t/data/map_hem/HEM12-HEM14.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= HEM12-HEM14.fa
  32 ALPHABET= ACGT
  33 Sequence name            Weight Length  Sequence name            Weight Length
  34 -------------            ------ ------  -------------            ------ ------
  35 SGD_Scer_YDR047W         1.0000   1000  MIT_Spar_c130_3923       1.0000   1000
  36 MIT_Sbay_c896_21277      1.0000   1000  WashU_Skud_Contig1362.1  1.0000    761
  37 SGD_Scer_YER014W         1.0000    322  MIT_Spar_c425_6072       1.0000    322
  38 MIT_Smik_c283_5928       1.0000    322  MIT_Sbay_c84_6418        1.0000    322
  39 ********************************************************************************
  40
  41 ********************************************************************************
  42 COMMAND LINE SUMMARY
  43 ********************************************************************************
  44 This information can also be useful in the event you wish to report a
  45 problem with the MEME software.
  46
  47 command: meme HEM12-HEM14.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
  48
  49 model:  mod=          oops    nmotifs=         5    evt=           inf
  50 object function=  E-value of product of p-values
  51 width:  minw=            6    maxw=           20    minic=        0.00
  52 width:  wg=             11    ws=              1    endgaps=       yes
  53 nsites: minsites=        8    maxsites=        8    wnsites=       0.8
  54 theta:  prob=            1    spmap=         uni    spfuzz=        0.5
  55 em:     prior=   dirichlet    b=            0.01    maxiter=        50
  56         distance=    1e-05
  57 data:   n=            5049    N=               8
  58 strands: + -
  59 sample: seed=            0    seqfrac=         1
  60 Letter frequencies in dataset:
  61 A 0.296 C 0.204 G 0.204 T 0.296
  62 Background letter frequencies (from yeast.nc.1.freq):
  63 A 0.324 C 0.176 G 0.176 T 0.324
  64 ********************************************************************************
  65
  66
  67 ********************************************************************************
  68 MOTIF  1        width =   15   sites =   8   llr = 132   E-value = 1.4e-008
  69 ********************************************************************************
  70 --------------------------------------------------------------------------------
  71         Motif 1 Description
  72 --------------------------------------------------------------------------------
  73 Simplified        A  a:::::aa1:65:58
  74 pos.-specific     C  :a5aa:::4a4:5:3
  75 probability       G  :::::a::4:::5::
  76 matrix            T  ::5:::::1::5:5:
  77
  78          bits    2.5  * ***   *
  79                  2.3  * ***   *
  80                  2.0  * ***   *
  81                  1.8  * ***   *
  82 Information      1.5 ** ***** *  *
  83 content          1.3 ** ***** *  *
  84 (23.8 bits)      1.0 ******** ** * *
  85                  0.8 ******** ** * *
  86                  0.5 ***************
  87                  0.3 ***************
  88                  0.0 ---------------
  89
  90 Multilevel           ACCCCGAACCAACAA
  91 consensus              T     G CTGTC
  92 sequence
  93
  94 --------------------------------------------------------------------------------
  95
  96 --------------------------------------------------------------------------------
  97         Motif 1 sites sorted by position p-value
  98 --------------------------------------------------------------------------------
  99 Sequence name            Strand  Start   P-value                 Site
 100 -------------            ------  ----- ---------            ---------------
 101 MIT_Sbay_c896_21277          +    213  2.96e-09 GCGTCAAAAA ACCCCGAACCCTGTA TAAACGAGGA
 102 MIT_Spar_c130_3923           +    242  1.00e-08 TGCCACCAAA ACCCCGAACCCTGTC CCGTATATAC
 103 SGD_Scer_YDR047W             +    245  1.00e-08 GCCGCCAAAA ACCCCGAACCCTGTC CTGTATATAC
 104 MIT_Smik_c283_5928           +    117  2.85e-08 TTAAATACGG ACTCCGAAGCAACAA GGTCGAAGGC
 105 MIT_Spar_c425_6072           +    120  2.85e-08 ATACTCCGCG ACTCCGAAGCAACAA AATGTCGAAG
 106 SGD_Scer_YER014W             +    121  2.85e-08 ATACTCCGCG ACTCCGAAGCAACAA AGTGTCGAAG
 107 WashU_Skud_Contig1362.1      +    208  5.25e-08 CTGCCAAAAA ACCCCGAATCATGTA GAAGCGAGAA
 108 MIT_Sbay_c84_6418            +    113  8.97e-08 ATACTCTGCG ACTCCGAAACAACAA AATCTCGAAG
 109 --------------------------------------------------------------------------------
 110
 111 --------------------------------------------------------------------------------
 112         Motif 1 block diagrams
 113 --------------------------------------------------------------------------------
 114 SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
 115 -------------            ----------------  -------------
 116 MIT_Sbay_c896_21277                 3e-09  212_[+1]_773
 117 MIT_Spar_c130_3923                  1e-08  241_[+1]_744
 118 SGD_Scer_YDR047W                    1e-08  244_[+1]_741
 119 MIT_Smik_c283_5928                2.9e-08  116_[+1]_191
 120 MIT_Spar_c425_6072                2.9e-08  119_[+1]_188
 121 SGD_Scer_YER014W                  2.9e-08  120_[+1]_187
 122 WashU_Skud_Contig1362.1           5.3e-08  207_[+1]_539
 123 MIT_Sbay_c84_6418                   9e-08  112_[+1]_195
 124 --------------------------------------------------------------------------------
 125
 126 --------------------------------------------------------------------------------
 127         Motif 1 in BLOCKS format
 128 --------------------------------------------------------------------------------
 129 BL   MOTIF 1 width=15 seqs=8
 130 MIT_Sbay_c896_21277      (  213) ACCCCGAACCCTGTA  1
 131 MIT_Spar_c130_3923       (  242) ACCCCGAACCCTGTC  1
 132 SGD_Scer_YDR047W         (  245) ACCCCGAACCCTGTC  1
 133 MIT_Smik_c283_5928       (  117) ACTCCGAAGCAACAA  1
 134 MIT_Spar_c425_6072       (  120) ACTCCGAAGCAACAA  1
 135 SGD_Scer_YER014W         (  121) ACTCCGAAGCAACAA  1
 136 WashU_Skud_Contig1362.1  (  208) ACCCCGAATCATGTA  1
 137 MIT_Sbay_c84_6418        (  113) ACTCCGAAACAACAA  1
 138 //
 139
 140 --------------------------------------------------------------------------------
 141
 142 --------------------------------------------------------------------------------
 143         Motif 1 position-specific scoring matrix
 144 --------------------------------------------------------------------------------
 145 log-odds matrix: alength= 4 w= 15 n= 4937 bayes= 9.26708 E= 1.4e-008
 146    162   -965   -965   -965
 147   -965    251   -965   -965
 148   -965    151   -965     62
 149   -965    251   -965   -965
 150   -965    251   -965   -965
 151   -965   -965    251   -965
 152    162   -965   -965   -965
 153    162   -965   -965   -965
 154   -137    109    109   -137
 155   -965    251   -965   -965
 156     95    109   -965   -965
 157     62   -965   -965     62
 158   -965    151    151   -965
 159     62   -965   -965     62
 160    121     51   -965   -965
 161 --------------------------------------------------------------------------------
 162
 163 --------------------------------------------------------------------------------
 164         Motif 1 position-specific probability matrix
 165 --------------------------------------------------------------------------------
 166 letter-probability matrix: alength= 4 w= 15 nsites= 8 E= 1.4e-008
 167  1.000000  0.000000  0.000000  0.000000
 168  0.000000  1.000000  0.000000  0.000000
 169  0.000000  0.500000  0.000000  0.500000
 170  0.000000  1.000000  0.000000  0.000000
 171  0.000000  1.000000  0.000000  0.000000
 172  0.000000  0.000000  1.000000  0.000000
 173  1.000000  0.000000  0.000000  0.000000
 174  1.000000  0.000000  0.000000  0.000000
 175  0.125000  0.375000  0.375000  0.125000
 176  0.000000  1.000000  0.000000  0.000000
 177  0.625000  0.375000  0.000000  0.000000
 178  0.500000  0.000000  0.000000  0.500000
 179  0.000000  0.500000  0.500000  0.000000
 180  0.500000  0.000000  0.000000  0.500000
 181  0.750000  0.250000  0.000000  0.000000
 182 --------------------------------------------------------------------------------
 183
 184 --------------------------------------------------------------------------------
 185         Motif 1 regular expression
 186 --------------------------------------------------------------------------------
 187 AC[CT]CCGAA[CG]C[AC][AT][CG][AT][AC]
 188 --------------------------------------------------------------------------------
 189
 190
 191
 192
 193 Time  2.78 secs.
 194
 195 ********************************************************************************
 196
 197
 198 ********************************************************************************
 199 MOTIF  2        width =   20   sites =   8   llr = 144   E-value = 2.6e-007
 200 ********************************************************************************
 201 --------------------------------------------------------------------------------
 202         Motif 2 Description
 203 --------------------------------------------------------------------------------
 204 Simplified        A  61:888::9:166::138::
 205 pos.-specific     C  48131:a1::813:1:5::8
 206 probability       G  :11::3:91a::::88:3a:
 207 matrix            T  ::8:1:::::131a113::3
 208
 209          bits    2.5       *  *        *
 210                  2.3       *  *        *
 211                  2.0       ** *        *
 212                  1.8       ** *        *
 213 Information      1.5       ** *   *    **
 214 content          1.3  *    *****  ***  **
 215 (26.0 bits)      1.0 ** * ******  *** ***
 216                  0.8 ***********  *** ***
 217                  0.5 ********************
 218                  0.3 ********************
 219                  0.0 --------------------
 220
 221 Multilevel           ACTAAACGAGCAATGGCAGC
 222 consensus            C  C G     TC   AG T
 223 sequence                             T
 224
 225 --------------------------------------------------------------------------------
 226
 227 --------------------------------------------------------------------------------
 228         Motif 2 sites sorted by position p-value
 229 --------------------------------------------------------------------------------
 230 Sequence name            Strand  Start   P-value                    Site
 231 -------------            ------  ----- ---------            --------------------
 232 SGD_Scer_YER014W             +    168  5.54e-13 GCGTTTTGTA ACTAAACGAGCAATGGCAGC TTTCAATTAA
 233 MIT_Smik_c283_5928           +    162  8.88e-12 GCATTTTACA ACTAAACGAGCAATGGTAGC TTTTGATTGA
 234 MIT_Spar_c425_6072           +    167  5.42e-11 GCGTTTTGCA ACTAAACGAGTAATGGCAGC TTTTAATTAA
 235 MIT_Sbay_c84_6418            +    163  5.99e-10 AATATTCACC ACTAAACGAGCAATGACAGT TATATTCAAA
 236 MIT_Sbay_c896_21277          -    914  4.51e-09 TTTTCCCGAG CAGAAACGAGCCCTGGAAGC TGCCTTCATT
 237 MIT_Spar_c130_3923           -    836  3.57e-08 TGTCTTTCCA ACTCAGCGAGATTTGTCGGC CGGAAAAAAA
 238 WashU_Skud_Contig1362.1      +    659  6.59e-08 AACATGCCGT CCCCTACCAGCTCTCGAAGC GGGCCTAGCA
 239 SGD_Scer_YDR047W             -    382  1.24e-07 TTGTAGTATA CGTACGCGGGCAATTGTGGT GACAGTATCT
 240 --------------------------------------------------------------------------------
 241
 242 --------------------------------------------------------------------------------
 243         Motif 2 block diagrams
 244 --------------------------------------------------------------------------------
 245 SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
 246 -------------            ----------------  -------------
 247 SGD_Scer_YER014W                  5.5e-13  167_[+2]_135
 248 MIT_Smik_c283_5928                8.9e-12  161_[+2]_141
 249 MIT_Spar_c425_6072                5.4e-11  166_[+2]_136
 250 MIT_Sbay_c84_6418                   6e-10  162_[+2]_140
 251 MIT_Sbay_c896_21277               4.5e-09  913_[-2]_67
 252 MIT_Spar_c130_3923                3.6e-08  835_[-2]_145
 253 WashU_Skud_Contig1362.1           6.6e-08  658_[+2]_83
 254 SGD_Scer_YDR047W                  1.2e-07  381_[-2]_599
 255 --------------------------------------------------------------------------------
 256
 257 --------------------------------------------------------------------------------
 258         Motif 2 in BLOCKS format
 259 --------------------------------------------------------------------------------
 260 BL   MOTIF 2 width=20 seqs=8
 261 SGD_Scer_YER014W         (  168) ACTAAACGAGCAATGGCAGC  1
 262 MIT_Smik_c283_5928       (  162) ACTAAACGAGCAATGGTAGC  1
 263 MIT_Spar_c425_6072       (  167) ACTAAACGAGTAATGGCAGC  1
 264 MIT_Sbay_c84_6418        (  163) ACTAAACGAGCAATGACAGT  1
 265 MIT_Sbay_c896_21277      (  914) CAGAAACGAGCCCTGGAAGC  1
 266 MIT_Spar_c130_3923       (  836) ACTCAGCGAGATTTGTCGGC  1
 267 WashU_Skud_Contig1362.1  (  659) CCCCTACCAGCTCTCGAAGC  1
 268 SGD_Scer_YDR047W         (  382) CGTACGCGGGCAATTGTGGT  1
 269 //
 270
 271 --------------------------------------------------------------------------------
 272
 273 --------------------------------------------------------------------------------
 274         Motif 2 position-specific scoring matrix
 275 --------------------------------------------------------------------------------
 276 log-odds matrix: alength= 4 w= 20 n= 4897 bayes= 9.25532 E= 2.6e-007
 277     95    109   -965   -965
 278   -137    209    -49   -965
 279   -965    -49    -49    121
 280    121     51   -965   -965
 281    121    -49   -965   -137
 282    121   -965     51   -965
 283   -965    251   -965   -965
 284   -965    -49    232   -965
 285    143   -965    -49   -965
 286   -965   -965    251   -965
 287   -137    209   -965   -137
 288     95    -49   -965    -38
 289     95     51   -965   -137
 290   -965   -965   -965    162
 291   -965    -49    209   -137
 292   -137   -965    209   -137
 293    -38    151   -965    -38
 294    121   -965     51   -965
 295   -965   -965    251   -965
 296   -965    209   -965    -38
 297 --------------------------------------------------------------------------------
 298
 299 --------------------------------------------------------------------------------
 300         Motif 2 position-specific probability matrix
 301 --------------------------------------------------------------------------------
 302 letter-probability matrix: alength= 4 w= 20 nsites= 8 E= 2.6e-007
 303  0.625000  0.375000  0.000000  0.000000
 304  0.125000  0.750000  0.125000  0.000000
 305  0.000000  0.125000  0.125000  0.750000
 306  0.750000  0.250000  0.000000  0.000000
 307  0.750000  0.125000  0.000000  0.125000
 308  0.750000  0.000000  0.250000  0.000000
 309  0.000000  1.000000  0.000000  0.000000
 310  0.000000  0.125000  0.875000  0.000000
 311  0.875000  0.000000  0.125000  0.000000
 312  0.000000  0.000000  1.000000  0.000000
 313  0.125000  0.750000  0.000000  0.125000
 314  0.625000  0.125000  0.000000  0.250000
 315  0.625000  0.250000  0.000000  0.125000
 316  0.000000  0.000000  0.000000  1.000000
 317  0.000000  0.125000  0.750000  0.125000
 318  0.125000  0.000000  0.750000  0.125000
 319  0.250000  0.500000  0.000000  0.250000
 320  0.750000  0.000000  0.250000  0.000000
 321  0.000000  0.000000  1.000000  0.000000
 322  0.000000  0.750000  0.000000  0.250000
 323 --------------------------------------------------------------------------------
 324
 325 --------------------------------------------------------------------------------
 326         Motif 2 regular expression
 327 --------------------------------------------------------------------------------
 328 [AC]CT[AC]A[AG]CGAGC[AT][AC]TGG[CAT][AG]G[CT]
 329 --------------------------------------------------------------------------------
 330
 331
 332
 333
 334 Time  5.72 secs.
 335
 336 ********************************************************************************
 337
 338
 339 ********************************************************************************
 340 MOTIF  3        width =   18   sites =   8   llr = 139   E-value = 1.4e-007
 341 ********************************************************************************
 342 --------------------------------------------------------------------------------
 343         Motif 3 Description
 344 --------------------------------------------------------------------------------
 345 Simplified        A  ::::aa:::a63614a86
 346 pos.-specific     C  14a3::::a:::311:::
 347 probability       G  9::5::6a::48:15:34
 348 matrix            T  :6:3::4:::::16::::
 349
 350          bits    2.5   *    **
 351                  2.3   *    **
 352                  2.0 * *    **
 353                  1.8 * *    **
 354 Information      1.5 * * ** *** *   *
 355 content          1.3 * * ****** *   *
 356 (25.1 bits)      1.0 *** ********   ***
 357                  0.8 ************  ****
 358                  0.5 ************* ****
 359                  0.3 ******************
 360                  0.0 ------------------
 361
 362 Multilevel           GTCGAAGGCAAGATGAAA
 363 consensus             C C  T   GAC A GG
 364 sequence                T
 365
 366 --------------------------------------------------------------------------------
 367
 368 --------------------------------------------------------------------------------
 369         Motif 3 sites sorted by position p-value
 370 --------------------------------------------------------------------------------
 371 Sequence name            Strand  Start   P-value                   Site
 372 -------------            ------  ----- ---------            ------------------
 373 MIT_Spar_c425_6072           +    138  4.37e-11 GCAACAAAAT GTCGAAGGCAAGATGAAA GGCGTTTTGC
 374 MIT_Smik_c283_5928           +    133  7.23e-11 AAGCAACAAG GTCGAAGGCAAGCTGAAA GGCATTTTAC
 375 SGD_Scer_YDR047W             -    769  2.84e-09 ACACTAGTAA GTCTAATGCAGGATGAAG AAACGAAGAA
 376 SGD_Scer_YER014W             +    139  7.28e-09 GCAACAAAGT GTCGAAGGCAAGTTCAAA GGCGTTTTGT
 377 MIT_Sbay_c896_21277          -    742  9.47e-09 ACGCTGCTAG GCCCAAGGCAGAACGAAA TAAGAAATGA
 378 MIT_Sbay_c84_6418            +    131  1.10e-08 ACAACAAAAT CTCGAAGGCAAGCTAAGG TAAAAATATT
 379 WashU_Skud_Contig1362.1      -    743  2.13e-08          A GCCCAATGCAAGAAAAAA GCAGCGCAGC
 380 MIT_Spar_c130_3923           -    774  6.83e-08 ACGCTAGTAA GCCTAATGCAGAAGAAGG AAAGGACACG
 381 --------------------------------------------------------------------------------
 382
 383 --------------------------------------------------------------------------------
 384         Motif 3 block diagrams
 385 --------------------------------------------------------------------------------
 386 SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
 387 -------------            ----------------  -------------
 388 MIT_Spar_c425_6072                4.4e-11  137_[+3]_167
 389 MIT_Smik_c283_5928                7.2e-11  132_[+3]_172
 390 SGD_Scer_YDR047W                  2.8e-09  768_[-3]_214
 391 SGD_Scer_YER014W                  7.3e-09  138_[+3]_166
 392 MIT_Sbay_c896_21277               9.5e-09  741_[-3]_241
 393 MIT_Sbay_c84_6418                 1.1e-08  130_[+3]_174
 394 WashU_Skud_Contig1362.1           2.1e-08  742_[-3]_1
 395 MIT_Spar_c130_3923                6.8e-08  773_[-3]_209
 396 --------------------------------------------------------------------------------
 397
 398 --------------------------------------------------------------------------------
 399         Motif 3 in BLOCKS format
 400 --------------------------------------------------------------------------------
 401 BL   MOTIF 3 width=18 seqs=8
 402 MIT_Spar_c425_6072       (  138) GTCGAAGGCAAGATGAAA  1
 403 MIT_Smik_c283_5928       (  133) GTCGAAGGCAAGCTGAAA  1
 404 SGD_Scer_YDR047W         (  769) GTCTAATGCAGGATGAAG  1
 405 SGD_Scer_YER014W         (  139) GTCGAAGGCAAGTTCAAA  1
 406 MIT_Sbay_c896_21277      (  742) GCCCAAGGCAGAACGAAA  1
 407 MIT_Sbay_c84_6418        (  131) CTCGAAGGCAAGCTAAGG  1
 408 WashU_Skud_Contig1362.1  (  743) GCCCAATGCAAGAAAAAA  1
 409 MIT_Spar_c130_3923       (  774) GCCTAATGCAGAAGAAGG  1
 410 //
 411
 412 --------------------------------------------------------------------------------
 413
 414 --------------------------------------------------------------------------------
 415         Motif 3 position-specific scoring matrix
 416 --------------------------------------------------------------------------------
 417 log-odds matrix: alength= 4 w= 18 n= 4913 bayes= 9.26004 E= 1.4e-007
 418   -965    -49    232   -965
 419   -965    109   -965     95
 420   -965    251   -965   -965
 421   -965     51    151    -38
 422    162   -965   -965   -965
 423    162   -965   -965   -965
 424   -965   -965    183     21
 425   -965   -965    251   -965
 426   -965    251   -965   -965
 427    162   -965   -965   -965
 428     95   -965    109   -965
 429    -38   -965    209   -965
 430     95     51   -965   -137
 431   -137    -49    -49     95
 432     21    -49    151   -965
 433    162   -965   -965   -965
 434    121   -965     51   -965
 435     95   -965    109   -965
 436 --------------------------------------------------------------------------------
 437
 438 --------------------------------------------------------------------------------
 439         Motif 3 position-specific probability matrix
 440 --------------------------------------------------------------------------------
 441 letter-probability matrix: alength= 4 w= 18 nsites= 8 E= 1.4e-007
 442  0.000000  0.125000  0.875000  0.000000
 443  0.000000  0.375000  0.000000  0.625000
 444  0.000000  1.000000  0.000000  0.000000
 445  0.000000  0.250000  0.500000  0.250000
 446  1.000000  0.000000  0.000000  0.000000
 447  1.000000  0.000000  0.000000  0.000000
 448  0.000000  0.000000  0.625000  0.375000
 449  0.000000  0.000000  1.000000  0.000000
 450  0.000000  1.000000  0.000000  0.000000
 451  1.000000  0.000000  0.000000  0.000000
 452  0.625000  0.000000  0.375000  0.000000
 453  0.250000  0.000000  0.750000  0.000000
 454  0.625000  0.250000  0.000000  0.125000
 455  0.125000  0.125000  0.125000  0.625000
 456  0.375000  0.125000  0.500000  0.000000
 457  1.000000  0.000000  0.000000  0.000000
 458  0.750000  0.000000  0.250000  0.000000
 459  0.625000  0.000000  0.375000  0.000000
 460 --------------------------------------------------------------------------------
 461
 462 --------------------------------------------------------------------------------
 463         Motif 3 regular expression
 464 --------------------------------------------------------------------------------
 465 G[TC]C[GCT]AA[GT]GCA[AG][GA][AC]T[GA]A[AG][AG]
 466 --------------------------------------------------------------------------------
 467
 468
 469
 470
 471 Time  8.67 secs.
 472
 473 ********************************************************************************
 474
 475
 476 ********************************************************************************
 477 MOTIF  4        width =   20   sites =   8   llr = 132   E-value = 6.8e-002
 478 ********************************************************************************
 479 --------------------------------------------------------------------------------
 480         Motif 4 Description
 481 --------------------------------------------------------------------------------
 482 Simplified        A  6::5:93:::1955985431
 483 pos.-specific     C  ::::::1a:96:::::1:36
 484 probability       G  :3953:6:a:31441:4653
 485 matrix            T  481:81:::1::11:3::::
 486
 487          bits    2.5        **
 488                  2.3        **
 489                  2.0        **
 490                  1.8   *    ***
 491 Information      1.5   *    ***
 492 content          1.3   *    *** *  *  *
 493 (23.8 bits)      1.0  ***********  *  * *
 494                  0.8 ************  ******
 495                  0.5 ********************
 496                  0.3 ********************
 497                  0.0 --------------------
 498
 499 Multilevel           ATGATAGCGCCAAAAAAGGC
 500 consensus            TG GG A   G GG TGAAG
 501 sequence                               C
 502
 503 --------------------------------------------------------------------------------
 504
 505 --------------------------------------------------------------------------------
 506         Motif 4 sites sorted by position p-value
 507 --------------------------------------------------------------------------------
 508 Sequence name            Strand  Start   P-value                    Site
 509 -------------            ------  ----- ---------            --------------------
 510 MIT_Sbay_c896_21277          +    244  1.24e-12 AGGAAGCTGC ATGGTAGCGCCAGAAAAGGC AGATAACCTT
 511 MIT_Spar_c130_3923           +    292  4.51e-10 AAAATCGTGT ATGGTAGCGCCAAGATAGCG AATAAACTAT
 512 SGD_Scer_YDR047W             +    294  7.62e-10 AAGATCGTGT ATGATAGCGCCAAGATGGCG GATAAACTAA
 513 WashU_Skud_Contig1362.1      +    251  2.49e-09 GAGGAAGTGT ATGGTAGCGCCAAGGAAAAC GGGCAATACT
 514 SGD_Scer_YER014W             -      8  4.22e-09 TAAAGTGCAA TTGAGAACGCCAAAAAGAGC TTGTATA
 515 MIT_Spar_c425_6072           -      8  4.66e-09 GAAGGTACAA TTGGGAACGCGGGAAAGGGC TCGAATA
 516 MIT_Smik_c283_5928           -     22  7.67e-07 AACCATATCT AGTATAGCGCGATTAAAGAA ATAGTGGAGA
 517 MIT_Sbay_c84_6418            -     23  1.04e-06 ACAGTCTCGC TGGATTCCGTAAGAAACAGC GGAATAAAGG
 518 --------------------------------------------------------------------------------
 519
 520 --------------------------------------------------------------------------------
 521         Motif 4 block diagrams
 522 --------------------------------------------------------------------------------
 523 SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
 524 -------------            ----------------  -------------
 525 MIT_Sbay_c896_21277               1.2e-12  243_[+4]_737
 526 MIT_Spar_c130_3923                4.5e-10  291_[+4]_689
 527 SGD_Scer_YDR047W                  7.6e-10  293_[+4]_687
 528 WashU_Skud_Contig1362.1           2.5e-09  250_[+4]_491
 529 SGD_Scer_YER014W                  4.2e-09  7_[-4]_295
 530 MIT_Spar_c425_6072                4.7e-09  7_[-4]_295
 531 MIT_Smik_c283_5928                7.7e-07  21_[-4]_281
 532 MIT_Sbay_c84_6418                   1e-06  22_[-4]_280
 533 --------------------------------------------------------------------------------
 534
 535 --------------------------------------------------------------------------------
 536         Motif 4 in BLOCKS format
 537 --------------------------------------------------------------------------------
 538 BL   MOTIF 4 width=20 seqs=8
 539 MIT_Sbay_c896_21277      (  244) ATGGTAGCGCCAGAAAAGGC  1
 540 MIT_Spar_c130_3923       (  292) ATGGTAGCGCCAAGATAGCG  1
 541 SGD_Scer_YDR047W         (  294) ATGATAGCGCCAAGATGGCG  1
 542 WashU_Skud_Contig1362.1  (  251) ATGGTAGCGCCAAGGAAAAC  1
 543 SGD_Scer_YER014W         (    8) TTGAGAACGCCAAAAAGAGC  1
 544 MIT_Spar_c425_6072       (    8) TTGGGAACGCGGGAAAGGGC  1
 545 MIT_Smik_c283_5928       (   22) AGTATAGCGCGATTAAAGAA  1
 546 MIT_Sbay_c84_6418        (   23) TGGATTCCGTAAGAAACAGC  1
 547 //
 548
 549 --------------------------------------------------------------------------------
 550
 551 --------------------------------------------------------------------------------
 552         Motif 4 position-specific scoring matrix
 553 --------------------------------------------------------------------------------
 554 log-odds matrix: alength= 4 w= 20 n= 4897 bayes= 9.25532 E= 6.8e-002
 555     95   -965   -965     21
 556   -965   -965     51    121
 557   -965   -965    232   -137
 558     62   -965    151   -965
 559   -965   -965     51    121
 560    143   -965   -965   -137
 561    -38    -49    183   -965
 562   -965    251   -965   -965
 563   -965   -965    251   -965
 564   -965    232   -965   -137
 565   -137    183     51   -965
 566    143   -965    -49   -965
 567     62   -965    109   -137
 568     62   -965    109   -137
 569    143   -965    -49   -965
 570    121   -965   -965    -38
 571     62    -49    109   -965
 572     21   -965    183   -965
 573    -38     51    151   -965
 574   -137    183     51   -965
 575 --------------------------------------------------------------------------------
 576
 577 --------------------------------------------------------------------------------
 578         Motif 4 position-specific probability matrix
 579 --------------------------------------------------------------------------------
 580 letter-probability matrix: alength= 4 w= 20 nsites= 8 E= 6.8e-002
 581  0.625000  0.000000  0.000000  0.375000
 582  0.000000  0.000000  0.250000  0.750000
 583  0.000000  0.000000  0.875000  0.125000
 584  0.500000  0.000000  0.500000  0.000000
 585  0.000000  0.000000  0.250000  0.750000
 586  0.875000  0.000000  0.000000  0.125000
 587  0.250000  0.125000  0.625000  0.000000
 588  0.000000  1.000000  0.000000  0.000000
 589  0.000000  0.000000  1.000000  0.000000
 590  0.000000  0.875000  0.000000  0.125000
 591  0.125000  0.625000  0.250000  0.000000
 592  0.875000  0.000000  0.125000  0.000000
 593  0.500000  0.000000  0.375000  0.125000
 594  0.500000  0.000000  0.375000  0.125000
 595  0.875000  0.000000  0.125000  0.000000
 596  0.750000  0.000000  0.000000  0.250000
 597  0.500000  0.125000  0.375000  0.000000
 598  0.375000  0.000000  0.625000  0.000000
 599  0.250000  0.250000  0.500000  0.000000
 600  0.125000  0.625000  0.250000  0.000000
 601 --------------------------------------------------------------------------------
 602
 603 --------------------------------------------------------------------------------
 604         Motif 4 regular expression
 605 --------------------------------------------------------------------------------
 606 [AT][TG]G[AG][TG]A[GA]CGC[CG]A[AG][AG]A[AT][AG][GA][GAC][CG]
 607 --------------------------------------------------------------------------------
 608
 609
 610
 611
 612 Time 11.28 secs.
 613
 614 ********************************************************************************
 615
 616
 617 ********************************************************************************
 618 MOTIF  5        width =   14   sites =   8   llr = 115   E-value = 4.7e-003
 619 ********************************************************************************
 620 --------------------------------------------------------------------------------
 621         Motif 5 Description
 622 --------------------------------------------------------------------------------
 623 Simplified        A  ::5::1::::::::
 624 pos.-specific     C  a::35:::a433a5
 625 probability       G  ::51:9::::4:::
 626 matrix            T  :a:65:aa:648:5
 627
 628          bits    2.5 *       *   *
 629                  2.3 *       *   *
 630                  2.0 *       *   *
 631                  1.8 *    *  *   *
 632 Information      1.5 **   ****   *
 633 content          1.3 **   ****   *
 634 (20.8 bits)      1.0 *** ****** ***
 635                  0.8 ********** ***
 636                  0.5 **************
 637                  0.3 **************
 638                  0.0 --------------
 639
 640 Multilevel           CTATCGTTCTGTCC
 641 consensus              GCT    CTC T
 642 sequence                       C
 643
 644 --------------------------------------------------------------------------------
 645
 646 --------------------------------------------------------------------------------
 647         Motif 5 sites sorted by position p-value
 648 --------------------------------------------------------------------------------
 649 Sequence name            Strand  Start   P-value                 Site
 650 -------------            ------  ----- ---------            --------------
 651 MIT_Spar_c130_3923           +    714  1.93e-09 CTCTAAAATG CTGCCGTTCCGTCC CATTGAGTTT
 652 SGD_Scer_YDR047W             +    714  1.93e-09 TTAAAAAATG CTGCCGTTCCGTCC CATTGAGTTT
 653 MIT_Sbay_c896_21277          +    705  8.69e-08 CAGCCAAACA CTGGCGTTCCGCCC GTCCCATCCA
 654 MIT_Smik_c283_5928           +     77  2.04e-07 GCAAATCCCT CTATTGTTCTTTCC ATTACTCTTT
 655 MIT_Spar_c425_6072           +     75  3.04e-07 GCGGATCTCT CTATTGTTCTCTCT ATTATTCTTT
 656 SGD_Scer_YER014W             +     75  3.04e-07 GCGAATATCT CTATTGTTCTCTCT ATTATACTAT
 657 MIT_Sbay_c84_6418            +     70  4.30e-07 TCGCATCCTT CTATTGTTCTTCCT TATTGTTCTC
 658 WashU_Skud_Contig1362.1      -    282  5.90e-07 TGGCTGAGCT CTGTCATTCTTTCT AAGTATTGCC
 659 --------------------------------------------------------------------------------
 660
 661 --------------------------------------------------------------------------------
 662         Motif 5 block diagrams
 663 --------------------------------------------------------------------------------
 664 SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
 665 -------------            ----------------  -------------
 666 MIT_Spar_c130_3923                1.9e-09  713_[+5]_273
 667 SGD_Scer_YDR047W                  1.9e-09  713_[+5]_273
 668 MIT_Sbay_c896_21277               8.7e-08  704_[+5]_282
 669 MIT_Smik_c283_5928                  2e-07  76_[+5]_232
 670 MIT_Spar_c425_6072                  3e-07  74_[+5]_234
 671 SGD_Scer_YER014W                    3e-07  74_[+5]_234
 672 MIT_Sbay_c84_6418                 4.3e-07  69_[+5]_239
 673 WashU_Skud_Contig1362.1           5.9e-07  281_[-5]_466
 674 --------------------------------------------------------------------------------
 675
 676 --------------------------------------------------------------------------------
 677         Motif 5 in BLOCKS format
 678 --------------------------------------------------------------------------------
 679 BL   MOTIF 5 width=14 seqs=8
 680 MIT_Spar_c130_3923       (  714) CTGCCGTTCCGTCC  1
 681 SGD_Scer_YDR047W         (  714) CTGCCGTTCCGTCC  1
 682 MIT_Sbay_c896_21277      (  705) CTGGCGTTCCGCCC  1
 683 MIT_Smik_c283_5928       (   77) CTATTGTTCTTTCC  1
 684 MIT_Spar_c425_6072       (   75) CTATTGTTCTCTCT  1
 685 SGD_Scer_YER014W         (   75) CTATTGTTCTCTCT  1
 686 MIT_Sbay_c84_6418        (   70) CTATTGTTCTTCCT  1
 687 WashU_Skud_Contig1362.1  (  282) CTGTCATTCTTTCT  1
 688 //
 689
 690 --------------------------------------------------------------------------------
 691
 692 --------------------------------------------------------------------------------
 693         Motif 5 position-specific scoring matrix
 694 --------------------------------------------------------------------------------
 695 log-odds matrix: alength= 4 w= 14 n= 4945 bayes= 9.26942 E= 4.7e-003
 696   -965    251   -965   -965
 697   -965   -965   -965    162
 698     62   -965    151   -965
 699   -965     51    -49     95
 700   -965    151   -965     62
 701   -137   -965    232   -965
 702   -965   -965   -965    162
 703   -965   -965   -965    162
 704   -965    251   -965   -965
 705   -965    109   -965     95
 706   -965     51    109     21
 707   -965     51   -965    121
 708   -965    251   -965   -965
 709   -965    151   -965     62
 710 --------------------------------------------------------------------------------
 711
 712 --------------------------------------------------------------------------------
 713         Motif 5 position-specific probability matrix
 714 --------------------------------------------------------------------------------
 715 letter-probability matrix: alength= 4 w= 14 nsites= 8 E= 4.7e-003
 716  0.000000  1.000000  0.000000  0.000000
 717  0.000000  0.000000  0.000000  1.000000
 718  0.500000  0.000000  0.500000  0.000000
 719  0.000000  0.250000  0.125000  0.625000
 720  0.000000  0.500000  0.000000  0.500000
 721  0.125000  0.000000  0.875000  0.000000
 722  0.000000  0.000000  0.000000  1.000000
 723  0.000000  0.000000  0.000000  1.000000
 724  0.000000  1.000000  0.000000  0.000000
 725  0.000000  0.375000  0.000000  0.625000
 726  0.000000  0.250000  0.375000  0.375000
 727  0.000000  0.250000  0.000000  0.750000
 728  0.000000  1.000000  0.000000  0.000000
 729  0.000000  0.500000  0.000000  0.500000
 730 --------------------------------------------------------------------------------
 731
 732 --------------------------------------------------------------------------------
 733         Motif 5 regular expression
 734 --------------------------------------------------------------------------------
 735 CT[AG][TC][CT]GTTC[TC][GTC][TC]C[CT]
 736 --------------------------------------------------------------------------------
 737
 738
 739
 740
 741 Time 13.87 secs.
 742
 743 ********************************************************************************
 744
 745
 746 ********************************************************************************
 747 SUMMARY OF MOTIFS
 748 ********************************************************************************
 749
 750 --------------------------------------------------------------------------------
 751         Combined block diagrams: non-overlapping sites with p-value < 0.0001
 752 --------------------------------------------------------------------------------
 753 SEQUENCE NAME            COMBINED P-VALUE  MOTIF DIAGRAM
 754 -------------            ----------------  -------------
 755 SGD_Scer_YDR047W                 7.31e-20  108_[+5(5.48e-05)]_122_[+1(1.00e-08)]_34_[+4(7.62e-10)]_68_[-2(1.24e-07)]_312_[+5(1.93e-09)]_41_[-3(2.84e-09)]_214
 756 MIT_Spar_c130_3923               2.71e-19  241_[+1(1.00e-08)]_35_[+4(4.51e-10)]_5_[-2(1.77e-05)]_377_[+5(1.93e-09)]_46_[-3(6.83e-08)]_3_[+5(7.96e-06)]_27_[-2(3.57e-08)]_145
 757 MIT_Sbay_c896_21277              2.82e-22  212_[+1(2.96e-09)]_16_[+4(1.24e-12)]_398_[+3(9.45e-05)]_25_[+5(8.69e-08)]_23_[-3(9.47e-09)]_154_[-2(4.51e-09)]_67
 758 WashU_Skud_Contig1362.1          2.00e-16  207_[+1(5.25e-08)]_28_[+4(2.49e-09)]_11_[-5(5.90e-07)]_363_[+2(6.59e-08)]_64_[-3(2.13e-08)]_1
 759 SGD_Scer_YER014W                 1.10e-23  7_[-4(4.22e-09)]_47_[+5(3.04e-07)]_32_[+1(2.85e-08)]_3_[+3(7.28e-09)]_11_[+2(5.54e-13)]_135
 760 MIT_Spar_c425_6072               7.28e-24  7_[-4(4.66e-09)]_47_[+5(3.04e-07)]_31_[+1(2.85e-08)]_3_[+3(4.37e-11)]_11_[+2(5.42e-11)]_136
 761 MIT_Smik_c283_5928               1.78e-22  21_[-4(7.67e-07)]_35_[+5(2.04e-07)]_26_[+1(2.85e-08)]_1_[+3(7.23e-11)]_11_[+2(8.88e-12)]_141
 762 MIT_Sbay_c84_6418                7.50e-18  22_[-4(1.04e-06)]_6_[+5(5.48e-05)]_7_[+5(4.30e-07)]_29_[+1(8.97e-08)]_3_[+3(1.10e-08)]_14_[+2(5.99e-10)]_140
 763 --------------------------------------------------------------------------------
 764
 765 ********************************************************************************
 766
 767
 768 ********************************************************************************
 769 Stopped because nmotifs = 5 reached.
 770 ********************************************************************************
 771
 772 CPU: dhn02990.mrc-dunn.cam.ac.uk
 773
 774 ********************************************************************************