t/data/map_hem/HEM13-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= HEM13-HEM14.fa
  32 ALPHABET= ACGT
  33 Sequence name            Weight Length  Sequence name            Weight Length
  34 -------------            ------ ------  -------------            ------ ------
  35 SGD_Scer_YDR044W         1.0000   1000  MIT_Spar_c130_3912       1.0000   1000
  36 MIT_Sbay_c896_21290      1.0000   1000  WashU_Smik_Contig2283.3  1.0000   1000
  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 HEM13-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=            5288    N=               8
  58 strands: + -
  59 sample: seed=            0    seqfrac=         1
  60 Letter frequencies in dataset:
  61 A 0.305 C 0.195 G 0.195 T 0.305
  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 =   20   sites =   8   llr = 168   E-value = 5.3e-017
  69 ********************************************************************************
  70 --------------------------------------------------------------------------------
  71         Motif 1 Description
  72 --------------------------------------------------------------------------------
  73 Simplified        A  1:::::::::9:::1:114:
  74 pos.-specific     C  :::494:a:1115a181:::
  75 probability       G  9556::5:a9:9::6339:9
  76 matrix            T  :55:165:::::5:1:5:61
  77
  78          bits    2.5        **    *
  79                  2.3        **    *
  80                  2.0        *** * *
  81                  1.8 *   *  *** * * * * *
  82 Information      1.5 *  **  *** * * * * *
  83 content          1.3 *  **  ***** * * * *
  84 (30.2 bits)      1.0 ************** * * *
  85                  0.8 **************** ***
  86                  0.5 **************** ***
  87                  0.3 ********************
  88                  0.0 --------------------
  89
  90 Multilevel           GGGGCTGCGGAGCCGCTGTG
  91 consensus             TTC CT     T  GG A
  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 SGD_Scer_YDR044W             +    344  3.65e-14 AAAAGTAGAA GGGCCCGCGGAGCCGCTGTG AAAGATTTCT
 102 MIT_Spar_c425_6072           -    113  1.77e-11 TCGACATTTT GTTGCTTCGGAGTCGCGGAG TATTTAAAAA
 103 SGD_Scer_YER014W             -    114  1.77e-11 TCGACACTTT GTTGCTTCGGAGTCGCGGAG TATTCAAAAA
 104 WashU_Smik_Contig2283.3      +    341  8.23e-11 AAAAAGAAAA GGGCCCGCGGCCCCGCCGTG AAACACTTCG
 105 MIT_Spar_c130_3912           +    336  1.07e-10 TAAAAGAAGA AGGGCTGCGGAGCCACTGTG AAAGACTTGT
 106 MIT_Sbay_c896_21290          +    343  2.63e-10 AAAAAGAAAA GGGCCCGCGCAGCCTGTGTG AAATGTTCGT
 107 MIT_Sbay_c84_6418            -    106  8.94e-10 TCGAGATTTT GTTGTTTCGGAGTCGCAGAG TATAAAAAAA
 108 MIT_Smik_c283_5928           -    110  7.48e-09 CTTCGACCTT GTTGCTTCGGAGTCCGTATT TAAAAAAGAA
 109 --------------------------------------------------------------------------------
 110
 111 --------------------------------------------------------------------------------
 112         Motif 1 block diagrams
 113 --------------------------------------------------------------------------------
 114 SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
 115 -------------            ----------------  -------------
 116 SGD_Scer_YDR044W                  3.7e-14  343_[+1]_637
 117 MIT_Spar_c425_6072                1.8e-11  112_[-1]_190
 118 SGD_Scer_YER014W                  1.8e-11  113_[-1]_189
 119 WashU_Smik_Contig2283.3           8.2e-11  340_[+1]_640
 120 MIT_Spar_c130_3912                1.1e-10  335_[+1]_645
 121 MIT_Sbay_c896_21290               2.6e-10  342_[+1]_638
 122 MIT_Sbay_c84_6418                 8.9e-10  105_[-1]_197
 123 MIT_Smik_c283_5928                7.5e-09  109_[-1]_193
 124 --------------------------------------------------------------------------------
 125
 126 --------------------------------------------------------------------------------
 127         Motif 1 in BLOCKS format
 128 --------------------------------------------------------------------------------
 129 BL   MOTIF 1 width=20 seqs=8
 130 SGD_Scer_YDR044W         (  344) GGGCCCGCGGAGCCGCTGTG  1
 131 MIT_Spar_c425_6072       (  113) GTTGCTTCGGAGTCGCGGAG  1
 132 SGD_Scer_YER014W         (  114) GTTGCTTCGGAGTCGCGGAG  1
 133 WashU_Smik_Contig2283.3  (  341) GGGCCCGCGGCCCCGCCGTG  1
 134 MIT_Spar_c130_3912       (  336) AGGGCTGCGGAGCCACTGTG  1
 135 MIT_Sbay_c896_21290      (  343) GGGCCCGCGCAGCCTGTGTG  1
 136 MIT_Sbay_c84_6418        (  106) GTTGTTTCGGAGTCGCAGAG  1
 137 MIT_Smik_c283_5928       (  110) GTTGCTTCGGAGTCCGTATT  1
 138 //
 139
 140 --------------------------------------------------------------------------------
 141
 142 --------------------------------------------------------------------------------
 143         Motif 1 position-specific scoring matrix
 144 --------------------------------------------------------------------------------
 145 log-odds matrix: alength= 4 w= 20 n= 5136 bayes= 9.32418 E= 5.3e-017
 146   -137   -965    232   -965
 147   -965   -965    151     62
 148   -965   -965    151     62
 149   -965    109    183   -965
 150   -965    232   -965   -137
 151   -965    109   -965     95
 152   -965   -965    151     62
 153   -965    251   -965   -965
 154   -965   -965    251   -965
 155   -965    -49    232   -965
 156    143    -49   -965   -965
 157   -965    -49    232   -965
 158   -965    151   -965     62
 159   -965    251   -965   -965
 160   -137    -49    183   -137
 161   -965    209     51   -965
 162   -137    -49     51     62
 163   -137   -965    232   -965
 164     21   -965   -965     95
 165   -965   -965    232   -137
 166 --------------------------------------------------------------------------------
 167
 168 --------------------------------------------------------------------------------
 169         Motif 1 position-specific probability matrix
 170 --------------------------------------------------------------------------------
 171 letter-probability matrix: alength= 4 w= 20 nsites= 8 E= 5.3e-017
 172  0.125000  0.000000  0.875000  0.000000
 173  0.000000  0.000000  0.500000  0.500000
 174  0.000000  0.000000  0.500000  0.500000
 175  0.000000  0.375000  0.625000  0.000000
 176  0.000000  0.875000  0.000000  0.125000
 177  0.000000  0.375000  0.000000  0.625000
 178  0.000000  0.000000  0.500000  0.500000
 179  0.000000  1.000000  0.000000  0.000000
 180  0.000000  0.000000  1.000000  0.000000
 181  0.000000  0.125000  0.875000  0.000000
 182  0.875000  0.125000  0.000000  0.000000
 183  0.000000  0.125000  0.875000  0.000000
 184  0.000000  0.500000  0.000000  0.500000
 185  0.000000  1.000000  0.000000  0.000000
 186  0.125000  0.125000  0.625000  0.125000
 187  0.000000  0.750000  0.250000  0.000000
 188  0.125000  0.125000  0.250000  0.500000
 189  0.125000  0.000000  0.875000  0.000000
 190  0.375000  0.000000  0.000000  0.625000
 191  0.000000  0.000000  0.875000  0.125000
 192 --------------------------------------------------------------------------------
 193
 194 --------------------------------------------------------------------------------
 195         Motif 1 regular expression
 196 --------------------------------------------------------------------------------
 197 G[GT][GT][GC]C[TC][GT]CGGAG[CT]CG[CG][TG]G[TA]G
 198 --------------------------------------------------------------------------------
 199
 200
 201
 202
 203 Time  3.15 secs.
 204
 205 ********************************************************************************
 206
 207
 208 ********************************************************************************
 209 MOTIF  2        width =   20   sites =   8   llr = 157   E-value = 1.6e-011
 210 ********************************************************************************
 211 --------------------------------------------------------------------------------
 212         Motif 2 Description
 213 --------------------------------------------------------------------------------
 214 Simplified        A  9453a:aa:aa:5:8185a:
 215 pos.-specific     C  ::3:::::a::::::4::::
 216 probability       G  1638:a::::::5a1434:1
 217 matrix            T  :::::::::::a::11:1:9
 218
 219          bits    2.5      *  *    *
 220                  2.3      *  *    *
 221                  2.0      *  *    *
 222                  1.8      *  *    *
 223 Information      1.5    ********* *    *
 224 content          1.3 ** ********* *    **
 225 (28.3 bits)      1.0 ** ***********  * **
 226                  0.8 ** ************ * **
 227                  0.5 ********************
 228                  0.3 ********************
 229                  0.0 --------------------
 230
 231 Multilevel           AGAGAGAACAATAGACAAAT
 232 consensus             ACA        G  GGG
 233 sequence               G
 234
 235 --------------------------------------------------------------------------------
 236
 237 --------------------------------------------------------------------------------
 238         Motif 2 sites sorted by position p-value
 239 --------------------------------------------------------------------------------
 240 Sequence name            Strand  Start   P-value                    Site
 241 -------------            ------  ----- ---------            --------------------
 242 MIT_Spar_c425_6072           -     69  2.68e-11 AAAGAATAAT AGAGAGAACAATAGAGAGAT CCGCGAAGGA
 243 MIT_Spar_c130_3912           +    167  9.91e-11 GCCTTTTCGA AACGAGAACAATGGACAAAT CAAGCTTTAT
 244 MIT_Sbay_c896_21290          +    173  2.20e-10 GCTTTCTCGA AGGGAGAACAATGGATAAAT CAAAGCTTAT
 245 SGD_Scer_YER014W             -     69  3.83e-10 ATAGTATAAT AGAGAGAACAATAGAGATAT TCGCGAAGAA
 246 WashU_Smik_Contig2283.3      +    163  9.67e-10 GCCTTTTCAA AAAGAGAACAATGGTCAAAT AAAGGTTTAT
 247 SGD_Scer_YDR044W             +    171  1.97e-09 AGCCTTTCGA AACGAGAACAATGGGCAAAG CAAGCTTTAT
 248 MIT_Smik_c283_5928           -     71  2.41e-09 AAAGAGTAAT GGAAAGAACAATAGAGGGAT TTGCAAAAGA
 249 MIT_Sbay_c84_6418            -     64  3.09e-09 GAGAACAATA AGGAAGAACAATAGAAGGAT GCGAAAGGAC
 250 --------------------------------------------------------------------------------
 251
 252 --------------------------------------------------------------------------------
 253         Motif 2 block diagrams
 254 --------------------------------------------------------------------------------
 255 SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
 256 -------------            ----------------  -------------
 257 MIT_Spar_c425_6072                2.7e-11  68_[-2]_234
 258 MIT_Spar_c130_3912                9.9e-11  166_[+2]_814
 259 MIT_Sbay_c896_21290               2.2e-10  172_[+2]_808
 260 SGD_Scer_YER014W                  3.8e-10  68_[-2]_234
 261 WashU_Smik_Contig2283.3           9.7e-10  162_[+2]_818
 262 SGD_Scer_YDR044W                    2e-09  170_[+2]_810
 263 MIT_Smik_c283_5928                2.4e-09  70_[-2]_232
 264 MIT_Sbay_c84_6418                 3.1e-09  63_[-2]_239
 265 --------------------------------------------------------------------------------
 266
 267 --------------------------------------------------------------------------------
 268         Motif 2 in BLOCKS format
 269 --------------------------------------------------------------------------------
 270 BL   MOTIF 2 width=20 seqs=8
 271 MIT_Spar_c425_6072       (   69) AGAGAGAACAATAGAGAGAT  1
 272 MIT_Spar_c130_3912       (  167) AACGAGAACAATGGACAAAT  1
 273 MIT_Sbay_c896_21290      (  173) AGGGAGAACAATGGATAAAT  1
 274 SGD_Scer_YER014W         (   69) AGAGAGAACAATAGAGATAT  1
 275 WashU_Smik_Contig2283.3  (  163) AAAGAGAACAATGGTCAAAT  1
 276 SGD_Scer_YDR044W         (  171) AACGAGAACAATGGGCAAAG  1
 277 MIT_Smik_c283_5928       (   71) GGAAAGAACAATAGAGGGAT  1
 278 MIT_Sbay_c84_6418        (   64) AGGAAGAACAATAGAAGGAT  1
 279 //
 280
 281 --------------------------------------------------------------------------------
 282
 283 --------------------------------------------------------------------------------
 284         Motif 2 position-specific scoring matrix
 285 --------------------------------------------------------------------------------
 286 log-odds matrix: alength= 4 w= 20 n= 5136 bayes= 9.32418 E= 1.6e-011
 287    143   -965    -49   -965
 288     21   -965    183   -965
 289     62     51     51   -965
 290    -38   -965    209   -965
 291    162   -965   -965   -965
 292   -965   -965    251   -965
 293    162   -965   -965   -965
 294    162   -965   -965   -965
 295   -965    251   -965   -965
 296    162   -965   -965   -965
 297    162   -965   -965   -965
 298   -965   -965   -965    162
 299     62   -965    151   -965
 300   -965   -965    251   -965
 301    121   -965    -49   -137
 302   -137    109    109   -137
 303    121   -965     51   -965
 304     62   -965    109   -137
 305    162   -965   -965   -965
 306   -965   -965    -49    143
 307 --------------------------------------------------------------------------------
 308
 309 --------------------------------------------------------------------------------
 310         Motif 2 position-specific probability matrix
 311 --------------------------------------------------------------------------------
 312 letter-probability matrix: alength= 4 w= 20 nsites= 8 E= 1.6e-011
 313  0.875000  0.000000  0.125000  0.000000
 314  0.375000  0.000000  0.625000  0.000000
 315  0.500000  0.250000  0.250000  0.000000
 316  0.250000  0.000000  0.750000  0.000000
 317  1.000000  0.000000  0.000000  0.000000
 318  0.000000  0.000000  1.000000  0.000000
 319  1.000000  0.000000  0.000000  0.000000
 320  1.000000  0.000000  0.000000  0.000000
 321  0.000000  1.000000  0.000000  0.000000
 322  1.000000  0.000000  0.000000  0.000000
 323  1.000000  0.000000  0.000000  0.000000
 324  0.000000  0.000000  0.000000  1.000000
 325  0.500000  0.000000  0.500000  0.000000
 326  0.000000  0.000000  1.000000  0.000000
 327  0.750000  0.000000  0.125000  0.125000
 328  0.125000  0.375000  0.375000  0.125000
 329  0.750000  0.000000  0.250000  0.000000
 330  0.500000  0.000000  0.375000  0.125000
 331  1.000000  0.000000  0.000000  0.000000
 332  0.000000  0.000000  0.125000  0.875000
 333 --------------------------------------------------------------------------------
 334
 335 --------------------------------------------------------------------------------
 336         Motif 2 regular expression
 337 --------------------------------------------------------------------------------
 338 A[GA][ACG][GA]AGAACAAT[AG]GA[CG][AG][AG]AT
 339 --------------------------------------------------------------------------------
 340
 341
 342
 343
 344 Time  6.10 secs.
 345
 346 ********************************************************************************
 347
 348
 349 ********************************************************************************
 350 MOTIF  3        width =   20   sites =   8   llr = 156   E-value = 2.4e-010
 351 ********************************************************************************
 352 --------------------------------------------------------------------------------
 353         Motif 3 Description
 354 --------------------------------------------------------------------------------
 355 Simplified        A  ::1:1:::::51:16:9aa9
 356 pos.-specific     C  :::a:5:4:4:1:::3::::
 357 probability       G  ::9:45a:::58:54:1:::
 358 matrix            T  aa::5::6a6::a4:8:::1
 359
 360          bits    2.5    *  *
 361                  2.3    *  *
 362                  2.0    *  *
 363                  1.8   **  *
 364 Information      1.5 **** ** *   *    **
 365 content          1.3 **** ** *  **   ***
 366 (28.1 bits)      1.0 **** ******** ******
 367                  0.8 **** ***************
 368                  0.5 ********************
 369                  0.3 ********************
 370                  0.0 --------------------
 371
 372 Multilevel           TTGCTCGTTTAGTGATAAAA
 373 consensus                GG C CG  TGC
 374 sequence
 375
 376 --------------------------------------------------------------------------------
 377
 378 --------------------------------------------------------------------------------
 379         Motif 3 sites sorted by position p-value
 380 --------------------------------------------------------------------------------
 381 Sequence name            Strand  Start   P-value                    Site
 382 -------------            ------  ----- ---------            --------------------
 383 WashU_Smik_Contig2283.3      +    630  6.53e-12 TCTTGAGGAT TTGCGGGTTCGGTGATAAAA AATGTATTGT
 384 MIT_Spar_c130_3912           +    624  2.08e-10 TCTAGAGGAT TTGCAGGCTCGGTGATAAAA TGTATTGTTG
 385 MIT_Smik_c283_5928           -    155  3.18e-10 AAAGCTACCA TTGCTCGTTTAGTTGTAAAA TGCCTTTCAG
 386 SGD_Scer_YER014W             -    161  5.75e-10 AAAGCTGCCA TTGCTCGTTTAGTTACAAAA CGCCTTTGAA
 387 SGD_Scer_YDR044W             +    629  5.75e-10 TCCAGAGGAT TTGCGGGCTTGATGATAAAA TGTATTGTTG
 388 MIT_Sbay_c896_21290          +    628  2.12e-09 TCTTGGGGAT TTGCGGGCTCGCTAATAAAA AGTGTCTTGT
 389 MIT_Sbay_c84_6418            -    156  3.04e-09 ATAACTGTCA TTGCTCGTTTAGTGGTGAAT ATTTTTACCT
 390 MIT_Spar_c425_6072           -    160  4.65e-09 AAAGCTGCCA TTACTCGTTTAGTTGCAAAA CGCCTTTCAT
 391 --------------------------------------------------------------------------------
 392
 393 --------------------------------------------------------------------------------
 394         Motif 3 block diagrams
 395 --------------------------------------------------------------------------------
 396 SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
 397 -------------            ----------------  -------------
 398 WashU_Smik_Contig2283.3           6.5e-12  629_[+3]_351
 399 MIT_Spar_c130_3912                2.1e-10  623_[+3]_357
 400 MIT_Smik_c283_5928                3.2e-10  154_[-3]_148
 401 SGD_Scer_YER014W                  5.8e-10  160_[-3]_142
 402 SGD_Scer_YDR044W                  5.8e-10  628_[+3]_352
 403 MIT_Sbay_c896_21290               2.1e-09  627_[+3]_353
 404 MIT_Sbay_c84_6418                   3e-09  155_[-3]_147
 405 MIT_Spar_c425_6072                4.7e-09  159_[-3]_143
 406 --------------------------------------------------------------------------------
 407
 408 --------------------------------------------------------------------------------
 409         Motif 3 in BLOCKS format
 410 --------------------------------------------------------------------------------
 411 BL   MOTIF 3 width=20 seqs=8
 412 WashU_Smik_Contig2283.3  (  630) TTGCGGGTTCGGTGATAAAA  1
 413 MIT_Spar_c130_3912       (  624) TTGCAGGCTCGGTGATAAAA  1
 414 MIT_Smik_c283_5928       (  155) TTGCTCGTTTAGTTGTAAAA  1
 415 SGD_Scer_YER014W         (  161) TTGCTCGTTTAGTTACAAAA  1
 416 SGD_Scer_YDR044W         (  629) TTGCGGGCTTGATGATAAAA  1
 417 MIT_Sbay_c896_21290      (  628) TTGCGGGCTCGCTAATAAAA  1
 418 MIT_Sbay_c84_6418        (  156) TTGCTCGTTTAGTGGTGAAT  1
 419 MIT_Spar_c425_6072       (  160) TTACTCGTTTAGTTGCAAAA  1
 420 //
 421
 422 --------------------------------------------------------------------------------
 423
 424 --------------------------------------------------------------------------------
 425         Motif 3 position-specific scoring matrix
 426 --------------------------------------------------------------------------------
 427 log-odds matrix: alength= 4 w= 20 n= 5136 bayes= 9.32418 E= 2.4e-010
 428   -965   -965   -965    162
 429   -965   -965   -965    162
 430   -137   -965    232   -965
 431   -965    251   -965   -965
 432   -137   -965    109     62
 433   -965    151    151   -965
 434   -965   -965    251   -965
 435   -965    109   -965     95
 436   -965   -965   -965    162
 437   -965    109   -965     95
 438     62   -965    151   -965
 439   -137    -49    209   -965
 440   -965   -965   -965    162
 441   -137   -965    151     21
 442     95   -965    109   -965
 443   -965     51   -965    121
 444    143   -965    -49   -965
 445    162   -965   -965   -965
 446    162   -965   -965   -965
 447    143   -965   -965   -137
 448 --------------------------------------------------------------------------------
 449
 450 --------------------------------------------------------------------------------
 451         Motif 3 position-specific probability matrix
 452 --------------------------------------------------------------------------------
 453 letter-probability matrix: alength= 4 w= 20 nsites= 8 E= 2.4e-010
 454  0.000000  0.000000  0.000000  1.000000
 455  0.000000  0.000000  0.000000  1.000000
 456  0.125000  0.000000  0.875000  0.000000
 457  0.000000  1.000000  0.000000  0.000000
 458  0.125000  0.000000  0.375000  0.500000
 459  0.000000  0.500000  0.500000  0.000000
 460  0.000000  0.000000  1.000000  0.000000
 461  0.000000  0.375000  0.000000  0.625000
 462  0.000000  0.000000  0.000000  1.000000
 463  0.000000  0.375000  0.000000  0.625000
 464  0.500000  0.000000  0.500000  0.000000
 465  0.125000  0.125000  0.750000  0.000000
 466  0.000000  0.000000  0.000000  1.000000
 467  0.125000  0.000000  0.500000  0.375000
 468  0.625000  0.000000  0.375000  0.000000
 469  0.000000  0.250000  0.000000  0.750000
 470  0.875000  0.000000  0.125000  0.000000
 471  1.000000  0.000000  0.000000  0.000000
 472  1.000000  0.000000  0.000000  0.000000
 473  0.875000  0.000000  0.000000  0.125000
 474 --------------------------------------------------------------------------------
 475
 476 --------------------------------------------------------------------------------
 477         Motif 3 regular expression
 478 --------------------------------------------------------------------------------
 479 TTGC[TG][CG]G[TC]T[TC][AG]GT[GT][AG][TC]AAAA
 480 --------------------------------------------------------------------------------
 481
 482
 483
 484
 485 Time  8.96 secs.
 486
 487 ********************************************************************************
 488
 489
 490 ********************************************************************************
 491 MOTIF  4        width =   15   sites =   8   llr = 123   E-value = 9.2e-006
 492 ********************************************************************************
 493 --------------------------------------------------------------------------------
 494         Motif 4 Description
 495 --------------------------------------------------------------------------------
 496 Simplified        A  1a9:::aa:1:1a44
 497 pos.-specific     C  3::::a:::351:::
 498 probability       G  6:1aa:::a5:3:16
 499 matrix            T  :::::::::155:5:
 500
 501          bits    2.5    ***  *
 502                  2.3    ***  *
 503                  2.0    ***  *
 504                  1.8    ***  *
 505 Information      1.5  * ******   *
 506 content          1.3  ********   * *
 507 (22.2 bits)      1.0 ********* * * *
 508                  0.8 ********* * * *
 509                  0.5 *********** * *
 510                  0.3 ***************
 511                  0.0 ---------------
 512
 513 Multilevel           GAAGGCAAGGCTATG
 514 consensus            C        CTG AA
 515 sequence
 516
 517 --------------------------------------------------------------------------------
 518
 519 --------------------------------------------------------------------------------
 520         Motif 4 sites sorted by position p-value
 521 --------------------------------------------------------------------------------
 522 Sequence name            Strand  Start   P-value                 Site
 523 -------------            ------  ----- ---------            ---------------
 524 WashU_Smik_Contig2283.3      +    710  5.26e-10 ATTAACAAGG GAAGGCAAGGCTATG TTCTATTGAG
 525 MIT_Sbay_c896_21290          +    703  3.55e-09 AAAATATCAA CAAGGCAAGGCTATG CCTTTCGAAG
 526 MIT_Spar_c130_3912           +    702  3.55e-09 ATCAACAGGG CAAGGCAAGGCTATG CTCTTTTGGA
 527 MIT_Smik_c283_5928           +    136  5.90e-08 CAACAAGGTC GAAGGCAAGCTGAAA GGCATTTTAC
 528 MIT_Sbay_c84_6418            +    134  1.20e-07 ACAAAATCTC GAAGGCAAGCTAAGG TAAAAATATT
 529 SGD_Scer_YDR044W             +    705  1.33e-07 ATATCAACAA AAGGGCAAGGCTATG CCTTCTGGAA
 530 MIT_Spar_c425_6072           +    141  1.99e-07 ACAAAATGTC GAAGGCAAGATGAAA GGCGTTTTGC
 531 SGD_Scer_YER014W             +    142  3.03e-07 ACAAAGTGTC GAAGGCAAGTTCAAA GGCGTTTTGT
 532 --------------------------------------------------------------------------------
 533
 534 --------------------------------------------------------------------------------
 535         Motif 4 block diagrams
 536 --------------------------------------------------------------------------------
 537 SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
 538 -------------            ----------------  -------------
 539 WashU_Smik_Contig2283.3           5.3e-10  709_[+4]_276
 540 MIT_Sbay_c896_21290               3.5e-09  702_[+4]_283
 541 MIT_Spar_c130_3912                3.5e-09  701_[+4]_284
 542 MIT_Smik_c283_5928                5.9e-08  135_[+4]_172
 543 MIT_Sbay_c84_6418                 1.2e-07  133_[+4]_174
 544 SGD_Scer_YDR044W                  1.3e-07  704_[+4]_281
 545 MIT_Spar_c425_6072                  2e-07  140_[+4]_167
 546 SGD_Scer_YER014W                    3e-07  141_[+4]_166
 547 --------------------------------------------------------------------------------
 548
 549 --------------------------------------------------------------------------------
 550         Motif 4 in BLOCKS format
 551 --------------------------------------------------------------------------------
 552 BL   MOTIF 4 width=15 seqs=8
 553 WashU_Smik_Contig2283.3  (  710) GAAGGCAAGGCTATG  1
 554 MIT_Sbay_c896_21290      (  703) CAAGGCAAGGCTATG  1
 555 MIT_Spar_c130_3912       (  702) CAAGGCAAGGCTATG  1
 556 MIT_Smik_c283_5928       (  136) GAAGGCAAGCTGAAA  1
 557 MIT_Sbay_c84_6418        (  134) GAAGGCAAGCTAAGG  1
 558 SGD_Scer_YDR044W         (  705) AAGGGCAAGGCTATG  1
 559 MIT_Spar_c425_6072       (  141) GAAGGCAAGATGAAA  1
 560 SGD_Scer_YER014W         (  142) GAAGGCAAGTTCAAA  1
 561 //
 562
 563 --------------------------------------------------------------------------------
 564
 565 --------------------------------------------------------------------------------
 566         Motif 4 position-specific scoring matrix
 567 --------------------------------------------------------------------------------
 568 log-odds matrix: alength= 4 w= 15 n= 5176 bayes= 9.33539 E= 9.2e-006
 569   -137     51    183   -965
 570    162   -965   -965   -965
 571    143   -965    -49   -965
 572   -965   -965    251   -965
 573   -965   -965    251   -965
 574   -965    251   -965   -965
 575    162   -965   -965   -965
 576    162   -965   -965   -965
 577   -965   -965    251   -965
 578   -137     51    151   -137
 579   -965    151   -965     62
 580   -137    -49     51     62
 581    162   -965   -965   -965
 582     21   -965    -49     62
 583     21   -965    183   -965
 584 --------------------------------------------------------------------------------
 585
 586 --------------------------------------------------------------------------------
 587         Motif 4 position-specific probability matrix
 588 --------------------------------------------------------------------------------
 589 letter-probability matrix: alength= 4 w= 15 nsites= 8 E= 9.2e-006
 590  0.125000  0.250000  0.625000  0.000000
 591  1.000000  0.000000  0.000000  0.000000
 592  0.875000  0.000000  0.125000  0.000000
 593  0.000000  0.000000  1.000000  0.000000
 594  0.000000  0.000000  1.000000  0.000000
 595  0.000000  1.000000  0.000000  0.000000
 596  1.000000  0.000000  0.000000  0.000000
 597  1.000000  0.000000  0.000000  0.000000
 598  0.000000  0.000000  1.000000  0.000000
 599  0.125000  0.250000  0.500000  0.125000
 600  0.000000  0.500000  0.000000  0.500000
 601  0.125000  0.125000  0.250000  0.500000
 602  1.000000  0.000000  0.000000  0.000000
 603  0.375000  0.000000  0.125000  0.500000
 604  0.375000  0.000000  0.625000  0.000000
 605 --------------------------------------------------------------------------------
 606
 607 --------------------------------------------------------------------------------
 608         Motif 4 regular expression
 609 --------------------------------------------------------------------------------
 610 [GC]AAGGCAAG[GC][CT][TG]A[TA][GA]
 611 --------------------------------------------------------------------------------
 612
 613
 614
 615
 616 Time 11.74 secs.
 617
 618 ********************************************************************************
 619
 620
 621 ********************************************************************************
 622 MOTIF  5        width =   19   sites =   8   llr = 137   E-value = 5.5e-005
 623 ********************************************************************************
 624 --------------------------------------------------------------------------------
 625         Motif 5 Description
 626 --------------------------------------------------------------------------------
 627 Simplified        A  5a559:a:3::1a5aaa98
 628 pos.-specific     C  ::51:::::15:::::::1
 629 probability       G  5:::1::a8:54:::::1:
 630 matrix            T  :::4:a:::9:5:5::::1
 631
 632          bits    2.5        *
 633                  2.3        *
 634                  2.0        *
 635                  1.8        *
 636 Information      1.5  *   **** * * ***
 637 content          1.3  *  ******* * ****
 638 (24.7 bits)      1.0 *** ******* * ****
 639                  0.8 *** ******* * *****
 640                  0.5 *** ***************
 641                  0.3 *******************
 642                  0.0 -------------------
 643
 644 Multilevel           AAAAATAGGTCTAAAAAAA
 645 consensus            G CT    A GG T
 646 sequence
 647
 648 --------------------------------------------------------------------------------
 649
 650 --------------------------------------------------------------------------------
 651         Motif 5 sites sorted by position p-value
 652 --------------------------------------------------------------------------------
 653 Sequence name            Strand  Start   P-value                   Site
 654 -------------            ------  ----- ---------            -------------------
 655 WashU_Smik_Contig2283.3      +    112  5.17e-11 TAACAGGTGA GACAATAGGTGGAAAAAAA GGAAAATATG
 656 SGD_Scer_YDR044W             +    119  5.17e-11 AACAAAGAAA GACAATAGGTGGAAAAAAA AAGGAAAATC
 657 MIT_Spar_c425_6072           +    277  1.49e-09 ACCGAAGAAT GAATATAGGTCTATAAAAA TTCAATAATT
 658 MIT_Spar_c130_3912           +    116  1.75e-09 AACAAAGAAA GACAATAGGCGGAAAAAAA GGAAAATCCG
 659 MIT_Sbay_c896_21290          +    120  6.56e-09 ATTGGCAGCG AACAATAGGTGAAAAAAAA AAAGAAAATG
 660 SGD_Scer_YER014W             +    270  1.56e-08 TTAAAAAATT AAATATAGGTCTATAAAAC TCGATAATTA
 661 MIT_Smik_c283_5928           +    272  2.46e-08 ATCAAATGTT AAATATAGATCTATAAAAA TTGAATAGTA
 662 MIT_Sbay_c84_6418            +    261  1.48e-07 TATTTATATT AAACGTAGATCTATAAAGT TTAAATAGTT
 663 --------------------------------------------------------------------------------
 664
 665 --------------------------------------------------------------------------------
 666         Motif 5 block diagrams
 667 --------------------------------------------------------------------------------
 668 SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
 669 -------------            ----------------  -------------
 670 WashU_Smik_Contig2283.3           5.2e-11  111_[+5]_870
 671 SGD_Scer_YDR044W                  5.2e-11  118_[+5]_863
 672 MIT_Spar_c425_6072                1.5e-09  276_[+5]_27
 673 MIT_Spar_c130_3912                1.8e-09  115_[+5]_866
 674 MIT_Sbay_c896_21290               6.6e-09  119_[+5]_862
 675 SGD_Scer_YER014W                  1.6e-08  269_[+5]_34
 676 MIT_Smik_c283_5928                2.5e-08  271_[+5]_32
 677 MIT_Sbay_c84_6418                 1.5e-07  260_[+5]_43
 678 --------------------------------------------------------------------------------
 679
 680 --------------------------------------------------------------------------------
 681         Motif 5 in BLOCKS format
 682 --------------------------------------------------------------------------------
 683 BL   MOTIF 5 width=19 seqs=8
 684 WashU_Smik_Contig2283.3  (  112) GACAATAGGTGGAAAAAAA  1
 685 SGD_Scer_YDR044W         (  119) GACAATAGGTGGAAAAAAA  1
 686 MIT_Spar_c425_6072       (  277) GAATATAGGTCTATAAAAA  1
 687 MIT_Spar_c130_3912       (  116) GACAATAGGCGGAAAAAAA  1
 688 MIT_Sbay_c896_21290      (  120) AACAATAGGTGAAAAAAAA  1
 689 SGD_Scer_YER014W         (  270) AAATATAGGTCTATAAAAC  1
 690 MIT_Smik_c283_5928       (  272) AAATATAGATCTATAAAAA  1
 691 MIT_Sbay_c84_6418        (  261) AAACGTAGATCTATAAAGT  1
 692 //
 693
 694 --------------------------------------------------------------------------------
 695
 696 --------------------------------------------------------------------------------
 697         Motif 5 position-specific scoring matrix
 698 --------------------------------------------------------------------------------
 699 log-odds matrix: alength= 4 w= 19 n= 5144 bayes= 9.32643 E= 5.5e-005
 700     62   -965    151   -965
 701    162   -965   -965   -965
 702     62    151   -965   -965
 703     62    -49   -965     21
 704    143   -965    -49   -965
 705   -965   -965   -965    162
 706    162   -965   -965   -965
 707   -965   -965    251   -965
 708    -38   -965    209   -965
 709   -965    -49   -965    143
 710   -965    151    151   -965
 711   -137   -965    109     62
 712    162   -965   -965   -965
 713     62   -965   -965     62
 714    162   -965   -965   -965
 715    162   -965   -965   -965
 716    162   -965   -965   -965
 717    143   -965    -49   -965
 718    121    -49   -965   -137
 719 --------------------------------------------------------------------------------
 720
 721 --------------------------------------------------------------------------------
 722         Motif 5 position-specific probability matrix
 723 --------------------------------------------------------------------------------
 724 letter-probability matrix: alength= 4 w= 19 nsites= 8 E= 5.5e-005
 725  0.500000  0.000000  0.500000  0.000000
 726  1.000000  0.000000  0.000000  0.000000
 727  0.500000  0.500000  0.000000  0.000000
 728  0.500000  0.125000  0.000000  0.375000
 729  0.875000  0.000000  0.125000  0.000000
 730  0.000000  0.000000  0.000000  1.000000
 731  1.000000  0.000000  0.000000  0.000000
 732  0.000000  0.000000  1.000000  0.000000
 733  0.250000  0.000000  0.750000  0.000000
 734  0.000000  0.125000  0.000000  0.875000
 735  0.000000  0.500000  0.500000  0.000000
 736  0.125000  0.000000  0.375000  0.500000
 737  1.000000  0.000000  0.000000  0.000000
 738  0.500000  0.000000  0.000000  0.500000
 739  1.000000  0.000000  0.000000  0.000000
 740  1.000000  0.000000  0.000000  0.000000
 741  1.000000  0.000000  0.000000  0.000000
 742  0.875000  0.000000  0.125000  0.000000
 743  0.750000  0.125000  0.000000  0.125000
 744 --------------------------------------------------------------------------------
 745
 746 --------------------------------------------------------------------------------
 747         Motif 5 regular expression
 748 --------------------------------------------------------------------------------
 749 [AG]A[AC][AT]ATAG[GA]T[CG][TG]A[AT]AAAAA
 750 --------------------------------------------------------------------------------
 751
 752
 753
 754
 755 Time 14.61 secs.
 756
 757 ********************************************************************************
 758
 759
 760 ********************************************************************************
 761 SUMMARY OF MOTIFS
 762 ********************************************************************************
 763
 764 --------------------------------------------------------------------------------
 765         Combined block diagrams: non-overlapping sites with p-value < 0.0001
 766 --------------------------------------------------------------------------------
 767 SEQUENCE NAME            COMBINED P-VALUE  MOTIF DIAGRAM
 768 -------------            ----------------  -------------
 769 SGD_Scer_YDR044W                 1.10e-26  118_[+5(5.17e-11)]_33_[+2(1.97e-09)]_153_[+1(3.65e-14)]_265_[+3(5.75e-10)]_56_[+4(1.33e-07)]_153_[+2(7.52e-05)]_108
 770 MIT_Spar_c130_3912               4.24e-25  115_[+5(1.75e-09)]_32_[+2(9.91e-11)]_149_[+1(1.07e-10)]_268_[+3(2.08e-10)]_58_[+4(3.55e-09)]_254_[-4(6.48e-05)]_15
 771 MIT_Sbay_c896_21290              6.48e-23  119_[+5(6.56e-09)]_34_[+2(2.20e-10)]_114_[+1(4.06e-05)]_16_[+1(2.63e-10)]_265_[+3(2.12e-09)]_55_[+4(3.55e-09)]_283
 772 WashU_Smik_Contig2283.3          6.34e-28  111_[+5(5.17e-11)]_32_[+2(9.67e-10)]_158_[+1(8.23e-11)]_5_[-4(1.66e-05)]_249_[+3(6.53e-12)]_60_[+4(5.26e-10)]_276
 773 SGD_Scer_YER014W                 1.51e-24  68_[-2(3.83e-10)]_25_[-1(1.77e-11)]_8_[+4(3.03e-07)]_4_[-3(5.75e-10)]_89_[+5(1.56e-08)]_34
 774 MIT_Spar_c425_6072               6.46e-26  68_[-2(2.68e-11)]_24_[-1(1.77e-11)]_8_[+4(1.99e-07)]_4_[-3(4.65e-09)]_97_[+5(1.49e-09)]_6_[+5(6.43e-06)]_2
 775 MIT_Smik_c283_5928               4.72e-22  70_[-2(2.41e-09)]_19_[-1(7.48e-09)]_6_[+4(5.90e-08)]_4_[-3(3.18e-10)]_97_[+5(2.46e-08)]_32
 776 MIT_Sbay_c84_6418                7.03e-21  63_[-2(3.09e-09)]_22_[-1(8.94e-10)]_8_[+4(1.20e-07)]_7_[-3(3.04e-09)]_85_[+5(1.48e-07)]_43
 777 --------------------------------------------------------------------------------
 778
 779 ********************************************************************************
 780
 781
 782 ********************************************************************************
 783 Stopped because nmotifs = 5 reached.
 784 ********************************************************************************
 785
 786 CPU: dhn02990.mrc-dunn.cam.ac.uk
 787
 788 ********************************************************************************