t/data/map_hem/HEM1-HEM3.meme.txt

   1 ********************************************************************************
   2 MEME - Motif discovery tool
   3 ********************************************************************************
   4 MEME version 3.5.4 (Release date:    )
   5
   6 For further information on how to interpret these results or to get
   7 a copy of the MEME software please access http://meme.nbcr.net.
   8
   9 This file may be used as input to the MAST algorithm for searching
  10 sequence databases for matches to groups of motifs.  MAST is available
  11 for interactive use and downloading at http://meme.nbcr.net.
  12 ********************************************************************************
  13
  14
  15 ********************************************************************************
  16 REFERENCE
  17 ********************************************************************************
  18 If you use this program in your research, please cite:
  19
  20 Timothy L. Bailey and Charles Elkan,
  21 "Fitting a mixture model by expectation maximization to discover
  22 motifs in biopolymers", Proceedings of the Second International
  23 Conference on Intelligent Systems for Molecular Biology, pp. 28-36,
  24 AAAI Press, Menlo Park, California, 1994.
  25 ********************************************************************************
  26
  27
  28 ********************************************************************************
  29 TRAINING SET
  30 ********************************************************************************
  31 DATAFILE= HEM1-HEM3.fa
  32 ALPHABET= ACGT
  33 Sequence name            Weight Length  Sequence name            Weight Length
  34 -------------            ------ ------  -------------            ------ ------
  35 SGD_Scer_YDR232W         1.0000    498  MIT_Spar_c117_4603       1.0000    498
  36 MIT_Smik_c228_4055       1.0000    498  WashU_Skud_Contig2069.5  1.0000    498
  37 WashU_Sbay_Contig461.5   1.0000    498  SGD_Scer_YDL205C         1.0000    860
  38 MIT_Spar_c429_3020       1.0000    860  MIT_Smik_c193_2483       1.0000    860
  39 MIT_Sbay_c841_3215       1.0000    860  WashU_Skud_Contig1850.5  1.0000    860
  40 ********************************************************************************
  41
  42 ********************************************************************************
  43 COMMAND LINE SUMMARY
  44 ********************************************************************************
  45 This information can also be useful in the event you wish to report a
  46 problem with the MEME software.
  47
  48 command: meme HEM1-HEM3.fa -nostatus -dna -revcomp -nmotifs 5 -bfile yeast.nc.1.freq -maxw 20 -mod oops -dir /Volumes/DATA/Home/ajr/sw/powerpc/meme-3.5.4
  49
  50 model:  mod=          oops    nmotifs=         5    evt=           inf
  51 object function=  E-value of product of p-values
  52 width:  minw=            6    maxw=           20    minic=        0.00
  53 width:  wg=             11    ws=              1    endgaps=       yes
  54 nsites: minsites=       10    maxsites=       10    wnsites=       0.8
  55 theta:  prob=            1    spmap=         uni    spfuzz=        0.5
  56 em:     prior=   dirichlet    b=            0.01    maxiter=        50
  57         distance=    1e-05
  58 data:   n=            6790    N=              10
  59 strands: + -
  60 sample: seed=            0    seqfrac=         1
  61 Letter frequencies in dataset:
  62 A 0.293 C 0.207 G 0.207 T 0.293
  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 = 225   E-value = 3.0e-032
  70 ********************************************************************************
  71 --------------------------------------------------------------------------------
  72         Motif 1 Description
  73 --------------------------------------------------------------------------------
  74 Simplified        A  :68:aa:1:4:aa::55a:9
  75 pos.-specific     C  1::a::::11a::::5::::
  76 probability       G  94:::::785:::aa:5:91
  77 matrix            T  ::2:::a21:::::::::1:
  78
  79          bits    2.5    *      *  **
  80                  2.3    *      *  **
  81                  2.0 *  *      *  **   *
  82                  1.8 *  *      *  **   *
  83 Information      1.5 *  **** * *****  **
  84 content          1.3 *  **** * *****  ***
  85 (32.4 bits)      1.0 ********* **********
  86                  0.8 ********************
  87                  0.5 ********************
  88                  0.3 ********************
  89                  0.0 --------------------
  90
  91 Multilevel           GAACAATGGGCAAGGAAAGA
  92 consensus             GT    T A     CG
  93 sequence
  94
  95 --------------------------------------------------------------------------------
  96
  97 --------------------------------------------------------------------------------
  98         Motif 1 sites sorted by position p-value
  99 --------------------------------------------------------------------------------
 100 Sequence name            Strand  Start   P-value                    Site
 101 -------------            ------  ----- ---------            --------------------
 102 WashU_Sbay_Contig461.5       +    278  1.41e-12 CACCGGGACA GAACAATGGGCAAGGCAAGA TGAAAAATCT
 103 MIT_Smik_c228_4055           +    283  1.41e-12 CATTGAATTA GAACAATGGGCAAGGCAAGA TGAAAATTTC
 104 MIT_Spar_c117_4603           +    280  1.41e-12 GCATGGGTCA GAACAATGGGCAAGGCAAGA TGAAAAATTT
 105 SGD_Scer_YDR232W             +    285  1.41e-12 GCATGGATCA GAACAATGGGCAAGGCAAGA TGAAAAATTT
 106 MIT_Sbay_c841_3215           +    363  6.65e-11 AGAGCCCAAG GGACAATAGACAAGGAGAGA ACCACCAACT
 107 WashU_Skud_Contig1850.5      +    365  1.00e-10 AAAGCTCCAG GAACAATGCCCAAGGAGAGA AAGAGTGCTA
 108 MIT_Spar_c429_3020           +    367  1.18e-10 CGCTCCCCAG GGTCAATTGACAAGGAGAGA AGGAATGTTA
 109 SGD_Scer_YDL205C             +    364  1.18e-10 CGCTCCCCAG GGTCAATTGACAAGGAGAGA AGGAATGTTA
 110 WashU_Skud_Contig2069.5      +    283  1.74e-10 CACTGGATCG GAACAATGGGCAAGGCAATG TGAAAAATTT
 111 MIT_Smik_c193_2483           +    366  3.73e-10 AAATCCCCAG CGACAATGTACAAGGAGAGA AGAAATGATA
 112 --------------------------------------------------------------------------------
 113
 114 --------------------------------------------------------------------------------
 115         Motif 1 block diagrams
 116 --------------------------------------------------------------------------------
 117 SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
 118 -------------            ----------------  -------------
 119 WashU_Sbay_Contig461.5            1.4e-12  277_[+1]_201
 120 MIT_Smik_c228_4055                1.4e-12  282_[+1]_196
 121 MIT_Spar_c117_4603                1.4e-12  279_[+1]_199
 122 SGD_Scer_YDR232W                  1.4e-12  284_[+1]_194
 123 MIT_Sbay_c841_3215                6.6e-11  362_[+1]_478
 124 WashU_Skud_Contig1850.5             1e-10  364_[+1]_476
 125 MIT_Spar_c429_3020                1.2e-10  366_[+1]_474
 126 SGD_Scer_YDL205C                  1.2e-10  363_[+1]_477
 127 WashU_Skud_Contig2069.5           1.7e-10  282_[+1]_196
 128 MIT_Smik_c193_2483                3.7e-10  365_[+1]_475
 129 --------------------------------------------------------------------------------
 130
 131 --------------------------------------------------------------------------------
 132         Motif 1 in BLOCKS format
 133 --------------------------------------------------------------------------------
 134 BL   MOTIF 1 width=20 seqs=10
 135 WashU_Sbay_Contig461.5   (  278) GAACAATGGGCAAGGCAAGA  1
 136 MIT_Smik_c228_4055       (  283) GAACAATGGGCAAGGCAAGA  1
 137 MIT_Spar_c117_4603       (  280) GAACAATGGGCAAGGCAAGA  1
 138 SGD_Scer_YDR232W         (  285) GAACAATGGGCAAGGCAAGA  1
 139 MIT_Sbay_c841_3215       (  363) GGACAATAGACAAGGAGAGA  1
 140 WashU_Skud_Contig1850.5  (  365) GAACAATGCCCAAGGAGAGA  1
 141 MIT_Spar_c429_3020       (  367) GGTCAATTGACAAGGAGAGA  1
 142 SGD_Scer_YDL205C         (  364) GGTCAATTGACAAGGAGAGA  1
 143 WashU_Skud_Contig2069.5  (  283) GAACAATGGGCAAGGCAATG  1
 144 MIT_Smik_c193_2483       (  366) CGACAATGTACAAGGAGAGA  1
 145 //
 146
 147 --------------------------------------------------------------------------------
 148
 149 --------------------------------------------------------------------------------
 150         Motif 1 position-specific scoring matrix
 151 --------------------------------------------------------------------------------
 152 log-odds matrix: alength= 4 w= 20 n= 6600 bayes= 9.36413 E= 3.0e-032
 153   -997    -81    236   -997
 154     89   -997    119   -997
 155    130   -997   -997    -70
 156   -997    251   -997   -997
 157    162   -997   -997   -997
 158    162   -997   -997   -997
 159   -997   -997   -997    162
 160   -169   -997    199    -70
 161   -997    -81    219   -169
 162     30    -81    151   -997
 163   -997    251   -997   -997
 164    162   -997   -997   -997
 165    162   -997   -997   -997
 166   -997   -997    251   -997
 167   -997   -997    251   -997
 168     62    151   -997   -997
 169     62   -997    151   -997
 170    162   -997   -997   -997
 171   -997   -997    236   -169
 172    147   -997    -81   -997
 173 --------------------------------------------------------------------------------
 174
 175 --------------------------------------------------------------------------------
 176         Motif 1 position-specific probability matrix
 177 --------------------------------------------------------------------------------
 178 letter-probability matrix: alength= 4 w= 20 nsites= 10 E= 3.0e-032
 179  0.000000  0.100000  0.900000  0.000000
 180  0.600000  0.000000  0.400000  0.000000
 181  0.800000  0.000000  0.000000  0.200000
 182  0.000000  1.000000  0.000000  0.000000
 183  1.000000  0.000000  0.000000  0.000000
 184  1.000000  0.000000  0.000000  0.000000
 185  0.000000  0.000000  0.000000  1.000000
 186  0.100000  0.000000  0.700000  0.200000
 187  0.000000  0.100000  0.800000  0.100000
 188  0.400000  0.100000  0.500000  0.000000
 189  0.000000  1.000000  0.000000  0.000000
 190  1.000000  0.000000  0.000000  0.000000
 191  1.000000  0.000000  0.000000  0.000000
 192  0.000000  0.000000  1.000000  0.000000
 193  0.000000  0.000000  1.000000  0.000000
 194  0.500000  0.500000  0.000000  0.000000
 195  0.500000  0.000000  0.500000  0.000000
 196  1.000000  0.000000  0.000000  0.000000
 197  0.000000  0.000000  0.900000  0.100000
 198  0.900000  0.000000  0.100000  0.000000
 199 --------------------------------------------------------------------------------
 200
 201 --------------------------------------------------------------------------------
 202         Motif 1 regular expression
 203 --------------------------------------------------------------------------------
 204 G[AG][AT]CAAT[GT]G[GA]CAAGG[AC][AG]AGA
 205 --------------------------------------------------------------------------------
 206
 207
 208
 209
 210 Time  4.86 secs.
 211
 212 ********************************************************************************
 213
 214
 215 ********************************************************************************
 216 MOTIF  2        width =   20   sites =  10   llr = 213   E-value = 1.1e-027
 217 ********************************************************************************
 218 --------------------------------------------------------------------------------
 219         Motif 2 Description
 220 --------------------------------------------------------------------------------
 221 Simplified        A  :::a::::::5343::::13
 222 pos.-specific     C  a:5::::::9::52296593
 223 probability       G  ::::::aa:::7157::5:4
 224 matrix            T  :a5:aa::a15:::114:::
 225
 226          bits    2.5 *     **
 227                  2.3 *     **
 228                  2.0 *     ** *     *  *
 229                  1.8 *     ** *     *  *
 230 Information      1.5 ** *******     * **
 231 content          1.3 ** ******* *  *****
 232 (30.7 bits)      1.0 ********** *  *****
 233                  0.8 ********** *********
 234                  0.5 ********************
 235                  0.3 ********************
 236                  0.0 --------------------
 237
 238 Multilevel           CTCATTGGTCAGCGGCCCCG
 239 consensus              T       TAAAC TG A
 240 sequence                          C     C
 241
 242 --------------------------------------------------------------------------------
 243
 244 --------------------------------------------------------------------------------
 245         Motif 2 sites sorted by position p-value
 246 --------------------------------------------------------------------------------
 247 Sequence name            Strand  Start   P-value                    Site
 248 -------------            ------  ----- ---------            --------------------
 249 WashU_Skud_Contig2069.5      -    358  1.23e-13 GCCTTCGTCG CTCATTGGTCTGCGGCCGCG GACGCTTTTT
 250 MIT_Spar_c117_4603           -    356  1.23e-13 GCCTTCGTCG CTCATTGGTCTGCGGCCGCG GGCGCTTTTT
 251 SGD_Scer_YDR232W             -    361  1.23e-13 GCCTTCGTCG CTCATTGGTCTGCGGCCGCG GGCGCTTTTT
 252 WashU_Sbay_Contig461.5       -    355  4.09e-12 GTCTTCGTCG CTCATTGGTCTGCGCCCGCC GGCGTTTTTT
 253 MIT_Spar_c429_3020           +    344  8.68e-11 TCATCGGTTT CTTATTGGTCAGACGCTCCC CAGGGTCAAT
 254 SGD_Scer_YDL205C             +    341  8.68e-11 TCATCGGTTT CTTATTGGTCAGACGCTCCC CAGGGTCAAT
 255 MIT_Smik_c228_4055           -    358  3.24e-10 GCTTTCGTCG CTCATTGGTCTGCGCTTGCG GGCGCTTTTT
 256 WashU_Skud_Contig1850.5      +    344  5.80e-10 TCATCGTTTT CTTATTGGTCAAAAGCTCCA GGAACAATGC
 257 MIT_Sbay_c841_3215           +    342  2.64e-09 TCATCGTTAT CTTATTGGTCAAGAGCCCAA GGGACAATAG
 258 MIT_Smik_c193_2483           +    345  5.92e-09 TCATCGTTAT CTTATTGGTTAAAATCCCCA GCGACAATGT
 259 --------------------------------------------------------------------------------
 260
 261 --------------------------------------------------------------------------------
 262         Motif 2 block diagrams
 263 --------------------------------------------------------------------------------
 264 SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
 265 -------------            ----------------  -------------
 266 WashU_Skud_Contig2069.5           1.2e-13  357_[-2]_121
 267 MIT_Spar_c117_4603                1.2e-13  355_[-2]_123
 268 SGD_Scer_YDR232W                  1.2e-13  360_[-2]_118
 269 WashU_Sbay_Contig461.5            4.1e-12  354_[-2]_124
 270 MIT_Spar_c429_3020                8.7e-11  343_[+2]_497
 271 SGD_Scer_YDL205C                  8.7e-11  340_[+2]_500
 272 MIT_Smik_c228_4055                3.2e-10  357_[-2]_121
 273 WashU_Skud_Contig1850.5           5.8e-10  343_[+2]_497
 274 MIT_Sbay_c841_3215                2.6e-09  341_[+2]_499
 275 MIT_Smik_c193_2483                5.9e-09  344_[+2]_496
 276 --------------------------------------------------------------------------------
 277
 278 --------------------------------------------------------------------------------
 279         Motif 2 in BLOCKS format
 280 --------------------------------------------------------------------------------
 281 BL   MOTIF 2 width=20 seqs=10
 282 WashU_Skud_Contig2069.5  (  358) CTCATTGGTCTGCGGCCGCG  1
 283 MIT_Spar_c117_4603       (  356) CTCATTGGTCTGCGGCCGCG  1
 284 SGD_Scer_YDR232W         (  361) CTCATTGGTCTGCGGCCGCG  1
 285 WashU_Sbay_Contig461.5   (  355) CTCATTGGTCTGCGCCCGCC  1
 286 MIT_Spar_c429_3020       (  344) CTTATTGGTCAGACGCTCCC  1
 287 SGD_Scer_YDL205C         (  341) CTTATTGGTCAGACGCTCCC  1
 288 MIT_Smik_c228_4055       (  358) CTCATTGGTCTGCGCTTGCG  1
 289 WashU_Skud_Contig1850.5  (  344) CTTATTGGTCAAAAGCTCCA  1
 290 MIT_Sbay_c841_3215       (  342) CTTATTGGTCAAGAGCCCAA  1
 291 MIT_Smik_c193_2483       (  345) CTTATTGGTTAAAATCCCCA  1
 292 //
 293
 294 --------------------------------------------------------------------------------
 295
 296 --------------------------------------------------------------------------------
 297         Motif 2 position-specific scoring matrix
 298 --------------------------------------------------------------------------------
 299 log-odds matrix: alength= 4 w= 20 n= 6600 bayes= 9.36413 E= 1.1e-027
 300   -997    251   -997   -997
 301   -997   -997   -997    162
 302   -997    151   -997     62
 303    162   -997   -997   -997
 304   -997   -997   -997    162
 305   -997   -997   -997    162
 306   -997   -997    251   -997
 307   -997   -997    251   -997
 308   -997   -997   -997    162
 309   -997    236   -997   -169
 310     62   -997   -997     62
 311    -11   -997    199   -997
 312     30    151    -81   -997
 313    -11     19    151   -997
 314   -997     19    199   -169
 315   -997    236   -997   -169
 316   -997    177   -997     30
 317   -997    151    151   -997
 318   -169    236   -997   -997
 319    -11     77    119   -997
 320 --------------------------------------------------------------------------------
 321
 322 --------------------------------------------------------------------------------
 323         Motif 2 position-specific probability matrix
 324 --------------------------------------------------------------------------------
 325 letter-probability matrix: alength= 4 w= 20 nsites= 10 E= 1.1e-027
 326  0.000000  1.000000  0.000000  0.000000
 327  0.000000  0.000000  0.000000  1.000000
 328  0.000000  0.500000  0.000000  0.500000
 329  1.000000  0.000000  0.000000  0.000000
 330  0.000000  0.000000  0.000000  1.000000
 331  0.000000  0.000000  0.000000  1.000000
 332  0.000000  0.000000  1.000000  0.000000
 333  0.000000  0.000000  1.000000  0.000000
 334  0.000000  0.000000  0.000000  1.000000
 335  0.000000  0.900000  0.000000  0.100000
 336  0.500000  0.000000  0.000000  0.500000
 337  0.300000  0.000000  0.700000  0.000000
 338  0.400000  0.500000  0.100000  0.000000
 339  0.300000  0.200000  0.500000  0.000000
 340  0.000000  0.200000  0.700000  0.100000
 341  0.000000  0.900000  0.000000  0.100000
 342  0.000000  0.600000  0.000000  0.400000
 343  0.000000  0.500000  0.500000  0.000000
 344  0.100000  0.900000  0.000000  0.000000
 345  0.300000  0.300000  0.400000  0.000000
 346 --------------------------------------------------------------------------------
 347
 348 --------------------------------------------------------------------------------
 349         Motif 2 regular expression
 350 --------------------------------------------------------------------------------
 351 CT[CT]ATTGGTC[AT][GA][CA][GAC][GC]C[CT][CG]C[GAC]
 352 --------------------------------------------------------------------------------
 353
 354
 355
 356
 357 Time  9.68 secs.
 358
 359 ********************************************************************************
 360
 361
 362 ********************************************************************************
 363 MOTIF  3        width =   15   sites =  10   llr = 175   E-value = 1.1e-018
 364 ********************************************************************************
 365 --------------------------------------------------------------------------------
 366         Motif 3 Description
 367 --------------------------------------------------------------------------------
 368 Simplified        A  :51:a:::::576::
 369 pos.-specific     C  ::5a:aa5:a:::4:
 370 probability       G  ::4::::5::5346a
 371 matrix            T  a5::::::a::::::
 372
 373          bits    2.5    * **  *    *
 374                  2.3    * **  *    *
 375                  2.0    * **  *    *
 376                  1.8    * **  *    *
 377 Information      1.5 *  *******   **
 378 content          1.3 *  *******   **
 379 (25.2 bits)      1.0 * *************
 380                  0.8 * *************
 381                  0.5 ***************
 382                  0.3 ***************
 383                  0.0 ---------------
 384
 385 Multilevel           TACCACCCTCAAAGG
 386 consensus             TG    G  GGGC
 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_Contig461.5       +    431  1.76e-09 AGGTCCGCTA TAGCACCGTCGAGGG GGACCGCTAT
 397 MIT_Smik_c228_4055           +    431  3.51e-09 AAGTTTATTA TAGCACCGTCGGGGG GAAGCATTAT
 398 MIT_Spar_c117_4603           +    430  3.51e-09 AAGCTTATTA TAGCACCGTCGGGGG GACCACTATA
 399 SGD_Scer_YDR232W             +    435  3.51e-09 AAGCTTATTA TAGCACCGTCGGGGG TACCACCACT
 400 WashU_Skud_Contig1850.5      +    729  7.37e-09 TCACCCTTAT TTCCACCCTCAAAGG ATAAAGCTTG
 401 MIT_Sbay_c841_3215           +    748  1.49e-08 TCACCCTTAT TTCCACCCTCAAACG ACAAGGCTTG
 402 MIT_Smik_c193_2483           +    722  1.49e-08 TCACCCTTAT TTCCACCCTCAAACG ATAAAGCTTG
 403 MIT_Spar_c429_3020           +    722  1.49e-08 TCACCCTTAT TTCCACCCTCAAACG ATAAAGCTTG
 404 SGD_Scer_YDL205C             +    721  1.49e-08 TCACCCTTAT TTCCACCCTCAAACG ATAAAGCTTG
 405 WashU_Skud_Contig2069.5      +    432  2.21e-08 AAGTCCGTCA TAACACCGTCGAAGG GGCACCACTA
 406 --------------------------------------------------------------------------------
 407
 408 --------------------------------------------------------------------------------
 409         Motif 3 block diagrams
 410 --------------------------------------------------------------------------------
 411 SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
 412 -------------            ----------------  -------------
 413 WashU_Sbay_Contig461.5            1.8e-09  430_[+3]_53
 414 MIT_Smik_c228_4055                3.5e-09  430_[+3]_53
 415 MIT_Spar_c117_4603                3.5e-09  429_[+3]_54
 416 SGD_Scer_YDR232W                  3.5e-09  434_[+3]_49
 417 WashU_Skud_Contig1850.5           7.4e-09  728_[+3]_117
 418 MIT_Sbay_c841_3215                1.5e-08  747_[+3]_98
 419 MIT_Smik_c193_2483                1.5e-08  721_[+3]_124
 420 MIT_Spar_c429_3020                1.5e-08  721_[+3]_124
 421 SGD_Scer_YDL205C                  1.5e-08  720_[+3]_125
 422 WashU_Skud_Contig2069.5           2.2e-08  431_[+3]_52
 423 --------------------------------------------------------------------------------
 424
 425 --------------------------------------------------------------------------------
 426         Motif 3 in BLOCKS format
 427 --------------------------------------------------------------------------------
 428 BL   MOTIF 3 width=15 seqs=10
 429 WashU_Sbay_Contig461.5   (  431) TAGCACCGTCGAGGG  1
 430 MIT_Smik_c228_4055       (  431) TAGCACCGTCGGGGG  1
 431 MIT_Spar_c117_4603       (  430) TAGCACCGTCGGGGG  1
 432 SGD_Scer_YDR232W         (  435) TAGCACCGTCGGGGG  1
 433 WashU_Skud_Contig1850.5  (  729) TTCCACCCTCAAAGG  1
 434 MIT_Sbay_c841_3215       (  748) TTCCACCCTCAAACG  1
 435 MIT_Smik_c193_2483       (  722) TTCCACCCTCAAACG  1
 436 MIT_Spar_c429_3020       (  722) TTCCACCCTCAAACG  1
 437 SGD_Scer_YDL205C         (  721) TTCCACCCTCAAACG  1
 438 WashU_Skud_Contig2069.5  (  432) TAACACCGTCGAAGG  1
 439 //
 440
 441 --------------------------------------------------------------------------------
 442
 443 --------------------------------------------------------------------------------
 444         Motif 3 position-specific scoring matrix
 445 --------------------------------------------------------------------------------
 446 log-odds matrix: alength= 4 w= 15 n= 6650 bayes= 9.37504 E= 1.1e-018
 447   -997   -997   -997    162
 448     62   -997   -997     62
 449   -169    151    119   -997
 450   -997    251   -997   -997
 451    162   -997   -997   -997
 452   -997    251   -997   -997
 453   -997    251   -997   -997
 454   -997    151    151   -997
 455   -997   -997   -997    162
 456   -997    251   -997   -997
 457     62   -997    151   -997
 458    111   -997     77   -997
 459     89   -997    119   -997
 460   -997    119    177   -997
 461   -997   -997    251   -997
 462 --------------------------------------------------------------------------------
 463
 464 --------------------------------------------------------------------------------
 465         Motif 3 position-specific probability matrix
 466 --------------------------------------------------------------------------------
 467 letter-probability matrix: alength= 4 w= 15 nsites= 10 E= 1.1e-018
 468  0.000000  0.000000  0.000000  1.000000
 469  0.500000  0.000000  0.000000  0.500000
 470  0.100000  0.500000  0.400000  0.000000
 471  0.000000  1.000000  0.000000  0.000000
 472  1.000000  0.000000  0.000000  0.000000
 473  0.000000  1.000000  0.000000  0.000000
 474  0.000000  1.000000  0.000000  0.000000
 475  0.000000  0.500000  0.500000  0.000000
 476  0.000000  0.000000  0.000000  1.000000
 477  0.000000  1.000000  0.000000  0.000000
 478  0.500000  0.000000  0.500000  0.000000
 479  0.700000  0.000000  0.300000  0.000000
 480  0.600000  0.000000  0.400000  0.000000
 481  0.000000  0.400000  0.600000  0.000000
 482  0.000000  0.000000  1.000000  0.000000
 483 --------------------------------------------------------------------------------
 484
 485 --------------------------------------------------------------------------------
 486         Motif 3 regular expression
 487 --------------------------------------------------------------------------------
 488 T[AT][CG]CACC[CG]TC[AG][AG][AG][GC]G
 489 --------------------------------------------------------------------------------
 490
 491
 492
 493
 494 Time 14.37 secs.
 495
 496 ********************************************************************************
 497
 498
 499 ********************************************************************************
 500 MOTIF  4        width =   20   sites =  10   llr = 206   E-value = 1.9e-024
 501 ********************************************************************************
 502 --------------------------------------------------------------------------------
 503         Motif 4 Description
 504 --------------------------------------------------------------------------------
 505 Simplified        A  4:a612::5:::::4214::
 506 pos.-specific     C  5::1::5::a4:::32:6:7
 507 probability       G  1a:398:a5:5:::168:a2
 508 matrix            T  ::::::5:::1aaa2:1::1
 509
 510          bits    2.5  *     * *        *
 511                  2.3  *     * *        *
 512                  2.0  *  *  * *        *
 513                  1.8  *  *  * *        *
 514 Information      1.5  ** ** * * ***  * *
 515 content          1.3  ** ** * * ***  ****
 516 (29.7 bits)      1.0  ** ********** *****
 517                  0.8 ************** *****
 518                  0.5 ************** *****
 519                  0.3 ********************
 520                  0.0 --------------------
 521
 522 Multilevel           CGAAGGCGACGTTTAGGCGC
 523 consensus            A  G AT G C   CA A G
 524 sequence                           TC
 525
 526 --------------------------------------------------------------------------------
 527
 528 --------------------------------------------------------------------------------
 529         Motif 4 sites sorted by position p-value
 530 --------------------------------------------------------------------------------
 531 Sequence name            Strand  Start   P-value                    Site
 532 -------------            ------  ----- ---------            --------------------
 533 SGD_Scer_YDR232W             +    384  9.38e-12 CAATGAGCGA CGAAGGCGGCCTTTCCGAGC GGTAGGGTAA
 534 MIT_Spar_c429_3020           +    670  1.07e-11 GAGCGAGGTT AGAGGGTGACGTTTAGGCGC ATAGGCAACC
 535 WashU_Skud_Contig1850.5      +    677  3.00e-11 GAACAAAGTT GGAAGGTGACGTTTAGGCGC ATAGGCAATC
 536 SGD_Scer_YDL205C             +    669  5.20e-11 GAACAAGGTT AGACGGTGACGTTTAGGCGC ATAGGCAATC
 537 WashU_Skud_Contig2069.5      +    381  7.97e-11 CAATGAGCGA CGAAGGCGGCCTTTCGTAGC AGCAGGGTAA
 538 MIT_Sbay_c841_3215           +    696  2.22e-10 AAACAACATT AGAGGGTGACGTTTTAGCGC ATAGGCAATC
 539 MIT_Spar_c117_4603           +    379  2.42e-10 CAATGAGCGA CGAAGGCGGCCTTTCCGAGT GGTAGGGTAA
 540 MIT_Smik_c193_2483           +    670  7.21e-10 GGACAAGGTC AGAGGATGACGTTTAAGCGC ATAGGCAATC
 541 WashU_Sbay_Contig461.5       +    378  1.03e-09 CAATGAGCGA CGAAGACGGCTTTTGGGCGG GGCAGGGTAA
 542 MIT_Smik_c228_4055           +    381  5.22e-09 CAATGAGCGA CGAAAGCGGCCTTTTGAAGG GTAGGGTAAT
 543 --------------------------------------------------------------------------------
 544
 545 --------------------------------------------------------------------------------
 546         Motif 4 block diagrams
 547 --------------------------------------------------------------------------------
 548 SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
 549 -------------            ----------------  -------------
 550 SGD_Scer_YDR232W                  9.4e-12  383_[+4]_95
 551 MIT_Spar_c429_3020                1.1e-11  669_[+4]_171
 552 WashU_Skud_Contig1850.5             3e-11  676_[+4]_164
 553 SGD_Scer_YDL205C                  5.2e-11  668_[+4]_172
 554 WashU_Skud_Contig2069.5             8e-11  380_[+4]_98
 555 MIT_Sbay_c841_3215                2.2e-10  695_[+4]_145
 556 MIT_Spar_c117_4603                2.4e-10  378_[+4]_100
 557 MIT_Smik_c193_2483                7.2e-10  669_[+4]_171
 558 WashU_Sbay_Contig461.5              1e-09  377_[+4]_101
 559 MIT_Smik_c228_4055                5.2e-09  380_[+4]_98
 560 --------------------------------------------------------------------------------
 561
 562 --------------------------------------------------------------------------------
 563         Motif 4 in BLOCKS format
 564 --------------------------------------------------------------------------------
 565 BL   MOTIF 4 width=20 seqs=10
 566 SGD_Scer_YDR232W         (  384) CGAAGGCGGCCTTTCCGAGC  1
 567 MIT_Spar_c429_3020       (  670) AGAGGGTGACGTTTAGGCGC  1
 568 WashU_Skud_Contig1850.5  (  677) GGAAGGTGACGTTTAGGCGC  1
 569 SGD_Scer_YDL205C         (  669) AGACGGTGACGTTTAGGCGC  1
 570 WashU_Skud_Contig2069.5  (  381) CGAAGGCGGCCTTTCGTAGC  1
 571 MIT_Sbay_c841_3215       (  696) AGAGGGTGACGTTTTAGCGC  1
 572 MIT_Spar_c117_4603       (  379) CGAAGGCGGCCTTTCCGAGT  1
 573 MIT_Smik_c193_2483       (  670) AGAGGATGACGTTTAAGCGC  1
 574 WashU_Sbay_Contig461.5   (  378) CGAAGACGGCTTTTGGGCGG  1
 575 MIT_Smik_c228_4055       (  381) CGAAAGCGGCCTTTTGAAGG  1
 576 //
 577
 578 --------------------------------------------------------------------------------
 579
 580 --------------------------------------------------------------------------------
 581         Motif 4 position-specific scoring matrix
 582 --------------------------------------------------------------------------------
 583 log-odds matrix: alength= 4 w= 20 n= 6600 bayes= 9.36413 E= 1.9e-024
 584     30    151    -81   -997
 585   -997   -997    251   -997
 586    162   -997   -997   -997
 587     89    -81     77   -997
 588   -169   -997    236   -997
 589    -70   -997    219   -997
 590   -997    151   -997     62
 591   -997   -997    251   -997
 592     62   -997    151   -997
 593   -997    251   -997   -997
 594   -997    119    151   -169
 595   -997   -997   -997    162
 596   -997   -997   -997    162
 597   -997   -997   -997    162
 598     30     77    -81    -70
 599    -70     19    177   -997
 600   -169   -997    219   -169
 601     30    177   -997   -997
 602   -997   -997    251   -997
 603   -997    199     19   -169
 604 --------------------------------------------------------------------------------
 605
 606 --------------------------------------------------------------------------------
 607         Motif 4 position-specific probability matrix
 608 --------------------------------------------------------------------------------
 609 letter-probability matrix: alength= 4 w= 20 nsites= 10 E= 1.9e-024
 610  0.400000  0.500000  0.100000  0.000000
 611  0.000000  0.000000  1.000000  0.000000
 612  1.000000  0.000000  0.000000  0.000000
 613  0.600000  0.100000  0.300000  0.000000
 614  0.100000  0.000000  0.900000  0.000000
 615  0.200000  0.000000  0.800000  0.000000
 616  0.000000  0.500000  0.000000  0.500000
 617  0.000000  0.000000  1.000000  0.000000
 618  0.500000  0.000000  0.500000  0.000000
 619  0.000000  1.000000  0.000000  0.000000
 620  0.000000  0.400000  0.500000  0.100000
 621  0.000000  0.000000  0.000000  1.000000
 622  0.000000  0.000000  0.000000  1.000000
 623  0.000000  0.000000  0.000000  1.000000
 624  0.400000  0.300000  0.100000  0.200000
 625  0.200000  0.200000  0.600000  0.000000
 626  0.100000  0.000000  0.800000  0.100000
 627  0.400000  0.600000  0.000000  0.000000
 628  0.000000  0.000000  1.000000  0.000000
 629  0.000000  0.700000  0.200000  0.100000
 630 --------------------------------------------------------------------------------
 631
 632 --------------------------------------------------------------------------------
 633         Motif 4 regular expression
 634 --------------------------------------------------------------------------------
 635 [CA]GA[AG]G[GA][CT]G[AG]C[GC]TTT[ACT][GAC]G[CA]G[CG]
 636 --------------------------------------------------------------------------------
 637
 638
 639
 640
 641 Time 18.89 secs.
 642
 643 ********************************************************************************
 644
 645
 646 ********************************************************************************
 647 MOTIF  5        width =   15   sites =  10   llr = 163   E-value = 1.8e-014
 648 ********************************************************************************
 649 --------------------------------------------------------------------------------
 650         Motif 5 Description
 651 --------------------------------------------------------------------------------
 652 Simplified        A  ::::::::4::::::
 653 pos.-specific     C  a7:116a::84a11:
 654 probability       G  ::9:14::61::::6
 655 matrix            T  :3198::a:16:994
 656
 657          bits    2.5 *     *    *
 658                  2.3 *     *    *
 659                  2.0 * *   *    *
 660                  1.8 * *   *    *
 661 Information      1.5 * *  *** * *
 662 content          1.3 **** ***** ****
 663 (23.5 bits)      1.0 ***************
 664                  0.8 ***************
 665                  0.5 ***************
 666                  0.3 ***************
 667                  0.0 ---------------
 668
 669 Multilevel           CCGTTCCTGCTCTTG
 670 consensus             T   G  A C   T
 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 WashU_Sbay_Contig461.5       +    308  2.85e-10 TGAAAAATCT CCGTTCCTGCTCTTG CTTGATATAT
 681 WashU_Skud_Contig2069.5      +    313  2.85e-10 TGAAAAATTT CCGTTCCTGCTCTTG CTTCATATAT
 682 MIT_Smik_c228_4055           +    312  1.62e-09 ATGAAAATTT CCGTTCCTGCTCTTT CTTCATATAT
 683 SGD_Scer_YDR232W             +    315  1.62e-09 TGAAAAATTT CCGTTCCTGCTCTTT CTTCATATAT
 684 MIT_Spar_c117_4603           +    310  1.17e-08 TGAAAAATTT CTGTTCCTGCTCTTT CTTCATATAT
 685 MIT_Smik_c193_2483           -    552  1.46e-08 CCGACATACG CCGTCGCTACCCTTG CAGTTCAAGT
 686 MIT_Spar_c429_3020           -    553  1.46e-08 CACCGACATT CTGTTGCTACCCTTG TAGTTCAAGT
 687 WashU_Skud_Contig1850.5      -    555  4.54e-08 CCGACACATT CCGTTGCTATCCTTG TAGTTCCGTT
 688 SGD_Scer_YDL205C             -    550  6.46e-08 CCGACACATT CTGCTGCTACCCTTG TAGTTTAAGT
 689 MIT_Sbay_c841_3215           -    516  1.21e-06 TCTTGCAAGC CCTTGCCTGGTCCCT GGCAGCGCGG
 690 --------------------------------------------------------------------------------
 691
 692 --------------------------------------------------------------------------------
 693         Motif 5 block diagrams
 694 --------------------------------------------------------------------------------
 695 SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
 696 -------------            ----------------  -------------
 697 WashU_Sbay_Contig461.5            2.8e-10  307_[+5]_176
 698 WashU_Skud_Contig2069.5           2.8e-10  312_[+5]_171
 699 MIT_Smik_c228_4055                1.6e-09  311_[+5]_172
 700 SGD_Scer_YDR232W                  1.6e-09  314_[+5]_169
 701 MIT_Spar_c117_4603                1.2e-08  309_[+5]_174
 702 MIT_Smik_c193_2483                1.5e-08  551_[-5]_294
 703 MIT_Spar_c429_3020                1.5e-08  552_[-5]_293
 704 WashU_Skud_Contig1850.5           4.5e-08  554_[-5]_291
 705 SGD_Scer_YDL205C                  6.5e-08  549_[-5]_296
 706 MIT_Sbay_c841_3215                1.2e-06  515_[-5]_330
 707 --------------------------------------------------------------------------------
 708
 709 --------------------------------------------------------------------------------
 710         Motif 5 in BLOCKS format
 711 --------------------------------------------------------------------------------
 712 BL   MOTIF 5 width=15 seqs=10
 713 WashU_Sbay_Contig461.5   (  308) CCGTTCCTGCTCTTG  1
 714 WashU_Skud_Contig2069.5  (  313) CCGTTCCTGCTCTTG  1
 715 MIT_Smik_c228_4055       (  312) CCGTTCCTGCTCTTT  1
 716 SGD_Scer_YDR232W         (  315) CCGTTCCTGCTCTTT  1
 717 MIT_Spar_c117_4603       (  310) CTGTTCCTGCTCTTT  1
 718 MIT_Smik_c193_2483       (  552) CCGTCGCTACCCTTG  1
 719 MIT_Spar_c429_3020       (  553) CTGTTGCTACCCTTG  1
 720 WashU_Skud_Contig1850.5  (  555) CCGTTGCTATCCTTG  1
 721 SGD_Scer_YDL205C         (  550) CTGCTGCTACCCTTG  1
 722 MIT_Sbay_c841_3215       (  516) CCTTGCCTGGTCCCT  1
 723 //
 724
 725 --------------------------------------------------------------------------------
 726
 727 --------------------------------------------------------------------------------
 728         Motif 5 position-specific scoring matrix
 729 --------------------------------------------------------------------------------
 730 log-odds matrix: alength= 4 w= 15 n= 6650 bayes= 9.37504 E= 1.8e-014
 731   -997    251   -997   -997
 732   -997    199   -997    -11
 733   -997   -997    236   -169
 734   -997    -81   -997    147
 735   -997    -81    -81    130
 736   -997    177    119   -997
 737   -997    251   -997   -997
 738   -997   -997   -997    162
 739     30   -997    177   -997
 740   -997    219    -81   -169
 741   -997    119   -997     89
 742   -997    251   -997   -997
 743   -997    -81   -997    147
 744   -997    -81   -997    147
 745   -997   -997    177     30
 746 --------------------------------------------------------------------------------
 747
 748 --------------------------------------------------------------------------------
 749         Motif 5 position-specific probability matrix
 750 --------------------------------------------------------------------------------
 751 letter-probability matrix: alength= 4 w= 15 nsites= 10 E= 1.8e-014
 752  0.000000  1.000000  0.000000  0.000000
 753  0.000000  0.700000  0.000000  0.300000
 754  0.000000  0.000000  0.900000  0.100000
 755  0.000000  0.100000  0.000000  0.900000
 756  0.000000  0.100000  0.100000  0.800000
 757  0.000000  0.600000  0.400000  0.000000
 758  0.000000  1.000000  0.000000  0.000000
 759  0.000000  0.000000  0.000000  1.000000
 760  0.400000  0.000000  0.600000  0.000000
 761  0.000000  0.800000  0.100000  0.100000
 762  0.000000  0.400000  0.000000  0.600000
 763  0.000000  1.000000  0.000000  0.000000
 764  0.000000  0.100000  0.000000  0.900000
 765  0.000000  0.100000  0.000000  0.900000
 766  0.000000  0.000000  0.600000  0.400000
 767 --------------------------------------------------------------------------------
 768
 769 --------------------------------------------------------------------------------
 770         Motif 5 regular expression
 771 --------------------------------------------------------------------------------
 772 C[CT]GTT[CG]CT[GA]C[TC]CTT[GT]
 773 --------------------------------------------------------------------------------
 774
 775
 776
 777
 778 Time 23.30 secs.
 779
 780 ********************************************************************************
 781
 782
 783 ********************************************************************************
 784 SUMMARY OF MOTIFS
 785 ********************************************************************************
 786
 787 --------------------------------------------------------------------------------
 788         Combined block diagrams: non-overlapping sites with p-value < 0.0001
 789 --------------------------------------------------------------------------------
 790 SEQUENCE NAME            COMBINED P-VALUE  MOTIF DIAGRAM
 791 -------------            ----------------  -------------
 792 SGD_Scer_YDR232W                 1.98e-32  284_[+1(1.41e-12)]_10_[+5(1.62e-09)]_31_[-2(1.23e-13)]_3_[+4(9.38e-12)]_31_[+3(3.51e-09)]_49
 793 MIT_Spar_c117_4603               2.87e-30  279_[+1(1.41e-12)]_10_[+5(1.17e-08)]_31_[-2(1.23e-13)]_3_[+4(2.42e-10)]_31_[+3(3.51e-09)]_54
 794 MIT_Smik_c228_4055               1.44e-26  282_[+1(1.41e-12)]_9_[+5(1.62e-09)]_31_[-2(3.24e-10)]_3_[+4(5.22e-09)]_30_[+3(3.51e-09)]_53
 795 WashU_Skud_Contig2069.5          1.65e-29  111_[-5(2.14e-05)]_156_[+1(1.74e-10)]_10_[+5(2.85e-10)]_30_[-2(1.23e-13)]_3_[+4(7.97e-11)]_31_[+3(2.21e-08)]_52
 796 WashU_Sbay_Contig461.5           4.83e-30  185_[-2(9.76e-05)]_72_[+1(1.41e-12)]_10_[+5(2.85e-10)]_32_[-2(4.09e-12)]_3_[+4(1.03e-09)]_11_[-5(1.98e-05)]_7_[+3(1.76e-09)]_53
 797 SGD_Scer_YDL205C                 6.25e-24  48_[-1(4.94e-05)]_272_[+2(8.68e-11)]_3_[+1(1.18e-10)]_166_[-5(6.46e-08)]_104_[+4(5.20e-11)]_32_[+3(1.49e-08)]_125
 798 MIT_Spar_c429_3020               3.47e-25  41_[-1(2.08e-05)]_282_[+2(8.68e-11)]_3_[+1(1.18e-10)]_166_[-5(1.46e-08)]_46_[-2(5.52e-05)]_36_[+4(1.07e-11)]_32_[+3(1.49e-08)]_124
 799 MIT_Smik_c193_2483               2.83e-21  344_[+2(5.92e-09)]_1_[+1(3.73e-10)]_166_[-5(1.46e-08)]_[-3(3.86e-06)]_88_[+4(7.21e-10)]_32_[+3(1.49e-08)]_124
 800 MIT_Sbay_c841_3215               5.49e-21  49_[-1(4.94e-05)]_272_[+2(2.64e-09)]_1_[+1(6.65e-11)]_133_[-5(1.21e-06)]_165_[+4(2.22e-10)]_32_[+3(1.49e-08)]_98
 801 WashU_Skud_Contig1850.5          7.09e-24  47_[-1(5.92e-05)]_276_[+2(5.80e-10)]_1_[+1(1.00e-10)]_170_[-5(4.54e-08)]_107_[+4(3.00e-11)]_32_[+3(7.37e-09)]_117
 802 --------------------------------------------------------------------------------
 803
 804 ********************************************************************************
 805
 806
 807 ********************************************************************************
 808 Stopped because nmotifs = 5 reached.
 809 ********************************************************************************
 810
 811 CPU: dhn02990.mrc-dunn.cam.ac.uk
 812
 813 ********************************************************************************