t/data/map_hem/HEM3-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= HEM3-HEM13.fa
  32 ALPHABET= ACGT
  33 Sequence name            Weight Length  Sequence name            Weight Length
  34 -------------            ------ ------  -------------            ------ ------
  35 SGD_Scer_YDL205C         1.0000    860  MIT_Spar_c429_3020       1.0000    860
  36 MIT_Smik_c193_2483       1.0000    860  MIT_Sbay_c841_3215       1.0000    860
  37 WashU_Skud_Contig1850.5  1.0000    860  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 HEM3-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=            8300    N=               9
  59 strands: + -
  60 sample: seed=            0    seqfrac=         1
  61 Letter frequencies in dataset:
  62 A 0.301 C 0.199 G 0.199 T 0.301
  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 = 197   E-value = 2.8e-022
  70 ********************************************************************************
  71 --------------------------------------------------------------------------------
  72         Motif 1 Description
  73 --------------------------------------------------------------------------------
  74 Simplified        A  :::::9692aa4:4::aa:a
  75 pos.-specific     C  :::::::::::::::3::9:
  76 probability       G  aa:aa1412::666:6::::
  77 matrix            T  ::a:::::6:::4:a1::1:
  78
  79          bits    2.5 ** **
  80                  2.3 ** **
  81                  2.0 ** **             *
  82                  1.8 ** **             *
  83 Information      1.5 *****    **   * ****
  84 content          1.3 ****** * **   * ****
  85 (31.6 bits)      1.0 ******** ***********
  86                  0.8 ******** ***********
  87                  0.5 ********************
  88                  0.3 ********************
  89                  0.0 --------------------
  90
  91 Multilevel           GGTGGAAATAAGGGTGAACA
  92 consensus                  G A  ATA C
  93 sequence                     G
  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_Contig1850.5      -    716  1.22e-12 ATCCTTTGAG GGTGGAAATAAGGGTGAACA ATAAGGGGAG
 103 MIT_Sbay_c841_3215           -    735  1.22e-12 GTCGTTTGAG GGTGGAAATAAGGGTGAACA ATAAGGGGAG
 104 MIT_Spar_c429_3020           -    709  1.22e-12 ATCGTTTGAG GGTGGAAATAAGGGTGAACA ATAAGGGGAG
 105 SGD_Scer_YDL205C             -    708  1.22e-12 ATCGTTTGAG GGTGGAAATAAGGGTGAACA ATAAGGGGAG
 106 MIT_Smik_c193_2483           -    709  1.22e-10 ATCGTTTGAG GGTGGAAATAAGGGTGAATA ATAAGGGGAG
 107 MIT_Spar_c130_3912           +    679  1.35e-10 CAACGATTGT GGTGGAGAGAAATATCAACA GGGCAAGGCA
 108 SGD_Scer_YDR044W             +    684  3.84e-10 CAACAATTAC GGTGGGGAGAAATATCAACA AAAGGGCAAG
 109 MIT_Sbay_c896_21290          +    685  5.43e-10 CGACTAAAAC GGTGGAGGAAAATATCAACA AGGCAAGGCT
 110 WashU_Smik_Contig2283.3      +    687  5.84e-10 CAACAATTAC GGTGGAGAAAAATATTAACA AGGGAAGGCA
 111 --------------------------------------------------------------------------------
 112
 113 --------------------------------------------------------------------------------
 114         Motif 1 block diagrams
 115 --------------------------------------------------------------------------------
 116 SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
 117 -------------            ----------------  -------------
 118 WashU_Skud_Contig1850.5           1.2e-12  715_[-1]_125
 119 MIT_Sbay_c841_3215                1.2e-12  734_[-1]_106
 120 MIT_Spar_c429_3020                1.2e-12  708_[-1]_132
 121 SGD_Scer_YDL205C                  1.2e-12  707_[-1]_133
 122 MIT_Smik_c193_2483                1.2e-10  708_[-1]_132
 123 MIT_Spar_c130_3912                1.4e-10  678_[+1]_302
 124 SGD_Scer_YDR044W                  3.8e-10  683_[+1]_297
 125 MIT_Sbay_c896_21290               5.4e-10  684_[+1]_296
 126 WashU_Smik_Contig2283.3           5.8e-10  686_[+1]_294
 127 --------------------------------------------------------------------------------
 128
 129 --------------------------------------------------------------------------------
 130         Motif 1 in BLOCKS format
 131 --------------------------------------------------------------------------------
 132 BL   MOTIF 1 width=20 seqs=9
 133 WashU_Skud_Contig1850.5  (  716) GGTGGAAATAAGGGTGAACA  1
 134 MIT_Sbay_c841_3215       (  735) GGTGGAAATAAGGGTGAACA  1
 135 MIT_Spar_c429_3020       (  709) GGTGGAAATAAGGGTGAACA  1
 136 SGD_Scer_YDL205C         (  708) GGTGGAAATAAGGGTGAACA  1
 137 MIT_Smik_c193_2483       (  709) GGTGGAAATAAGGGTGAATA  1
 138 MIT_Spar_c130_3912       (  679) GGTGGAGAGAAATATCAACA  1
 139 SGD_Scer_YDR044W         (  684) GGTGGGGAGAAATATCAACA  1
 140 MIT_Sbay_c896_21290      (  685) GGTGGAGGAAAATATCAACA  1
 141 WashU_Smik_Contig2283.3  (  687) GGTGGAGAAAAATATTAACA  1
 142 //
 143
 144 --------------------------------------------------------------------------------
 145
 146 --------------------------------------------------------------------------------
 147         Motif 1 position-specific scoring matrix
 148 --------------------------------------------------------------------------------
 149 log-odds matrix: alength= 4 w= 20 n= 8129 bayes= 9.81734 E= 2.8e-022
 150   -982   -982    251   -982
 151   -982   -982    251   -982
 152   -982   -982   -982    162
 153   -982   -982    251   -982
 154   -982   -982    251   -982
 155    145   -982    -66   -982
 156     78   -982    134   -982
 157    145   -982    -66   -982
 158    -55   -982     34     78
 159    162   -982   -982   -982
 160    162   -982   -982   -982
 161     45   -982    166   -982
 162   -982   -982    166     45
 163     45   -982    166   -982
 164   -982   -982   -982    162
 165   -982     92    166   -154
 166    162   -982   -982   -982
 167    162   -982   -982   -982
 168   -982    234   -982   -154
 169    162   -982   -982   -982
 170 --------------------------------------------------------------------------------
 171
 172 --------------------------------------------------------------------------------
 173         Motif 1 position-specific probability matrix
 174 --------------------------------------------------------------------------------
 175 letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 2.8e-022
 176  0.000000  0.000000  1.000000  0.000000
 177  0.000000  0.000000  1.000000  0.000000
 178  0.000000  0.000000  0.000000  1.000000
 179  0.000000  0.000000  1.000000  0.000000
 180  0.000000  0.000000  1.000000  0.000000
 181  0.888889  0.000000  0.111111  0.000000
 182  0.555556  0.000000  0.444444  0.000000
 183  0.888889  0.000000  0.111111  0.000000
 184  0.222222  0.000000  0.222222  0.555556
 185  1.000000  0.000000  0.000000  0.000000
 186  1.000000  0.000000  0.000000  0.000000
 187  0.444444  0.000000  0.555556  0.000000
 188  0.000000  0.000000  0.555556  0.444444
 189  0.444444  0.000000  0.555556  0.000000
 190  0.000000  0.000000  0.000000  1.000000
 191  0.000000  0.333333  0.555556  0.111111
 192  1.000000  0.000000  0.000000  0.000000
 193  1.000000  0.000000  0.000000  0.000000
 194  0.000000  0.888889  0.000000  0.111111
 195  1.000000  0.000000  0.000000  0.000000
 196 --------------------------------------------------------------------------------
 197
 198 --------------------------------------------------------------------------------
 199         Motif 1 regular expression
 200 --------------------------------------------------------------------------------
 201 GGTGGA[AG]A[TAG]AA[GA][GT][GA]T[GC]AACA
 202 --------------------------------------------------------------------------------
 203
 204
 205
 206
 207 Time  7.14 secs.
 208
 209 ********************************************************************************
 210
 211
 212 ********************************************************************************
 213 MOTIF  2        width =   20   sites =   9   llr = 199   E-value = 2.7e-023
 214 ********************************************************************************
 215 --------------------------------------------------------------------------------
 216         Motif 2 Description
 217 --------------------------------------------------------------------------------
 218 Simplified        A  3::1:a:6:::a7::::1:1
 219 pos.-specific     C  ::a:6:4:::a:316:a878
 220 probability       G  7a:94:::6a:::::1:::1
 221 matrix            T  ::::::644::::949:13:
 222
 223          bits    2.5  **      **     *
 224                  2.3  **      **     *
 225                  2.0  ***     **     *
 226                  1.8  ***     **     *
 227 Information      1.5  *****   ***    *  *
 228 content          1.3 ******   *** * *****
 229 (31.9 bits)      1.0 ******* ************
 230                  0.8 ********************
 231                  0.5 ********************
 232                  0.3 ********************
 233                  0.0 --------------------
 234
 235 Multilevel           GGCGCATAGGCAATCTCCCC
 236 consensus            A   G CTT   C T   T
 237 sequence
 238
 239 --------------------------------------------------------------------------------
 240
 241 --------------------------------------------------------------------------------
 242         Motif 2 sites sorted by position p-value
 243 --------------------------------------------------------------------------------
 244 Sequence name            Strand  Start   P-value                    Site
 245 -------------            ------  ----- ---------            --------------------
 246 WashU_Skud_Contig1850.5      +    692  2.30e-13 GTGACGTTTA GGCGCATAGGCAATCTCCCC TTATTGTTCA
 247 SGD_Scer_YDL205C             +    684  2.30e-13 GTGACGTTTA GGCGCATAGGCAATCTCCCC TTATTGTTCA
 248 MIT_Sbay_c841_3215           +    711  3.52e-12 GTGACGTTTT AGCGCATAGGCAATCTCCCC TTATTGTTCA
 249 MIT_Smik_c193_2483           +    685  3.52e-12 ATGACGTTTA AGCGCATAGGCAATCTCCCC TTATTATTCA
 250 MIT_Spar_c429_3020           +    685  4.30e-12 GTGACGTTTA GGCGCATAGGCAACCTCCCC TTATTGTTCA
 251 WashU_Smik_Contig2283.3      +    739  3.24e-11 ATTGAGAAGC GGCGGACTTGCACTTTCCTC GAAGAAAAAA
 252 SGD_Scer_YDR044W             +    733  3.60e-10 TCTGGAAAGT GGCAGACTTGCACTTTCCTC GAAAAGAAAA
 253 MIT_Spar_c130_3912           +    730  1.03e-09 TTTTGGAAGT GGCGGACTTGCACTTTCTTG AAAAGAAAAA
 254 MIT_Sbay_c896_21290          +    731  2.40e-09 TTCGAAGAAA AGCGGACTTGCAATTGCACA ACCGTATCGA
 255 --------------------------------------------------------------------------------
 256
 257 --------------------------------------------------------------------------------
 258         Motif 2 block diagrams
 259 --------------------------------------------------------------------------------
 260 SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
 261 -------------            ----------------  -------------
 262 WashU_Skud_Contig1850.5           2.3e-13  691_[+2]_149
 263 SGD_Scer_YDL205C                  2.3e-13  683_[+2]_157
 264 MIT_Sbay_c841_3215                3.5e-12  710_[+2]_130
 265 MIT_Smik_c193_2483                3.5e-12  684_[+2]_156
 266 MIT_Spar_c429_3020                4.3e-12  684_[+2]_156
 267 WashU_Smik_Contig2283.3           3.2e-11  738_[+2]_242
 268 SGD_Scer_YDR044W                  3.6e-10  732_[+2]_248
 269 MIT_Spar_c130_3912                  1e-09  729_[+2]_251
 270 MIT_Sbay_c896_21290               2.4e-09  730_[+2]_250
 271 --------------------------------------------------------------------------------
 272
 273 --------------------------------------------------------------------------------
 274         Motif 2 in BLOCKS format
 275 --------------------------------------------------------------------------------
 276 BL   MOTIF 2 width=20 seqs=9
 277 WashU_Skud_Contig1850.5  (  692) GGCGCATAGGCAATCTCCCC  1
 278 SGD_Scer_YDL205C         (  684) GGCGCATAGGCAATCTCCCC  1
 279 MIT_Sbay_c841_3215       (  711) AGCGCATAGGCAATCTCCCC  1
 280 MIT_Smik_c193_2483       (  685) AGCGCATAGGCAATCTCCCC  1
 281 MIT_Spar_c429_3020       (  685) GGCGCATAGGCAACCTCCCC  1
 282 WashU_Smik_Contig2283.3  (  739) GGCGGACTTGCACTTTCCTC  1
 283 SGD_Scer_YDR044W         (  733) GGCAGACTTGCACTTTCCTC  1
 284 MIT_Spar_c130_3912       (  730) GGCGGACTTGCACTTTCTTG  1
 285 MIT_Sbay_c896_21290      (  731) AGCGGACTTGCAATTGCACA  1
 286 //
 287
 288 --------------------------------------------------------------------------------
 289
 290 --------------------------------------------------------------------------------
 291         Motif 2 position-specific scoring matrix
 292 --------------------------------------------------------------------------------
 293 log-odds matrix: alength= 4 w= 20 n= 8129 bayes= 9.81734 E= 2.7e-023
 294      4   -982    192   -982
 295   -982   -982    251   -982
 296   -982    251   -982   -982
 297   -154   -982    234   -982
 298   -982    166    134   -982
 299    162   -982   -982   -982
 300   -982    134   -982     78
 301     78   -982   -982     45
 302   -982   -982    166     45
 303   -982   -982    251   -982
 304   -982    251   -982   -982
 305    162   -982   -982   -982
 306    104     92   -982   -982
 307   -982    -66   -982    145
 308   -982    166   -982     45
 309   -982   -982    -66    145
 310   -982    251   -982   -982
 311   -154    215   -982   -154
 312   -982    192   -982      4
 313   -154    215    -66   -982
 314 --------------------------------------------------------------------------------
 315
 316 --------------------------------------------------------------------------------
 317         Motif 2 position-specific probability matrix
 318 --------------------------------------------------------------------------------
 319 letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 2.7e-023
 320  0.333333  0.000000  0.666667  0.000000
 321  0.000000  0.000000  1.000000  0.000000
 322  0.000000  1.000000  0.000000  0.000000
 323  0.111111  0.000000  0.888889  0.000000
 324  0.000000  0.555556  0.444444  0.000000
 325  1.000000  0.000000  0.000000  0.000000
 326  0.000000  0.444444  0.000000  0.555556
 327  0.555556  0.000000  0.000000  0.444444
 328  0.000000  0.000000  0.555556  0.444444
 329  0.000000  0.000000  1.000000  0.000000
 330  0.000000  1.000000  0.000000  0.000000
 331  1.000000  0.000000  0.000000  0.000000
 332  0.666667  0.333333  0.000000  0.000000
 333  0.000000  0.111111  0.000000  0.888889
 334  0.000000  0.555556  0.000000  0.444444
 335  0.000000  0.000000  0.111111  0.888889
 336  0.000000  1.000000  0.000000  0.000000
 337  0.111111  0.777778  0.000000  0.111111
 338  0.000000  0.666667  0.000000  0.333333
 339  0.111111  0.777778  0.111111  0.000000
 340 --------------------------------------------------------------------------------
 341
 342 --------------------------------------------------------------------------------
 343         Motif 2 regular expression
 344 --------------------------------------------------------------------------------
 345 [GA]GCG[CG]A[TC][AT][GT]GCA[AC]T[CT]TCC[CT]C
 346 --------------------------------------------------------------------------------
 347
 348
 349
 350
 351 Time 14.04 secs.
 352
 353 ********************************************************************************
 354
 355
 356 ********************************************************************************
 357 MOTIF  3        width =   15   sites =   9   llr = 162   E-value = 1.1e-016
 358 ********************************************************************************
 359 --------------------------------------------------------------------------------
 360         Motif 3 Description
 361 --------------------------------------------------------------------------------
 362 Simplified        A  1:::::6::6:::a:
 363 pos.-specific     C  :79:1::a9:6a::a
 364 probability       G  ::189:::::4:a::
 365 matrix            T  93:2:a4:14:::::
 366
 367          bits    2.5        *   ** *
 368                  2.3        *   ** *
 369                  2.0   * *  **  ** *
 370                  1.8   * *  **  ** *
 371 Information      1.5   **** ** *****
 372 content          1.3  ***** ** *****
 373 (26.0 bits)      1.0 ****** ** *****
 374                  0.8 ***************
 375                  0.5 ***************
 376                  0.3 ***************
 377                  0.0 ---------------
 378
 379 Multilevel           TCCGGTACCACCGAC
 380 consensus             T T  T  TG
 381 sequence
 382
 383 --------------------------------------------------------------------------------
 384
 385 --------------------------------------------------------------------------------
 386         Motif 3 sites sorted by position p-value
 387 --------------------------------------------------------------------------------
 388 Sequence name            Strand  Start   P-value                 Site
 389 -------------            ------  ----- ---------            ---------------
 390 MIT_Smik_c193_2483           -    572  1.00e-10 TCTTGCCATA TCCGGTACCACCGAC ATACGCCGTC
 391 MIT_Spar_c429_3020           -    571  1.00e-10 CTTTGTCACA TCCGGTACCACCGAC ATTCTGTTGC
 392 MIT_Sbay_c896_21290          +    312  2.46e-09 GAAAAATGGC TTCGGTTCCTGCGAC TCGTTTAAAA
 393 SGD_Scer_YDL205C             -    570  2.75e-09 GCATTATCAC ACCGGTACCACCGAC ACATTCTGCT
 394 WashU_Skud_Contig1850.5      -    575  3.32e-09 TCTTGCCACA TCCGCTACCACCGAC ACATTCCGTT
 395 MIT_Sbay_c841_3215           -    581  6.14e-09 CTTTGCCCCA TCCGGTACTACCGAC ACATTGGCCG
 396 WashU_Smik_Contig2283.3      +    309  6.34e-09 AATTTTGGTT TCGGGTTCCTGCGAC TCGTTTAAAA
 397 MIT_Spar_c130_3912           +    306  1.39e-08 GAAATTTGGA TTCTGTTCCTGCGAC TCGTTTAAAA
 398 SGD_Scer_YDR044W             +    313  1.39e-08 GAAATTTGGC TTCTGTTCCTGCGAC TCGTTTAAAA
 399 --------------------------------------------------------------------------------
 400
 401 --------------------------------------------------------------------------------
 402         Motif 3 block diagrams
 403 --------------------------------------------------------------------------------
 404 SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
 405 -------------            ----------------  -------------
 406 MIT_Smik_c193_2483                  1e-10  571_[-3]_274
 407 MIT_Spar_c429_3020                  1e-10  570_[-3]_275
 408 MIT_Sbay_c896_21290               2.5e-09  311_[+3]_674
 409 SGD_Scer_YDL205C                  2.7e-09  569_[-3]_276
 410 WashU_Skud_Contig1850.5           3.3e-09  574_[-3]_271
 411 MIT_Sbay_c841_3215                6.1e-09  580_[-3]_265
 412 WashU_Smik_Contig2283.3           6.3e-09  308_[+3]_677
 413 MIT_Spar_c130_3912                1.4e-08  305_[+3]_680
 414 SGD_Scer_YDR044W                  1.4e-08  312_[+3]_673
 415 --------------------------------------------------------------------------------
 416
 417 --------------------------------------------------------------------------------
 418         Motif 3 in BLOCKS format
 419 --------------------------------------------------------------------------------
 420 BL   MOTIF 3 width=15 seqs=9
 421 MIT_Smik_c193_2483       (  572) TCCGGTACCACCGAC  1
 422 MIT_Spar_c429_3020       (  571) TCCGGTACCACCGAC  1
 423 MIT_Sbay_c896_21290      (  312) TTCGGTTCCTGCGAC  1
 424 SGD_Scer_YDL205C         (  570) ACCGGTACCACCGAC  1
 425 WashU_Skud_Contig1850.5  (  575) TCCGCTACCACCGAC  1
 426 MIT_Sbay_c841_3215       (  581) TCCGGTACTACCGAC  1
 427 WashU_Smik_Contig2283.3  (  309) TCGGGTTCCTGCGAC  1
 428 MIT_Spar_c130_3912       (  306) TTCTGTTCCTGCGAC  1
 429 SGD_Scer_YDR044W         (  313) TTCTGTTCCTGCGAC  1
 430 //
 431
 432 --------------------------------------------------------------------------------
 433
 434 --------------------------------------------------------------------------------
 435         Motif 3 position-specific scoring matrix
 436 --------------------------------------------------------------------------------
 437 log-odds matrix: alength= 4 w= 15 n= 8174 bayes= 9.82531 E= 1.1e-016
 438   -154   -982   -982    145
 439   -982    192   -982      4
 440   -982    234    -66   -982
 441   -982   -982    215    -55
 442   -982    -66    234   -982
 443   -982   -982   -982    162
 444     78   -982   -982     45
 445   -982    251   -982   -982
 446   -982    234   -982   -154
 447     78   -982   -982     45
 448   -982    166    134   -982
 449   -982    251   -982   -982
 450   -982   -982    251   -982
 451    162   -982   -982   -982
 452   -982    251   -982   -982
 453 --------------------------------------------------------------------------------
 454
 455 --------------------------------------------------------------------------------
 456         Motif 3 position-specific probability matrix
 457 --------------------------------------------------------------------------------
 458 letter-probability matrix: alength= 4 w= 15 nsites= 9 E= 1.1e-016
 459  0.111111  0.000000  0.000000  0.888889
 460  0.000000  0.666667  0.000000  0.333333
 461  0.000000  0.888889  0.111111  0.000000
 462  0.000000  0.000000  0.777778  0.222222
 463  0.000000  0.111111  0.888889  0.000000
 464  0.000000  0.000000  0.000000  1.000000
 465  0.555556  0.000000  0.000000  0.444444
 466  0.000000  1.000000  0.000000  0.000000
 467  0.000000  0.888889  0.000000  0.111111
 468  0.555556  0.000000  0.000000  0.444444
 469  0.000000  0.555556  0.444444  0.000000
 470  0.000000  1.000000  0.000000  0.000000
 471  0.000000  0.000000  1.000000  0.000000
 472  1.000000  0.000000  0.000000  0.000000
 473  0.000000  1.000000  0.000000  0.000000
 474 --------------------------------------------------------------------------------
 475
 476 --------------------------------------------------------------------------------
 477         Motif 3 regular expression
 478 --------------------------------------------------------------------------------
 479 T[CT]C[GT]GT[AT]CC[AT][CG]CGAC
 480 --------------------------------------------------------------------------------
 481
 482
 483
 484
 485 Time 20.83 secs.
 486
 487 ********************************************************************************
 488
 489
 490 ********************************************************************************
 491 MOTIF  4        width =   20   sites =   9   llr = 178   E-value = 5.9e-016
 492 ********************************************************************************
 493 --------------------------------------------------------------------------------
 494         Motif 4 Description
 495 --------------------------------------------------------------------------------
 496 Simplified        A  ::2::19a91:a:99:9a2:
 497 pos.-specific     C  1:214::::2:::::a:::1
 498 probability       G  ::2:481:17a:a11:1:39
 499 matrix            T  9a3911::::::::::::4:
 500
 501          bits    2.5           * *  *
 502                  2.3           * *  *
 503                  2.0           * *  *   *
 504                  1.8           * *  *   *
 505 Information      1.5  *     *  ***  * * *
 506 content          1.3 ** * ************* *
 507 (28.5 bits)      1.0 ** *************** *
 508                  0.8 ** *************** *
 509                  0.5 ** *****************
 510                  0.3 ** *****************
 511                  0.0 --------------------
 512
 513 Multilevel           TTTTCGAAAGGAGAACAATG
 514 consensus              A G    C        G
 515 sequence               C               A
 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_c130_3912           +    160  6.95e-11 TTATATAGCC TTTTCGAAACGAGAACAATG GACAAATCAA
 525 MIT_Sbay_c896_21290          +    166  9.05e-11 TTATATAGCT TTCTCGAAGGGAGAACAATG GATAAATCAA
 526 MIT_Smik_c193_2483           +    648  1.24e-10 CGCAAGGCGT TTATGGAAAGGAGGACAAGG TCAGAGGATG
 527 SGD_Scer_YDL205C             +    647  1.24e-10 CAAGGCGTTT TTGTTGAAAGGAGAACAAGG TTAGACGGTG
 528 SGD_Scer_YDR044W             +    164  4.24e-10 CTTATATAGC CTTTCGAAACGAGAACAATG GGCAAAGCAA
 529 MIT_Spar_c429_3020           +    648  6.04e-10 CAAGGCGTTT TTATGGAAAGGAGAGCGAGG TTAGAGGGTG
 530 MIT_Sbay_c841_3215           +    670  1.69e-09 CAAAGGCGCT TTGTGGGAAGGAGAACAAAC AACATTAGAG
 531 WashU_Skud_Contig1850.5      +    655  2.34e-09 ACAAGGCTTT TTCCGTAAAGGAGAACAAAG TTGGAAGGTG
 532 WashU_Smik_Contig2283.3      +    156  3.18e-09 TTATATAGCC TTTTCAAAAAGAGAACAATG GTCAAATAAA
 533 --------------------------------------------------------------------------------
 534
 535 --------------------------------------------------------------------------------
 536         Motif 4 block diagrams
 537 --------------------------------------------------------------------------------
 538 SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
 539 -------------            ----------------  -------------
 540 MIT_Spar_c130_3912                6.9e-11  159_[+4]_821
 541 MIT_Sbay_c896_21290               9.1e-11  165_[+4]_815
 542 MIT_Smik_c193_2483                1.2e-10  647_[+4]_193
 543 SGD_Scer_YDL205C                  1.2e-10  646_[+4]_194
 544 SGD_Scer_YDR044W                  4.2e-10  163_[+4]_817
 545 MIT_Spar_c429_3020                  6e-10  647_[+4]_193
 546 MIT_Sbay_c841_3215                1.7e-09  669_[+4]_171
 547 WashU_Skud_Contig1850.5           2.3e-09  654_[+4]_186
 548 WashU_Smik_Contig2283.3           3.2e-09  155_[+4]_825
 549 --------------------------------------------------------------------------------
 550
 551 --------------------------------------------------------------------------------
 552         Motif 4 in BLOCKS format
 553 --------------------------------------------------------------------------------
 554 BL   MOTIF 4 width=20 seqs=9
 555 MIT_Spar_c130_3912       (  160) TTTTCGAAACGAGAACAATG  1
 556 MIT_Sbay_c896_21290      (  166) TTCTCGAAGGGAGAACAATG  1
 557 MIT_Smik_c193_2483       (  648) TTATGGAAAGGAGGACAAGG  1
 558 SGD_Scer_YDL205C         (  647) TTGTTGAAAGGAGAACAAGG  1
 559 SGD_Scer_YDR044W         (  164) CTTTCGAAACGAGAACAATG  1
 560 MIT_Spar_c429_3020       (  648) TTATGGAAAGGAGAGCGAGG  1
 561 MIT_Sbay_c841_3215       (  670) TTGTGGGAAGGAGAACAAAC  1
 562 WashU_Skud_Contig1850.5  (  655) TTCCGTAAAGGAGAACAAAG  1
 563 WashU_Smik_Contig2283.3  (  156) TTTTCAAAAAGAGAACAATG  1
 564 //
 565
 566 --------------------------------------------------------------------------------
 567
 568 --------------------------------------------------------------------------------
 569         Motif 4 position-specific scoring matrix
 570 --------------------------------------------------------------------------------
 571 log-odds matrix: alength= 4 w= 20 n= 8129 bayes= 9.81734 E= 5.9e-016
 572   -982    -66   -982    145
 573   -982   -982   -982    162
 574    -55     34     34      4
 575   -982    -66   -982    145
 576   -982    134    134   -154
 577   -154   -982    215   -154
 578    145   -982    -66   -982
 579    162   -982   -982   -982
 580    145   -982    -66   -982
 581   -154     34    192   -982
 582   -982   -982    251   -982
 583    162   -982   -982   -982
 584   -982   -982    251   -982
 585    145   -982    -66   -982
 586    145   -982    -66   -982
 587   -982    251   -982   -982
 588    145   -982    -66   -982
 589    162   -982   -982   -982
 590    -55   -982     92     45
 591   -982    -66    234   -982
 592 --------------------------------------------------------------------------------
 593
 594 --------------------------------------------------------------------------------
 595         Motif 4 position-specific probability matrix
 596 --------------------------------------------------------------------------------
 597 letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 5.9e-016
 598  0.000000  0.111111  0.000000  0.888889
 599  0.000000  0.000000  0.000000  1.000000
 600  0.222222  0.222222  0.222222  0.333333
 601  0.000000  0.111111  0.000000  0.888889
 602  0.000000  0.444444  0.444444  0.111111
 603  0.111111  0.000000  0.777778  0.111111
 604  0.888889  0.000000  0.111111  0.000000
 605  1.000000  0.000000  0.000000  0.000000
 606  0.888889  0.000000  0.111111  0.000000
 607  0.111111  0.222222  0.666667  0.000000
 608  0.000000  0.000000  1.000000  0.000000
 609  1.000000  0.000000  0.000000  0.000000
 610  0.000000  0.000000  1.000000  0.000000
 611  0.888889  0.000000  0.111111  0.000000
 612  0.888889  0.000000  0.111111  0.000000
 613  0.000000  1.000000  0.000000  0.000000
 614  0.888889  0.000000  0.111111  0.000000
 615  1.000000  0.000000  0.000000  0.000000
 616  0.222222  0.000000  0.333333  0.444444
 617  0.000000  0.111111  0.888889  0.000000
 618 --------------------------------------------------------------------------------
 619
 620 --------------------------------------------------------------------------------
 621         Motif 4 regular expression
 622 --------------------------------------------------------------------------------
 623 TT[TACGA]T[CG]GAAA[GC]GAGAACAA[TGA]G
 624 --------------------------------------------------------------------------------
 625
 626
 627
 628
 629 Time 27.50 secs.
 630
 631 ********************************************************************************
 632
 633
 634 ********************************************************************************
 635 MOTIF  5        width =   20   sites =   9   llr = 178   E-value = 5.2e-014
 636 ********************************************************************************
 637 --------------------------------------------------------------------------------
 638         Motif 5 Description
 639 --------------------------------------------------------------------------------
 640 Simplified        A  :::::::::::3:::a::::
 641 pos.-specific     C  84::1122:34:4a::::::
 642 probability       G  :::::::::::1::::::a:
 643 matrix            T  26aa9988a7666:a:aa:a
 644
 645          bits    2.5              *    *
 646                  2.3              *    *
 647                  2.0              *    *
 648                  1.8              *    *
 649 Information      1.5 * **    *    *******
 650 content          1.3 * ****  *    *******
 651 (28.6 bits)      1.0 *********** ********
 652                  0.8 *********** ********
 653                  0.5 *********** ********
 654                  0.3 ********************
 655                  0.0 --------------------
 656
 657 Multilevel           CTTTTTTTTTTTTCTATTGT
 658 consensus            TC    CC CCAC
 659 sequence
 660
 661 --------------------------------------------------------------------------------
 662
 663 --------------------------------------------------------------------------------
 664         Motif 5 sites sorted by position p-value
 665 --------------------------------------------------------------------------------
 666 Sequence name            Strand  Start   P-value                    Site
 667 -------------            ------  ----- ---------            --------------------
 668 WashU_Smik_Contig2283.3      -    113  4.87e-11 CACATATTTT CCTTTTTTTCCACCTATTGT CTCACCTGTT
 669 MIT_Spar_c130_3912           -    117  1.86e-10 CACGGATTTT CCTTTTTTTCCGCCTATTGT CTTTCTTTGT
 670 WashU_Skud_Contig1850.5      +     46  2.33e-10 AGTTTTCCTG CTTTTTTTTTTTTCTATTGT TCTAGAAACT
 671 MIT_Smik_c193_2483           +     49  6.29e-10 ACTATCTGGC CTTTTTCTTTTTTCTATTGT TCTAGATACT
 672 MIT_Spar_c429_3020           +     47  7.60e-10 GATTTTCTTG CCTTTTCCTTTTTCTATTGT TCTAGATACT
 673 SGD_Scer_YDL205C             +     47  1.27e-09 ATTTTCTTCG CTTTTCTTTTTTTCTATTGT TCTAGATATT
 674 MIT_Sbay_c896_21290          -    121  1.43e-09 CGCATTTTCT TTTTTTTTTTCACCTATTGT TCGCTGCCAA
 675 SGD_Scer_YDR044W             -    120  1.50e-09 CGGATTTTCC TTTTTTTTTCCACCTATTGT CTTTCTTTGT
 676 MIT_Sbay_c841_3215           +     48  1.62e-09 TATTTTTTTT CCTTCTTCTTTTTCTATTGT TCTAGATGCT
 677 --------------------------------------------------------------------------------
 678
 679 --------------------------------------------------------------------------------
 680         Motif 5 block diagrams
 681 --------------------------------------------------------------------------------
 682 SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
 683 -------------            ----------------  -------------
 684 WashU_Smik_Contig2283.3           4.9e-11  112_[-5]_868
 685 MIT_Spar_c130_3912                1.9e-10  116_[-5]_864
 686 WashU_Skud_Contig1850.5           2.3e-10  45_[+5]_795
 687 MIT_Smik_c193_2483                6.3e-10  48_[+5]_792
 688 MIT_Spar_c429_3020                7.6e-10  46_[+5]_794
 689 SGD_Scer_YDL205C                  1.3e-09  46_[+5]_794
 690 MIT_Sbay_c896_21290               1.4e-09  120_[-5]_860
 691 SGD_Scer_YDR044W                  1.5e-09  119_[-5]_861
 692 MIT_Sbay_c841_3215                1.6e-09  47_[+5]_793
 693 --------------------------------------------------------------------------------
 694
 695 --------------------------------------------------------------------------------
 696         Motif 5 in BLOCKS format
 697 --------------------------------------------------------------------------------
 698 BL   MOTIF 5 width=20 seqs=9
 699 WashU_Smik_Contig2283.3  (  113) CCTTTTTTTCCACCTATTGT  1
 700 MIT_Spar_c130_3912       (  117) CCTTTTTTTCCGCCTATTGT  1
 701 WashU_Skud_Contig1850.5  (   46) CTTTTTTTTTTTTCTATTGT  1
 702 MIT_Smik_c193_2483       (   49) CTTTTTCTTTTTTCTATTGT  1
 703 MIT_Spar_c429_3020       (   47) CCTTTTCCTTTTTCTATTGT  1
 704 SGD_Scer_YDL205C         (   47) CTTTTCTTTTTTTCTATTGT  1
 705 MIT_Sbay_c896_21290      (  121) TTTTTTTTTTCACCTATTGT  1
 706 SGD_Scer_YDR044W         (  120) TTTTTTTTTCCACCTATTGT  1
 707 MIT_Sbay_c841_3215       (   48) CCTTCTTCTTTTTCTATTGT  1
 708 //
 709
 710 --------------------------------------------------------------------------------
 711
 712 --------------------------------------------------------------------------------
 713         Motif 5 position-specific scoring matrix
 714 --------------------------------------------------------------------------------
 715 log-odds matrix: alength= 4 w= 20 n= 8129 bayes= 9.81734 E= 5.2e-014
 716   -982    215   -982    -55
 717   -982    134   -982     78
 718   -982   -982   -982    162
 719   -982   -982   -982    162
 720   -982    -66   -982    145
 721   -982    -66   -982    145
 722   -982     34   -982    126
 723   -982     34   -982    126
 724   -982   -982   -982    162
 725   -982     92   -982    104
 726   -982    134   -982     78
 727      4   -982    -66     78
 728   -982    134   -982     78
 729   -982    251   -982   -982
 730   -982   -982   -982    162
 731    162   -982   -982   -982
 732   -982   -982   -982    162
 733   -982   -982   -982    162
 734   -982   -982    251   -982
 735   -982   -982   -982    162
 736 --------------------------------------------------------------------------------
 737
 738 --------------------------------------------------------------------------------
 739         Motif 5 position-specific probability matrix
 740 --------------------------------------------------------------------------------
 741 letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 5.2e-014
 742  0.000000  0.777778  0.000000  0.222222
 743  0.000000  0.444444  0.000000  0.555556
 744  0.000000  0.000000  0.000000  1.000000
 745  0.000000  0.000000  0.000000  1.000000
 746  0.000000  0.111111  0.000000  0.888889
 747  0.000000  0.111111  0.000000  0.888889
 748  0.000000  0.222222  0.000000  0.777778
 749  0.000000  0.222222  0.000000  0.777778
 750  0.000000  0.000000  0.000000  1.000000
 751  0.000000  0.333333  0.000000  0.666667
 752  0.000000  0.444444  0.000000  0.555556
 753  0.333333  0.000000  0.111111  0.555556
 754  0.000000  0.444444  0.000000  0.555556
 755  0.000000  1.000000  0.000000  0.000000
 756  0.000000  0.000000  0.000000  1.000000
 757  1.000000  0.000000  0.000000  0.000000
 758  0.000000  0.000000  0.000000  1.000000
 759  0.000000  0.000000  0.000000  1.000000
 760  0.000000  0.000000  1.000000  0.000000
 761  0.000000  0.000000  0.000000  1.000000
 762 --------------------------------------------------------------------------------
 763
 764 --------------------------------------------------------------------------------
 765         Motif 5 regular expression
 766 --------------------------------------------------------------------------------
 767 [CT][TC]TTTT[TC][TC]T[TC][TC][TA][TC]CTATTGT
 768 --------------------------------------------------------------------------------
 769
 770
 771
 772
 773 Time 34.04 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_YDL205C                 3.32e-30  46_[+5(1.27e-09)]_156_[+5(7.84e-05)]_327_[-3(2.75e-09)]_62_[+4(1.24e-10)]_17_[+2(2.30e-13)]_4_[-1(1.22e-12)]_133
 788 MIT_Spar_c429_3020               6.35e-30  46_[+5(7.60e-10)]_170_[+5(7.84e-05)]_251_[+1(3.79e-05)]_43_[-3(1.00e-10)]_62_[+4(6.04e-10)]_17_[+2(4.30e-12)]_4_[-1(1.22e-12)]_132
 789 MIT_Smik_c193_2483               7.78e-29  48_[+5(6.29e-10)]_174_[+5(2.65e-05)]_309_[-3(1.00e-10)]_61_[+4(1.24e-10)]_17_[+2(3.52e-12)]_4_[-1(1.22e-10)]_132
 790 MIT_Sbay_c841_3215               1.43e-27  47_[+5(1.62e-09)]_297_[-5(2.91e-05)]_196_[-3(6.14e-09)]_74_[+4(1.69e-09)]_21_[+2(3.52e-12)]_4_[-1(1.22e-12)]_106
 791 WashU_Skud_Contig1850.5          1.30e-29  45_[+5(2.33e-10)]_131_[-4(6.41e-05)]_19_[+5(7.84e-05)]_319_[-3(3.32e-09)]_1_[-3(6.63e-05)]_49_[+4(2.34e-09)]_17_[+2(2.30e-13)]_4_[-1(1.22e-12)]_125
 792 SGD_Scer_YDR044W                 2.91e-23  119_[-5(1.50e-09)]_24_[+4(4.24e-10)]_18_[+3(7.91e-05)]_42_[+4(4.47e-05)]_34_[+3(1.39e-08)]_271_[+4(2.94e-05)]_65_[+1(3.84e-10)]_29_[+2(3.60e-10)]_248
 793 MIT_Spar_c130_3912               7.46e-25  116_[-5(1.86e-10)]_23_[+4(6.95e-11)]_126_[+3(1.39e-08)]_358_[+1(1.35e-10)]_31_[+2(1.03e-09)]_251
 794 MIT_Sbay_c896_21290              1.06e-23  85_[-5(1.91e-05)]_15_[-5(1.43e-09)]_25_[+4(9.05e-11)]_126_[+3(2.46e-09)]_140_[-5(3.09e-05)]_198_[+1(5.43e-10)]_26_[+2(2.40e-09)]_48_[+5(4.88e-05)]_182
 795 WashU_Smik_Contig2283.3          5.66e-25  86_[+1(4.04e-05)]_6_[-5(4.87e-11)]_23_[+4(3.18e-09)]_133_[+3(6.34e-09)]_144_[-5(8.86e-05)]_199_[+1(5.84e-10)]_32_[+2(3.24e-11)]_27_[-1(3.56e-05)]_195
 796 --------------------------------------------------------------------------------
 797
 798 ********************************************************************************
 799
 800
 801 ********************************************************************************
 802 Stopped because nmotifs = 5 reached.
 803 ********************************************************************************
 804
 805 CPU: dhn02990.mrc-dunn.cam.ac.uk
 806
 807 ********************************************************************************