branch-1-6/t/data/map_hem/HEM1-HEM12.meme.txt

   1 ********************************************************************************
   2 MEME - Motif discovery tool
   3 ********************************************************************************
   4 MEME version 3.5.4 (Release date:    )
   5
   6 For further information on how to interpret these results or to get
   7 a copy of the MEME software please access http://meme.nbcr.net.
   8
   9 This file may be used as input to the MAST algorithm for searching
  10 sequence databases for matches to groups of motifs.  MAST is available
  11 for interactive use and downloading at http://meme.nbcr.net.
  12 ********************************************************************************
  13
  14
  15 ********************************************************************************
  16 REFERENCE
  17 ********************************************************************************
  18 If you use this program in your research, please cite:
  19
  20 Timothy L. Bailey and Charles Elkan,
  21 "Fitting a mixture model by expectation maximization to discover
  22 motifs in biopolymers", Proceedings of the Second International
  23 Conference on Intelligent Systems for Molecular Biology, pp. 28-36,
  24 AAAI Press, Menlo Park, California, 1994.
  25 ********************************************************************************
  26
  27
  28 ********************************************************************************
  29 TRAINING SET
  30 ********************************************************************************
  31 DATAFILE= HEM1-HEM12.fa
  32 ALPHABET= ACGT
  33 Sequence name            Weight Length  Sequence name            Weight Length
  34 -------------            ------ ------  -------------            ------ ------
  35 SGD_Scer_YDR232W         1.0000    498  MIT_Spar_c117_4603       1.0000    498
  36 MIT_Smik_c228_4055       1.0000    498  WashU_Skud_Contig2069.5  1.0000    498
  37 WashU_Sbay_Contig461.5   1.0000    498  SGD_Scer_YDR047W         1.0000   1000
  38 MIT_Spar_c130_3923       1.0000   1000  MIT_Sbay_c896_21277      1.0000   1000
  39 WashU_Skud_Contig1362.1  1.0000    761
  40 ********************************************************************************
  41
  42 ********************************************************************************
  43 COMMAND LINE SUMMARY
  44 ********************************************************************************
  45 This information can also be useful in the event you wish to report a
  46 problem with the MEME software.
  47
  48 command: meme HEM1-HEM12.fa -nostatus -dna -revcomp -nmotifs 5 -bfile yeast.nc.1.freq -maxw 20 -mod oops -dir /Volumes/DATA/Home/ajr/sw/powerpc/meme-3.5.4
  49
  50 model:  mod=          oops    nmotifs=         5    evt=           inf
  51 object function=  E-value of product of p-values
  52 width:  minw=            6    maxw=           20    minic=        0.00
  53 width:  wg=             11    ws=              1    endgaps=       yes
  54 nsites: minsites=        9    maxsites=        9    wnsites=       0.8
  55 theta:  prob=            1    spmap=         uni    spfuzz=        0.5
  56 em:     prior=   dirichlet    b=            0.01    maxiter=        50
  57         distance=    1e-05
  58 data:   n=            6251    N=               9
  59 strands: + -
  60 sample: seed=            0    seqfrac=         1
  61 Letter frequencies in dataset:
  62 A 0.280 C 0.220 G 0.220 T 0.280
  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 = 195   E-value = 1.4e-022
  70 ********************************************************************************
  71 --------------------------------------------------------------------------------
  72         Motif 1 Description
  73 --------------------------------------------------------------------------------
  74 Simplified        A  116::::8:8:1a9::943:
  75 pos.-specific     C  9::3a172:189::2:::6:
  76 probability       G  :947:63:a1:::1:a:61a
  77 matrix            T  :::::3::::2:::8:1:::
  78
  79          bits    2.5     *   *      *   *
  80                  2.3     *   *      *   *
  81                  2.0 **  *   *  *   *   *
  82                  1.8 **  *   *  *   *   *
  83 Information      1.5 ** ** * * ***  *   *
  84 content          1.3 ** ** * * **** *   *
  85 (31.3 bits)      1.0 ***** *** ******** *
  86                  0.8 ********************
  87                  0.5 ********************
  88                  0.3 ********************
  89                  0.0 --------------------
  90
  91 Multilevel           CGAGCGCAGACCAATGAGCG
  92 consensus              GC TGC  T   C  AA
  93 sequence
  94
  95 --------------------------------------------------------------------------------
  96
  97 --------------------------------------------------------------------------------
  98         Motif 1 sites sorted by position p-value
  99 --------------------------------------------------------------------------------
 100 Sequence name            Strand  Start   P-value                    Site
 101 -------------            ------  ----- ---------            --------------------
 102 WashU_Sbay_Contig461.5       +    357  3.08e-14 AAAACGCCGG CGGGCGCAGACCAATGAGCG ACGAAGACGG
 103 WashU_Skud_Contig2069.5      +    360  1.83e-13 AAAGCGTCCG CGGCCGCAGACCAATGAGCG ACGAAGGCGG
 104 MIT_Spar_c117_4603           +    358  1.83e-13 AAAGCGCCCG CGGCCGCAGACCAATGAGCG ACGAAGGCGG
 105 SGD_Scer_YDR232W             +    363  1.83e-13 AAAGCGCCCG CGGCCGCAGACCAATGAGCG ACGAAGGCGG
 106 MIT_Smik_c228_4055           +    360  1.47e-11 AAAGCGCCCG CAAGCGCAGACCAATGAGCG ACGAAAGCGG
 107 MIT_Sbay_c896_21277          +    892  2.69e-10 GCCTAATTCT CGAGCTGAGGCCAATGAAGG CAGCTTCCAG
 108 MIT_Spar_c130_3923           +    931  7.23e-10 AGCTGATCCT CGAGCTGCGATCAACGAAAG CCCCATCCAA
 109 SGD_Scer_YDR047W             +    922  1.02e-09 ACCTGAACTT CGAGCCGCGATCAACGAAAG CTCTCATCCA
 110 WashU_Skud_Contig1362.1      +    294  1.77e-08 AAAGAATGAC AGAGCTCAGCCAAGTGTAAG CTAAGTGTTG
 111 --------------------------------------------------------------------------------
 112
 113 --------------------------------------------------------------------------------
 114         Motif 1 block diagrams
 115 --------------------------------------------------------------------------------
 116 SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
 117 -------------            ----------------  -------------
 118 WashU_Sbay_Contig461.5            3.1e-14  356_[+1]_122
 119 WashU_Skud_Contig2069.5           1.8e-13  359_[+1]_119
 120 MIT_Spar_c117_4603                1.8e-13  357_[+1]_121
 121 SGD_Scer_YDR232W                  1.8e-13  362_[+1]_116
 122 MIT_Smik_c228_4055                1.5e-11  359_[+1]_119
 123 MIT_Sbay_c896_21277               2.7e-10  891_[+1]_89
 124 MIT_Spar_c130_3923                7.2e-10  930_[+1]_50
 125 SGD_Scer_YDR047W                    1e-09  921_[+1]_59
 126 WashU_Skud_Contig1362.1           1.8e-08  293_[+1]_448
 127 --------------------------------------------------------------------------------
 128
 129 --------------------------------------------------------------------------------
 130         Motif 1 in BLOCKS format
 131 --------------------------------------------------------------------------------
 132 BL   MOTIF 1 width=20 seqs=9
 133 WashU_Sbay_Contig461.5   (  357) CGGGCGCAGACCAATGAGCG  1
 134 WashU_Skud_Contig2069.5  (  360) CGGCCGCAGACCAATGAGCG  1
 135 MIT_Spar_c117_4603       (  358) CGGCCGCAGACCAATGAGCG  1
 136 SGD_Scer_YDR232W         (  363) CGGCCGCAGACCAATGAGCG  1
 137 MIT_Smik_c228_4055       (  360) CAAGCGCAGACCAATGAGCG  1
 138 MIT_Sbay_c896_21277      (  892) CGAGCTGAGGCCAATGAAGG  1
 139 MIT_Spar_c130_3923       (  931) CGAGCTGCGATCAACGAAAG  1
 140 SGD_Scer_YDR047W         (  922) CGAGCCGCGATCAACGAAAG  1
 141 WashU_Skud_Contig1362.1  (  294) AGAGCTCAGCCAAGTGTAAG  1
 142 //
 143
 144 --------------------------------------------------------------------------------
 145
 146 --------------------------------------------------------------------------------
 147         Motif 1 position-specific scoring matrix
 148 --------------------------------------------------------------------------------
 149 log-odds matrix: alength= 4 w= 20 n= 6080 bayes= 9.39779 E= 1.4e-022
 150   -154    234   -982   -982
 151   -154   -982    234   -982
 152     78   -982    134   -982
 153   -982     92    192   -982
 154   -982    251   -982   -982
 155   -982    -66    166      4
 156   -982    192     92   -982
 157    126     34   -982   -982
 158   -982   -982    251   -982
 159    126    -66    -66   -982
 160   -982    215   -982    -55
 161   -154    234   -982   -982
 162    162   -982   -982   -982
 163    145   -982    -66   -982
 164   -982     34   -982    126
 165   -982   -982    251   -982
 166    145   -982   -982   -154
 167     45   -982    166   -982
 168      4    166    -66   -982
 169   -982   -982    251   -982
 170 --------------------------------------------------------------------------------
 171
 172 --------------------------------------------------------------------------------
 173         Motif 1 position-specific probability matrix
 174 --------------------------------------------------------------------------------
 175 letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 1.4e-022
 176  0.111111  0.888889  0.000000  0.000000
 177  0.111111  0.000000  0.888889  0.000000
 178  0.555556  0.000000  0.444444  0.000000
 179  0.000000  0.333333  0.666667  0.000000
 180  0.000000  1.000000  0.000000  0.000000
 181  0.000000  0.111111  0.555556  0.333333
 182  0.000000  0.666667  0.333333  0.000000
 183  0.777778  0.222222  0.000000  0.000000
 184  0.000000  0.000000  1.000000  0.000000
 185  0.777778  0.111111  0.111111  0.000000
 186  0.000000  0.777778  0.000000  0.222222
 187  0.111111  0.888889  0.000000  0.000000
 188  1.000000  0.000000  0.000000  0.000000
 189  0.888889  0.000000  0.111111  0.000000
 190  0.000000  0.222222  0.000000  0.777778
 191  0.000000  0.000000  1.000000  0.000000
 192  0.888889  0.000000  0.000000  0.111111
 193  0.444444  0.000000  0.555556  0.000000
 194  0.333333  0.555556  0.111111  0.000000
 195  0.000000  0.000000  1.000000  0.000000
 196 --------------------------------------------------------------------------------
 197
 198 --------------------------------------------------------------------------------
 199         Motif 1 regular expression
 200 --------------------------------------------------------------------------------
 201 CG[AG][GC]C[GT][CG][AC]GA[CT]CAA[TC]GA[GA][CA]G
 202 --------------------------------------------------------------------------------
 203
 204
 205
 206
 207 Time  4.41 secs.
 208
 209 ********************************************************************************
 210
 211
 212 ********************************************************************************
 213 MOTIF  2        width =   20   sites =   9   llr = 179   E-value = 3.0e-017
 214 ********************************************************************************
 215 --------------------------------------------------------------------------------
 216         Motif 2 Description
 217 --------------------------------------------------------------------------------
 218 Simplified        A  1:4a1a9:4::::614:8:a
 219 pos.-specific     C  :14::::a111:4:1:::9:
 220 probability       G  991:9:1:46::644:a21:
 221 matrix            T  :::::::::39a::36::::
 222
 223          bits    2.5        *        *
 224                  2.3        *        *
 225                  2.0 **  *  *        * *
 226                  1.8 **  *  *        * *
 227 Information      1.5 ** *** *   **   * **
 228 content          1.3 ** *****  ***   * **
 229 (28.7 bits)      1.0 ** *****  ****  ****
 230                  0.8 ************** *****
 231                  0.5 ************** *****
 232                  0.3 ********************
 233                  0.0 --------------------
 234
 235 Multilevel           GGAAGAACAGTTGAGTGACA
 236 consensus              C     GT  CGTA G
 237 sequence
 238
 239 --------------------------------------------------------------------------------
 240
 241 --------------------------------------------------------------------------------
 242         Motif 2 sites sorted by position p-value
 243 --------------------------------------------------------------------------------
 244 Sequence name            Strand  Start   P-value                    Site
 245 -------------            ------  ----- ---------            --------------------
 246 WashU_Skud_Contig2069.5      +    162  7.75e-12 CCGTGTGGAG GGAAGAACGGTTGAGAGACA GCAGAGCACA
 247 SGD_Scer_YDR232W             +    165  7.75e-12 GGCGTGTAAA GGAAGAACGGTTGAGAGACA GCAGAGCAGG
 248 WashU_Sbay_Contig461.5       +    161  8.83e-11 GCGTGTGGAG GGAAGAACCGTTGAGAGACA ACAGAGCAGG
 249 MIT_Spar_c117_4603           +    160  2.12e-10 GGCGTGTAAA GGAAGAACGGTTGAGAGAGA GCAGAGCAGG
 250 MIT_Spar_c130_3923           +    170  2.30e-10 TGACAAAAAG GGCAGAACATTTCGTTGGCA AAATTTAAAC
 251 SGD_Scer_YDR047W             +    173  4.04e-10 AGATGAAAAT GGCAGAACATTTCGCTGGCA AAATTAAAAC
 252 MIT_Smik_c228_4055           +    161  6.70e-10 GACGTGTGAA GCCAGAACGGTTGAATGACA GTAGAGGAGG
 253 WashU_Skud_Contig1362.1      +    137  8.43e-10 ACATACGAAA GGCAGAACACCTCGTTGACA AAACTGAAAC
 254 MIT_Sbay_c896_21277          +    143  3.02e-08 TGACACGAAT AGGAAAGCATTTCGTTGACA AAAATAAAAT
 255 --------------------------------------------------------------------------------
 256
 257 --------------------------------------------------------------------------------
 258         Motif 2 block diagrams
 259 --------------------------------------------------------------------------------
 260 SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
 261 -------------            ----------------  -------------
 262 WashU_Skud_Contig2069.5           7.7e-12  161_[+2]_317
 263 SGD_Scer_YDR232W                  7.7e-12  164_[+2]_314
 264 WashU_Sbay_Contig461.5            8.8e-11  160_[+2]_318
 265 MIT_Spar_c117_4603                2.1e-10  159_[+2]_319
 266 MIT_Spar_c130_3923                2.3e-10  169_[+2]_811
 267 SGD_Scer_YDR047W                    4e-10  172_[+2]_808
 268 MIT_Smik_c228_4055                6.7e-10  160_[+2]_318
 269 WashU_Skud_Contig1362.1           8.4e-10  136_[+2]_605
 270 MIT_Sbay_c896_21277                 3e-08  142_[+2]_838
 271 --------------------------------------------------------------------------------
 272
 273 --------------------------------------------------------------------------------
 274         Motif 2 in BLOCKS format
 275 --------------------------------------------------------------------------------
 276 BL   MOTIF 2 width=20 seqs=9
 277 WashU_Skud_Contig2069.5  (  162) GGAAGAACGGTTGAGAGACA  1
 278 SGD_Scer_YDR232W         (  165) GGAAGAACGGTTGAGAGACA  1
 279 WashU_Sbay_Contig461.5   (  161) GGAAGAACCGTTGAGAGACA  1
 280 MIT_Spar_c117_4603       (  160) GGAAGAACGGTTGAGAGAGA  1
 281 MIT_Spar_c130_3923       (  170) GGCAGAACATTTCGTTGGCA  1
 282 SGD_Scer_YDR047W         (  173) GGCAGAACATTTCGCTGGCA  1
 283 MIT_Smik_c228_4055       (  161) GCCAGAACGGTTGAATGACA  1
 284 WashU_Skud_Contig1362.1  (  137) GGCAGAACACCTCGTTGACA  1
 285 MIT_Sbay_c896_21277      (  143) AGGAAAGCATTTCGTTGACA  1
 286 //
 287
 288 --------------------------------------------------------------------------------
 289
 290 --------------------------------------------------------------------------------
 291         Motif 2 position-specific scoring matrix
 292 --------------------------------------------------------------------------------
 293 log-odds matrix: alength= 4 w= 20 n= 6080 bayes= 9.39779 E= 3.0e-017
 294   -154   -982    234   -982
 295   -982    -66    234   -982
 296     45    134    -66   -982
 297    162   -982   -982   -982
 298   -154   -982    234   -982
 299    162   -982   -982   -982
 300    145   -982    -66   -982
 301   -982    251   -982   -982
 302     45    -66    134   -982
 303   -982    -66    166      4
 304   -982    -66   -982    145
 305   -982   -982   -982    162
 306   -982    134    166   -982
 307     78   -982    134   -982
 308   -154    -66    134      4
 309     45   -982   -982     78
 310   -982   -982    251   -982
 311    126   -982     34   -982
 312   -982    234    -66   -982
 313    162   -982   -982   -982
 314 --------------------------------------------------------------------------------
 315
 316 --------------------------------------------------------------------------------
 317         Motif 2 position-specific probability matrix
 318 --------------------------------------------------------------------------------
 319 letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 3.0e-017
 320  0.111111  0.000000  0.888889  0.000000
 321  0.000000  0.111111  0.888889  0.000000
 322  0.444444  0.444444  0.111111  0.000000
 323  1.000000  0.000000  0.000000  0.000000
 324  0.111111  0.000000  0.888889  0.000000
 325  1.000000  0.000000  0.000000  0.000000
 326  0.888889  0.000000  0.111111  0.000000
 327  0.000000  1.000000  0.000000  0.000000
 328  0.444444  0.111111  0.444444  0.000000
 329  0.000000  0.111111  0.555556  0.333333
 330  0.000000  0.111111  0.000000  0.888889
 331  0.000000  0.000000  0.000000  1.000000
 332  0.000000  0.444444  0.555556  0.000000
 333  0.555556  0.000000  0.444444  0.000000
 334  0.111111  0.111111  0.444444  0.333333
 335  0.444444  0.000000  0.000000  0.555556
 336  0.000000  0.000000  1.000000  0.000000
 337  0.777778  0.000000  0.222222  0.000000
 338  0.000000  0.888889  0.111111  0.000000
 339  1.000000  0.000000  0.000000  0.000000
 340 --------------------------------------------------------------------------------
 341
 342 --------------------------------------------------------------------------------
 343         Motif 2 regular expression
 344 --------------------------------------------------------------------------------
 345 GG[AC]AGAAC[AG][GT]TT[GC][AG][GT][TA]G[AG]CA
 346 --------------------------------------------------------------------------------
 347
 348
 349
 350
 351 Time  8.63 secs.
 352
 353 ********************************************************************************
 354
 355
 356 ********************************************************************************
 357 MOTIF  3        width =   20   sites =   9   llr = 181   E-value = 3.1e-017
 358 ********************************************************************************
 359 --------------------------------------------------------------------------------
 360         Motif 3 Description
 361 --------------------------------------------------------------------------------
 362 Simplified        A  8aaa64:::::1:::1112:
 363 pos.-specific     C  1:::4:1:a9::2aa3:62a
 364 probability       G  1::::::4::a:::::81::
 365 matrix            T  :::::696:1:98::6126:
 366
 367          bits    2.5         * *  **    *
 368                  2.3         * *  **    *
 369                  2.0         ***  **    *
 370                  1.8         ***  **    *
 371 Information      1.5  ***    ***  **    *
 372 content          1.3  ***  * ***  ** *  *
 373 (29.1 bits)      1.0  **** ********* *  *
 374                  0.8 *************** *  *
 375                  0.5 ********************
 376                  0.3 ********************
 377                  0.0 --------------------
 378
 379 Multilevel           AAAAATTTCCGTTCCTGCTC
 380 consensus                CA G    C  C TA
 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 WashU_Skud_Contig2069.5      +    305  9.40e-12 AGGCAATGTG AAAAATTTCCGTTCCTGCTC TTGCTTCATA
 391 SGD_Scer_YDR232W             +    307  9.40e-12 AGGCAAGATG AAAAATTTCCGTTCCTGCTC TTTCTTCATA
 392 MIT_Smik_c228_4055           +    304  6.77e-11 AAGGCAAGAT GAAAATTTCCGTTCCTGCTC TTTCTTCATA
 393 WashU_Sbay_Contig461.5       +    300  7.67e-11 AGGCAAGATG AAAAATCTCCGTTCCTGCTC TTGCTTGATA
 394 SGD_Scer_YDR047W             +    647  1.22e-10 CTGTGCATTT AAAACATGCCGTTCCCGTAC CAAGTTATAT
 395 MIT_Spar_c130_3923           +    645  2.75e-10 GGCGCAATTC AAAACATGCCGTCCCCGTAC TAAGTTATGT
 396 MIT_Spar_c117_4603           +    302  3.58e-10 AGGCAAGATG AAAAATTTCTGTTCCTGCTC TTTCTTCATA
 397 WashU_Skud_Contig1362.1      +    647  5.76e-09 TGGAACAAAT CAAACATGCCGTCCCCTACC AGCTCTCGAA
 398 MIT_Sbay_c896_21277          +    651  9.67e-09 TTGACAAGAC AAAACATGCCGATCCAAGCC AGGCGAAACG
 399 --------------------------------------------------------------------------------
 400
 401 --------------------------------------------------------------------------------
 402         Motif 3 block diagrams
 403 --------------------------------------------------------------------------------
 404 SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
 405 -------------            ----------------  -------------
 406 WashU_Skud_Contig2069.5           9.4e-12  304_[+3]_174
 407 SGD_Scer_YDR232W                  9.4e-12  306_[+3]_172
 408 MIT_Smik_c228_4055                6.8e-11  303_[+3]_175
 409 WashU_Sbay_Contig461.5            7.7e-11  299_[+3]_179
 410 SGD_Scer_YDR047W                  1.2e-10  646_[+3]_334
 411 MIT_Spar_c130_3923                2.7e-10  644_[+3]_336
 412 MIT_Spar_c117_4603                3.6e-10  301_[+3]_177
 413 WashU_Skud_Contig1362.1           5.8e-09  646_[+3]_95
 414 MIT_Sbay_c896_21277               9.7e-09  650_[+3]_330
 415 --------------------------------------------------------------------------------
 416
 417 --------------------------------------------------------------------------------
 418         Motif 3 in BLOCKS format
 419 --------------------------------------------------------------------------------
 420 BL   MOTIF 3 width=20 seqs=9
 421 WashU_Skud_Contig2069.5  (  305) AAAAATTTCCGTTCCTGCTC  1
 422 SGD_Scer_YDR232W         (  307) AAAAATTTCCGTTCCTGCTC  1
 423 MIT_Smik_c228_4055       (  304) GAAAATTTCCGTTCCTGCTC  1
 424 WashU_Sbay_Contig461.5   (  300) AAAAATCTCCGTTCCTGCTC  1
 425 SGD_Scer_YDR047W         (  647) AAAACATGCCGTTCCCGTAC  1
 426 MIT_Spar_c130_3923       (  645) AAAACATGCCGTCCCCGTAC  1
 427 MIT_Spar_c117_4603       (  302) AAAAATTTCTGTTCCTGCTC  1
 428 WashU_Skud_Contig1362.1  (  647) CAAACATGCCGTCCCCTACC  1
 429 MIT_Sbay_c896_21277      (  651) AAAACATGCCGATCCAAGCC  1
 430 //
 431
 432 --------------------------------------------------------------------------------
 433
 434 --------------------------------------------------------------------------------
 435         Motif 3 position-specific scoring matrix
 436 --------------------------------------------------------------------------------
 437 log-odds matrix: alength= 4 w= 20 n= 6080 bayes= 9.39779 E= 3.1e-017
 438    126    -66    -66   -982
 439    162   -982   -982   -982
 440    162   -982   -982   -982
 441    162   -982   -982   -982
 442     78    134   -982   -982
 443     45   -982   -982     78
 444   -982    -66   -982    145
 445   -982   -982    134     78
 446   -982    251   -982   -982
 447   -982    234   -982   -154
 448   -982   -982    251   -982
 449   -154   -982   -982    145
 450   -982     34   -982    126
 451   -982    251   -982   -982
 452   -982    251   -982   -982
 453   -154     92   -982     78
 454   -154   -982    215   -154
 455   -154    166    -66    -55
 456    -55     34   -982     78
 457   -982    251   -982   -982
 458 --------------------------------------------------------------------------------
 459
 460 --------------------------------------------------------------------------------
 461         Motif 3 position-specific probability matrix
 462 --------------------------------------------------------------------------------
 463 letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 3.1e-017
 464  0.777778  0.111111  0.111111  0.000000
 465  1.000000  0.000000  0.000000  0.000000
 466  1.000000  0.000000  0.000000  0.000000
 467  1.000000  0.000000  0.000000  0.000000
 468  0.555556  0.444444  0.000000  0.000000
 469  0.444444  0.000000  0.000000  0.555556
 470  0.000000  0.111111  0.000000  0.888889
 471  0.000000  0.000000  0.444444  0.555556
 472  0.000000  1.000000  0.000000  0.000000
 473  0.000000  0.888889  0.000000  0.111111
 474  0.000000  0.000000  1.000000  0.000000
 475  0.111111  0.000000  0.000000  0.888889
 476  0.000000  0.222222  0.000000  0.777778
 477  0.000000  1.000000  0.000000  0.000000
 478  0.000000  1.000000  0.000000  0.000000
 479  0.111111  0.333333  0.000000  0.555556
 480  0.111111  0.000000  0.777778  0.111111
 481  0.111111  0.555556  0.111111  0.222222
 482  0.222222  0.222222  0.000000  0.555556
 483  0.000000  1.000000  0.000000  0.000000
 484 --------------------------------------------------------------------------------
 485
 486 --------------------------------------------------------------------------------
 487         Motif 3 regular expression
 488 --------------------------------------------------------------------------------
 489 AAAA[AC][TA]T[TG]CCGT[TC]CC[TC]G[CT][TAC]C
 490 --------------------------------------------------------------------------------
 491
 492
 493
 494
 495 Time 12.69 secs.
 496
 497 ********************************************************************************
 498
 499
 500 ********************************************************************************
 501 MOTIF  4        width =   20   sites =   9   llr = 171   E-value = 9.5e-014
 502 ********************************************************************************
 503 --------------------------------------------------------------------------------
 504         Motif 4 Description
 505 --------------------------------------------------------------------------------
 506 Simplified        A  23aa22::::::::::1611
 507 pos.-specific     C  7:::1:a::991::86:236
 508 probability       G  17::48:6a1:3::147:62
 509 matrix            T  ::::2::4::16aa1:22:1
 510
 511          bits    2.5       * *
 512                  2.3       * *
 513                  2.0       * ***
 514                  1.8       * ***
 515 Information      1.5   ** ** *** ****
 516 content          1.3  *** ** *** ****
 517 (27.5 bits)      1.0 **** ****** ***** *
 518                  0.8 **** ************ **
 519                  0.5 **** ***************
 520                  0.3 ********************
 521                  0.0 --------------------
 522
 523 Multilevel           CGAAGGCGGCCTTTCCGAGC
 524 consensus            AA  AA T   G   GTCCG
 525 sequence                 T            T
 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_YDR232W             +    384  4.75e-14 CAATGAGCGA CGAAGGCGGCCTTTCCGAGC GGTAGGGTAA
 535 WashU_Skud_Contig2069.5      +    381  3.48e-12 CAATGAGCGA CGAAGGCGGCCTTTCGTAGC AGCAGGGTAA
 536 MIT_Spar_c117_4603           +    379  6.28e-12 CAATGAGCGA CGAAGGCGGCCTTTCCGAGT GGTAGGGTAA
 537 MIT_Spar_c130_3923           +    708  1.69e-09 ATTATACTCT AAAATGCTGCCGTTCCGTCC CATTGAGTTT
 538 SGD_Scer_YDR047W             +    708  1.69e-09 AATTTGTTAA AAAATGCTGCCGTTCCGTCC CATTGAGTTT
 539 MIT_Smik_c228_4055           +    381  3.64e-09 CAATGAGCGA CGAAAGCGGCCTTTTGAAGG GTAGGGTAAT
 540 WashU_Sbay_Contig461.5       +    378  5.96e-09 CAATGAGCGA CGAAGACGGCTTTTGGGCGG GGCAGGGTAA
 541 MIT_Sbay_c896_21277          +    699  7.77e-09 ACTACGCAGC CAAACACTGGCGTTCCGCCC GTCCCATCCA
 542 WashU_Skud_Contig1362.1      -    483  5.15e-08 AACGCTTATA GGAAAGCTGCCCTTCGTAAA ACAGCTTGCT
 543 --------------------------------------------------------------------------------
 544
 545 --------------------------------------------------------------------------------
 546         Motif 4 block diagrams
 547 --------------------------------------------------------------------------------
 548 SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
 549 -------------            ----------------  -------------
 550 SGD_Scer_YDR232W                  4.8e-14  383_[+4]_95
 551 WashU_Skud_Contig2069.5           3.5e-12  380_[+4]_98
 552 MIT_Spar_c117_4603                6.3e-12  378_[+4]_100
 553 MIT_Spar_c130_3923                1.7e-09  707_[+4]_273
 554 SGD_Scer_YDR047W                  1.7e-09  707_[+4]_273
 555 MIT_Smik_c228_4055                3.6e-09  380_[+4]_98
 556 WashU_Sbay_Contig461.5              6e-09  377_[+4]_101
 557 MIT_Sbay_c896_21277               7.8e-09  698_[+4]_282
 558 WashU_Skud_Contig1362.1           5.1e-08  482_[-4]_259
 559 --------------------------------------------------------------------------------
 560
 561 --------------------------------------------------------------------------------
 562         Motif 4 in BLOCKS format
 563 --------------------------------------------------------------------------------
 564 BL   MOTIF 4 width=20 seqs=9
 565 SGD_Scer_YDR232W         (  384) CGAAGGCGGCCTTTCCGAGC  1
 566 WashU_Skud_Contig2069.5  (  381) CGAAGGCGGCCTTTCGTAGC  1
 567 MIT_Spar_c117_4603       (  379) CGAAGGCGGCCTTTCCGAGT  1
 568 MIT_Spar_c130_3923       (  708) AAAATGCTGCCGTTCCGTCC  1
 569 SGD_Scer_YDR047W         (  708) AAAATGCTGCCGTTCCGTCC  1
 570 MIT_Smik_c228_4055       (  381) CGAAAGCGGCCTTTTGAAGG  1
 571 WashU_Sbay_Contig461.5   (  378) CGAAGACGGCTTTTGGGCGG  1
 572 MIT_Sbay_c896_21277      (  699) CAAACACTGGCGTTCCGCCC  1
 573 WashU_Skud_Contig1362.1  (  483) GGAAAGCTGCCCTTCGTAAA  1
 574 //
 575
 576 --------------------------------------------------------------------------------
 577
 578 --------------------------------------------------------------------------------
 579         Motif 4 position-specific scoring matrix
 580 --------------------------------------------------------------------------------
 581 log-odds matrix: alength= 4 w= 20 n= 6080 bayes= 9.39779 E= 9.5e-014
 582    -55    192    -66   -982
 583      4   -982    192   -982
 584    162   -982   -982   -982
 585    162   -982   -982   -982
 586    -55    -66    134    -55
 587    -55   -982    215   -982
 588   -982    251   -982   -982
 589   -982   -982    166     45
 590   -982   -982    251   -982
 591   -982    234    -66   -982
 592   -982    234   -982   -154
 593   -982    -66     92     78
 594   -982   -982   -982    162
 595   -982   -982   -982    162
 596   -982    215    -66   -154
 597   -982    166    134   -982
 598   -154   -982    192    -55
 599     78     34   -982    -55
 600   -154     92    166   -982
 601   -154    166     34   -154
 602 --------------------------------------------------------------------------------
 603
 604 --------------------------------------------------------------------------------
 605         Motif 4 position-specific probability matrix
 606 --------------------------------------------------------------------------------
 607 letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 9.5e-014
 608  0.222222  0.666667  0.111111  0.000000
 609  0.333333  0.000000  0.666667  0.000000
 610  1.000000  0.000000  0.000000  0.000000
 611  1.000000  0.000000  0.000000  0.000000
 612  0.222222  0.111111  0.444444  0.222222
 613  0.222222  0.000000  0.777778  0.000000
 614  0.000000  1.000000  0.000000  0.000000
 615  0.000000  0.000000  0.555556  0.444444
 616  0.000000  0.000000  1.000000  0.000000
 617  0.000000  0.888889  0.111111  0.000000
 618  0.000000  0.888889  0.000000  0.111111
 619  0.000000  0.111111  0.333333  0.555556
 620  0.000000  0.000000  0.000000  1.000000
 621  0.000000  0.000000  0.000000  1.000000
 622  0.000000  0.777778  0.111111  0.111111
 623  0.000000  0.555556  0.444444  0.000000
 624  0.111111  0.000000  0.666667  0.222222
 625  0.555556  0.222222  0.000000  0.222222
 626  0.111111  0.333333  0.555556  0.000000
 627  0.111111  0.555556  0.222222  0.111111
 628 --------------------------------------------------------------------------------
 629
 630 --------------------------------------------------------------------------------
 631         Motif 4 regular expression
 632 --------------------------------------------------------------------------------
 633 [CA][GA]AA[GAT][GA]C[GT]GCC[TG]TTC[CG][GT][ACT][GC][CG]
 634 --------------------------------------------------------------------------------
 635
 636
 637
 638
 639 Time 16.70 secs.
 640
 641 ********************************************************************************
 642
 643
 644 ********************************************************************************
 645 MOTIF  5        width =   20   sites =   9   llr = 178   E-value = 2.7e-015
 646 ********************************************************************************
 647 --------------------------------------------------------------------------------
 648         Motif 5 Description
 649 --------------------------------------------------------------------------------
 650 Simplified        A  :68:86:::::76::27a29
 651 pos.-specific     C  :::9:1:3::a134:8::::
 652 probability       G  a:2:2:37aa:::69:3:71
 653 matrix            T  :4:1:37::::21:1:::1:
 654
 655          bits    2.5 *       ***
 656                  2.3 *       ***
 657                  2.0 *  *    ***   *
 658                  1.8 *  *    ***   *
 659 Information      1.5 *  *   ****  *** *
 660 content          1.3 *  *   ****  *** * *
 661 (28.5 bits)      1.0 * *** *****  *******
 662                  0.8 ***** *****  *******
 663                  0.5 ***** **************
 664                  0.3 ********************
 665                  0.0 --------------------
 666
 667 Multilevel           GAACAATGGGCAAGGCAAGA
 668 consensus             TG GTGC   TCC AG A
 669 sequence
 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_Contig461.5       +    278  7.65e-13 CACCGGGACA GAACAATGGGCAAGGCAAGA TGAAAAATCT
 679 MIT_Smik_c228_4055           +    283  7.65e-13 CATTGAATTA GAACAATGGGCAAGGCAAGA TGAAAATTTC
 680 MIT_Spar_c117_4603           +    280  7.65e-13 GCATGGGTCA GAACAATGGGCAAGGCAAGA TGAAAAATTT
 681 SGD_Scer_YDR232W             +    285  7.65e-13 GCATGGATCA GAACAATGGGCAAGGCAAGA TGAAAAATTT
 682 WashU_Skud_Contig2069.5      +    283  7.37e-10 CACTGGATCG GAACAATGGGCAAGGCAATG TGAAAAATTT
 683 SGD_Scer_YDR047W             +    871  2.30e-09 TAATGTAGCC GTGCATGCGGCTCCGCGAAA AGAGCTCTGC
 684 WashU_Skud_Contig1362.1      +    334  3.13e-09 ACAAGGGAAG GTACATTGGGCCCCGAAAAA ATTTGCTAAT
 685 MIT_Spar_c130_3923           +    880  4.62e-09 TTATATAGCC GTACGTGCGGCTCCTCGAGA AAGGCCCTGC
 686 MIT_Sbay_c896_21277          +    841  2.58e-08 TTTTATAGCC GTGTGCGCGGCATCGAGAGA CAGGTTCAGC
 687 --------------------------------------------------------------------------------
 688
 689 --------------------------------------------------------------------------------
 690         Motif 5 block diagrams
 691 --------------------------------------------------------------------------------
 692 SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
 693 -------------            ----------------  -------------
 694 WashU_Sbay_Contig461.5            7.6e-13  277_[+5]_201
 695 MIT_Smik_c228_4055                7.6e-13  282_[+5]_196
 696 MIT_Spar_c117_4603                7.6e-13  279_[+5]_199
 697 SGD_Scer_YDR232W                  7.6e-13  284_[+5]_194
 698 WashU_Skud_Contig2069.5           7.4e-10  282_[+5]_196
 699 SGD_Scer_YDR047W                  2.3e-09  870_[+5]_110
 700 WashU_Skud_Contig1362.1           3.1e-09  333_[+5]_408
 701 MIT_Spar_c130_3923                4.6e-09  879_[+5]_101
 702 MIT_Sbay_c896_21277               2.6e-08  840_[+5]_140
 703 --------------------------------------------------------------------------------
 704
 705 --------------------------------------------------------------------------------
 706         Motif 5 in BLOCKS format
 707 --------------------------------------------------------------------------------
 708 BL   MOTIF 5 width=20 seqs=9
 709 WashU_Sbay_Contig461.5   (  278) GAACAATGGGCAAGGCAAGA  1
 710 MIT_Smik_c228_4055       (  283) GAACAATGGGCAAGGCAAGA  1
 711 MIT_Spar_c117_4603       (  280) GAACAATGGGCAAGGCAAGA  1
 712 SGD_Scer_YDR232W         (  285) GAACAATGGGCAAGGCAAGA  1
 713 WashU_Skud_Contig2069.5  (  283) GAACAATGGGCAAGGCAATG  1
 714 SGD_Scer_YDR047W         (  871) GTGCATGCGGCTCCGCGAAA  1
 715 WashU_Skud_Contig1362.1  (  334) GTACATTGGGCCCCGAAAAA  1
 716 MIT_Spar_c130_3923       (  880) GTACGTGCGGCTCCTCGAGA  1
 717 MIT_Sbay_c896_21277      (  841) GTGTGCGCGGCATCGAGAGA  1
 718 //
 719
 720 --------------------------------------------------------------------------------
 721
 722 --------------------------------------------------------------------------------
 723         Motif 5 position-specific scoring matrix
 724 --------------------------------------------------------------------------------
 725 log-odds matrix: alength= 4 w= 20 n= 6080 bayes= 9.39779 E= 2.7e-015
 726   -982   -982    251   -982
 727     78   -982   -982     45
 728    126   -982     34   -982
 729   -982    234   -982   -154
 730    126   -982     34   -982
 731     78    -66   -982      4
 732   -982   -982     92    104
 733   -982     92    192   -982
 734   -982   -982    251   -982
 735   -982   -982    251   -982
 736   -982    251   -982   -982
 737    104    -66   -982    -55
 738     78     92   -982   -154
 739   -982    134    166   -982
 740   -982   -982    234   -154
 741    -55    215   -982   -982
 742    104   -982     92   -982
 743    162   -982   -982   -982
 744    -55   -982    192   -154
 745    145   -982    -66   -982
 746 --------------------------------------------------------------------------------
 747
 748 --------------------------------------------------------------------------------
 749         Motif 5 position-specific probability matrix
 750 --------------------------------------------------------------------------------
 751 letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 2.7e-015
 752  0.000000  0.000000  1.000000  0.000000
 753  0.555556  0.000000  0.000000  0.444444
 754  0.777778  0.000000  0.222222  0.000000
 755  0.000000  0.888889  0.000000  0.111111
 756  0.777778  0.000000  0.222222  0.000000
 757  0.555556  0.111111  0.000000  0.333333
 758  0.000000  0.000000  0.333333  0.666667
 759  0.000000  0.333333  0.666667  0.000000
 760  0.000000  0.000000  1.000000  0.000000
 761  0.000000  0.000000  1.000000  0.000000
 762  0.000000  1.000000  0.000000  0.000000
 763  0.666667  0.111111  0.000000  0.222222
 764  0.555556  0.333333  0.000000  0.111111
 765  0.000000  0.444444  0.555556  0.000000
 766  0.000000  0.000000  0.888889  0.111111
 767  0.222222  0.777778  0.000000  0.000000
 768  0.666667  0.000000  0.333333  0.000000
 769  1.000000  0.000000  0.000000  0.000000
 770  0.222222  0.000000  0.666667  0.111111
 771  0.888889  0.000000  0.111111  0.000000
 772 --------------------------------------------------------------------------------
 773
 774 --------------------------------------------------------------------------------
 775         Motif 5 regular expression
 776 --------------------------------------------------------------------------------
 777 G[AT][AG]C[AG][AT][TG][GC]GGC[AT][AC][GC]G[CA][AG]A[GA]A
 778 --------------------------------------------------------------------------------
 779
 780
 781
 782
 783 Time 20.54 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_YDR232W                 2.02e-39  164_[+2(7.75e-12)]_100_[+5(7.65e-13)]_2_[+3(9.40e-12)]_36_[+1(1.83e-13)]_1_[+4(4.75e-14)]_95
 798 MIT_Spar_c117_4603               1.73e-34  159_[+2(2.12e-10)]_100_[+5(7.65e-13)]_2_[+3(3.58e-10)]_36_[+1(1.83e-13)]_1_[+4(6.28e-12)]_100
 799 MIT_Smik_c228_4055               3.04e-30  160_[+2(6.70e-10)]_102_[+5(7.65e-13)]_1_[+3(6.77e-11)]_36_[+1(1.47e-11)]_1_[+4(3.64e-09)]_98
 800 WashU_Skud_Contig2069.5          9.14e-35  161_[+2(7.75e-12)]_101_[+5(7.37e-10)]_2_[+3(9.40e-12)]_35_[+1(1.83e-13)]_1_[+4(3.48e-12)]_98
 801 WashU_Sbay_Contig461.5           2.20e-33  160_[+2(8.83e-11)]_7_[+1(7.03e-05)]_70_[+5(7.65e-13)]_2_[+3(7.67e-11)]_37_[+1(3.08e-14)]_1_[+4(5.96e-09)]_6_[+5(2.10e-06)]_75
 802 SGD_Scer_YDR047W                 5.13e-24  172_[+2(4.04e-10)]_47_[+3(8.04e-06)]_387_[+3(1.22e-10)]_41_[+4(1.69e-09)]_17_[-5(6.96e-05)]_106_[+5(2.30e-09)]_31_[+1(1.02e-09)]_3_[-4(1.74e-05)]_36
 803 MIT_Spar_c130_3923               9.08e-24  169_[+2(2.30e-10)]_47_[+3(8.58e-05)]_388_[+3(2.75e-10)]_43_[+4(1.69e-09)]_17_[-5(6.49e-06)]_37_[-5(2.93e-05)]_58_[+5(4.62e-09)]_31_[+1(7.23e-10)]_8_[+4(7.15e-06)]_22
 804 MIT_Sbay_c896_21277              2.02e-19  142_[+2(3.02e-08)]_45_[+3(6.78e-05)]_259_[-4(2.48e-06)]_144_[+3(9.67e-09)]_28_[+4(7.77e-09)]_122_[+5(2.58e-08)]_31_[+1(2.69e-10)]_89
 805 WashU_Skud_Contig1362.1          4.91e-20  41_[-1(2.10e-05)]_75_[+2(8.43e-10)]_137_[+1(1.77e-08)]_20_[+5(3.13e-09)]_129_[-4(5.15e-08)]_144_[+3(5.76e-09)]_31_[+4(1.33e-05)]_44
 806 --------------------------------------------------------------------------------
 807
 808 ********************************************************************************
 809
 810
 811 ********************************************************************************
 812 Stopped because nmotifs = 5 reached.
 813 ********************************************************************************
 814
 815 CPU: dhn02990.mrc-dunn.cam.ac.uk
 816
 817 ********************************************************************************