t/data/map_hem/HEM2-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= HEM2-HEM15.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_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 HEM2-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=            8635    N=              10
  59 strands: + -
  60 sample: seed=            0    seqfrac=         1
  61 Letter frequencies in dataset:
  62 A 0.321 C 0.179 G 0.179 T 0.321
  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 = 215   E-value = 5.2e-026
  70 ********************************************************************************
  71 --------------------------------------------------------------------------------
  72         Motif 1 Description
  73 --------------------------------------------------------------------------------
  74 Simplified        A  2:1861:5aa5:a::::a5:
  75 pos.-specific     C  5:5:::95:::a:5a:a:5a
  76 probability       G  314249:::::::5:5::::
  77 matrix            T  :9::::1:::5::::5::::
  78
  79          bits    2.5            *  * *  *
  80                  2.3            *  * *  *
  81                  2.0      **    *  * *  *
  82                  1.8      **    *  * *  *
  83 Information      1.5      ** ** **** ** *
  84 content          1.3  *   ** ** **** ** *
  85 (31.0 bits)      1.0  ********* *********
  86                  0.8 ********** *********
  87                  0.5 ********************
  88                  0.3 ********************
  89                  0.0 --------------------
  90
  91 Multilevel           CTCAAGCAAAACACCGCAAC
  92 consensus            G GGG  C  T  G T  C
  93 sequence             A
  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     +    179  2.28e-13 GGCAGCTTGC CTCAGGCCAATCACCGCACC GAACAGGGAT
 103 MIT_Smik_c273_7756           +    178  2.28e-13 TGTATGTTGC CTCAGGCCAATCACCGCACC GAATAAGGAT
 104 MIT_Spar_c19_8512            +    180  2.28e-13 GGCAGCTTGC CTCAGGCCAATCACCGCACC GAACAGGGAT
 105 SGD_Scer_YGL040C             +    179  6.49e-13 GGAAGCTTGC CTCAAGCCAATCACCGCACC GAACAGGGAT
 106 MIT_Sbay_c77_8808            +    180  3.46e-11 GGCAGCCTGC CGCAGGCCAATCACCGCACC GCCCGGAGAT
 107 MIT_Spar_c278_20970          -    508  1.13e-10 TTGTTGAACA GTGAAGCAAAACAGCTCAAC AGCAGGGCAA
 108 WashU_Sbay_Contig480.2       -    518  2.09e-10 TGTTGAACAG GTGGAGCAAAACAGCTCAAC AGCAGAACAA
 109 SGD_Scer_YOR176W             -    506  5.11e-10 TTGTTGAACA GTAAAGCAAAACAGCTCAAC AGCAGGACAA
 110 MIT_Smik_c935_20455          -    492  1.39e-09 TTGTTGAACA ATGAAGTAAAACAGCTCAAC AGCAGAGCAA
 111 WashU_Skud_Contig2050.4      -    509  1.85e-09 TGTTGAACAG ATGGAACAAAACAGCTCAAC AGCAGAACAA
 112 --------------------------------------------------------------------------------
 113
 114 --------------------------------------------------------------------------------
 115         Motif 1 block diagrams
 116 --------------------------------------------------------------------------------
 117 SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
 118 -------------            ----------------  -------------
 119 WashU_Skud_Contig2052.17          2.3e-13  178_[+1]_802
 120 MIT_Smik_c273_7756                2.3e-13  177_[+1]_803
 121 MIT_Spar_c19_8512                 2.3e-13  179_[+1]_801
 122 SGD_Scer_YGL040C                  6.5e-13  178_[+1]_802
 123 MIT_Sbay_c77_8808                 3.5e-11  179_[+1]_801
 124 MIT_Spar_c278_20970               1.1e-10  507_[-1]_200
 125 WashU_Sbay_Contig480.2            2.1e-10  517_[-1]_190
 126 SGD_Scer_YOR176W                  5.1e-10  505_[-1]_202
 127 MIT_Smik_c935_20455               1.4e-09  491_[-1]_216
 128 WashU_Skud_Contig2050.4           1.8e-09  508_[-1]_199
 129 --------------------------------------------------------------------------------
 130
 131 --------------------------------------------------------------------------------
 132         Motif 1 in BLOCKS format
 133 --------------------------------------------------------------------------------
 134 BL   MOTIF 1 width=20 seqs=10
 135 WashU_Skud_Contig2052.17 (  179) CTCAGGCCAATCACCGCACC  1
 136 MIT_Smik_c273_7756       (  178) CTCAGGCCAATCACCGCACC  1
 137 MIT_Spar_c19_8512        (  180) CTCAGGCCAATCACCGCACC  1
 138 SGD_Scer_YGL040C         (  179) CTCAAGCCAATCACCGCACC  1
 139 MIT_Sbay_c77_8808        (  180) CGCAGGCCAATCACCGCACC  1
 140 MIT_Spar_c278_20970      (  508) GTGAAGCAAAACAGCTCAAC  1
 141 WashU_Sbay_Contig480.2   (  518) GTGGAGCAAAACAGCTCAAC  1
 142 SGD_Scer_YOR176W         (  506) GTAAAGCAAAACAGCTCAAC  1
 143 MIT_Smik_c935_20455      (  492) ATGAAGTAAAACAGCTCAAC  1
 144 WashU_Skud_Contig2050.4  (  509) ATGGAACAAAACAGCTCAAC  1
 145 //
 146
 147 --------------------------------------------------------------------------------
 148
 149 --------------------------------------------------------------------------------
 150         Motif 1 position-specific scoring matrix
 151 --------------------------------------------------------------------------------
 152 log-odds matrix: alength= 4 w= 20 n= 8445 bayes= 9.72024 E= 5.2e-026
 153    -70    151     77   -997
 154   -997   -997    -81    147
 155   -169    151    119   -997
 156    130   -997     19   -997
 157     89   -997    119   -997
 158   -169   -997    236   -997
 159   -997    236   -997   -169
 160     62    151   -997   -997
 161    162   -997   -997   -997
 162    162   -997   -997   -997
 163     62   -997   -997     62
 164   -997    251   -997   -997
 165    162   -997   -997   -997
 166   -997    151    151   -997
 167   -997    251   -997   -997
 168   -997   -997    151     62
 169   -997    251   -997   -997
 170    162   -997   -997   -997
 171     62    151   -997   -997
 172   -997    251   -997   -997
 173 --------------------------------------------------------------------------------
 174
 175 --------------------------------------------------------------------------------
 176         Motif 1 position-specific probability matrix
 177 --------------------------------------------------------------------------------
 178 letter-probability matrix: alength= 4 w= 20 nsites= 10 E= 5.2e-026
 179  0.200000  0.500000  0.300000  0.000000
 180  0.000000  0.000000  0.100000  0.900000
 181  0.100000  0.500000  0.400000  0.000000
 182  0.800000  0.000000  0.200000  0.000000
 183  0.600000  0.000000  0.400000  0.000000
 184  0.100000  0.000000  0.900000  0.000000
 185  0.000000  0.900000  0.000000  0.100000
 186  0.500000  0.500000  0.000000  0.000000
 187  1.000000  0.000000  0.000000  0.000000
 188  1.000000  0.000000  0.000000  0.000000
 189  0.500000  0.000000  0.000000  0.500000
 190  0.000000  1.000000  0.000000  0.000000
 191  1.000000  0.000000  0.000000  0.000000
 192  0.000000  0.500000  0.500000  0.000000
 193  0.000000  1.000000  0.000000  0.000000
 194  0.000000  0.000000  0.500000  0.500000
 195  0.000000  1.000000  0.000000  0.000000
 196  1.000000  0.000000  0.000000  0.000000
 197  0.500000  0.500000  0.000000  0.000000
 198  0.000000  1.000000  0.000000  0.000000
 199 --------------------------------------------------------------------------------
 200
 201 --------------------------------------------------------------------------------
 202         Motif 1 regular expression
 203 --------------------------------------------------------------------------------
 204 [CGA]T[CG][AG][AG]GC[AC]AA[AT]CA[CG]C[GT]CA[AC]C
 205 --------------------------------------------------------------------------------
 206
 207
 208
 209
 210 Time  7.72 secs.
 211
 212 ********************************************************************************
 213
 214
 215 ********************************************************************************
 216 MOTIF  2        width =   20   sites =  10   llr = 180   E-value = 8.7e-013
 217 ********************************************************************************
 218 --------------------------------------------------------------------------------
 219         Motif 2 Description
 220 --------------------------------------------------------------------------------
 221 Simplified        A  :3:::69932:::::::49a
 222 pos.-specific     C  8:1:a11:::3627:39:1:
 223 probability       G  1::::3::41546:a:16::
 224 matrix            T  179a:::1372:23:7::::
 225
 226          bits    2.5     *         *
 227                  2.3     *         *
 228                  2.0     *         * *
 229                  1.8     *         * *
 230 Information      1.5 *  **      *  * *  *
 231 content          1.3 * *** **   * ** ****
 232 (26.0 bits)      1.0 * *** **   *********
 233                  0.8 ********  **********
 234                  0.5 ********************
 235                  0.3 ********************
 236                  0.0 --------------------
 237
 238 Multilevel           CTTTCAAAGTGCGCGTCGAA
 239 consensus             A   G  AACGCT C A
 240 sequence                     T T T
 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_Skud_Contig2050.4      +    556  3.60e-13 TTCACTGGAT CTTTCAAAGTGCGCGTCGAA ACCACAAACC
 250 WashU_Sbay_Contig480.2       +    561  5.54e-13 TGGCAGAGAT CTTTCGAAGTGCGCGTCGAA ACCACAAACC
 251 MIT_Spar_c278_20970          +    550  5.52e-12 CAGTGAAGAT CTTTCGAATTGCGCGTCGAA ACCACAAACC
 252 SGD_Scer_YOR176W             +    548  1.17e-10 CATTGAAGAT CTTTCACATTGCGCGTCGAA ACCACAAACC
 253 MIT_Smik_c935_20455          +    534  2.24e-09 CAATAGAGTT CTCTCCAATTGCGCGTCAAA ACCACAAACC
 254 WashU_Skud_Contig2052.17     -    268  2.94e-09 ATGACCAAGA CATTCAAAAACGGCGTCAAA AAAAAAAAAG
 255 MIT_Smik_c273_7756           -    258  7.80e-09 TGATCAAAGT CATTCAAAGGCGCTGCCGAA AAAAATTGGT
 256 MIT_Spar_c19_8512            -    263  1.90e-08 CGATAAAAGT CATTCAAAATTGTTGCCGAA AAAAAAAAAT
 257 MIT_Sbay_c77_8808            -    258  8.58e-08 TGATCAAAAT TTTTCGAAAACGCTGCCAAA TAGAAAAAGG
 258 SGD_Scer_YGL040C             +    647  2.66e-07 TTTTGTATAT GTTTCAATGTTCTCGTGACA ATGCAGGCTT
 259 --------------------------------------------------------------------------------
 260
 261 --------------------------------------------------------------------------------
 262         Motif 2 block diagrams
 263 --------------------------------------------------------------------------------
 264 SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
 265 -------------            ----------------  -------------
 266 WashU_Skud_Contig2050.4           3.6e-13  555_[+2]_152
 267 WashU_Sbay_Contig480.2            5.5e-13  560_[+2]_147
 268 MIT_Spar_c278_20970               5.5e-12  549_[+2]_158
 269 SGD_Scer_YOR176W                  1.2e-10  547_[+2]_160
 270 MIT_Smik_c935_20455               2.2e-09  533_[+2]_174
 271 WashU_Skud_Contig2052.17          2.9e-09  267_[-2]_713
 272 MIT_Smik_c273_7756                7.8e-09  257_[-2]_723
 273 MIT_Spar_c19_8512                 1.9e-08  262_[-2]_718
 274 MIT_Sbay_c77_8808                 8.6e-08  257_[-2]_723
 275 SGD_Scer_YGL040C                  2.7e-07  646_[+2]_334
 276 --------------------------------------------------------------------------------
 277
 278 --------------------------------------------------------------------------------
 279         Motif 2 in BLOCKS format
 280 --------------------------------------------------------------------------------
 281 BL   MOTIF 2 width=20 seqs=10
 282 WashU_Skud_Contig2050.4  (  556) CTTTCAAAGTGCGCGTCGAA  1
 283 WashU_Sbay_Contig480.2   (  561) CTTTCGAAGTGCGCGTCGAA  1
 284 MIT_Spar_c278_20970      (  550) CTTTCGAATTGCGCGTCGAA  1
 285 SGD_Scer_YOR176W         (  548) CTTTCACATTGCGCGTCGAA  1
 286 MIT_Smik_c935_20455      (  534) CTCTCCAATTGCGCGTCAAA  1
 287 WashU_Skud_Contig2052.17 (  268) CATTCAAAAACGGCGTCAAA  1
 288 MIT_Smik_c273_7756       (  258) CATTCAAAGGCGCTGCCGAA  1
 289 MIT_Spar_c19_8512        (  263) CATTCAAAATTGTTGCCGAA  1
 290 MIT_Sbay_c77_8808        (  258) TTTTCGAAAACGCTGCCAAA  1
 291 SGD_Scer_YGL040C         (  647) GTTTCAATGTTCTCGTGACA  1
 292 //
 293
 294 --------------------------------------------------------------------------------
 295
 296 --------------------------------------------------------------------------------
 297         Motif 2 position-specific scoring matrix
 298 --------------------------------------------------------------------------------
 299 log-odds matrix: alength= 4 w= 20 n= 8445 bayes= 9.72024 E= 8.7e-013
 300   -997    219    -81   -169
 301    -11   -997   -997    111
 302   -997    -81   -997    147
 303   -997   -997   -997    162
 304   -997    251   -997   -997
 305     89    -81     77   -997
 306    147    -81   -997   -997
 307    147   -997   -997   -169
 308    -11   -997    119    -11
 309    -70   -997    -81    111
 310   -997     77    151    -70
 311   -997    177    119   -997
 312   -997     19    177    -70
 313   -997    199   -997    -11
 314   -997   -997    251   -997
 315   -997     77   -997    111
 316   -997    236    -81   -997
 317     30   -997    177   -997
 318    147    -81   -997   -997
 319    162   -997   -997   -997
 320 --------------------------------------------------------------------------------
 321
 322 --------------------------------------------------------------------------------
 323         Motif 2 position-specific probability matrix
 324 --------------------------------------------------------------------------------
 325 letter-probability matrix: alength= 4 w= 20 nsites= 10 E= 8.7e-013
 326  0.000000  0.800000  0.100000  0.100000
 327  0.300000  0.000000  0.000000  0.700000
 328  0.000000  0.100000  0.000000  0.900000
 329  0.000000  0.000000  0.000000  1.000000
 330  0.000000  1.000000  0.000000  0.000000
 331  0.600000  0.100000  0.300000  0.000000
 332  0.900000  0.100000  0.000000  0.000000
 333  0.900000  0.000000  0.000000  0.100000
 334  0.300000  0.000000  0.400000  0.300000
 335  0.200000  0.000000  0.100000  0.700000
 336  0.000000  0.300000  0.500000  0.200000
 337  0.000000  0.600000  0.400000  0.000000
 338  0.000000  0.200000  0.600000  0.200000
 339  0.000000  0.700000  0.000000  0.300000
 340  0.000000  0.000000  1.000000  0.000000
 341  0.000000  0.300000  0.000000  0.700000
 342  0.000000  0.900000  0.100000  0.000000
 343  0.400000  0.000000  0.600000  0.000000
 344  0.900000  0.100000  0.000000  0.000000
 345  1.000000  0.000000  0.000000  0.000000
 346 --------------------------------------------------------------------------------
 347
 348 --------------------------------------------------------------------------------
 349         Motif 2 regular expression
 350 --------------------------------------------------------------------------------
 351 C[TA]TTC[AG]AA[GAT][TA][GCT][CG][GCT][CT]G[TC]C[GA]AA
 352 --------------------------------------------------------------------------------
 353
 354
 355
 356
 357 Time 15.21 secs.
 358
 359 ********************************************************************************
 360
 361
 362 ********************************************************************************
 363 MOTIF  3        width =   20   sites =  10   llr = 185   E-value = 8.7e-014
 364 ********************************************************************************
 365 --------------------------------------------------------------------------------
 366         Motif 3 Description
 367 --------------------------------------------------------------------------------
 368 Simplified        A  :556:15:255:::1:2:::
 369 pos.-specific     C  55::a:5:435:8a415::9
 370 probability       G  :::::9:9:2::::::3:::
 371 matrix            T  5:54:::14::a2:59:aa1
 372
 373          bits    2.5     *        *
 374                  2.3     *        *
 375                  2.0     ** *     *     *
 376                  1.8     ** *     *     *
 377 Information      1.5     ** *   ***   ***
 378 content          1.3     ** *   *** * ***
 379 (26.7 bits)      1.0 **  ****  **** * ***
 380                  0.8 ** *****  **** *****
 381                  0.5 ********************
 382                  0.3 ********************
 383                  0.0 --------------------
 384
 385 Multilevel           CAAACGAGCAATCCTTCTTC
 386 consensus            TCTT  C TCC T C G
 387 sequence                     AG      A
 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_Smik_c935_20455          +    153  1.95e-11 CCAAAAGACT CCTTCGCGTCCTCCTTCTTC AAGTCTCATA
 397 MIT_Spar_c278_20970          +    158  1.95e-11 TAAAAGTATT CCTTCGCGTCCTCCTTCTTC AATCCCATAT
 398 SGD_Scer_YOR176W             +    156  1.95e-11 CAAAAGTATT CCTTCGCGTCCTCCTTCTTC AATCCCATAT
 399 WashU_Sbay_Contig480.2       +    206  4.98e-11 AAGAAGTATT CCTACGCGAGCTCCCTCTTC AAGTGCCAAA
 400 WashU_Skud_Contig2052.17     -    199  4.36e-10 ACGCAACGGG TAAACGAGCAATCCCTGTTC GGTGCGGTGA
 401 MIT_Spar_c19_8512            -    200  4.36e-10 AAACTACGGG TAAACGAGCAATCCCTGTTC GGTGCGGTGA
 402 SGD_Scer_YGL040C             -    199  4.36e-10 AAAATACGGG TAAACGAGCAATCCCTGTTC GGTGCGGTGA
 403 MIT_Smik_c273_7756           -    198  1.99e-09 GAACAACGGG TAAACGAGCAATCCTTATTC GGTGCGGTGA
 404 WashU_Skud_Contig2050.4      +    162  3.33e-08 AAGAAGTATT CCTTCGCGTGCTTCTCCTTT CTGTGTCAAA
 405 MIT_Sbay_c77_8808            +    824  6.99e-07 TACATAGAAC TAAACAATAAATTCATATTC AATAATACTT
 406 --------------------------------------------------------------------------------
 407
 408 --------------------------------------------------------------------------------
 409         Motif 3 block diagrams
 410 --------------------------------------------------------------------------------
 411 SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
 412 -------------            ----------------  -------------
 413 MIT_Smik_c935_20455               1.9e-11  152_[+3]_555
 414 MIT_Spar_c278_20970               1.9e-11  157_[+3]_550
 415 SGD_Scer_YOR176W                  1.9e-11  155_[+3]_552
 416 WashU_Sbay_Contig480.2              5e-11  205_[+3]_502
 417 WashU_Skud_Contig2052.17          4.4e-10  198_[-3]_782
 418 MIT_Spar_c19_8512                 4.4e-10  199_[-3]_781
 419 SGD_Scer_YGL040C                  4.4e-10  198_[-3]_782
 420 MIT_Smik_c273_7756                  2e-09  197_[-3]_783
 421 WashU_Skud_Contig2050.4           3.3e-08  161_[+3]_546
 422 MIT_Sbay_c77_8808                   7e-07  823_[+3]_157
 423 --------------------------------------------------------------------------------
 424
 425 --------------------------------------------------------------------------------
 426         Motif 3 in BLOCKS format
 427 --------------------------------------------------------------------------------
 428 BL   MOTIF 3 width=20 seqs=10
 429 MIT_Smik_c935_20455      (  153) CCTTCGCGTCCTCCTTCTTC  1
 430 MIT_Spar_c278_20970      (  158) CCTTCGCGTCCTCCTTCTTC  1
 431 SGD_Scer_YOR176W         (  156) CCTTCGCGTCCTCCTTCTTC  1
 432 WashU_Sbay_Contig480.2   (  206) CCTACGCGAGCTCCCTCTTC  1
 433 WashU_Skud_Contig2052.17 (  199) TAAACGAGCAATCCCTGTTC  1
 434 MIT_Spar_c19_8512        (  200) TAAACGAGCAATCCCTGTTC  1
 435 SGD_Scer_YGL040C         (  199) TAAACGAGCAATCCCTGTTC  1
 436 MIT_Smik_c273_7756       (  198) TAAACGAGCAATCCTTATTC  1
 437 WashU_Skud_Contig2050.4  (  162) CCTTCGCGTGCTTCTCCTTT  1
 438 MIT_Sbay_c77_8808        (  824) TAAACAATAAATTCATATTC  1
 439 //
 440
 441 --------------------------------------------------------------------------------
 442
 443 --------------------------------------------------------------------------------
 444         Motif 3 position-specific scoring matrix
 445 --------------------------------------------------------------------------------
 446 log-odds matrix: alength= 4 w= 20 n= 8445 bayes= 9.72024 E= 8.7e-014
 447   -997    151   -997     62
 448     62    151   -997   -997
 449     62   -997   -997     62
 450     89   -997   -997     30
 451   -997    251   -997   -997
 452   -169   -997    236   -997
 453     62    151   -997   -997
 454   -997   -997    236   -169
 455    -70    119   -997     30
 456     62     77     19   -997
 457     62    151   -997   -997
 458   -997   -997   -997    162
 459   -997    219   -997    -70
 460   -997    251   -997   -997
 461   -169    119   -997     62
 462   -997    -81   -997    147
 463    -70    151     77   -997
 464   -997   -997   -997    162
 465   -997   -997   -997    162
 466   -997    236   -997   -169
 467 --------------------------------------------------------------------------------
 468
 469 --------------------------------------------------------------------------------
 470         Motif 3 position-specific probability matrix
 471 --------------------------------------------------------------------------------
 472 letter-probability matrix: alength= 4 w= 20 nsites= 10 E= 8.7e-014
 473  0.000000  0.500000  0.000000  0.500000
 474  0.500000  0.500000  0.000000  0.000000
 475  0.500000  0.000000  0.000000  0.500000
 476  0.600000  0.000000  0.000000  0.400000
 477  0.000000  1.000000  0.000000  0.000000
 478  0.100000  0.000000  0.900000  0.000000
 479  0.500000  0.500000  0.000000  0.000000
 480  0.000000  0.000000  0.900000  0.100000
 481  0.200000  0.400000  0.000000  0.400000
 482  0.500000  0.300000  0.200000  0.000000
 483  0.500000  0.500000  0.000000  0.000000
 484  0.000000  0.000000  0.000000  1.000000
 485  0.000000  0.800000  0.000000  0.200000
 486  0.000000  1.000000  0.000000  0.000000
 487  0.100000  0.400000  0.000000  0.500000
 488  0.000000  0.100000  0.000000  0.900000
 489  0.200000  0.500000  0.300000  0.000000
 490  0.000000  0.000000  0.000000  1.000000
 491  0.000000  0.000000  0.000000  1.000000
 492  0.000000  0.900000  0.000000  0.100000
 493 --------------------------------------------------------------------------------
 494
 495 --------------------------------------------------------------------------------
 496         Motif 3 regular expression
 497 --------------------------------------------------------------------------------
 498 [CT][AC][AT][AT]CG[AC]G[CTA][ACG][AC]T[CT]C[TC]T[CGA]TTC
 499 --------------------------------------------------------------------------------
 500
 501
 502
 503
 504 Time 22.63 secs.
 505
 506 ********************************************************************************
 507
 508
 509 ********************************************************************************
 510 MOTIF  4        width =   20   sites =  10   llr = 177   E-value = 3.5e-011
 511 ********************************************************************************
 512 --------------------------------------------------------------------------------
 513         Motif 4 Description
 514 --------------------------------------------------------------------------------
 515 Simplified        A  7:2a19aa2:61:4969a:9
 516 pos.-specific     C  1a7:5:::5a:16::4::1:
 517 probability       G  2:::31::::4246::::::
 518 matrix            T  ::1:1:::3::6::1:1:91
 519
 520          bits    2.5  *       *
 521                  2.3  *       *
 522                  2.0  *       *
 523                  1.8  *       *
 524 Information      1.5  * *  ** *  *    *
 525 content          1.3  * * *** *  *** ****
 526 (25.6 bits)      1.0  *** *** ** ********
 527                  0.8 ******** ** ********
 528                  0.5 *********** ********
 529                  0.3 ********************
 530                  0.0 --------------------
 531
 532 Multilevel           ACCACAAACCATCGAAAATA
 533 consensus            G A G   T GGGA C
 534 sequence                     A
 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_Skud_Contig2050.4      +    576  3.12e-12 GCGCGTCGAA ACCACAAACCGTCGAAAATA TTGATCATCT
 544 MIT_Smik_c935_20455          +    554  3.12e-12 GCGCGTCAAA ACCACAAACCGTCGAAAATA ATGATCATCT
 545 MIT_Spar_c278_20970          +    570  3.12e-12 GCGCGTCGAA ACCACAAACCGTCGAAAATA ATGGTCATCT
 546 WashU_Sbay_Contig480.2       +    581  5.53e-11 GCGCGTCGAA ACCACAAACCATCAAAAATA TCGACCATCT
 547 SGD_Scer_YOR176W             +    568  1.19e-10 GCGCGTCGAA ACCACAAACCGTCGAAAACA ATGGTCATCT
 548 WashU_Skud_Contig2052.17     +     87  2.26e-09 AGCTAATTTA GCCAGAAATCATGAACAATA GGATGACGCA
 549 MIT_Spar_c19_8512            +     89  2.98e-08 GGCTGATTGG GCCAAAAAACAAGGACAATA GAATGACACA
 550 MIT_Smik_c273_7756           +     89  9.01e-08 GCTAAATAGG CCAATAAATCAGGAACAATA GAATGACGCA
 551 SGD_Scer_YGL040C             -    535  1.20e-07 TTTTTAATTA ACTAGAAATCAGCGTCAATT ATAGTTTCTG
 552 MIT_Sbay_c77_8808            +    771  2.18e-07 CAATATGTGG ACAAGGAAACACGAAATATA TTGGGATAAA
 553 --------------------------------------------------------------------------------
 554
 555 --------------------------------------------------------------------------------
 556         Motif 4 block diagrams
 557 --------------------------------------------------------------------------------
 558 SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
 559 -------------            ----------------  -------------
 560 WashU_Skud_Contig2050.4           3.1e-12  575_[+4]_132
 561 MIT_Smik_c935_20455               3.1e-12  553_[+4]_154
 562 MIT_Spar_c278_20970               3.1e-12  569_[+4]_138
 563 WashU_Sbay_Contig480.2            5.5e-11  580_[+4]_127
 564 SGD_Scer_YOR176W                  1.2e-10  567_[+4]_140
 565 WashU_Skud_Contig2052.17          2.3e-09  86_[+4]_894
 566 MIT_Spar_c19_8512                   3e-08  88_[+4]_892
 567 MIT_Smik_c273_7756                  9e-08  88_[+4]_892
 568 SGD_Scer_YGL040C                  1.2e-07  534_[-4]_446
 569 MIT_Sbay_c77_8808                 2.2e-07  770_[+4]_210
 570 --------------------------------------------------------------------------------
 571
 572 --------------------------------------------------------------------------------
 573         Motif 4 in BLOCKS format
 574 --------------------------------------------------------------------------------
 575 BL   MOTIF 4 width=20 seqs=10
 576 WashU_Skud_Contig2050.4  (  576) ACCACAAACCGTCGAAAATA  1
 577 MIT_Smik_c935_20455      (  554) ACCACAAACCGTCGAAAATA  1
 578 MIT_Spar_c278_20970      (  570) ACCACAAACCGTCGAAAATA  1
 579 WashU_Sbay_Contig480.2   (  581) ACCACAAACCATCAAAAATA  1
 580 SGD_Scer_YOR176W         (  568) ACCACAAACCGTCGAAAACA  1
 581 WashU_Skud_Contig2052.17 (   87) GCCAGAAATCATGAACAATA  1
 582 MIT_Spar_c19_8512        (   89) GCCAAAAAACAAGGACAATA  1
 583 MIT_Smik_c273_7756       (   89) CCAATAAATCAGGAACAATA  1
 584 SGD_Scer_YGL040C         (  535) ACTAGAAATCAGCGTCAATT  1
 585 MIT_Sbay_c77_8808        (  771) ACAAGGAAACACGAAATATA  1
 586 //
 587
 588 --------------------------------------------------------------------------------
 589
 590 --------------------------------------------------------------------------------
 591         Motif 4 position-specific scoring matrix
 592 --------------------------------------------------------------------------------
 593 log-odds matrix: alength= 4 w= 20 n= 8445 bayes= 9.72024 E= 3.5e-011
 594    111    -81     19   -997
 595   -997    251   -997   -997
 596    -70    199   -997   -169
 597    162   -997   -997   -997
 598   -169    151     77   -169
 599    147   -997    -81   -997
 600    162   -997   -997   -997
 601    162   -997   -997   -997
 602    -70    151   -997    -11
 603   -997    251   -997   -997
 604     89   -997    119   -997
 605   -169    -81     19     89
 606   -997    177    119   -997
 607     30   -997    177   -997
 608    147   -997   -997   -169
 609     89    119   -997   -997
 610    147   -997   -997   -169
 611    162   -997   -997   -997
 612   -997    -81   -997    147
 613    147   -997   -997   -169
 614 --------------------------------------------------------------------------------
 615
 616 --------------------------------------------------------------------------------
 617         Motif 4 position-specific probability matrix
 618 --------------------------------------------------------------------------------
 619 letter-probability matrix: alength= 4 w= 20 nsites= 10 E= 3.5e-011
 620  0.700000  0.100000  0.200000  0.000000
 621  0.000000  1.000000  0.000000  0.000000
 622  0.200000  0.700000  0.000000  0.100000
 623  1.000000  0.000000  0.000000  0.000000
 624  0.100000  0.500000  0.300000  0.100000
 625  0.900000  0.000000  0.100000  0.000000
 626  1.000000  0.000000  0.000000  0.000000
 627  1.000000  0.000000  0.000000  0.000000
 628  0.200000  0.500000  0.000000  0.300000
 629  0.000000  1.000000  0.000000  0.000000
 630  0.600000  0.000000  0.400000  0.000000
 631  0.100000  0.100000  0.200000  0.600000
 632  0.000000  0.600000  0.400000  0.000000
 633  0.400000  0.000000  0.600000  0.000000
 634  0.900000  0.000000  0.000000  0.100000
 635  0.600000  0.400000  0.000000  0.000000
 636  0.900000  0.000000  0.000000  0.100000
 637  1.000000  0.000000  0.000000  0.000000
 638  0.000000  0.100000  0.000000  0.900000
 639  0.900000  0.000000  0.000000  0.100000
 640 --------------------------------------------------------------------------------
 641
 642 --------------------------------------------------------------------------------
 643         Motif 4 regular expression
 644 --------------------------------------------------------------------------------
 645 [AG]C[CA]A[CG]AAA[CTA]C[AG][TG][CG][GA]A[AC]AATA
 646 --------------------------------------------------------------------------------
 647
 648
 649
 650
 651 Time 29.89 secs.
 652
 653 ********************************************************************************
 654
 655
 656 ********************************************************************************
 657 MOTIF  5        width =   15   sites =  10   llr = 143   E-value = 2.9e-005
 658 ********************************************************************************
 659 --------------------------------------------------------------------------------
 660         Motif 5 Description
 661 --------------------------------------------------------------------------------
 662 Simplified        A  :6::11:1::3116:
 663 pos.-specific     C  ::4a::::a8:12:1
 664 probability       G  9::::8:9:118:3:
 665 matrix            T  146:91a::16:719
 666
 667          bits    2.5    *    *
 668                  2.3    *    *
 669                  2.0 *  *   **
 670                  1.8 *  *   **
 671 Information      1.5 *  * ***** *
 672 content          1.3 *  ******* *  *
 673 (20.7 bits)      1.0 * ******** *  *
 674                  0.8 ********** ** *
 675                  0.5 ***************
 676                  0.3 ***************
 677                  0.0 ---------------
 678
 679 Multilevel           GATCTGTGCCTGTAT
 680 consensus             TC       A CG
 681 sequence
 682
 683 --------------------------------------------------------------------------------
 684
 685 --------------------------------------------------------------------------------
 686         Motif 5 sites sorted by position p-value
 687 --------------------------------------------------------------------------------
 688 Sequence name            Strand  Start   P-value                 Site
 689 -------------            ------  ----- ---------            ---------------
 690 WashU_Sbay_Contig480.2       -    655  3.42e-10 CTTCTTATCT GACCTGTGCCTGTAT GAAGAGCTTC
 691 MIT_Smik_c935_20455          -    630  3.42e-10 CTTCTTGTTA GACCTGTGCCTGTAT GGAGTATTTC
 692 MIT_Spar_c278_20970          -    645  3.42e-10 ATTCTTTCTG GACCTGTGCCTGTAT CGTGTCTTTG
 693 SGD_Scer_YOR176W             -    641  3.42e-10 CTTCTTGCTT GACCTGTGCCTGTAT TTTGTCCTTG
 694 WashU_Skud_Contig2050.4      -    650  1.56e-08 TCTTCTTGTT GATCTGTGCCTGAAT GGAATATTTC
 695 SGD_Scer_YGL040C             +    944  5.03e-08 TGTCATCTGT GTTCTGTGCCAGTAC ACCGGACTCG
 696 MIT_Spar_c19_8512            +    985  1.58e-07 TATGATCTGT GTTCTATGCCAGTGT A
 697 MIT_Smik_c273_7756           -    540  3.80e-06 TTATTGTTTA GTTCTGTGCGGCCTT GTTTTAAGCA
 698 WashU_Skud_Contig2052.17     -    662  5.05e-06 GTTATTGTTT GTTCAGTGCTAATGT ATTTATGGGT
 699 MIT_Sbay_c77_8808            -    324  5.92e-06 GATTTGTTCA TATCTTTACCTGCGT GCCCTAAAAT
 700 --------------------------------------------------------------------------------
 701
 702 --------------------------------------------------------------------------------
 703         Motif 5 block diagrams
 704 --------------------------------------------------------------------------------
 705 SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
 706 -------------            ----------------  -------------
 707 WashU_Sbay_Contig480.2            3.4e-10  654_[-5]_58
 708 MIT_Smik_c935_20455               3.4e-10  629_[-5]_83
 709 MIT_Spar_c278_20970               3.4e-10  644_[-5]_68
 710 SGD_Scer_YOR176W                  3.4e-10  640_[-5]_72
 711 WashU_Skud_Contig2050.4           1.6e-08  649_[-5]_63
 712 SGD_Scer_YGL040C                    5e-08  943_[+5]_42
 713 MIT_Spar_c19_8512                 1.6e-07  984_[+5]_1
 714 MIT_Smik_c273_7756                3.8e-06  539_[-5]_446
 715 WashU_Skud_Contig2052.17            5e-06  661_[-5]_324
 716 MIT_Sbay_c77_8808                 5.9e-06  323_[-5]_662
 717 --------------------------------------------------------------------------------
 718
 719 --------------------------------------------------------------------------------
 720         Motif 5 in BLOCKS format
 721 --------------------------------------------------------------------------------
 722 BL   MOTIF 5 width=15 seqs=10
 723 WashU_Sbay_Contig480.2   (  655) GACCTGTGCCTGTAT  1
 724 MIT_Smik_c935_20455      (  630) GACCTGTGCCTGTAT  1
 725 MIT_Spar_c278_20970      (  645) GACCTGTGCCTGTAT  1
 726 SGD_Scer_YOR176W         (  641) GACCTGTGCCTGTAT  1
 727 WashU_Skud_Contig2050.4  (  650) GATCTGTGCCTGAAT  1
 728 SGD_Scer_YGL040C         (  944) GTTCTGTGCCAGTAC  1
 729 MIT_Spar_c19_8512        (  985) GTTCTATGCCAGTGT  1
 730 MIT_Smik_c273_7756       (  540) GTTCTGTGCGGCCTT  1
 731 WashU_Skud_Contig2052.17 (  662) GTTCAGTGCTAATGT  1
 732 MIT_Sbay_c77_8808        (  324) TATCTTTACCTGCGT  1
 733 //
 734
 735 --------------------------------------------------------------------------------
 736
 737 --------------------------------------------------------------------------------
 738         Motif 5 position-specific scoring matrix
 739 --------------------------------------------------------------------------------
 740 log-odds matrix: alength= 4 w= 15 n= 8495 bayes= 9.72877 E= 2.9e-005
 741   -997   -997    236   -169
 742     89   -997   -997     30
 743   -997    119   -997     89
 744   -997    251   -997   -997
 745   -169   -997   -997    147
 746   -169   -997    219   -169
 747   -997   -997   -997    162
 748   -169   -997    236   -997
 749   -997    251   -997   -997
 750   -997    219    -81   -169
 751    -11   -997    -81     89
 752   -169    -81    219   -997
 753   -169     19   -997    111
 754     89   -997     77   -169
 755   -997    -81   -997    147
 756 --------------------------------------------------------------------------------
 757
 758 --------------------------------------------------------------------------------
 759         Motif 5 position-specific probability matrix
 760 --------------------------------------------------------------------------------
 761 letter-probability matrix: alength= 4 w= 15 nsites= 10 E= 2.9e-005
 762  0.000000  0.000000  0.900000  0.100000
 763  0.600000  0.000000  0.000000  0.400000
 764  0.000000  0.400000  0.000000  0.600000
 765  0.000000  1.000000  0.000000  0.000000
 766  0.100000  0.000000  0.000000  0.900000
 767  0.100000  0.000000  0.800000  0.100000
 768  0.000000  0.000000  0.000000  1.000000
 769  0.100000  0.000000  0.900000  0.000000
 770  0.000000  1.000000  0.000000  0.000000
 771  0.000000  0.800000  0.100000  0.100000
 772  0.300000  0.000000  0.100000  0.600000
 773  0.100000  0.100000  0.800000  0.000000
 774  0.100000  0.200000  0.000000  0.700000
 775  0.600000  0.000000  0.300000  0.100000
 776  0.000000  0.100000  0.000000  0.900000
 777 --------------------------------------------------------------------------------
 778
 779 --------------------------------------------------------------------------------
 780         Motif 5 regular expression
 781 --------------------------------------------------------------------------------
 782 G[AT][TC]CTGTGCC[TA]G[TC][AG]T
 783 --------------------------------------------------------------------------------
 784
 785
 786
 787
 788 Time 37.04 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                 7.45e-21  178_[+1(6.49e-13)]_[-3(4.36e-10)]_316_[-4(1.20e-07)]_92_[+2(2.66e-07)]_127_[+1(6.62e-05)]_130_[+5(5.03e-08)]_42
 803 MIT_Spar_c19_8512                1.88e-22  88_[+4(2.98e-08)]_71_[+1(2.28e-13)]_[-3(4.36e-10)]_43_[-2(1.90e-08)]_150_[+3(3.32e-05)]_465_[-3(5.73e-05)]_47_[+5(1.58e-07)]_1
 804 MIT_Smik_c273_7756               1.86e-20  88_[+4(9.01e-08)]_69_[+1(2.28e-13)]_[-3(1.99e-09)]_40_[-2(7.80e-09)]_262_[-5(3.80e-06)]_446
 805 MIT_Sbay_c77_8808                1.33e-14  179_[+1(3.46e-11)]_58_[-2(8.58e-08)]_46_[-5(5.92e-06)]_432_[+4(2.18e-07)]_33_[+3(6.99e-07)]_90_[-1(4.25e-05)]_47
 806 WashU_Skud_Contig2052.17         7.44e-23  86_[+4(2.26e-09)]_72_[+1(2.28e-13)]_[-3(4.36e-10)]_49_[-2(2.94e-09)]_374_[-5(5.05e-06)]_131_[+3(3.98e-05)]_143_[+1(9.33e-05)]_10
 807 SGD_Scer_YOR176W                 4.25e-28  100_[-4(3.19e-05)]_35_[+3(1.95e-11)]_136_[+3(4.98e-05)]_174_[-1(5.11e-10)]_22_[+2(1.17e-10)]_[+4(1.19e-10)]_53_[-5(3.42e-10)]_72
 808 MIT_Spar_c278_20970              1.73e-31  48_[+3(3.79e-05)]_89_[+3(1.95e-11)]_330_[-1(1.13e-10)]_22_[+2(5.52e-12)]_[+4(3.12e-12)]_55_[-5(3.42e-10)]_68
 809 MIT_Smik_c935_20455              5.70e-28  152_[+3(1.95e-11)]_127_[+3(4.68e-06)]_172_[-1(1.39e-09)]_22_[+2(2.24e-09)]_[+4(3.12e-12)]_56_[-5(3.42e-10)]_83
 810 WashU_Skud_Contig2050.4          8.21e-27  161_[+3(3.33e-08)]_256_[+4(2.13e-05)]_51_[-1(1.85e-09)]_2_[+1(8.00e-05)]_5_[+2(3.60e-13)]_[+4(3.12e-12)]_54_[-5(1.56e-08)]_63
 811 WashU_Sbay_Contig480.2           1.32e-30  205_[+3(4.98e-11)]_292_[-1(2.09e-10)]_23_[+2(5.54e-13)]_[+4(5.53e-11)]_10_[-3(4.52e-05)]_24_[-5(3.42e-10)]_58
 812 --------------------------------------------------------------------------------
 813
 814 ********************************************************************************
 815
 816
 817 ********************************************************************************
 818 Stopped because nmotifs = 5 reached.
 819 ********************************************************************************
 820
 821 CPU: dhn02990.mrc-dunn.cam.ac.uk
 822
 823 ********************************************************************************