branch-1-6/t/data/map_hem/HEM4-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= HEM4-HEM14.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_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 HEM4-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=            4463    N=               9
  59 strands: + -
  60 sample: seed=            0    seqfrac=         1
  61 Letter frequencies in dataset:
  62 A 0.321 C 0.179 G 0.179 T 0.321
  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 = 6.5e-023
  70 ********************************************************************************
  71 --------------------------------------------------------------------------------
  72         Motif 1 Description
  73 --------------------------------------------------------------------------------
  74 Simplified        A  :7:::a:6:::aa1:a9:6a
  75 pos.-specific     C  9279::4:4a:::6a::4::
  76 probability       G  ::314:6:6:a::3::1:4:
  77 matrix            T  11::6::4:::::::::6::
  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           CACCTAGAGCGAACCAATAA
  92 consensus             CG G CTC    G   CG
  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_Contig1682.4      +    231  7.13e-12 GAGATATGTA CACCTAGAGCGAACCAATGA TAATTTGTTT
 103 MIT_Spar_c261_21317          +    229  7.13e-12 TGAATATGTA CACCTAGAGCGAACCAATGA TAATTTGTTT
 104 SGD_Scer_YOR278W             +    225  7.13e-12 AAGATATGTA CACCTAGAGCGAACCAATGA TAATTTGTTT
 105 MIT_Smik_c492_20940          +    234  2.25e-11 AAGATATGTA CACCTAGAGCGAACCAATAA TAATTTGTTT
 106 WashU_Sbay_Contig635.57      +    237  9.57e-11 AAAACATGTA CACCTAGAGCGAACCAGTGA TAATTTGCTT
 107 MIT_Spar_c425_6072           +    115  1.35e-10 TTTAAATACT CCGCGACTCCGAAGCAACAA AATGTCGAAG
 108 SGD_Scer_YER014W             +    116  1.35e-10 TTTGAATACT CCGCGACTCCGAAGCAACAA AGTGTCGAAG
 109 MIT_Sbay_c84_6418            +    108  1.06e-09 TTTTTATACT CTGCGACTCCGAAACAACAA AATCTCGAAG
 110 MIT_Smik_c283_5928           +    112  1.44e-09 CTTTTTTAAA TACGGACTCCGAAGCAACAA GGTCGAAGGC
 111 --------------------------------------------------------------------------------
 112
 113 --------------------------------------------------------------------------------
 114         Motif 1 block diagrams
 115 --------------------------------------------------------------------------------
 116 SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
 117 -------------            ----------------  -------------
 118 WashU_Skud_Contig1682.4           7.1e-12  230_[+1]_385
 119 MIT_Spar_c261_21317               7.1e-12  228_[+1]_387
 120 SGD_Scer_YOR278W                  7.1e-12  224_[+1]_391
 121 MIT_Smik_c492_20940               2.3e-11  233_[+1]_382
 122 WashU_Sbay_Contig635.57           9.6e-11  236_[+1]_379
 123 MIT_Spar_c425_6072                1.4e-10  114_[+1]_188
 124 SGD_Scer_YER014W                  1.4e-10  115_[+1]_187
 125 MIT_Sbay_c84_6418                 1.1e-09  107_[+1]_195
 126 MIT_Smik_c283_5928                1.4e-09  111_[+1]_191
 127 --------------------------------------------------------------------------------
 128
 129 --------------------------------------------------------------------------------
 130         Motif 1 in BLOCKS format
 131 --------------------------------------------------------------------------------
 132 BL   MOTIF 1 width=20 seqs=9
 133 WashU_Skud_Contig1682.4  (  231) CACCTAGAGCGAACCAATGA  1
 134 MIT_Spar_c261_21317      (  229) CACCTAGAGCGAACCAATGA  1
 135 SGD_Scer_YOR278W         (  225) CACCTAGAGCGAACCAATGA  1
 136 MIT_Smik_c492_20940      (  234) CACCTAGAGCGAACCAATAA  1
 137 WashU_Sbay_Contig635.57  (  237) CACCTAGAGCGAACCAGTGA  1
 138 MIT_Spar_c425_6072       (  115) CCGCGACTCCGAAGCAACAA  1
 139 SGD_Scer_YER014W         (  116) CCGCGACTCCGAAGCAACAA  1
 140 MIT_Sbay_c84_6418        (  108) CTGCGACTCCGAAACAACAA  1
 141 MIT_Smik_c283_5928       (  112) TACGGACTCCGAAGCAACAA  1
 142 //
 143
 144 --------------------------------------------------------------------------------
 145
 146 --------------------------------------------------------------------------------
 147         Motif 1 position-specific scoring matrix
 148 --------------------------------------------------------------------------------
 149 log-odds matrix: alength= 4 w= 20 n= 4292 bayes= 8.89448 E= 6.5e-023
 150   -982    234   -982   -154
 151    104     34   -982   -154
 152   -982    192     92   -982
 153   -982    234    -66   -982
 154   -982   -982    134     78
 155    162   -982   -982   -982
 156   -982    134    166   -982
 157     78   -982   -982     45
 158   -982    134    166   -982
 159   -982    251   -982   -982
 160   -982   -982    251   -982
 161    162   -982   -982   -982
 162    162   -982   -982   -982
 163   -154    166     92   -982
 164   -982    251   -982   -982
 165    162   -982   -982   -982
 166    145   -982    -66   -982
 167   -982    134   -982     78
 168     78   -982    134   -982
 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= 6.5e-023
 176  0.000000  0.888889  0.000000  0.111111
 177  0.666667  0.222222  0.000000  0.111111
 178  0.000000  0.666667  0.333333  0.000000
 179  0.000000  0.888889  0.111111  0.000000
 180  0.000000  0.000000  0.444444  0.555556
 181  1.000000  0.000000  0.000000  0.000000
 182  0.000000  0.444444  0.555556  0.000000
 183  0.555556  0.000000  0.000000  0.444444
 184  0.000000  0.444444  0.555556  0.000000
 185  0.000000  1.000000  0.000000  0.000000
 186  0.000000  0.000000  1.000000  0.000000
 187  1.000000  0.000000  0.000000  0.000000
 188  1.000000  0.000000  0.000000  0.000000
 189  0.111111  0.555556  0.333333  0.000000
 190  0.000000  1.000000  0.000000  0.000000
 191  1.000000  0.000000  0.000000  0.000000
 192  0.888889  0.000000  0.111111  0.000000
 193  0.000000  0.444444  0.000000  0.555556
 194  0.555556  0.000000  0.444444  0.000000
 195  1.000000  0.000000  0.000000  0.000000
 196 --------------------------------------------------------------------------------
 197
 198 --------------------------------------------------------------------------------
 199         Motif 1 regular expression
 200 --------------------------------------------------------------------------------
 201 C[AC][CG]C[TG]A[GC][AT][GC]CGAA[CG]CAA[TC][AG]A
 202 --------------------------------------------------------------------------------
 203
 204
 205
 206
 207 Time  2.29 secs.
 208
 209 ********************************************************************************
 210
 211
 212 ********************************************************************************
 213 MOTIF  2        width =   15   sites =   9   llr = 142   E-value = 7.6e-011
 214 ********************************************************************************
 215 --------------------------------------------------------------------------------
 216         Motif 2 Description
 217 --------------------------------------------------------------------------------
 218 Simplified        A  ::a:128::::2:::
 219 pos.-specific     C  a6::981:::27291
 220 probability       G  :4:a:::1227:81:
 221 matrix            T  ::::::198811::9
 222
 223          bits    2.5 *  *
 224                  2.3 *  *
 225                  2.0 *  **        *
 226                  1.8 *  **       **
 227 Information      1.5 ******      **
 228 content          1.3 ****** *  * ***
 229 (22.8 bits)      1.0 ****** ********
 230                  0.8 ***************
 231                  0.5 ***************
 232                  0.3 ***************
 233                  0.0 ---------------
 234
 235 Multilevel           CCAGCCATTTGCGCT
 236 consensus             G   A  GGCAC
 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_Sbay_Contig635.57      +    344  1.85e-10 TGGTCTACTT CCAGCCATTTGCGCT TGACATAGAC
 247 WashU_Skud_Contig1682.4      +    337  1.85e-10 TGGTCTACTT CCAGCCATTTGCGCT TTACATAGAC
 248 MIT_Smik_c492_20940          +    342  1.85e-10 TTGTCTACTT CCAGCCATTTGCGCT TTATATAGAC
 249 MIT_Spar_c261_21317          +    336  1.85e-10 TGGTCTACTT CCAGCCATTTGCGCT TTATATAGAC
 250 SGD_Scer_YOR278W             +    333  1.85e-10 TGGTCTACTT CCAGCCATTTGCGCT TTATATAGAC
 251 SGD_Scer_YER014W             +    174  2.34e-07 TGTAACTAAA CGAGCAATGGCAGCT TTCAATTAAA
 252 MIT_Smik_c283_5928           +    168  4.95e-07 TACAACTAAA CGAGCAATGGTAGCT TTTGATTGAA
 253 MIT_Spar_c425_6072           +      5  4.95e-07       TATT CGAGCCCTTTCCCGC GTTCCCAATT
 254 MIT_Sbay_c84_6418            +     44  1.47e-06 CGGAATCCAG CGAGACTGTTGTCCT TTCGCATCCT
 255 --------------------------------------------------------------------------------
 256
 257 --------------------------------------------------------------------------------
 258         Motif 2 block diagrams
 259 --------------------------------------------------------------------------------
 260 SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
 261 -------------            ----------------  -------------
 262 WashU_Sbay_Contig635.57           1.8e-10  343_[+2]_277
 263 WashU_Skud_Contig1682.4           1.8e-10  336_[+2]_284
 264 MIT_Smik_c492_20940               1.8e-10  341_[+2]_279
 265 MIT_Spar_c261_21317               1.8e-10  335_[+2]_285
 266 SGD_Scer_YOR278W                  1.8e-10  332_[+2]_288
 267 SGD_Scer_YER014W                  2.3e-07  173_[+2]_134
 268 MIT_Smik_c283_5928                4.9e-07  167_[+2]_140
 269 MIT_Spar_c425_6072                4.9e-07  4_[+2]_303
 270 MIT_Sbay_c84_6418                 1.5e-06  43_[+2]_264
 271 --------------------------------------------------------------------------------
 272
 273 --------------------------------------------------------------------------------
 274         Motif 2 in BLOCKS format
 275 --------------------------------------------------------------------------------
 276 BL   MOTIF 2 width=15 seqs=9
 277 WashU_Sbay_Contig635.57  (  344) CCAGCCATTTGCGCT  1
 278 WashU_Skud_Contig1682.4  (  337) CCAGCCATTTGCGCT  1
 279 MIT_Smik_c492_20940      (  342) CCAGCCATTTGCGCT  1
 280 MIT_Spar_c261_21317      (  336) CCAGCCATTTGCGCT  1
 281 SGD_Scer_YOR278W         (  333) CCAGCCATTTGCGCT  1
 282 SGD_Scer_YER014W         (  174) CGAGCAATGGCAGCT  1
 283 MIT_Smik_c283_5928       (  168) CGAGCAATGGTAGCT  1
 284 MIT_Spar_c425_6072       (    5) CGAGCCCTTTCCCGC  1
 285 MIT_Sbay_c84_6418        (   44) CGAGACTGTTGTCCT  1
 286 //
 287
 288 --------------------------------------------------------------------------------
 289
 290 --------------------------------------------------------------------------------
 291         Motif 2 position-specific scoring matrix
 292 --------------------------------------------------------------------------------
 293 log-odds matrix: alength= 4 w= 15 n= 4337 bayes= 8.90956 E= 7.6e-011
 294   -982    251   -982   -982
 295   -982    166    134   -982
 296    162   -982   -982   -982
 297   -982   -982    251   -982
 298   -154    234   -982   -982
 299    -55    215   -982   -982
 300    126    -66   -982   -154
 301   -982   -982    -66    145
 302   -982   -982     34    126
 303   -982   -982     34    126
 304   -982     34    192   -154
 305    -55    192   -982   -154
 306   -982     34    215   -982
 307   -982    234    -66   -982
 308   -982    -66   -982    145
 309 --------------------------------------------------------------------------------
 310
 311 --------------------------------------------------------------------------------
 312         Motif 2 position-specific probability matrix
 313 --------------------------------------------------------------------------------
 314 letter-probability matrix: alength= 4 w= 15 nsites= 9 E= 7.6e-011
 315  0.000000  1.000000  0.000000  0.000000
 316  0.000000  0.555556  0.444444  0.000000
 317  1.000000  0.000000  0.000000  0.000000
 318  0.000000  0.000000  1.000000  0.000000
 319  0.111111  0.888889  0.000000  0.000000
 320  0.222222  0.777778  0.000000  0.000000
 321  0.777778  0.111111  0.000000  0.111111
 322  0.000000  0.000000  0.111111  0.888889
 323  0.000000  0.000000  0.222222  0.777778
 324  0.000000  0.000000  0.222222  0.777778
 325  0.000000  0.222222  0.666667  0.111111
 326  0.222222  0.666667  0.000000  0.111111
 327  0.000000  0.222222  0.777778  0.000000
 328  0.000000  0.888889  0.111111  0.000000
 329  0.000000  0.111111  0.000000  0.888889
 330 --------------------------------------------------------------------------------
 331
 332 --------------------------------------------------------------------------------
 333         Motif 2 regular expression
 334 --------------------------------------------------------------------------------
 335 C[CG]AGC[CA]AT[TG][TG][GC][CA][GC]CT
 336 --------------------------------------------------------------------------------
 337
 338
 339
 340
 341 Time  4.39 secs.
 342
 343 ********************************************************************************
 344
 345
 346 ********************************************************************************
 347 MOTIF  3        width =   20   sites =   9   llr = 181   E-value = 1.1e-018
 348 ********************************************************************************
 349 --------------------------------------------------------------------------------
 350         Motif 3 Description
 351 --------------------------------------------------------------------------------
 352 Simplified        A  ::::4a6::a4:1:7a33:1
 353 pos.-specific     C  1:a:::::a:::2:1::66:
 354 probability       G  9::4::4a:::a6:2:1139
 355 matrix            T  :a:66:::::6:1a::6:1:
 356
 357          bits    2.5   *    **  *
 358                  2.3   *    **  *
 359                  2.0 * *    **  *       *
 360                  1.8 * *    **  *       *
 361 Information      1.5 ***  * *** * * *   *
 362 content          1.3 ***  * *** * * *   *
 363 (29.0 bits)      1.0 **** ***** * * *  **
 364                  0.8 **************** ***
 365                  0.5 **************** ***
 366                  0.3 ********************
 367                  0.0 --------------------
 368
 369 Multilevel           GTCTTAAGCATGGTAATCCG
 370 consensus               GA G   A C G AAG
 371 sequence
 372
 373 --------------------------------------------------------------------------------
 374
 375 --------------------------------------------------------------------------------
 376         Motif 3 sites sorted by position p-value
 377 --------------------------------------------------------------------------------
 378 Sequence name            Strand  Start   P-value                    Site
 379 -------------            ------  ----- ---------            --------------------
 380 WashU_Sbay_Contig635.57      +    384  5.08e-12 GAGGCGTGAT GTCTTAAGCATGGTAATCCG GAAGATCAGT
 381 WashU_Skud_Contig1682.4      +    377  5.08e-12 GAGGCGTGAT GTCTTAAGCATGGTAATCCG GAAGATCAGT
 382 MIT_Smik_c492_20940          +    382  5.08e-12 GAGGCGTGAT GTCTTAAGCATGGTAATCCG GAAGATCAGT
 383 MIT_Spar_c261_21317          +    376  5.08e-12 GAGGCGTGAT GTCTTAAGCATGGTAATCCG GAAGATCAGT
 384 SGD_Scer_YOR278W             +    373  5.08e-12 GAGGCGTGAT GTCTTAAGCATGGTAATCCG GAAGATCAGT
 385 MIT_Smik_c283_5928           +    133  7.06e-10 AAGCAACAAG GTCGAAGGCAAGCTGAAAGG CATTTTACAA
 386 MIT_Spar_c425_6072           +    138  1.93e-09 GCAACAAAAT GTCGAAGGCAAGATGAAAGG CGTTTTGCAA
 387 SGD_Scer_YER014W             +    139  2.96e-09 GCAACAAAGT GTCGAAGGCAAGTTCAAAGG CGTTTTGTAA
 388 MIT_Sbay_c84_6418            +    131  2.41e-08 ACAACAAAAT CTCGAAGGCAAGCTAAGGTA AAAATATTCA
 389 --------------------------------------------------------------------------------
 390
 391 --------------------------------------------------------------------------------
 392         Motif 3 block diagrams
 393 --------------------------------------------------------------------------------
 394 SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
 395 -------------            ----------------  -------------
 396 WashU_Sbay_Contig635.57           5.1e-12  383_[+3]_232
 397 WashU_Skud_Contig1682.4           5.1e-12  376_[+3]_239
 398 MIT_Smik_c492_20940               5.1e-12  381_[+3]_234
 399 MIT_Spar_c261_21317               5.1e-12  375_[+3]_240
 400 SGD_Scer_YOR278W                  5.1e-12  372_[+3]_243
 401 MIT_Smik_c283_5928                7.1e-10  132_[+3]_170
 402 MIT_Spar_c425_6072                1.9e-09  137_[+3]_165
 403 SGD_Scer_YER014W                    3e-09  138_[+3]_164
 404 MIT_Sbay_c84_6418                 2.4e-08  130_[+3]_172
 405 --------------------------------------------------------------------------------
 406
 407 --------------------------------------------------------------------------------
 408         Motif 3 in BLOCKS format
 409 --------------------------------------------------------------------------------
 410 BL   MOTIF 3 width=20 seqs=9
 411 WashU_Sbay_Contig635.57  (  384) GTCTTAAGCATGGTAATCCG  1
 412 WashU_Skud_Contig1682.4  (  377) GTCTTAAGCATGGTAATCCG  1
 413 MIT_Smik_c492_20940      (  382) GTCTTAAGCATGGTAATCCG  1
 414 MIT_Spar_c261_21317      (  376) GTCTTAAGCATGGTAATCCG  1
 415 SGD_Scer_YOR278W         (  373) GTCTTAAGCATGGTAATCCG  1
 416 MIT_Smik_c283_5928       (  133) GTCGAAGGCAAGCTGAAAGG  1
 417 MIT_Spar_c425_6072       (  138) GTCGAAGGCAAGATGAAAGG  1
 418 SGD_Scer_YER014W         (  139) GTCGAAGGCAAGTTCAAAGG  1
 419 MIT_Sbay_c84_6418        (  131) CTCGAAGGCAAGCTAAGGTA  1
 420 //
 421
 422 --------------------------------------------------------------------------------
 423
 424 --------------------------------------------------------------------------------
 425         Motif 3 position-specific scoring matrix
 426 --------------------------------------------------------------------------------
 427 log-odds matrix: alength= 4 w= 20 n= 4292 bayes= 8.89448 E= 1.1e-018
 428   -982    -66    234   -982
 429   -982   -982   -982    162
 430   -982    251   -982   -982
 431   -982   -982    134     78
 432     45   -982   -982     78
 433    162   -982   -982   -982
 434     78   -982    134   -982
 435   -982   -982    251   -982
 436   -982    251   -982   -982
 437    162   -982   -982   -982
 438     45   -982   -982     78
 439   -982   -982    251   -982
 440   -154     34    166   -154
 441   -982   -982   -982    162
 442    104    -66     34   -982
 443    162   -982   -982   -982
 444      4   -982    -66     78
 445      4    166    -66   -982
 446   -982    166     92   -154
 447   -154   -982    234   -982
 448 --------------------------------------------------------------------------------
 449
 450 --------------------------------------------------------------------------------
 451         Motif 3 position-specific probability matrix
 452 --------------------------------------------------------------------------------
 453 letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 1.1e-018
 454  0.000000  0.111111  0.888889  0.000000
 455  0.000000  0.000000  0.000000  1.000000
 456  0.000000  1.000000  0.000000  0.000000
 457  0.000000  0.000000  0.444444  0.555556
 458  0.444444  0.000000  0.000000  0.555556
 459  1.000000  0.000000  0.000000  0.000000
 460  0.555556  0.000000  0.444444  0.000000
 461  0.000000  0.000000  1.000000  0.000000
 462  0.000000  1.000000  0.000000  0.000000
 463  1.000000  0.000000  0.000000  0.000000
 464  0.444444  0.000000  0.000000  0.555556
 465  0.000000  0.000000  1.000000  0.000000
 466  0.111111  0.222222  0.555556  0.111111
 467  0.000000  0.000000  0.000000  1.000000
 468  0.666667  0.111111  0.222222  0.000000
 469  1.000000  0.000000  0.000000  0.000000
 470  0.333333  0.000000  0.111111  0.555556
 471  0.333333  0.555556  0.111111  0.000000
 472  0.000000  0.555556  0.333333  0.111111
 473  0.111111  0.000000  0.888889  0.000000
 474 --------------------------------------------------------------------------------
 475
 476 --------------------------------------------------------------------------------
 477         Motif 3 regular expression
 478 --------------------------------------------------------------------------------
 479 GTC[TG][TA]A[AG]GCA[TA]G[GC]T[AG]A[TA][CA][CG]G
 480 --------------------------------------------------------------------------------
 481
 482
 483
 484
 485 Time  6.42 secs.
 486
 487 ********************************************************************************
 488
 489
 490 ********************************************************************************
 491 MOTIF  4        width =   15   sites =   9   llr = 134   E-value = 6.1e-007
 492 ********************************************************************************
 493 --------------------------------------------------------------------------------
 494         Motif 4 Description
 495 --------------------------------------------------------------------------------
 496 Simplified        A  :9:a:2:::a:8499
 497 pos.-specific     C  7::::::a:::::1:
 498 probability       G  :1::48:::::2::1
 499 matrix            T  3:a:6:a:a:a:6::
 500
 501          bits    2.5        *
 502                  2.3        *
 503                  2.0        *
 504                  1.8        *
 505 Information      1.5   ** ******
 506 content          1.3 **** ******  **
 507 (21.5 bits)      1.0 ************ **
 508                  0.8 ***************
 509                  0.5 ***************
 510                  0.3 ***************
 511                  0.0 ---------------
 512
 513 Multilevel           CATATGTCTATATAA
 514 consensus            T   GA     GA
 515 sequence
 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_Smik_c492_20940          -    357  1.53e-08 ATCACGCCTC CATATGTCTATATAA AGCGCAAATG
 525 MIT_Spar_c261_21317          -    351  1.53e-08 ATCACGCCTC CATATGTCTATATAA AGCGCAAATG
 526 SGD_Scer_YOR278W             -    348  1.53e-08 ATCACGCCTC CATATGTCTATATAA AGCGCAAATG
 527 WashU_Skud_Contig1682.4      -    352  3.10e-08 ATCACGCCTC CATATGTCTATGTAA AGCGCAAATG
 528 MIT_Spar_c425_6072           +    280  5.61e-08 GAAGAATGAA TATAGGTCTATAAAA ATTCAATAAT
 529 SGD_Scer_YER014W             +    273  5.61e-08 AAAAATTAAA TATAGGTCTATAAAA CTCGATAATT
 530 WashU_Sbay_Contig635.57      -    359  1.88e-07 ATCACGCCTC CATATGTCTATGTCA AGCGCAAATG
 531 MIT_Smik_c283_5928           +    275  3.48e-07 AAATGTTAAA TATAGATCTATAAAA ATTGAATAGT
 532 MIT_Sbay_c84_6418            +    264  7.23e-07 TTATATTAAA CGTAGATCTATAAAG TTTAAATAGT
 533 --------------------------------------------------------------------------------
 534
 535 --------------------------------------------------------------------------------
 536         Motif 4 block diagrams
 537 --------------------------------------------------------------------------------
 538 SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
 539 -------------            ----------------  -------------
 540 MIT_Smik_c492_20940               1.5e-08  356_[-4]_264
 541 MIT_Spar_c261_21317               1.5e-08  350_[-4]_270
 542 SGD_Scer_YOR278W                  1.5e-08  347_[-4]_273
 543 WashU_Skud_Contig1682.4           3.1e-08  351_[-4]_269
 544 MIT_Spar_c425_6072                5.6e-08  279_[+4]_28
 545 SGD_Scer_YER014W                  5.6e-08  272_[+4]_35
 546 WashU_Sbay_Contig635.57           1.9e-07  358_[-4]_262
 547 MIT_Smik_c283_5928                3.5e-07  274_[+4]_33
 548 MIT_Sbay_c84_6418                 7.2e-07  263_[+4]_44
 549 --------------------------------------------------------------------------------
 550
 551 --------------------------------------------------------------------------------
 552         Motif 4 in BLOCKS format
 553 --------------------------------------------------------------------------------
 554 BL   MOTIF 4 width=15 seqs=9
 555 MIT_Smik_c492_20940      (  357) CATATGTCTATATAA  1
 556 MIT_Spar_c261_21317      (  351) CATATGTCTATATAA  1
 557 SGD_Scer_YOR278W         (  348) CATATGTCTATATAA  1
 558 WashU_Skud_Contig1682.4  (  352) CATATGTCTATGTAA  1
 559 MIT_Spar_c425_6072       (  280) TATAGGTCTATAAAA  1
 560 SGD_Scer_YER014W         (  273) TATAGGTCTATAAAA  1
 561 WashU_Sbay_Contig635.57  (  359) CATATGTCTATGTCA  1
 562 MIT_Smik_c283_5928       (  275) TATAGATCTATAAAA  1
 563 MIT_Sbay_c84_6418        (  264) CGTAGATCTATAAAG  1
 564 //
 565
 566 --------------------------------------------------------------------------------
 567
 568 --------------------------------------------------------------------------------
 569         Motif 4 position-specific scoring matrix
 570 --------------------------------------------------------------------------------
 571 log-odds matrix: alength= 4 w= 15 n= 4337 bayes= 8.90956 E= 6.1e-007
 572   -982    192   -982      4
 573    145   -982    -66   -982
 574   -982   -982   -982    162
 575    162   -982   -982   -982
 576   -982   -982    134     78
 577    -55   -982    215   -982
 578   -982   -982   -982    162
 579   -982    251   -982   -982
 580   -982   -982   -982    162
 581    162   -982   -982   -982
 582   -982   -982   -982    162
 583    126   -982     34   -982
 584     45   -982   -982     78
 585    145    -66   -982   -982
 586    145   -982    -66   -982
 587 --------------------------------------------------------------------------------
 588
 589 --------------------------------------------------------------------------------
 590         Motif 4 position-specific probability matrix
 591 --------------------------------------------------------------------------------
 592 letter-probability matrix: alength= 4 w= 15 nsites= 9 E= 6.1e-007
 593  0.000000  0.666667  0.000000  0.333333
 594  0.888889  0.000000  0.111111  0.000000
 595  0.000000  0.000000  0.000000  1.000000
 596  1.000000  0.000000  0.000000  0.000000
 597  0.000000  0.000000  0.444444  0.555556
 598  0.222222  0.000000  0.777778  0.000000
 599  0.000000  0.000000  0.000000  1.000000
 600  0.000000  1.000000  0.000000  0.000000
 601  0.000000  0.000000  0.000000  1.000000
 602  1.000000  0.000000  0.000000  0.000000
 603  0.000000  0.000000  0.000000  1.000000
 604  0.777778  0.000000  0.222222  0.000000
 605  0.444444  0.000000  0.000000  0.555556
 606  0.888889  0.111111  0.000000  0.000000
 607  0.888889  0.000000  0.111111  0.000000
 608 --------------------------------------------------------------------------------
 609
 610 --------------------------------------------------------------------------------
 611         Motif 4 regular expression
 612 --------------------------------------------------------------------------------
 613 [CT]ATA[TG][GA]TCTAT[AG][TA]AA
 614 --------------------------------------------------------------------------------
 615
 616
 617
 618
 619 Time  8.49 secs.
 620
 621 ********************************************************************************
 622
 623
 624 ********************************************************************************
 625 MOTIF  5        width =   20   sites =   9   llr = 162   E-value = 6.6e-011
 626 ********************************************************************************
 627 --------------------------------------------------------------------------------
 628         Motif 5 Description
 629 --------------------------------------------------------------------------------
 630 Simplified        A  27a973:384:aa:a9693a
 631 pos.-specific     C  1:::::6::::::9::::::
 632 probability       G  7::::74126a::::1:17:
 633 matrix            T  :3:13::6:::::1::4:::
 634
 635          bits    2.5           *
 636                  2.3           *
 637                  2.0           *  *
 638                  1.8           *  *
 639 Information      1.5   *   *   *****    *
 640 content          1.3   *  **   ****** ***
 641 (25.9 bits)      1.0 * ** ** ******** ***
 642                  0.8 ******* ************
 643                  0.5 ******* ************
 644                  0.3 ********************
 645                  0.0 --------------------
 646
 647 Multilevel           GAAAAGCTAGGAACAAAAGA
 648 consensus            AT  TAGAGA      T A
 649 sequence
 650
 651 --------------------------------------------------------------------------------
 652
 653 --------------------------------------------------------------------------------
 654         Motif 5 sites sorted by position p-value
 655 --------------------------------------------------------------------------------
 656 Sequence name            Strand  Start   P-value                    Site
 657 -------------            ------  ----- ---------            --------------------
 658 MIT_Smik_c492_20940          +    309  2.27e-12 TTTCAATAAT GAAAAGCTAGGAACAAAAGA AATTTGTCTA
 659 SGD_Scer_YOR278W             +    300  7.58e-11 TTTCAATAAT GAAAAGCTAGGAACAAAAAA AATTGGTCTA
 660 WashU_Sbay_Contig635.57      +    312  8.91e-10 TTTCATTAAA GAAAAGCTAGGAACAAAGAA ATTGGTCTAC
 661 WashU_Skud_Contig1682.4      +    304  8.91e-10 TTTCAATAAT GAAAAGCTAGGAATAAAAGA GATTGGTCTA
 662 MIT_Spar_c261_21317          +    304  8.91e-10 TTTCAATAAT GAAAAGCTAGGAACAGAAAA ATTGGTCTAC
 663 MIT_Smik_c283_5928           -     76  1.57e-09 AAAGAAAAGA GTAATGGAAAGAACAATAGA GGGATTTGCA
 664 MIT_Spar_c425_6072           -     74  3.54e-08 AAGAAAAAGA ATAATAGAGAGAACAATAGA GAGATCCGCG
 665 SGD_Scer_YER014W             -     74  3.54e-08 AAGAAATAGT ATAATAGAGAGAACAATAGA GATATTCGCG
 666 MIT_Sbay_c84_6418            -     69  4.79e-08 AAAACGAGAA CAATAAGGAAGAACAATAGA AGGATGCGAA
 667 --------------------------------------------------------------------------------
 668
 669 --------------------------------------------------------------------------------
 670         Motif 5 block diagrams
 671 --------------------------------------------------------------------------------
 672 SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
 673 -------------            ----------------  -------------
 674 MIT_Smik_c492_20940               2.3e-12  308_[+5]_307
 675 SGD_Scer_YOR278W                  7.6e-11  299_[+5]_316
 676 WashU_Sbay_Contig635.57           8.9e-10  311_[+5]_304
 677 WashU_Skud_Contig1682.4           8.9e-10  303_[+5]_312
 678 MIT_Spar_c261_21317               8.9e-10  303_[+5]_312
 679 MIT_Smik_c283_5928                1.6e-09  75_[-5]_227
 680 MIT_Spar_c425_6072                3.5e-08  73_[-5]_229
 681 SGD_Scer_YER014W                  3.5e-08  73_[-5]_229
 682 MIT_Sbay_c84_6418                 4.8e-08  68_[-5]_234
 683 --------------------------------------------------------------------------------
 684
 685 --------------------------------------------------------------------------------
 686         Motif 5 in BLOCKS format
 687 --------------------------------------------------------------------------------
 688 BL   MOTIF 5 width=20 seqs=9
 689 MIT_Smik_c492_20940      (  309) GAAAAGCTAGGAACAAAAGA  1
 690 SGD_Scer_YOR278W         (  300) GAAAAGCTAGGAACAAAAAA  1
 691 WashU_Sbay_Contig635.57  (  312) GAAAAGCTAGGAACAAAGAA  1
 692 WashU_Skud_Contig1682.4  (  304) GAAAAGCTAGGAATAAAAGA  1
 693 MIT_Spar_c261_21317      (  304) GAAAAGCTAGGAACAGAAAA  1
 694 MIT_Smik_c283_5928       (   76) GTAATGGAAAGAACAATAGA  1
 695 MIT_Spar_c425_6072       (   74) ATAATAGAGAGAACAATAGA  1
 696 SGD_Scer_YER014W         (   74) ATAATAGAGAGAACAATAGA  1
 697 MIT_Sbay_c84_6418        (   69) CAATAAGGAAGAACAATAGA  1
 698 //
 699
 700 --------------------------------------------------------------------------------
 701
 702 --------------------------------------------------------------------------------
 703         Motif 5 position-specific scoring matrix
 704 --------------------------------------------------------------------------------
 705 log-odds matrix: alength= 4 w= 20 n= 4292 bayes= 8.89448 E= 6.6e-011
 706    -55    -66    192   -982
 707    104   -982   -982      4
 708    162   -982   -982   -982
 709    145   -982   -982   -154
 710    104   -982   -982      4
 711      4   -982    192   -982
 712   -982    166    134   -982
 713      4   -982    -66     78
 714    126   -982     34   -982
 715     45   -982    166   -982
 716   -982   -982    251   -982
 717    162   -982   -982   -982
 718    162   -982   -982   -982
 719   -982    234   -982   -154
 720    162   -982   -982   -982
 721    145   -982    -66   -982
 722     78   -982   -982     45
 723    145   -982    -66   -982
 724      4   -982    192   -982
 725    162   -982   -982   -982
 726 --------------------------------------------------------------------------------
 727
 728 --------------------------------------------------------------------------------
 729         Motif 5 position-specific probability matrix
 730 --------------------------------------------------------------------------------
 731 letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 6.6e-011
 732  0.222222  0.111111  0.666667  0.000000
 733  0.666667  0.000000  0.000000  0.333333
 734  1.000000  0.000000  0.000000  0.000000
 735  0.888889  0.000000  0.000000  0.111111
 736  0.666667  0.000000  0.000000  0.333333
 737  0.333333  0.000000  0.666667  0.000000
 738  0.000000  0.555556  0.444444  0.000000
 739  0.333333  0.000000  0.111111  0.555556
 740  0.777778  0.000000  0.222222  0.000000
 741  0.444444  0.000000  0.555556  0.000000
 742  0.000000  0.000000  1.000000  0.000000
 743  1.000000  0.000000  0.000000  0.000000
 744  1.000000  0.000000  0.000000  0.000000
 745  0.000000  0.888889  0.000000  0.111111
 746  1.000000  0.000000  0.000000  0.000000
 747  0.888889  0.000000  0.111111  0.000000
 748  0.555556  0.000000  0.000000  0.444444
 749  0.888889  0.000000  0.111111  0.000000
 750  0.333333  0.000000  0.666667  0.000000
 751  1.000000  0.000000  0.000000  0.000000
 752 --------------------------------------------------------------------------------
 753
 754 --------------------------------------------------------------------------------
 755         Motif 5 regular expression
 756 --------------------------------------------------------------------------------
 757 [GA][AT]AA[AT][GA][CG][TA][AG][GA]GAACAA[AT]A[GA]A
 758 --------------------------------------------------------------------------------
 759
 760
 761
 762
 763 Time 10.53 secs.
 764
 765 ********************************************************************************
 766
 767
 768 ********************************************************************************
 769 SUMMARY OF MOTIFS
 770 ********************************************************************************
 771
 772 --------------------------------------------------------------------------------
 773         Combined block diagrams: non-overlapping sites with p-value < 0.0001
 774 --------------------------------------------------------------------------------
 775 SEQUENCE NAME            COMBINED P-VALUE  MOTIF DIAGRAM
 776 -------------            ----------------  -------------
 777 SGD_Scer_YOR278W                 3.99e-29  224_[+1(7.13e-12)]_55_[+5(7.58e-11)]_13_[+2(1.85e-10)]_[-4(1.53e-08)]_10_[+3(5.08e-12)]_243
 778 MIT_Spar_c261_21317              4.14e-28  228_[+1(7.13e-12)]_55_[+5(8.91e-10)]_12_[+2(1.85e-10)]_[-4(1.53e-08)]_10_[+3(5.08e-12)]_240
 779 MIT_Smik_c492_20940              4.23e-30  233_[+1(2.25e-11)]_55_[+5(2.27e-12)]_13_[+2(1.85e-10)]_[-4(1.53e-08)]_10_[+3(5.08e-12)]_234
 780 WashU_Skud_Contig1682.4          8.07e-28  230_[+1(7.13e-12)]_53_[+5(8.91e-10)]_13_[+2(1.85e-10)]_[-4(3.10e-08)]_10_[+3(5.08e-12)]_239
 781 WashU_Sbay_Contig635.57          5.21e-26  27_[+2(5.31e-05)]_194_[+1(9.57e-11)]_55_[+5(8.91e-10)]_12_[+2(1.85e-10)]_[-4(1.88e-07)]_10_[+3(5.08e-12)]_232
 782 SGD_Scer_YER014W                 8.73e-21  73_[-5(3.54e-08)]_22_[+1(1.35e-10)]_3_[+3(2.96e-09)]_15_[+2(2.34e-07)]_84_[+4(5.61e-08)]_35
 783 MIT_Spar_c425_6072               1.18e-20  4_[+2(4.95e-07)]_54_[-5(3.54e-08)]_21_[+1(1.35e-10)]_3_[+3(1.93e-09)]_15_[+2(1.10e-05)]_92_[+4(5.61e-08)]_28
 784 MIT_Smik_c283_5928               1.26e-20  75_[-5(1.57e-09)]_16_[+1(1.44e-09)]_1_[+3(7.06e-10)]_15_[+2(4.95e-07)]_92_[+4(3.48e-07)]_33
 785 MIT_Sbay_c84_6418                3.25e-17  43_[+2(1.47e-06)]_10_[-5(4.79e-08)]_19_[+1(1.06e-09)]_3_[+3(2.41e-08)]_113_[+4(7.23e-07)]_6_[-3(8.88e-05)]_18
 786 --------------------------------------------------------------------------------
 787
 788 ********************************************************************************
 789
 790
 791 ********************************************************************************
 792 Stopped because nmotifs = 5 reached.
 793 ********************************************************************************
 794
 795 CPU: dhn02990.mrc-dunn.cam.ac.uk
 796
 797 ********************************************************************************