGTCTCTACAAGACCCA  1
 559 MIT_Smik_c283_5928       (  112) TACGGACTCCGAAGCAACAA  1
 560 WashU_Skud_Contig2052.17 (  460) CATCGACGCTAAAACACAAA  1
 561 MIT_Spar_c19_8512        (  311) CTGCCTCTTTACAACACCCA  1
 562 MIT_Sbay_c77_8808        (  766) TGTGGACAAGGAAACACGAA  1
 563 MIT_Smik_c273_7756       (  311) CTGGGCGTTTCAAACATACA  1
 564 //
 565
 566 --------------------------------------------------------------------------------
 567
 568 --------------------------------------------------------------------------------
 569         Motif 4 position-specific scoring matrix
 570 --------------------------------------------------------------------------------
 571 log-odds matrix: alength= 4 w= 20 n= 6117 bayes= 9.40656 E= 1.9e-005
 572   -982    215   -982    -55
 573    -55     34     34      4
 574   -982    -66    192    -55
 575   -982    192     92   -982
 576   -982    -66    234   -982
 577    104    -66   -982    -55
 578   -982    234    -66   -982
 579   -154   -982    -66    126
 580   -154    192   -982    -55
 581   -982    134    -66     45
 582      4    -66    166   -982
 583    126     34   -982   -982
 584    162   -982   -982   -982
 585    104   -982     92   -982
 586   -982    234    -66   -982
 587    162   -982   -982   -982
 588     45    134   -982   -154
 589    -55    192    -66   -982
 590    104     92   -982   -982
 591    162   -982   -982   -982
 592 --------------------------------------------------------------------------------
 593
 594 --------------------------------------------------------------------------------
 595         Motif 4 position-specific probability matrix
 596 --------------------------------------------------------------------------------
 597 letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 1.9e-005
 598  0.000000  0.777778  0.000000  0.222222
 599  0.222222  0.222222  0.222222  0.333333
 600  0.000000  0.111111  0.666667  0.222222
 601  0.000000  0.666667  0.333333  0.000000
 602  0.000000  0.111111  0.888889  0.000000
 603  0.666667  0.111111  0.000000  0.222222
 604  0.000000  0.888889  0.111111  0.000000
 605  0.111111  0.000000  0.111111  0.777778
 606  0.111111  0.666667  0.000000  0.222222
 607  0.000000  0.444444  0.111111  0.444444
 608  0.333333  0.111111  0.555556  0.000000
 609  0.777778  0.222222  0.000000  0.000000
 610  1.000000  0.000000  0.000000  0.000000
 611  0.666667  0.000000  0.333333  0.000000
 612  0.000000  0.888889  0.111111  0.000000
 613  1.000000  0.000000  0.000000  0.000000
 614  0.444444  0.444444  0.000000  0.111111
 615  0.222222  0.666667  0.111111  0.000000
 616  0.666667  0.333333  0.000000  0.000000
 617  1.000000  0.000000  0.000000  0.000000
 618 --------------------------------------------------------------------------------
 619
 620 --------------------------------------------------------------------------------
 621         Motif 4 regular expression
 622 --------------------------------------------------------------------------------
 623 [CT][TACGA][GT][CG]G[AT]CT[CT][CT][GA][AC]A[AG]CA[AC][CA][AC]A
 624 --------------------------------------------------------------------------------
 625
 626
 627
 628
 629 Time 16.27 secs.
 630
 631 ********************************************************************************
 632
 633
 634 ********************************************************************************
 635 MOTIF  5        width =   20   sites =   9   llr = 142   E-value = 8.9e-002
 636 ********************************************************************************
 637 --------------------------------------------------------------------------------
 638         Motif 5 Description
 639 --------------------------------------------------------------------------------
 640 Simplified        A  :22::::41::::128:999
 641 pos.-specific     C  :1:971::6:a1::::::::
 642 probability       G  ::7:1112::::2:1:1:::
 643 matrix            T  a71128933a:989729111
 644
 645          bits    2.5           *
 646                  2.3           *
 647                  2.0    *      *
 648                  1.8    *      *
 649 Information      1.5 *  *     **
 650 content          1.3 *  *  *  ***    *
 651 (22.7 bits)      1.0 * *** *  *****  ****
 652                  0.8 * ***** ****** *****
 653                  0.5 ******* ************
 654                  0.3 ********************
 655                  0.0 --------------------
 656
 657 Multilevel           TTGCCTTACTCTTTTATAAA
 658 consensus             AA T  TT   G AT
 659 sequence                    G
 660
 661 --------------------------------------------------------------------------------
 662
 663 --------------------------------------------------------------------------------
 664         Motif 5 sites sorted by position p-value
 665 --------------------------------------------------------------------------------
 666 Sequence name            Strand  Start   P-value                    Site
 667 -------------            ------  ----- ---------            --------------------
 668 MIT_Spar_c19_8512            +    143  7.75e-12 ATTTATTAGG TTGCCTTACTCTTTTATAAA TCAAGCGGGC
 669 MIT_Sbay_c77_8808            +    147  1.19e-11 TTTTATTGTG TTGCCTTGCTCTTTTATAAA TCAGGCAGCC
 670 WashU_Skud_Contig2052.17     +    142  1.97e-11 TTCATATAAG TTGCCTTTCTCTTTTATAAA TTGGGCAGGC
 671 SGD_Scer_YGL040C             +    142  3.83e-10 ATTTATTAGG TTGCCTTACTCTTATATAAA TCAAGCGGGA
 672 MIT_Smik_c273_7756           +    567  2.20e-08 AACAATAAAG TTACCTTGATCTTTAATAAA ATATTCCCCC
 673 MIT_Smik_c283_5928           +     92  1.78e-07 GTTCTTTCCA TTACTCTTTTCTTTTTTAAA TACGGACTCC
 674 MIT_Spar_c425_6072           +     91  4.97e-07 TTCTCTCTAT TATTCTTTTTCTTTTTTAAA TACTCCGCGA
 675 SGD_Scer_YER014W             +    206  1.59e-06 AAAGAAAGGT TAGCGTTACTCTGTGATTTT TTTCATGTAA
 676 MIT_Sbay_c84_6418            -     27  2.13e-06 GACAACAGTC TCGCTGGATTCCGTAAGAAA CAGCGGAATA
 677 --------------------------------------------------------------------------------
 678
 679 --------------------------------------------------------------------------------
 680         Motif 5 block diagrams
 681 --------------------------------------------------------------------------------
 682 SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
 683 -------------            ----------------  -------------
 684 MIT_Spar_c19_8512                 7.7e-12  142_[+5]_838
 685 MIT_Sbay_c77_8808                 1.2e-11  146_[+5]_834
 686 WashU_Skud_Contig2052.17            2e-11  141_[+5]_839
 687 SGD_Scer_YGL040C                  3.8e-10  141_[+5]_839
 688 MIT_Smik_c273_7756                2.2e-08  566_[+5]_414
 689 MIT_Smik_c283_5928                1.8e-07  91_[+5]_211
 690 MIT_Spar_c425_6072                  5e-07  90_[+5]_212
 691 SGD_Scer_YER014W                  1.6e-06  205_[+5]_97
 692 MIT_Sbay_c84_6418                 2.1e-06  26_[-5]_276
 693 --------------------------------------------------------------------------------
 694
 695 --------------------------------------------------------------------------------
 696         Motif 5 in BLOCKS format
 697 --------------------------------------------------------------------------------
 698 BL   MOTIF 5 width=20 seqs=9
 699 MIT_Spar_c19_8512        (  143) TTGCCTTACTCTTTTATAAA  1
 700 MIT_Sbay_c77_8808        (  147) TTGCCTTGCTCTTTTATAAA  1
 701 WashU_Skud_Contig2052.17 (  142) TTGCCTTTCTCTTTTATAAA  1
 702 SGD_Scer_YGL040C         (  142) TTGCCTTACTCTTATATAAA  1
 703 MIT_Smik_c273_7756       (  567) TTACCTTGATCTTTAATAAA  1
 704 MIT_Smik_c283_5928       (   92) TTACTCTTTTCTTTTTTAAA  1
 705 MIT_Spar_c425_6072       (   91) TATTCTTTTTCTTTTTTAAA  1
 706 SGD_Scer_YER014W         (  206) TAGCGTTACTCTGTGATTTT  1
 707 MIT_Sbay_c84_6418        (   27) TCGCTGGATTCCGTAAGAAA  1
 708 //
 709
 710 --------------------------------------------------------------------------------
 711
 712 --------------------------------------------------------------------------------
 713         Motif 5 position-specific scoring matrix
 714 --------------------------------------------------------------------------------
 715 log-odds matrix: alength= 4 w= 20 n= 6117 bayes= 9.40656 E= 8.9e-002
 716   -982   -982   -982    162
 717    -55    -66   -982    104
 718    -55   -982    192   -154
 719   -982    234   -982   -154
 720   -982    192    -66    -55
 721   -982    -66    -66    126
 722   -982   -982    -66    145
 723     45   -982     34      4
 724   -154    166   -982      4
 725   -982   -982   -982    162
 726   -982    251   -982   -982
 727   -982    -66   -982    145
 728   -982   -982     34    126
 729   -154   -982   -982    145
 730    -55   -982    -66    104
 731    126   -982   -982    -55
 732   -982   -982    -66    145
 733    145   -982   -982   -154
 734    145   -982   -982   -154
 735    145   -982   -982   -154
 736 --------------------------------------------------------------------------------
 737
 738 --------------------------------------------------------------------------------
 739         Motif 5 position-specific probability matrix
 740 --------------------------------------------------------------------------------
 741 letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 8.9e-002
 742  0.000000  0.000000  0.000000  1.000000
 743  0.222222  0.111111  0.000000  0.666667
 744  0.222222  0.000000  0.666667  0.111111
 745  0.000000  0.888889  0.000000  0.111111
 746  0.000000  0.666667  0.111111  0.222222
 747  0.000000  0.111111  0.111111  0.777778
 748  0.000000  0.000000  0.111111  0.888889
 749  0.444444  0.000000  0.222222  0.333333
 750  0.111111  0.555556  0.000000  0.333333
 751  0.000000  0.000000  0.000000  1.000000
 752  0.000000  1.000000  0.000000  0.000000
 753  0.000000  0.111111  0.000000  0.888889
 754  0.000000  0.000000  0.222222  0.777778
 755  0.111111  0.000000  0.000000  0.888889
 756  0.222222  0.000000  0.111111  0.666667
 757  0.777778  0.000000  0.000000  0.222222
 758  0.000000  0.000000  0.111111  0.888889
 759  0.888889  0.000000  0.000000  0.111111
 760  0.888889  0.000000  0.000000  0.111111
 761  0.888889  0.000000  0.000000  0.111111
 762 --------------------------------------------------------------------------------
 763
 764 --------------------------------------------------------------------------------
 765         Motif 5 regular expression
 766 --------------------------------------------------------------------------------
 767 T[TA][GA]C[CT]TT[ATG][CT]TCT[TG]T[TA][AT]TAAA
 768 --------------------------------------------------------------------------------
 769
 770
 771
 772
 773 Time 20.21 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_YGL040C                 6.13e-24  97_[+3(2.54e-09)]_24_[+5(3.83e-10)]_10_[-2(7.15e-09)]_13_[+1(4.10e-12)]_96_[+4(8.20e-09)]_665
 788 MIT_Spar_c19_8512                1.11e-26  98_[+3(1.07e-09)]_24_[+5(7.75e-12)]_10_[-2(1.54e-10)]_13_[+1(4.10e-12)]_13_[+5(5.08e-05)]_57_[+4(5.58e-08)]_670
 789 MIT_Smik_c273_7756               4.21e-19  98_[+3(1.39e-10)]_52_[-2(2.10e-08)]_13_[+1(6.00e-10)]_92_[-4(8.97e-07)]_236_[+5(2.20e-08)]_414
 790 MIT_Sbay_c77_8808                9.48e-21  101_[+3(1.50e-09)]_25_[+5(1.19e-11)]_6_[-2(7.55e-09)]_12_[+1(5.23e-09)]_250_[-3(4.01e-05)]_276_[+4(8.32e-07)]_141_[+2(5.20e-05)]_59
 791 WashU_Skud_Contig2052.17         1.47e-26  96_[+3(7.49e-10)]_25_[+5(1.97e-11)]_10_[-2(1.54e-10)]_13_[+1(4.10e-12)]_98_[-4(1.54e-05)]_122_[-4(4.18e-08)]_191_[-1(9.59e-05)]_80_[-4(2.53e-05)]_16_[-1(9.59e-05)]_174
 792 SGD_Scer_YER014W                 1.85e-24  65_[-3(6.53e-09)]_30_[+4(3.47e-12)]_2_[+2(4.64e-08)]_16_[-1(1.37e-11)]_17_[+5(1.59e-06)]_97
 793 MIT_Spar_c425_6072               5.95e-25  65_[-3(6.11e-10)]_5_[+5(4.97e-07)]_4_[+4(3.47e-12)]_2_[+2(2.87e-08)]_16_[-1(2.28e-10)]_14_[+1(4.94e-05)]_101
 794 MIT_Smik_c283_5928               4.38e-23  67_[-3(2.37e-09)]_4_[+5(1.78e-07)]_[+4(1.07e-08)]_[+2(1.35e-09)]_16_[-1(1.09e-10)]_140
 795 MIT_Sbay_c84_6418                1.54e-25  26_[-5(2.13e-06)]_14_[-3(3.82e-11)]_27_[+4(4.98e-12)]_2_[+2(4.02e-08)]_19_[-1(1.01e-10)]_139
 796 --------------------------------------------------------------------------------
 797
 798 ********************************************************************************
 799
 800
 801 ********************************************************************************
 802 Stopped because nmotifs = 5 reached.
 803 ********************************************************************************
 804
 805 CPU: dhn02990.mrc-dunn.cam.ac.uk
 806
 807 ********************************************************************************