t/data/map_hem/HEM12-HEM15.meme.txt

   1 ********************************************************************************
   2 MEME - Motif discovery tool
   3 ********************************************************************************
   4 MEME version 3.5.4 (Release date:    )
   5
   6 For further information on how to interpret these results or to get
   7 a copy of the MEME software please access http://meme.nbcr.net.
   8
   9 This file may be used as input to the MAST algorithm for searching
  10 sequence databases for matches to groups of motifs.  MAST is available
  11 for interactive use and downloading at http://meme.nbcr.net.
  12 ********************************************************************************
  13
  14
  15 ********************************************************************************
  16 REFERENCE
  17 ********************************************************************************
  18 If you use this program in your research, please cite:
  19
  20 Timothy L. Bailey and Charles Elkan,
  21 "Fitting a mixture model by expectation maximization to discover
  22 motifs in biopolymers", Proceedings of the Second International
  23 Conference on Intelligent Systems for Molecular Biology, pp. 28-36,
  24 AAAI Press, Menlo Park, California, 1994.
  25 ********************************************************************************
  26
  27
  28 ********************************************************************************
  29 TRAINING SET
  30 ********************************************************************************
  31 DATAFILE= HEM12-HEM15.fa
  32 ALPHABET= ACGT
  33 Sequence name            Weight Length  Sequence name            Weight Length
  34 -------------            ------ ------  -------------            ------ ------
  35 SGD_Scer_YDR047W         1.0000   1000  MIT_Spar_c130_3923       1.0000   1000
  36 MIT_Sbay_c896_21277      1.0000   1000  WashU_Skud_Contig1362.1  1.0000    761
  37 SGD_Scer_YOR176W         1.0000    727  MIT_Spar_c278_20970      1.0000    727
  38 MIT_Smik_c935_20455      1.0000    727  WashU_Skud_Contig2050.4  1.0000    727
  39 WashU_Sbay_Contig480.2   1.0000    727
  40 ********************************************************************************
  41
  42 ********************************************************************************
  43 COMMAND LINE SUMMARY
  44 ********************************************************************************
  45 This information can also be useful in the event you wish to report a
  46 problem with the MEME software.
  47
  48 command: meme HEM12-HEM15.fa -nostatus -dna -revcomp -nmotifs 5 -bfile yeast.nc.1.freq -maxw 20 -mod oops -dir /Volumes/DATA/Home/ajr/sw/powerpc/meme-3.5.4
  49
  50 model:  mod=          oops    nmotifs=         5    evt=           inf
  51 object function=  E-value of product of p-values
  52 width:  minw=            6    maxw=           20    minic=        0.00
  53 width:  wg=             11    ws=              1    endgaps=       yes
  54 nsites: minsites=        9    maxsites=        9    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=            7396    N=               9
  59 strands: + -
  60 sample: seed=            0    seqfrac=         1
  61 Letter frequencies in dataset:
  62 A 0.298 C 0.202 G 0.202 T 0.298
  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 =   9   llr = 199   E-value = 4.8e-024
  70 ********************************************************************************
  71 --------------------------------------------------------------------------------
  72         Motif 1 Description
  73 --------------------------------------------------------------------------------
  74 Simplified        A  ::::1236aaa::6:6aa::
  75 pos.-specific     C  1828327::::aa4a:::9a
  76 probability       G  81816::4:::::::4::::
  77 matrix            T  11:1:6::::::::::::1:
  78
  79          bits    2.5            ** *    *
  80                  2.3            ** *    *
  81                  2.0            ** *   **
  82                  1.8   *        ** *   **
  83 Information      1.5 ****    ***** * ****
  84 content          1.3 ****  * ***** * ****
  85 (31.9 bits)      1.0 ***** **************
  86                  0.8 ***** **************
  87                  0.5 ********************
  88                  0.3 ********************
  89                  0.0 --------------------
  90
  91 Multilevel           GCGCGTCAAAACCACAAACC
  92 consensus              C CAAG     C G
  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_Sbay_Contig480.2       +    571  6.74e-13 CTTTCGAAGT GCGCGTCGAAACCACAAACC ATCAAAAATA
 103 WashU_Skud_Contig2050.4      +    566  6.74e-13 CTTTCAAAGT GCGCGTCGAAACCACAAACC GTCGAAAATA
 104 MIT_Spar_c278_20970          +    560  6.74e-13 CTTTCGAATT GCGCGTCGAAACCACAAACC GTCGAAAATA
 105 SGD_Scer_YOR176W             +    558  6.74e-13 CTTTCACATT GCGCGTCGAAACCACAAACC GTCGAAAACA
 106 MIT_Smik_c935_20455          +    544  1.42e-12 CTCTCCAATT GCGCGTCAAAACCACAAACC GTCGAAAATA
 107 MIT_Sbay_c896_21277          +    203  2.13e-10 CTTTTCCATG GCGTCAAAAAACCCCGAACC CTGTATAAAC
 108 SGD_Scer_YDR047W             +    235  2.25e-10 TTCCTCTCCT GCCGCCAAAAACCCCGAACC CTGTCCTGTA
 109 MIT_Spar_c130_3923           +    232  1.41e-09 TTTTCTCTCC TGCCACCAAAACCCCGAACC CTGTCCCGTA
 110 WashU_Skud_Contig1362.1      +    198  2.94e-09 TTTTTTCCTG CTGCCAAAAAACCCCGAATC ATGTAGAAGC
 111 --------------------------------------------------------------------------------
 112
 113 --------------------------------------------------------------------------------
 114         Motif 1 block diagrams
 115 --------------------------------------------------------------------------------
 116 SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
 117 -------------            ----------------  -------------
 118 WashU_Sbay_Contig480.2            6.7e-13  570_[+1]_137
 119 WashU_Skud_Contig2050.4           6.7e-13  565_[+1]_142
 120 MIT_Spar_c278_20970               6.7e-13  559_[+1]_148
 121 SGD_Scer_YOR176W                  6.7e-13  557_[+1]_150
 122 MIT_Smik_c935_20455               1.4e-12  543_[+1]_164
 123 MIT_Sbay_c896_21277               2.1e-10  202_[+1]_778
 124 SGD_Scer_YDR047W                  2.2e-10  234_[+1]_746
 125 MIT_Spar_c130_3923                1.4e-09  231_[+1]_749
 126 WashU_Skud_Contig1362.1           2.9e-09  197_[+1]_544
 127 --------------------------------------------------------------------------------
 128
 129 --------------------------------------------------------------------------------
 130         Motif 1 in BLOCKS format
 131 --------------------------------------------------------------------------------
 132 BL   MOTIF 1 width=20 seqs=9
 133 WashU_Sbay_Contig480.2   (  571) GCGCGTCGAAACCACAAACC  1
 134 WashU_Skud_Contig2050.4  (  566) GCGCGTCGAAACCACAAACC  1
 135 MIT_Spar_c278_20970      (  560) GCGCGTCGAAACCACAAACC  1
 136 SGD_Scer_YOR176W         (  558) GCGCGTCGAAACCACAAACC  1
 137 MIT_Smik_c935_20455      (  544) GCGCGTCAAAACCACAAACC  1
 138 MIT_Sbay_c896_21277      (  203) GCGTCAAAAAACCCCGAACC  1
 139 SGD_Scer_YDR047W         (  235) GCCGCCAAAAACCCCGAACC  1
 140 MIT_Spar_c130_3923       (  232) TGCCACCAAAACCCCGAACC  1
 141 WashU_Skud_Contig1362.1  (  198) CTGCCAAAAAACCCCGAATC  1
 142 //
 143
 144 --------------------------------------------------------------------------------
 145
 146 --------------------------------------------------------------------------------
 147         Motif 1 position-specific scoring matrix
 148 --------------------------------------------------------------------------------
 149 log-odds matrix: alength= 4 w= 20 n= 7225 bayes= 9.64706 E= 4.8e-024
 150   -982    -66    215   -154
 151   -982    215    -66   -154
 152   -982     34    215   -982
 153   -982    215    -66   -154
 154   -154     92    166   -982
 155    -55     34   -982     78
 156      4    192   -982   -982
 157     78   -982    134   -982
 158    162   -982   -982   -982
 159    162   -982   -982   -982
 160    162   -982   -982   -982
 161   -982    251   -982   -982
 162   -982    251   -982   -982
 163     78    134   -982   -982
 164   -982    251   -982   -982
 165     78   -982    134   -982
 166    162   -982   -982   -982
 167    162   -982   -982   -982
 168   -982    234   -982   -154
 169   -982    251   -982   -982
 170 --------------------------------------------------------------------------------
 171
 172 --------------------------------------------------------------------------------
 173         Motif 1 position-specific probability matrix
 174 --------------------------------------------------------------------------------
 175 letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 4.8e-024
 176  0.000000  0.111111  0.777778  0.111111
 177  0.000000  0.777778  0.111111  0.111111
 178  0.000000  0.222222  0.777778  0.000000
 179  0.000000  0.777778  0.111111  0.111111
 180  0.111111  0.333333  0.555556  0.000000
 181  0.222222  0.222222  0.000000  0.555556
 182  0.333333  0.666667  0.000000  0.000000
 183  0.555556  0.000000  0.444444  0.000000
 184  1.000000  0.000000  0.000000  0.000000
 185  1.000000  0.000000  0.000000  0.000000
 186  1.000000  0.000000  0.000000  0.000000
 187  0.000000  1.000000  0.000000  0.000000
 188  0.000000  1.000000  0.000000  0.000000
 189  0.555556  0.444444  0.000000  0.000000
 190  0.000000  1.000000  0.000000  0.000000
 191  0.555556  0.000000  0.444444  0.000000
 192  1.000000  0.000000  0.000000  0.000000
 193  1.000000  0.000000  0.000000  0.000000
 194  0.000000  0.888889  0.000000  0.111111
 195  0.000000  1.000000  0.000000  0.000000
 196 --------------------------------------------------------------------------------
 197
 198 --------------------------------------------------------------------------------
 199         Motif 1 regular expression
 200 --------------------------------------------------------------------------------
 201 GC[GC]C[GC][TAC][CA][AG]AAACC[AC]C[AG]AACC
 202 --------------------------------------------------------------------------------
 203
 204
 205
 206
 207 Time  5.88 secs.
 208
 209 ********************************************************************************
 210
 211
 212 ********************************************************************************
 213 MOTIF  2        width =   20   sites =   9   llr = 171   E-value = 5.0e-014
 214 ********************************************************************************
 215 --------------------------------------------------------------------------------
 216         Motif 2 Description
 217 --------------------------------------------------------------------------------
 218 Simplified        A  91:a12:::6::::1::12:
 219 pos.-specific     C  1:::1:881:8:a2239:48
 220 probability       G  :91:2:22::2a:827:1::
 221 matrix            T  ::9:68::94::::4:1832
 222
 223          bits    2.5            **
 224                  2.3            **
 225                  2.0  *         **   *
 226                  1.8  *    **  ****  *
 227 Information      1.5  * *  **  **** **  *
 228 content          1.3 ****  *** **** **  *
 229 (27.4 bits)      1.0 ****  *** **** **  *
 230                  0.8 **** ********* *** *
 231                  0.5 **** ********* *****
 232                  0.3 ********************
 233                  0.0 --------------------
 234
 235 Multilevel           AGTATTCCTACGCGTGCTCC
 236 consensus                GAGG TG  CCC  TT
 237 sequence                           G   A
 238
 239 --------------------------------------------------------------------------------
 240
 241 --------------------------------------------------------------------------------
 242         Motif 2 sites sorted by position p-value
 243 --------------------------------------------------------------------------------
 244 Sequence name            Strand  Start   P-value                    Site
 245 -------------            ------  ----- ---------            --------------------
 246 MIT_Spar_c278_20970          +    152  2.21e-12 ACCGACTAAA AGTATTCCTTCGCGTCCTCC TTCTTCAATC
 247 SGD_Scer_YOR176W             +    150  2.21e-12 ACCGACCAAA AGTATTCCTTCGCGTCCTCC TTCTTCAATC
 248 WashU_Skud_Contig2050.4      +    156  3.61e-12 GACCAAAAGA AGTATTCCTTCGCGTGCTTC TCCTTTCTGT
 249 WashU_Sbay_Contig480.2       +    200  7.52e-12 GACCAAAAGA AGTATTCCTACGCGAGCTCC CTCTTCAAGT
 250 MIT_Smik_c935_20455          +    147  3.24e-09 GGCCGACCAA AAGACTCCTTCGCGTCCTCC TTCTTCAAGT
 251 WashU_Skud_Contig1362.1      -    674  4.27e-09 CGTTCGATCG AGTAATGCTAGGCCCGCTTC GAGAGCTGGT
 252 SGD_Scer_YDR047W             -    388  1.16e-08 AACATGTTGT AGTATACGTACGCGGGCAAT TGTGGTGACA
 253 MIT_Spar_c130_3923           -    386  2.39e-08 ATCATATTTT AGTAGACGCACGCGGGCGAT TATAACGAAA
 254 MIT_Sbay_c896_21277          -    675  2.87e-08 TGTTTGGCTG CGTAGTGCTAGGCCCGTTTC GCCTGGCTTG
 255 --------------------------------------------------------------------------------
 256
 257 --------------------------------------------------------------------------------
 258         Motif 2 block diagrams
 259 --------------------------------------------------------------------------------
 260 SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
 261 -------------            ----------------  -------------
 262 MIT_Spar_c278_20970               2.2e-12  151_[+2]_556
 263 SGD_Scer_YOR176W                  2.2e-12  149_[+2]_558
 264 WashU_Skud_Contig2050.4           3.6e-12  155_[+2]_552
 265 WashU_Sbay_Contig480.2            7.5e-12  199_[+2]_508
 266 MIT_Smik_c935_20455               3.2e-09  146_[+2]_561
 267 WashU_Skud_Contig1362.1           4.3e-09  673_[-2]_68
 268 SGD_Scer_YDR047W                  1.2e-08  387_[-2]_593
 269 MIT_Spar_c130_3923                2.4e-08  385_[-2]_595
 270 MIT_Sbay_c896_21277               2.9e-08  674_[-2]_306
 271 --------------------------------------------------------------------------------
 272
 273 --------------------------------------------------------------------------------
 274         Motif 2 in BLOCKS format
 275 --------------------------------------------------------------------------------
 276 BL   MOTIF 2 width=20 seqs=9
 277 MIT_Spar_c278_20970      (  152) AGTATTCCTTCGCGTCCTCC  1
 278 SGD_Scer_YOR176W         (  150) AGTATTCCTTCGCGTCCTCC  1
 279 WashU_Skud_Contig2050.4  (  156) AGTATTCCTTCGCGTGCTTC  1
 280 WashU_Sbay_Contig480.2   (  200) AGTATTCCTACGCGAGCTCC  1
 281 MIT_Smik_c935_20455      (  147) AAGACTCCTTCGCGTCCTCC  1
 282 WashU_Skud_Contig1362.1  (  674) AGTAATGCTAGGCCCGCTTC  1
 283 SGD_Scer_YDR047W         (  388) AGTATACGTACGCGGGCAAT  1
 284 MIT_Spar_c130_3923       (  386) AGTAGACGCACGCGGGCGAT  1
 285 MIT_Sbay_c896_21277      (  675) CGTAGTGCTAGGCCCGTTTC  1
 286 //
 287
 288 --------------------------------------------------------------------------------
 289
 290 --------------------------------------------------------------------------------
 291         Motif 2 position-specific scoring matrix
 292 --------------------------------------------------------------------------------
 293 log-odds matrix: alength= 4 w= 20 n= 7225 bayes= 9.64706 E= 5.0e-014
 294    145    -66   -982   -982
 295   -154   -982    234   -982
 296   -982   -982    -66    145
 297    162   -982   -982   -982
 298   -154    -66     34     78
 299    -55   -982   -982    126
 300   -982    215     34   -982
 301   -982    215     34   -982
 302   -982    -66   -982    145
 303     78   -982   -982     45
 304   -982    215     34   -982
 305   -982   -982    251   -982
 306   -982    251   -982   -982
 307   -982     34    215   -982
 308   -154     34     34     45
 309   -982     92    192   -982
 310   -982    234   -982   -154
 311   -154   -982    -66    126
 312    -55    134   -982      4
 313   -982    215   -982    -55
 314 --------------------------------------------------------------------------------
 315
 316 --------------------------------------------------------------------------------
 317         Motif 2 position-specific probability matrix
 318 --------------------------------------------------------------------------------
 319 letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 5.0e-014
 320  0.888889  0.111111  0.000000  0.000000
 321  0.111111  0.000000  0.888889  0.000000
 322  0.000000  0.000000  0.111111  0.888889
 323  1.000000  0.000000  0.000000  0.000000
 324  0.111111  0.111111  0.222222  0.555556
 325  0.222222  0.000000  0.000000  0.777778
 326  0.000000  0.777778  0.222222  0.000000
 327  0.000000  0.777778  0.222222  0.000000
 328  0.000000  0.111111  0.000000  0.888889
 329  0.555556  0.000000  0.000000  0.444444
 330  0.000000  0.777778  0.222222  0.000000
 331  0.000000  0.000000  1.000000  0.000000
 332  0.000000  1.000000  0.000000  0.000000
 333  0.000000  0.222222  0.777778  0.000000
 334  0.111111  0.222222  0.222222  0.444444
 335  0.000000  0.333333  0.666667  0.000000
 336  0.000000  0.888889  0.000000  0.111111
 337  0.111111  0.000000  0.111111  0.777778
 338  0.222222  0.444444  0.000000  0.333333
 339  0.000000  0.777778  0.000000  0.222222
 340 --------------------------------------------------------------------------------
 341
 342 --------------------------------------------------------------------------------
 343         Motif 2 regular expression
 344 --------------------------------------------------------------------------------
 345 AGTA[TG][TA][CG][CG]T[AT][CG]GC[GC][TCG][GC]CT[CTA][CT]
 346 --------------------------------------------------------------------------------
 347
 348
 349
 350
 351 Time 11.70 secs.
 352
 353 ********************************************************************************
 354
 355
 356 ********************************************************************************
 357 MOTIF  3        width =   20   sites =   9   llr = 168   E-value = 2.4e-011
 358 ********************************************************************************
 359 --------------------------------------------------------------------------------
 360         Motif 3 Description
 361 --------------------------------------------------------------------------------
 362 Simplified        A  ::::::::11::7:21::::
 363 pos.-specific     C  :428:1a2:::2116:1:::
 364 probability       G  a:::19:17:1718::8:::
 365 matrix            T  :6829::7299111291aaa
 366
 367          bits    2.5 *     *
 368                  2.3 *     *
 369                  2.0 *    **
 370                  1.8 *    **
 371 Information      1.5 *  * **      *  ****
 372 content          1.3 *  ****   ** *  ****
 373 (27.0 bits)      1.0 ******* **** * *****
 374                  0.8 ************ *******
 375                  0.5 ************ *******
 376                  0.3 ********************
 377                  0.0 --------------------
 378
 379 Multilevel           GTTCTGCTGTTGAGCTGTTT
 380 consensus             CCT   CT  C  A
 381 sequence                           T
 382
 383 --------------------------------------------------------------------------------
 384
 385 --------------------------------------------------------------------------------
 386         Motif 3 sites sorted by position p-value
 387 --------------------------------------------------------------------------------
 388 Sequence name            Strand  Start   P-value                    Site
 389 -------------            ------  ----- ---------            --------------------
 390 MIT_Smik_c935_20455          +    484  3.60e-13 AGCTTTTTTT GCTCTGCTGTTGAGCTGTTT TACTTCATTG
 391 WashU_Sbay_Contig480.2       +    510  1.02e-12 GCTGTTTTTT GTTCTGCTGTTGAGCTGTTT TGCTCCACCT
 392 WashU_Skud_Contig2050.4      +    501  1.02e-12 GCTGTTTTTT GTTCTGCTGTTGAGCTGTTT TGTTCCATCT
 393 MIT_Spar_c278_20970          +    500  1.41e-12 AGCTTTTTTT GCCCTGCTGTTGAGCTGTTT TGCTTCACTG
 394 SGD_Scer_YOR176W             +    498  2.49e-12 AGCTTTTTTT GTCCTGCTGTTGAGCTGTTT TGCTTTACTG
 395 WashU_Skud_Contig1362.1      -    125  2.43e-08 TCAACGAGGT GTTCTGCCTTTCGTATGTTT ATTGCTCGAA
 396 MIT_Spar_c130_3923           -    609  7.51e-08 CGCCAGTGGT GCTTTGCTTTGCCGTAGTTT GTAAAAAAAA
 397 MIT_Sbay_c896_21277          +    770  1.89e-07 CTAGCAGCGT GCTTGCCGGATGAGTTTTTT CCATTTTCCT
 398 SGD_Scer_YDR047W             -    161  2.04e-07 CCAGCGAAAT GTTCTGCCATTTTCATCTTT ACCGCTCGAA
 399 --------------------------------------------------------------------------------
 400
 401 --------------------------------------------------------------------------------
 402         Motif 3 block diagrams
 403 --------------------------------------------------------------------------------
 404 SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
 405 -------------            ----------------  -------------
 406 MIT_Smik_c935_20455               3.6e-13  483_[+3]_224
 407 WashU_Sbay_Contig480.2              1e-12  509_[+3]_198
 408 WashU_Skud_Contig2050.4             1e-12  500_[+3]_207
 409 MIT_Spar_c278_20970               1.4e-12  499_[+3]_208
 410 SGD_Scer_YOR176W                  2.5e-12  497_[+3]_210
 411 WashU_Skud_Contig1362.1           2.4e-08  124_[-3]_617
 412 MIT_Spar_c130_3923                7.5e-08  608_[-3]_372
 413 MIT_Sbay_c896_21277               1.9e-07  769_[+3]_211
 414 SGD_Scer_YDR047W                    2e-07  160_[-3]_820
 415 --------------------------------------------------------------------------------
 416
 417 --------------------------------------------------------------------------------
 418         Motif 3 in BLOCKS format
 419 --------------------------------------------------------------------------------
 420 BL   MOTIF 3 width=20 seqs=9
 421 MIT_Smik_c935_20455      (  484) GCTCTGCTGTTGAGCTGTTT  1
 422 WashU_Sbay_Contig480.2   (  510) GTTCTGCTGTTGAGCTGTTT  1
 423 WashU_Skud_Contig2050.4  (  501) GTTCTGCTGTTGAGCTGTTT  1
 424 MIT_Spar_c278_20970      (  500) GCCCTGCTGTTGAGCTGTTT  1
 425 SGD_Scer_YOR176W         (  498) GTCCTGCTGTTGAGCTGTTT  1
 426 WashU_Skud_Contig1362.1  (  125) GTTCTGCCTTTCGTATGTTT  1
 427 MIT_Spar_c130_3923       (  609) GCTTTGCTTTGCCGTAGTTT  1
 428 MIT_Sbay_c896_21277      (  770) GCTTGCCGGATGAGTTTTTT  1
 429 SGD_Scer_YDR047W         (  161) GTTCTGCCATTTTCATCTTT  1
 430 //
 431
 432 --------------------------------------------------------------------------------
 433
 434 --------------------------------------------------------------------------------
 435         Motif 3 position-specific scoring matrix
 436 --------------------------------------------------------------------------------
 437 log-odds matrix: alength= 4 w= 20 n= 7225 bayes= 9.64706 E= 2.4e-011
 438   -982   -982    251   -982
 439   -982    134   -982     78
 440   -982     34   -982    126
 441   -982    215   -982    -55
 442   -982   -982    -66    145
 443   -982    -66    234   -982
 444   -982    251   -982   -982
 445   -982     34    -66    104
 446   -154   -982    192    -55
 447   -154   -982   -982    145
 448   -982   -982    -66    145
 449   -982     34    192   -154
 450    104    -66    -66   -154
 451   -982    -66    215   -154
 452    -55    166   -982    -55
 453   -154   -982   -982    145
 454   -982    -66    215   -154
 455   -982   -982   -982    162
 456   -982   -982   -982    162
 457   -982   -982   -982    162
 458 --------------------------------------------------------------------------------
 459
 460 --------------------------------------------------------------------------------
 461         Motif 3 position-specific probability matrix
 462 --------------------------------------------------------------------------------
 463 letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 2.4e-011
 464  0.000000  0.000000  1.000000  0.000000
 465  0.000000  0.444444  0.000000  0.555556
 466  0.000000  0.222222  0.000000  0.777778
 467  0.000000  0.777778  0.000000  0.222222
 468  0.000000  0.000000  0.111111  0.888889
 469  0.000000  0.111111  0.888889  0.000000
 470  0.000000  1.000000  0.000000  0.000000
 471  0.000000  0.222222  0.111111  0.666667
 472  0.111111  0.000000  0.666667  0.222222
 473  0.111111  0.000000  0.000000  0.888889
 474  0.000000  0.000000  0.111111  0.888889
 475  0.000000  0.222222  0.666667  0.111111
 476  0.666667  0.111111  0.111111  0.111111
 477  0.000000  0.111111  0.777778  0.111111
 478  0.222222  0.555556  0.000000  0.222222
 479  0.111111  0.000000  0.000000  0.888889
 480  0.000000  0.111111  0.777778  0.111111
 481  0.000000  0.000000  0.000000  1.000000
 482  0.000000  0.000000  0.000000  1.000000
 483  0.000000  0.000000  0.000000  1.000000
 484 --------------------------------------------------------------------------------
 485
 486 --------------------------------------------------------------------------------
 487         Motif 3 regular expression
 488 --------------------------------------------------------------------------------
 489 G[TC][TC][CT]TGC[TC][GT]TT[GC]AG[CAT]TGTTT
 490 --------------------------------------------------------------------------------
 491
 492
 493
 494
 495 Time 17.31 secs.
 496
 497 ********************************************************************************
 498
 499
 500 ********************************************************************************
 501 MOTIF  4        width =   20   sites =   9   llr = 165   E-value = 1.1e-009
 502 ********************************************************************************
 503 --------------------------------------------------------------------------------
 504         Motif 4 Description
 505 --------------------------------------------------------------------------------
 506 Simplified        A  8282::a:8:3::3734a93
 507 pos.-specific     C  17:1:a:a:31:a3:14:::
 508 probability       G  ::17a:::2761::34::17
 509 matrix            T  111::::::::9:3:11:::
 510
 511          bits    2.5     ** *    *
 512                  2.3     ** *    *
 513                  2.0     ** *    *
 514                  1.8     ** *    *
 515 Information      1.5     **** *  *    *
 516 content          1.3     **** * **    ***
 517 (26.4 bits)      1.0  * ******* ** *  ***
 518                  0.8 ************* *  ***
 519                  0.5 ************* * ****
 520                  0.3 ********************
 521                  0.0 --------------------
 522
 523 Multilevel           ACAGGCACAGGTCAAGAAAG
 524 consensus             A A    GCA  CGAC  A
 525 sequence                          T
 526
 527 --------------------------------------------------------------------------------
 528
 529 --------------------------------------------------------------------------------
 530         Motif 4 sites sorted by position p-value
 531 --------------------------------------------------------------------------------
 532 Sequence name            Strand  Start   P-value                    Site
 533 -------------            ------  ----- ---------            --------------------
 534 SGD_Scer_YOR176W             +    643  5.51e-13 AGGACAAAAT ACAGGCACAGGTCAAGCAAG AAGACAAACC
 535 MIT_Spar_c278_20970          +    647  1.12e-12 AAGACACGAT ACAGGCACAGGTCCAGAAAG AATACAAAAC
 536 MIT_Smik_c935_20455          +    632  6.03e-12 AATACTCCAT ACAGGCACAGGTCTAACAAG AAGACAACGC
 537 WashU_Sbay_Contig480.2       +    657  2.48e-10 AGCTCTTCAT ACAGGCACAGGTCAGATAAG AAGACAATTC
 538 MIT_Spar_c130_3923           -    808  3.78e-09 GCCGGAAAAA AAAAGCACGCATCCGGCAAG GAAAGGACGC
 539 SGD_Scer_YDR047W             -    798  3.78e-09 GCCGGAAAAA AAAAGCACGCATCCGGCAAG CACACTAGTA
 540 WashU_Skud_Contig2050.4      +    652  2.81e-08 AATATTCCAT TCAGGCACAGATCAACAAGA AGACAAAAAG
 541 WashU_Skud_Contig1362.1      +     48  4.74e-08 AGCAAGCTCA ATTGGCACAGCTCTAAAAAA AGCCTTGTGA
 542 MIT_Sbay_c896_21277          -    831  1.01e-07 TCTCTCGATG CCGCGCACACGGCTATAAAA CTGACCTTTC
 543 --------------------------------------------------------------------------------
 544
 545 --------------------------------------------------------------------------------
 546         Motif 4 block diagrams
 547 --------------------------------------------------------------------------------
 548 SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
 549 -------------            ----------------  -------------
 550 SGD_Scer_YOR176W                  5.5e-13  642_[+4]_65
 551 MIT_Spar_c278_20970               1.1e-12  646_[+4]_61
 552 MIT_Smik_c935_20455                 6e-12  631_[+4]_76
 553 WashU_Sbay_Contig480.2            2.5e-10  656_[+4]_51
 554 MIT_Spar_c130_3923                3.8e-09  807_[-4]_173
 555 SGD_Scer_YDR047W                  3.8e-09  797_[-4]_183
 556 WashU_Skud_Contig2050.4           2.8e-08  651_[+4]_56
 557 WashU_Skud_Contig1362.1           4.7e-08  47_[+4]_694
 558 MIT_Sbay_c896_21277                 1e-07  830_[-4]_150
 559 --------------------------------------------------------------------------------
 560
 561 --------------------------------------------------------------------------------
 562         Motif 4 in BLOCKS format
 563 --------------------------------------------------------------------------------
 564 BL   MOTIF 4 width=20 seqs=9
 565 SGD_Scer_YOR176W         (  643) ACAGGCACAGGTCAAGCAAG  1
 566 MIT_Spar_c278_20970      (  647) ACAGGCACAGGTCCAGAAAG  1
 567 MIT_Smik_c935_20455      (  632) ACAGGCACAGGTCTAACAAG  1
 568 WashU_Sbay_Contig480.2   (  657) ACAGGCACAGGTCAGATAAG  1
 569 MIT_Spar_c130_3923       (  808) AAAAGCACGCATCCGGCAAG  1
 570 SGD_Scer_YDR047W         (  798) AAAAGCACGCATCCGGCAAG  1
 571 WashU_Skud_Contig2050.4  (  652) TCAGGCACAGATCAACAAGA  1
 572 WashU_Skud_Contig1362.1  (   48) ATTGGCACAGCTCTAAAAAA  1
 573 MIT_Sbay_c896_21277      (  831) CCGCGCACACGGCTATAAAA  1
 574 //
 575
 576 --------------------------------------------------------------------------------
 577
 578 --------------------------------------------------------------------------------
 579         Motif 4 position-specific scoring matrix
 580 --------------------------------------------------------------------------------
 581 log-odds matrix: alength= 4 w= 20 n= 7225 bayes= 9.64706 E= 1.1e-009
 582    126    -66   -982   -154
 583    -55    192   -982   -154
 584    126   -982    -66   -154
 585    -55    -66    192   -982
 586   -982   -982    251   -982
 587   -982    251   -982   -982
 588    162   -982   -982   -982
 589   -982    251   -982   -982
 590    126   -982     34   -982
 591   -982     92    192   -982
 592      4    -66    166   -982
 593   -982   -982    -66    145
 594   -982    251   -982   -982
 595      4     92   -982      4
 596    104   -982     92   -982
 597      4    -66    134   -154
 598     45    134   -982   -154
 599    162   -982   -982   -982
 600    145   -982    -66   -982
 601      4   -982    192   -982
 602 --------------------------------------------------------------------------------
 603
 604 --------------------------------------------------------------------------------
 605         Motif 4 position-specific probability matrix
 606 --------------------------------------------------------------------------------
 607 letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 1.1e-009
 608  0.777778  0.111111  0.000000  0.111111
 609  0.222222  0.666667  0.000000  0.111111
 610  0.777778  0.000000  0.111111  0.111111
 611  0.222222  0.111111  0.666667  0.000000
 612  0.000000  0.000000  1.000000  0.000000
 613  0.000000  1.000000  0.000000  0.000000
 614  1.000000  0.000000  0.000000  0.000000
 615  0.000000  1.000000  0.000000  0.000000
 616  0.777778  0.000000  0.222222  0.000000
 617  0.000000  0.333333  0.666667  0.000000
 618  0.333333  0.111111  0.555556  0.000000
 619  0.000000  0.000000  0.111111  0.888889
 620  0.000000  1.000000  0.000000  0.000000
 621  0.333333  0.333333  0.000000  0.333333
 622  0.666667  0.000000  0.333333  0.000000
 623  0.333333  0.111111  0.444444  0.111111
 624  0.444444  0.444444  0.000000  0.111111
 625  1.000000  0.000000  0.000000  0.000000
 626  0.888889  0.000000  0.111111  0.000000
 627  0.333333  0.000000  0.666667  0.000000
 628 --------------------------------------------------------------------------------
 629
 630 --------------------------------------------------------------------------------
 631         Motif 4 regular expression
 632 --------------------------------------------------------------------------------
 633 A[CA]A[GA]GCAC[AG][GC][GA]TC[ACT][AG][GA][AC]AA[GA]
 634 --------------------------------------------------------------------------------
 635
 636
 637
 638
 639 Time 22.56 secs.
 640
 641 ********************************************************************************
 642
 643
 644 ********************************************************************************
 645 MOTIF  5        width =   20   sites =   9   llr = 160   E-value = 3.0e-008
 646 ********************************************************************************
 647 --------------------------------------------------------------------------------
 648         Motif 5 Description
 649 --------------------------------------------------------------------------------
 650 Simplified        A  91:1::3:::3:::::::1:
 651 pos.-specific     C  :::611:::::89::613::
 652 probability       G  17::::::::121:::::4:
 653 matrix            T  :2a3997aaa6::aa4974a
 654
 655          bits    2.5
 656                  2.3
 657                  2.0             *
 658                  1.8            **
 659 Information      1.5   *    *** ****    *
 660 content          1.3 * * ** *** **** *  *
 661 (25.6 bits)      1.0 *** ** *** ******* *
 662                  0.8 ********** ******* *
 663                  0.5 ********** *********
 664                  0.3 ********************
 665                  0.0 --------------------
 666
 667 Multilevel           AGTCTTTTTTTCCTTCTTGT
 668 consensus             T T  A   AG   T CT
 669 sequence
 670
 671 --------------------------------------------------------------------------------
 672
 673 --------------------------------------------------------------------------------
 674         Motif 5 sites sorted by position p-value
 675 --------------------------------------------------------------------------------
 676 Sequence name            Strand  Start   P-value                    Site
 677 -------------            ------  ----- ---------            --------------------
 678 MIT_Spar_c130_3923           +    733  2.54e-10 CGTCCCATTG AGTTTTATTTTCCTTCTCGT AGCACCTTCT
 679 WashU_Sbay_Contig480.2       +    102  1.11e-09 AGAGAAGAAA ATTTTTTTTTTCCTTCTTGT ATGGTCAGTT
 680 WashU_Skud_Contig2050.4      +     58  1.57e-09 ATAAGCAAGA AATCTTTTTTTCCTTCTTTT ACGGTCTATT
 681 WashU_Skud_Contig1362.1      +    713  1.57e-09 GTTGCCGTTT AGTCTTATTTTCCTTTCCGT GCTGCGCTGC
 682 MIT_Spar_c278_20970          +    480  1.72e-09 AAATGCGAAG AGTCTTTTTTAGCTTTTTTT GCCCTGCTGT
 683 SGD_Scer_YDR047W             +    733  3.76e-09 CGTCCCATTG AGTTTTATTTTCCTTCTCAT GGCACCTTCT
 684 MIT_Smik_c935_20455          +     57  4.88e-09 ATATGTGATG AGTCCTTTTTACGTTCTTGT ATAACCTAAG
 685 MIT_Sbay_c896_21277          +     10  2.83e-08  AGTGTTAAC AGTATCTTTTGCCTTTTTTT ATTCTAATAG
 686 SGD_Scer_YOR176W             +    478  3.32e-08 AGTGCGAAGA GTTCTTTTTTAGCTTTTTTT GTCCTGCTGT
 687 --------------------------------------------------------------------------------
 688
 689 --------------------------------------------------------------------------------
 690         Motif 5 block diagrams
 691 --------------------------------------------------------------------------------
 692 SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
 693 -------------            ----------------  -------------
 694 MIT_Spar_c130_3923                2.5e-10  732_[+5]_248
 695 WashU_Sbay_Contig480.2            1.1e-09  101_[+5]_606
 696 WashU_Skud_Contig2050.4           1.6e-09  57_[+5]_650
 697 WashU_Skud_Contig1362.1           1.6e-09  712_[+5]_29
 698 MIT_Spar_c278_20970               1.7e-09  479_[+5]_228
 699 SGD_Scer_YDR047W                  3.8e-09  732_[+5]_248
 700 MIT_Smik_c935_20455               4.9e-09  56_[+5]_651
 701 MIT_Sbay_c896_21277               2.8e-08  9_[+5]_971
 702 SGD_Scer_YOR176W                  3.3e-08  477_[+5]_230
 703 --------------------------------------------------------------------------------
 704
 705 --------------------------------------------------------------------------------
 706         Motif 5 in BLOCKS format
 707 --------------------------------------------------------------------------------
 708 BL   MOTIF 5 width=20 seqs=9
 709 MIT_Spar_c130_3923       (  733) AGTTTTATTTTCCTTCTCGT  1
 710 WashU_Sbay_Contig480.2   (  102) ATTTTTTTTTTCCTTCTTGT  1
 711 WashU_Skud_Contig2050.4  (   58) AATCTTTTTTTCCTTCTTTT  1
 712 WashU_Skud_Contig1362.1  (  713) AGTCTTATTTTCCTTTCCGT  1
 713 MIT_Spar_c278_20970      (  480) AGTCTTTTTTAGCTTTTTTT  1
 714 SGD_Scer_YDR047W         (  733) AGTTTTATTTTCCTTCTCAT  1
 715 MIT_Smik_c935_20455      (   57) AGTCCTTTTTACGTTCTTGT  1
 716 MIT_Sbay_c896_21277      (   10) AGTATCTTTTGCCTTTTTTT  1
 717 SGD_Scer_YOR176W         (  478) GTTCTTTTTTAGCTTTTTTT  1
 718 //
 719
 720 --------------------------------------------------------------------------------
 721
 722 --------------------------------------------------------------------------------
 723         Motif 5 position-specific scoring matrix
 724 --------------------------------------------------------------------------------
 725 log-odds matrix: alength= 4 w= 20 n= 7225 bayes= 9.64706 E= 3.0e-008
 726    145   -982    -66   -982
 727   -154   -982    192    -55
 728   -982   -982   -982    162
 729   -154    166   -982      4
 730   -982    -66   -982    145
 731   -982    -66   -982    145
 732      4   -982   -982    104
 733   -982   -982   -982    162
 734   -982   -982   -982    162
 735   -982   -982   -982    162
 736      4   -982    -66     78
 737   -982    215     34   -982
 738   -982    234    -66   -982
 739   -982   -982   -982    162
 740   -982   -982   -982    162
 741   -982    166   -982     45
 742   -982    -66   -982    145
 743   -982     92   -982    104
 744   -154   -982    134     45
 745   -982   -982   -982    162
 746 --------------------------------------------------------------------------------
 747
 748 --------------------------------------------------------------------------------
 749         Motif 5 position-specific probability matrix
 750 --------------------------------------------------------------------------------
 751 letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 3.0e-008
 752  0.888889  0.000000  0.111111  0.000000
 753  0.111111  0.000000  0.666667  0.222222
 754  0.000000  0.000000  0.000000  1.000000
 755  0.111111  0.555556  0.000000  0.333333
 756  0.000000  0.111111  0.000000  0.888889
 757  0.000000  0.111111  0.000000  0.888889
 758  0.333333  0.000000  0.000000  0.666667
 759  0.000000  0.000000  0.000000  1.000000
 760  0.000000  0.000000  0.000000  1.000000
 761  0.000000  0.000000  0.000000  1.000000
 762  0.333333  0.000000  0.111111  0.555556
 763  0.000000  0.777778  0.222222  0.000000
 764  0.000000  0.888889  0.111111  0.000000
 765  0.000000  0.000000  0.000000  1.000000
 766  0.000000  0.000000  0.000000  1.000000
 767  0.000000  0.555556  0.000000  0.444444
 768  0.000000  0.111111  0.000000  0.888889
 769  0.000000  0.333333  0.000000  0.666667
 770  0.111111  0.000000  0.444444  0.444444
 771  0.000000  0.000000  0.000000  1.000000
 772 --------------------------------------------------------------------------------
 773
 774 --------------------------------------------------------------------------------
 775         Motif 5 regular expression
 776 --------------------------------------------------------------------------------
 777 A[GT]T[CT]TT[TA]TTT[TA][CG]CTT[CT]T[TC][GT]T
 778 --------------------------------------------------------------------------------
 779
 780
 781
 782
 783 Time 27.84 secs.
 784
 785 ********************************************************************************
 786
 787
 788 ********************************************************************************
 789 SUMMARY OF MOTIFS
 790 ********************************************************************************
 791
 792 --------------------------------------------------------------------------------
 793         Combined block diagrams: non-overlapping sites with p-value < 0.0001
 794 --------------------------------------------------------------------------------
 795 SEQUENCE NAME            COMBINED P-VALUE  MOTIF DIAGRAM
 796 -------------            ----------------  -------------
 797 SGD_Scer_YDR047W                 1.02e-19  160_[-3(2.04e-07)]_31_[+5(1.41e-05)]_3_[+1(2.25e-10)]_133_[-2(1.16e-08)]_88_[+4(6.35e-05)]_217_[+5(3.76e-09)]_45_[-4(3.78e-09)]_183
 798 MIT_Spar_c130_3923               3.55e-20  231_[+1(1.41e-09)]_134_[-2(2.39e-08)]_178_[+3(8.67e-05)]_5_[-3(7.51e-08)]_104_[+5(2.54e-10)]_55_[-4(3.78e-09)]_173
 799 MIT_Sbay_c896_21277              2.88e-17  9_[+5(2.83e-08)]_148_[+5(7.36e-05)]_5_[+1(2.13e-10)]_452_[-2(2.87e-08)]_75_[+3(1.89e-07)]_41_[-4(1.01e-07)]_150
 800 WashU_Skud_Contig1362.1          7.74e-20  47_[+4(4.74e-08)]_57_[-3(2.43e-08)]_53_[+1(2.94e-09)]_70_[+4(1.81e-05)]_366_[-2(4.27e-09)]_19_[+5(1.57e-09)]_29
 801 SGD_Scer_YOR176W                 1.14e-33  149_[+2(2.21e-12)]_26_[-3(1.12e-05)]_90_[+2(6.19e-05)]_152_[+5(3.32e-08)]_[+3(2.49e-12)]_40_[+1(6.74e-13)]_65_[+4(5.51e-13)]_65
 802 MIT_Spar_c278_20970              7.69e-35  57_[+5(1.77e-06)]_29_[-4(3.91e-05)]_25_[+2(2.21e-12)]_27_[-2(6.64e-05)]_261_[+5(1.72e-09)]_[+3(1.41e-12)]_40_[+1(6.74e-13)]_67_[+4(1.12e-12)]_3_[-3(6.33e-05)]_38
 803 MIT_Smik_c935_20455              6.08e-31  56_[+5(4.88e-09)]_70_[+2(3.24e-09)]_317_[+3(3.60e-13)]_40_[+1(1.42e-12)]_68_[+4(6.03e-12)]_76
 804 WashU_Skud_Contig2050.4          1.32e-30  57_[+5(1.57e-09)]_78_[+2(3.61e-12)]_304_[+5(7.50e-05)]_1_[+3(1.02e-12)]_45_[+1(6.74e-13)]_66_[+4(2.81e-08)]_56
 805 WashU_Sbay_Contig480.2           2.10e-32  101_[+5(1.11e-09)]_78_[+2(7.52e-12)]_37_[-5(3.91e-05)]_77_[+3(3.61e-05)]_44_[+2(3.84e-06)]_51_[+5(6.08e-06)]_1_[+3(1.02e-12)]_41_[+1(6.74e-13)]_66_[+4(2.48e-10)]_51
 806 --------------------------------------------------------------------------------
 807
 808 ********************************************************************************
 809
 810
 811 ********************************************************************************
 812 Stopped because nmotifs = 5 reached.
 813 ********************************************************************************
 814
 815 CPU: dhn02990.mrc-dunn.cam.ac.uk
 816
 817 ********************************************************************************