t/data/map_hem/HEM2-HEM4.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-HEM4.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_YOR278W         1.0000    635
  38 MIT_Spar_c261_21317      1.0000    635  MIT_Smik_c492_20940      1.0000    635
  39 WashU_Skud_Contig1682.4  1.0000    635  WashU_Sbay_Contig635.57  1.0000    635
  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-HEM4.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=            8175    N=              10
  59 strands: + -
  60 sample: seed=            0    seqfrac=         1
  61 Letter frequencies in dataset:
  62 A 0.324 C 0.176 G 0.176 T 0.324
  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 = 209   E-value = 6.2e-024
  70 ********************************************************************************
  71 --------------------------------------------------------------------------------
  72         Motif 1 Description
  73 --------------------------------------------------------------------------------
  74 Simplified        A  :aa:5a5:::a:::44:416
  75 pos.-specific     C  a:::5:5a:5:5a:169:::
  76 probability       G  ::::::::55:::5:::694
  77 matrix            T  :::a::::5::5:55:1:::
  78
  79          bits    2.5 *      *    *
  80                  2.3 *      *    *
  81                  2.0 *      *    *   * *
  82                  1.8 *      *    *   * *
  83 Information      1.5 **** * * ** *   * *
  84 content          1.3 **** * * ** *  ****
  85 (30.1 bits)      1.0 ************** *****
  86                  0.8 ************** *****
  87                  0.5 ************** *****
  88                  0.3 ********************
  89                  0.0 --------------------
  90
  91 Multilevel           CAATAAACGCACCGTCCGGA
  92 consensus                C C TG T TAA A G
  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 MIT_Sbay_c77_8808            +    187  6.45e-12 TGCCGCAGGC CAATCACCGCACCGCCCGGA GATGCTCGTT
 103 WashU_Skud_Contig2052.17     +    186  6.21e-11 TGCCTCAGGC CAATCACCGCACCGAACAGG GATTGCTCGT
 104 MIT_Spar_c19_8512            +    187  6.21e-11 TGCCTCAGGC CAATCACCGCACCGAACAGG GATTGCTCGT
 105 SGD_Scer_YGL040C             +    186  6.21e-11 TGCCTCAAGC CAATCACCGCACCGAACAGG GATTGCTCGT
 106 WashU_Sbay_Contig635.57      -    400  2.02e-10 AGCCATCATT CAATAAACTGATCTTCCGGA TTACCATGCT
 107 WashU_Skud_Contig1682.4      -    393  2.02e-10 AACCATCATT CAATAAACTGATCTTCCGGA TTACCATGCT
 108 MIT_Smik_c492_20940          -    398  2.02e-10 AACCATCATT CAATAAACTGATCTTCCGGA TTACCATGCT
 109 MIT_Spar_c261_21317          -    392  2.02e-10 AACCATCATT CAATAAACTGATCTTCCGGA TTACCATGCT
 110 SGD_Scer_YOR278W             -    389  2.02e-10 AACCATCATT CAATAAACTGATCTTCCGGA TTACCATGCT
 111 MIT_Smik_c273_7756           +    185  3.21e-09 TGCCTCAGGC CAATCACCGCACCGAATAAG GATTGCTCGT
 112 --------------------------------------------------------------------------------
 113
 114 --------------------------------------------------------------------------------
 115         Motif 1 block diagrams
 116 --------------------------------------------------------------------------------
 117 SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
 118 -------------            ----------------  -------------
 119 MIT_Sbay_c77_8808                 6.4e-12  186_[+1]_794
 120 WashU_Skud_Contig2052.17          6.2e-11  185_[+1]_795
 121 MIT_Spar_c19_8512                 6.2e-11  186_[+1]_794
 122 SGD_Scer_YGL040C                  6.2e-11  185_[+1]_795
 123 WashU_Sbay_Contig635.57             2e-10  399_[-1]_216
 124 WashU_Skud_Contig1682.4             2e-10  392_[-1]_223
 125 MIT_Smik_c492_20940                 2e-10  397_[-1]_218
 126 MIT_Spar_c261_21317                 2e-10  391_[-1]_224
 127 SGD_Scer_YOR278W                    2e-10  388_[-1]_227
 128 MIT_Smik_c273_7756                3.2e-09  184_[+1]_796
 129 --------------------------------------------------------------------------------
 130
 131 --------------------------------------------------------------------------------
 132         Motif 1 in BLOCKS format
 133 --------------------------------------------------------------------------------
 134 BL   MOTIF 1 width=20 seqs=10
 135 MIT_Sbay_c77_8808        (  187) CAATCACCGCACCGCCCGGA  1
 136 WashU_Skud_Contig2052.17 (  186) CAATCACCGCACCGAACAGG  1
 137 MIT_Spar_c19_8512        (  187) CAATCACCGCACCGAACAGG  1
 138 SGD_Scer_YGL040C         (  186) CAATCACCGCACCGAACAGG  1
 139 WashU_Sbay_Contig635.57  (  400) CAATAAACTGATCTTCCGGA  1
 140 WashU_Skud_Contig1682.4  (  393) CAATAAACTGATCTTCCGGA  1
 141 MIT_Smik_c492_20940      (  398) CAATAAACTGATCTTCCGGA  1
 142 MIT_Spar_c261_21317      (  392) CAATAAACTGATCTTCCGGA  1
 143 SGD_Scer_YOR278W         (  389) CAATAAACTGATCTTCCGGA  1
 144 MIT_Smik_c273_7756       (  185) CAATCACCGCACCGAATAAG  1
 145 //
 146
 147 --------------------------------------------------------------------------------
 148
 149 --------------------------------------------------------------------------------
 150         Motif 1 position-specific scoring matrix
 151 --------------------------------------------------------------------------------
 152 log-odds matrix: alength= 4 w= 20 n= 7985 bayes= 9.63934 E= 6.2e-024
 153   -997    251   -997   -997
 154    162   -997   -997   -997
 155    162   -997   -997   -997
 156   -997   -997   -997    162
 157     62    151   -997   -997
 158    162   -997   -997   -997
 159     62    151   -997   -997
 160   -997    251   -997   -997
 161   -997   -997    151     62
 162   -997    151    151   -997
 163    162   -997   -997   -997
 164   -997    151   -997     62
 165   -997    251   -997   -997
 166   -997   -997    151     62
 167     30    -81   -997     62
 168     30    177   -997   -997
 169   -997    236   -997   -169
 170     30   -997    177   -997
 171   -169   -997    236   -997
 172     89   -997    119   -997
 173 --------------------------------------------------------------------------------
 174
 175 --------------------------------------------------------------------------------
 176         Motif 1 position-specific probability matrix
 177 --------------------------------------------------------------------------------
 178 letter-probability matrix: alength= 4 w= 20 nsites= 10 E= 6.2e-024
 179  0.000000  1.000000  0.000000  0.000000
 180  1.000000  0.000000  0.000000  0.000000
 181  1.000000  0.000000  0.000000  0.000000
 182  0.000000  0.000000  0.000000  1.000000
 183  0.500000  0.500000  0.000000  0.000000
 184  1.000000  0.000000  0.000000  0.000000
 185  0.500000  0.500000  0.000000  0.000000
 186  0.000000  1.000000  0.000000  0.000000
 187  0.000000  0.000000  0.500000  0.500000
 188  0.000000  0.500000  0.500000  0.000000
 189  1.000000  0.000000  0.000000  0.000000
 190  0.000000  0.500000  0.000000  0.500000
 191  0.000000  1.000000  0.000000  0.000000
 192  0.000000  0.000000  0.500000  0.500000
 193  0.400000  0.100000  0.000000  0.500000
 194  0.400000  0.600000  0.000000  0.000000
 195  0.000000  0.900000  0.000000  0.100000
 196  0.400000  0.000000  0.600000  0.000000
 197  0.100000  0.000000  0.900000  0.000000
 198  0.600000  0.000000  0.400000  0.000000
 199 --------------------------------------------------------------------------------
 200
 201 --------------------------------------------------------------------------------
 202         Motif 1 regular expression
 203 --------------------------------------------------------------------------------
 204 CAAT[AC]A[AC]C[GT][CG]A[CT]C[GT][TA][CA]C[GA]G[AG]
 205 --------------------------------------------------------------------------------
 206
 207
 208
 209
 210 Time  6.87 secs.
 211
 212 ********************************************************************************
 213
 214
 215 ********************************************************************************
 216 MOTIF  2        width =   15   sites =  10   llr = 166   E-value = 1.6e-014
 217 ********************************************************************************
 218 --------------------------------------------------------------------------------
 219         Motif 2 Description
 220 --------------------------------------------------------------------------------
 221 Simplified        A  7:51a::5::::::5
 222 pos.-specific     C  :::8::915:aa:a5
 223 probability       G  395::41::a::1::
 224 matrix            T  :1:1:6:45:::9::
 225
 226          bits    2.5          *** *
 227                  2.3          *** *
 228                  2.0  *    *  *** *
 229                  1.8  *    *  *** *
 230 Information      1.5  * ** *  *** *
 231 content          1.3  * ** *  *****
 232 (23.9 bits)      1.0 ******* *******
 233                  0.8 ******* *******
 234                  0.5 ******* *******
 235                  0.3 ***************
 236                  0.0 ---------------
 237
 238 Multilevel           AGACATCACGCCTCA
 239 consensus            G G  G TT     C
 240 sequence
 241
 242 --------------------------------------------------------------------------------
 243
 244 --------------------------------------------------------------------------------
 245         Motif 2 sites sorted by position p-value
 246 --------------------------------------------------------------------------------
 247 Sequence name            Strand  Start   P-value                 Site
 248 -------------            ------  ----- ---------            ---------------
 249 WashU_Sbay_Contig635.57      -    373  1.33e-09 ACCATGCTTA AGACATCACGCCTCC ATATGTCTAT
 250 WashU_Skud_Contig1682.4      -    366  1.33e-09 ACCATGCTTA AGACATCACGCCTCC ATATGTCTAT
 251 MIT_Smik_c492_20940          -    371  1.33e-09 ACCATGCTTA AGACATCACGCCTCC ATATGTCTAT
 252 MIT_Spar_c261_21317          -    365  1.33e-09 ACCATGCTTA AGACATCACGCCTCC ATATGTCTAT
 253 SGD_Scer_YOR278W             -    362  1.33e-09 ACCATGCTTA AGACATCACGCCTCC ATATGTCTAT
 254 WashU_Skud_Contig2052.17     +    168  5.67e-09 TAAATTGGGC AGGCAGCTTGCCTCA GGCCAATCAC
 255 MIT_Spar_c19_8512            +    169  7.74e-09 TAAATCAAGC GGGCAGCTTGCCTCA GGCCAATCAC
 256 MIT_Sbay_c77_8808            +    169  4.53e-08 TTTATAAATC AGGCAGCCTGCCGCA GGCCAATCAC
 257 SGD_Scer_YGL040C             +    168  7.07e-08 TAAATCAAGC GGGAAGCTTGCCTCA AGCCAATCAC
 258 MIT_Smik_c273_7756           +    167  6.43e-07 TAAATCAAGA GTGTATGTTGCCTCA GGCCAATCAC
 259 --------------------------------------------------------------------------------
 260
 261 --------------------------------------------------------------------------------
 262         Motif 2 block diagrams
 263 --------------------------------------------------------------------------------
 264 SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
 265 -------------            ----------------  -------------
 266 WashU_Sbay_Contig635.57           1.3e-09  372_[-2]_248
 267 WashU_Skud_Contig1682.4           1.3e-09  365_[-2]_255
 268 MIT_Smik_c492_20940               1.3e-09  370_[-2]_250
 269 MIT_Spar_c261_21317               1.3e-09  364_[-2]_256
 270 SGD_Scer_YOR278W                  1.3e-09  361_[-2]_259
 271 WashU_Skud_Contig2052.17          5.7e-09  167_[+2]_818
 272 MIT_Spar_c19_8512                 7.7e-09  168_[+2]_817
 273 MIT_Sbay_c77_8808                 4.5e-08  168_[+2]_817
 274 SGD_Scer_YGL040C                  7.1e-08  167_[+2]_818
 275 MIT_Smik_c273_7756                6.4e-07  166_[+2]_819
 276 --------------------------------------------------------------------------------
 277
 278 --------------------------------------------------------------------------------
 279         Motif 2 in BLOCKS format
 280 --------------------------------------------------------------------------------
 281 BL   MOTIF 2 width=15 seqs=10
 282 WashU_Sbay_Contig635.57  (  373) AGACATCACGCCTCC  1
 283 WashU_Skud_Contig1682.4  (  366) AGACATCACGCCTCC  1
 284 MIT_Smik_c492_20940      (  371) AGACATCACGCCTCC  1
 285 MIT_Spar_c261_21317      (  365) AGACATCACGCCTCC  1
 286 SGD_Scer_YOR278W         (  362) AGACATCACGCCTCC  1
 287 WashU_Skud_Contig2052.17 (  168) AGGCAGCTTGCCTCA  1
 288 MIT_Spar_c19_8512        (  169) GGGCAGCTTGCCTCA  1
 289 MIT_Sbay_c77_8808        (  169) AGGCAGCCTGCCGCA  1
 290 SGD_Scer_YGL040C         (  168) GGGAAGCTTGCCTCA  1
 291 MIT_Smik_c273_7756       (  167) GTGTATGTTGCCTCA  1
 292 //
 293
 294 --------------------------------------------------------------------------------
 295
 296 --------------------------------------------------------------------------------
 297         Motif 2 position-specific scoring matrix
 298 --------------------------------------------------------------------------------
 299 log-odds matrix: alength= 4 w= 15 n= 8035 bayes= 9.64836 E= 1.6e-014
 300    111   -997     77   -997
 301   -997   -997    236   -169
 302     62   -997    151   -997
 303   -169    219   -997   -169
 304    162   -997   -997   -997
 305   -997   -997    119     89
 306   -997    236    -81   -997
 307     62    -81   -997     30
 308   -997    151   -997     62
 309   -997   -997    251   -997
 310   -997    251   -997   -997
 311   -997    251   -997   -997
 312   -997   -997    -81    147
 313   -997    251   -997   -997
 314     62    151   -997   -997
 315 --------------------------------------------------------------------------------
 316
 317 --------------------------------------------------------------------------------
 318         Motif 2 position-specific probability matrix
 319 --------------------------------------------------------------------------------
 320 letter-probability matrix: alength= 4 w= 15 nsites= 10 E= 1.6e-014
 321  0.700000  0.000000  0.300000  0.000000
 322  0.000000  0.000000  0.900000  0.100000
 323  0.500000  0.000000  0.500000  0.000000
 324  0.100000  0.800000  0.000000  0.100000
 325  1.000000  0.000000  0.000000  0.000000
 326  0.000000  0.000000  0.400000  0.600000
 327  0.000000  0.900000  0.100000  0.000000
 328  0.500000  0.100000  0.000000  0.400000
 329  0.000000  0.500000  0.000000  0.500000
 330  0.000000  0.000000  1.000000  0.000000
 331  0.000000  1.000000  0.000000  0.000000
 332  0.000000  1.000000  0.000000  0.000000
 333  0.000000  0.000000  0.100000  0.900000
 334  0.000000  1.000000  0.000000  0.000000
 335  0.500000  0.500000  0.000000  0.000000
 336 --------------------------------------------------------------------------------
 337
 338 --------------------------------------------------------------------------------
 339         Motif 2 regular expression
 340 --------------------------------------------------------------------------------
 341 [AG]G[AG]CA[TG]C[AT][CT]GCCTC[AC]
 342 --------------------------------------------------------------------------------
 343
 344
 345
 346
 347 Time 13.73 secs.
 348
 349 ********************************************************************************
 350
 351
 352 ********************************************************************************
 353 MOTIF  3        width =   20   sites =  10   llr = 189   E-value = 4.3e-016
 354 ********************************************************************************
 355 --------------------------------------------------------------------------------
 356         Motif 3 Description
 357 --------------------------------------------------------------------------------
 358 Simplified        A  :a1:1a:71::7:911596:
 359 pos.-specific     C  1:1:::5:7a:::::6:::7
 360 probability       G  :::a4::1:::3a191514:
 361 matrix            T  9:8:5:522:a::::2:::3
 362
 363          bits    2.5    *     *  *
 364                  2.3    *     *  *
 365                  2.0    *     *  * *
 366                  1.8    *     *  * *
 367 Information      1.5  * * *   ** * *
 368 content          1.3 ** * *   ** ***  * *
 369 (27.3 bits)      1.0 ** * ** ******* ****
 370                  0.8 **** ** ************
 371                  0.5 ********************
 372                  0.3 ********************
 373                  0.0 --------------------
 374
 375 Multilevel           TATGTACACCTAGAGCAAAC
 376 consensus                G TTT  G   TG GT
 377 sequence
 378
 379 --------------------------------------------------------------------------------
 380
 381 --------------------------------------------------------------------------------
 382         Motif 3 sites sorted by position p-value
 383 --------------------------------------------------------------------------------
 384 Sequence name            Strand  Start   P-value                    Site
 385 -------------            ------  ----- ---------            --------------------
 386 WashU_Skud_Contig1682.4      +    225  1.88e-12 GAAGTAGAGA TATGTACACCTAGAGCGAAC CAATGATAAT
 387 MIT_Smik_c492_20940          +    228  1.88e-12 GAAGTGAAGA TATGTACACCTAGAGCGAAC CAATAATAAT
 388 MIT_Spar_c261_21317          +    223  1.88e-12 ACAAAATGAA TATGTACACCTAGAGCGAAC CAATGATAAT
 389 SGD_Scer_YOR278W             +    219  1.88e-12 GAAGTGAAGA TATGTACACCTAGAGCGAAC CAATGATAAT
 390 WashU_Sbay_Contig635.57      +    231  4.24e-11 GTAAAAAAAA CATGTACACCTAGAGCGAAC CAGTGATAAT
 391 MIT_Spar_c19_8512            +     21  3.25e-09 ATATTCTAAA TATGGATTCCTAGGGCAGGC AATAATATGG
 392 WashU_Skud_Contig2052.17     +     21  7.96e-09 TGTTTTCTGA TATGGATGCCTGGAGAAAAT ATTAATATGT
 393 MIT_Smik_c273_7756           +     21  1.42e-08 GTTTTCTTAA TACGGATATCTAGAGTAAGT CACAATTTAA
 394 SGD_Scer_YGL040C             +     21  2.94e-08 ATTTTCTAGG TATGAATTACTGGAGTAAGC AATAATATGA
 395 MIT_Sbay_c77_8808            +     22  8.75e-08 GTTTTTCTGG TAAGGATATCTGGAAGAAGT AACAATACGT
 396 --------------------------------------------------------------------------------
 397
 398 --------------------------------------------------------------------------------
 399         Motif 3 block diagrams
 400 --------------------------------------------------------------------------------
 401 SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
 402 -------------            ----------------  -------------
 403 WashU_Skud_Contig1682.4           1.9e-12  224_[+3]_391
 404 MIT_Smik_c492_20940               1.9e-12  227_[+3]_388
 405 MIT_Spar_c261_21317               1.9e-12  222_[+3]_393
 406 SGD_Scer_YOR278W                  1.9e-12  218_[+3]_397
 407 WashU_Sbay_Contig635.57           4.2e-11  230_[+3]_385
 408 MIT_Spar_c19_8512                 3.2e-09  20_[+3]_960
 409 WashU_Skud_Contig2052.17            8e-09  20_[+3]_960
 410 MIT_Smik_c273_7756                1.4e-08  20_[+3]_960
 411 SGD_Scer_YGL040C                  2.9e-08  20_[+3]_960
 412 MIT_Sbay_c77_8808                 8.8e-08  21_[+3]_959
 413 --------------------------------------------------------------------------------
 414
 415 --------------------------------------------------------------------------------
 416         Motif 3 in BLOCKS format
 417 --------------------------------------------------------------------------------
 418 BL   MOTIF 3 width=20 seqs=10
 419 WashU_Skud_Contig1682.4  (  225) TATGTACACCTAGAGCGAAC  1
 420 MIT_Smik_c492_20940      (  228) TATGTACACCTAGAGCGAAC  1
 421 MIT_Spar_c261_21317      (  223) TATGTACACCTAGAGCGAAC  1
 422 SGD_Scer_YOR278W         (  219) TATGTACACCTAGAGCGAAC  1
 423 WashU_Sbay_Contig635.57  (  231) CATGTACACCTAGAGCGAAC  1
 424 MIT_Spar_c19_8512        (   21) TATGGATTCCTAGGGCAGGC  1
 425 WashU_Skud_Contig2052.17 (   21) TATGGATGCCTGGAGAAAAT  1
 426 MIT_Smik_c273_7756       (   21) TACGGATATCTAGAGTAAGT  1
 427 SGD_Scer_YGL040C         (   21) TATGAATTACTGGAGTAAGC  1
 428 MIT_Sbay_c77_8808        (   22) TAAGGATATCTGGAAGAAGT  1
 429 //
 430
 431 --------------------------------------------------------------------------------
 432
 433 --------------------------------------------------------------------------------
 434         Motif 3 position-specific scoring matrix
 435 --------------------------------------------------------------------------------
 436 log-odds matrix: alength= 4 w= 20 n= 7985 bayes= 9.63934 E= 4.3e-016
 437   -997    -81   -997    147
 438    162   -997   -997   -997
 439   -169    -81   -997    130
 440   -997   -997    251   -997
 441   -169   -997    119     62
 442    162   -997   -997   -997
 443   -997    151   -997     62
 444    111   -997    -81    -70
 445   -169    199   -997    -70
 446   -997    251   -997   -997
 447   -997   -997   -997    162
 448    111   -997     77   -997
 449   -997   -997    251   -997
 450    147   -997    -81   -997
 451   -169   -997    236   -997
 452   -169    177    -81    -70
 453     62   -997    151   -997
 454    147   -997    -81   -997
 455     89   -997    119   -997
 456   -997    199   -997    -11
 457 --------------------------------------------------------------------------------
 458
 459 --------------------------------------------------------------------------------
 460         Motif 3 position-specific probability matrix
 461 --------------------------------------------------------------------------------
 462 letter-probability matrix: alength= 4 w= 20 nsites= 10 E= 4.3e-016
 463  0.000000  0.100000  0.000000  0.900000
 464  1.000000  0.000000  0.000000  0.000000
 465  0.100000  0.100000  0.000000  0.800000
 466  0.000000  0.000000  1.000000  0.000000
 467  0.100000  0.000000  0.400000  0.500000
 468  1.000000  0.000000  0.000000  0.000000
 469  0.000000  0.500000  0.000000  0.500000
 470  0.700000  0.000000  0.100000  0.200000
 471  0.100000  0.700000  0.000000  0.200000
 472  0.000000  1.000000  0.000000  0.000000
 473  0.000000  0.000000  0.000000  1.000000
 474  0.700000  0.000000  0.300000  0.000000
 475  0.000000  0.000000  1.000000  0.000000
 476  0.900000  0.000000  0.100000  0.000000
 477  0.100000  0.000000  0.900000  0.000000
 478  0.100000  0.600000  0.100000  0.200000
 479  0.500000  0.000000  0.500000  0.000000
 480  0.900000  0.000000  0.100000  0.000000
 481  0.600000  0.000000  0.400000  0.000000
 482  0.000000  0.700000  0.000000  0.300000
 483 --------------------------------------------------------------------------------
 484
 485 --------------------------------------------------------------------------------
 486         Motif 3 regular expression
 487 --------------------------------------------------------------------------------
 488 TATG[TG]A[CT][AT][CT]CT[AG]GAG[CT][AG]A[AG][CT]
 489 --------------------------------------------------------------------------------
 490
 491
 492
 493
 494 Time 20.40 secs.
 495
 496 ********************************************************************************
 497
 498
 499 ********************************************************************************
 500 MOTIF  4        width =   20   sites =  10   llr = 176   E-value = 2.5e-011
 501 ********************************************************************************
 502 --------------------------------------------------------------------------------
 503         Motif 4 Description
 504 --------------------------------------------------------------------------------
 505 Simplified        A  ::6:11::72::7::1:::2
 506 pos.-specific     C  a:19::882:68::::29:6
 507 probability       G  ::::1:11:62:1:126192
 508 matrix            T  :a31891112222a972:1:
 509
 510          bits    2.5 *
 511                  2.3 *
 512                  2.0 *  *             **
 513                  1.8 *  *             **
 514 Information      1.5 ** *  **   * *   **
 515 content          1.3 ** * ***   * **  **
 516 (25.4 bits)      1.0 ** * ***  ** ** ****
 517                  0.8 ** ********* *******
 518                  0.5 ********************
 519                  0.3 ********************
 520                  0.0 --------------------
 521
 522 Multilevel           CTACTTCCAGCCATTTGCGC
 523 consensus              T     CAGTT  GC  A
 524 sequence                      TT     T  G
 525
 526 --------------------------------------------------------------------------------
 527
 528 --------------------------------------------------------------------------------
 529         Motif 4 sites sorted by position p-value
 530 --------------------------------------------------------------------------------
 531 Sequence name            Strand  Start   P-value                    Site
 532 -------------            ------  ----- ---------            --------------------
 533 WashU_Sbay_Contig635.57      +    338  1.95e-13 AGAAATTGGT CTACTTCCAGCCATTTGCGC TTGACATAGA
 534 WashU_Skud_Contig1682.4      +    331  1.95e-13 AGAGATTGGT CTACTTCCAGCCATTTGCGC TTTACATAGA
 535 MIT_Smik_c492_20940          +    336  1.95e-13 AGAAATTTGT CTACTTCCAGCCATTTGCGC TTTATATAGA
 536 MIT_Spar_c261_21317          +    330  1.95e-13 AAAAATTGGT CTACTTCCAGCCATTTGCGC TTTATATAGA
 537 SGD_Scer_YOR278W             +    327  1.95e-13 AAAAATTGGT CTACTTCCAGCCATTTGCGC TTTATATAGA
 538 SGD_Scer_YGL040C             +    444  9.32e-08 ACGTGTACGC CTTCTTCCCTTCTTTGCCTC TTGTGCCACT
 539 MIT_Smik_c273_7756           +    243  2.84e-07 TTTTTTTCAT CTTCTACCAATTTTTTTCGG CAGCGCCTTT
 540 WashU_Skud_Contig2052.17     -    956  5.15e-07 TGTAGTTTTC CTTCGTTCAGCCATGACGGA AACTACATAA
 541 MIT_Spar_c19_8512            -    872  8.90e-07 TCATTAACCT CTCCATCTTTGTATTGGCGG TACGACATAT
 542 MIT_Sbay_c77_8808            +    255  1.31e-06 TTGCCTTTTT CTATTTGGCAGCGTTTTCGA AAAATTTTGA
 543 --------------------------------------------------------------------------------
 544
 545 --------------------------------------------------------------------------------
 546         Motif 4 block diagrams
 547 --------------------------------------------------------------------------------
 548 SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
 549 -------------            ----------------  -------------
 550 WashU_Sbay_Contig635.57           1.9e-13  337_[+4]_278
 551 WashU_Skud_Contig1682.4           1.9e-13  330_[+4]_285
 552 MIT_Smik_c492_20940               1.9e-13  335_[+4]_280
 553 MIT_Spar_c261_21317               1.9e-13  329_[+4]_286
 554 SGD_Scer_YOR278W                  1.9e-13  326_[+4]_289
 555 SGD_Scer_YGL040C                  9.3e-08  443_[+4]_537
 556 MIT_Smik_c273_7756                2.8e-07  242_[+4]_738
 557 WashU_Skud_Contig2052.17          5.1e-07  955_[-4]_25
 558 MIT_Spar_c19_8512                 8.9e-07  871_[-4]_109
 559 MIT_Sbay_c77_8808                 1.3e-06  254_[+4]_726
 560 --------------------------------------------------------------------------------
 561
 562 --------------------------------------------------------------------------------
 563         Motif 4 in BLOCKS format
 564 --------------------------------------------------------------------------------
 565 BL   MOTIF 4 width=20 seqs=10
 566 WashU_Sbay_Contig635.57  (  338) CTACTTCCAGCCATTTGCGC  1
 567 WashU_Skud_Contig1682.4  (  331) CTACTTCCAGCCATTTGCGC  1
 568 MIT_Smik_c492_20940      (  336) CTACTTCCAGCCATTTGCGC  1
 569 MIT_Spar_c261_21317      (  330) CTACTTCCAGCCATTTGCGC  1
 570 SGD_Scer_YOR278W         (  327) CTACTTCCAGCCATTTGCGC  1
 571 SGD_Scer_YGL040C         (  444) CTTCTTCCCTTCTTTGCCTC  1
 572 MIT_Smik_c273_7756       (  243) CTTCTACCAATTTTTTTCGG  1
 573 WashU_Skud_Contig2052.17 (  956) CTTCGTTCAGCCATGACGGA  1
 574 MIT_Spar_c19_8512        (  872) CTCCATCTTTGTATTGGCGG  1
 575 MIT_Sbay_c77_8808        (  255) CTATTTGGCAGCGTTTTCGA  1
 576 //
 577
 578 --------------------------------------------------------------------------------
 579
 580 --------------------------------------------------------------------------------
 581         Motif 4 position-specific scoring matrix
 582 --------------------------------------------------------------------------------
 583 log-odds matrix: alength= 4 w= 20 n= 7985 bayes= 9.63934 E= 2.5e-011
 584   -997    251   -997   -997
 585   -997   -997   -997    162
 586     89    -81   -997    -11
 587   -997    236   -997   -169
 588   -169   -997    -81    130
 589   -169   -997   -997    147
 590   -997    219    -81   -169
 591   -997    219    -81   -169
 592    111     19   -997   -169
 593    -70   -997    177    -70
 594   -997    177     19    -70
 595   -997    219   -997    -70
 596    111   -997    -81    -70
 597   -997   -997   -997    162
 598   -997   -997    -81    147
 599   -169   -997     19    111
 600   -997     19    177    -70
 601   -997    236    -81   -997
 602   -997   -997    236   -169
 603    -70    177     19   -997
 604 --------------------------------------------------------------------------------
 605
 606 --------------------------------------------------------------------------------
 607         Motif 4 position-specific probability matrix
 608 --------------------------------------------------------------------------------
 609 letter-probability matrix: alength= 4 w= 20 nsites= 10 E= 2.5e-011
 610  0.000000  1.000000  0.000000  0.000000
 611  0.000000  0.000000  0.000000  1.000000
 612  0.600000  0.100000  0.000000  0.300000
 613  0.000000  0.900000  0.000000  0.100000
 614  0.100000  0.000000  0.100000  0.800000
 615  0.100000  0.000000  0.000000  0.900000
 616  0.000000  0.800000  0.100000  0.100000
 617  0.000000  0.800000  0.100000  0.100000
 618  0.700000  0.200000  0.000000  0.100000
 619  0.200000  0.000000  0.600000  0.200000
 620  0.000000  0.600000  0.200000  0.200000
 621  0.000000  0.800000  0.000000  0.200000
 622  0.700000  0.000000  0.100000  0.200000
 623  0.000000  0.000000  0.000000  1.000000
 624  0.000000  0.000000  0.100000  0.900000
 625  0.100000  0.000000  0.200000  0.700000
 626  0.000000  0.200000  0.600000  0.200000
 627  0.000000  0.900000  0.100000  0.000000
 628  0.000000  0.000000  0.900000  0.100000
 629  0.200000  0.600000  0.200000  0.000000
 630 --------------------------------------------------------------------------------
 631
 632 --------------------------------------------------------------------------------
 633         Motif 4 regular expression
 634 --------------------------------------------------------------------------------
 635 CT[AT]CTTCC[AC][GAT][CGT][CT][AT]TT[TG][GCT]CG[CAG]
 636 --------------------------------------------------------------------------------
 637
 638
 639
 640
 641 Time 26.90 secs.
 642
 643 ********************************************************************************
 644
 645
 646 ********************************************************************************
 647 MOTIF  5        width =   20   sites =  10   llr = 171   E-value = 2.2e-009
 648 ********************************************************************************
 649 --------------------------------------------------------------------------------
 650         Motif 5 Description
 651 --------------------------------------------------------------------------------
 652 Simplified        A  8a327aaa21:71:9a1987
 653 pos.-specific     C  1::::::::8::::1:6:12
 654 probability       G  ::18::::81:269::1111
 655 matrix            T  1:6:3:::::a131::2:::
 656
 657          bits    2.5
 658                  2.3
 659                  2.0              *
 660                  1.8              *
 661 Information      1.5  * * ******  * *
 662 content          1.3  * * ******  *** *
 663 (24.6 bits)      1.0  * * ******  *** **
 664                  0.8 ** *****************
 665                  0.5 ********************
 666                  0.3 ********************
 667                  0.0 --------------------
 668
 669 Multilevel           AATGAAAAGCTAGGAACAAA
 670 consensus              AAT   A  GT   T  C
 671 sequence
 672
 673 --------------------------------------------------------------------------------
 674
 675 --------------------------------------------------------------------------------
 676         Motif 5 sites sorted by position p-value
 677 --------------------------------------------------------------------------------
 678 Sequence name            Strand  Start   P-value                    Site
 679 -------------            ------  ----- ---------            --------------------
 680 MIT_Smik_c492_20940          +    306  4.19e-12 AGATTTCAAT AATGAAAAGCTAGGAACAAA AGAAATTTGT
 681 SGD_Scer_YOR278W             +    297  4.19e-12 AGATTTCAAT AATGAAAAGCTAGGAACAAA AAAAATTGGT
 682 WashU_Sbay_Contig635.57      +    309  1.29e-11 AGATTTCATT AAAGAAAAGCTAGGAACAAA GAAATTGGTC
 683 MIT_Spar_c261_21317          +    301  4.20e-11 AGATTTCAAT AATGAAAAGCTAGGAACAGA AAAATTGGTC
 684 WashU_Skud_Contig1682.4      +    301  6.30e-11 AGATTTCAAT AATGAAAAGCTAGGAATAAA AGAGATTGGT
 685 MIT_Sbay_c77_8808            +    327  4.84e-08 TTAGGGCACG CAGGTAAAGATATGAACAAA TCATATTGAT
 686 MIT_Spar_c19_8512            +    700  7.12e-08 TTCTTGATTG AAAATAAAGCTGTGAAGAAC TAAATAATAA
 687 WashU_Skud_Contig2052.17     -    224  8.93e-08 TGATGCGGAA AATGAAAAACTTTGAACGCA ACGGGTAAAC
 688 SGD_Scer_YGL040C             +    692  5.38e-07 TGTGCGAATT AAAGTAAAGCTAATCAAAAC TAAACAATAA
 689 MIT_Smik_c273_7756           -    444  7.12e-07 TAACGATAAC TATAAAAAAGTGGGAATAAG ATATACACAT
 690 --------------------------------------------------------------------------------
 691
 692 --------------------------------------------------------------------------------
 693         Motif 5 block diagrams
 694 --------------------------------------------------------------------------------
 695 SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
 696 -------------            ----------------  -------------
 697 MIT_Smik_c492_20940               4.2e-12  305_[+5]_310
 698 SGD_Scer_YOR278W                  4.2e-12  296_[+5]_319
 699 WashU_Sbay_Contig635.57           1.3e-11  308_[+5]_307
 700 MIT_Spar_c261_21317               4.2e-11  300_[+5]_315
 701 WashU_Skud_Contig1682.4           6.3e-11  300_[+5]_315
 702 MIT_Sbay_c77_8808                 4.8e-08  326_[+5]_654
 703 MIT_Spar_c19_8512                 7.1e-08  699_[+5]_281
 704 WashU_Skud_Contig2052.17          8.9e-08  223_[-5]_757
 705 SGD_Scer_YGL040C                  5.4e-07  691_[+5]_289
 706 MIT_Smik_c273_7756                7.1e-07  443_[-5]_537
 707 --------------------------------------------------------------------------------
 708
 709 --------------------------------------------------------------------------------
 710         Motif 5 in BLOCKS format
 711 --------------------------------------------------------------------------------
 712 BL   MOTIF 5 width=20 seqs=10
 713 MIT_Smik_c492_20940      (  306) AATGAAAAGCTAGGAACAAA  1
 714 SGD_Scer_YOR278W         (  297) AATGAAAAGCTAGGAACAAA  1
 715 WashU_Sbay_Contig635.57  (  309) AAAGAAAAGCTAGGAACAAA  1
 716 MIT_Spar_c261_21317      (  301) AATGAAAAGCTAGGAACAGA  1
 717 WashU_Skud_Contig1682.4  (  301) AATGAAAAGCTAGGAATAAA  1
 718 MIT_Sbay_c77_8808        (  327) CAGGTAAAGATATGAACAAA  1
 719 MIT_Spar_c19_8512        (  700) AAAATAAAGCTGTGAAGAAC  1
 720 WashU_Skud_Contig2052.17 (  224) AATGAAAAACTTTGAACGCA  1
 721 SGD_Scer_YGL040C         (  692) AAAGTAAAGCTAATCAAAAC  1
 722 MIT_Smik_c273_7756       (  444) TATAAAAAAGTGGGAATAAG  1
 723 //
 724
 725 --------------------------------------------------------------------------------
 726
 727 --------------------------------------------------------------------------------
 728         Motif 5 position-specific scoring matrix
 729 --------------------------------------------------------------------------------
 730 log-odds matrix: alength= 4 w= 20 n= 7985 bayes= 9.63934 E= 2.2e-009
 731    130    -81   -997   -169
 732    162   -997   -997   -997
 733    -11   -997    -81     89
 734    -70   -997    219   -997
 735    111   -997   -997    -11
 736    162   -997   -997   -997
 737    162   -997   -997   -997
 738    162   -997   -997   -997
 739    -70   -997    219   -997
 740   -169    219    -81   -997
 741   -997   -997   -997    162
 742    111   -997     19   -169
 743   -169   -997    177    -11
 744   -997   -997    236   -169
 745    147    -81   -997   -997
 746    162   -997   -997   -997
 747   -169    177    -81    -70
 748    147   -997    -81   -997
 749    130    -81    -81   -997
 750    111     19    -81   -997
 751 --------------------------------------------------------------------------------
 752
 753 --------------------------------------------------------------------------------
 754         Motif 5 position-specific probability matrix
 755 --------------------------------------------------------------------------------
 756 letter-probability matrix: alength= 4 w= 20 nsites= 10 E= 2.2e-009
 757  0.800000  0.100000  0.000000  0.100000
 758  1.000000  0.000000  0.000000  0.000000
 759  0.300000  0.000000  0.100000  0.600000
 760  0.200000  0.000000  0.800000  0.000000
 761  0.700000  0.000000  0.000000  0.300000
 762  1.000000  0.000000  0.000000  0.000000
 763  1.000000  0.000000  0.000000  0.000000
 764  1.000000  0.000000  0.000000  0.000000
 765  0.200000  0.000000  0.800000  0.000000
 766  0.100000  0.800000  0.100000  0.000000
 767  0.000000  0.000000  0.000000  1.000000
 768  0.700000  0.000000  0.200000  0.100000
 769  0.100000  0.000000  0.600000  0.300000
 770  0.000000  0.000000  0.900000  0.100000
 771  0.900000  0.100000  0.000000  0.000000
 772  1.000000  0.000000  0.000000  0.000000
 773  0.100000  0.600000  0.100000  0.200000
 774  0.900000  0.000000  0.100000  0.000000
 775  0.800000  0.100000  0.100000  0.000000
 776  0.700000  0.200000  0.100000  0.000000
 777 --------------------------------------------------------------------------------
 778
 779 --------------------------------------------------------------------------------
 780         Motif 5 regular expression
 781 --------------------------------------------------------------------------------
 782 AA[TA][GA][AT]AAA[GA]CT[AG][GT]GAA[CT]AA[AC]
 783 --------------------------------------------------------------------------------
 784
 785
 786
 787
 788 Time 33.38 secs.
 789
 790 ********************************************************************************
 791
 792
 793 ********************************************************************************
 794 SUMMARY OF MOTIFS
 795 ********************************************************************************
 796
 797 --------------------------------------------------------------------------------
 798         Combined block diagrams: non-overlapping sites with p-value < 0.0001
 799 --------------------------------------------------------------------------------
 800 SEQUENCE NAME            COMBINED P-VALUE  MOTIF DIAGRAM
 801 -------------            ----------------  -------------
 802 SGD_Scer_YGL040C                 5.35e-17  20_[+3(2.94e-08)]_127_[+2(7.07e-08)]_3_[+1(6.21e-11)]_36_[-5(4.31e-05)]_84_[-4(9.17e-05)]_78_[+4(9.32e-08)]_228_[+5(5.38e-07)]_41_[-2(3.82e-05)]_74_[-3(7.54e-05)]_139
 803 MIT_Spar_c19_8512                1.12e-18  20_[+3(3.25e-09)]_128_[+2(7.74e-09)]_3_[+1(6.21e-11)]_37_[-5(8.15e-05)]_436_[+5(7.12e-08)]_152_[-4(8.90e-07)]_109
 804 MIT_Smik_c273_7756               2.75e-14  20_[+3(1.42e-08)]_126_[+2(6.43e-07)]_3_[+1(3.21e-09)]_38_[+4(2.84e-07)]_181_[-5(7.12e-07)]_537
 805 MIT_Sbay_c77_8808                1.49e-17  21_[+3(8.75e-08)]_127_[+2(4.53e-08)]_3_[+1(6.45e-12)]_48_[+4(1.31e-06)]_52_[+5(4.84e-08)]_183_[+2(7.84e-05)]_348_[+4(1.00e-05)]_88
 806 WashU_Skud_Contig2052.17         1.43e-18  20_[+3(7.96e-09)]_127_[+2(5.67e-09)]_3_[+1(6.21e-11)]_18_[-5(8.93e-08)]_712_[-4(5.15e-07)]_25
 807 SGD_Scer_YOR278W                 3.31e-33  218_[+3(1.88e-12)]_58_[+5(4.19e-12)]_10_[+4(1.95e-13)]_15_[-2(1.33e-09)]_12_[-1(2.02e-10)]_181_[-5(9.56e-06)]_26
 808 MIT_Spar_c261_21317              2.99e-32  222_[+3(1.88e-12)]_23_[+5(1.02e-05)]_15_[+5(4.20e-11)]_9_[+4(1.95e-13)]_15_[-2(1.33e-09)]_12_[-1(2.02e-10)]_224
 809 MIT_Smik_c492_20940              3.31e-33  227_[+3(1.88e-12)]_23_[+5(1.02e-05)]_15_[+5(4.19e-12)]_10_[+4(1.95e-13)]_15_[-2(1.33e-09)]_12_[-1(2.02e-10)]_218
 810 WashU_Skud_Contig1682.4          4.41e-32  224_[+3(1.88e-12)]_56_[+5(6.30e-11)]_10_[+4(1.95e-13)]_15_[-2(1.33e-09)]_12_[-1(2.02e-10)]_223
 811 WashU_Sbay_Contig635.57          1.91e-31  230_[+3(4.24e-11)]_58_[+5(1.29e-11)]_9_[+4(1.95e-13)]_15_[-2(1.33e-09)]_12_[-1(2.02e-10)]_216
 812 --------------------------------------------------------------------------------
 813
 814 ********************************************************************************
 815
 816
 817 ********************************************************************************
 818 Stopped because nmotifs = 5 reached.
 819 ********************************************************************************
 820
 821 CPU: dhn02990.mrc-dunn.cam.ac.uk
 822
 823 ********************************************************************************