t/data/map_hem/HEM3-HEM4.meme.txt

   1 ********************************************************************************
   2 MEME - Motif discovery tool
   3 ********************************************************************************
   4 MEME version 3.5.4 (Release date:    )
   5
   6 For further information on how to interpret these results or to get
   7 a copy of the MEME software please access http://meme.nbcr.net.
   8
   9 This file may be used as input to the MAST algorithm for searching
  10 sequence databases for matches to groups of motifs.  MAST is available
  11 for interactive use and downloading at http://meme.nbcr.net.
  12 ********************************************************************************
  13
  14
  15 ********************************************************************************
  16 REFERENCE
  17 ********************************************************************************
  18 If you use this program in your research, please cite:
  19
  20 Timothy L. Bailey and Charles Elkan,
  21 "Fitting a mixture model by expectation maximization to discover
  22 motifs in biopolymers", Proceedings of the Second International
  23 Conference on Intelligent Systems for Molecular Biology, pp. 28-36,
  24 AAAI Press, Menlo Park, California, 1994.
  25 ********************************************************************************
  26
  27
  28 ********************************************************************************
  29 TRAINING SET
  30 ********************************************************************************
  31 DATAFILE= HEM3-HEM4.fa
  32 ALPHABET= ACGT
  33 Sequence name            Weight Length  Sequence name            Weight Length
  34 -------------            ------ ------  -------------            ------ ------
  35 SGD_Scer_YDL205C         1.0000    860  MIT_Spar_c429_3020       1.0000    860
  36 MIT_Smik_c193_2483       1.0000    860  MIT_Sbay_c841_3215       1.0000    860
  37 WashU_Skud_Contig1850.5  1.0000    860  SGD_Scer_YOR278W         1.0000    635
  38 MIT_Spar_c261_21317      1.0000    635  MIT_Smik_c492_20940      1.0000    635
  39 WashU_Skud_Contig1682.4  1.0000    635  WashU_Sbay_Contig635.57  1.0000    635
  40 ********************************************************************************
  41
  42 ********************************************************************************
  43 COMMAND LINE SUMMARY
  44 ********************************************************************************
  45 This information can also be useful in the event you wish to report a
  46 problem with the MEME software.
  47
  48 command: meme HEM3-HEM4.fa -nostatus -dna -revcomp -nmotifs 5 -bfile yeast.nc.1.freq -maxw 20 -mod oops -dir /Volumes/DATA/Home/ajr/sw/powerpc/meme-3.5.4
  49
  50 model:  mod=          oops    nmotifs=         5    evt=           inf
  51 object function=  E-value of product of p-values
  52 width:  minw=            6    maxw=           20    minic=        0.00
  53 width:  wg=             11    ws=              1    endgaps=       yes
  54 nsites: minsites=       10    maxsites=       10    wnsites=       0.8
  55 theta:  prob=            1    spmap=         uni    spfuzz=        0.5
  56 em:     prior=   dirichlet    b=            0.01    maxiter=        50
  57         distance=    1e-05
  58 data:   n=            7475    N=              10
  59 strands: + -
  60 sample: seed=            0    seqfrac=         1
  61 Letter frequencies in dataset:
  62 A 0.310 C 0.190 G 0.190 T 0.310
  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 = 217   E-value = 9.7e-028
  70 ********************************************************************************
  71 --------------------------------------------------------------------------------
  72         Motif 1 Description
  73 --------------------------------------------------------------------------------
  74 Simplified        A  5:a:::5:::5::5:::a5a
  75 pos.-specific     C  5a::aa5::::a55::5:2:
  76 probability       G  :::a::::5:5:5::21:::
  77 matrix            T  :::::::a5a::::a84:3:
  78
  79          bits    2.5  * ***     *
  80                  2.3  * ***     *
  81                  2.0  * ***     *
  82                  1.8  * ***     *
  83 Information      1.5  ***** * * ** *  * *
  84 content          1.3  ***** * * ** *  * *
  85 (31.3 bits)      1.0 **************** * *
  86                  0.8 ****************** *
  87                  0.5 ****************** *
  88                  0.3 ********************
  89                  0.0 --------------------
  90
  91 Multilevel           ACAGCCATGTACCATTCAAA
  92 consensus            C     C T G GC GT T
  93 sequence                               C
  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_Contig1850.5      +    115  4.59e-11 AAAAAGCAAT ACAGCCCTGTACCATTCAAA CACGAACGCC
 103 MIT_Sbay_c841_3215           +    116  4.59e-11 AAAACGCAAT ACAGCCCTGTACCATTCAAA TACGAACGCC
 104 MIT_Smik_c193_2483           +    117  4.59e-11 AAAAAGTAAT ACAGCCCTGTACCATTCAAA CACGAGCGCC
 105 WashU_Skud_Contig1682.4      +    337  1.14e-10 TGGTCTACTT CCAGCCATTTGCGCTTTACA TAGACATATG
 106 MIT_Smik_c492_20940          +    342  1.41e-10 TTGTCTACTT CCAGCCATTTGCGCTTTATA TAGACATATG
 107 MIT_Spar_c261_21317          +    336  1.41e-10 TGGTCTACTT CCAGCCATTTGCGCTTTATA TAGACATATG
 108 SGD_Scer_YOR278W             +    333  1.41e-10 TGGTCTACTT CCAGCCATTTGCGCTTTATA TAGACATATG
 109 MIT_Spar_c429_3020           +    115  1.41e-10 AAAATGTAAA ACAGCCCTGTACCATGCAAA CACGAGCCTC
 110 SGD_Scer_YDL205C             +    115  1.41e-10 AAAATCTAAT ACAGCCCTGTACCATGCAAA CACGAGCGTC
 111 WashU_Sbay_Contig635.57      +    344  2.72e-10 TGGTCTACTT CCAGCCATTTGCGCTTGACA TAGACATATG
 112 --------------------------------------------------------------------------------
 113
 114 --------------------------------------------------------------------------------
 115         Motif 1 block diagrams
 116 --------------------------------------------------------------------------------
 117 SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
 118 -------------            ----------------  -------------
 119 WashU_Skud_Contig1850.5           4.6e-11  114_[+1]_726
 120 MIT_Sbay_c841_3215                4.6e-11  115_[+1]_725
 121 MIT_Smik_c193_2483                4.6e-11  116_[+1]_724
 122 WashU_Skud_Contig1682.4           1.1e-10  336_[+1]_279
 123 MIT_Smik_c492_20940               1.4e-10  341_[+1]_274
 124 MIT_Spar_c261_21317               1.4e-10  335_[+1]_280
 125 SGD_Scer_YOR278W                  1.4e-10  332_[+1]_283
 126 MIT_Spar_c429_3020                1.4e-10  114_[+1]_726
 127 SGD_Scer_YDL205C                  1.4e-10  114_[+1]_726
 128 WashU_Sbay_Contig635.57           2.7e-10  343_[+1]_272
 129 --------------------------------------------------------------------------------
 130
 131 --------------------------------------------------------------------------------
 132         Motif 1 in BLOCKS format
 133 --------------------------------------------------------------------------------
 134 BL   MOTIF 1 width=20 seqs=10
 135 WashU_Skud_Contig1850.5  (  115) ACAGCCCTGTACCATTCAAA  1
 136 MIT_Sbay_c841_3215       (  116) ACAGCCCTGTACCATTCAAA  1
 137 MIT_Smik_c193_2483       (  117) ACAGCCCTGTACCATTCAAA  1
 138 WashU_Skud_Contig1682.4  (  337) CCAGCCATTTGCGCTTTACA  1
 139 MIT_Smik_c492_20940      (  342) CCAGCCATTTGCGCTTTATA  1
 140 MIT_Spar_c261_21317      (  336) CCAGCCATTTGCGCTTTATA  1
 141 SGD_Scer_YOR278W         (  333) CCAGCCATTTGCGCTTTATA  1
 142 MIT_Spar_c429_3020       (  115) ACAGCCCTGTACCATGCAAA  1
 143 SGD_Scer_YDL205C         (  115) ACAGCCCTGTACCATGCAAA  1
 144 WashU_Sbay_Contig635.57  (  344) CCAGCCATTTGCGCTTGACA  1
 145 //
 146
 147 --------------------------------------------------------------------------------
 148
 149 --------------------------------------------------------------------------------
 150         Motif 1 position-specific scoring matrix
 151 --------------------------------------------------------------------------------
 152 log-odds matrix: alength= 4 w= 20 n= 7285 bayes= 9.5068 E= 9.7e-028
 153     62    151   -997   -997
 154   -997    251   -997   -997
 155    162   -997   -997   -997
 156   -997   -997    251   -997
 157   -997    251   -997   -997
 158   -997    251   -997   -997
 159     62    151   -997   -997
 160   -997   -997   -997    162
 161   -997   -997    151     62
 162   -997   -997   -997    162
 163     62   -997    151   -997
 164   -997    251   -997   -997
 165   -997    151    151   -997
 166     62    151   -997   -997
 167   -997   -997   -997    162
 168   -997   -997     19    130
 169   -997    151    -81     30
 170    162   -997   -997   -997
 171     62     19   -997    -11
 172    162   -997   -997   -997
 173 --------------------------------------------------------------------------------
 174
 175 --------------------------------------------------------------------------------
 176         Motif 1 position-specific probability matrix
 177 --------------------------------------------------------------------------------
 178 letter-probability matrix: alength= 4 w= 20 nsites= 10 E= 9.7e-028
 179  0.500000  0.500000  0.000000  0.000000
 180  0.000000  1.000000  0.000000  0.000000
 181  1.000000  0.000000  0.000000  0.000000
 182  0.000000  0.000000  1.000000  0.000000
 183  0.000000  1.000000  0.000000  0.000000
 184  0.000000  1.000000  0.000000  0.000000
 185  0.500000  0.500000  0.000000  0.000000
 186  0.000000  0.000000  0.000000  1.000000
 187  0.000000  0.000000  0.500000  0.500000
 188  0.000000  0.000000  0.000000  1.000000
 189  0.500000  0.000000  0.500000  0.000000
 190  0.000000  1.000000  0.000000  0.000000
 191  0.000000  0.500000  0.500000  0.000000
 192  0.500000  0.500000  0.000000  0.000000
 193  0.000000  0.000000  0.000000  1.000000
 194  0.000000  0.000000  0.200000  0.800000
 195  0.000000  0.500000  0.100000  0.400000
 196  1.000000  0.000000  0.000000  0.000000
 197  0.500000  0.200000  0.000000  0.300000
 198  1.000000  0.000000  0.000000  0.000000
 199 --------------------------------------------------------------------------------
 200
 201 --------------------------------------------------------------------------------
 202         Motif 1 regular expression
 203 --------------------------------------------------------------------------------
 204 [AC]CAGCC[AC]T[GT]T[AG]C[CG][AC]T[TG][CT]A[ATC]A
 205 --------------------------------------------------------------------------------
 206
 207
 208
 209
 210 Time  5.67 secs.
 211
 212 ********************************************************************************
 213
 214
 215 ********************************************************************************
 216 MOTIF  2        width =   20   sites =  10   llr = 211   E-value = 3.2e-025
 217 ********************************************************************************
 218 --------------------------------------------------------------------------------
 219         Motif 2 Description
 220 --------------------------------------------------------------------------------
 221 Simplified        A  8::::::a5::a::::57::
 222 pos.-specific     C  ::::a:::5:a::5:::::a
 223 probability       G  1:55:::::5:::5a2::::
 224 matrix            T  1a55:aa::5::a::853a:
 225
 226          bits    2.5     *     *   *    *
 227                  2.3     *     *   *    *
 228                  2.0     *     *   *    *
 229                  1.8     *     *   *    *
 230 Information      1.5  *  ****  *****   **
 231 content          1.3  *  ****  *****   **
 232 (30.4 bits)      1.0  ***************  **
 233                  0.8 **************** ***
 234                  0.5 ********************
 235                  0.3 ********************
 236                  0.0 --------------------
 237
 238 Multilevel           ATGGCTTAAGCATCGTAATC
 239 consensus              TT    CT   G GTT
 240 sequence
 241
 242 --------------------------------------------------------------------------------
 243
 244 --------------------------------------------------------------------------------
 245         Motif 2 sites sorted by position p-value
 246 --------------------------------------------------------------------------------
 247 Sequence name            Strand  Start   P-value                    Site
 248 -------------            ------  ----- ---------            --------------------
 249 WashU_Sbay_Contig635.57      +    382  8.08e-11 TGGAGGCGTG ATGTCTTAAGCATGGTAATC CGGAAGATCA
 250 WashU_Skud_Contig1682.4      +    375  8.08e-11 TGGAGGCGTG ATGTCTTAAGCATGGTAATC CGGAAGATCA
 251 MIT_Smik_c492_20940          +    380  8.08e-11 TGGAGGCGTG ATGTCTTAAGCATGGTAATC CGGAAGATCA
 252 MIT_Spar_c261_21317          +    374  8.08e-11 TGGAGGCGTG ATGTCTTAAGCATGGTAATC CGGAAGATCA
 253 SGD_Scer_YOR278W             +    371  8.08e-11 TGGAGGCGTG ATGTCTTAAGCATGGTAATC CGGAAGATCA
 254 MIT_Smik_c193_2483           +    326  8.08e-11 AGAGGCCTTC ATTGCTTACTCATCGTTATC TTATTGGTTA
 255 MIT_Spar_c429_3020           +    325  5.11e-10 AAAGACCTTC ATTGCTTACTCATCGGTTTC TTATTGGTCA
 256 SGD_Scer_YDL205C             +    322  5.11e-10 AAAGACCTTC ATTGCTTACTCATCGGTTTC TTATTGGTCA
 257 MIT_Sbay_c841_3215           +    323  6.64e-10 AGAGGCCTTC TTTGCTTACTCATCGTTATC TTATTGGTCA
 258 WashU_Skud_Contig1850.5      +    325  7.76e-10 AGAGGCGTAC GTTGCTTACTCATCGTTTTC TTATTGGTCA
 259 --------------------------------------------------------------------------------
 260
 261 --------------------------------------------------------------------------------
 262         Motif 2 block diagrams
 263 --------------------------------------------------------------------------------
 264 SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
 265 -------------            ----------------  -------------
 266 WashU_Sbay_Contig635.57           8.1e-11  381_[+2]_234
 267 WashU_Skud_Contig1682.4           8.1e-11  374_[+2]_241
 268 MIT_Smik_c492_20940               8.1e-11  379_[+2]_236
 269 MIT_Spar_c261_21317               8.1e-11  373_[+2]_242
 270 SGD_Scer_YOR278W                  8.1e-11  370_[+2]_245
 271 MIT_Smik_c193_2483                8.1e-11  325_[+2]_515
 272 MIT_Spar_c429_3020                5.1e-10  324_[+2]_516
 273 SGD_Scer_YDL205C                  5.1e-10  321_[+2]_519
 274 MIT_Sbay_c841_3215                6.6e-10  322_[+2]_518
 275 WashU_Skud_Contig1850.5           7.8e-10  324_[+2]_516
 276 --------------------------------------------------------------------------------
 277
 278 --------------------------------------------------------------------------------
 279         Motif 2 in BLOCKS format
 280 --------------------------------------------------------------------------------
 281 BL   MOTIF 2 width=20 seqs=10
 282 WashU_Sbay_Contig635.57  (  382) ATGTCTTAAGCATGGTAATC  1
 283 WashU_Skud_Contig1682.4  (  375) ATGTCTTAAGCATGGTAATC  1
 284 MIT_Smik_c492_20940      (  380) ATGTCTTAAGCATGGTAATC  1
 285 MIT_Spar_c261_21317      (  374) ATGTCTTAAGCATGGTAATC  1
 286 SGD_Scer_YOR278W         (  371) ATGTCTTAAGCATGGTAATC  1
 287 MIT_Smik_c193_2483       (  326) ATTGCTTACTCATCGTTATC  1
 288 MIT_Spar_c429_3020       (  325) ATTGCTTACTCATCGGTTTC  1
 289 SGD_Scer_YDL205C         (  322) ATTGCTTACTCATCGGTTTC  1
 290 MIT_Sbay_c841_3215       (  323) TTTGCTTACTCATCGTTATC  1
 291 WashU_Skud_Contig1850.5  (  325) GTTGCTTACTCATCGTTTTC  1
 292 //
 293
 294 --------------------------------------------------------------------------------
 295
 296 --------------------------------------------------------------------------------
 297         Motif 2 position-specific scoring matrix
 298 --------------------------------------------------------------------------------
 299 log-odds matrix: alength= 4 w= 20 n= 7285 bayes= 9.5068 E= 3.2e-025
 300    130   -997    -81   -169
 301   -997   -997   -997    162
 302   -997   -997    151     62
 303   -997   -997    151     62
 304   -997    251   -997   -997
 305   -997   -997   -997    162
 306   -997   -997   -997    162
 307    162   -997   -997   -997
 308     62    151   -997   -997
 309   -997   -997    151     62
 310   -997    251   -997   -997
 311    162   -997   -997   -997
 312   -997   -997   -997    162
 313   -997    151    151   -997
 314   -997   -997    251   -997
 315   -997   -997     19    130
 316     62   -997   -997     62
 317    111   -997   -997    -11
 318   -997   -997   -997    162
 319   -997    251   -997   -997
 320 --------------------------------------------------------------------------------
 321
 322 --------------------------------------------------------------------------------
 323         Motif 2 position-specific probability matrix
 324 --------------------------------------------------------------------------------
 325 letter-probability matrix: alength= 4 w= 20 nsites= 10 E= 3.2e-025
 326  0.800000  0.000000  0.100000  0.100000
 327  0.000000  0.000000  0.000000  1.000000
 328  0.000000  0.000000  0.500000  0.500000
 329  0.000000  0.000000  0.500000  0.500000
 330  0.000000  1.000000  0.000000  0.000000
 331  0.000000  0.000000  0.000000  1.000000
 332  0.000000  0.000000  0.000000  1.000000
 333  1.000000  0.000000  0.000000  0.000000
 334  0.500000  0.500000  0.000000  0.000000
 335  0.000000  0.000000  0.500000  0.500000
 336  0.000000  1.000000  0.000000  0.000000
 337  1.000000  0.000000  0.000000  0.000000
 338  0.000000  0.000000  0.000000  1.000000
 339  0.000000  0.500000  0.500000  0.000000
 340  0.000000  0.000000  1.000000  0.000000
 341  0.000000  0.000000  0.200000  0.800000
 342  0.500000  0.000000  0.000000  0.500000
 343  0.700000  0.000000  0.000000  0.300000
 344  0.000000  0.000000  0.000000  1.000000
 345  0.000000  1.000000  0.000000  0.000000
 346 --------------------------------------------------------------------------------
 347
 348 --------------------------------------------------------------------------------
 349         Motif 2 regular expression
 350 --------------------------------------------------------------------------------
 351 AT[GT][GT]CTTA[AC][GT]CAT[CG]G[TG][AT][AT]TC
 352 --------------------------------------------------------------------------------
 353
 354
 355
 356
 357 Time 11.21 secs.
 358
 359 ********************************************************************************
 360
 361
 362 ********************************************************************************
 363 MOTIF  3        width =   20   sites =  10   llr = 207   E-value = 5.5e-024
 364 ********************************************************************************
 365 --------------------------------------------------------------------------------
 366         Motif 3 Description
 367 --------------------------------------------------------------------------------
 368 Simplified        A  :519a:a5:a255:9:::aa
 369 pos.-specific     C  5:::::::a::::::::5::
 370 probability       G  559::a::::8::::::5::
 371 matrix            T  :::1:::5:::55a1aa:::
 372
 373          bits    2.5      *  *
 374                  2.3      *  *
 375                  2.0   *  *  *
 376                  1.8   *  *  *
 377 Information      1.5 * * *** ***  * *****
 378 content          1.3 * ***** ***  *******
 379 (29.8 bits)      1.0 ******* ***  *******
 380                  0.8 ******* ***  *******
 381                  0.5 ********************
 382                  0.3 ********************
 383                  0.0 --------------------
 384
 385 Multilevel           CAGAAGAACAGAATATTCAA
 386 consensus            GG     T  ATT    G
 387 sequence
 388
 389 --------------------------------------------------------------------------------
 390
 391 --------------------------------------------------------------------------------
 392         Motif 3 sites sorted by position p-value
 393 --------------------------------------------------------------------------------
 394 Sequence name            Strand  Start   P-value                    Site
 395 -------------            ------  ----- ---------            --------------------
 396 WashU_Sbay_Contig635.57      +    402  7.26e-11 CATGGTAATC CGGAAGATCAGTTTATTGAA TGATGGCTCT
 397 WashU_Skud_Contig1682.4      +    395  7.26e-11 CATGGTAATC CGGAAGATCAGTTTATTGAA TGATGGTTCT
 398 MIT_Smik_c492_20940          +    400  7.26e-11 CATGGTAATC CGGAAGATCAGTTTATTGAA TGATGGTTCT
 399 MIT_Spar_c261_21317          +    394  7.26e-11 CATGGTAATC CGGAAGATCAGTTTATTGAA TGATGGTTCT
 400 SGD_Scer_YOR278W             +    391  7.26e-11 CATGGTAATC CGGAAGATCAGTTTATTGAA TGATGGTTTT
 401 MIT_Spar_c429_3020           +     87  2.07e-10 AATACGGGAT GAGAAGAACAGAATATTCAA AATGTAAAAC
 402 SGD_Scer_YDL205C             +     87  2.07e-10 AATACGGGAT GAGAAGAACAGAATATTCAA AATCTAATAC
 403 MIT_Smik_c193_2483           +     89  1.38e-09 AATACGGGAT GAAAAGAACAGAATATTCAA AAAGTAATAC
 404 WashU_Skud_Contig1850.5      +     87  2.47e-09 ATATGGGGAT GAGAAGAACAAAATTTTCAA AAAGCAATAC
 405 MIT_Sbay_c841_3215           +     88  2.47e-09 AATATGGGAT GAGTAGAACAAAATATTCAA AACGCAATAC
 406 --------------------------------------------------------------------------------
 407
 408 --------------------------------------------------------------------------------
 409         Motif 3 block diagrams
 410 --------------------------------------------------------------------------------
 411 SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
 412 -------------            ----------------  -------------
 413 WashU_Sbay_Contig635.57           7.3e-11  401_[+3]_214
 414 WashU_Skud_Contig1682.4           7.3e-11  394_[+3]_221
 415 MIT_Smik_c492_20940               7.3e-11  399_[+3]_216
 416 MIT_Spar_c261_21317               7.3e-11  393_[+3]_222
 417 SGD_Scer_YOR278W                  7.3e-11  390_[+3]_225
 418 MIT_Spar_c429_3020                2.1e-10  86_[+3]_754
 419 SGD_Scer_YDL205C                  2.1e-10  86_[+3]_754
 420 MIT_Smik_c193_2483                1.4e-09  88_[+3]_752
 421 WashU_Skud_Contig1850.5           2.5e-09  86_[+3]_754
 422 MIT_Sbay_c841_3215                2.5e-09  87_[+3]_753
 423 --------------------------------------------------------------------------------
 424
 425 --------------------------------------------------------------------------------
 426         Motif 3 in BLOCKS format
 427 --------------------------------------------------------------------------------
 428 BL   MOTIF 3 width=20 seqs=10
 429 WashU_Sbay_Contig635.57  (  402) CGGAAGATCAGTTTATTGAA  1
 430 WashU_Skud_Contig1682.4  (  395) CGGAAGATCAGTTTATTGAA  1
 431 MIT_Smik_c492_20940      (  400) CGGAAGATCAGTTTATTGAA  1
 432 MIT_Spar_c261_21317      (  394) CGGAAGATCAGTTTATTGAA  1
 433 SGD_Scer_YOR278W         (  391) CGGAAGATCAGTTTATTGAA  1
 434 MIT_Spar_c429_3020       (   87) GAGAAGAACAGAATATTCAA  1
 435 SGD_Scer_YDL205C         (   87) GAGAAGAACAGAATATTCAA  1
 436 MIT_Smik_c193_2483       (   89) GAAAAGAACAGAATATTCAA  1
 437 WashU_Skud_Contig1850.5  (   87) GAGAAGAACAAAATTTTCAA  1
 438 MIT_Sbay_c841_3215       (   88) GAGTAGAACAAAATATTCAA  1
 439 //
 440
 441 --------------------------------------------------------------------------------
 442
 443 --------------------------------------------------------------------------------
 444         Motif 3 position-specific scoring matrix
 445 --------------------------------------------------------------------------------
 446 log-odds matrix: alength= 4 w= 20 n= 7285 bayes= 9.5068 E= 5.5e-024
 447   -997    151    151   -997
 448     62   -997    151   -997
 449   -169   -997    236   -997
 450    147   -997   -997   -169
 451    162   -997   -997   -997
 452   -997   -997    251   -997
 453    162   -997   -997   -997
 454     62   -997   -997     62
 455   -997    251   -997   -997
 456    162   -997   -997   -997
 457    -70   -997    219   -997
 458     62   -997   -997     62
 459     62   -997   -997     62
 460   -997   -997   -997    162
 461    147   -997   -997   -169
 462   -997   -997   -997    162
 463   -997   -997   -997    162
 464   -997    151    151   -997
 465    162   -997   -997   -997
 466    162   -997   -997   -997
 467 --------------------------------------------------------------------------------
 468
 469 --------------------------------------------------------------------------------
 470         Motif 3 position-specific probability matrix
 471 --------------------------------------------------------------------------------
 472 letter-probability matrix: alength= 4 w= 20 nsites= 10 E= 5.5e-024
 473  0.000000  0.500000  0.500000  0.000000
 474  0.500000  0.000000  0.500000  0.000000
 475  0.100000  0.000000  0.900000  0.000000
 476  0.900000  0.000000  0.000000  0.100000
 477  1.000000  0.000000  0.000000  0.000000
 478  0.000000  0.000000  1.000000  0.000000
 479  1.000000  0.000000  0.000000  0.000000
 480  0.500000  0.000000  0.000000  0.500000
 481  0.000000  1.000000  0.000000  0.000000
 482  1.000000  0.000000  0.000000  0.000000
 483  0.200000  0.000000  0.800000  0.000000
 484  0.500000  0.000000  0.000000  0.500000
 485  0.500000  0.000000  0.000000  0.500000
 486  0.000000  0.000000  0.000000  1.000000
 487  0.900000  0.000000  0.000000  0.100000
 488  0.000000  0.000000  0.000000  1.000000
 489  0.000000  0.000000  0.000000  1.000000
 490  0.000000  0.500000  0.500000  0.000000
 491  1.000000  0.000000  0.000000  0.000000
 492  1.000000  0.000000  0.000000  0.000000
 493 --------------------------------------------------------------------------------
 494
 495 --------------------------------------------------------------------------------
 496         Motif 3 regular expression
 497 --------------------------------------------------------------------------------
 498 [CG][AG]GAAGA[AT]CA[GA][AT][AT]TATT[CG]AA
 499 --------------------------------------------------------------------------------
 500
 501
 502
 503
 504 Time 16.58 secs.
 505
 506 ********************************************************************************
 507
 508
 509 ********************************************************************************
 510 MOTIF  4        width =   15   sites =  10   llr = 165   E-value = 1.7e-014
 511 ********************************************************************************
 512 --------------------------------------------------------------------------------
 513         Motif 4 Description
 514 --------------------------------------------------------------------------------
 515 Simplified        A  9:555:a:5:aa11a
 516 pos.-specific     C  1a5:::::5:::66:
 517 probability       G  ::::5a:a:a::33:
 518 matrix            T  :::5:::::::::::
 519
 520          bits    2.5  *   * * *
 521                  2.3  *   * * *
 522                  2.0  *   * * *
 523                  1.8  *   * * *
 524 Information      1.5  *   *** ***  *
 525 content          1.3 **   *** ***  *
 526 (23.9 bits)      1.0 *** ***********
 527                  0.8 *** ***********
 528                  0.5 ***************
 529                  0.3 ***************
 530                  0.0 ---------------
 531
 532 Multilevel           ACAAAGAGAGAACCA
 533 consensus              CTG   C   GG
 534 sequence
 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_Sbay_Contig635.57      +    238  2.42e-09 AAACATGTAC ACCTAGAGCGAACCA GTGATAATTT
 544 WashU_Skud_Contig1682.4      +    232  2.42e-09 AGATATGTAC ACCTAGAGCGAACCA ATGATAATTT
 545 MIT_Smik_c492_20940          +    235  2.42e-09 AGATATGTAC ACCTAGAGCGAACCA ATAATAATTT
 546 MIT_Spar_c261_21317          +    230  2.42e-09 GAATATGTAC ACCTAGAGCGAACCA ATGATAATTT
 547 SGD_Scer_YOR278W             +    226  2.42e-09 AGATATGTAC ACCTAGAGCGAACCA ATGATAATTT
 548 MIT_Sbay_c841_3215           +    372  6.95e-09 GGGACAATAG ACAAGGAGAGAACCA CCAACTTTGG
 549 MIT_Spar_c429_3020           +    376  3.49e-08 GGGTCAATTG ACAAGGAGAGAAGGA ATGTTACATC
 550 SGD_Scer_YDL205C             +    373  3.49e-08 GGGTCAATTG ACAAGGAGAGAAGGA ATGTTATATG
 551 MIT_Smik_c193_2483           +    375  1.07e-07 GCGACAATGT ACAAGGAGAGAAGAA ATGATATGTC
 552 WashU_Skud_Contig1850.5      +    374  1.53e-07 GGAACAATGC CCAAGGAGAGAAAGA GTGCTACGTC
 553 --------------------------------------------------------------------------------
 554
 555 --------------------------------------------------------------------------------
 556         Motif 4 block diagrams
 557 --------------------------------------------------------------------------------
 558 SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
 559 -------------            ----------------  -------------
 560 WashU_Sbay_Contig635.57           2.4e-09  237_[+4]_383
 561 WashU_Skud_Contig1682.4           2.4e-09  231_[+4]_389
 562 MIT_Smik_c492_20940               2.4e-09  234_[+4]_386
 563 MIT_Spar_c261_21317               2.4e-09  229_[+4]_391
 564 SGD_Scer_YOR278W                  2.4e-09  225_[+4]_395
 565 MIT_Sbay_c841_3215                6.9e-09  371_[+4]_474
 566 MIT_Spar_c429_3020                3.5e-08  375_[+4]_470
 567 SGD_Scer_YDL205C                  3.5e-08  372_[+4]_473
 568 MIT_Smik_c193_2483                1.1e-07  374_[+4]_471
 569 WashU_Skud_Contig1850.5           1.5e-07  373_[+4]_472
 570 --------------------------------------------------------------------------------
 571
 572 --------------------------------------------------------------------------------
 573         Motif 4 in BLOCKS format
 574 --------------------------------------------------------------------------------
 575 BL   MOTIF 4 width=15 seqs=10
 576 WashU_Sbay_Contig635.57  (  238) ACCTAGAGCGAACCA  1
 577 WashU_Skud_Contig1682.4  (  232) ACCTAGAGCGAACCA  1
 578 MIT_Smik_c492_20940      (  235) ACCTAGAGCGAACCA  1
 579 MIT_Spar_c261_21317      (  230) ACCTAGAGCGAACCA  1
 580 SGD_Scer_YOR278W         (  226) ACCTAGAGCGAACCA  1
 581 MIT_Sbay_c841_3215       (  372) ACAAGGAGAGAACCA  1
 582 MIT_Spar_c429_3020       (  376) ACAAGGAGAGAAGGA  1
 583 SGD_Scer_YDL205C         (  373) ACAAGGAGAGAAGGA  1
 584 MIT_Smik_c193_2483       (  375) ACAAGGAGAGAAGAA  1
 585 WashU_Skud_Contig1850.5  (  374) CCAAGGAGAGAAAGA  1
 586 //
 587
 588 --------------------------------------------------------------------------------
 589
 590 --------------------------------------------------------------------------------
 591         Motif 4 position-specific scoring matrix
 592 --------------------------------------------------------------------------------
 593 log-odds matrix: alength= 4 w= 15 n= 7335 bayes= 9.51668 E= 1.7e-014
 594    147    -81   -997   -997
 595   -997    251   -997   -997
 596     62    151   -997   -997
 597     62   -997   -997     62
 598     62   -997    151   -997
 599   -997   -997    251   -997
 600    162   -997   -997   -997
 601   -997   -997    251   -997
 602     62    151   -997   -997
 603   -997   -997    251   -997
 604    162   -997   -997   -997
 605    162   -997   -997   -997
 606   -169    177     77   -997
 607   -169    177     77   -997
 608    162   -997   -997   -997
 609 --------------------------------------------------------------------------------
 610
 611 --------------------------------------------------------------------------------
 612         Motif 4 position-specific probability matrix
 613 --------------------------------------------------------------------------------
 614 letter-probability matrix: alength= 4 w= 15 nsites= 10 E= 1.7e-014
 615  0.900000  0.100000  0.000000  0.000000
 616  0.000000  1.000000  0.000000  0.000000
 617  0.500000  0.500000  0.000000  0.000000
 618  0.500000  0.000000  0.000000  0.500000
 619  0.500000  0.000000  0.500000  0.000000
 620  0.000000  0.000000  1.000000  0.000000
 621  1.000000  0.000000  0.000000  0.000000
 622  0.000000  0.000000  1.000000  0.000000
 623  0.500000  0.500000  0.000000  0.000000
 624  0.000000  0.000000  1.000000  0.000000
 625  1.000000  0.000000  0.000000  0.000000
 626  1.000000  0.000000  0.000000  0.000000
 627  0.100000  0.600000  0.300000  0.000000
 628  0.100000  0.600000  0.300000  0.000000
 629  1.000000  0.000000  0.000000  0.000000
 630 --------------------------------------------------------------------------------
 631
 632 --------------------------------------------------------------------------------
 633         Motif 4 regular expression
 634 --------------------------------------------------------------------------------
 635 AC[AC][AT][AG]GAG[AC]GAA[CG][CG]A
 636 --------------------------------------------------------------------------------
 637
 638
 639
 640
 641 Time 21.88 secs.
 642
 643 ********************************************************************************
 644
 645
 646 ********************************************************************************
 647 MOTIF  5        width =   20   sites =  10   llr = 194   E-value = 4.5e-019
 648 ********************************************************************************
 649 --------------------------------------------------------------------------------
 650         Motif 5 Description
 651 --------------------------------------------------------------------------------
 652 Simplified        A  aaaa:55a:5aa454a88a9
 653 pos.-specific     C  :::::5::::::51::::::
 654 probability       G  ::::a:::a5::::6:22:1
 655 matrix            T  ::::::5:::::14::::::
 656
 657          bits    2.5     *   *
 658                  2.3     *   *
 659                  2.0     *   *
 660                  1.8     *   *
 661 Information      1.5 *****  ** **   *  *
 662 content          1.3 *****  ** **  **  **
 663 (28.0 bits)      1.0 ****** *****  ******
 664                  0.8 ****** ****** ******
 665                  0.5 ************* ******
 666                  0.3 ********************
 667                  0.0 --------------------
 668
 669 Multilevel           AAAAGAAAGAAACAGAAAAA
 670 consensus                 CT  G  ATA GG
 671 sequence
 672
 673 --------------------------------------------------------------------------------
 674
 675 --------------------------------------------------------------------------------
 676         Motif 5 sites sorted by position p-value
 677 --------------------------------------------------------------------------------
 678 Sequence name            Strand  Start   P-value                    Site
 679 -------------            ------  ----- ---------            --------------------
 680 MIT_Spar_c261_21317          +    305  8.38e-12 TTCAATAATG AAAAGCTAGGAACAGAAAAA TTGGTCTACT
 681 SGD_Scer_YOR278W             +    301  1.32e-10 TTCAATAATG AAAAGCTAGGAACAAAAAAA ATTGGTCTAC
 682 WashU_Sbay_Contig635.57      +    313  5.24e-10 TTCATTAAAG AAAAGCTAGGAACAAAGAAA TTGGTCTACT
 683 MIT_Smik_c492_20940          +    310  5.24e-10 TTCAATAATG AAAAGCTAGGAACAAAAGAA ATTTGTCTAC
 684 MIT_Sbay_c841_3215           -    231  9.80e-10 TTAGACATAA AAAAGAAAGAAACCGAAAAA TTAAAGGAAC
 685 WashU_Skud_Contig1850.5      -    231  1.03e-09 TAAACATAAA AAAAGAAAGAAAATGAAAAA ATTGAAGGAA
 686 MIT_Spar_c429_3020           -    232  1.03e-09 CAAACATAAA AAAAGAAAGAAAATGAAAAA AATGAAGGAA
 687 SGD_Scer_YDL205C             -    230  1.03e-09 CAAACATAAA AAAAGAAAGAAAATGAAAAA GTAAAGGAAC
 688 MIT_Smik_c193_2483           -    235  2.33e-09 AAAACATAGA AAAAGAAAGAAAATGAGAAA AACTGAAGGA
 689 WashU_Skud_Contig1682.4      +    305  7.25e-09 TTCAATAATG AAAAGCTAGGAATAAAAGAG ATTGGTCTAC
 690 --------------------------------------------------------------------------------
 691
 692 --------------------------------------------------------------------------------
 693         Motif 5 block diagrams
 694 --------------------------------------------------------------------------------
 695 SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
 696 -------------            ----------------  -------------
 697 MIT_Spar_c261_21317               8.4e-12  304_[+5]_311
 698 SGD_Scer_YOR278W                  1.3e-10  300_[+5]_315
 699 WashU_Sbay_Contig635.57           5.2e-10  312_[+5]_303
 700 MIT_Smik_c492_20940               5.2e-10  309_[+5]_306
 701 MIT_Sbay_c841_3215                9.8e-10  230_[-5]_610
 702 WashU_Skud_Contig1850.5             1e-09  230_[-5]_610
 703 MIT_Spar_c429_3020                  1e-09  231_[-5]_609
 704 SGD_Scer_YDL205C                    1e-09  229_[-5]_611
 705 MIT_Smik_c193_2483                2.3e-09  234_[-5]_606
 706 WashU_Skud_Contig1682.4           7.3e-09  304_[+5]_311
 707 --------------------------------------------------------------------------------
 708
 709 --------------------------------------------------------------------------------
 710         Motif 5 in BLOCKS format
 711 --------------------------------------------------------------------------------
 712 BL   MOTIF 5 width=20 seqs=10
 713 MIT_Spar_c261_21317      (  305) AAAAGCTAGGAACAGAAAAA  1
 714 SGD_Scer_YOR278W         (  301) AAAAGCTAGGAACAAAAAAA  1
 715 WashU_Sbay_Contig635.57  (  313) AAAAGCTAGGAACAAAGAAA  1
 716 MIT_Smik_c492_20940      (  310) AAAAGCTAGGAACAAAAGAA  1
 717 MIT_Sbay_c841_3215       (  231) AAAAGAAAGAAACCGAAAAA  1
 718 WashU_Skud_Contig1850.5  (  231) AAAAGAAAGAAAATGAAAAA  1
 719 MIT_Spar_c429_3020       (  232) AAAAGAAAGAAAATGAAAAA  1
 720 SGD_Scer_YDL205C         (  230) AAAAGAAAGAAAATGAAAAA  1
 721 MIT_Smik_c193_2483       (  235) AAAAGAAAGAAAATGAGAAA  1
 722 WashU_Skud_Contig1682.4  (  305) AAAAGCTAGGAATAAAAGAG  1
 723 //
 724
 725 --------------------------------------------------------------------------------
 726
 727 --------------------------------------------------------------------------------
 728         Motif 5 position-specific scoring matrix
 729 --------------------------------------------------------------------------------
 730 log-odds matrix: alength= 4 w= 20 n= 7285 bayes= 9.5068 E= 4.5e-019
 731    162   -997   -997   -997
 732    162   -997   -997   -997
 733    162   -997   -997   -997
 734    162   -997   -997   -997
 735   -997   -997    251   -997
 736     62    151   -997   -997
 737     62   -997   -997     62
 738    162   -997   -997   -997
 739   -997   -997    251   -997
 740     62   -997    151   -997
 741    162   -997   -997   -997
 742    162   -997   -997   -997
 743     30    151   -997   -169
 744     62    -81   -997     30
 745     30   -997    177   -997
 746    162   -997   -997   -997
 747    130   -997     19   -997
 748    130   -997     19   -997
 749    162   -997   -997   -997
 750    147   -997    -81   -997
 751 --------------------------------------------------------------------------------
 752
 753 --------------------------------------------------------------------------------
 754         Motif 5 position-specific probability matrix
 755 --------------------------------------------------------------------------------
 756 letter-probability matrix: alength= 4 w= 20 nsites= 10 E= 4.5e-019
 757  1.000000  0.000000  0.000000  0.000000
 758  1.000000  0.000000  0.000000  0.000000
 759  1.000000  0.000000  0.000000  0.000000
 760  1.000000  0.000000  0.000000  0.000000
 761  0.000000  0.000000  1.000000  0.000000
 762  0.500000  0.500000  0.000000  0.000000
 763  0.500000  0.000000  0.000000  0.500000
 764  1.000000  0.000000  0.000000  0.000000
 765  0.000000  0.000000  1.000000  0.000000
 766  0.500000  0.000000  0.500000  0.000000
 767  1.000000  0.000000  0.000000  0.000000
 768  1.000000  0.000000  0.000000  0.000000
 769  0.400000  0.500000  0.000000  0.100000
 770  0.500000  0.100000  0.000000  0.400000
 771  0.400000  0.000000  0.600000  0.000000
 772  1.000000  0.000000  0.000000  0.000000
 773  0.800000  0.000000  0.200000  0.000000
 774  0.800000  0.000000  0.200000  0.000000
 775  1.000000  0.000000  0.000000  0.000000
 776  0.900000  0.000000  0.100000  0.000000
 777 --------------------------------------------------------------------------------
 778
 779 --------------------------------------------------------------------------------
 780         Motif 5 regular expression
 781 --------------------------------------------------------------------------------
 782 AAAAG[AC][AT]AG[AG]AA[CA][AT][GA]A[AG][AG]AA
 783 --------------------------------------------------------------------------------
 784
 785
 786
 787
 788 Time 27.05 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_YDL205C                 6.52e-24  48_[-5(3.42e-05)]_18_[+3(2.07e-10)]_8_[+1(1.41e-10)]_95_[-5(1.03e-09)]_72_[+2(5.11e-10)]_31_[+4(3.49e-08)]_473
 803 MIT_Spar_c429_3020               6.52e-24  86_[+3(2.07e-10)]_8_[+1(1.41e-10)]_97_[-5(1.03e-09)]_11_[-5(7.48e-05)]_42_[+2(5.11e-10)]_31_[+4(3.49e-08)]_430_[-5(9.37e-05)]_20
 804 MIT_Smik_c193_2483               1.47e-23  88_[+3(1.38e-09)]_8_[+1(4.59e-11)]_98_[-5(2.33e-09)]_11_[-5(5.68e-05)]_40_[+2(8.08e-11)]_29_[+4(1.07e-07)]_410_[+3(7.71e-05)]_41
 805 MIT_Sbay_c841_3215               6.24e-24  49_[-5(2.22e-05)]_18_[+3(2.47e-09)]_8_[+1(4.59e-11)]_95_[-5(9.80e-10)]_10_[-5(1.66e-05)]_42_[+2(6.64e-10)]_29_[+4(6.95e-09)]_474
 806 WashU_Skud_Contig1850.5          1.39e-22  30_[-5(2.12e-05)]_36_[+3(2.47e-09)]_8_[+1(4.59e-11)]_96_[-5(1.03e-09)]_4_[-5(8.25e-06)]_50_[+2(7.76e-10)]_29_[+4(1.53e-07)]_246_[-1(7.52e-05)]_206
 807 SGD_Scer_YOR278W                 1.13e-27  225_[+4(2.42e-09)]_60_[+5(1.32e-10)]_12_[+1(1.41e-10)]_18_[+2(8.08e-11)]_[+3(7.26e-11)]_106_[-4(9.20e-05)]_24_[+3(1.41e-05)]_60
 808 MIT_Spar_c261_21317              8.21e-29  197_[+5(7.95e-06)]_12_[+4(2.42e-09)]_60_[+5(8.38e-12)]_11_[+1(1.41e-10)]_18_[+2(8.08e-11)]_[+3(7.26e-11)]_222
 809 MIT_Smik_c492_20940              4.15e-27  234_[+4(2.42e-09)]_60_[+5(5.24e-10)]_12_[+1(1.41e-10)]_18_[+2(8.08e-11)]_[+3(7.26e-11)]_196_[-5(9.37e-05)]
 810 WashU_Skud_Contig1682.4          4.10e-26  231_[+4(2.42e-09)]_58_[+5(7.25e-09)]_12_[+1(1.14e-10)]_18_[+2(8.08e-11)]_[+3(7.26e-11)]_221
 811 WashU_Sbay_Contig635.57          7.73e-27  237_[+4(2.42e-09)]_60_[+5(5.24e-10)]_11_[+1(2.72e-10)]_18_[+2(8.08e-11)]_[+3(7.26e-11)]_25_[+5(8.91e-05)]_126_[+2(8.80e-05)]_23
 812 --------------------------------------------------------------------------------
 813
 814 ********************************************************************************
 815
 816
 817 ********************************************************************************
 818 Stopped because nmotifs = 5 reached.
 819 ********************************************************************************
 820
 821 CPU: dhn02990.mrc-dunn.cam.ac.uk
 822
 823 ********************************************************************************