t/data/map_hem/HEM1-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= HEM1-HEM15.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_YOR176W         1.0000    727
  38 MIT_Spar_c278_20970      1.0000    727  MIT_Smik_c935_20455      1.0000    727
  39 WashU_Skud_Contig2050.4  1.0000    727  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 HEM1-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=       10    maxsites=       10    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=            6125    N=              10
  59 strands: + -
  60 sample: seed=            0    seqfrac=         1
  61 Letter frequencies in dataset:
  62 A 0.296 C 0.204 G 0.204 T 0.296
  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 =  10   llr = 225   E-value = 1.2e-031
  70 ********************************************************************************
  71 --------------------------------------------------------------------------------
  72         Motif 1 Description
  73 --------------------------------------------------------------------------------
  74 Simplified        A  4a5::5:::5:1aa61:5:5
  75 pos.-specific     C  6::::5:a::a::::5a:55
  76 probability       G  ::2:a:a:a::9::44:55:
  77 matrix            T  ::3a:::::5::::::::::
  78
  79          bits    2.5     * *** *     *
  80                  2.3     * *** *     *
  81                  2.0     * *** **    *
  82                  1.8     * *** **    *
  83 Information      1.5  * ** *** ****  * *
  84 content          1.3 ** ** *** ****  * *
  85 (32.4 bits)      1.0 ** ****** **********
  86                  0.8 ** ****** **********
  87                  0.5 ** *****************
  88                  0.3 ********************
  89                  0.0 --------------------
  90
  91 Multilevel           CAATGAGCGACGAAACCACA
  92 consensus            A T  C   T    GG GGC
  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_Contig2069.5      +    371  4.19e-12 GGCCGCAGAC CAATGAGCGACGAAGGCGGC CTTTCGTAGC
 103 MIT_Spar_c117_4603           +    369  4.19e-12 GGCCGCAGAC CAATGAGCGACGAAGGCGGC CTTTCCGAGT
 104 SGD_Scer_YDR232W             +    374  4.19e-12 GGCCGCAGAC CAATGAGCGACGAAGGCGGC CTTTCCGAGC
 105 MIT_Smik_c228_4055           +    371  6.28e-12 AAGCGCAGAC CAATGAGCGACGAAAGCGGC CTTTTGAAGG
 106 SGD_Scer_YOR176W             +    554  3.36e-11 AGATCTTTCA CATTGCGCGTCGAAACCACA AACCGTCGAA
 107 WashU_Sbay_Contig480.2       +    567  8.33e-11 AGATCTTTCG AAGTGCGCGTCGAAACCACA AACCATCAAA
 108 WashU_Skud_Contig2050.4      +    562  8.33e-11 GGATCTTTCA AAGTGCGCGTCGAAACCACA AACCGTCGAA
 109 WashU_Sbay_Contig461.5       +    368  8.75e-11 GGGCGCAGAC CAATGAGCGACGAAGACGGC TTTTGGGCGG
 110 MIT_Spar_c278_20970          +    556  9.22e-11 AGATCTTTCG AATTGCGCGTCGAAACCACA AACCGTCGAA
 111 MIT_Smik_c935_20455          +    540  3.96e-10 AGTTCTCTCC AATTGCGCGTCAAAACCACA AACCGTCGAA
 112 --------------------------------------------------------------------------------
 113
 114 --------------------------------------------------------------------------------
 115         Motif 1 block diagrams
 116 --------------------------------------------------------------------------------
 117 SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
 118 -------------            ----------------  -------------
 119 WashU_Skud_Contig2069.5           4.2e-12  370_[+1]_108
 120 MIT_Spar_c117_4603                4.2e-12  368_[+1]_110
 121 SGD_Scer_YDR232W                  4.2e-12  373_[+1]_105
 122 MIT_Smik_c228_4055                6.3e-12  370_[+1]_108
 123 SGD_Scer_YOR176W                  3.4e-11  553_[+1]_154
 124 WashU_Sbay_Contig480.2            8.3e-11  566_[+1]_141
 125 WashU_Skud_Contig2050.4           8.3e-11  561_[+1]_146
 126 WashU_Sbay_Contig461.5            8.7e-11  367_[+1]_111
 127 MIT_Spar_c278_20970               9.2e-11  555_[+1]_152
 128 MIT_Smik_c935_20455                 4e-10  539_[+1]_168
 129 --------------------------------------------------------------------------------
 130
 131 --------------------------------------------------------------------------------
 132         Motif 1 in BLOCKS format
 133 --------------------------------------------------------------------------------
 134 BL   MOTIF 1 width=20 seqs=10
 135 WashU_Skud_Contig2069.5  (  371) CAATGAGCGACGAAGGCGGC  1
 136 MIT_Spar_c117_4603       (  369) CAATGAGCGACGAAGGCGGC  1
 137 SGD_Scer_YDR232W         (  374) CAATGAGCGACGAAGGCGGC  1
 138 MIT_Smik_c228_4055       (  371) CAATGAGCGACGAAAGCGGC  1
 139 SGD_Scer_YOR176W         (  554) CATTGCGCGTCGAAACCACA  1
 140 WashU_Sbay_Contig480.2   (  567) AAGTGCGCGTCGAAACCACA  1
 141 WashU_Skud_Contig2050.4  (  562) AAGTGCGCGTCGAAACCACA  1
 142 WashU_Sbay_Contig461.5   (  368) CAATGAGCGACGAAGACGGC  1
 143 MIT_Spar_c278_20970      (  556) AATTGCGCGTCGAAACCACA  1
 144 MIT_Smik_c935_20455      (  540) AATTGCGCGTCAAAACCACA  1
 145 //
 146
 147 --------------------------------------------------------------------------------
 148
 149 --------------------------------------------------------------------------------
 150         Motif 1 position-specific scoring matrix
 151 --------------------------------------------------------------------------------
 152 log-odds matrix: alength= 4 w= 20 n= 5935 bayes= 9.21067 E= 1.2e-031
 153     30    177   -997   -997
 154    162   -997   -997   -997
 155     62   -997     19    -11
 156   -997   -997   -997    162
 157   -997   -997    251   -997
 158     62    151   -997   -997
 159   -997   -997    251   -997
 160   -997    251   -997   -997
 161   -997   -997    251   -997
 162     62   -997   -997     62
 163   -997    251   -997   -997
 164   -169   -997    236   -997
 165    162   -997   -997   -997
 166    162   -997   -997   -997
 167     89   -997    119   -997
 168   -169    151    119   -997
 169   -997    251   -997   -997
 170     62   -997    151   -997
 171   -997    151    151   -997
 172     62    151   -997   -997
 173 --------------------------------------------------------------------------------
 174
 175 --------------------------------------------------------------------------------
 176         Motif 1 position-specific probability matrix
 177 --------------------------------------------------------------------------------
 178 letter-probability matrix: alength= 4 w= 20 nsites= 10 E= 1.2e-031
 179  0.400000  0.600000  0.000000  0.000000
 180  1.000000  0.000000  0.000000  0.000000
 181  0.500000  0.000000  0.200000  0.300000
 182  0.000000  0.000000  0.000000  1.000000
 183  0.000000  0.000000  1.000000  0.000000
 184  0.500000  0.500000  0.000000  0.000000
 185  0.000000  0.000000  1.000000  0.000000
 186  0.000000  1.000000  0.000000  0.000000
 187  0.000000  0.000000  1.000000  0.000000
 188  0.500000  0.000000  0.000000  0.500000
 189  0.000000  1.000000  0.000000  0.000000
 190  0.100000  0.000000  0.900000  0.000000
 191  1.000000  0.000000  0.000000  0.000000
 192  1.000000  0.000000  0.000000  0.000000
 193  0.600000  0.000000  0.400000  0.000000
 194  0.100000  0.500000  0.400000  0.000000
 195  0.000000  1.000000  0.000000  0.000000
 196  0.500000  0.000000  0.500000  0.000000
 197  0.000000  0.500000  0.500000  0.000000
 198  0.500000  0.500000  0.000000  0.000000
 199 --------------------------------------------------------------------------------
 200
 201 --------------------------------------------------------------------------------
 202         Motif 1 regular expression
 203 --------------------------------------------------------------------------------
 204 [CA]A[ATG]TG[AC]GCG[AT]CGAA[AG][CG]C[AG][CG][AC]
 205 --------------------------------------------------------------------------------
 206
 207
 208
 209
 210 Time  3.95 secs.
 211
 212 ********************************************************************************
 213
 214
 215 ********************************************************************************
 216 MOTIF  2        width =   20   sites =  10   llr = 209   E-value = 9.7e-026
 217 ********************************************************************************
 218 --------------------------------------------------------------------------------
 219         Motif 2 Description
 220 --------------------------------------------------------------------------------
 221 Simplified        A  ::2::::1:::::::::::9
 222 pos.-specific     C  94:4:a6:3a:a41:a::9:
 223 probability       G  1:5:4:4:6:1:1:3:::1:
 224 matrix            T  :6366::91:9:597:aa:1
 225
 226          bits    2.5      *   * *   *
 227                  2.3      *   * *   *
 228                  2.0 *    *   * *   *  *
 229                  1.8 *    *   * *   *  *
 230 Information      1.5 *    **  * *   ****
 231 content          1.3 *    *** *** * *****
 232 (30.1 bits)      1.0 ** ********* *******
 233                  0.8 ** *****************
 234                  0.5 ********************
 235                  0.3 ********************
 236                  0.0 --------------------
 237
 238 Multilevel           CTGTTCCTGCTCTTTCTTCA
 239 consensus             CTCG G C   C G
 240 sequence               A
 241
 242 --------------------------------------------------------------------------------
 243
 244 --------------------------------------------------------------------------------
 245         Motif 2 sites sorted by position p-value
 246 --------------------------------------------------------------------------------
 247 Sequence name            Strand  Start   P-value                    Site
 248 -------------            ------  ----- ---------            --------------------
 249 MIT_Smik_c228_4055           +    312  4.12e-12 ATGAAAATTT CCGTTCCTGCTCTTTCTTCA TATATGAACA
 250 SGD_Scer_YDR232W             +    315  4.12e-12 TGAAAAATTT CCGTTCCTGCTCTTTCTTCA TATATGAACA
 251 MIT_Spar_c117_4603           +    310  6.47e-12 TGAAAAATTT CTGTTCCTGCTCTTTCTTCA TATATGAACA
 252 WashU_Skud_Contig2069.5      +    313  8.03e-12 TGAAAAATTT CCGTTCCTGCTCTTGCTTCA TATATGACAA
 253 MIT_Smik_c935_20455          +    154  7.23e-11 CAAAAGACTC CTTCGCGTCCTCCTTCTTCA AGTCTCATAT
 254 MIT_Spar_c278_20970          +    159  7.23e-11 AAAAGTATTC CTTCGCGTCCTCCTTCTTCA ATCCCATATC
 255 SGD_Scer_YOR176W             +    157  7.23e-11 AAAAGTATTC CTTCGCGTCCTCCTTCTTCA ATCCCATATC
 256 WashU_Sbay_Contig461.5       +    308  1.78e-10 TGAAAAATCT CCGTTCCTGCTCTTGCTTGA TATATTAACA
 257 WashU_Sbay_Contig480.2       +    207  1.47e-09 AGAAGTATTC CTACGCGAGCTCCCTCTTCA AGTGCCAAAT
 258 WashU_Skud_Contig2050.4      +    157  2.43e-08 ACCAAAAGAA GTATTCCTTCGCGTGCTTCT CCTTTCTGTG
 259 --------------------------------------------------------------------------------
 260
 261 --------------------------------------------------------------------------------
 262         Motif 2 block diagrams
 263 --------------------------------------------------------------------------------
 264 SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
 265 -------------            ----------------  -------------
 266 MIT_Smik_c228_4055                4.1e-12  311_[+2]_167
 267 SGD_Scer_YDR232W                  4.1e-12  314_[+2]_164
 268 MIT_Spar_c117_4603                6.5e-12  309_[+2]_169
 269 WashU_Skud_Contig2069.5             8e-12  312_[+2]_166
 270 MIT_Smik_c935_20455               7.2e-11  153_[+2]_554
 271 MIT_Spar_c278_20970               7.2e-11  158_[+2]_549
 272 SGD_Scer_YOR176W                  7.2e-11  156_[+2]_551
 273 WashU_Sbay_Contig461.5            1.8e-10  307_[+2]_171
 274 WashU_Sbay_Contig480.2            1.5e-09  206_[+2]_501
 275 WashU_Skud_Contig2050.4           2.4e-08  156_[+2]_551
 276 --------------------------------------------------------------------------------
 277
 278 --------------------------------------------------------------------------------
 279         Motif 2 in BLOCKS format
 280 --------------------------------------------------------------------------------
 281 BL   MOTIF 2 width=20 seqs=10
 282 MIT_Smik_c228_4055       (  312) CCGTTCCTGCTCTTTCTTCA  1
 283 SGD_Scer_YDR232W         (  315) CCGTTCCTGCTCTTTCTTCA  1
 284 MIT_Spar_c117_4603       (  310) CTGTTCCTGCTCTTTCTTCA  1
 285 WashU_Skud_Contig2069.5  (  313) CCGTTCCTGCTCTTGCTTCA  1
 286 MIT_Smik_c935_20455      (  154) CTTCGCGTCCTCCTTCTTCA  1
 287 MIT_Spar_c278_20970      (  159) CTTCGCGTCCTCCTTCTTCA  1
 288 SGD_Scer_YOR176W         (  157) CTTCGCGTCCTCCTTCTTCA  1
 289 WashU_Sbay_Contig461.5   (  308) CCGTTCCTGCTCTTGCTTGA  1
 290 WashU_Sbay_Contig480.2   (  207) CTACGCGAGCTCCCTCTTCA  1
 291 WashU_Skud_Contig2050.4  (  157) GTATTCCTTCGCGTGCTTCT  1
 292 //
 293
 294 --------------------------------------------------------------------------------
 295
 296 --------------------------------------------------------------------------------
 297         Motif 2 position-specific scoring matrix
 298 --------------------------------------------------------------------------------
 299 log-odds matrix: alength= 4 w= 20 n= 5935 bayes= 9.21067 E= 9.7e-026
 300   -997    236    -81   -997
 301   -997    119   -997     89
 302    -70   -997    151    -11
 303   -997    119   -997     89
 304   -997   -997    119     89
 305   -997    251   -997   -997
 306   -997    177    119   -997
 307   -169   -997   -997    147
 308   -997     77    177   -169
 309   -997    251   -997   -997
 310   -997   -997    -81    147
 311   -997    251   -997   -997
 312   -997    119    -81     62
 313   -997    -81   -997    147
 314   -997   -997     77    111
 315   -997    251   -997   -997
 316   -997   -997   -997    162
 317   -997   -997   -997    162
 318   -997    236    -81   -997
 319    147   -997   -997   -169
 320 --------------------------------------------------------------------------------
 321
 322 --------------------------------------------------------------------------------
 323         Motif 2 position-specific probability matrix
 324 --------------------------------------------------------------------------------
 325 letter-probability matrix: alength= 4 w= 20 nsites= 10 E= 9.7e-026
 326  0.000000  0.900000  0.100000  0.000000
 327  0.000000  0.400000  0.000000  0.600000
 328  0.200000  0.000000  0.500000  0.300000
 329  0.000000  0.400000  0.000000  0.600000
 330  0.000000  0.000000  0.400000  0.600000
 331  0.000000  1.000000  0.000000  0.000000
 332  0.000000  0.600000  0.400000  0.000000
 333  0.100000  0.000000  0.000000  0.900000
 334  0.000000  0.300000  0.600000  0.100000
 335  0.000000  1.000000  0.000000  0.000000
 336  0.000000  0.000000  0.100000  0.900000
 337  0.000000  1.000000  0.000000  0.000000
 338  0.000000  0.400000  0.100000  0.500000
 339  0.000000  0.100000  0.000000  0.900000
 340  0.000000  0.000000  0.300000  0.700000
 341  0.000000  1.000000  0.000000  0.000000
 342  0.000000  0.000000  0.000000  1.000000
 343  0.000000  0.000000  0.000000  1.000000
 344  0.000000  0.900000  0.100000  0.000000
 345  0.900000  0.000000  0.000000  0.100000
 346 --------------------------------------------------------------------------------
 347
 348 --------------------------------------------------------------------------------
 349         Motif 2 regular expression
 350 --------------------------------------------------------------------------------
 351 C[TC][GTA][TC][TG]C[CG]T[GC]CTC[TC]T[TG]CTTCA
 352 --------------------------------------------------------------------------------
 353
 354
 355
 356
 357 Time  7.93 secs.
 358
 359 ********************************************************************************
 360
 361
 362 ********************************************************************************
 363 MOTIF  3        width =   20   sites =  10   llr = 194   E-value = 5.5e-020
 364 ********************************************************************************
 365 --------------------------------------------------------------------------------
 366         Motif 3 Description
 367 --------------------------------------------------------------------------------
 368 Simplified        A  :1:3::111:1:11:91:::
 369 pos.-specific     C  122:6661:9::1::1:8::
 370 probability       G  :::7::3:91:a:3a:9::7
 371 matrix            T  978:44:8::9:86:::2a3
 372
 373          bits    2.5            *  *
 374                  2.3            *  *
 375                  2.0         ** *  * *
 376                  1.8         ** *  * *
 377 Information      1.5         ** *  * ***
 378 content          1.3 *  ***  ****  ******
 379 (28.0 bits)      1.0 * ***** ****  ******
 380                  0.8 ************* ******
 381                  0.5 ********************
 382                  0.3 ********************
 383                  0.0 --------------------
 384
 385 Multilevel           TTTGCCCTGCTGTTGAGCTG
 386 consensus             CCATTG      G   T T
 387 sequence
 388
 389 --------------------------------------------------------------------------------
 390
 391 --------------------------------------------------------------------------------
 392         Motif 3 sites sorted by position p-value
 393 --------------------------------------------------------------------------------
 394 Sequence name            Strand  Start   P-value                    Site
 395 -------------            ------  ----- ---------            --------------------
 396 MIT_Spar_c278_20970          +    497  1.95e-13 TTTAGCTTTT TTTGCCCTGCTGTTGAGCTG TTTTGCTTCA
 397 MIT_Smik_c935_20455          +    481  1.64e-12 TTCAGCTTTT TTTGCTCTGCTGTTGAGCTG TTTTACTTCA
 398 SGD_Scer_YOR176W             +    495  1.64e-12 TTTAGCTTTT TTTGTCCTGCTGTTGAGCTG TTTTGCTTTA
 399 WashU_Sbay_Contig480.2       +    507  8.61e-12 TTAGCTGTTT TTTGTTCTGCTGTTGAGCTG TTTTGCTCCA
 400 WashU_Skud_Contig2050.4      +    498  8.61e-12 TCAGCTGTTT TTTGTTCTGCTGTTGAGCTG TTTTGTTCCA
 401 MIT_Spar_c117_4603           -    457  3.51e-09 ACTGCAATGC TTCACCGTGCTGTGGAACTT GATATAGTGG
 402 WashU_Sbay_Contig461.5       -    260  8.74e-09 TGCCCATTGT TCTGTCCCGGTGCTGCGCTG TTGGAACCAC
 403 SGD_Scer_YDR232W             -    465  2.27e-08 ACTACAATGC TTTACCGAGCAGTGGAGTTT GATATAGTGG
 404 WashU_Skud_Contig2069.5      -    460  2.39e-08 GCTGTAATGG CCTACCATGCTGAAGAGCTG ATATAGTGGT
 405 MIT_Smik_c228_4055           -    459  3.73e-08 ACAGCAATGT TACGCTGTACTGTGGAGTTT GATATAATGC
 406 --------------------------------------------------------------------------------
 407
 408 --------------------------------------------------------------------------------
 409         Motif 3 block diagrams
 410 --------------------------------------------------------------------------------
 411 SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
 412 -------------            ----------------  -------------
 413 MIT_Spar_c278_20970               1.9e-13  496_[+3]_211
 414 MIT_Smik_c935_20455               1.6e-12  480_[+3]_227
 415 SGD_Scer_YOR176W                  1.6e-12  494_[+3]_213
 416 WashU_Sbay_Contig480.2            8.6e-12  506_[+3]_201
 417 WashU_Skud_Contig2050.4           8.6e-12  497_[+3]_210
 418 MIT_Spar_c117_4603                3.5e-09  456_[-3]_22
 419 WashU_Sbay_Contig461.5            8.7e-09  259_[-3]_219
 420 SGD_Scer_YDR232W                  2.3e-08  464_[-3]_14
 421 WashU_Skud_Contig2069.5           2.4e-08  459_[-3]_19
 422 MIT_Smik_c228_4055                3.7e-08  458_[-3]_20
 423 --------------------------------------------------------------------------------
 424
 425 --------------------------------------------------------------------------------
 426         Motif 3 in BLOCKS format
 427 --------------------------------------------------------------------------------
 428 BL   MOTIF 3 width=20 seqs=10
 429 MIT_Spar_c278_20970      (  497) TTTGCCCTGCTGTTGAGCTG  1
 430 MIT_Smik_c935_20455      (  481) TTTGCTCTGCTGTTGAGCTG  1
 431 SGD_Scer_YOR176W         (  495) TTTGTCCTGCTGTTGAGCTG  1
 432 WashU_Sbay_Contig480.2   (  507) TTTGTTCTGCTGTTGAGCTG  1
 433 WashU_Skud_Contig2050.4  (  498) TTTGTTCTGCTGTTGAGCTG  1
 434 MIT_Spar_c117_4603       (  457) TTCACCGTGCTGTGGAACTT  1
 435 WashU_Sbay_Contig461.5   (  260) TCTGTCCCGGTGCTGCGCTG  1
 436 SGD_Scer_YDR232W         (  465) TTTACCGAGCAGTGGAGTTT  1
 437 WashU_Skud_Contig2069.5  (  460) CCTACCATGCTGAAGAGCTG  1
 438 MIT_Smik_c228_4055       (  459) TACGCTGTACTGTGGAGTTT  1
 439 //
 440
 441 --------------------------------------------------------------------------------
 442
 443 --------------------------------------------------------------------------------
 444         Motif 3 position-specific scoring matrix
 445 --------------------------------------------------------------------------------
 446 log-odds matrix: alength= 4 w= 20 n= 5935 bayes= 9.21067 E= 5.5e-020
 447   -997    -81   -997    147
 448   -169     19   -997    111
 449   -997     19   -997    130
 450    -11   -997    199   -997
 451   -997    177   -997     30
 452   -997    177   -997     30
 453   -169    177     77   -997
 454   -169    -81   -997    130
 455   -169   -997    236   -997
 456   -997    236    -81   -997
 457   -169   -997   -997    147
 458   -997   -997    251   -997
 459   -169    -81   -997    130
 460   -169   -997     77     89
 461   -997   -997    251   -997
 462    147    -81   -997   -997
 463   -169   -997    236   -997
 464   -997    219   -997    -70
 465   -997   -997   -997    162
 466   -997   -997    199    -11
 467 --------------------------------------------------------------------------------
 468
 469 --------------------------------------------------------------------------------
 470         Motif 3 position-specific probability matrix
 471 --------------------------------------------------------------------------------
 472 letter-probability matrix: alength= 4 w= 20 nsites= 10 E= 5.5e-020
 473  0.000000  0.100000  0.000000  0.900000
 474  0.100000  0.200000  0.000000  0.700000
 475  0.000000  0.200000  0.000000  0.800000
 476  0.300000  0.000000  0.700000  0.000000
 477  0.000000  0.600000  0.000000  0.400000
 478  0.000000  0.600000  0.000000  0.400000
 479  0.100000  0.600000  0.300000  0.000000
 480  0.100000  0.100000  0.000000  0.800000
 481  0.100000  0.000000  0.900000  0.000000
 482  0.000000  0.900000  0.100000  0.000000
 483  0.100000  0.000000  0.000000  0.900000
 484  0.000000  0.000000  1.000000  0.000000
 485  0.100000  0.100000  0.000000  0.800000
 486  0.100000  0.000000  0.300000  0.600000
 487  0.000000  0.000000  1.000000  0.000000
 488  0.900000  0.100000  0.000000  0.000000
 489  0.100000  0.000000  0.900000  0.000000
 490  0.000000  0.800000  0.000000  0.200000
 491  0.000000  0.000000  0.000000  1.000000
 492  0.000000  0.000000  0.700000  0.300000
 493 --------------------------------------------------------------------------------
 494
 495 --------------------------------------------------------------------------------
 496         Motif 3 regular expression
 497 --------------------------------------------------------------------------------
 498 T[TC][TC][GA][CT][CT][CG]TGCTGT[TG]GAG[CT]T[GT]
 499 --------------------------------------------------------------------------------
 500
 501
 502
 503
 504 Time 11.72 secs.
 505
 506 ********************************************************************************
 507
 508
 509 ********************************************************************************
 510 MOTIF  4        width =   20   sites =  10   llr = 192   E-value = 5.7e-019
 511 ********************************************************************************
 512 --------------------------------------------------------------------------------
 513         Motif 4 Description
 514 --------------------------------------------------------------------------------
 515 Simplified        A  :1:19421:1::::1:5:9:
 516 pos.-specific     C  :::9:1621:5a3::a58::
 517 probability       G  :1::::2219::::9:::1:
 518 matrix            T  a8a:15:58:5:7a:::2:a
 519
 520          bits    2.5            *   *
 521                  2.3            *   *
 522                  2.0    *     * *  **
 523                  1.8    *     * *  **
 524 Information      1.5 * **     * * *** * *
 525 content          1.3 * ***    * * *** ***
 526 (27.7 bits)      1.0 * *** * ************
 527                  0.8 ***** * ************
 528                  0.5 ***** * ************
 529                  0.3 ********************
 530                  0.0 --------------------
 531
 532 Multilevel           TTTCATCTTGCCTTGCACAT
 533 consensus                 AAC  T C   CT
 534 sequence                   GG
 535
 536 --------------------------------------------------------------------------------
 537
 538 --------------------------------------------------------------------------------
 539         Motif 4 sites sorted by position p-value
 540 --------------------------------------------------------------------------------
 541 Sequence name            Strand  Start   P-value                    Site
 542 -------------            ------  ----- ---------            --------------------
 543 WashU_Sbay_Contig461.5       -    283  6.64e-13 AACGGAGATT TTTCATCTTGCCTTGCCCAT TGTTCTGTCC
 544 MIT_Smik_c228_4055           -    288  6.64e-13 GAACGGAAAT TTTCATCTTGCCTTGCCCAT TGTTCTAATT
 545 MIT_Spar_c117_4603           -    285  6.64e-13 AACAGAAATT TTTCATCTTGCCTTGCCCAT TGTTCTGACC
 546 SGD_Scer_YDR232W             -    290  6.64e-13 AACGGAAATT TTTCATCTTGCCTTGCCCAT TGTTCTGATC
 547 WashU_Skud_Contig2069.5      -    288  1.75e-10 AACGGAAATT TTTCACATTGCCTTGCCCAT TGTTCCGATC
 548 MIT_Spar_c278_20970          +    302  3.17e-10 AGTAGAGATA TTTCAAGCTGTCCTGCACAT GCTACATATT
 549 MIT_Smik_c935_20455          +    298  3.30e-09 AATAAAGAAG TTTCAACGTGTCCTGCATGT TCTACAAATT
 550 WashU_Skud_Contig2050.4      +    308  1.63e-08 ATAATTAAAA TGTCTTCAGGTCTTGCACAT ACTCCTACAT
 551 SGD_Scer_YOR176W             +    301  5.38e-08 AGCGGAGATG TTTCAAGGCATCCTACACAT GCTACATATT
 552 WashU_Sbay_Contig480.2       +    345  5.53e-08 GAAAGATGTT TATAAAACTGTCTTGCATAT GCTCTATTTA
 553 --------------------------------------------------------------------------------
 554
 555 --------------------------------------------------------------------------------
 556         Motif 4 block diagrams
 557 --------------------------------------------------------------------------------
 558 SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
 559 -------------            ----------------  -------------
 560 WashU_Sbay_Contig461.5            6.6e-13  282_[-4]_196
 561 MIT_Smik_c228_4055                6.6e-13  287_[-4]_191
 562 MIT_Spar_c117_4603                6.6e-13  284_[-4]_194
 563 SGD_Scer_YDR232W                  6.6e-13  289_[-4]_189
 564 WashU_Skud_Contig2069.5           1.7e-10  287_[-4]_191
 565 MIT_Spar_c278_20970               3.2e-10  301_[+4]_406
 566 MIT_Smik_c935_20455               3.3e-09  297_[+4]_410
 567 WashU_Skud_Contig2050.4           1.6e-08  307_[+4]_400
 568 SGD_Scer_YOR176W                  5.4e-08  300_[+4]_407
 569 WashU_Sbay_Contig480.2            5.5e-08  344_[+4]_363
 570 --------------------------------------------------------------------------------
 571
 572 --------------------------------------------------------------------------------
 573         Motif 4 in BLOCKS format
 574 --------------------------------------------------------------------------------
 575 BL   MOTIF 4 width=20 seqs=10
 576 WashU_Sbay_Contig461.5   (  283) TTTCATCTTGCCTTGCCCAT  1
 577 MIT_Smik_c228_4055       (  288) TTTCATCTTGCCTTGCCCAT  1
 578 MIT_Spar_c117_4603       (  285) TTTCATCTTGCCTTGCCCAT  1
 579 SGD_Scer_YDR232W         (  290) TTTCATCTTGCCTTGCCCAT  1
 580 WashU_Skud_Contig2069.5  (  288) TTTCACATTGCCTTGCCCAT  1
 581 MIT_Spar_c278_20970      (  302) TTTCAAGCTGTCCTGCACAT  1
 582 MIT_Smik_c935_20455      (  298) TTTCAACGTGTCCTGCATGT  1
 583 WashU_Skud_Contig2050.4  (  308) TGTCTTCAGGTCTTGCACAT  1
 584 SGD_Scer_YOR176W         (  301) TTTCAAGGCATCCTACACAT  1
 585 WashU_Sbay_Contig480.2   (  345) TATAAAACTGTCTTGCATAT  1
 586 //
 587
 588 --------------------------------------------------------------------------------
 589
 590 --------------------------------------------------------------------------------
 591         Motif 4 position-specific scoring matrix
 592 --------------------------------------------------------------------------------
 593 log-odds matrix: alength= 4 w= 20 n= 5935 bayes= 9.21067 E= 5.7e-019
 594   -997   -997   -997    162
 595   -169   -997    -81    130
 596   -997   -997   -997    162
 597   -169    236   -997   -997
 598    147   -997   -997   -169
 599     30    -81   -997     62
 600    -70    177     19   -997
 601   -169     19     19     62
 602   -997    -81    -81    130
 603   -169   -997    236   -997
 604   -997    151   -997     62
 605   -997    251   -997   -997
 606   -997     77   -997    111
 607   -997   -997   -997    162
 608   -169   -997    236   -997
 609   -997    251   -997   -997
 610     62    151   -997   -997
 611   -997    219   -997    -70
 612    147   -997    -81   -997
 613   -997   -997   -997    162
 614 --------------------------------------------------------------------------------
 615
 616 --------------------------------------------------------------------------------
 617         Motif 4 position-specific probability matrix
 618 --------------------------------------------------------------------------------
 619 letter-probability matrix: alength= 4 w= 20 nsites= 10 E= 5.7e-019
 620  0.000000  0.000000  0.000000  1.000000
 621  0.100000  0.000000  0.100000  0.800000
 622  0.000000  0.000000  0.000000  1.000000
 623  0.100000  0.900000  0.000000  0.000000
 624  0.900000  0.000000  0.000000  0.100000
 625  0.400000  0.100000  0.000000  0.500000
 626  0.200000  0.600000  0.200000  0.000000
 627  0.100000  0.200000  0.200000  0.500000
 628  0.000000  0.100000  0.100000  0.800000
 629  0.100000  0.000000  0.900000  0.000000
 630  0.000000  0.500000  0.000000  0.500000
 631  0.000000  1.000000  0.000000  0.000000
 632  0.000000  0.300000  0.000000  0.700000
 633  0.000000  0.000000  0.000000  1.000000
 634  0.100000  0.000000  0.900000  0.000000
 635  0.000000  1.000000  0.000000  0.000000
 636  0.500000  0.500000  0.000000  0.000000
 637  0.000000  0.800000  0.000000  0.200000
 638  0.900000  0.000000  0.100000  0.000000
 639  0.000000  0.000000  0.000000  1.000000
 640 --------------------------------------------------------------------------------
 641
 642 --------------------------------------------------------------------------------
 643         Motif 4 regular expression
 644 --------------------------------------------------------------------------------
 645 TTTCA[TA][CAG][TCG]TG[CT]C[TC]TGC[AC][CT]AT
 646 --------------------------------------------------------------------------------
 647
 648
 649
 650
 651 Time 15.38 secs.
 652
 653 ********************************************************************************
 654
 655
 656 ********************************************************************************
 657 MOTIF  5        width =   20   sites =  10   llr = 188   E-value = 9.3e-018
 658 ********************************************************************************
 659 --------------------------------------------------------------------------------
 660         Motif 5 Description
 661 --------------------------------------------------------------------------------
 662 Simplified        A  216895a11:3::::13:11
 663 pos.-specific     C  6931:2::5:678:7::69:
 664 probability       G  1:1:13:91a::17:972:9
 665 matrix            T  1::1::::3:13133::2::
 666
 667          bits    2.5          *
 668                  2.3          *
 669                  2.0  *     * *     *  **
 670                  1.8  *     * *     *  **
 671 Information      1.5  *    ** *  *  *  **
 672 content          1.3  *  * ** * ****** **
 673 (27.1 bits)      1.0  *  * ** * *********
 674                  0.8 ***** ** ***********
 675                  0.5 ********************
 676                  0.3 ********************
 677                  0.0 --------------------
 678
 679 Multilevel           CCAAAAAGCGCCCGCGGCCG
 680 consensus            A C  G  T AT TT AG
 681 sequence                  C           T
 682
 683 --------------------------------------------------------------------------------
 684
 685 --------------------------------------------------------------------------------
 686         Motif 5 sites sorted by position p-value
 687 --------------------------------------------------------------------------------
 688 Sequence name            Strand  Start   P-value                    Site
 689 -------------            ------  ----- ---------            --------------------
 690 MIT_Spar_c117_4603           +    344  3.06e-14 TGAACAATGA CCAAAAAGCGCCCGCGGCCG CAGACCAATG
 691 SGD_Scer_YDR232W             +    349  3.06e-14 TGAACAATGA CCAAAAAGCGCCCGCGGCCG CAGACCAATG
 692 WashU_Skud_Contig2069.5      +    346  1.65e-12 ATGACAATGA CCAAAAAGCGTCCGCGGCCG CAGACCAATG
 693 MIT_Smik_c228_4055           +    346  1.43e-10 TGAACAATGA CCAAAAAGCGCCCGCAAGCG CAGACCAATG
 694 MIT_Spar_c278_20970          +    126  3.60e-09 TTGGTGCCAA ACCAAGAGTGACCTTGACCG ACTAAAAGTA
 695 SGD_Scer_YOR176W             +    124  3.90e-09 TTGGTGTCAA GCCAAGAGTGACCTTGACCG ACCAAAAGTA
 696 WashU_Sbay_Contig461.5       +    343  4.91e-09 TAACAATGAC CAAAAAAACGCCGGCGGGCG CAGACCAATG
 697 MIT_Smik_c935_20455          +    122  5.29e-09 TAATGATCAG ACCAACAGTGATCTTGGCCG ACCAAAAGAC
 698 WashU_Skud_Contig2050.4      +    242  1.18e-07 TTCTCCTTCG TCGCAGAGAGCTCGCGGTAG CATTTCATTG
 699 WashU_Sbay_Contig480.2       +    282  2.27e-07 ATGCCTCTCG CCATGCAGGGCTTGCGGTCA TGTTTTCTAC
 700 --------------------------------------------------------------------------------
 701
 702 --------------------------------------------------------------------------------
 703         Motif 5 block diagrams
 704 --------------------------------------------------------------------------------
 705 SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
 706 -------------            ----------------  -------------
 707 MIT_Spar_c117_4603                3.1e-14  343_[+5]_135
 708 SGD_Scer_YDR232W                  3.1e-14  348_[+5]_130
 709 WashU_Skud_Contig2069.5           1.6e-12  345_[+5]_133
 710 MIT_Smik_c228_4055                1.4e-10  345_[+5]_133
 711 MIT_Spar_c278_20970               3.6e-09  125_[+5]_582
 712 SGD_Scer_YOR176W                  3.9e-09  123_[+5]_584
 713 WashU_Sbay_Contig461.5            4.9e-09  342_[+5]_136
 714 MIT_Smik_c935_20455               5.3e-09  121_[+5]_586
 715 WashU_Skud_Contig2050.4           1.2e-07  241_[+5]_466
 716 WashU_Sbay_Contig480.2            2.3e-07  281_[+5]_426
 717 --------------------------------------------------------------------------------
 718
 719 --------------------------------------------------------------------------------
 720         Motif 5 in BLOCKS format
 721 --------------------------------------------------------------------------------
 722 BL   MOTIF 5 width=20 seqs=10
 723 MIT_Spar_c117_4603       (  344) CCAAAAAGCGCCCGCGGCCG  1
 724 SGD_Scer_YDR232W         (  349) CCAAAAAGCGCCCGCGGCCG  1
 725 WashU_Skud_Contig2069.5  (  346) CCAAAAAGCGTCCGCGGCCG  1
 726 MIT_Smik_c228_4055       (  346) CCAAAAAGCGCCCGCAAGCG  1
 727 MIT_Spar_c278_20970      (  126) ACCAAGAGTGACCTTGACCG  1
 728 SGD_Scer_YOR176W         (  124) GCCAAGAGTGACCTTGACCG  1
 729 WashU_Sbay_Contig461.5   (  343) CAAAAAAACGCCGGCGGGCG  1
 730 MIT_Smik_c935_20455      (  122) ACCAACAGTGATCTTGGCCG  1
 731 WashU_Skud_Contig2050.4  (  242) TCGCAGAGAGCTCGCGGTAG  1
 732 WashU_Sbay_Contig480.2   (  282) CCATGCAGGGCTTGCGGTCA  1
 733 //
 734
 735 --------------------------------------------------------------------------------
 736
 737 --------------------------------------------------------------------------------
 738         Motif 5 position-specific scoring matrix
 739 --------------------------------------------------------------------------------
 740 log-odds matrix: alength= 4 w= 20 n= 5935 bayes= 9.21067 E= 9.3e-018
 741    -70    177    -81   -169
 742   -169    236   -997   -997
 743     89     77    -81   -997
 744    130    -81   -997   -169
 745    147   -997    -81   -997
 746     62     19     77   -997
 747    162   -997   -997   -997
 748   -169   -997    236   -997
 749   -169    151    -81    -11
 750   -997   -997    251   -997
 751    -11    177   -997   -169
 752   -997    199   -997    -11
 753   -997    219    -81   -169
 754   -997   -997    199    -11
 755   -997    199   -997    -11
 756   -169   -997    236   -997
 757    -11   -997    199   -997
 758   -997    177     19    -70
 759   -169    236   -997   -997
 760   -169   -997    236   -997
 761 --------------------------------------------------------------------------------
 762
 763 --------------------------------------------------------------------------------
 764         Motif 5 position-specific probability matrix
 765 --------------------------------------------------------------------------------
 766 letter-probability matrix: alength= 4 w= 20 nsites= 10 E= 9.3e-018
 767  0.200000  0.600000  0.100000  0.100000
 768  0.100000  0.900000  0.000000  0.000000
 769  0.600000  0.300000  0.100000  0.000000
 770  0.800000  0.100000  0.000000  0.100000
 771  0.900000  0.000000  0.100000  0.000000
 772  0.500000  0.200000  0.300000  0.000000
 773  1.000000  0.000000  0.000000  0.000000
 774  0.100000  0.000000  0.900000  0.000000
 775  0.100000  0.500000  0.100000  0.300000
 776  0.000000  0.000000  1.000000  0.000000
 777  0.300000  0.600000  0.000000  0.100000
 778  0.000000  0.700000  0.000000  0.300000
 779  0.000000  0.800000  0.100000  0.100000
 780  0.000000  0.000000  0.700000  0.300000
 781  0.000000  0.700000  0.000000  0.300000
 782  0.100000  0.000000  0.900000  0.000000
 783  0.300000  0.000000  0.700000  0.000000
 784  0.000000  0.600000  0.200000  0.200000
 785  0.100000  0.900000  0.000000  0.000000
 786  0.100000  0.000000  0.900000  0.000000
 787 --------------------------------------------------------------------------------
 788
 789 --------------------------------------------------------------------------------
 790         Motif 5 regular expression
 791 --------------------------------------------------------------------------------
 792 [CA]C[AC]AA[AGC]AG[CT]G[CA][CT]C[GT][CT]G[GA][CGT]CG
 793 --------------------------------------------------------------------------------
 794
 795
 796
 797
 798 Time 18.95 secs.
 799
 800 ********************************************************************************
 801
 802
 803 ********************************************************************************
 804 SUMMARY OF MOTIFS
 805 ********************************************************************************
 806
 807 --------------------------------------------------------------------------------
 808         Combined block diagrams: non-overlapping sites with p-value < 0.0001
 809 --------------------------------------------------------------------------------
 810 SEQUENCE NAME            COMBINED P-VALUE  MOTIF DIAGRAM
 811 -------------            ----------------  -------------
 812 SGD_Scer_YDR232W                 2.26e-35  131_[-2(4.87e-05)]_138_[-4(6.64e-13)]_5_[+2(4.12e-12)]_14_[+5(3.06e-14)]_5_[+1(4.19e-12)]_71_[-3(2.27e-08)]_14
 813 MIT_Spar_c117_4603               5.83e-36  284_[-4(6.64e-13)]_5_[+2(6.47e-12)]_14_[+5(3.06e-14)]_5_[+1(4.19e-12)]_68_[-3(3.51e-09)]_22
 814 MIT_Smik_c228_4055               1.73e-31  287_[-4(6.64e-13)]_4_[+2(4.12e-12)]_14_[+5(1.43e-10)]_5_[+1(6.28e-12)]_68_[-3(3.73e-08)]_20
 815 WashU_Skud_Contig2069.5          4.17e-31  264_[-3(3.20e-06)]_3_[-4(1.75e-10)]_5_[+2(8.03e-12)]_13_[+5(1.65e-12)]_5_[+1(4.19e-12)]_69_[-3(2.39e-08)]_19
 816 WashU_Sbay_Contig461.5           5.52e-28  168_[+1(4.58e-05)]_71_[-3(8.74e-09)]_3_[-4(6.64e-13)]_5_[+2(1.78e-10)]_15_[+5(4.91e-09)]_5_[+1(8.75e-11)]_111
 817 SGD_Scer_YOR176W                 6.45e-27  123_[+5(3.90e-09)]_13_[+2(7.23e-11)]_124_[+4(5.38e-08)]_81_[+3(6.18e-05)]_73_[+3(1.64e-12)]_39_[+1(3.36e-11)]_80_[-2(1.18e-05)]_54
 818 MIT_Spar_c278_20970              1.57e-29  125_[+5(3.60e-09)]_13_[+2(7.23e-11)]_123_[+4(3.17e-10)]_83_[+3(6.18e-05)]_72_[+3(1.95e-13)]_39_[+1(9.22e-11)]_128_[+3(8.37e-05)]_4
 819 MIT_Smik_c935_20455              6.31e-27  121_[+5(5.29e-09)]_12_[+2(7.23e-11)]_18_[-2(1.21e-05)]_86_[+4(3.30e-09)]_163_[+3(1.64e-12)]_39_[+1(3.96e-10)]_168
 820 WashU_Skud_Contig2050.4          1.40e-22  67_[-1(8.16e-05)]_4_[-2(9.76e-05)]_15_[+5(6.67e-06)]_10_[+2(2.43e-08)]_65_[+5(1.18e-07)]_46_[+4(1.63e-08)]_170_[+3(8.61e-12)]_44_[+1(8.33e-11)]_146
 821 WashU_Sbay_Contig480.2           5.90e-23  29_[-5(7.21e-05)]_121_[+5(9.26e-05)]_16_[+2(1.47e-09)]_55_[+5(2.27e-07)]_43_[+4(5.53e-08)]_142_[+3(8.61e-12)]_11_[-3(9.47e-05)]_9_[+1(8.33e-11)]_42_[-2(6.80e-06)]_14_[-4(5.59e-06)]_45
 822 --------------------------------------------------------------------------------
 823
 824 ********************************************************************************
 825
 826
 827 ********************************************************************************
 828 Stopped because nmotifs = 5 reached.
 829 ********************************************************************************
 830
 831 CPU: dhn02990.mrc-dunn.cam.ac.uk
 832
 833 ********************************************************************************