t/data/map_hem/HEM3-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= HEM3-HEM14.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_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 HEM3-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=            5588    N=               9
  59 strands: + -
  60 sample: seed=            0    seqfrac=         1
  61 Letter frequencies in dataset:
  62 A 0.311 C 0.189 G 0.189 T 0.311
  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 = 1.6e-024
  70 ********************************************************************************
  71 --------------------------------------------------------------------------------
  72         Motif 1 Description
  73 --------------------------------------------------------------------------------
  74 Simplified        A  4:1:::::a::1:::6::::
  75 pos.-specific     C  6:98964:::::::a:87a1
  76 probability       G  :::::::::::9::::::::
  77 matrix            T  :a:2146a:aa:aa:423:9
  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           CTCCCCTTATTGTTCACCCT
  92 consensus            A  T TC        TTT
  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_Contig1850.5      +    706  7.49e-13 CATAGGCAAT CTCCCCTTATTGTTCACCCT TATTTCCACC
 103 MIT_Sbay_c841_3215           +    725  7.49e-13 CATAGGCAAT CTCCCCTTATTGTTCACCCT TATTTCCACC
 104 MIT_Spar_c429_3020           +    699  7.49e-13 CATAGGCAAC CTCCCCTTATTGTTCACCCT TATTTCCACC
 105 SGD_Scer_YDL205C             +    698  7.49e-13 CATAGGCAAT CTCCCCTTATTGTTCACCCT TATTTCCACC
 106 MIT_Smik_c193_2483           +    699  4.36e-11 CATAGGCAAT CTCCCCTTATTATTCACCCT TATTTCCACC
 107 MIT_Spar_c425_6072           +     69  2.43e-10 TCCTTCGCGG ATCTCTCTATTGTTCTCTCT ATTATTCTTT
 108 MIT_Sbay_c84_6418            +     64  6.44e-10 GTCCTTTCGC ATCCTTCTATTGTTCTTCCT TATTGTTCTC
 109 MIT_Smik_c283_5928           +     71  6.44e-10 TCTTTTGCAA ATCCCTCTATTGTTCTTTCC ATTACTCTTT
 110 SGD_Scer_YER014W             +     69  1.29e-09 TTCTTCGCGA ATATCTCTATTGTTCTCTCT ATTATACTAT
 111 --------------------------------------------------------------------------------
 112
 113 --------------------------------------------------------------------------------
 114         Motif 1 block diagrams
 115 --------------------------------------------------------------------------------
 116 SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
 117 -------------            ----------------  -------------
 118 WashU_Skud_Contig1850.5           7.5e-13  705_[+1]_135
 119 MIT_Sbay_c841_3215                7.5e-13  724_[+1]_116
 120 MIT_Spar_c429_3020                7.5e-13  698_[+1]_142
 121 SGD_Scer_YDL205C                  7.5e-13  697_[+1]_143
 122 MIT_Smik_c193_2483                4.4e-11  698_[+1]_142
 123 MIT_Spar_c425_6072                2.4e-10  68_[+1]_234
 124 MIT_Sbay_c84_6418                 6.4e-10  63_[+1]_239
 125 MIT_Smik_c283_5928                6.4e-10  70_[+1]_232
 126 SGD_Scer_YER014W                  1.3e-09  68_[+1]_234
 127 --------------------------------------------------------------------------------
 128
 129 --------------------------------------------------------------------------------
 130         Motif 1 in BLOCKS format
 131 --------------------------------------------------------------------------------
 132 BL   MOTIF 1 width=20 seqs=9
 133 WashU_Skud_Contig1850.5  (  706) CTCCCCTTATTGTTCACCCT  1
 134 MIT_Sbay_c841_3215       (  725) CTCCCCTTATTGTTCACCCT  1
 135 MIT_Spar_c429_3020       (  699) CTCCCCTTATTGTTCACCCT  1
 136 SGD_Scer_YDL205C         (  698) CTCCCCTTATTGTTCACCCT  1
 137 MIT_Smik_c193_2483       (  699) CTCCCCTTATTATTCACCCT  1
 138 MIT_Spar_c425_6072       (   69) ATCTCTCTATTGTTCTCTCT  1
 139 MIT_Sbay_c84_6418        (   64) ATCCTTCTATTGTTCTTCCT  1
 140 MIT_Smik_c283_5928       (   71) ATCCCTCTATTGTTCTTTCC  1
 141 SGD_Scer_YER014W         (   69) ATATCTCTATTGTTCTCTCT  1
 142 //
 143
 144 --------------------------------------------------------------------------------
 145
 146 --------------------------------------------------------------------------------
 147         Motif 1 position-specific scoring matrix
 148 --------------------------------------------------------------------------------
 149 log-odds matrix: alength= 4 w= 20 n= 5417 bayes= 9.23095 E= 1.6e-024
 150     45    166   -982   -982
 151   -982   -982   -982    162
 152   -154    234   -982   -982
 153   -982    215   -982    -55
 154   -982    234   -982   -154
 155   -982    166   -982     45
 156   -982    134   -982     78
 157   -982   -982   -982    162
 158    162   -982   -982   -982
 159   -982   -982   -982    162
 160   -982   -982   -982    162
 161   -154   -982    234   -982
 162   -982   -982   -982    162
 163   -982   -982   -982    162
 164   -982    251   -982   -982
 165     78   -982   -982     45
 166   -982    215   -982    -55
 167   -982    192   -982      4
 168   -982    251   -982   -982
 169   -982    -66   -982    145
 170 --------------------------------------------------------------------------------
 171
 172 --------------------------------------------------------------------------------
 173         Motif 1 position-specific probability matrix
 174 --------------------------------------------------------------------------------
 175 letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 1.6e-024
 176  0.444444  0.555556  0.000000  0.000000
 177  0.000000  0.000000  0.000000  1.000000
 178  0.111111  0.888889  0.000000  0.000000
 179  0.000000  0.777778  0.000000  0.222222
 180  0.000000  0.888889  0.000000  0.111111
 181  0.000000  0.555556  0.000000  0.444444
 182  0.000000  0.444444  0.000000  0.555556
 183  0.000000  0.000000  0.000000  1.000000
 184  1.000000  0.000000  0.000000  0.000000
 185  0.000000  0.000000  0.000000  1.000000
 186  0.000000  0.000000  0.000000  1.000000
 187  0.111111  0.000000  0.888889  0.000000
 188  0.000000  0.000000  0.000000  1.000000
 189  0.000000  0.000000  0.000000  1.000000
 190  0.000000  1.000000  0.000000  0.000000
 191  0.555556  0.000000  0.000000  0.444444
 192  0.000000  0.777778  0.000000  0.222222
 193  0.000000  0.666667  0.000000  0.333333
 194  0.000000  1.000000  0.000000  0.000000
 195  0.000000  0.111111  0.000000  0.888889
 196 --------------------------------------------------------------------------------
 197
 198 --------------------------------------------------------------------------------
 199         Motif 1 regular expression
 200 --------------------------------------------------------------------------------
 201 [CA]TC[CT]C[CT][TC]TATTGTTC[AT][CT][CT]CT
 202 --------------------------------------------------------------------------------
 203
 204
 205
 206
 207 Time  3.32 secs.
 208
 209 ********************************************************************************
 210
 211
 212 ********************************************************************************
 213 MOTIF  2        width =   20   sites =   9   llr = 193   E-value = 8.8e-023
 214 ********************************************************************************
 215 --------------------------------------------------------------------------------
 216         Motif 2 Description
 217 --------------------------------------------------------------------------------
 218 Simplified        A  ::a:::::aa7:4a:aa82:
 219 pos.-specific     C  96:a6a46:::9::6::::6
 220 probability       G  14:::::4::316::::28:
 221 matrix            T  ::::4:6:::::::4::::4
 222
 223          bits    2.5    * *
 224                  2.3    * *
 225                  2.0 *  * *     *
 226                  1.8 *  * *     *
 227 Information      1.5 **** * *** * * ** *
 228 content          1.3 **** * *** * * ** *
 229 (30.9 bits)      1.0 ********************
 230                  0.8 ********************
 231                  0.5 ********************
 232                  0.3 ********************
 233                  0.0 --------------------
 234
 235 Multilevel           CCACCCTCAAACGACAAAGC
 236 consensus             G  T CG  G A T  GAT
 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 MIT_Sbay_c841_3215           +    750  5.90e-12 ACCCTTATTT CCACCCTCAAACGACAAGGC TTGTTATGTT
 247 MIT_Smik_c193_2483           +    724  8.81e-12 ACCCTTATTT CCACCCTCAAACGATAAAGC TTGCTGCGCT
 248 MIT_Spar_c429_3020           +    724  8.81e-12 ACCCTTATTT CCACCCTCAAACGATAAAGC TTGTCTACAT
 249 SGD_Scer_YDL205C             +    723  8.81e-12 ACCCTTATTT CCACCCTCAAACGATAAAGC TTGCTACTTT
 250 SGD_Scer_YER014W             +    119  1.14e-10 GAATACTCCG CGACTCCGAAGCAACAAAGT GTCGAAGGCA
 251 WashU_Skud_Contig1850.5      +    731  1.80e-10 ACCCTTATTT CCACCCTCAAAGGATAAAGC TTGTTGCATT
 252 MIT_Sbay_c84_6418            +    111  4.97e-10 TTATACTCTG CGACTCCGAAACAACAAAAT CTCGAAGGCA
 253 MIT_Spar_c425_6072           +    118  5.35e-10 AAATACTCCG CGACTCCGAAGCAACAAAAT GTCGAAGGCA
 254 MIT_Smik_c283_5928           +    115  8.73e-10 TTTTAAATAC GGACTCCGAAGCAACAAGGT CGAAGGCAAG
 255 --------------------------------------------------------------------------------
 256
 257 --------------------------------------------------------------------------------
 258         Motif 2 block diagrams
 259 --------------------------------------------------------------------------------
 260 SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
 261 -------------            ----------------  -------------
 262 MIT_Sbay_c841_3215                5.9e-12  749_[+2]_91
 263 MIT_Smik_c193_2483                8.8e-12  723_[+2]_117
 264 MIT_Spar_c429_3020                8.8e-12  723_[+2]_117
 265 SGD_Scer_YDL205C                  8.8e-12  722_[+2]_118
 266 SGD_Scer_YER014W                  1.1e-10  118_[+2]_184
 267 WashU_Skud_Contig1850.5           1.8e-10  730_[+2]_110
 268 MIT_Sbay_c84_6418                   5e-10  110_[+2]_192
 269 MIT_Spar_c425_6072                5.3e-10  117_[+2]_185
 270 MIT_Smik_c283_5928                8.7e-10  114_[+2]_188
 271 --------------------------------------------------------------------------------
 272
 273 --------------------------------------------------------------------------------
 274         Motif 2 in BLOCKS format
 275 --------------------------------------------------------------------------------
 276 BL   MOTIF 2 width=20 seqs=9
 277 MIT_Sbay_c841_3215       (  750) CCACCCTCAAACGACAAGGC  1
 278 MIT_Smik_c193_2483       (  724) CCACCCTCAAACGATAAAGC  1
 279 MIT_Spar_c429_3020       (  724) CCACCCTCAAACGATAAAGC  1
 280 SGD_Scer_YDL205C         (  723) CCACCCTCAAACGATAAAGC  1
 281 SGD_Scer_YER014W         (  119) CGACTCCGAAGCAACAAAGT  1
 282 WashU_Skud_Contig1850.5  (  731) CCACCCTCAAAGGATAAAGC  1
 283 MIT_Sbay_c84_6418        (  111) CGACTCCGAAACAACAAAAT  1
 284 MIT_Spar_c425_6072       (  118) CGACTCCGAAGCAACAAAAT  1
 285 MIT_Smik_c283_5928       (  115) GGACTCCGAAGCAACAAGGT  1
 286 //
 287
 288 --------------------------------------------------------------------------------
 289
 290 --------------------------------------------------------------------------------
 291         Motif 2 position-specific scoring matrix
 292 --------------------------------------------------------------------------------
 293 log-odds matrix: alength= 4 w= 20 n= 5417 bayes= 9.23095 E= 8.8e-023
 294   -982    234    -66   -982
 295   -982    166    134   -982
 296    162   -982   -982   -982
 297   -982    251   -982   -982
 298   -982    166   -982     45
 299   -982    251   -982   -982
 300   -982    134   -982     78
 301   -982    166    134   -982
 302    162   -982   -982   -982
 303    162   -982   -982   -982
 304    104   -982     92   -982
 305   -982    234    -66   -982
 306     45   -982    166   -982
 307    162   -982   -982   -982
 308   -982    166   -982     45
 309    162   -982   -982   -982
 310    162   -982   -982   -982
 311    126   -982     34   -982
 312    -55   -982    215   -982
 313   -982    166   -982     45
 314 --------------------------------------------------------------------------------
 315
 316 --------------------------------------------------------------------------------
 317         Motif 2 position-specific probability matrix
 318 --------------------------------------------------------------------------------
 319 letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 8.8e-023
 320  0.000000  0.888889  0.111111  0.000000
 321  0.000000  0.555556  0.444444  0.000000
 322  1.000000  0.000000  0.000000  0.000000
 323  0.000000  1.000000  0.000000  0.000000
 324  0.000000  0.555556  0.000000  0.444444
 325  0.000000  1.000000  0.000000  0.000000
 326  0.000000  0.444444  0.000000  0.555556
 327  0.000000  0.555556  0.444444  0.000000
 328  1.000000  0.000000  0.000000  0.000000
 329  1.000000  0.000000  0.000000  0.000000
 330  0.666667  0.000000  0.333333  0.000000
 331  0.000000  0.888889  0.111111  0.000000
 332  0.444444  0.000000  0.555556  0.000000
 333  1.000000  0.000000  0.000000  0.000000
 334  0.000000  0.555556  0.000000  0.444444
 335  1.000000  0.000000  0.000000  0.000000
 336  1.000000  0.000000  0.000000  0.000000
 337  0.777778  0.000000  0.222222  0.000000
 338  0.222222  0.000000  0.777778  0.000000
 339  0.000000  0.555556  0.000000  0.444444
 340 --------------------------------------------------------------------------------
 341
 342 --------------------------------------------------------------------------------
 343         Motif 2 regular expression
 344 --------------------------------------------------------------------------------
 345 C[CG]AC[CT]C[TC][CG]AA[AG]C[GA]A[CT]AA[AG][GA][CT]
 346 --------------------------------------------------------------------------------
 347
 348
 349
 350
 351 Time  6.50 secs.
 352
 353 ********************************************************************************
 354
 355
 356 ********************************************************************************
 357 MOTIF  3        width =   20   sites =   9   llr = 178   E-value = 2.3e-016
 358 ********************************************************************************
 359 --------------------------------------------------------------------------------
 360         Motif 3 Description
 361 --------------------------------------------------------------------------------
 362 Simplified        A  9a::9496:41:94:34:71
 363 pos.-specific     C  1:a::6:4:::31:6::91:
 364 probability       G  ::::1:1:a69::6:76:29
 365 matrix            T  :::a:::::::7::4::1::
 366
 367          bits    2.5   *     *
 368                  2.3   *     *
 369                  2.0   *     * *      * *
 370                  1.8   *     * *      * *
 371 Information      1.5  ***    * *      * *
 372 content          1.3 ***** * * * *  * * *
 373 (28.5 bits)      1.0 ****************** *
 374                  0.8 ********************
 375                  0.5 ********************
 376                  0.3 ********************
 377                  0.0 --------------------
 378
 379 Multilevel           AACTACAAGGGTAGCGGCAG
 380 consensus                 A C A C ATAA G
 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 SGD_Scer_YDL205C             +    545  1.06e-11 AGTTAACTTA AACTACAAGGGTAGCAGCAG AATGTGTCGG
 391 MIT_Spar_c429_3020           +    548  4.76e-11 AGTTAACTTG AACTACAAGGGTAGCAACAG AATGTCGGTG
 392 MIT_Smik_c193_2483           +    547  1.28e-10 ACTTGACTTG AACTGCAAGGGTAGCGACGG CGTATGTCGG
 393 MIT_Spar_c425_6072           +    166  1.56e-10 GGCGTTTTGC AACTAAACGAGTAATGGCAG CTTTTAATTA
 394 SGD_Scer_YER014W             +    167  1.77e-10 GGCGTTTTGT AACTAAACGAGCAATGGCAG CTTTCAATTA
 395 MIT_Sbay_c84_6418            +    162  1.74e-09 AAATATTCAC CACTAAACGAGCAATGACAG TTATATTCAA
 396 WashU_Skud_Contig1850.5      +    550  1.74e-09 CGCAAAACGG AACTACAAGGATAGCAACGG AATGTGTCGG
 397 MIT_Smik_c283_5928           +    161  2.36e-09 GGCATTTTAC AACTAAACGAGCAATGGTAG CTTTTGATTG
 398 MIT_Sbay_c841_3215           +    557  4.89e-09 CGTAAGATAG AACTACGAGGGTCGCGGCCA ATGTGTCGGT
 399 --------------------------------------------------------------------------------
 400
 401 --------------------------------------------------------------------------------
 402         Motif 3 block diagrams
 403 --------------------------------------------------------------------------------
 404 SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
 405 -------------            ----------------  -------------
 406 SGD_Scer_YDL205C                  1.1e-11  544_[+3]_296
 407 MIT_Spar_c429_3020                4.8e-11  547_[+3]_293
 408 MIT_Smik_c193_2483                1.3e-10  546_[+3]_294
 409 MIT_Spar_c425_6072                1.6e-10  165_[+3]_137
 410 SGD_Scer_YER014W                  1.8e-10  166_[+3]_136
 411 MIT_Sbay_c84_6418                 1.7e-09  161_[+3]_141
 412 WashU_Skud_Contig1850.5           1.7e-09  549_[+3]_291
 413 MIT_Smik_c283_5928                2.4e-09  160_[+3]_142
 414 MIT_Sbay_c841_3215                4.9e-09  556_[+3]_284
 415 --------------------------------------------------------------------------------
 416
 417 --------------------------------------------------------------------------------
 418         Motif 3 in BLOCKS format
 419 --------------------------------------------------------------------------------
 420 BL   MOTIF 3 width=20 seqs=9
 421 SGD_Scer_YDL205C         (  545) AACTACAAGGGTAGCAGCAG  1
 422 MIT_Spar_c429_3020       (  548) AACTACAAGGGTAGCAACAG  1
 423 MIT_Smik_c193_2483       (  547) AACTGCAAGGGTAGCGACGG  1
 424 MIT_Spar_c425_6072       (  166) AACTAAACGAGTAATGGCAG  1
 425 SGD_Scer_YER014W         (  167) AACTAAACGAGCAATGGCAG  1
 426 MIT_Sbay_c84_6418        (  162) CACTAAACGAGCAATGACAG  1
 427 WashU_Skud_Contig1850.5  (  550) AACTACAAGGATAGCAACGG  1
 428 MIT_Smik_c283_5928       (  161) AACTAAACGAGCAATGGTAG  1
 429 MIT_Sbay_c841_3215       (  557) AACTACGAGGGTCGCGGCCA  1
 430 //
 431
 432 --------------------------------------------------------------------------------
 433
 434 --------------------------------------------------------------------------------
 435         Motif 3 position-specific scoring matrix
 436 --------------------------------------------------------------------------------
 437 log-odds matrix: alength= 4 w= 20 n= 5417 bayes= 9.23095 E= 2.3e-016
 438    145    -66   -982   -982
 439    162   -982   -982   -982
 440   -982    251   -982   -982
 441   -982   -982   -982    162
 442    145   -982    -66   -982
 443     45    166   -982   -982
 444    145   -982    -66   -982
 445     78    134   -982   -982
 446   -982   -982    251   -982
 447     45   -982    166   -982
 448   -154   -982    234   -982
 449   -982     92   -982    104
 450    145    -66   -982   -982
 451     45   -982    166   -982
 452   -982    166   -982     45
 453      4   -982    192   -982
 454     45   -982    166   -982
 455   -982    234   -982   -154
 456    104    -66     34   -982
 457   -154   -982    234   -982
 458 --------------------------------------------------------------------------------
 459
 460 --------------------------------------------------------------------------------
 461         Motif 3 position-specific probability matrix
 462 --------------------------------------------------------------------------------
 463 letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 2.3e-016
 464  0.888889  0.111111  0.000000  0.000000
 465  1.000000  0.000000  0.000000  0.000000
 466  0.000000  1.000000  0.000000  0.000000
 467  0.000000  0.000000  0.000000  1.000000
 468  0.888889  0.000000  0.111111  0.000000
 469  0.444444  0.555556  0.000000  0.000000
 470  0.888889  0.000000  0.111111  0.000000
 471  0.555556  0.444444  0.000000  0.000000
 472  0.000000  0.000000  1.000000  0.000000
 473  0.444444  0.000000  0.555556  0.000000
 474  0.111111  0.000000  0.888889  0.000000
 475  0.000000  0.333333  0.000000  0.666667
 476  0.888889  0.111111  0.000000  0.000000
 477  0.444444  0.000000  0.555556  0.000000
 478  0.000000  0.555556  0.000000  0.444444
 479  0.333333  0.000000  0.666667  0.000000
 480  0.444444  0.000000  0.555556  0.000000
 481  0.000000  0.888889  0.000000  0.111111
 482  0.666667  0.111111  0.222222  0.000000
 483  0.111111  0.000000  0.888889  0.000000
 484 --------------------------------------------------------------------------------
 485
 486 --------------------------------------------------------------------------------
 487         Motif 3 regular expression
 488 --------------------------------------------------------------------------------
 489 AACTA[CA]A[AC]G[GA]G[TC]A[GA][CT][GA][GA]C[AG]G
 490 --------------------------------------------------------------------------------
 491
 492
 493
 494
 495 Time  9.58 secs.
 496
 497 ********************************************************************************
 498
 499
 500 ********************************************************************************
 501 MOTIF  4        width =   11   sites =   9   llr = 119   E-value = 1.7e-006
 502 ********************************************************************************
 503 --------------------------------------------------------------------------------
 504         Motif 4 Description
 505 --------------------------------------------------------------------------------
 506 Simplified        A  2aa::6a4:1:
 507 pos.-specific     C  :::::4:6:8:
 508 probability       G  8::aa:::a::
 509 matrix            T  :::::::::1a
 510
 511          bits    2.5    **   *
 512                  2.3    **   *
 513                  2.0    **   *
 514                  1.8    **   *
 515 Information      1.5 ***** * * *
 516 content          1.3 ***** * ***
 517 (19.1 bits)      1.0 ***********
 518                  0.8 ***********
 519                  0.5 ***********
 520                  0.3 ***********
 521                  0.0 -----------
 522
 523 Multilevel           GAAGGAACGCT
 524 consensus            A    C A
 525 sequence
 526
 527 --------------------------------------------------------------------------------
 528
 529 --------------------------------------------------------------------------------
 530         Motif 4 sites sorted by position p-value
 531 --------------------------------------------------------------------------------
 532 Sequence name            Strand  Start   P-value               Site
 533 -------------            ------  ----- ---------            -----------
 534 WashU_Skud_Contig1850.5      -    217  1.62e-07 TGAAAAAATT GAAGGAACGCT TTATATAAAC
 535 MIT_Smik_c193_2483           -    220  1.62e-07 GAGAAAAACT GAAGGAACGCT TAATATAAAC
 536 MIT_Spar_c429_3020           -    218  1.62e-07 TGAAAAAAAT GAAGGAACGCT TTATATAAAC
 537 MIT_Sbay_c84_6418            +    134  2.68e-07 ACAAAATCTC GAAGGCAAGCT AAGGTAAAAA
 538 MIT_Smik_c283_5928           +    136  2.68e-07 CAACAAGGTC GAAGGCAAGCT GAAAGGCATT
 539 MIT_Sbay_c841_3215           -    218  7.62e-07 CCGAAAAATT AAAGGAACGCT TATTTAAACG
 540 SGD_Scer_YDL205C             -    217  7.62e-07 ATGAAAAAGT AAAGGAACGCT TTATATAAAC
 541 MIT_Spar_c425_6072           +    141  2.30e-06 ACAAAATGTC GAAGGCAAGAT GAAAGGCGTT
 542 SGD_Scer_YER014W             +    142  2.30e-06 ACAAAGTGTC GAAGGCAAGTT CAAAGGCGTT
 543 --------------------------------------------------------------------------------
 544
 545 --------------------------------------------------------------------------------
 546         Motif 4 block diagrams
 547 --------------------------------------------------------------------------------
 548 SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
 549 -------------            ----------------  -------------
 550 WashU_Skud_Contig1850.5           1.6e-07  216_[-4]_633
 551 MIT_Smik_c193_2483                1.6e-07  219_[-4]_630
 552 MIT_Spar_c429_3020                1.6e-07  217_[-4]_632
 553 MIT_Sbay_c84_6418                 2.7e-07  133_[+4]_178
 554 MIT_Smik_c283_5928                2.7e-07  135_[+4]_176
 555 MIT_Sbay_c841_3215                7.6e-07  217_[-4]_632
 556 SGD_Scer_YDL205C                  7.6e-07  216_[-4]_633
 557 MIT_Spar_c425_6072                2.3e-06  140_[+4]_171
 558 SGD_Scer_YER014W                  2.3e-06  141_[+4]_170
 559 --------------------------------------------------------------------------------
 560
 561 --------------------------------------------------------------------------------
 562         Motif 4 in BLOCKS format
 563 --------------------------------------------------------------------------------
 564 BL   MOTIF 4 width=11 seqs=9
 565 WashU_Skud_Contig1850.5  (  217) GAAGGAACGCT  1
 566 MIT_Smik_c193_2483       (  220) GAAGGAACGCT  1
 567 MIT_Spar_c429_3020       (  218) GAAGGAACGCT  1
 568 MIT_Sbay_c84_6418        (  134) GAAGGCAAGCT  1
 569 MIT_Smik_c283_5928       (  136) GAAGGCAAGCT  1
 570 MIT_Sbay_c841_3215       (  218) AAAGGAACGCT  1
 571 SGD_Scer_YDL205C         (  217) AAAGGAACGCT  1
 572 MIT_Spar_c425_6072       (  141) GAAGGCAAGAT  1
 573 SGD_Scer_YER014W         (  142) GAAGGCAAGTT  1
 574 //
 575
 576 --------------------------------------------------------------------------------
 577
 578 --------------------------------------------------------------------------------
 579         Motif 4 position-specific scoring matrix
 580 --------------------------------------------------------------------------------
 581 log-odds matrix: alength= 4 w= 11 n= 5498 bayes= 9.2524 E= 1.7e-006
 582    -55   -982    215   -982
 583    162   -982   -982   -982
 584    162   -982   -982   -982
 585   -982   -982    251   -982
 586   -982   -982    251   -982
 587     78    134   -982   -982
 588    162   -982   -982   -982
 589     45    166   -982   -982
 590   -982   -982    251   -982
 591   -154    215   -982   -154
 592   -982   -982   -982    162
 593 --------------------------------------------------------------------------------
 594
 595 --------------------------------------------------------------------------------
 596         Motif 4 position-specific probability matrix
 597 --------------------------------------------------------------------------------
 598 letter-probability matrix: alength= 4 w= 11 nsites= 9 E= 1.7e-006
 599  0.222222  0.000000  0.777778  0.000000
 600  1.000000  0.000000  0.000000  0.000000
 601  1.000000  0.000000  0.000000  0.000000
 602  0.000000  0.000000  1.000000  0.000000
 603  0.000000  0.000000  1.000000  0.000000
 604  0.555556  0.444444  0.000000  0.000000
 605  1.000000  0.000000  0.000000  0.000000
 606  0.444444  0.555556  0.000000  0.000000
 607  0.000000  0.000000  1.000000  0.000000
 608  0.111111  0.777778  0.000000  0.111111
 609  0.000000  0.000000  0.000000  1.000000
 610 --------------------------------------------------------------------------------
 611
 612 --------------------------------------------------------------------------------
 613         Motif 4 regular expression
 614 --------------------------------------------------------------------------------
 615 [GA]AAGG[AC]A[CA]GCT
 616 --------------------------------------------------------------------------------
 617
 618
 619
 620
 621 Time 12.58 secs.
 622
 623 ********************************************************************************
 624
 625
 626 ********************************************************************************
 627 MOTIF  5        width =   20   sites =   9   llr = 167   E-value = 6.6e-012
 628 ********************************************************************************
 629 --------------------------------------------------------------------------------
 630         Motif 5 Description
 631 --------------------------------------------------------------------------------
 632 Simplified        A  9:a:2:::4:a4492::7a9
 633 pos.-specific     C  :6::66a::::66:1:71::
 634 probability       G  1::a2:::6::::1:2:2::
 635 matrix            T  :4:::4:a:a::::783::1
 636
 637          bits    2.5    *  *
 638                  2.3    *  *
 639                  2.0    *  *
 640                  1.8    *  *
 641 Information      1.5   **  ** **       *
 642 content          1.3 * **  ** **  *  * *
 643 (26.7 bits)      1.0 **** ********* ** **
 644                  0.8 ************** *****
 645                  0.5 ********************
 646                  0.3 ********************
 647                  0.0 --------------------
 648
 649 Multilevel           ACAGCCCTGTACCATTCAAA
 650 consensus             T  AT  A  AA AGTG
 651 sequence                 G
 652
 653 --------------------------------------------------------------------------------
 654
 655 --------------------------------------------------------------------------------
 656         Motif 5 sites sorted by position p-value
 657 --------------------------------------------------------------------------------
 658 Sequence name            Strand  Start   P-value                    Site
 659 -------------            ------  ----- ---------            --------------------
 660 WashU_Skud_Contig1850.5      +    115  6.64e-13 AAAAAGCAAT ACAGCCCTGTACCATTCAAA CACGAACGCC
 661 MIT_Sbay_c841_3215           +    116  6.64e-13 AAAACGCAAT ACAGCCCTGTACCATTCAAA TACGAACGCC
 662 MIT_Smik_c193_2483           +    117  6.64e-13 AAAAAGTAAT ACAGCCCTGTACCATTCAAA CACGAGCGCC
 663 MIT_Spar_c429_3020           +    115  1.38e-12 AAAATGTAAA ACAGCCCTGTACCATGCAAA CACGAGCCTC
 664 SGD_Scer_YDL205C             +    115  1.38e-12 AAAATCTAAT ACAGCCCTGTACCATGCAAA CACGAGCGTC
 665 MIT_Smik_c283_5928           +    276  3.37e-08 AATGTTAAAT ATAGATCTATAAAAATTGAA TAGTAATAAT
 666 MIT_Spar_c425_6072           +    281  3.48e-08 AAGAATGAAT ATAGGTCTATAAAAATTCAA TAATTATAGA
 667 SGD_Scer_YER014W             +    274  3.63e-08 AAAATTAAAT ATAGGTCTATAAAACTCGAT AATTATAATG
 668 MIT_Sbay_c84_6418            +    265  4.65e-08 TATATTAAAC GTAGATCTATAAAGTTTAAA TAGTTTATAA
 669 --------------------------------------------------------------------------------
 670
 671 --------------------------------------------------------------------------------
 672         Motif 5 block diagrams
 673 --------------------------------------------------------------------------------
 674 SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
 675 -------------            ----------------  -------------
 676 WashU_Skud_Contig1850.5           6.6e-13  114_[+5]_726
 677 MIT_Sbay_c841_3215                6.6e-13  115_[+5]_725
 678 MIT_Smik_c193_2483                6.6e-13  116_[+5]_724
 679 MIT_Spar_c429_3020                1.4e-12  114_[+5]_726
 680 SGD_Scer_YDL205C                  1.4e-12  114_[+5]_726
 681 MIT_Smik_c283_5928                3.4e-08  275_[+5]_27
 682 MIT_Spar_c425_6072                3.5e-08  280_[+5]_22
 683 SGD_Scer_YER014W                  3.6e-08  273_[+5]_29
 684 MIT_Sbay_c84_6418                 4.7e-08  264_[+5]_38
 685 --------------------------------------------------------------------------------
 686
 687 --------------------------------------------------------------------------------
 688         Motif 5 in BLOCKS format
 689 --------------------------------------------------------------------------------
 690 BL   MOTIF 5 width=20 seqs=9
 691 WashU_Skud_Contig1850.5  (  115) ACAGCCCTGTACCATTCAAA  1
 692 MIT_Sbay_c841_3215       (  116) ACAGCCCTGTACCATTCAAA  1
 693 MIT_Smik_c193_2483       (  117) ACAGCCCTGTACCATTCAAA  1
 694 MIT_Spar_c429_3020       (  115) ACAGCCCTGTACCATGCAAA  1
 695 SGD_Scer_YDL205C         (  115) ACAGCCCTGTACCATGCAAA  1
 696 MIT_Smik_c283_5928       (  276) ATAGATCTATAAAAATTGAA  1
 697 MIT_Spar_c425_6072       (  281) ATAGGTCTATAAAAATTCAA  1
 698 SGD_Scer_YER014W         (  274) ATAGGTCTATAAAACTCGAT  1
 699 MIT_Sbay_c84_6418        (  265) GTAGATCTATAAAGTTTAAA  1
 700 //
 701
 702 --------------------------------------------------------------------------------
 703
 704 --------------------------------------------------------------------------------
 705         Motif 5 position-specific scoring matrix
 706 --------------------------------------------------------------------------------
 707 log-odds matrix: alength= 4 w= 20 n= 5417 bayes= 9.23095 E= 6.6e-012
 708    145   -982    -66   -982
 709   -982    166   -982     45
 710    162   -982   -982   -982
 711   -982   -982    251   -982
 712    -55    166     34   -982
 713   -982    166   -982     45
 714   -982    251   -982   -982
 715   -982   -982   -982    162
 716     45   -982    166   -982
 717   -982   -982   -982    162
 718    162   -982   -982   -982
 719     45    166   -982   -982
 720     45    166   -982   -982
 721    145   -982    -66   -982
 722    -55    -66   -982    104
 723   -982   -982     34    126
 724   -982    192   -982      4
 725    104    -66     34   -982
 726    162   -982   -982   -982
 727    145   -982   -982   -154
 728 --------------------------------------------------------------------------------
 729
 730 --------------------------------------------------------------------------------
 731         Motif 5 position-specific probability matrix
 732 --------------------------------------------------------------------------------
 733 letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 6.6e-012
 734  0.888889  0.000000  0.111111  0.000000
 735  0.000000  0.555556  0.000000  0.444444
 736  1.000000  0.000000  0.000000  0.000000
 737  0.000000  0.000000  1.000000  0.000000
 738  0.222222  0.555556  0.222222  0.000000
 739  0.000000  0.555556  0.000000  0.444444
 740  0.000000  1.000000  0.000000  0.000000
 741  0.000000  0.000000  0.000000  1.000000
 742  0.444444  0.000000  0.555556  0.000000
 743  0.000000  0.000000  0.000000  1.000000
 744  1.000000  0.000000  0.000000  0.000000
 745  0.444444  0.555556  0.000000  0.000000
 746  0.444444  0.555556  0.000000  0.000000
 747  0.888889  0.000000  0.111111  0.000000
 748  0.222222  0.111111  0.000000  0.666667
 749  0.000000  0.000000  0.222222  0.777778
 750  0.000000  0.666667  0.000000  0.333333
 751  0.666667  0.111111  0.222222  0.000000
 752  1.000000  0.000000  0.000000  0.000000
 753  0.888889  0.000000  0.000000  0.111111
 754 --------------------------------------------------------------------------------
 755
 756 --------------------------------------------------------------------------------
 757         Motif 5 regular expression
 758 --------------------------------------------------------------------------------
 759 A[CT]AG[CAG][CT]CT[GA]TA[CA][CA]A[TA][TG][CT][AG]AA
 760 --------------------------------------------------------------------------------
 761
 762
 763
 764
 765 Time 15.70 secs.
 766
 767 ********************************************************************************
 768
 769
 770 ********************************************************************************
 771 SUMMARY OF MOTIFS
 772 ********************************************************************************
 773
 774 --------------------------------------------------------------------------------
 775         Combined block diagrams: non-overlapping sites with p-value < 0.0001
 776 --------------------------------------------------------------------------------
 777 SEQUENCE NAME            COMBINED P-VALUE  MOTIF DIAGRAM
 778 -------------            ----------------  -------------
 779 SGD_Scer_YDL205C                 2.08e-30  114_[+5(1.38e-12)]_82_[-4(7.62e-07)]_154_[+4(3.75e-05)]_152_[+3(1.06e-11)]_133_[+1(7.49e-13)]_5_[+2(8.81e-12)]_118
 780 MIT_Spar_c429_3020               1.99e-30  53_[+1(9.52e-05)]_41_[+5(1.38e-12)]_83_[-4(1.62e-07)]_156_[+4(3.75e-05)]_152_[+3(4.76e-11)]_131_[+1(7.49e-13)]_5_[+2(8.81e-12)]_117
 781 MIT_Smik_c193_2483               1.21e-28  116_[+5(6.64e-13)]_83_[-4(1.62e-07)]_316_[+3(1.28e-10)]_132_[+1(4.36e-11)]_5_[+2(8.81e-12)]_117
 782 MIT_Sbay_c841_3215               2.40e-28  54_[+1(9.52e-05)]_41_[+5(6.64e-13)]_60_[+5(4.92e-05)]_2_[-4(7.62e-07)]_328_[+3(4.89e-09)]_107_[-1(5.66e-05)]_21_[+1(7.49e-13)]_5_[+2(5.90e-12)]_91
 783 WashU_Skud_Contig1850.5          5.34e-28  114_[+5(6.64e-13)]_82_[-4(1.62e-07)]_289_[+2(7.24e-05)]_13_[+3(1.74e-09)]_136_[+1(7.49e-13)]_5_[+2(1.80e-10)]_110
 784 SGD_Scer_YER014W                 1.36e-22  68_[+1(1.29e-09)]_30_[+2(1.14e-10)]_3_[+4(2.30e-06)]_14_[+3(1.77e-10)]_87_[+5(3.63e-08)]_29
 785 MIT_Spar_c425_6072               1.03e-22  68_[+1(2.43e-10)]_29_[+2(5.35e-10)]_3_[+4(2.30e-06)]_14_[+3(1.56e-10)]_57_[+4(9.30e-05)]_27_[+5(3.48e-08)]_22
 786 MIT_Smik_c283_5928               6.69e-22  70_[+1(6.44e-10)]_24_[+2(8.73e-10)]_1_[+4(2.68e-07)]_14_[+3(2.36e-09)]_95_[+5(3.37e-08)]_27
 787 MIT_Sbay_c84_6418                4.02e-22  63_[+1(6.44e-10)]_27_[+2(4.97e-10)]_3_[+4(2.68e-07)]_17_[+3(1.74e-09)]_83_[+5(4.65e-08)]_38
 788 --------------------------------------------------------------------------------
 789
 790 ********************************************************************************
 791
 792
 793 ********************************************************************************
 794 Stopped because nmotifs = 5 reached.
 795 ********************************************************************************
 796
 797 CPU: dhn02990.mrc-dunn.cam.ac.uk
 798
 799 ********************************************************************************