branch-1-6/t/data/map_hem/HEM2-HEM13.meme.txt

   1 ********************************************************************************
   2 MEME - Motif discovery tool
   3 ********************************************************************************
   4 MEME version 3.5.4 (Release date:    )
   5
   6 For further information on how to interpret these results or to get
   7 a copy of the MEME software please access http://meme.nbcr.net.
   8
   9 This file may be used as input to the MAST algorithm for searching
  10 sequence databases for matches to groups of motifs.  MAST is available
  11 for interactive use and downloading at http://meme.nbcr.net.
  12 ********************************************************************************
  13
  14
  15 ********************************************************************************
  16 REFERENCE
  17 ********************************************************************************
  18 If you use this program in your research, please cite:
  19
  20 Timothy L. Bailey and Charles Elkan,
  21 "Fitting a mixture model by expectation maximization to discover
  22 motifs in biopolymers", Proceedings of the Second International
  23 Conference on Intelligent Systems for Molecular Biology, pp. 28-36,
  24 AAAI Press, Menlo Park, California, 1994.
  25 ********************************************************************************
  26
  27
  28 ********************************************************************************
  29 TRAINING SET
  30 ********************************************************************************
  31 DATAFILE= HEM2-HEM13.fa
  32 ALPHABET= ACGT
  33 Sequence name            Weight Length  Sequence name            Weight Length
  34 -------------            ------ ------  -------------            ------ ------
  35 SGD_Scer_YGL040C         1.0000   1000  MIT_Spar_c19_8512        1.0000   1000
  36 MIT_Smik_c273_7756       1.0000   1000  MIT_Sbay_c77_8808        1.0000   1000
  37 WashU_Skud_Contig2052.17 1.0000   1000  SGD_Scer_YDR044W         1.0000   1000
  38 MIT_Spar_c130_3912       1.0000   1000  MIT_Sbay_c896_21290      1.0000   1000
  39 WashU_Smik_Contig2283.3  1.0000   1000
  40 ********************************************************************************
  41
  42 ********************************************************************************
  43 COMMAND LINE SUMMARY
  44 ********************************************************************************
  45 This information can also be useful in the event you wish to report a
  46 problem with the MEME software.
  47
  48 command: meme HEM2-HEM13.fa -nostatus -dna -revcomp -nmotifs 5 -bfile yeast.nc.1.freq -maxw 20 -mod oops -dir /Volumes/DATA/Home/ajr/sw/powerpc/meme-3.5.4
  49
  50 model:  mod=          oops    nmotifs=         5    evt=           inf
  51 object function=  E-value of product of p-values
  52 width:  minw=            6    maxw=           20    minic=        0.00
  53 width:  wg=             11    ws=              1    endgaps=       yes
  54 nsites: minsites=        9    maxsites=        9    wnsites=       0.8
  55 theta:  prob=            1    spmap=         uni    spfuzz=        0.5
  56 em:     prior=   dirichlet    b=            0.01    maxiter=        50
  57         distance=    1e-05
  58 data:   n=            9000    N=               9
  59 strands: + -
  60 sample: seed=            0    seqfrac=         1
  61 Letter frequencies in dataset:
  62 A 0.314 C 0.186 G 0.186 T 0.314
  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 = 9.2e-022
  70 ********************************************************************************
  71 --------------------------------------------------------------------------------
  72         Motif 1 Description
  73 --------------------------------------------------------------------------------
  74 Simplified        A  ::::::4:12a1:::::::8
  75 pos.-specific     C  a144:a::1::::::66::1
  76 probability       G  :66:a:6a28:::a8::1a1
  77 matrix            T  :3:6::::6::9a:2449::
  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           CGGTGCGGTGATTGGCCTGA
  92 consensus             TCC  A GA    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_Contig2052.17     -    180  1.35e-13 AATCCCTGTT CGGTGCGGTGATTGGCCTGA GGCAAGCTGC
 103 MIT_Smik_c273_7756           -    179  1.35e-13 AATCCTTATT CGGTGCGGTGATTGGCCTGA GGCAACATAC
 104 MIT_Spar_c19_8512            -    181  1.35e-13 AATCCCTGTT CGGTGCGGTGATTGGCCTGA GGCAAGCTGC
 105 SGD_Scer_YGL040C             -    180  1.17e-12 AATCCCTGTT CGGTGCGGTGATTGGCTTGA GGCAAGCTTC
 106 MIT_Sbay_c77_8808            -    181  2.88e-12 CATCTCCGGG CGGTGCGGTGATTGGCCTGC GGCAGGCTGC
 107 WashU_Smik_Contig2283.3      +    542  2.66e-10 ACGTTGAAAA CTCCGCAGGGATTGGTTTGG AAAATTATAG
 108 SGD_Scer_YDR044W             +    540  1.12e-09 ACAGTAAAAA CTCCGCAGGAAATGGTTTGA AGAATCTTAA
 109 MIT_Spar_c130_3912           +    534  1.20e-09 ACATTGAAAA CCCCGCAGCAATTGTTCTGA AGAATCTTAA
 110 MIT_Sbay_c896_21290          +    542  1.43e-09 ACTTTTAAAA CTCCGCAGAGATTGTTTGGA GGGACCTTGA
 111 --------------------------------------------------------------------------------
 112
 113 --------------------------------------------------------------------------------
 114         Motif 1 block diagrams
 115 --------------------------------------------------------------------------------
 116 SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
 117 -------------            ----------------  -------------
 118 WashU_Skud_Contig2052.17          1.4e-13  179_[-1]_801
 119 MIT_Smik_c273_7756                1.4e-13  178_[-1]_802
 120 MIT_Spar_c19_8512                 1.4e-13  180_[-1]_800
 121 SGD_Scer_YGL040C                  1.2e-12  179_[-1]_801
 122 MIT_Sbay_c77_8808                 2.9e-12  180_[-1]_800
 123 WashU_Smik_Contig2283.3           2.7e-10  541_[+1]_439
 124 SGD_Scer_YDR044W                  1.1e-09  539_[+1]_441
 125 MIT_Spar_c130_3912                1.2e-09  533_[+1]_447
 126 MIT_Sbay_c896_21290               1.4e-09  541_[+1]_439
 127 --------------------------------------------------------------------------------
 128
 129 --------------------------------------------------------------------------------
 130         Motif 1 in BLOCKS format
 131 --------------------------------------------------------------------------------
 132 BL   MOTIF 1 width=20 seqs=9
 133 WashU_Skud_Contig2052.17 (  180) CGGTGCGGTGATTGGCCTGA  1
 134 MIT_Smik_c273_7756       (  179) CGGTGCGGTGATTGGCCTGA  1
 135 MIT_Spar_c19_8512        (  181) CGGTGCGGTGATTGGCCTGA  1
 136 SGD_Scer_YGL040C         (  180) CGGTGCGGTGATTGGCTTGA  1
 137 MIT_Sbay_c77_8808        (  181) CGGTGCGGTGATTGGCCTGC  1
 138 WashU_Smik_Contig2283.3  (  542) CTCCGCAGGGATTGGTTTGG  1
 139 SGD_Scer_YDR044W         (  540) CTCCGCAGGAAATGGTTTGA  1
 140 MIT_Spar_c130_3912       (  534) CCCCGCAGCAATTGTTCTGA  1
 141 MIT_Sbay_c896_21290      (  542) CTCCGCAGAGATTGTTTGGA  1
 142 //
 143
 144 --------------------------------------------------------------------------------
 145
 146 --------------------------------------------------------------------------------
 147         Motif 1 position-specific scoring matrix
 148 --------------------------------------------------------------------------------
 149 log-odds matrix: alength= 4 w= 20 n= 8829 bayes= 9.93664 E= 9.2e-022
 150   -982    251   -982   -982
 151   -982    -66    166      4
 152   -982    134    166   -982
 153   -982    134   -982     78
 154   -982   -982    251   -982
 155   -982    251   -982   -982
 156     45   -982    166   -982
 157   -982   -982    251   -982
 158   -154    -66     34     78
 159    -55   -982    215   -982
 160    162   -982   -982   -982
 161   -154   -982   -982    145
 162   -982   -982   -982    162
 163   -982   -982    251   -982
 164   -982   -982    215    -55
 165   -982    166   -982     45
 166   -982    166   -982     45
 167   -982   -982    -66    145
 168   -982   -982    251   -982
 169    126    -66    -66   -982
 170 --------------------------------------------------------------------------------
 171
 172 --------------------------------------------------------------------------------
 173         Motif 1 position-specific probability matrix
 174 --------------------------------------------------------------------------------
 175 letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 9.2e-022
 176  0.000000  1.000000  0.000000  0.000000
 177  0.000000  0.111111  0.555556  0.333333
 178  0.000000  0.444444  0.555556  0.000000
 179  0.000000  0.444444  0.000000  0.555556
 180  0.000000  0.000000  1.000000  0.000000
 181  0.000000  1.000000  0.000000  0.000000
 182  0.444444  0.000000  0.555556  0.000000
 183  0.000000  0.000000  1.000000  0.000000
 184  0.111111  0.111111  0.222222  0.555556
 185  0.222222  0.000000  0.777778  0.000000
 186  1.000000  0.000000  0.000000  0.000000
 187  0.111111  0.000000  0.000000  0.888889
 188  0.000000  0.000000  0.000000  1.000000
 189  0.000000  0.000000  1.000000  0.000000
 190  0.000000  0.000000  0.777778  0.222222
 191  0.000000  0.555556  0.000000  0.444444
 192  0.000000  0.555556  0.000000  0.444444
 193  0.000000  0.000000  0.111111  0.888889
 194  0.000000  0.000000  1.000000  0.000000
 195  0.777778  0.111111  0.111111  0.000000
 196 --------------------------------------------------------------------------------
 197
 198 --------------------------------------------------------------------------------
 199         Motif 1 regular expression
 200 --------------------------------------------------------------------------------
 201 C[GT][GC][TC]GC[GA]G[TG][GA]ATTG[GT][CT][CT]TGA
 202 --------------------------------------------------------------------------------
 203
 204
 205
 206
 207 Time  8.40 secs.
 208
 209 ********************************************************************************
 210
 211
 212 ********************************************************************************
 213 MOTIF  2        width =   20   sites =   9   llr = 167   E-value = 2.0e-010
 214 ********************************************************************************
 215 --------------------------------------------------------------------------------
 216         Motif 2 Description
 217 --------------------------------------------------------------------------------
 218 Simplified        A  4a:aa:a:43:19464a493
 219 pos.-specific     C  ::a::::::1:::4:6:11:
 220 probability       G  6::::::a62491:4::::7
 221 matrix            T  :::::a:::36::1:::4::
 222
 223          bits    2.5   *    *
 224                  2.3   *    *
 225                  2.0   *    *   *
 226                  1.8   *    *   *
 227 Information      1.5  *******   *    *
 228 content          1.3  *******   **   * **
 229 (26.8 bits)      1.0 ********* *** *** **
 230                  0.8 ********* *** *** **
 231                  0.5 ********* ******* **
 232                  0.3 ********* **********
 233                  0.0 --------------------
 234
 235 Multilevel           GACAATAGGATGAAACAAAG
 236 consensus            A       ATG  CGA T A
 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 WashU_Skud_Contig2052.17     +    100  8.72e-11 AGAAATCATG AACAATAGGATGACGCATAG ACGTCACTAC
 247 WashU_Smik_Contig2283.3      +    112  3.17e-10 TAACAGGTGA GACAATAGGTGGAAAAAAAG GAAAATATGT
 248 MIT_Spar_c130_3912           +    116  6.61e-10 AACAAAGAAA GACAATAGGCGGAAAAAAAG GAAAATCCGT
 249 SGD_Scer_YGL040C             +    101  8.03e-10 GAAAATCAAA GACAATAGAGTGGCGCATAG ATGTTGCTAG
 250 MIT_Spar_c19_8512            +    102  1.36e-09 AAAAAACAAG GACAATAGAATGACACATAA AGTTTGCTAG
 251 SGD_Scer_YDR044W             +    119  1.86e-09 AACAAAGAAA GACAATAGGTGGAAAAAAAA AGGAAAATCC
 252 MIT_Sbay_c77_8808            +    105  3.82e-09 AACTAACATT AACAATAGAGTGATGCATAG ACGTCACTAG
 253 MIT_Smik_c273_7756           +    102  5.03e-09 ATAAATCAGG AACAATAGAATGACGCACCG AGTTTGCTAG
 254 MIT_Sbay_c896_21290          +    120  2.10e-08 ATTGGCAGCG AACAATAGGTGAAAAAAAAA AAGAAAATGC
 255 --------------------------------------------------------------------------------
 256
 257 --------------------------------------------------------------------------------
 258         Motif 2 block diagrams
 259 --------------------------------------------------------------------------------
 260 SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
 261 -------------            ----------------  -------------
 262 WashU_Skud_Contig2052.17          8.7e-11  99_[+2]_881
 263 WashU_Smik_Contig2283.3           3.2e-10  111_[+2]_869
 264 MIT_Spar_c130_3912                6.6e-10  115_[+2]_865
 265 SGD_Scer_YGL040C                    8e-10  100_[+2]_880
 266 MIT_Spar_c19_8512                 1.4e-09  101_[+2]_879
 267 SGD_Scer_YDR044W                  1.9e-09  118_[+2]_862
 268 MIT_Sbay_c77_8808                 3.8e-09  104_[+2]_876
 269 MIT_Smik_c273_7756                  5e-09  101_[+2]_879
 270 MIT_Sbay_c896_21290               2.1e-08  119_[+2]_861
 271 --------------------------------------------------------------------------------
 272
 273 --------------------------------------------------------------------------------
 274         Motif 2 in BLOCKS format
 275 --------------------------------------------------------------------------------
 276 BL   MOTIF 2 width=20 seqs=9
 277 WashU_Skud_Contig2052.17 (  100) AACAATAGGATGACGCATAG  1
 278 WashU_Smik_Contig2283.3  (  112) GACAATAGGTGGAAAAAAAG  1
 279 MIT_Spar_c130_3912       (  116) GACAATAGGCGGAAAAAAAG  1
 280 SGD_Scer_YGL040C         (  101) GACAATAGAGTGGCGCATAG  1
 281 MIT_Spar_c19_8512        (  102) GACAATAGAATGACACATAA  1
 282 SGD_Scer_YDR044W         (  119) GACAATAGGTGGAAAAAAAA  1
 283 MIT_Sbay_c77_8808        (  105) AACAATAGAGTGATGCATAG  1
 284 MIT_Smik_c273_7756       (  102) AACAATAGAATGACGCACCG  1
 285 MIT_Sbay_c896_21290      (  120) AACAATAGGTGAAAAAAAAA  1
 286 //
 287
 288 --------------------------------------------------------------------------------
 289
 290 --------------------------------------------------------------------------------
 291         Motif 2 position-specific scoring matrix
 292 --------------------------------------------------------------------------------
 293 log-odds matrix: alength= 4 w= 20 n= 8829 bayes= 9.93664 E= 2.0e-010
 294     45   -982    166   -982
 295    162   -982   -982   -982
 296   -982    251   -982   -982
 297    162   -982   -982   -982
 298    162   -982   -982   -982
 299   -982   -982   -982    162
 300    162   -982   -982   -982
 301   -982   -982    251   -982
 302     45   -982    166   -982
 303      4    -66     34      4
 304   -982   -982    134     78
 305   -154   -982    234   -982
 306    145   -982    -66   -982
 307     45    134   -982   -154
 308     78   -982    134   -982
 309     45    166   -982   -982
 310    162   -982   -982   -982
 311     45    -66   -982     45
 312    145    -66   -982   -982
 313      4   -982    192   -982
 314 --------------------------------------------------------------------------------
 315
 316 --------------------------------------------------------------------------------
 317         Motif 2 position-specific probability matrix
 318 --------------------------------------------------------------------------------
 319 letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 2.0e-010
 320  0.444444  0.000000  0.555556  0.000000
 321  1.000000  0.000000  0.000000  0.000000
 322  0.000000  1.000000  0.000000  0.000000
 323  1.000000  0.000000  0.000000  0.000000
 324  1.000000  0.000000  0.000000  0.000000
 325  0.000000  0.000000  0.000000  1.000000
 326  1.000000  0.000000  0.000000  0.000000
 327  0.000000  0.000000  1.000000  0.000000
 328  0.444444  0.000000  0.555556  0.000000
 329  0.333333  0.111111  0.222222  0.333333
 330  0.000000  0.000000  0.444444  0.555556
 331  0.111111  0.000000  0.888889  0.000000
 332  0.888889  0.000000  0.111111  0.000000
 333  0.444444  0.444444  0.000000  0.111111
 334  0.555556  0.000000  0.444444  0.000000
 335  0.444444  0.555556  0.000000  0.000000
 336  1.000000  0.000000  0.000000  0.000000
 337  0.444444  0.111111  0.000000  0.444444
 338  0.888889  0.111111  0.000000  0.000000
 339  0.333333  0.000000  0.666667  0.000000
 340 --------------------------------------------------------------------------------
 341
 342 --------------------------------------------------------------------------------
 343         Motif 2 regular expression
 344 --------------------------------------------------------------------------------
 345 [GA]ACAATAG[GA][ATG][TG]GA[AC][AG][CA]A[AT]A[GA]
 346 --------------------------------------------------------------------------------
 347
 348
 349
 350
 351 Time 16.42 secs.
 352
 353 ********************************************************************************
 354
 355
 356 ********************************************************************************
 357 MOTIF  3        width =   18   sites =   9   llr = 161   E-value = 2.9e-010
 358 ********************************************************************************
 359 --------------------------------------------------------------------------------
 360         Motif 3 Description
 361 --------------------------------------------------------------------------------
 362 Simplified        A  a97926:1a9:::8a:2:
 363 pos.-specific     C  ::3::::6::::a::427
 364 probability       G  ::::84a1:1aa:::34:
 365 matrix            T  :1:1:::2:::::2:213
 366
 367          bits    2.5       *   ***
 368                  2.3       *   ***
 369                  2.0       *   ***
 370                  1.8       *   ***
 371 Information      1.5 *   * * * *** *
 372 content          1.3 *   * * ***** *  *
 373 (25.8 bits)      1.0 ******* ***** *  *
 374                  0.8 ******* ******** *
 375                  0.5 ******************
 376                  0.3 ******************
 377                  0.0 ------------------
 378
 379 Multilevel           AAAAGAGCAAGGCAACGC
 380 consensus              C AG T     T GAT
 381 sequence                            TC
 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_Spar_c130_3912           +    695  1.68e-11 GAGAAATATC AACAGGGCAAGGCAAGGC TATGCTCTTT
 391 MIT_Sbay_c77_8808            -    144  1.90e-10 CCTGATTTAT AAAAGAGCAAGGCAACAC AATAAAAGGC
 392 SGD_Scer_YDR044W             +    703  6.56e-10 AAATATCAAC AAAAGGGCAAGGCTATGC CTTCTGGAAA
 393 WashU_Smik_Contig2283.3      +    703  3.25e-09 GAAAAATATT AACAAGGGAAGGCAAGGC TATGTTCTAT
 394 MIT_Spar_c19_8512            -    140  3.60e-09 CTTGATTTAT AAAAGAGTAAGGCAACCT AATAAATGCT
 395 MIT_Sbay_c896_21290          +    701  6.28e-09 GGAAAATATC AACAAGGCAAGGCTATGC CTTTCGAAGA
 396 MIT_Smik_c273_7756           -    833  1.56e-08 GTTTTCTACA AAATGAGCAGGGCAAGAC GAAATTTCCG
 397 WashU_Skud_Contig2052.17     -    139  1.98e-08 CCCAATTTAT AAAAGAGAAAGGCAACTT ATATGAAGAG
 398 SGD_Scer_YGL040C             -    139  2.12e-08 CTTGATTTAT ATAAGAGTAAGGCAACCT AATAAATGCT
 399 --------------------------------------------------------------------------------
 400
 401 --------------------------------------------------------------------------------
 402         Motif 3 block diagrams
 403 --------------------------------------------------------------------------------
 404 SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
 405 -------------            ----------------  -------------
 406 MIT_Spar_c130_3912                1.7e-11  694_[+3]_288
 407 MIT_Sbay_c77_8808                 1.9e-10  143_[-3]_839
 408 SGD_Scer_YDR044W                  6.6e-10  702_[+3]_280
 409 WashU_Smik_Contig2283.3           3.3e-09  702_[+3]_280
 410 MIT_Spar_c19_8512                 3.6e-09  139_[-3]_843
 411 MIT_Sbay_c896_21290               6.3e-09  700_[+3]_282
 412 MIT_Smik_c273_7756                1.6e-08  832_[-3]_150
 413 WashU_Skud_Contig2052.17            2e-08  138_[-3]_844
 414 SGD_Scer_YGL040C                  2.1e-08  138_[-3]_844
 415 --------------------------------------------------------------------------------
 416
 417 --------------------------------------------------------------------------------
 418         Motif 3 in BLOCKS format
 419 --------------------------------------------------------------------------------
 420 BL   MOTIF 3 width=18 seqs=9
 421 MIT_Spar_c130_3912       (  695) AACAGGGCAAGGCAAGGC  1
 422 MIT_Sbay_c77_8808        (  144) AAAAGAGCAAGGCAACAC  1
 423 SGD_Scer_YDR044W         (  703) AAAAGGGCAAGGCTATGC  1
 424 WashU_Smik_Contig2283.3  (  703) AACAAGGGAAGGCAAGGC  1
 425 MIT_Spar_c19_8512        (  140) AAAAGAGTAAGGCAACCT  1
 426 MIT_Sbay_c896_21290      (  701) AACAAGGCAAGGCTATGC  1
 427 MIT_Smik_c273_7756       (  833) AAATGAGCAGGGCAAGAC  1
 428 WashU_Skud_Contig2052.17 (  139) AAAAGAGAAAGGCAACTT  1
 429 SGD_Scer_YGL040C         (  139) ATAAGAGTAAGGCAACCT  1
 430 //
 431
 432 --------------------------------------------------------------------------------
 433
 434 --------------------------------------------------------------------------------
 435         Motif 3 position-specific scoring matrix
 436 --------------------------------------------------------------------------------
 437 log-odds matrix: alength= 4 w= 18 n= 8847 bayes= 9.93958 E= 2.9e-010
 438    162   -982   -982   -982
 439    145   -982   -982   -154
 440    104     92   -982   -982
 441    145   -982   -982   -154
 442    -55   -982    215   -982
 443     78   -982    134   -982
 444   -982   -982    251   -982
 445   -154    166    -66    -55
 446    162   -982   -982   -982
 447    145   -982    -66   -982
 448   -982   -982    251   -982
 449   -982   -982    251   -982
 450   -982    251   -982   -982
 451    126   -982   -982    -55
 452    162   -982   -982   -982
 453   -982    134     92    -55
 454    -55     34    134   -154
 455   -982    192   -982      4
 456 --------------------------------------------------------------------------------
 457
 458 --------------------------------------------------------------------------------
 459         Motif 3 position-specific probability matrix
 460 --------------------------------------------------------------------------------
 461 letter-probability matrix: alength= 4 w= 18 nsites= 9 E= 2.9e-010
 462  1.000000  0.000000  0.000000  0.000000
 463  0.888889  0.000000  0.000000  0.111111
 464  0.666667  0.333333  0.000000  0.000000
 465  0.888889  0.000000  0.000000  0.111111
 466  0.222222  0.000000  0.777778  0.000000
 467  0.555556  0.000000  0.444444  0.000000
 468  0.000000  0.000000  1.000000  0.000000
 469  0.111111  0.555556  0.111111  0.222222
 470  1.000000  0.000000  0.000000  0.000000
 471  0.888889  0.000000  0.111111  0.000000
 472  0.000000  0.000000  1.000000  0.000000
 473  0.000000  0.000000  1.000000  0.000000
 474  0.000000  1.000000  0.000000  0.000000
 475  0.777778  0.000000  0.000000  0.222222
 476  1.000000  0.000000  0.000000  0.000000
 477  0.000000  0.444444  0.333333  0.222222
 478  0.222222  0.222222  0.444444  0.111111
 479  0.000000  0.666667  0.000000  0.333333
 480 --------------------------------------------------------------------------------
 481
 482 --------------------------------------------------------------------------------
 483         Motif 3 regular expression
 484 --------------------------------------------------------------------------------
 485 AA[AC]A[GA][AG]G[CT]AAGGC[AT]A[CGT][GAC][CT]
 486 --------------------------------------------------------------------------------
 487
 488
 489
 490
 491 Time 24.29 secs.
 492
 493 ********************************************************************************
 494
 495
 496 ********************************************************************************
 497 MOTIF  4        width =   15   sites =   9   llr = 139   E-value = 2.6e-006
 498 ********************************************************************************
 499 --------------------------------------------------------------------------------
 500         Motif 4 Description
 501 --------------------------------------------------------------------------------
 502 Simplified        A  :::::::2:8:::::
 503 pos.-specific     C  3:9:a:::318771:
 504 probability       G  :9:::a::::1:34:
 505 matrix            T  711a::a87113:4a
 506
 507          bits    2.5     **
 508                  2.3     **
 509                  2.0  ** **
 510                  1.8  ** **
 511 Information      1.5  ******   * * *
 512 content          1.3  ******   *** *
 513 (22.3 bits)      1.0 ******* * *** *
 514                  0.8 ***************
 515                  0.5 ***************
 516                  0.3 ***************
 517                  0.0 ---------------
 518
 519 Multilevel           TGCTCGTTTACCCGT
 520 consensus            C      AC  TGT
 521 sequence
 522
 523 --------------------------------------------------------------------------------
 524
 525 --------------------------------------------------------------------------------
 526         Motif 4 sites sorted by position p-value
 527 --------------------------------------------------------------------------------
 528 Sequence name            Strand  Start   P-value                 Site
 529 -------------            ------  ----- ---------            ---------------
 530 WashU_Skud_Contig2052.17     +    209  3.42e-10 GAACAGGGAT TGCTCGTTTACCCGT TGCGTTCAAA
 531 MIT_Smik_c273_7756           +    208  3.42e-10 GAATAAGGAT TGCTCGTTTACCCGT TGTTCGATTT
 532 MIT_Spar_c19_8512            +    210  3.42e-10 GAACAGGGAT TGCTCGTTTACCCGT AGTTTGAATT
 533 SGD_Scer_YGL040C             +    209  3.42e-10 GAACAGGGAT TGCTCGTTTACCCGT ATTTTGATTT
 534 MIT_Sbay_c77_8808            +    209  5.96e-09 CGCCCGGAGA TGCTCGTTTACCGTT GTGCACCAAA
 535 MIT_Spar_c130_3912           -    591  1.14e-07 GAGTTTCGTC CGCTCGTACACTGTT GGGAGAAACA
 536 SGD_Scer_YDR044W             -    597  3.16e-07 GGAGTTTGTC CTCTCGTTCACTGTT GGGAAAAACA
 537 WashU_Smik_Contig2283.3      -    597  7.66e-07 GAAGTTCATC CGCTCGTACCTTCTT GAAAGACAAT
 538 MIT_Sbay_c896_21290          +    366  1.10e-06 CTGTGTGAAA TGTTCGTTTTGCCCT TCCCAGAGAG
 539 --------------------------------------------------------------------------------
 540
 541 --------------------------------------------------------------------------------
 542         Motif 4 block diagrams
 543 --------------------------------------------------------------------------------
 544 SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
 545 -------------            ----------------  -------------
 546 WashU_Skud_Contig2052.17          3.4e-10  208_[+4]_777
 547 MIT_Smik_c273_7756                3.4e-10  207_[+4]_778
 548 MIT_Spar_c19_8512                 3.4e-10  209_[+4]_776
 549 SGD_Scer_YGL040C                  3.4e-10  208_[+4]_777
 550 MIT_Sbay_c77_8808                   6e-09  208_[+4]_777
 551 MIT_Spar_c130_3912                1.1e-07  590_[-4]_395
 552 SGD_Scer_YDR044W                  3.2e-07  596_[-4]_389
 553 WashU_Smik_Contig2283.3           7.7e-07  596_[-4]_389
 554 MIT_Sbay_c896_21290               1.1e-06  365_[+4]_620
 555 --------------------------------------------------------------------------------
 556
 557 --------------------------------------------------------------------------------
 558         Motif 4 in BLOCKS format
 559 --------------------------------------------------------------------------------
 560 BL   MOTIF 4 width=15 seqs=9
 561 WashU_Skud_Contig2052.17 (  209) TGCTCGTTTACCCGT  1
 562 MIT_Smik_c273_7756       (  208) TGCTCGTTTACCCGT  1
 563 MIT_Spar_c19_8512        (  210) TGCTCGTTTACCCGT  1
 564 SGD_Scer_YGL040C         (  209) TGCTCGTTTACCCGT  1
 565 MIT_Sbay_c77_8808        (  209) TGCTCGTTTACCGTT  1
 566 MIT_Spar_c130_3912       (  591) CGCTCGTACACTGTT  1
 567 SGD_Scer_YDR044W         (  597) CTCTCGTTCACTGTT  1
 568 WashU_Smik_Contig2283.3  (  597) CGCTCGTACCTTCTT  1
 569 MIT_Sbay_c896_21290      (  366) TGTTCGTTTTGCCCT  1
 570 //
 571
 572 --------------------------------------------------------------------------------
 573
 574 --------------------------------------------------------------------------------
 575         Motif 4 position-specific scoring matrix
 576 --------------------------------------------------------------------------------
 577 log-odds matrix: alength= 4 w= 15 n= 8874 bayes= 9.94398 E= 2.6e-006
 578   -982     92   -982    104
 579   -982   -982    234   -154
 580   -982    234   -982   -154
 581   -982   -982   -982    162
 582   -982    251   -982   -982
 583   -982   -982    251   -982
 584   -982   -982   -982    162
 585    -55   -982   -982    126
 586   -982     92   -982    104
 587    126    -66   -982   -154
 588   -982    215    -66   -154
 589   -982    192   -982      4
 590   -982    192     92   -982
 591   -982    -66    134     45
 592   -982   -982   -982    162
 593 --------------------------------------------------------------------------------
 594
 595 --------------------------------------------------------------------------------
 596         Motif 4 position-specific probability matrix
 597 --------------------------------------------------------------------------------
 598 letter-probability matrix: alength= 4 w= 15 nsites= 9 E= 2.6e-006
 599  0.000000  0.333333  0.000000  0.666667
 600  0.000000  0.000000  0.888889  0.111111
 601  0.000000  0.888889  0.000000  0.111111
 602  0.000000  0.000000  0.000000  1.000000
 603  0.000000  1.000000  0.000000  0.000000
 604  0.000000  0.000000  1.000000  0.000000
 605  0.000000  0.000000  0.000000  1.000000
 606  0.222222  0.000000  0.000000  0.777778
 607  0.000000  0.333333  0.000000  0.666667
 608  0.777778  0.111111  0.000000  0.111111
 609  0.000000  0.777778  0.111111  0.111111
 610  0.000000  0.666667  0.000000  0.333333
 611  0.000000  0.666667  0.333333  0.000000
 612  0.000000  0.111111  0.444444  0.444444
 613  0.000000  0.000000  0.000000  1.000000
 614 --------------------------------------------------------------------------------
 615
 616 --------------------------------------------------------------------------------
 617         Motif 4 regular expression
 618 --------------------------------------------------------------------------------
 619 [TC]GCTCGT[TA][TC]AC[CT][CG][GT]T
 620 --------------------------------------------------------------------------------
 621
 622
 623
 624
 625 Time 32.02 secs.
 626
 627 ********************************************************************************
 628
 629
 630 ********************************************************************************
 631 MOTIF  5        width =   20   sites =   9   llr = 157   E-value = 4.5e-006
 632 ********************************************************************************
 633 --------------------------------------------------------------------------------
 634         Motif 5 Description
 635 --------------------------------------------------------------------------------
 636 Simplified        A  a:21::1178:99:1794a8
 637 pos.-specific     C  ::::3::::1:1:163:1:2
 638 probability       G  ::177199319::91:13::
 639 matrix            T  :a72:9::::1:1:2::1::
 640
 641          bits    2.5
 642                  2.3
 643                  2.0       **  *  *
 644                  1.8       **  *  *
 645 Information      1.5 **  * **  *  *    *
 646 content          1.3 **  ****  ** *  * *
 647 (25.2 bits)      1.0 ** ****** **** ** **
 648                  0.8 ** *********** ** **
 649                  0.5 ***************** **
 650                  0.3 ********************
 651                  0.0 --------------------
 652
 653 Multilevel           ATTGGTGGAAGAAGCAAAAA
 654 consensus              ATC   G     TC G C
 655 sequence
 656
 657 --------------------------------------------------------------------------------
 658
 659 --------------------------------------------------------------------------------
 660         Motif 5 sites sorted by position p-value
 661 --------------------------------------------------------------------------------
 662 Sequence name            Strand  Start   P-value                    Site
 663 -------------            ------  ----- ---------            --------------------
 664 WashU_Smik_Contig2283.3      +    249  2.56e-12 CTGGGGCATT ATTGGTGGAAGAAGCCAGAA AAGACGAAAG
 665 MIT_Sbay_c896_21290          +    259  2.92e-12 CTGGGGCATA ATTGGTGGGAGAAGCCAGAA AATGCGAAAG
 666 MIT_Spar_c130_3912           +    253  2.92e-12 CTGGGGCATT ATTGGTGGGAGAAGCCAGAA AAGGCGAAAG
 667 SGD_Scer_YDR044W             +    261  1.67e-09 CTGGAGCGTT ATTGGTGGGAGAACCAGAAA AGGCGAAAGC
 668 MIT_Sbay_c77_8808            +     27  1.46e-08 TCTGGTAAGG ATATCTGGAAGAAGTAACAA TACGTATAAA
 669 MIT_Smik_c273_7756           -    234  3.53e-08 GCCGAAAAAA ATTGGTAGAAGATGAAAAAA AAAATCGAAC
 670 MIT_Spar_c19_8512            +     45  7.16e-08 GCAGGCAATA ATATGGGGAAGCAGTAAAAC TTTTTGTTTT
 671 WashU_Skud_Contig2052.17     +    962  8.03e-08 AGTTTCCGTC ATGGCTGAACGAAGGAAAAC TACATCACCT
 672 SGD_Scer_YGL040C             +     26  1.04e-07 CTAGGTATGA ATTACTGGAGTAAGCAATAA TATGAGTAAG
 673 --------------------------------------------------------------------------------
 674
 675 --------------------------------------------------------------------------------
 676         Motif 5 block diagrams
 677 --------------------------------------------------------------------------------
 678 SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
 679 -------------            ----------------  -------------
 680 WashU_Smik_Contig2283.3           2.6e-12  248_[+5]_732
 681 MIT_Sbay_c896_21290               2.9e-12  258_[+5]_722
 682 MIT_Spar_c130_3912                2.9e-12  252_[+5]_728
 683 SGD_Scer_YDR044W                  1.7e-09  260_[+5]_720
 684 MIT_Sbay_c77_8808                 1.5e-08  26_[+5]_954
 685 MIT_Smik_c273_7756                3.5e-08  233_[-5]_747
 686 MIT_Spar_c19_8512                 7.2e-08  44_[+5]_936
 687 WashU_Skud_Contig2052.17            8e-08  961_[+5]_19
 688 SGD_Scer_YGL040C                    1e-07  25_[+5]_955
 689 --------------------------------------------------------------------------------
 690
 691 --------------------------------------------------------------------------------
 692         Motif 5 in BLOCKS format
 693 --------------------------------------------------------------------------------
 694 BL   MOTIF 5 width=20 seqs=9
 695 WashU_Smik_Contig2283.3  (  249) ATTGGTGGAAGAAGCCAGAA  1
 696 MIT_Sbay_c896_21290      (  259) ATTGGTGGGAGAAGCCAGAA  1
 697 MIT_Spar_c130_3912       (  253) ATTGGTGGGAGAAGCCAGAA  1
 698 SGD_Scer_YDR044W         (  261) ATTGGTGGGAGAACCAGAAA  1
 699 MIT_Sbay_c77_8808        (   27) ATATCTGGAAGAAGTAACAA  1
 700 MIT_Smik_c273_7756       (  234) ATTGGTAGAAGATGAAAAAA  1
 701 MIT_Spar_c19_8512        (   45) ATATGGGGAAGCAGTAAAAC  1
 702 WashU_Skud_Contig2052.17 (  962) ATGGCTGAACGAAGGAAAAC  1
 703 SGD_Scer_YGL040C         (   26) ATTACTGGAGTAAGCAATAA  1
 704 //
 705
 706 --------------------------------------------------------------------------------
 707
 708 --------------------------------------------------------------------------------
 709         Motif 5 position-specific scoring matrix
 710 --------------------------------------------------------------------------------
 711 log-odds matrix: alength= 4 w= 20 n= 8829 bayes= 9.93664 E= 4.5e-006
 712    162   -982   -982   -982
 713   -982   -982   -982    162
 714    -55   -982    -66    104
 715   -154   -982    192    -55
 716   -982     92    192   -982
 717   -982   -982    -66    145
 718   -154   -982    234   -982
 719   -154   -982    234   -982
 720    104   -982     92   -982
 721    126    -66    -66   -982
 722   -982   -982    234   -154
 723    145    -66   -982   -982
 724    145   -982   -982   -154
 725   -982    -66    234   -982
 726   -154    166    -66    -55
 727    104     92   -982   -982
 728    145   -982    -66   -982
 729     45    -66     92   -154
 730    162   -982   -982   -982
 731    126     34   -982   -982
 732 --------------------------------------------------------------------------------
 733
 734 --------------------------------------------------------------------------------
 735         Motif 5 position-specific probability matrix
 736 --------------------------------------------------------------------------------
 737 letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 4.5e-006
 738  1.000000  0.000000  0.000000  0.000000
 739  0.000000  0.000000  0.000000  1.000000
 740  0.222222  0.000000  0.111111  0.666667
 741  0.111111  0.000000  0.666667  0.222222
 742  0.000000  0.333333  0.666667  0.000000
 743  0.000000  0.000000  0.111111  0.888889
 744  0.111111  0.000000  0.888889  0.000000
 745  0.111111  0.000000  0.888889  0.000000
 746  0.666667  0.000000  0.333333  0.000000
 747  0.777778  0.111111  0.111111  0.000000
 748  0.000000  0.000000  0.888889  0.111111
 749  0.888889  0.111111  0.000000  0.000000
 750  0.888889  0.000000  0.000000  0.111111
 751  0.000000  0.111111  0.888889  0.000000
 752  0.111111  0.555556  0.111111  0.222222
 753  0.666667  0.333333  0.000000  0.000000
 754  0.888889  0.000000  0.111111  0.000000
 755  0.444444  0.111111  0.333333  0.111111
 756  1.000000  0.000000  0.000000  0.000000
 757  0.777778  0.222222  0.000000  0.000000
 758 --------------------------------------------------------------------------------
 759
 760 --------------------------------------------------------------------------------
 761         Motif 5 regular expression
 762 --------------------------------------------------------------------------------
 763 AT[TA][GT][GC]TGG[AG]AGAAG[CT][AC]A[AG]A[AC]
 764 --------------------------------------------------------------------------------
 765
 766
 767
 768
 769 Time 39.67 secs.
 770
 771 ********************************************************************************
 772
 773
 774 ********************************************************************************
 775 SUMMARY OF MOTIFS
 776 ********************************************************************************
 777
 778 --------------------------------------------------------------------------------
 779         Combined block diagrams: non-overlapping sites with p-value < 0.0001
 780 --------------------------------------------------------------------------------
 781 SEQUENCE NAME            COMBINED P-VALUE  MOTIF DIAGRAM
 782 -------------            ----------------  -------------
 783 SGD_Scer_YGL040C                 1.75e-23  25_[+5(1.04e-07)]_55_[+2(8.03e-10)]_18_[-3(2.12e-08)]_23_[-1(1.17e-12)]_9_[+4(3.42e-10)]_178_[-3(7.59e-05)]_498_[-2(2.36e-05)]_63
 784 MIT_Spar_c19_8512                4.98e-25  44_[+5(7.16e-08)]_37_[+2(1.36e-09)]_18_[-3(3.60e-09)]_23_[-1(1.35e-13)]_9_[+4(3.42e-10)]_8_[-2(8.78e-05)]_191_[-3(9.88e-05)]_101_[+2(6.40e-05)]_317_[+2(1.09e-05)]_81
 785 MIT_Smik_c273_7756               3.49e-24  25_[+5(8.56e-07)]_56_[+2(5.03e-09)]_57_[-1(1.35e-13)]_9_[+4(3.42e-10)]_11_[-5(3.53e-08)]_529_[+5(2.17e-05)]_30_[-3(1.56e-08)]_150
 786 MIT_Sbay_c77_8808                4.86e-24  26_[+5(1.46e-08)]_58_[+2(3.82e-09)]_19_[-3(1.90e-10)]_19_[-1(2.88e-12)]_8_[+4(5.96e-09)]_465_[-2(9.60e-06)]_54_[+5(6.34e-05)]_218
 787 WashU_Skud_Contig2052.17         2.08e-25  99_[+2(8.72e-11)]_19_[-3(1.98e-08)]_23_[-1(1.35e-13)]_9_[+4(3.42e-10)]_322_[-5(2.17e-05)]_101_[-4(3.66e-05)]_280_[+5(8.03e-08)]_19
 788 SGD_Scer_YDR044W                 1.15e-20  118_[+2(1.86e-09)]_40_[+3(9.53e-06)]_64_[+5(1.67e-09)]_153_[+1(5.50e-05)]_86_[+1(1.12e-09)]_37_[-4(3.16e-07)]_91_[+3(6.56e-10)]_280
 789 MIT_Spar_c130_3912               1.46e-25  115_[+2(6.61e-10)]_117_[+5(2.92e-12)]_261_[+1(1.20e-09)]_37_[-4(1.14e-07)]_89_[+3(1.68e-11)]_288
 790 MIT_Sbay_c896_21290              9.74e-21  84_[+5(7.87e-05)]_15_[+2(2.10e-08)]_119_[+5(2.92e-12)]_87_[+4(1.10e-06)]_161_[+1(1.43e-09)]_37_[-4(1.81e-05)]_87_[+3(6.28e-09)]_282
 791 WashU_Smik_Contig2283.3          1.35e-23  111_[+2(3.17e-10)]_81_[+1(3.33e-05)]_16_[+5(2.56e-12)]_273_[+1(2.66e-10)]_35_[-4(7.66e-07)]_91_[+3(3.25e-09)]_280
 792 --------------------------------------------------------------------------------
 793
 794 ********************************************************************************
 795
 796
 797 ********************************************************************************
 798 Stopped because nmotifs = 5 reached.
 799 ********************************************************************************
 800
 801 CPU: dhn02990.mrc-dunn.cam.ac.uk
 802
 803 ********************************************************************************