t/data/map_hem/HEM4-HEM12.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= HEM4-HEM12.fa
  32 ALPHABET= ACGT
  33 Sequence name            Weight Length  Sequence name            Weight Length
  34 -------------            ------ ------  -------------            ------ ------
  35 SGD_Scer_YOR278W         1.0000    635  MIT_Spar_c261_21317      1.0000    635
  36 MIT_Smik_c492_20940      1.0000    635  WashU_Skud_Contig1682.4  1.0000    635
  37 WashU_Sbay_Contig635.57  1.0000    635  SGD_Scer_YDR047W         1.0000   1000
  38 MIT_Spar_c130_3923       1.0000   1000  MIT_Sbay_c896_21277      1.0000   1000
  39 WashU_Skud_Contig1362.1  1.0000    761
  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 HEM4-HEM12.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=            6936    N=               9
  59 strands: + -
  60 sample: seed=            0    seqfrac=         1
  61 Letter frequencies in dataset:
  62 A 0.299 C 0.201 G 0.201 T 0.299
  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 = 188   E-value = 6.5e-019
  70 ********************************************************************************
  71 --------------------------------------------------------------------------------
  72         Motif 1 Description
  73 --------------------------------------------------------------------------------
  74 Simplified        A  :9a4a:a::6::1:::1718
  75 pos.-specific     C  21:::a::64a:684a9::2
  76 probability       G  :::6::::4::a:::::21:
  77 matrix            T  8::::::a::::326::18:
  78
  79          bits    2.5      *    **   *
  80                  2.3      *    **   *
  81                  2.0      *    **   **
  82                  1.8      *    **   **
  83 Information      1.5   * ***** ** * **
  84 content          1.3  ** ***** ** * **
  85 (30.1 bits)      1.0 ************ ****  *
  86                  0.8 ***************** **
  87                  0.5 ********************
  88                  0.3 ********************
  89                  0.0 --------------------
  90
  91 Multilevel           TAAGACATCACGCCTCCATA
  92 consensus            C  A    GC  TTC  G C
  93 sequence
  94
  95 --------------------------------------------------------------------------------
  96
  97 --------------------------------------------------------------------------------
  98         Motif 1 sites sorted by position p-value
  99 --------------------------------------------------------------------------------
 100 Sequence name            Strand  Start   P-value                    Site
 101 -------------            ------  ----- ---------            --------------------
 102 WashU_Sbay_Contig635.57      -    370  3.48e-12 TTACCATGCT TAAGACATCACGCCTCCATA TGTCTATGTC
 103 WashU_Skud_Contig1682.4      -    363  3.48e-12 TTACCATGCT TAAGACATCACGCCTCCATA TGTCTATGTA
 104 MIT_Smik_c492_20940          -    368  3.48e-12 TTACCATGCT TAAGACATCACGCCTCCATA TGTCTATATA
 105 MIT_Spar_c261_21317          -    362  3.48e-12 TTACCATGCT TAAGACATCACGCCTCCATA TGTCTATATA
 106 SGD_Scer_YOR278W             -    359  3.48e-12 TTACCATGCT TAAGACATCACGCCTCCATA TGTCTATATA
 107 MIT_Spar_c130_3923           +    644  1.59e-10 TGGCGCAATT CAAAACATGCCGTCCCCGTA CTAAGTTATG
 108 SGD_Scer_YDR047W             +    646  4.90e-10 GCTGTGCATT TAAAACATGCCGTTCCCGTA CCAAGTTATA
 109 WashU_Skud_Contig1362.1      +    646  3.58e-09 CTGGAACAAA TCAAACATGCCGTCCCCTAC CAGCTCTCGA
 110 MIT_Sbay_c896_21277          +    650  9.08e-09 ATTGACAAGA CAAAACATGCCGATCCAAGC CAGGCGAAAC
 111 --------------------------------------------------------------------------------
 112
 113 --------------------------------------------------------------------------------
 114         Motif 1 block diagrams
 115 --------------------------------------------------------------------------------
 116 SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
 117 -------------            ----------------  -------------
 118 WashU_Sbay_Contig635.57           3.5e-12  369_[-1]_246
 119 WashU_Skud_Contig1682.4           3.5e-12  362_[-1]_253
 120 MIT_Smik_c492_20940               3.5e-12  367_[-1]_248
 121 MIT_Spar_c261_21317               3.5e-12  361_[-1]_254
 122 SGD_Scer_YOR278W                  3.5e-12  358_[-1]_257
 123 MIT_Spar_c130_3923                1.6e-10  643_[+1]_337
 124 SGD_Scer_YDR047W                  4.9e-10  645_[+1]_335
 125 WashU_Skud_Contig1362.1           3.6e-09  645_[+1]_96
 126 MIT_Sbay_c896_21277               9.1e-09  649_[+1]_331
 127 --------------------------------------------------------------------------------
 128
 129 --------------------------------------------------------------------------------
 130         Motif 1 in BLOCKS format
 131 --------------------------------------------------------------------------------
 132 BL   MOTIF 1 width=20 seqs=9
 133 WashU_Sbay_Contig635.57  (  370) TAAGACATCACGCCTCCATA  1
 134 WashU_Skud_Contig1682.4  (  363) TAAGACATCACGCCTCCATA  1
 135 MIT_Smik_c492_20940      (  368) TAAGACATCACGCCTCCATA  1
 136 MIT_Spar_c261_21317      (  362) TAAGACATCACGCCTCCATA  1
 137 SGD_Scer_YOR278W         (  359) TAAGACATCACGCCTCCATA  1
 138 MIT_Spar_c130_3923       (  644) CAAAACATGCCGTCCCCGTA  1
 139 SGD_Scer_YDR047W         (  646) TAAAACATGCCGTTCCCGTA  1
 140 WashU_Skud_Contig1362.1  (  646) TCAAACATGCCGTCCCCTAC  1
 141 MIT_Sbay_c896_21277      (  650) CAAAACATGCCGATCCAAGC  1
 142 //
 143
 144 --------------------------------------------------------------------------------
 145
 146 --------------------------------------------------------------------------------
 147         Motif 1 position-specific scoring matrix
 148 --------------------------------------------------------------------------------
 149 log-odds matrix: alength= 4 w= 20 n= 6765 bayes= 9.55203 E= 6.5e-019
 150   -982     34   -982    126
 151    145    -66   -982   -982
 152    162   -982   -982   -982
 153     45   -982    166   -982
 154    162   -982   -982   -982
 155   -982    251   -982   -982
 156    162   -982   -982   -982
 157   -982   -982   -982    162
 158   -982    166    134   -982
 159     78    134   -982   -982
 160   -982    251   -982   -982
 161   -982   -982    251   -982
 162   -154    166   -982      4
 163   -982    215   -982    -55
 164   -982    134   -982     78
 165   -982    251   -982   -982
 166   -154    234   -982   -982
 167    104   -982     34   -154
 168   -154   -982    -66    126
 169    126     34   -982   -982
 170 --------------------------------------------------------------------------------
 171
 172 --------------------------------------------------------------------------------
 173         Motif 1 position-specific probability matrix
 174 --------------------------------------------------------------------------------
 175 letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 6.5e-019
 176  0.000000  0.222222  0.000000  0.777778
 177  0.888889  0.111111  0.000000  0.000000
 178  1.000000  0.000000  0.000000  0.000000
 179  0.444444  0.000000  0.555556  0.000000
 180  1.000000  0.000000  0.000000  0.000000
 181  0.000000  1.000000  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  0.555556  0.444444  0.000000
 185  0.555556  0.444444  0.000000  0.000000
 186  0.000000  1.000000  0.000000  0.000000
 187  0.000000  0.000000  1.000000  0.000000
 188  0.111111  0.555556  0.000000  0.333333
 189  0.000000  0.777778  0.000000  0.222222
 190  0.000000  0.444444  0.000000  0.555556
 191  0.000000  1.000000  0.000000  0.000000
 192  0.111111  0.888889  0.000000  0.000000
 193  0.666667  0.000000  0.222222  0.111111
 194  0.111111  0.000000  0.111111  0.777778
 195  0.777778  0.222222  0.000000  0.000000
 196 --------------------------------------------------------------------------------
 197
 198 --------------------------------------------------------------------------------
 199         Motif 1 regular expression
 200 --------------------------------------------------------------------------------
 201 [TC]AA[GA]ACAT[CG][AC]CG[CT][CT][TC]CC[AG]T[AC]
 202 --------------------------------------------------------------------------------
 203
 204
 205
 206
 207 Time  5.21 secs.
 208
 209 ********************************************************************************
 210
 211
 212 ********************************************************************************
 213 MOTIF  2        width =   20   sites =   9   llr = 180   E-value = 1.7e-016
 214 ********************************************************************************
 215 --------------------------------------------------------------------------------
 216         Motif 2 Description
 217 --------------------------------------------------------------------------------
 218 Simplified        A  ::1:7:::73:::3:::::9
 219 pos.-specific     C  :188::aa2::::7:8::11
 220 probability       G  1::128::1:1:a:a:112:
 221 matrix            T  991112:::79a:::2997:
 222
 223          bits    2.5       **    * *
 224                  2.3       **    * *
 225                  2.0       **    * *
 226                  1.8       **    * *
 227 Information      1.5    * ***   ** **
 228 content          1.3 **** ***  ******** *
 229 (28.8 bits)      1.0 **** ***  ******** *
 230                  0.8 **** ***************
 231                  0.5 ********************
 232                  0.3 ********************
 233                  0.0 --------------------
 234
 235 Multilevel           TTCCAGCCATTTGCGCTTTA
 236 consensus                GT  CA   A T  G
 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_Contig1682.4      +    335  6.64e-13 ATTGGTCTAC TTCCAGCCATTTGCGCTTTA CATAGACATA
 247 MIT_Smik_c492_20940          +    340  6.64e-13 ATTTGTCTAC TTCCAGCCATTTGCGCTTTA TATAGACATA
 248 MIT_Spar_c261_21317          +    334  6.64e-13 ATTGGTCTAC TTCCAGCCATTTGCGCTTTA TATAGACATA
 249 SGD_Scer_YOR278W             +    331  6.64e-13 ATTGGTCTAC TTCCAGCCATTTGCGCTTTA TATAGACATA
 250 WashU_Sbay_Contig635.57      +    342  1.74e-12 ATTGGTCTAC TTCCAGCCATTTGCGCTTGA CATAGACATA
 251 MIT_Spar_c130_3923           +    720  2.83e-09 AATGCTGCCG TTCCGTCCCATTGAGTTTTA TTTTCCTTCT
 252 SGD_Scer_YDR047W             +    720  2.83e-09 AATGCTGCCG TTCCGTCCCATTGAGTTTTA TTTTCCTTCT
 253 MIT_Sbay_c896_21277          +    833  4.51e-08 AAGGTCAGTT TTATAGCCGTGTGCGCGGCA TCGAGAGACA
 254 WashU_Skud_Contig1362.1      -     39  7.81e-08 TTTTTTTAGA GCTGTGCCAATTGAGCTTGC TACCAATCTA
 255 --------------------------------------------------------------------------------
 256
 257 --------------------------------------------------------------------------------
 258         Motif 2 block diagrams
 259 --------------------------------------------------------------------------------
 260 SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
 261 -------------            ----------------  -------------
 262 WashU_Skud_Contig1682.4           6.6e-13  334_[+2]_281
 263 MIT_Smik_c492_20940               6.6e-13  339_[+2]_276
 264 MIT_Spar_c261_21317               6.6e-13  333_[+2]_282
 265 SGD_Scer_YOR278W                  6.6e-13  330_[+2]_285
 266 WashU_Sbay_Contig635.57           1.7e-12  341_[+2]_274
 267 MIT_Spar_c130_3923                2.8e-09  719_[+2]_261
 268 SGD_Scer_YDR047W                  2.8e-09  719_[+2]_261
 269 MIT_Sbay_c896_21277               4.5e-08  832_[+2]_148
 270 WashU_Skud_Contig1362.1           7.8e-08  38_[-2]_703
 271 --------------------------------------------------------------------------------
 272
 273 --------------------------------------------------------------------------------
 274         Motif 2 in BLOCKS format
 275 --------------------------------------------------------------------------------
 276 BL   MOTIF 2 width=20 seqs=9
 277 WashU_Skud_Contig1682.4  (  335) TTCCAGCCATTTGCGCTTTA  1
 278 MIT_Smik_c492_20940      (  340) TTCCAGCCATTTGCGCTTTA  1
 279 MIT_Spar_c261_21317      (  334) TTCCAGCCATTTGCGCTTTA  1
 280 SGD_Scer_YOR278W         (  331) TTCCAGCCATTTGCGCTTTA  1
 281 WashU_Sbay_Contig635.57  (  342) TTCCAGCCATTTGCGCTTGA  1
 282 MIT_Spar_c130_3923       (  720) TTCCGTCCCATTGAGTTTTA  1
 283 SGD_Scer_YDR047W         (  720) TTCCGTCCCATTGAGTTTTA  1
 284 MIT_Sbay_c896_21277      (  833) TTATAGCCGTGTGCGCGGCA  1
 285 WashU_Skud_Contig1362.1  (   39) GCTGTGCCAATTGAGCTTGC  1
 286 //
 287
 288 --------------------------------------------------------------------------------
 289
 290 --------------------------------------------------------------------------------
 291         Motif 2 position-specific scoring matrix
 292 --------------------------------------------------------------------------------
 293 log-odds matrix: alength= 4 w= 20 n= 6765 bayes= 9.55203 E= 1.7e-016
 294   -982   -982    -66    145
 295   -982    -66   -982    145
 296   -154    215   -982   -154
 297   -982    215    -66   -154
 298    104   -982     34   -154
 299   -982   -982    215    -55
 300   -982    251   -982   -982
 301   -982    251   -982   -982
 302    104     34    -66   -982
 303      4   -982   -982    104
 304   -982   -982    -66    145
 305   -982   -982   -982    162
 306   -982   -982    251   -982
 307      4    192   -982   -982
 308   -982   -982    251   -982
 309   -982    215   -982    -55
 310   -982   -982    -66    145
 311   -982   -982    -66    145
 312   -982    -66     34    104
 313    145    -66   -982   -982
 314 --------------------------------------------------------------------------------
 315
 316 --------------------------------------------------------------------------------
 317         Motif 2 position-specific probability matrix
 318 --------------------------------------------------------------------------------
 319 letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 1.7e-016
 320  0.000000  0.000000  0.111111  0.888889
 321  0.000000  0.111111  0.000000  0.888889
 322  0.111111  0.777778  0.000000  0.111111
 323  0.000000  0.777778  0.111111  0.111111
 324  0.666667  0.000000  0.222222  0.111111
 325  0.000000  0.000000  0.777778  0.222222
 326  0.000000  1.000000  0.000000  0.000000
 327  0.000000  1.000000  0.000000  0.000000
 328  0.666667  0.222222  0.111111  0.000000
 329  0.333333  0.000000  0.000000  0.666667
 330  0.000000  0.000000  0.111111  0.888889
 331  0.000000  0.000000  0.000000  1.000000
 332  0.000000  0.000000  1.000000  0.000000
 333  0.333333  0.666667  0.000000  0.000000
 334  0.000000  0.000000  1.000000  0.000000
 335  0.000000  0.777778  0.000000  0.222222
 336  0.000000  0.000000  0.111111  0.888889
 337  0.000000  0.000000  0.111111  0.888889
 338  0.000000  0.111111  0.222222  0.666667
 339  0.888889  0.111111  0.000000  0.000000
 340 --------------------------------------------------------------------------------
 341
 342 --------------------------------------------------------------------------------
 343         Motif 2 regular expression
 344 --------------------------------------------------------------------------------
 345 TTCC[AG][GT]CC[AC][TA]TTG[CA]G[CT]TT[TG]A
 346 --------------------------------------------------------------------------------
 347
 348
 349
 350
 351 Time 10.37 secs.
 352
 353 ********************************************************************************
 354
 355
 356 ********************************************************************************
 357 MOTIF  3        width =   15   sites =   9   llr = 143   E-value = 1.2e-009
 358 ********************************************************************************
 359 --------------------------------------------------------------------------------
 360         Motif 3 Description
 361 --------------------------------------------------------------------------------
 362 Simplified        A  8::::1a9:9::9::
 363 pos.-specific     C  ::a62:::1::a:21
 364 probability       G  13::89:1911::8:
 365 matrix            T  17:4::::::9:1:9
 366
 367          bits    2.5   *        *
 368                  2.3   *        *
 369                  2.0   *  *  *  *
 370                  1.8   * **  *  * *
 371 Information      1.5   * *** *  * *
 372 content          1.3   * ******** **
 373 (22.9 bits)      1.0  **************
 374                  0.8 ***************
 375                  0.5 ***************
 376                  0.3 ***************
 377                  0.0 ---------------
 378
 379 Multilevel           ATCCGGAAGATCAGT
 380 consensus             G TC        C
 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 WashU_Sbay_Contig635.57      +    399  6.31e-10 AAGCATGGTA ATCCGGAAGATCAGT TTATTGAATG
 391 WashU_Skud_Contig1682.4      +    392  6.31e-10 AAGCATGGTA ATCCGGAAGATCAGT TTATTGAATG
 392 MIT_Smik_c492_20940          +    397  6.31e-10 AAGCATGGTA ATCCGGAAGATCAGT TTATTGAATG
 393 MIT_Spar_c261_21317          +    391  6.31e-10 AAGCATGGTA ATCCGGAAGATCAGT TTATTGAATG
 394 SGD_Scer_YOR278W             +    388  6.31e-10 AAGCATGGTA ATCCGGAAGATCAGT TTATTGAATG
 395 MIT_Sbay_c896_21277          +    817  1.82e-07 CATCTCGCTA AGCTGAAAGGTCAGT TTTATAGCCG
 396 MIT_Spar_c130_3923           -    922  1.82e-07 CGTTGATCGC AGCTCGAGGATCAGC TAGTGAAATA
 397 SGD_Scer_YDR047W             +    134  2.44e-07 TGTTACCTTC GTCTGGAACATCACT AATTCGAGCG
 398 WashU_Skud_Contig1362.1      +    363  9.95e-07 AATTTGCTAA TGCTCGAAGAGCTCT CAATCAATCA
 399 --------------------------------------------------------------------------------
 400
 401 --------------------------------------------------------------------------------
 402         Motif 3 block diagrams
 403 --------------------------------------------------------------------------------
 404 SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
 405 -------------            ----------------  -------------
 406 WashU_Sbay_Contig635.57           6.3e-10  398_[+3]_222
 407 WashU_Skud_Contig1682.4           6.3e-10  391_[+3]_229
 408 MIT_Smik_c492_20940               6.3e-10  396_[+3]_224
 409 MIT_Spar_c261_21317               6.3e-10  390_[+3]_230
 410 SGD_Scer_YOR278W                  6.3e-10  387_[+3]_233
 411 MIT_Sbay_c896_21277               1.8e-07  816_[+3]_169
 412 MIT_Spar_c130_3923                1.8e-07  921_[-3]_64
 413 SGD_Scer_YDR047W                  2.4e-07  133_[+3]_852
 414 WashU_Skud_Contig1362.1             1e-06  362_[+3]_384
 415 --------------------------------------------------------------------------------
 416
 417 --------------------------------------------------------------------------------
 418         Motif 3 in BLOCKS format
 419 --------------------------------------------------------------------------------
 420 BL   MOTIF 3 width=15 seqs=9
 421 WashU_Sbay_Contig635.57  (  399) ATCCGGAAGATCAGT  1
 422 WashU_Skud_Contig1682.4  (  392) ATCCGGAAGATCAGT  1
 423 MIT_Smik_c492_20940      (  397) ATCCGGAAGATCAGT  1
 424 MIT_Spar_c261_21317      (  391) ATCCGGAAGATCAGT  1
 425 SGD_Scer_YOR278W         (  388) ATCCGGAAGATCAGT  1
 426 MIT_Sbay_c896_21277      (  817) AGCTGAAAGGTCAGT  1
 427 MIT_Spar_c130_3923       (  922) AGCTCGAGGATCAGC  1
 428 SGD_Scer_YDR047W         (  134) GTCTGGAACATCACT  1
 429 WashU_Skud_Contig1362.1  (  363) TGCTCGAAGAGCTCT  1
 430 //
 431
 432 --------------------------------------------------------------------------------
 433
 434 --------------------------------------------------------------------------------
 435         Motif 3 position-specific scoring matrix
 436 --------------------------------------------------------------------------------
 437 log-odds matrix: alength= 4 w= 15 n= 6810 bayes= 9.56161 E= 1.2e-009
 438    126   -982    -66   -154
 439   -982   -982     92    104
 440   -982    251   -982   -982
 441   -982    166   -982     45
 442   -982     34    215   -982
 443   -154   -982    234   -982
 444    162   -982   -982   -982
 445    145   -982    -66   -982
 446   -982    -66    234   -982
 447    145   -982    -66   -982
 448   -982   -982    -66    145
 449   -982    251   -982   -982
 450    145   -982   -982   -154
 451   -982     34    215   -982
 452   -982    -66   -982    145
 453 --------------------------------------------------------------------------------
 454
 455 --------------------------------------------------------------------------------
 456         Motif 3 position-specific probability matrix
 457 --------------------------------------------------------------------------------
 458 letter-probability matrix: alength= 4 w= 15 nsites= 9 E= 1.2e-009
 459  0.777778  0.000000  0.111111  0.111111
 460  0.000000  0.000000  0.333333  0.666667
 461  0.000000  1.000000  0.000000  0.000000
 462  0.000000  0.555556  0.000000  0.444444
 463  0.000000  0.222222  0.777778  0.000000
 464  0.111111  0.000000  0.888889  0.000000
 465  1.000000  0.000000  0.000000  0.000000
 466  0.888889  0.000000  0.111111  0.000000
 467  0.000000  0.111111  0.888889  0.000000
 468  0.888889  0.000000  0.111111  0.000000
 469  0.000000  0.000000  0.111111  0.888889
 470  0.000000  1.000000  0.000000  0.000000
 471  0.888889  0.000000  0.000000  0.111111
 472  0.000000  0.222222  0.777778  0.000000
 473  0.000000  0.111111  0.000000  0.888889
 474 --------------------------------------------------------------------------------
 475
 476 --------------------------------------------------------------------------------
 477         Motif 3 regular expression
 478 --------------------------------------------------------------------------------
 479 A[TG]C[CT][GC]GAAGATCA[GC]T
 480 --------------------------------------------------------------------------------
 481
 482
 483
 484
 485 Time 15.31 secs.
 486
 487 ********************************************************************************
 488
 489
 490 ********************************************************************************
 491 MOTIF  4        width =   20   sites =   9   llr = 174   E-value = 1.7e-013
 492 ********************************************************************************
 493 --------------------------------------------------------------------------------
 494         Motif 4 Description
 495 --------------------------------------------------------------------------------
 496 Simplified        A  ::::6:::::4::a:3:93:
 497 pos.-specific     C  1911::4:a:486:248:46
 498 probability       G  ::::4a6a:::::::11:23
 499 matrix            T  9199:::::a124:8111:1
 500
 501          bits    2.5      * **
 502                  2.3      * **
 503                  2.0  *   * **
 504                  1.8  *   * **
 505 Information      1.5  *   ***** * *  *
 506 content          1.3 **** ***** * *  *
 507 (27.9 bits)      1.0 ********** **** ** *
 508                  0.8 ********** **** ****
 509                  0.5 *************** ****
 510                  0.3 ********************
 511                  0.0 --------------------
 512
 513 Multilevel           TCTTAGGGCTACCATCCACC
 514 consensus                G C   CTT CA  AG
 515 sequence                               G
 516
 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_c261_21317          +    548  3.46e-12 TTCGTTTTTC TCTTAGGGCTCCCATCCAAC TGTCGGCGAG
 525 WashU_Sbay_Contig635.57      +    555  1.43e-11 TTTCTCTTTT TCTTAGGGCTCCTATCCAGC TGCCTGCGAA
 526 MIT_Spar_c130_3923           -    287  2.21e-11 TTATTCGCTA TCTTGGCGCTACCATACACG ATTTTTTTTC
 527 SGD_Scer_YDR047W             -    289  3.04e-10 TTATCCGCCA TCTTGGCGCTATCATACACG ATCTTTTTCA
 528 MIT_Smik_c492_20940          +    546  5.86e-10 TTTCGCTTTT TCTTAGGGCTCCTATCTAAC TCTCGGGCGA
 529 WashU_Skud_Contig1362.1      -    246  1.17e-09 TGCCCGTTTT CCTTGGCGCTACCATACACT TCCTCTGTTT
 530 MIT_Sbay_c896_21277          -    239  5.15e-09 TATCTGCCTT TTCTGGCGCTACCATGCAGC TTCCTCGTTT
 531 WashU_Skud_Contig1682.4      +    542  1.02e-08 TTTCACTTTT TCTCAGGGCTTTTACCCAAC TGCCGACAAA
 532 SGD_Scer_YOR278W             +    531  1.19e-08 TCGCTTTATC TCTTAGGGCTCCTACTGTCG GTAGAGAAAA
 533 --------------------------------------------------------------------------------
 534
 535 --------------------------------------------------------------------------------
 536         Motif 4 block diagrams
 537 --------------------------------------------------------------------------------
 538 SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
 539 -------------            ----------------  -------------
 540 MIT_Spar_c261_21317               3.5e-12  547_[+4]_68
 541 WashU_Sbay_Contig635.57           1.4e-11  554_[+4]_61
 542 MIT_Spar_c130_3923                2.2e-11  286_[-4]_694
 543 SGD_Scer_YDR047W                    3e-10  288_[-4]_692
 544 MIT_Smik_c492_20940               5.9e-10  545_[+4]_70
 545 WashU_Skud_Contig1362.1           1.2e-09  245_[-4]_496
 546 MIT_Sbay_c896_21277               5.2e-09  238_[-4]_742
 547 WashU_Skud_Contig1682.4             1e-08  541_[+4]_74
 548 SGD_Scer_YOR278W                  1.2e-08  530_[+4]_85
 549 --------------------------------------------------------------------------------
 550
 551 --------------------------------------------------------------------------------
 552         Motif 4 in BLOCKS format
 553 --------------------------------------------------------------------------------
 554 BL   MOTIF 4 width=20 seqs=9
 555 MIT_Spar_c261_21317      (  548) TCTTAGGGCTCCCATCCAAC  1
 556 WashU_Sbay_Contig635.57  (  555) TCTTAGGGCTCCTATCCAGC  1
 557 MIT_Spar_c130_3923       (  287) TCTTGGCGCTACCATACACG  1
 558 SGD_Scer_YDR047W         (  289) TCTTGGCGCTATCATACACG  1
 559 MIT_Smik_c492_20940      (  546) TCTTAGGGCTCCTATCTAAC  1
 560 WashU_Skud_Contig1362.1  (  246) CCTTGGCGCTACCATACACT  1
 561 MIT_Sbay_c896_21277      (  239) TTCTGGCGCTACCATGCAGC  1
 562 WashU_Skud_Contig1682.4  (  542) TCTCAGGGCTTTTACCCAAC  1
 563 SGD_Scer_YOR278W         (  531) TCTTAGGGCTCCTACTGTCG  1
 564 //
 565
 566 --------------------------------------------------------------------------------
 567
 568 --------------------------------------------------------------------------------
 569         Motif 4 position-specific scoring matrix
 570 --------------------------------------------------------------------------------
 571 log-odds matrix: alength= 4 w= 20 n= 6765 bayes= 9.55203 E= 1.7e-013
 572   -982    -66   -982    145
 573   -982    234   -982   -154
 574   -982    -66   -982    145
 575   -982    -66   -982    145
 576     78   -982    134   -982
 577   -982   -982    251   -982
 578   -982    134    166   -982
 579   -982   -982    251   -982
 580   -982    251   -982   -982
 581   -982   -982   -982    162
 582     45    134   -982   -154
 583   -982    215   -982    -55
 584   -982    166   -982     45
 585    162   -982   -982   -982
 586   -982     34   -982    126
 587      4    134    -66   -154
 588   -982    215    -66   -154
 589    145   -982   -982   -154
 590      4    134     34   -982
 591   -982    166     92   -154
 592 --------------------------------------------------------------------------------
 593
 594 --------------------------------------------------------------------------------
 595         Motif 4 position-specific probability matrix
 596 --------------------------------------------------------------------------------
 597 letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 1.7e-013
 598  0.000000  0.111111  0.000000  0.888889
 599  0.000000  0.888889  0.000000  0.111111
 600  0.000000  0.111111  0.000000  0.888889
 601  0.000000  0.111111  0.000000  0.888889
 602  0.555556  0.000000  0.444444  0.000000
 603  0.000000  0.000000  1.000000  0.000000
 604  0.000000  0.444444  0.555556  0.000000
 605  0.000000  0.000000  1.000000  0.000000
 606  0.000000  1.000000  0.000000  0.000000
 607  0.000000  0.000000  0.000000  1.000000
 608  0.444444  0.444444  0.000000  0.111111
 609  0.000000  0.777778  0.000000  0.222222
 610  0.000000  0.555556  0.000000  0.444444
 611  1.000000  0.000000  0.000000  0.000000
 612  0.000000  0.222222  0.000000  0.777778
 613  0.333333  0.444444  0.111111  0.111111
 614  0.000000  0.777778  0.111111  0.111111
 615  0.888889  0.000000  0.000000  0.111111
 616  0.333333  0.444444  0.222222  0.000000
 617  0.000000  0.555556  0.333333  0.111111
 618 --------------------------------------------------------------------------------
 619
 620 --------------------------------------------------------------------------------
 621         Motif 4 regular expression
 622 --------------------------------------------------------------------------------
 623 TCTT[AG]G[GC]GCT[AC][CT][CT]A[TC][CA]CA[CAG][CG]
 624 --------------------------------------------------------------------------------
 625
 626
 627
 628
 629 Time 20.21 secs.
 630
 631 ********************************************************************************
 632
 633
 634 ********************************************************************************
 635 MOTIF  5        width =   20   sites =   9   llr = 167   E-value = 1.7e-011
 636 ********************************************************************************
 637 --------------------------------------------------------------------------------
 638         Motif 5 Description
 639 --------------------------------------------------------------------------------
 640 Simplified        A  921:9181:18181::881:
 641 pos.-specific     C  :1:118:99:2:118:1:98
 642 probability       G  ::9:::1::::9:61a12:2
 643 matrix            T  17:9:11:19::121:::::
 644
 645          bits    2.5                *
 646                  2.3                *
 647                  2.0   *    **  *   *  *
 648                  1.8   *    **  *   *  **
 649 Information      1.5   *    **  *  **  **
 650 content          1.3   **** **  *  **  **
 651 (26.7 bits)      1.0 * **** *****  ** ***
 652                  0.8 * *********** ******
 653                  0.5 ********************
 654                  0.3 ********************
 655                  0.0 --------------------
 656
 657 Multilevel           ATGTACACCTAGAGCGAACC
 658 consensus             A        C  T   G G
 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_Sbay_Contig635.57      +    232  3.60e-13 TAAAAAAAAC ATGTACACCTAGAGCGAACC AGTGATAATT
 669 WashU_Skud_Contig1682.4      +    226  3.60e-13 AAGTAGAGAT ATGTACACCTAGAGCGAACC AATGATAATT
 670 MIT_Smik_c492_20940          +    229  3.60e-13 AAGTGAAGAT ATGTACACCTAGAGCGAACC AATAATAATT
 671 MIT_Spar_c261_21317          +    224  3.60e-13 CAAAATGAAT ATGTACACCTAGAGCGAACC AATGATAATT
 672 SGD_Scer_YOR278W             +    220  3.60e-13 AAGTGAAGAT ATGTACACCTAGAGCGAACC AATGATAATT
 673 SGD_Scer_YDR047W             +    449  2.13e-07 TCGCAGTGCT ACGTACGCCAAAAACGCGCG CATGGAAGTA
 674 MIT_Sbay_c896_21277          +    384  2.80e-07 GCTTGGTAAC AAATAAACCTAGCCGGGGCC AGAATTTCAC
 675 MIT_Spar_c130_3923           +    120  3.31e-07 TATTTACTCT ATGTCCACTTCGTTTGAAAC ATCAGTGGTT
 676 WashU_Skud_Contig1362.1      +    684  7.95e-07 GAAGCGGGCC TAGCATTACTCGATCGAACG TTGCCGTTTA
 677 --------------------------------------------------------------------------------
 678
 679 --------------------------------------------------------------------------------
 680         Motif 5 block diagrams
 681 --------------------------------------------------------------------------------
 682 SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
 683 -------------            ----------------  -------------
 684 WashU_Sbay_Contig635.57           3.6e-13  231_[+5]_384
 685 WashU_Skud_Contig1682.4           3.6e-13  225_[+5]_390
 686 MIT_Smik_c492_20940               3.6e-13  228_[+5]_387
 687 MIT_Spar_c261_21317               3.6e-13  223_[+5]_392
 688 SGD_Scer_YOR278W                  3.6e-13  219_[+5]_396
 689 SGD_Scer_YDR047W                  2.1e-07  448_[+5]_532
 690 MIT_Sbay_c896_21277               2.8e-07  383_[+5]_597
 691 MIT_Spar_c130_3923                3.3e-07  119_[+5]_861
 692 WashU_Skud_Contig1362.1             8e-07  683_[+5]_58
 693 --------------------------------------------------------------------------------
 694
 695 --------------------------------------------------------------------------------
 696         Motif 5 in BLOCKS format
 697 --------------------------------------------------------------------------------
 698 BL   MOTIF 5 width=20 seqs=9
 699 WashU_Sbay_Contig635.57  (  232) ATGTACACCTAGAGCGAACC  1
 700 WashU_Skud_Contig1682.4  (  226) ATGTACACCTAGAGCGAACC  1
 701 MIT_Smik_c492_20940      (  229) ATGTACACCTAGAGCGAACC  1
 702 MIT_Spar_c261_21317      (  224) ATGTACACCTAGAGCGAACC  1
 703 SGD_Scer_YOR278W         (  220) ATGTACACCTAGAGCGAACC  1
 704 SGD_Scer_YDR047W         (  449) ACGTACGCCAAAAACGCGCG  1
 705 MIT_Sbay_c896_21277      (  384) AAATAAACCTAGCCGGGGCC  1
 706 MIT_Spar_c130_3923       (  120) ATGTCCACTTCGTTTGAAAC  1
 707 WashU_Skud_Contig1362.1  (  684) TAGCATTACTCGATCGAACG  1
 708 //
 709
 710 --------------------------------------------------------------------------------
 711
 712 --------------------------------------------------------------------------------
 713         Motif 5 position-specific scoring matrix
 714 --------------------------------------------------------------------------------
 715 log-odds matrix: alength= 4 w= 20 n= 6765 bayes= 9.55203 E= 1.7e-011
 716    145   -982   -982   -154
 717    -55    -66   -982    104
 718   -154   -982    234   -982
 719   -982    -66   -982    145
 720    145    -66   -982   -982
 721   -154    215   -982   -154
 722    126   -982    -66   -154
 723   -154    234   -982   -982
 724   -982    234   -982   -154
 725   -154   -982   -982    145
 726    126     34   -982   -982
 727   -154   -982    234   -982
 728    126    -66   -982   -154
 729   -154    -66    166    -55
 730   -982    215    -66   -154
 731   -982   -982    251   -982
 732    126    -66    -66   -982
 733    126   -982     34   -982
 734   -154    234   -982   -982
 735   -982    215     34   -982
 736 --------------------------------------------------------------------------------
 737
 738 --------------------------------------------------------------------------------
 739         Motif 5 position-specific probability matrix
 740 --------------------------------------------------------------------------------
 741 letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 1.7e-011
 742  0.888889  0.000000  0.000000  0.111111
 743  0.222222  0.111111  0.000000  0.666667
 744  0.111111  0.000000  0.888889  0.000000
 745  0.000000  0.111111  0.000000  0.888889
 746  0.888889  0.111111  0.000000  0.000000
 747  0.111111  0.777778  0.000000  0.111111
 748  0.777778  0.000000  0.111111  0.111111
 749  0.111111  0.888889  0.000000  0.000000
 750  0.000000  0.888889  0.000000  0.111111
 751  0.111111  0.000000  0.000000  0.888889
 752  0.777778  0.222222  0.000000  0.000000
 753  0.111111  0.000000  0.888889  0.000000
 754  0.777778  0.111111  0.000000  0.111111
 755  0.111111  0.111111  0.555556  0.222222
 756  0.000000  0.777778  0.111111  0.111111
 757  0.000000  0.000000  1.000000  0.000000
 758  0.777778  0.111111  0.111111  0.000000
 759  0.777778  0.000000  0.222222  0.000000
 760  0.111111  0.888889  0.000000  0.000000
 761  0.000000  0.777778  0.222222  0.000000
 762 --------------------------------------------------------------------------------
 763
 764 --------------------------------------------------------------------------------
 765         Motif 5 regular expression
 766 --------------------------------------------------------------------------------
 767 A[TA]GTACACCT[AC]GA[GT]CGA[AG]C[CG]
 768 --------------------------------------------------------------------------------
 769
 770
 771
 772
 773 Time 25.01 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_YOR278W                 4.46e-32  [-5(9.93e-05)]_199_[+5(3.60e-13)]_91_[+2(6.64e-13)]_8_[-1(3.48e-12)]_9_[+3(6.31e-10)]_128_[+4(1.19e-08)]_85
 788 MIT_Spar_c261_21317              1.84e-35  25_[+4(3.48e-05)]_54_[+1(1.15e-05)]_104_[+5(3.60e-13)]_90_[+2(6.64e-13)]_8_[-1(3.48e-12)]_9_[+3(6.31e-10)]_142_[+4(3.46e-12)]_68
 789 MIT_Smik_c492_20940              2.51e-33  228_[+5(3.60e-13)]_91_[+2(6.64e-13)]_8_[-1(3.48e-12)]_9_[+3(6.31e-10)]_134_[+4(5.86e-10)]_70
 790 WashU_Skud_Contig1682.4          3.86e-32  225_[+5(3.60e-13)]_89_[+2(6.64e-13)]_8_[-1(3.48e-12)]_9_[+3(6.31e-10)]_135_[+4(1.02e-08)]_74
 791 WashU_Sbay_Contig635.57          1.81e-34  231_[+5(3.60e-13)]_90_[+2(1.74e-12)]_8_[-1(3.48e-12)]_9_[+3(6.31e-10)]_141_[+4(1.43e-11)]_61
 792 SGD_Scer_YDR047W                 2.76e-19  133_[+3(2.44e-07)]_140_[-4(3.04e-10)]_140_[+5(2.13e-07)]_177_[+1(4.90e-10)]_54_[+2(2.83e-09)]_61_[-1(8.87e-05)]_22_[+3(5.89e-06)]_55_[-3(5.20e-05)]_73
 793 MIT_Spar_c130_3923               9.70e-21  42_[+3(1.33e-05)]_62_[+5(3.31e-07)]_147_[-4(2.21e-11)]_337_[+1(1.59e-10)]_56_[+2(2.83e-09)]_38_[-5(5.60e-05)]_13_[-1(8.87e-05)]_55_[-3(2.21e-05)]_21_[-3(1.82e-07)]_64
 794 MIT_Sbay_c896_21277              7.11e-16  118_[+3(1.87e-05)]_105_[-4(5.15e-09)]_125_[+5(2.80e-07)]_138_[-2(1.57e-05)]_88_[+1(9.08e-09)]_45_[+2(1.89e-05)]_17_[+4(7.61e-05)]_45_[+3(1.82e-07)]_1_[+2(4.51e-08)]_148
 795 WashU_Skud_Contig1362.1          4.40e-16  38_[-2(7.81e-08)]_187_[-4(1.17e-09)]_97_[+3(9.95e-07)]_268_[+1(3.58e-09)]_18_[+5(7.95e-07)]_58
 796 --------------------------------------------------------------------------------
 797
 798 ********************************************************************************
 799
 800
 801 ********************************************************************************
 802 Stopped because nmotifs = 5 reached.
 803 ********************************************************************************
 804
 805 CPU: dhn02990.mrc-dunn.cam.ac.uk
 806
 807 ********************************************************************************