t/data/map_hem/HEM14-HEM15.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= HEM14-HEM15.fa
  32 ALPHABET= ACGT
  33 Sequence name            Weight Length  Sequence name            Weight Length
  34 -------------            ------ ------  -------------            ------ ------
  35 SGD_Scer_YER014W         1.0000    322  MIT_Spar_c425_6072       1.0000    322
  36 MIT_Smik_c283_5928       1.0000    322  MIT_Sbay_c84_6418        1.0000    322
  37 SGD_Scer_YOR176W         1.0000    727  MIT_Spar_c278_20970      1.0000    727
  38 MIT_Smik_c935_20455      1.0000    727  WashU_Skud_Contig2050.4  1.0000    727
  39 WashU_Sbay_Contig480.2   1.0000    727
  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 HEM14-HEM15.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=            4923    N=               9
  59 strands: + -
  60 sample: seed=            0    seqfrac=         1
  61 Letter frequencies in dataset:
  62 A 0.317 C 0.183 G 0.183 T 0.317
  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 = 199   E-value = 3.0e-025
  70 ********************************************************************************
  71 --------------------------------------------------------------------------------
  72         Motif 1 Description
  73 --------------------------------------------------------------------------------
  74 Simplified        A  ::::1aa7:4a:aa92:1:1
  75 pos.-specific     C  a:4a::::a6:a:::662:9
  76 probability       G  :6::9::3::::::12:71:
  77 matrix            T  :46:::::::::::::4:9:
  78
  79          bits    2.5 *  *    *  *
  80                  2.3 *  *    *  *
  81                  2.0 *  **   *  *       *
  82                  1.8 *  **   *  *       *
  83 Information      1.5 *  **** * ****     *
  84 content          1.3 *  **** * *****  ***
  85 (31.9 bits)      1.0 *************** ****
  86                  0.8 ********************
  87                  0.5 ********************
  88                  0.3 ********************
  89                  0.0 --------------------
  90
  91 Multilevel           CGTCGAAACCACAAACCGTC
  92 consensus             TC    G A     ATC
  93 sequence                            G
  94
  95 --------------------------------------------------------------------------------
  96
  97 --------------------------------------------------------------------------------
  98         Motif 1 sites sorted by position p-value
  99 --------------------------------------------------------------------------------
 100 Sequence name            Strand  Start   P-value                    Site
 101 -------------            ------  ----- ---------            --------------------
 102 WashU_Skud_Contig2050.4      +    569  3.57e-13 TCAAAGTGCG CGTCGAAACCACAAACCGTC GAAAATATTG
 103 MIT_Spar_c278_20970          +    563  3.57e-13 TCGAATTGCG CGTCGAAACCACAAACCGTC GAAAATAATG
 104 SGD_Scer_YOR176W             +    561  3.57e-13 TCACATTGCG CGTCGAAACCACAAACCGTC GAAAACAATG
 105 WashU_Sbay_Contig480.2       +    574  2.79e-11 TCGAAGTGCG CGTCGAAACCACAAACCATC AAAAATATCG
 106 MIT_Smik_c935_20455          +    547  3.89e-11 TCCAATTGCG CGTCAAAACCACAAACCGTC GAAAATAATG
 107 SGD_Scer_YER014W             +    122  5.95e-11 TACTCCGCGA CTCCGAAGCAACAAAGTGTC GAAGGCAAGT
 108 MIT_Spar_c425_6072           +    121  1.08e-10 TACTCCGCGA CTCCGAAGCAACAAAATGTC GAAGGCAAGA
 109 MIT_Sbay_c84_6418            +    114  2.44e-10 TACTCTGCGA CTCCGAAACAACAAAATCTC GAAGGCAAGC
 110 MIT_Smik_c283_5928           +    118  2.73e-09 TAAATACGGA CTCCGAAGCAACAAGGTCGA AGGCAAGCTG
 111 --------------------------------------------------------------------------------
 112
 113 --------------------------------------------------------------------------------
 114         Motif 1 block diagrams
 115 --------------------------------------------------------------------------------
 116 SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
 117 -------------            ----------------  -------------
 118 WashU_Skud_Contig2050.4           3.6e-13  568_[+1]_139
 119 MIT_Spar_c278_20970               3.6e-13  562_[+1]_145
 120 SGD_Scer_YOR176W                  3.6e-13  560_[+1]_147
 121 WashU_Sbay_Contig480.2            2.8e-11  573_[+1]_134
 122 MIT_Smik_c935_20455               3.9e-11  546_[+1]_161
 123 SGD_Scer_YER014W                    6e-11  121_[+1]_181
 124 MIT_Spar_c425_6072                1.1e-10  120_[+1]_182
 125 MIT_Sbay_c84_6418                 2.4e-10  113_[+1]_189
 126 MIT_Smik_c283_5928                2.7e-09  117_[+1]_185
 127 --------------------------------------------------------------------------------
 128
 129 --------------------------------------------------------------------------------
 130         Motif 1 in BLOCKS format
 131 --------------------------------------------------------------------------------
 132 BL   MOTIF 1 width=20 seqs=9
 133 WashU_Skud_Contig2050.4  (  569) CGTCGAAACCACAAACCGTC  1
 134 MIT_Spar_c278_20970      (  563) CGTCGAAACCACAAACCGTC  1
 135 SGD_Scer_YOR176W         (  561) CGTCGAAACCACAAACCGTC  1
 136 WashU_Sbay_Contig480.2   (  574) CGTCGAAACCACAAACCATC  1
 137 MIT_Smik_c935_20455      (  547) CGTCAAAACCACAAACCGTC  1
 138 SGD_Scer_YER014W         (  122) CTCCGAAGCAACAAAGTGTC  1
 139 MIT_Spar_c425_6072       (  121) CTCCGAAGCAACAAAATGTC  1
 140 MIT_Sbay_c84_6418        (  114) CTCCGAAACAACAAAATCTC  1
 141 MIT_Smik_c283_5928       (  118) CTCCGAAGCAACAAGGTCGA  1
 142 //
 143
 144 --------------------------------------------------------------------------------
 145
 146 --------------------------------------------------------------------------------
 147         Motif 1 position-specific scoring matrix
 148 --------------------------------------------------------------------------------
 149 log-odds matrix: alength= 4 w= 20 n= 4752 bayes= 9.04166 E= 3.0e-025
 150   -982    251   -982   -982
 151   -982   -982    166     45
 152   -982    134   -982     78
 153   -982    251   -982   -982
 154   -154   -982    234   -982
 155    162   -982   -982   -982
 156    162   -982   -982   -982
 157    104   -982     92   -982
 158   -982    251   -982   -982
 159     45    166   -982   -982
 160    162   -982   -982   -982
 161   -982    251   -982   -982
 162    162   -982   -982   -982
 163    162   -982   -982   -982
 164    145   -982    -66   -982
 165    -55    166     34   -982
 166   -982    166   -982     45
 167   -154     34    192   -982
 168   -982   -982    -66    145
 169   -154    234   -982   -982
 170 --------------------------------------------------------------------------------
 171
 172 --------------------------------------------------------------------------------
 173         Motif 1 position-specific probability matrix
 174 --------------------------------------------------------------------------------
 175 letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 3.0e-025
 176  0.000000  1.000000  0.000000  0.000000
 177  0.000000  0.000000  0.555556  0.444444
 178  0.000000  0.444444  0.000000  0.555556
 179  0.000000  1.000000  0.000000  0.000000
 180  0.111111  0.000000  0.888889  0.000000
 181  1.000000  0.000000  0.000000  0.000000
 182  1.000000  0.000000  0.000000  0.000000
 183  0.666667  0.000000  0.333333  0.000000
 184  0.000000  1.000000  0.000000  0.000000
 185  0.444444  0.555556  0.000000  0.000000
 186  1.000000  0.000000  0.000000  0.000000
 187  0.000000  1.000000  0.000000  0.000000
 188  1.000000  0.000000  0.000000  0.000000
 189  1.000000  0.000000  0.000000  0.000000
 190  0.888889  0.000000  0.111111  0.000000
 191  0.222222  0.555556  0.222222  0.000000
 192  0.000000  0.555556  0.000000  0.444444
 193  0.111111  0.222222  0.666667  0.000000
 194  0.000000  0.000000  0.111111  0.888889
 195  0.111111  0.888889  0.000000  0.000000
 196 --------------------------------------------------------------------------------
 197
 198 --------------------------------------------------------------------------------
 199         Motif 1 regular expression
 200 --------------------------------------------------------------------------------
 201 C[GT][TC]CGAA[AG]C[CA]ACAAA[CAG][CT][GC]TC
 202 --------------------------------------------------------------------------------
 203
 204
 205
 206
 207 Time  2.80 secs.
 208
 209 ********************************************************************************
 210
 211
 212 ********************************************************************************
 213 MOTIF  2        width =   20   sites =   9   llr = 169   E-value = 2.7e-014
 214 ********************************************************************************
 215 --------------------------------------------------------------------------------
 216         Motif 2 Description
 217 --------------------------------------------------------------------------------
 218 Simplified        A  ::::1::1133:1:::::3:
 219 pos.-specific     C  :99::9:9::36279167::
 220 probability       G  ::::::9:813:::::::::
 221 matrix            T  a11a911:16:47319437a
 222
 223          bits    2.5
 224                  2.3
 225                  2.0  **  ***      *
 226                  1.8  **  ***      *
 227 Information      1.5 **** ***      *    *
 228 content          1.3 **** ****    *** * *
 229 (27.1 bits)      1.0 *********  * ***** *
 230                  0.8 ********* ** *******
 231                  0.5 ********* **********
 232                  0.3 ********************
 233                  0.0 --------------------
 234
 235 Multilevel           TCCTTCGCGTACTCCTCCTT
 236 consensus                     ACTCT  TTA
 237 sequence                       G
 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_Smik_c935_20455          +    152  1.72e-12 ACCAAAAGAC TCCTTCGCGTCCTCCTTCTT CAAGTCTCAT
 247 MIT_Spar_c278_20970          +    157  1.72e-12 CTAAAAGTAT TCCTTCGCGTCCTCCTTCTT CAATCCCATA
 248 SGD_Scer_YOR176W             +    155  1.72e-12 CCAAAAGTAT TCCTTCGCGTCCTCCTTCTT CAATCCCATA
 249 WashU_Skud_Contig2050.4      +    161  4.74e-12 AAAGAAGTAT TCCTTCGCGTGCTTCTCCTT TCTGTGTCAA
 250 WashU_Sbay_Contig480.2       +    205  6.16e-10 AAAGAAGTAT TCCTACGCGAGCTCCCTCTT CAAGTGCCAA
 251 MIT_Spar_c425_6072           +     59  2.17e-09 TGAATTGGTA TCCTTCGCGGATCTCTCTAT TGTTCTCTCT
 252 SGD_Scer_YER014W             +     59  3.35e-08 TGAATTGGTG TTCTTCGCGAATATCTCTAT TGTTCTCTCT
 253 MIT_Sbay_c84_6418            +     65  9.53e-08 TCCTTTCGCA TCCTTCTATTGTTCTTCCTT ATTGTTCTCG
 254 MIT_Smik_c283_5928           +     61  1.51e-07 TAAACTGCTA TCTTTTGCAAATCCCTCTAT TGTTCTTTCC
 255 --------------------------------------------------------------------------------
 256
 257 --------------------------------------------------------------------------------
 258         Motif 2 block diagrams
 259 --------------------------------------------------------------------------------
 260 SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
 261 -------------            ----------------  -------------
 262 MIT_Smik_c935_20455               1.7e-12  151_[+2]_556
 263 MIT_Spar_c278_20970               1.7e-12  156_[+2]_551
 264 SGD_Scer_YOR176W                  1.7e-12  154_[+2]_553
 265 WashU_Skud_Contig2050.4           4.7e-12  160_[+2]_547
 266 WashU_Sbay_Contig480.2            6.2e-10  204_[+2]_503
 267 MIT_Spar_c425_6072                2.2e-09  58_[+2]_244
 268 SGD_Scer_YER014W                  3.3e-08  58_[+2]_244
 269 MIT_Sbay_c84_6418                 9.5e-08  64_[+2]_238
 270 MIT_Smik_c283_5928                1.5e-07  60_[+2]_242
 271 --------------------------------------------------------------------------------
 272
 273 --------------------------------------------------------------------------------
 274         Motif 2 in BLOCKS format
 275 --------------------------------------------------------------------------------
 276 BL   MOTIF 2 width=20 seqs=9
 277 MIT_Smik_c935_20455      (  152) TCCTTCGCGTCCTCCTTCTT  1
 278 MIT_Spar_c278_20970      (  157) TCCTTCGCGTCCTCCTTCTT  1
 279 SGD_Scer_YOR176W         (  155) TCCTTCGCGTCCTCCTTCTT  1
 280 WashU_Skud_Contig2050.4  (  161) TCCTTCGCGTGCTTCTCCTT  1
 281 WashU_Sbay_Contig480.2   (  205) TCCTACGCGAGCTCCCTCTT  1
 282 MIT_Spar_c425_6072       (   59) TCCTTCGCGGATCTCTCTAT  1
 283 SGD_Scer_YER014W         (   59) TTCTTCGCGAATATCTCTAT  1
 284 MIT_Sbay_c84_6418        (   65) TCCTTCTATTGTTCTTCCTT  1
 285 MIT_Smik_c283_5928       (   61) TCTTTTGCAAATCCCTCTAT  1
 286 //
 287
 288 --------------------------------------------------------------------------------
 289
 290 --------------------------------------------------------------------------------
 291         Motif 2 position-specific scoring matrix
 292 --------------------------------------------------------------------------------
 293 log-odds matrix: alength= 4 w= 20 n= 4752 bayes= 9.04166 E= 2.7e-014
 294   -982   -982   -982    162
 295   -982    234   -982   -154
 296   -982    234   -982   -154
 297   -982   -982   -982    162
 298   -154   -982   -982    145
 299   -982    234   -982   -154
 300   -982   -982    234   -154
 301   -154    234   -982   -982
 302   -154   -982    215   -154
 303      4   -982    -66     78
 304      4     92     92   -982
 305   -982    166   -982     45
 306   -154     34   -982    104
 307   -982    192   -982      4
 308   -982    234   -982   -154
 309   -982    -66   -982    145
 310   -982    166   -982     45
 311   -982    192   -982      4
 312      4   -982   -982    104
 313   -982   -982   -982    162
 314 --------------------------------------------------------------------------------
 315
 316 --------------------------------------------------------------------------------
 317         Motif 2 position-specific probability matrix
 318 --------------------------------------------------------------------------------
 319 letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 2.7e-014
 320  0.000000  0.000000  0.000000  1.000000
 321  0.000000  0.888889  0.000000  0.111111
 322  0.000000  0.888889  0.000000  0.111111
 323  0.000000  0.000000  0.000000  1.000000
 324  0.111111  0.000000  0.000000  0.888889
 325  0.000000  0.888889  0.000000  0.111111
 326  0.000000  0.000000  0.888889  0.111111
 327  0.111111  0.888889  0.000000  0.000000
 328  0.111111  0.000000  0.777778  0.111111
 329  0.333333  0.000000  0.111111  0.555556
 330  0.333333  0.333333  0.333333  0.000000
 331  0.000000  0.555556  0.000000  0.444444
 332  0.111111  0.222222  0.000000  0.666667
 333  0.000000  0.666667  0.000000  0.333333
 334  0.000000  0.888889  0.000000  0.111111
 335  0.000000  0.111111  0.000000  0.888889
 336  0.000000  0.555556  0.000000  0.444444
 337  0.000000  0.666667  0.000000  0.333333
 338  0.333333  0.000000  0.000000  0.666667
 339  0.000000  0.000000  0.000000  1.000000
 340 --------------------------------------------------------------------------------
 341
 342 --------------------------------------------------------------------------------
 343         Motif 2 regular expression
 344 --------------------------------------------------------------------------------
 345 TCCTTCGCG[TA][ACG][CT][TC][CT]CT[CT][CT][TA]T
 346 --------------------------------------------------------------------------------
 347
 348
 349
 350
 351 Time  5.45 secs.
 352
 353 ********************************************************************************
 354
 355
 356 ********************************************************************************
 357 MOTIF  3        width =   20   sites =   9   llr = 159   E-value = 1.6e-009
 358 ********************************************************************************
 359 --------------------------------------------------------------------------------
 360         Motif 3 Description
 361 --------------------------------------------------------------------------------
 362 Simplified        A  :1:12::::23:1:8:1:2:
 363 pos.-specific     C  :::4291:6:1:21219:::
 364 probability       G  1:8::::6::6::9:8::8:
 365 matrix            T  9924619448:a7::1:a:a
 366
 367          bits    2.5
 368                  2.3
 369                  2.0      *       *  *
 370                  1.8      *       *  *
 371 Information      1.5   *  *     * * *****
 372 content          1.3 * *  **    * * *****
 373 (25.4 bits)      1.0 ***  ****  * *******
 374                  0.8 ***  ******* *******
 375                  0.5 ********************
 376                  0.3 ********************
 377                  0.0 --------------------
 378
 379 Multilevel           TTGCTCTGCTGTTGAGCTGT
 380 consensus              TTA  TTAA C C   A
 381 sequence                 C
 382
 383 --------------------------------------------------------------------------------
 384
 385 --------------------------------------------------------------------------------
 386         Motif 3 sites sorted by position p-value
 387 --------------------------------------------------------------------------------
 388 Sequence name            Strand  Start   P-value                    Site
 389 -------------            ------  ----- ---------            --------------------
 390 MIT_Smik_c935_20455          +    482  3.60e-13 TCAGCTTTTT TTGCTCTGCTGTTGAGCTGT TTTACTTCAT
 391 MIT_Spar_c278_20970          +    498  5.54e-13 TTAGCTTTTT TTGCCCTGCTGTTGAGCTGT TTTGCTTCAC
 392 WashU_Sbay_Contig480.2       +    508  1.71e-12 TAGCTGTTTT TTGTTCTGCTGTTGAGCTGT TTTGCTCCAC
 393 WashU_Skud_Contig2050.4      +    499  1.71e-12 CAGCTGTTTT TTGTTCTGCTGTTGAGCTGT TTTGTTCCAT
 394 SGD_Scer_YOR176W             +    496  3.87e-12 TTAGCTTTTT TTGTCCTGCTGTTGAGCTGT TTTGCTTTAC
 395 MIT_Sbay_c84_6418            +      8  1.48e-07    TGTCGAA GTTCTCCTTTATTCCGCTGT TTCTTACGGA
 396 SGD_Scer_YER014W             +     28  2.26e-07 GCGTTCTCAA TTGCACTTTACTCGATATGT TTGAATTGGT
 397 MIT_Smik_c283_5928           +     19  2.82e-07 CTCTCTCCAC TATTTCTTTAATCGCGCTAT ACTAGATATG
 398 MIT_Spar_c425_6072           -    281  8.96e-07 TCTATAATTA TTGAATTTTTATAGACCTAT ATTCATTCTT
 399 --------------------------------------------------------------------------------
 400
 401 --------------------------------------------------------------------------------
 402         Motif 3 block diagrams
 403 --------------------------------------------------------------------------------
 404 SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
 405 -------------            ----------------  -------------
 406 MIT_Smik_c935_20455               3.6e-13  481_[+3]_226
 407 MIT_Spar_c278_20970               5.5e-13  497_[+3]_210
 408 WashU_Sbay_Contig480.2            1.7e-12  507_[+3]_200
 409 WashU_Skud_Contig2050.4           1.7e-12  498_[+3]_209
 410 SGD_Scer_YOR176W                  3.9e-12  495_[+3]_212
 411 MIT_Sbay_c84_6418                 1.5e-07  7_[+3]_295
 412 SGD_Scer_YER014W                  2.3e-07  27_[+3]_275
 413 MIT_Smik_c283_5928                2.8e-07  18_[+3]_284
 414 MIT_Spar_c425_6072                  9e-07  280_[-3]_22
 415 --------------------------------------------------------------------------------
 416
 417 --------------------------------------------------------------------------------
 418         Motif 3 in BLOCKS format
 419 --------------------------------------------------------------------------------
 420 BL   MOTIF 3 width=20 seqs=9
 421 MIT_Smik_c935_20455      (  482) TTGCTCTGCTGTTGAGCTGT  1
 422 MIT_Spar_c278_20970      (  498) TTGCCCTGCTGTTGAGCTGT  1
 423 WashU_Sbay_Contig480.2   (  508) TTGTTCTGCTGTTGAGCTGT  1
 424 WashU_Skud_Contig2050.4  (  499) TTGTTCTGCTGTTGAGCTGT  1
 425 SGD_Scer_YOR176W         (  496) TTGTCCTGCTGTTGAGCTGT  1
 426 MIT_Sbay_c84_6418        (    8) GTTCTCCTTTATTCCGCTGT  1
 427 SGD_Scer_YER014W         (   28) TTGCACTTTACTCGATATGT  1
 428 MIT_Smik_c283_5928       (   19) TATTTCTTTAATCGCGCTAT  1
 429 MIT_Spar_c425_6072       (  281) TTGAATTTTTATAGACCTAT  1
 430 //
 431
 432 --------------------------------------------------------------------------------
 433
 434 --------------------------------------------------------------------------------
 435         Motif 3 position-specific scoring matrix
 436 --------------------------------------------------------------------------------
 437 log-odds matrix: alength= 4 w= 20 n= 4752 bayes= 9.04166 E= 1.6e-009
 438   -982   -982    -66    145
 439   -154   -982   -982    145
 440   -982   -982    215    -55
 441   -154    134   -982     45
 442    -55     34   -982     78
 443   -982    234   -982   -154
 444   -982    -66   -982    145
 445   -982   -982    166     45
 446   -982    166   -982     45
 447    -55   -982   -982    126
 448      4    -66    166   -982
 449   -982   -982   -982    162
 450   -154     34   -982    104
 451   -982    -66    234   -982
 452    126     34   -982   -982
 453   -982    -66    215   -154
 454   -154    234   -982   -982
 455   -982   -982   -982    162
 456    -55   -982    215   -982
 457   -982   -982   -982    162
 458 --------------------------------------------------------------------------------
 459
 460 --------------------------------------------------------------------------------
 461         Motif 3 position-specific probability matrix
 462 --------------------------------------------------------------------------------
 463 letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 1.6e-009
 464  0.000000  0.000000  0.111111  0.888889
 465  0.111111  0.000000  0.000000  0.888889
 466  0.000000  0.000000  0.777778  0.222222
 467  0.111111  0.444444  0.000000  0.444444
 468  0.222222  0.222222  0.000000  0.555556
 469  0.000000  0.888889  0.000000  0.111111
 470  0.000000  0.111111  0.000000  0.888889
 471  0.000000  0.000000  0.555556  0.444444
 472  0.000000  0.555556  0.000000  0.444444
 473  0.222222  0.000000  0.000000  0.777778
 474  0.333333  0.111111  0.555556  0.000000
 475  0.000000  0.000000  0.000000  1.000000
 476  0.111111  0.222222  0.000000  0.666667
 477  0.000000  0.111111  0.888889  0.000000
 478  0.777778  0.222222  0.000000  0.000000
 479  0.000000  0.111111  0.777778  0.111111
 480  0.111111  0.888889  0.000000  0.000000
 481  0.000000  0.000000  0.000000  1.000000
 482  0.222222  0.000000  0.777778  0.000000
 483  0.000000  0.000000  0.000000  1.000000
 484 --------------------------------------------------------------------------------
 485
 486 --------------------------------------------------------------------------------
 487         Motif 3 regular expression
 488 --------------------------------------------------------------------------------
 489 TT[GT][CT][TAC]CT[GT][CT][TA][GA]T[TC]G[AC]GCT[GA]T
 490 --------------------------------------------------------------------------------
 491
 492
 493
 494
 495 Time  7.97 secs.
 496
 497 ********************************************************************************
 498
 499
 500 ********************************************************************************
 501 MOTIF  4        width =   20   sites =   9   llr = 162   E-value = 7.2e-011
 502 ********************************************************************************
 503 --------------------------------------------------------------------------------
 504         Motif 4 Description
 505 --------------------------------------------------------------------------------
 506 Simplified        A  :412:::41:39:1aaa717
 507 pos.-specific     C  :166::1:78::a4:::3::
 508 probability       G  a4:2::612:71::::::91
 509 matrix            T  ::3:aa34:2:::4:::::2
 510
 511          bits    2.5 *           *
 512                  2.3 *           *
 513                  2.0 *           *     *
 514                  1.8 *           *     *
 515 Information      1.5 *   **   *  * *** *
 516 content          1.3 *   **  ***** *** *
 517 (26.0 bits)      1.0 *   **  ***** *****
 518                  0.8 ******* ***** *****
 519                  0.5 ******* ************
 520                  0.3 ********************
 521                  0.0 --------------------
 522
 523 Multilevel           GACCTTGACCGACCAAAAGA
 524 consensus             GTA  TTGTA  T   C T
 525 sequence                G
 526
 527 --------------------------------------------------------------------------------
 528
 529 --------------------------------------------------------------------------------
 530         Motif 4 sites sorted by position p-value
 531 --------------------------------------------------------------------------------
 532 Sequence name            Strand  Start   P-value                    Site
 533 -------------            ------  ----- ---------            --------------------
 534 SGD_Scer_YOR176W             +    133  2.43e-11 AGCCAAGAGT GACCTTGACCGACCAAAAGT ATTCCTTCGC
 535 MIT_Spar_c278_20970          +    135  8.09e-11 AACCAAGAGT GACCTTGACCGACTAAAAGT ATTCCTTCGC
 536 WashU_Sbay_Contig480.2       +    180  9.46e-11 GAGCCATAAT GCTCTTGACCGACCAAAAGA AGTATTCCTA
 537 MIT_Smik_c935_20455          +    131  9.46e-11 GACCAACAGT GATCTTGGCCGACCAAAAGA CTCCTTCGCG
 538 WashU_Skud_Contig2050.4      +    136  3.12e-10 GACCAACAAT GATATTGACCGACCAAAAGA AGTATTCCTT
 539 MIT_Spar_c425_6072           +    156  3.11e-09 CAAGATGAAA GGCGTTTTGCAACTAAACGA GTAATGGCAG
 540 MIT_Smik_c283_5928           +    151  1.64e-08 CAAGCTGAAA GGCATTTTACAACTAAACGA GCAATGGTAG
 541 SGD_Scer_YER014W             +    157  1.64e-08 CAAGTTCAAA GGCGTTTTGTAACTAAACGA GCAATGGCAG
 542 MIT_Sbay_c84_6418            -    203  3.27e-07 TCTCCAGTGA GGACTTCTCTGGCAAAAAAG TAGAATGACG
 543 --------------------------------------------------------------------------------
 544
 545 --------------------------------------------------------------------------------
 546         Motif 4 block diagrams
 547 --------------------------------------------------------------------------------
 548 SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
 549 -------------            ----------------  -------------
 550 SGD_Scer_YOR176W                  2.4e-11  132_[+4]_575
 551 MIT_Spar_c278_20970               8.1e-11  134_[+4]_573
 552 WashU_Sbay_Contig480.2            9.5e-11  179_[+4]_528
 553 MIT_Smik_c935_20455               9.5e-11  130_[+4]_577
 554 WashU_Skud_Contig2050.4           3.1e-10  135_[+4]_572
 555 MIT_Spar_c425_6072                3.1e-09  155_[+4]_147
 556 MIT_Smik_c283_5928                1.6e-08  150_[+4]_152
 557 SGD_Scer_YER014W                  1.6e-08  156_[+4]_146
 558 MIT_Sbay_c84_6418                 3.3e-07  202_[-4]_100
 559 --------------------------------------------------------------------------------
 560
 561 --------------------------------------------------------------------------------
 562         Motif 4 in BLOCKS format
 563 --------------------------------------------------------------------------------
 564 BL   MOTIF 4 width=20 seqs=9
 565 SGD_Scer_YOR176W         (  133) GACCTTGACCGACCAAAAGT  1
 566 MIT_Spar_c278_20970      (  135) GACCTTGACCGACTAAAAGT  1
 567 WashU_Sbay_Contig480.2   (  180) GCTCTTGACCGACCAAAAGA  1
 568 MIT_Smik_c935_20455      (  131) GATCTTGGCCGACCAAAAGA  1
 569 WashU_Skud_Contig2050.4  (  136) GATATTGACCGACCAAAAGA  1
 570 MIT_Spar_c425_6072       (  156) GGCGTTTTGCAACTAAACGA  1
 571 MIT_Smik_c283_5928       (  151) GGCATTTTACAACTAAACGA  1
 572 SGD_Scer_YER014W         (  157) GGCGTTTTGTAACTAAACGA  1
 573 MIT_Sbay_c84_6418        (  203) GGACTTCTCTGGCAAAAAAG  1
 574 //
 575
 576 --------------------------------------------------------------------------------
 577
 578 --------------------------------------------------------------------------------
 579         Motif 4 position-specific scoring matrix
 580 --------------------------------------------------------------------------------
 581 log-odds matrix: alength= 4 w= 20 n= 4752 bayes= 9.04166 E= 7.2e-011
 582   -982   -982    251   -982
 583     45    -66    134   -982
 584   -154    166   -982      4
 585    -55    166     34   -982
 586   -982   -982   -982    162
 587   -982   -982   -982    162
 588   -982    -66    166      4
 589     45   -982    -66     45
 590   -154    192     34   -982
 591   -982    215   -982    -55
 592      4   -982    192   -982
 593    145   -982    -66   -982
 594   -982    251   -982   -982
 595   -154    134   -982     45
 596    162   -982   -982   -982
 597    162   -982   -982   -982
 598    162   -982   -982   -982
 599    104     92   -982   -982
 600   -154   -982    234   -982
 601    104   -982    -66    -55
 602 --------------------------------------------------------------------------------
 603
 604 --------------------------------------------------------------------------------
 605         Motif 4 position-specific probability matrix
 606 --------------------------------------------------------------------------------
 607 letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 7.2e-011
 608  0.000000  0.000000  1.000000  0.000000
 609  0.444444  0.111111  0.444444  0.000000
 610  0.111111  0.555556  0.000000  0.333333
 611  0.222222  0.555556  0.222222  0.000000
 612  0.000000  0.000000  0.000000  1.000000
 613  0.000000  0.000000  0.000000  1.000000
 614  0.000000  0.111111  0.555556  0.333333
 615  0.444444  0.000000  0.111111  0.444444
 616  0.111111  0.666667  0.222222  0.000000
 617  0.000000  0.777778  0.000000  0.222222
 618  0.333333  0.000000  0.666667  0.000000
 619  0.888889  0.000000  0.111111  0.000000
 620  0.000000  1.000000  0.000000  0.000000
 621  0.111111  0.444444  0.000000  0.444444
 622  1.000000  0.000000  0.000000  0.000000
 623  1.000000  0.000000  0.000000  0.000000
 624  1.000000  0.000000  0.000000  0.000000
 625  0.666667  0.333333  0.000000  0.000000
 626  0.111111  0.000000  0.888889  0.000000
 627  0.666667  0.000000  0.111111  0.222222
 628 --------------------------------------------------------------------------------
 629
 630 --------------------------------------------------------------------------------
 631         Motif 4 regular expression
 632 --------------------------------------------------------------------------------
 633 G[AG][CT][CAG]TT[GT][AT][CG][CT][GA]AC[CT]AAA[AC]G[AT]
 634 --------------------------------------------------------------------------------
 635
 636
 637
 638
 639 Time 10.39 secs.
 640
 641 ********************************************************************************
 642
 643
 644 ********************************************************************************
 645 MOTIF  5        width =   20   sites =   9   llr = 144   E-value = 1.4e-003
 646 ********************************************************************************
 647 --------------------------------------------------------------------------------
 648         Motif 5 Description
 649 --------------------------------------------------------------------------------
 650 Simplified        A  a6a:::1:191169877a82
 651 pos.-specific     C  ::::7a6a1:71:::11::2
 652 probability       G  ::::::::2:1341221:26
 653 matrix            T  :4:a3:3:6114::::1:::
 654
 655          bits    2.5      * *
 656                  2.3      * *
 657                  2.0      * *
 658                  1.8      * *
 659 Information      1.5 * ** * *         *
 660 content          1.3 * **** *     *   *
 661 (23.0 bits)      1.0 * **** * *  ***  **
 662                  0.8 ******** ** **** ***
 663                  0.5 ******** ** **** ***
 664                  0.3 ********************
 665                  0.0 --------------------
 666
 667 Multilevel           AAATCCCCTACTAAAAAAAG
 668 consensus             T  T T G  GG GG  GA
 669 sequence                                C
 670
 671 --------------------------------------------------------------------------------
 672
 673 --------------------------------------------------------------------------------
 674         Motif 5 sites sorted by position p-value
 675 --------------------------------------------------------------------------------
 676 Sequence name            Strand  Start   P-value                    Site
 677 -------------            ------  ----- ---------            --------------------
 678 WashU_Sbay_Contig480.2       +    233  5.39e-12 TTCAAGTGCC AAATCCCCTACTGAAAAAAG CAACATGAGA
 679 MIT_Spar_c278_20970          +    184  1.13e-11 CTTCAATCCC ATATCCCCTACTGAAAAAAG CAGCGTGCGA
 680 SGD_Scer_YOR176W             +    182  1.61e-11 CTTCAATCCC ATATCCCCTACGAAAAAAAG CAGCATGAGA
 681 WashU_Skud_Contig2050.4      +    189  2.93e-10 TTTCTGTGTC AAATCCCCTACTGAAAAAGC AGCATTGGGA
 682 MIT_Smik_c935_20455          +    180  2.45e-09 TTCAAGTCTC ATATCCCCTACCAGAAAAAG TAGCAGGCGA
 683 MIT_Spar_c425_6072           +    232  1.36e-07 TTTTCACATA AAATCCTCGAAGAAGGAAAA ATTGATAATC
 684 MIT_Smik_c283_5928           +    228  5.40e-07 TTGTCCCACG AAATTCTCGTTGAAAGCAAG GTTCGTAAGG
 685 MIT_Sbay_c84_6418            +    154  6.05e-07 TAAGGTAAAA ATATTCACCACTAAACGAGC AATGACAGTT
 686 SGD_Scer_YER014W             +    236  1.24e-06 TTTCATGTAA AAATTCTCAAGAGAGATAAA GTTGTTAAAA
 687 --------------------------------------------------------------------------------
 688
 689 --------------------------------------------------------------------------------
 690         Motif 5 block diagrams
 691 --------------------------------------------------------------------------------
 692 SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
 693 -------------            ----------------  -------------
 694 WashU_Sbay_Contig480.2            5.4e-12  232_[+5]_475
 695 MIT_Spar_c278_20970               1.1e-11  183_[+5]_524
 696 SGD_Scer_YOR176W                  1.6e-11  181_[+5]_526
 697 WashU_Skud_Contig2050.4           2.9e-10  188_[+5]_519
 698 MIT_Smik_c935_20455               2.5e-09  179_[+5]_528
 699 MIT_Spar_c425_6072                1.4e-07  231_[+5]_71
 700 MIT_Smik_c283_5928                5.4e-07  227_[+5]_75
 701 MIT_Sbay_c84_6418                 6.1e-07  153_[+5]_149
 702 SGD_Scer_YER014W                  1.2e-06  235_[+5]_67
 703 --------------------------------------------------------------------------------
 704
 705 --------------------------------------------------------------------------------
 706         Motif 5 in BLOCKS format
 707 --------------------------------------------------------------------------------
 708 BL   MOTIF 5 width=20 seqs=9
 709 WashU_Sbay_Contig480.2   (  233) AAATCCCCTACTGAAAAAAG  1
 710 MIT_Spar_c278_20970      (  184) ATATCCCCTACTGAAAAAAG  1
 711 SGD_Scer_YOR176W         (  182) ATATCCCCTACGAAAAAAAG  1
 712 WashU_Skud_Contig2050.4  (  189) AAATCCCCTACTGAAAAAGC  1
 713 MIT_Smik_c935_20455      (  180) ATATCCCCTACCAGAAAAAG  1
 714 MIT_Spar_c425_6072       (  232) AAATCCTCGAAGAAGGAAAA  1
 715 MIT_Smik_c283_5928       (  228) AAATTCTCGTTGAAAGCAAG  1
 716 MIT_Sbay_c84_6418        (  154) ATATTCACCACTAAACGAGC  1
 717 SGD_Scer_YER014W         (  236) AAATTCTCAAGAGAGATAAA  1
 718 //
 719
 720 --------------------------------------------------------------------------------
 721
 722 --------------------------------------------------------------------------------
 723         Motif 5 position-specific scoring matrix
 724 --------------------------------------------------------------------------------
 725 log-odds matrix: alength= 4 w= 20 n= 4752 bayes= 9.04166 E= 1.4e-003
 726    162   -982   -982   -982
 727     78   -982   -982     45
 728    162   -982   -982   -982
 729   -982   -982   -982    162
 730   -982    192   -982      4
 731   -982    251   -982   -982
 732   -154    166   -982      4
 733   -982    251   -982   -982
 734   -154    -66     34     78
 735    145   -982   -982   -154
 736   -154    192    -66   -154
 737   -154    -66     92     45
 738     78   -982    134   -982
 739    145   -982    -66   -982
 740    126   -982     34   -982
 741    104    -66     34   -982
 742    104    -66    -66   -154
 743    162   -982   -982   -982
 744    126   -982     34   -982
 745    -55     34    166   -982
 746 --------------------------------------------------------------------------------
 747
 748 --------------------------------------------------------------------------------
 749         Motif 5 position-specific probability matrix
 750 --------------------------------------------------------------------------------
 751 letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 1.4e-003
 752  1.000000  0.000000  0.000000  0.000000
 753  0.555556  0.000000  0.000000  0.444444
 754  1.000000  0.000000  0.000000  0.000000
 755  0.000000  0.000000  0.000000  1.000000
 756  0.000000  0.666667  0.000000  0.333333
 757  0.000000  1.000000  0.000000  0.000000
 758  0.111111  0.555556  0.000000  0.333333
 759  0.000000  1.000000  0.000000  0.000000
 760  0.111111  0.111111  0.222222  0.555556
 761  0.888889  0.000000  0.000000  0.111111
 762  0.111111  0.666667  0.111111  0.111111
 763  0.111111  0.111111  0.333333  0.444444
 764  0.555556  0.000000  0.444444  0.000000
 765  0.888889  0.000000  0.111111  0.000000
 766  0.777778  0.000000  0.222222  0.000000
 767  0.666667  0.111111  0.222222  0.000000
 768  0.666667  0.111111  0.111111  0.111111
 769  1.000000  0.000000  0.000000  0.000000
 770  0.777778  0.000000  0.222222  0.000000
 771  0.222222  0.222222  0.555556  0.000000
 772 --------------------------------------------------------------------------------
 773
 774 --------------------------------------------------------------------------------
 775         Motif 5 regular expression
 776 --------------------------------------------------------------------------------
 777 A[AT]AT[CT]C[CT]C[TG]AC[TG][AG]A[AG][AG]AA[AG][GAC]
 778 --------------------------------------------------------------------------------
 779
 780
 781
 782
 783 Time 12.73 secs.
 784
 785 ********************************************************************************
 786
 787
 788 ********************************************************************************
 789 SUMMARY OF MOTIFS
 790 ********************************************************************************
 791
 792 --------------------------------------------------------------------------------
 793         Combined block diagrams: non-overlapping sites with p-value < 0.0001
 794 --------------------------------------------------------------------------------
 795 SEQUENCE NAME            COMBINED P-VALUE  MOTIF DIAGRAM
 796 -------------            ----------------  -------------
 797 SGD_Scer_YER014W                 3.19e-19  27_[+3(2.26e-07)]_11_[+2(3.35e-08)]_43_[+1(5.95e-11)]_15_[+4(1.64e-08)]_59_[+5(1.24e-06)]_67
 798 MIT_Spar_c425_6072               4.24e-21  58_[+2(2.17e-09)]_42_[+1(1.08e-10)]_15_[+4(3.11e-09)]_56_[+5(1.36e-07)]_29_[-3(8.96e-07)]_22
 799 MIT_Smik_c283_5928               2.54e-17  18_[+3(2.82e-07)]_22_[+2(1.51e-07)]_37_[+1(2.73e-09)]_13_[+4(1.64e-08)]_57_[+5(5.40e-07)]_28_[-3(2.96e-05)]_27
 800 MIT_Sbay_c84_6418                1.73e-17  7_[+3(1.48e-07)]_37_[+2(9.53e-08)]_29_[+1(2.44e-10)]_20_[+5(6.05e-07)]_29_[-4(3.27e-07)]_100
 801 SGD_Scer_YOR176W                 1.87e-35  132_[+4(2.43e-11)]_2_[+2(1.72e-12)]_7_[+5(1.61e-11)]_294_[+3(3.87e-12)]_45_[+1(3.57e-13)]_147
 802 MIT_Spar_c278_20970              6.54e-36  134_[+4(8.09e-11)]_2_[+2(1.72e-12)]_7_[+5(1.13e-11)]_155_[-2(5.46e-05)]_119_[+3(5.54e-13)]_45_[+1(3.57e-13)]_145
 803 MIT_Smik_c935_20455              7.71e-32  130_[+4(9.46e-11)]_1_[+2(1.72e-12)]_8_[+5(2.45e-09)]_282_[+3(3.60e-13)]_45_[+1(3.89e-11)]_161
 804 WashU_Skud_Contig2050.4          4.20e-33  135_[+4(3.12e-10)]_5_[+2(4.74e-12)]_8_[+5(2.93e-10)]_290_[+3(1.71e-12)]_50_[+1(3.57e-13)]_69_[-3(1.35e-06)]_50
 805 WashU_Sbay_Contig480.2           1.98e-31  40_[-4(5.82e-05)]_119_[+4(9.46e-11)]_5_[+2(6.16e-10)]_8_[+5(5.39e-12)]_255_[+3(1.71e-12)]_46_[+1(2.79e-11)]_134
 806 --------------------------------------------------------------------------------
 807
 808 ********************************************************************************
 809
 810
 811 ********************************************************************************
 812 Stopped because nmotifs = 5 reached.
 813 ********************************************************************************
 814
 815 CPU: dhn02990.mrc-dunn.cam.ac.uk
 816
 817 ********************************************************************************