t/data/map_hem/HEM2-HEM3.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-HEM3.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_YDL205C         1.0000    860
  38 MIT_Spar_c429_3020       1.0000    860  MIT_Smik_c193_2483       1.0000    860
  39 MIT_Sbay_c841_3215       1.0000    860  WashU_Skud_Contig1850.5  1.0000    860
  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-HEM3.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=            9300    N=              10
  59 strands: + -
  60 sample: seed=            0    seqfrac=         1
  61 Letter frequencies in dataset:
  62 A 0.317 C 0.183 G 0.183 T 0.317
  63 Background letter frequencies (from yeast.nc.1.freq):
  64 A 0.324 C 0.176 G 0.176 T 0.324
  65 ********************************************************************************
  66
  67
  68 ********************************************************************************
  69 MOTIF  1        width =   11   sites =  10   llr = 140   E-value = 1.1e-010
  70 ********************************************************************************
  71 --------------------------------------------------------------------------------
  72         Motif 1 Description
  73 --------------------------------------------------------------------------------
  74 Simplified        A  :::aa1:a1::
  75 pos.-specific     C  :a9:::5:9a:
  76 probability       G  a:1:::5:::6
  77 matrix            T  :::::9::::4
  78
  79          bits    2.5 **       *
  80                  2.3 **       *
  81                  2.0 ***     **
  82                  1.8 ***     **
  83 Information      1.5 ***** ****
  84 content          1.3 ***********
  85 (20.2 bits)      1.0 ***********
  86                  0.8 ***********
  87                  0.5 ***********
  88                  0.3 ***********
  89                  0.0 -----------
  90
  91 Multilevel           GCCAATCACCG
  92 consensus                  G   T
  93 sequence
  94
  95 --------------------------------------------------------------------------------
  96
  97 --------------------------------------------------------------------------------
  98         Motif 1 sites sorted by position p-value
  99 --------------------------------------------------------------------------------
 100 Sequence name            Strand  Start   P-value               Site
 101 -------------            ------  ----- ---------            -----------
 102 WashU_Skud_Contig2052.17     +    184  1.14e-07 CTTGCCTCAG GCCAATCACCG CACCGAACAG
 103 MIT_Sbay_c77_8808            +    185  1.14e-07 CCTGCCGCAG GCCAATCACCG CACCGCCCGG
 104 MIT_Smik_c273_7756           +    183  1.14e-07 GTTGCCTCAG GCCAATCACCG CACCGAATAA
 105 MIT_Spar_c19_8512            +    185  1.14e-07 CTTGCCTCAG GCCAATCACCG CACCGAACAG
 106 SGD_Scer_YGL040C             +    184  1.14e-07 CTTGCCTCAA GCCAATCACCG CACCGAACAG
 107 MIT_Sbay_c841_3215           +    151  3.24e-07 ACGCCAATCT GCCAATGACCT TGAAATCAAG
 108 MIT_Spar_c429_3020           +    150  3.24e-07 GCCTCAATCT GCCAATGACCT TGAATCCAAG
 109 SGD_Scer_YDL205C             +    150  3.24e-07 GCGTCAATCT GCCAATGACCT TGAATTCAGG
 110 MIT_Smik_c193_2483           +    152  1.57e-06 GCGCCAATTT GCCAATGAACT TGAAATCCAG
 111 WashU_Skud_Contig1850.5      -    817  1.69e-06 AACTGAATAA GCGAAAGACCG TCCCACTACC
 112 --------------------------------------------------------------------------------
 113
 114 --------------------------------------------------------------------------------
 115         Motif 1 block diagrams
 116 --------------------------------------------------------------------------------
 117 SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
 118 -------------            ----------------  -------------
 119 WashU_Skud_Contig2052.17          1.1e-07  183_[+1]_806
 120 MIT_Sbay_c77_8808                 1.1e-07  184_[+1]_805
 121 MIT_Smik_c273_7756                1.1e-07  182_[+1]_807
 122 MIT_Spar_c19_8512                 1.1e-07  184_[+1]_805
 123 SGD_Scer_YGL040C                  1.1e-07  183_[+1]_806
 124 MIT_Sbay_c841_3215                3.2e-07  150_[+1]_699
 125 MIT_Spar_c429_3020                3.2e-07  149_[+1]_700
 126 SGD_Scer_YDL205C                  3.2e-07  149_[+1]_700
 127 MIT_Smik_c193_2483                1.6e-06  151_[+1]_698
 128 WashU_Skud_Contig1850.5           1.7e-06  816_[-1]_33
 129 --------------------------------------------------------------------------------
 130
 131 --------------------------------------------------------------------------------
 132         Motif 1 in BLOCKS format
 133 --------------------------------------------------------------------------------
 134 BL   MOTIF 1 width=11 seqs=10
 135 WashU_Skud_Contig2052.17 (  184) GCCAATCACCG  1
 136 MIT_Sbay_c77_8808        (  185) GCCAATCACCG  1
 137 MIT_Smik_c273_7756       (  183) GCCAATCACCG  1
 138 MIT_Spar_c19_8512        (  185) GCCAATCACCG  1
 139 SGD_Scer_YGL040C         (  184) GCCAATCACCG  1
 140 MIT_Sbay_c841_3215       (  151) GCCAATGACCT  1
 141 MIT_Spar_c429_3020       (  150) GCCAATGACCT  1
 142 SGD_Scer_YDL205C         (  150) GCCAATGACCT  1
 143 MIT_Smik_c193_2483       (  152) GCCAATGAACT  1
 144 WashU_Skud_Contig1850.5  (  817) GCGAAAGACCG  1
 145 //
 146
 147 --------------------------------------------------------------------------------
 148
 149 --------------------------------------------------------------------------------
 150         Motif 1 position-specific scoring matrix
 151 --------------------------------------------------------------------------------
 152 log-odds matrix: alength= 4 w= 11 n= 9200 bayes= 9.84392 E= 1.1e-010
 153   -997   -997    251   -997
 154   -997    251   -997   -997
 155   -997    236    -81   -997
 156    162   -997   -997   -997
 157    162   -997   -997   -997
 158   -169   -997   -997    147
 159   -997    151    151   -997
 160    162   -997   -997   -997
 161   -169    236   -997   -997
 162   -997    251   -997   -997
 163   -997   -997    177     30
 164 --------------------------------------------------------------------------------
 165
 166 --------------------------------------------------------------------------------
 167         Motif 1 position-specific probability matrix
 168 --------------------------------------------------------------------------------
 169 letter-probability matrix: alength= 4 w= 11 nsites= 10 E= 1.1e-010
 170  0.000000  0.000000  1.000000  0.000000
 171  0.000000  1.000000  0.000000  0.000000
 172  0.000000  0.900000  0.100000  0.000000
 173  1.000000  0.000000  0.000000  0.000000
 174  1.000000  0.000000  0.000000  0.000000
 175  0.100000  0.000000  0.000000  0.900000
 176  0.000000  0.500000  0.500000  0.000000
 177  1.000000  0.000000  0.000000  0.000000
 178  0.100000  0.900000  0.000000  0.000000
 179  0.000000  1.000000  0.000000  0.000000
 180  0.000000  0.000000  0.600000  0.400000
 181 --------------------------------------------------------------------------------
 182
 183 --------------------------------------------------------------------------------
 184         Motif 1 regular expression
 185 --------------------------------------------------------------------------------
 186 GCCAAT[CG]ACC[GT]
 187 --------------------------------------------------------------------------------
 188
 189
 190
 191
 192 Time  9.05 secs.
 193
 194 ********************************************************************************
 195
 196
 197 ********************************************************************************
 198 MOTIF  2        width =   20   sites =  10   llr = 196   E-value = 5.0e-018
 199 ********************************************************************************
 200 --------------------------------------------------------------------------------
 201         Motif 2 Description
 202 --------------------------------------------------------------------------------
 203 Simplified        A  ::5::1:::a:::::7:::1
 204 pos.-specific     C  ::5:5:::5:aa9::::116
 205 probability       G  :5:::9::::::14:1311:
 206 matrix            T  a5:a5:aa5::::6a27883
 207
 208          bits    2.5           **
 209                  2.3           **
 210                  2.0      *    ***
 211                  1.8      *    ***
 212 Information      1.5 *  * *** **** *
 213 content          1.3 *  * *** **** *
 214 (28.2 bits)      1.0 *************** ***
 215                  0.8 *************** ****
 216                  0.5 ********************
 217                  0.3 ********************
 218                  0.0 --------------------
 219
 220 Multilevel           TGATCGTTCACCCTTATTTC
 221 consensus             TC T   T    G TG  T
 222 sequence
 223
 224 --------------------------------------------------------------------------------
 225
 226 --------------------------------------------------------------------------------
 227         Motif 2 sites sorted by position p-value
 228 --------------------------------------------------------------------------------
 229 Sequence name            Strand  Start   P-value                    Site
 230 -------------            ------  ----- ---------            --------------------
 231 SGD_Scer_YGL040C             +    209  7.10e-11 GAACAGGGAT TGCTCGTTTACCCGTATTTT GATTTTTTTT
 232 WashU_Skud_Contig1850.5      +    712  8.92e-11 CAATCTCCCC TTATTGTTCACCCTTATTTC CACCCTCAAA
 233 MIT_Sbay_c841_3215           +    731  8.92e-11 CAATCTCCCC TTATTGTTCACCCTTATTTC CACCCTCAAA
 234 MIT_Spar_c429_3020           +    705  8.92e-11 CAACCTCCCC TTATTGTTCACCCTTATTTC CACCCTCAAA
 235 SGD_Scer_YDL205C             +    704  8.92e-11 CAATCTCCCC TTATTGTTCACCCTTATTTC CACCCTCAAA
 236 MIT_Smik_c273_7756           +    208  1.21e-10 GAATAAGGAT TGCTCGTTTACCCGTTGTTC GATTTTTTTT
 237 MIT_Spar_c19_8512            +    210  1.21e-10 GAACAGGGAT TGCTCGTTTACCCGTAGTTT GAATTTTTTT
 238 MIT_Smik_c193_2483           +    705  2.20e-09 CAATCTCCCC TTATTATTCACCCTTATTTC CACCCTCAAA
 239 WashU_Skud_Contig2052.17     +    209  6.11e-09 GAACAGGGAT TGCTCGTTTACCCGTTGCGT TCAAAGTTTT
 240 MIT_Sbay_c77_8808            +    209  2.28e-08 CGCCCGGAGA TGCTCGTTTACCGTTGTGCA CCAAATTTTT
 241 --------------------------------------------------------------------------------
 242
 243 --------------------------------------------------------------------------------
 244         Motif 2 block diagrams
 245 --------------------------------------------------------------------------------
 246 SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
 247 -------------            ----------------  -------------
 248 SGD_Scer_YGL040C                  7.1e-11  208_[+2]_772
 249 WashU_Skud_Contig1850.5           8.9e-11  711_[+2]_129
 250 MIT_Sbay_c841_3215                8.9e-11  730_[+2]_110
 251 MIT_Spar_c429_3020                8.9e-11  704_[+2]_136
 252 SGD_Scer_YDL205C                  8.9e-11  703_[+2]_137
 253 MIT_Smik_c273_7756                1.2e-10  207_[+2]_773
 254 MIT_Spar_c19_8512                 1.2e-10  209_[+2]_771
 255 MIT_Smik_c193_2483                2.2e-09  704_[+2]_136
 256 WashU_Skud_Contig2052.17          6.1e-09  208_[+2]_772
 257 MIT_Sbay_c77_8808                 2.3e-08  208_[+2]_772
 258 --------------------------------------------------------------------------------
 259
 260 --------------------------------------------------------------------------------
 261         Motif 2 in BLOCKS format
 262 --------------------------------------------------------------------------------
 263 BL   MOTIF 2 width=20 seqs=10
 264 SGD_Scer_YGL040C         (  209) TGCTCGTTTACCCGTATTTT  1
 265 WashU_Skud_Contig1850.5  (  712) TTATTGTTCACCCTTATTTC  1
 266 MIT_Sbay_c841_3215       (  731) TTATTGTTCACCCTTATTTC  1
 267 MIT_Spar_c429_3020       (  705) TTATTGTTCACCCTTATTTC  1
 268 SGD_Scer_YDL205C         (  704) TTATTGTTCACCCTTATTTC  1
 269 MIT_Smik_c273_7756       (  208) TGCTCGTTTACCCGTTGTTC  1
 270 MIT_Spar_c19_8512        (  210) TGCTCGTTTACCCGTAGTTT  1
 271 MIT_Smik_c193_2483       (  705) TTATTATTCACCCTTATTTC  1
 272 WashU_Skud_Contig2052.17 (  209) TGCTCGTTTACCCGTTGCGT  1
 273 MIT_Sbay_c77_8808        (  209) TGCTCGTTTACCGTTGTGCA  1
 274 //
 275
 276 --------------------------------------------------------------------------------
 277
 278 --------------------------------------------------------------------------------
 279         Motif 2 position-specific scoring matrix
 280 --------------------------------------------------------------------------------
 281 log-odds matrix: alength= 4 w= 20 n= 9110 bayes= 9.82972 E= 5.0e-018
 282   -997   -997   -997    162
 283   -997   -997    151     62
 284     62    151   -997   -997
 285   -997   -997   -997    162
 286   -997    151   -997     62
 287   -169   -997    236   -997
 288   -997   -997   -997    162
 289   -997   -997   -997    162
 290   -997    151   -997     62
 291    162   -997   -997   -997
 292   -997    251   -997   -997
 293   -997    251   -997   -997
 294   -997    236    -81   -997
 295   -997   -997    119     89
 296   -997   -997   -997    162
 297    111   -997    -81    -70
 298   -997   -997     77    111
 299   -997    -81    -81    130
 300   -997    -81    -81    130
 301   -169    177   -997    -11
 302 --------------------------------------------------------------------------------
 303
 304 --------------------------------------------------------------------------------
 305         Motif 2 position-specific probability matrix
 306 --------------------------------------------------------------------------------
 307 letter-probability matrix: alength= 4 w= 20 nsites= 10 E= 5.0e-018
 308  0.000000  0.000000  0.000000  1.000000
 309  0.000000  0.000000  0.500000  0.500000
 310  0.500000  0.500000  0.000000  0.000000
 311  0.000000  0.000000  0.000000  1.000000
 312  0.000000  0.500000  0.000000  0.500000
 313  0.100000  0.000000  0.900000  0.000000
 314  0.000000  0.000000  0.000000  1.000000
 315  0.000000  0.000000  0.000000  1.000000
 316  0.000000  0.500000  0.000000  0.500000
 317  1.000000  0.000000  0.000000  0.000000
 318  0.000000  1.000000  0.000000  0.000000
 319  0.000000  1.000000  0.000000  0.000000
 320  0.000000  0.900000  0.100000  0.000000
 321  0.000000  0.000000  0.400000  0.600000
 322  0.000000  0.000000  0.000000  1.000000
 323  0.700000  0.000000  0.100000  0.200000
 324  0.000000  0.000000  0.300000  0.700000
 325  0.000000  0.100000  0.100000  0.800000
 326  0.000000  0.100000  0.100000  0.800000
 327  0.100000  0.600000  0.000000  0.300000
 328 --------------------------------------------------------------------------------
 329
 330 --------------------------------------------------------------------------------
 331         Motif 2 regular expression
 332 --------------------------------------------------------------------------------
 333 T[GT][AC]T[CT]GTT[CT]ACCC[TG]T[AT][TG]TT[CT]
 334 --------------------------------------------------------------------------------
 335
 336
 337
 338
 339 Time 18.20 secs.
 340
 341 ********************************************************************************
 342
 343
 344 ********************************************************************************
 345 MOTIF  3        width =   15   sites =  10   llr = 167   E-value = 8.5e-015
 346 ********************************************************************************
 347 --------------------------------------------------------------------------------
 348         Motif 3 Description
 349 --------------------------------------------------------------------------------
 350 Simplified        A  5:a:::a9:1:1:1:
 351 pos.-specific     C  :1:::a::39:5a98
 352 probability       G  :4:aa::13::3::1
 353 matrix            T  55::::::4:a1::1
 354
 355          bits    2.5    ***      *
 356                  2.3    ***      *
 357                  2.0    ***   *  **
 358                  1.8    ***   *  **
 359 Information      1.5   *****  ** ***
 360 content          1.3   ****** ** ***
 361 (24.1 bits)      1.0   ****** ** ***
 362                  0.8  ******* ******
 363                  0.5 ***************
 364                  0.3 ***************
 365                  0.0 ---------------
 366
 367 Multilevel           ATAGGCAATCTCCCC
 368 consensus            TG      C  G
 369 sequence                     G
 370
 371 --------------------------------------------------------------------------------
 372
 373 --------------------------------------------------------------------------------
 374         Motif 3 sites sorted by position p-value
 375 --------------------------------------------------------------------------------
 376 Sequence name            Strand  Start   P-value                 Site
 377 -------------            ------  ----- ---------            ---------------
 378 MIT_Spar_c429_3020           +    690  1.51e-09 GTTTAGGCGC ATAGGCAACCTCCCC TTATTGTTCA
 379 MIT_Spar_c19_8512            -    169  1.91e-09 GTGATTGGCC TGAGGCAAGCTGCCC GCTTGATTTA
 380 WashU_Skud_Contig1850.5      +    697  2.59e-09 GTTTAGGCGC ATAGGCAATCTCCCC TTATTGTTCA
 381 MIT_Sbay_c841_3215           +    716  2.59e-09 GTTTTAGCGC ATAGGCAATCTCCCC TTATTGTTCA
 382 MIT_Smik_c193_2483           +    690  2.59e-09 GTTTAAGCGC ATAGGCAATCTCCCC TTATTATTCA
 383 SGD_Scer_YDL205C             +    689  2.59e-09 GTTTAGGCGC ATAGGCAATCTCCCC TTATTGTTCA
 384 SGD_Scer_YGL040C             -    168  8.84e-09 GTGATTGGCT TGAGGCAAGCTTCCC GCTTGATTTA
 385 WashU_Skud_Contig2052.17     -    168  2.94e-08 GTGATTGGCC TGAGGCAAGCTGCCT GCCCAATTTA
 386 MIT_Sbay_c77_8808            +    167  1.36e-07 CTTTTATAAA TCAGGCAGCCTGCCG CAGGCCAATC
 387 MIT_Smik_c273_7756           -    167  3.45e-07 GTGATTGGCC TGAGGCAACATACAC TCTTGATTTA
 388 --------------------------------------------------------------------------------
 389
 390 --------------------------------------------------------------------------------
 391         Motif 3 block diagrams
 392 --------------------------------------------------------------------------------
 393 SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
 394 -------------            ----------------  -------------
 395 MIT_Spar_c429_3020                1.5e-09  689_[+3]_156
 396 MIT_Spar_c19_8512                 1.9e-09  168_[-3]_817
 397 WashU_Skud_Contig1850.5           2.6e-09  696_[+3]_149
 398 MIT_Sbay_c841_3215                2.6e-09  715_[+3]_130
 399 MIT_Smik_c193_2483                2.6e-09  689_[+3]_156
 400 SGD_Scer_YDL205C                  2.6e-09  688_[+3]_157
 401 SGD_Scer_YGL040C                  8.8e-09  167_[-3]_818
 402 WashU_Skud_Contig2052.17          2.9e-08  167_[-3]_818
 403 MIT_Sbay_c77_8808                 1.4e-07  166_[+3]_819
 404 MIT_Smik_c273_7756                3.4e-07  166_[-3]_819
 405 --------------------------------------------------------------------------------
 406
 407 --------------------------------------------------------------------------------
 408         Motif 3 in BLOCKS format
 409 --------------------------------------------------------------------------------
 410 BL   MOTIF 3 width=15 seqs=10
 411 MIT_Spar_c429_3020       (  690) ATAGGCAACCTCCCC  1
 412 MIT_Spar_c19_8512        (  169) TGAGGCAAGCTGCCC  1
 413 WashU_Skud_Contig1850.5  (  697) ATAGGCAATCTCCCC  1
 414 MIT_Sbay_c841_3215       (  716) ATAGGCAATCTCCCC  1
 415 MIT_Smik_c193_2483       (  690) ATAGGCAATCTCCCC  1
 416 SGD_Scer_YDL205C         (  689) ATAGGCAATCTCCCC  1
 417 SGD_Scer_YGL040C         (  168) TGAGGCAAGCTTCCC  1
 418 WashU_Skud_Contig2052.17 (  168) TGAGGCAAGCTGCCT  1
 419 MIT_Sbay_c77_8808        (  167) TCAGGCAGCCTGCCG  1
 420 MIT_Smik_c273_7756       (  167) TGAGGCAACATACAC  1
 421 //
 422
 423 --------------------------------------------------------------------------------
 424
 425 --------------------------------------------------------------------------------
 426         Motif 3 position-specific scoring matrix
 427 --------------------------------------------------------------------------------
 428 log-odds matrix: alength= 4 w= 15 n= 9160 bayes= 9.83763 E= 8.5e-015
 429     62   -997   -997     62
 430   -997    -81    119     62
 431    162   -997   -997   -997
 432   -997   -997    251   -997
 433   -997   -997    251   -997
 434   -997    251   -997   -997
 435    162   -997   -997   -997
 436    147   -997    -81   -997
 437   -997     77     77     30
 438   -169    236   -997   -997
 439   -997   -997   -997    162
 440   -169    151     77   -169
 441   -997    251   -997   -997
 442   -169    236   -997   -997
 443   -997    219    -81   -169
 444 --------------------------------------------------------------------------------
 445
 446 --------------------------------------------------------------------------------
 447         Motif 3 position-specific probability matrix
 448 --------------------------------------------------------------------------------
 449 letter-probability matrix: alength= 4 w= 15 nsites= 10 E= 8.5e-015
 450  0.500000  0.000000  0.000000  0.500000
 451  0.000000  0.100000  0.400000  0.500000
 452  1.000000  0.000000  0.000000  0.000000
 453  0.000000  0.000000  1.000000  0.000000
 454  0.000000  0.000000  1.000000  0.000000
 455  0.000000  1.000000  0.000000  0.000000
 456  1.000000  0.000000  0.000000  0.000000
 457  0.900000  0.000000  0.100000  0.000000
 458  0.000000  0.300000  0.300000  0.400000
 459  0.100000  0.900000  0.000000  0.000000
 460  0.000000  0.000000  0.000000  1.000000
 461  0.100000  0.500000  0.300000  0.100000
 462  0.000000  1.000000  0.000000  0.000000
 463  0.100000  0.900000  0.000000  0.000000
 464  0.000000  0.800000  0.100000  0.100000
 465 --------------------------------------------------------------------------------
 466
 467 --------------------------------------------------------------------------------
 468         Motif 3 regular expression
 469 --------------------------------------------------------------------------------
 470 [AT][TG]AGGCAA[TCG]CT[CG]CCC
 471 --------------------------------------------------------------------------------
 472
 473
 474
 475
 476 Time 27.22 secs.
 477
 478 ********************************************************************************
 479
 480
 481 ********************************************************************************
 482 MOTIF  4        width =   18   sites =  10   llr = 176   E-value = 2.3e-013
 483 ********************************************************************************
 484 --------------------------------------------------------------------------------
 485         Motif 4 Description
 486 --------------------------------------------------------------------------------
 487 Simplified        A  92:5718a:aa:a:9855
 488 pos.-specific     C  ::a:::::a:::::::::
 489 probability       G  ::::182::::::a12:5
 490 matrix            T  18:521:::::a::::5:
 491
 492          bits    2.5   *     *    *
 493                  2.3   *     *    *
 494                  2.0   *     *    *
 495                  1.8   *     *    *
 496 Information      1.5   *  * *******
 497 content          1.3 * *  * ********
 498 (25.4 bits)      1.0 ***  *********** *
 499                  0.8 ***  *********** *
 500                  0.5 ******************
 501                  0.3 ******************
 502                  0.0 ------------------
 503
 504 Multilevel           ATCAAGAACAATAGAAAA
 505 consensus             A TT G        GTG
 506 sequence
 507
 508 --------------------------------------------------------------------------------
 509
 510 --------------------------------------------------------------------------------
 511         Motif 4 sites sorted by position p-value
 512 --------------------------------------------------------------------------------
 513 Sequence name            Strand  Start   P-value                   Site
 514 -------------            ------  ----- ---------            ------------------
 515 MIT_Sbay_c841_3215           -     57  8.38e-10 CCATATTAGC ATCTAGAACAATAGAAAA AGAAGAAGGA
 516 MIT_Smik_c193_2483           -     58  8.38e-10 CCGTATTAGT ATCTAGAACAATAGAAAA AAGAAAAAGG
 517 MIT_Spar_c429_3020           -     56  8.38e-10 CCGTATTAGT ATCTAGAACAATAGAAAA AGGAAAAGGC
 518 SGD_Scer_YDL205C             -     56  8.38e-10 CCGTATTAAT ATCTAGAACAATAGAAAA AAAGAAAAGC
 519 MIT_Smik_c273_7756           +     96  2.49e-09 AGGCCAATAA ATCAGGAACAATAGAATG ACGCACCGAG
 520 MIT_Spar_c19_8512            +     96  5.09e-09 TGGGCCAAAA AACAAGGACAATAGAATG ACACATAAAG
 521 WashU_Skud_Contig1850.5      -     55  9.52e-09 CCATATTAGT TTCTAGAACAATAGAAAA AAAAAAAAGC
 522 WashU_Skud_Contig2052.17     +     94  9.81e-09 TTAGCCAGAA ATCATGAACAATAGGATG ACGCATAGAC
 523 SGD_Scer_YGL040C             +     95  2.62e-08 GGGCAAGAAA ATCAAAGACAATAGAGTG GCGCATAGAT
 524 MIT_Sbay_c77_8808            +     99  6.75e-08 GCTATGAACT AACATTAACAATAGAGTG ATGCATAGAC
 525 --------------------------------------------------------------------------------
 526
 527 --------------------------------------------------------------------------------
 528         Motif 4 block diagrams
 529 --------------------------------------------------------------------------------
 530 SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
 531 -------------            ----------------  -------------
 532 MIT_Sbay_c841_3215                8.4e-10  56_[-4]_786
 533 MIT_Smik_c193_2483                8.4e-10  57_[-4]_785
 534 MIT_Spar_c429_3020                8.4e-10  55_[-4]_787
 535 SGD_Scer_YDL205C                  8.4e-10  55_[-4]_787
 536 MIT_Smik_c273_7756                2.5e-09  95_[+4]_887
 537 MIT_Spar_c19_8512                 5.1e-09  95_[+4]_887
 538 WashU_Skud_Contig1850.5           9.5e-09  54_[-4]_788
 539 WashU_Skud_Contig2052.17          9.8e-09  93_[+4]_889
 540 SGD_Scer_YGL040C                  2.6e-08  94_[+4]_888
 541 MIT_Sbay_c77_8808                 6.8e-08  98_[+4]_884
 542 --------------------------------------------------------------------------------
 543
 544 --------------------------------------------------------------------------------
 545         Motif 4 in BLOCKS format
 546 --------------------------------------------------------------------------------
 547 BL   MOTIF 4 width=18 seqs=10
 548 MIT_Sbay_c841_3215       (   57) ATCTAGAACAATAGAAAA  1
 549 MIT_Smik_c193_2483       (   58) ATCTAGAACAATAGAAAA  1
 550 MIT_Spar_c429_3020       (   56) ATCTAGAACAATAGAAAA  1
 551 SGD_Scer_YDL205C         (   56) ATCTAGAACAATAGAAAA  1
 552 MIT_Smik_c273_7756       (   96) ATCAGGAACAATAGAATG  1
 553 MIT_Spar_c19_8512        (   96) AACAAGGACAATAGAATG  1
 554 WashU_Skud_Contig1850.5  (   55) TTCTAGAACAATAGAAAA  1
 555 WashU_Skud_Contig2052.17 (   94) ATCATGAACAATAGGATG  1
 556 SGD_Scer_YGL040C         (   95) ATCAAAGACAATAGAGTG  1
 557 MIT_Sbay_c77_8808        (   99) AACATTAACAATAGAGTG  1
 558 //
 559
 560 --------------------------------------------------------------------------------
 561
 562 --------------------------------------------------------------------------------
 563         Motif 4 position-specific scoring matrix
 564 --------------------------------------------------------------------------------
 565 log-odds matrix: alength= 4 w= 18 n= 9130 bayes= 9.83289 E= 2.3e-013
 566    147   -997   -997   -169
 567    -70   -997   -997    130
 568   -997    251   -997   -997
 569     62   -997   -997     62
 570    111   -997    -81    -70
 571   -169   -997    219   -169
 572    130   -997     19   -997
 573    162   -997   -997   -997
 574   -997    251   -997   -997
 575    162   -997   -997   -997
 576    162   -997   -997   -997
 577   -997   -997   -997    162
 578    162   -997   -997   -997
 579   -997   -997    251   -997
 580    147   -997    -81   -997
 581    130   -997     19   -997
 582     62   -997   -997     62
 583     62   -997    151   -997
 584 --------------------------------------------------------------------------------
 585
 586 --------------------------------------------------------------------------------
 587         Motif 4 position-specific probability matrix
 588 --------------------------------------------------------------------------------
 589 letter-probability matrix: alength= 4 w= 18 nsites= 10 E= 2.3e-013
 590  0.900000  0.000000  0.000000  0.100000
 591  0.200000  0.000000  0.000000  0.800000
 592  0.000000  1.000000  0.000000  0.000000
 593  0.500000  0.000000  0.000000  0.500000
 594  0.700000  0.000000  0.100000  0.200000
 595  0.100000  0.000000  0.800000  0.100000
 596  0.800000  0.000000  0.200000  0.000000
 597  1.000000  0.000000  0.000000  0.000000
 598  0.000000  1.000000  0.000000  0.000000
 599  1.000000  0.000000  0.000000  0.000000
 600  1.000000  0.000000  0.000000  0.000000
 601  0.000000  0.000000  0.000000  1.000000
 602  1.000000  0.000000  0.000000  0.000000
 603  0.000000  0.000000  1.000000  0.000000
 604  0.900000  0.000000  0.100000  0.000000
 605  0.800000  0.000000  0.200000  0.000000
 606  0.500000  0.000000  0.000000  0.500000
 607  0.500000  0.000000  0.500000  0.000000
 608 --------------------------------------------------------------------------------
 609
 610 --------------------------------------------------------------------------------
 611         Motif 4 regular expression
 612 --------------------------------------------------------------------------------
 613 A[TA]C[AT][AT]G[AG]ACAATAGA[AG][AT][AG]
 614 --------------------------------------------------------------------------------
 615
 616
 617
 618
 619 Time 35.82 secs.
 620
 621 ********************************************************************************
 622
 623
 624 ********************************************************************************
 625 MOTIF  5        width =   20   sites =  10   llr = 179   E-value = 9.4e-012
 626 ********************************************************************************
 627 --------------------------------------------------------------------------------
 628         Motif 5 Description
 629 --------------------------------------------------------------------------------
 630 Simplified        A  ::::::8::::::1:1211:
 631 pos.-specific     C  :1:11a2:12:61:49:4::
 632 probability       G  ::::1::::::::41:::::
 633 matrix            T  a9a98::a98a4955:859a
 634
 635          bits    2.5      *
 636                  2.3      *
 637                  2.0      *         *
 638                  1.8      *         *
 639 Information      1.5 * *  * *  *    *   *
 640 content          1.3 **** * ** ***  *  **
 641 (25.8 bits)      1.0 *************  ** **
 642                  0.8 ************* *** **
 643                  0.5 ********************
 644                  0.3 ********************
 645                  0.0 --------------------
 646
 647 Multilevel           TTTTTCATTTTCTTTCTTTT
 648 consensus                  C  C T GC AC
 649 sequence
 650
 651 --------------------------------------------------------------------------------
 652
 653 --------------------------------------------------------------------------------
 654         Motif 5 sites sorted by position p-value
 655 --------------------------------------------------------------------------------
 656 Sequence name            Strand  Start   P-value                    Site
 657 -------------            ------  ----- ---------            --------------------
 658 WashU_Skud_Contig1850.5      +    231  1.09e-10 TTCCTTCAAT TTTTTCATTTTCTTTCTTTT TTTATGTTTA
 659 MIT_Spar_c429_3020           +    232  1.09e-10 TTCCTTCATT TTTTTCATTTTCTTTCTTTT TTTATGTTTG
 660 SGD_Scer_YDL205C             +    230  1.09e-10 GTTCCTTTAC TTTTTCATTTTCTTTCTTTT TTTATGTTTG
 661 MIT_Sbay_c77_8808            +    234  1.86e-10 GTGCACCAAA TTTTTCATTTTTTGCCTTTT TCTATTTGGC
 662 MIT_Smik_c193_2483           +    235  1.28e-09 TCCTTCAGTT TTTCTCATTTTCTTTCTTTT TCTATGTTTT
 663 MIT_Sbay_c841_3215           +    261  2.16e-09 TTATGTCTAA TTTTTCATTTTTTTTCACTT GAAAATTGCT
 664 MIT_Spar_c19_8512            +    450  1.73e-08 GTACGTCTTG TTTTGCCTTCTTTGGCTCTT GTGTCACTGA
 665 SGD_Scer_YGL040C             +    446  2.06e-08 GTGTACGCCT TCTTCCCTTCTTTGCCTCTT GTGCCACTGT
 666 WashU_Skud_Contig2052.17     +    235  3.92e-08 GCGTTCAAAG TTTTTCATTTTCCGCATCAT CTACTTTTTT
 667 MIT_Smik_c273_7756           +    235  4.56e-08 TTCGATTTTT TTTTTCATCTTCTACCAATT TTTTTCGGCA
 668 --------------------------------------------------------------------------------
 669
 670 --------------------------------------------------------------------------------
 671         Motif 5 block diagrams
 672 --------------------------------------------------------------------------------
 673 SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
 674 -------------            ----------------  -------------
 675 WashU_Skud_Contig1850.5           1.1e-10  230_[+5]_610
 676 MIT_Spar_c429_3020                1.1e-10  231_[+5]_609
 677 SGD_Scer_YDL205C                  1.1e-10  229_[+5]_611
 678 MIT_Sbay_c77_8808                 1.9e-10  233_[+5]_747
 679 MIT_Smik_c193_2483                1.3e-09  234_[+5]_606
 680 MIT_Sbay_c841_3215                2.2e-09  260_[+5]_580
 681 MIT_Spar_c19_8512                 1.7e-08  449_[+5]_531
 682 SGD_Scer_YGL040C                  2.1e-08  445_[+5]_535
 683 WashU_Skud_Contig2052.17          3.9e-08  234_[+5]_746
 684 MIT_Smik_c273_7756                4.6e-08  234_[+5]_746
 685 --------------------------------------------------------------------------------
 686
 687 --------------------------------------------------------------------------------
 688         Motif 5 in BLOCKS format
 689 --------------------------------------------------------------------------------
 690 BL   MOTIF 5 width=20 seqs=10
 691 WashU_Skud_Contig1850.5  (  231) TTTTTCATTTTCTTTCTTTT  1
 692 MIT_Spar_c429_3020       (  232) TTTTTCATTTTCTTTCTTTT  1
 693 SGD_Scer_YDL205C         (  230) TTTTTCATTTTCTTTCTTTT  1
 694 MIT_Sbay_c77_8808        (  234) TTTTTCATTTTTTGCCTTTT  1
 695 MIT_Smik_c193_2483       (  235) TTTCTCATTTTCTTTCTTTT  1
 696 MIT_Sbay_c841_3215       (  261) TTTTTCATTTTTTTTCACTT  1
 697 MIT_Spar_c19_8512        (  450) TTTTGCCTTCTTTGGCTCTT  1
 698 SGD_Scer_YGL040C         (  446) TCTTCCCTTCTTTGCCTCTT  1
 699 WashU_Skud_Contig2052.17 (  235) TTTTTCATTTTCCGCATCAT  1
 700 MIT_Smik_c273_7756       (  235) TTTTTCATCTTCTACCAATT  1
 701 //
 702
 703 --------------------------------------------------------------------------------
 704
 705 --------------------------------------------------------------------------------
 706         Motif 5 position-specific scoring matrix
 707 --------------------------------------------------------------------------------
 708 log-odds matrix: alength= 4 w= 20 n= 9110 bayes= 9.82972 E= 9.4e-012
 709   -997   -997   -997    162
 710   -997    -81   -997    147
 711   -997   -997   -997    162
 712   -997    -81   -997    147
 713   -997    -81    -81    130
 714   -997    251   -997   -997
 715    130     19   -997   -997
 716   -997   -997   -997    162
 717   -997    -81   -997    147
 718   -997     19   -997    130
 719   -997   -997   -997    162
 720   -997    177   -997     30
 721   -997    -81   -997    147
 722   -169   -997    119     62
 723   -997    119    -81     62
 724   -169    236   -997   -997
 725    -70   -997   -997    130
 726   -169    119   -997     62
 727   -169   -997   -997    147
 728   -997   -997   -997    162
 729 --------------------------------------------------------------------------------
 730
 731 --------------------------------------------------------------------------------
 732         Motif 5 position-specific probability matrix
 733 --------------------------------------------------------------------------------
 734 letter-probability matrix: alength= 4 w= 20 nsites= 10 E= 9.4e-012
 735  0.000000  0.000000  0.000000  1.000000
 736  0.000000  0.100000  0.000000  0.900000
 737  0.000000  0.000000  0.000000  1.000000
 738  0.000000  0.100000  0.000000  0.900000
 739  0.000000  0.100000  0.100000  0.800000
 740  0.000000  1.000000  0.000000  0.000000
 741  0.800000  0.200000  0.000000  0.000000
 742  0.000000  0.000000  0.000000  1.000000
 743  0.000000  0.100000  0.000000  0.900000
 744  0.000000  0.200000  0.000000  0.800000
 745  0.000000  0.000000  0.000000  1.000000
 746  0.000000  0.600000  0.000000  0.400000
 747  0.000000  0.100000  0.000000  0.900000
 748  0.100000  0.000000  0.400000  0.500000
 749  0.000000  0.400000  0.100000  0.500000
 750  0.100000  0.900000  0.000000  0.000000
 751  0.200000  0.000000  0.000000  0.800000
 752  0.100000  0.400000  0.000000  0.500000
 753  0.100000  0.000000  0.000000  0.900000
 754  0.000000  0.000000  0.000000  1.000000
 755 --------------------------------------------------------------------------------
 756
 757 --------------------------------------------------------------------------------
 758         Motif 5 regular expression
 759 --------------------------------------------------------------------------------
 760 TTTTTC[AC]TT[TC]T[CT]T[TG][TC]C[TA][TC]TT
 761 --------------------------------------------------------------------------------
 762
 763
 764
 765
 766 Time 44.27 secs.
 767
 768 ********************************************************************************
 769
 770
 771 ********************************************************************************
 772 SUMMARY OF MOTIFS
 773 ********************************************************************************
 774
 775 --------------------------------------------------------------------------------
 776         Combined block diagrams: non-overlapping sites with p-value < 0.0001
 777 --------------------------------------------------------------------------------
 778 SEQUENCE NAME            COMBINED P-VALUE  MOTIF DIAGRAM
 779 -------------            ----------------  -------------
 780 SGD_Scer_YGL040C                 4.71e-19  94_[+4(2.62e-08)]_55_[-3(8.84e-09)]_1_[+1(1.14e-07)]_14_[+2(7.10e-11)]_6_[+5(2.48e-05)]_191_[+5(2.06e-08)]_95_[-5(3.50e-05)]_420
 781 MIT_Spar_c19_8512                3.44e-20  95_[+4(5.09e-09)]_55_[-3(1.91e-09)]_1_[+1(1.14e-07)]_14_[+2(1.21e-10)]_7_[+5(2.48e-05)]_193_[+5(1.73e-08)]_353_[+5(1.61e-05)]_65_[-5(3.99e-05)]_73
 782 MIT_Smik_c273_7756               5.44e-18  43_[-5(4.67e-06)]_32_[+4(2.49e-09)]_53_[-3(3.45e-07)]_1_[+1(1.14e-07)]_14_[+2(1.21e-10)]_7_[+5(4.56e-08)]_187_[+2(8.72e-05)]_539
 783 MIT_Sbay_c77_8808                3.80e-17  98_[+4(6.75e-08)]_50_[+3(1.36e-07)]_3_[+1(1.14e-07)]_13_[+2(2.28e-08)]_5_[+5(1.86e-10)]_508_[-5(4.64e-05)]_219
 784 WashU_Skud_Contig2052.17         6.49e-17  93_[+4(9.81e-09)]_56_[-3(2.94e-08)]_1_[+1(1.14e-07)]_14_[+2(6.11e-09)]_6_[+5(3.92e-08)]_265_[+5(1.82e-05)]_245_[+1(9.56e-05)]_205
 785 SGD_Scer_YDL205C                 7.24e-23  55_[-4(8.38e-10)]_76_[+1(3.24e-07)]_69_[+5(1.09e-10)]_4_[+5(6.12e-05)]_50_[+2(1.32e-05)]_345_[+3(2.59e-09)]_[+2(8.92e-11)]_137
 786 MIT_Spar_c429_3020               4.36e-23  55_[-4(8.38e-10)]_76_[+1(3.24e-07)]_71_[+5(1.09e-10)]_75_[+2(1.32e-05)]_160_[-5(7.29e-05)]_163_[+3(1.51e-09)]_[+2(8.92e-11)]_105_[+2(8.90e-05)]_11
 787 MIT_Smik_c193_2483               6.38e-20  57_[-4(8.38e-10)]_76_[+1(1.57e-06)]_72_[+5(1.28e-09)]_11_[+5(4.42e-05)]_42_[+2(1.03e-05)]_342_[+3(2.59e-09)]_[+2(2.20e-09)]_136
 788 MIT_Sbay_c841_3215               1.19e-21  56_[-4(8.38e-10)]_76_[+1(3.24e-07)]_69_[+5(3.18e-06)]_10_[+5(2.16e-09)]_44_[+2(1.03e-05)]_371_[+3(2.59e-09)]_[+2(8.92e-11)]_110
 789 WashU_Skud_Contig1850.5          3.30e-21  54_[-4(9.52e-09)]_158_[+5(1.09e-10)]_4_[+5(6.08e-06)]_52_[+2(1.38e-05)]_180_[-5(8.12e-05)]_43_[+3(2.88e-05)]_92_[+3(2.59e-09)]_[+2(8.92e-11)]_85_[-1(1.69e-06)]_33
 790 --------------------------------------------------------------------------------
 791
 792 ********************************************************************************
 793
 794
 795 ********************************************************************************
 796 Stopped because nmotifs = 5 reached.
 797 ********************************************************************************
 798
 799 CPU: dhn02990.mrc-dunn.cam.ac.uk
 800
 801 ********************************************************************************