******************************************************************************** MEME - Motif discovery tool ******************************************************************************** MEME version 4.10.0 (Release date: Wed May 21 10:35:36 2014 +1000) For further information on how to interpret these results or to get a copy of the MEME software please access http://meme.nbcr.net. This file may be used as input to the MAST algorithm for searching sequence databases for matches to groups of motifs. MAST is available for interactive use and downloading at http://meme.nbcr.net. ******************************************************************************** ******************************************************************************** REFERENCE ******************************************************************************** If you use this program in your research, please cite: Timothy L. Bailey and Charles Elkan, "Fitting a mixture model by expectation maximization to discover motifs in biopolymers", Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology, pp. 28-36, AAAI Press, Menlo Park, California, 1994. ******************************************************************************** ******************************************************************************** TRAINING SET ******************************************************************************** DATAFILE= motifs/204/204.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 10628 1.0000 500 11614 1.0000 500 1428 1.0000 500 1926 1.0000 500 20641 1.0000 500 2087 1.0000 500 21141 1.0000 500 21355 1.0000 500 22245 1.0000 500 22993 1.0000 500 25650 1.0000 500 25797 1.0000 500 262610 1.0000 500 262819 1.0000 500 263509 1.0000 500 268024 1.0000 500 3032 1.0000 500 31661 1.0000 500 35690 1.0000 500 38191 1.0000 500 38294 1.0000 500 5828 1.0000 500 6209 1.0000 500 7886 1.0000 500 8349 1.0000 500 8860 1.0000 500 ******************************************************************************** ******************************************************************************** COMMAND LINE SUMMARY ******************************************************************************** This information can also be useful in the event you wish to report a problem with the MEME software. command: meme motifs/204/204.seqs.fa -oc motifs/204 -dna -minw 12 -maxw 21 -nmotifs 3 -maxsize 500000 model: mod= zoops nmotifs= 3 evt= inf object function= E-value of product of p-values width: minw= 12 maxw= 21 minic= 0.00 width: wg= 11 ws= 1 endgaps= yes nsites: minsites= 2 maxsites= 26 wnsites= 0.8 theta: prob= 1 spmap= uni spfuzz= 0.5 global: substring= yes branching= no wbranch= no em: prior= dirichlet b= 0.01 maxiter= 50 distance= 1e-05 data: n= 13000 N= 26 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.253 C 0.235 G 0.242 T 0.270 Background letter frequencies (from dataset with add-one prior applied): A 0.253 C 0.235 G 0.242 T 0.270 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 12 sites = 24 llr = 221 E-value = 6.5e-005 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A ::1:::52:312 pos.-specific C :::::2::::2: probability G 182:a8:58476 matrix T 928a::5433:2 bits 2.1 * 1.9 ** 1.7 ** 1.5 ** ** Relative 1.3 ** *** * Entropy 1.0 ** **** * (13.3 bits) 0.8 ******* * 0.6 ******* * ** 0.4 ************ 0.2 ************ 0.0 ------------ Multilevel TGTTGGAGGGGG consensus CTTTACT sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 38294 176 5.86e-08 GGTTTGTCTT TGTTGGAGGGGG TTTGAATGGA 10628 246 9.35e-07 TTCGTGGTAC TGTTGGAAGAGG AAAGCCTACG 2087 173 1.44e-06 CTGTGGGATT TGTTGGTAGGGG GAGATGATGA 1926 24 3.04e-06 GCGTTGGAGG TGTTGGAGGTGT GCGAGCTGCT 11614 238 4.05e-06 GTTTGGGGTT TGGTGGTGGGGG TGCTGCCGCC 22993 8 5.11e-06 GTATTAA TGTTGGATTTGG CCTTCTTCTT 21141 307 5.11e-06 TTGGCCATCG TGTTGGTGTTGG TGTTGTGGCA 7886 41 6.77e-06 TCCCTCCTGC TGTTGGTTGTCG CCTCCTATTC 262819 314 7.34e-06 TATGCACGTT TGTTGGAATGGG TTGGAATGTG 8860 347 8.72e-06 TGGCAGGGGC GGTTGGTTGGGG CGTTCGATGA 5828 432 8.72e-06 AGCACGTAAT TGGTGGTTGTGG ATCTGGCGGG 6209 373 2.00e-05 CACTTGTTCA TGTTGCTGGAGA ATGTGTGGTG 268024 294 2.00e-05 AGCTGGTTGC TGGTGGTGGAGT ACGGGAGATC 1428 225 2.70e-05 GGCCTTCTGC TGTTGCTTGAGA GGCTTTGCTA 262610 242 3.18e-05 GCAGGTGTTG TGTTGGAATAGT TGAATCGAGT 38191 7 3.52e-05 TCGCCG TGATGGATGGCG TCTGCTCCAG 3032 279 4.90e-05 ATTGATTGTG TGTTGGATGTAT AAACTAAGAC 22245 234 4.90e-05 ATGATGATTG TGTTGCATTGCG TCCCCACAAT 21355 50 4.90e-05 GTGTATCTGT GTTTGGTGGAGG AACCGCGTTA 25650 31 6.56e-05 TGTCTTGTCT TTTTGGAGGGCA CGTACTACCT 25797 164 1.23e-04 CAATGACGAT GTTTGGATGACG GTCAGTTGGA 35690 12 1.29e-04 CAGTGTGGTG TTGTGGTGGTGA AAATCCAAAT 263509 285 1.53e-04 GGAACTGTCA TGTTGCAGGATT GTGAGGAGGA 31661 6 2.85e-04 TGGTA TGATGCAGTGAG AAGCAGTGAC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 38294 5.9e-08 175_[+1]_313 10628 9.4e-07 245_[+1]_243 2087 1.4e-06 172_[+1]_316 1926 3e-06 23_[+1]_465 11614 4.1e-06 237_[+1]_251 22993 5.1e-06 7_[+1]_481 21141 5.1e-06 306_[+1]_182 7886 6.8e-06 40_[+1]_448 262819 7.3e-06 313_[+1]_175 8860 8.7e-06 346_[+1]_142 5828 8.7e-06 431_[+1]_57 6209 2e-05 372_[+1]_116 268024 2e-05 293_[+1]_195 1428 2.7e-05 224_[+1]_264 262610 3.2e-05 241_[+1]_247 38191 3.5e-05 6_[+1]_482 3032 4.9e-05 278_[+1]_210 22245 4.9e-05 233_[+1]_255 21355 4.9e-05 49_[+1]_439 25650 6.6e-05 30_[+1]_458 25797 0.00012 163_[+1]_325 35690 0.00013 11_[+1]_477 263509 0.00015 284_[+1]_204 31661 0.00028 5_[+1]_483 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=12 seqs=24 38294 ( 176) TGTTGGAGGGGG 1 10628 ( 246) TGTTGGAAGAGG 1 2087 ( 173) TGTTGGTAGGGG 1 1926 ( 24) TGTTGGAGGTGT 1 11614 ( 238) TGGTGGTGGGGG 1 22993 ( 8) TGTTGGATTTGG 1 21141 ( 307) TGTTGGTGTTGG 1 7886 ( 41) TGTTGGTTGTCG 1 262819 ( 314) TGTTGGAATGGG 1 8860 ( 347) GGTTGGTTGGGG 1 5828 ( 432) TGGTGGTTGTGG 1 6209 ( 373) TGTTGCTGGAGA 1 268024 ( 294) TGGTGGTGGAGT 1 1428 ( 225) TGTTGCTTGAGA 1 262610 ( 242) TGTTGGAATAGT 1 38191 ( 7) TGATGGATGGCG 1 3032 ( 279) TGTTGGATGTAT 1 22245 ( 234) TGTTGCATTGCG 1 21355 ( 50) GTTTGGTGGAGG 1 25650 ( 31) TTTTGGAGGGCA 1 25797 ( 164) GTTTGGATGACG 1 35690 ( 12) TTGTGGTGGTGA 1 263509 ( 285) TGTTGCAGGATT 1 31661 ( 6) TGATGCAGTGAG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 12714 bayes= 9.49463 E= 6.5e-005 -1123 -1123 -95 169 -1123 -1123 178 -70 -160 -1123 -54 147 -1123 -1123 -1123 189 -1123 -1123 205 -1123 -1123 -17 171 -1123 110 -1123 -1123 76 -60 -1123 92 47 -1123 -1123 163 -11 40 -1123 63 11 -160 -17 146 -270 -60 -1123 137 -38 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 24 E= 6.5e-005 0.000000 0.000000 0.125000 0.875000 0.000000 0.000000 0.833333 0.166667 0.083333 0.000000 0.166667 0.750000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.208333 0.791667 0.000000 0.541667 0.000000 0.000000 0.458333 0.166667 0.000000 0.458333 0.375000 0.000000 0.000000 0.750000 0.250000 0.333333 0.000000 0.375000 0.291667 0.083333 0.208333 0.666667 0.041667 0.166667 0.000000 0.625000 0.208333 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- TGTTG[GC][AT][GT][GT][GAT][GC][GT] -------------------------------------------------------------------------------- Time 5.95 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 20 sites = 25 llr = 257 E-value = 8.0e-003 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A :9624262233812714481 pos.-specific C 8128282:664:66:64625 probability G ::::2::5:121:11:11:1 matrix T 1:2:2:232::131221::3 bits 2.1 1.9 1.7 1.5 Relative 1.3 ** * * Entropy 1.0 ** * * * * (14.8 bits) 0.8 ** * * * * ** ** 0.6 **** ** * ***** ** 0.4 **** ***** ***** ** 0.2 ******************** 0.0 -------------------- Multilevel CAACACAGCCCACCACACAC consensus CACATTTAA TATTCACT sequence A G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------------- 20641 395 5.65e-09 CATAGCAACA CATCACATCACACCACAAAC TTATCATCAG 35690 434 4.82e-08 CACGCATCTC CACCCCAGCACATCACACAA ACGACGTGTC 3032 421 1.24e-07 GCTACGCCAA CAACACAGCACTCAACGCAC CCTCCGCCCC 2087 343 2.34e-07 AATTCGGGGT CAACACAGTGAACAAAACAC AGAAATCAGT 38191 436 2.65e-07 TTGATCTCCG CAACACAACATACCACCCCT CCACTCATTG 5828 109 5.39e-07 GACCCTATTC CAACTCAGCCAACGTCTAAC GCCAATGCTC 25797 453 6.04e-07 ACCTCAACAA CAACACAGTAGAGCACAAAT AATCTGAATA 22993 110 9.44e-07 TTTCGTACTG CAACGCCTTCCAACACCAAC GAATCGTCAT 38294 237 1.98e-06 CTTTCTGCTG CACCTGTGCCAACCATCCAC CTCCCCCTTC 6209 142 4.78e-06 AACTCTTTGG CAACACTGCCGGCTACACCA TCAATATCAA 268024 353 4.78e-06 GTAGTAATTT CAACCAATTCCACCGTGCAC TACCGCGCAT 263509 469 4.78e-06 CTCTGCTTCC TCTCGCTGCCGACCACACAC CTTTTTTCGT 10628 389 4.78e-06 GAAGATATCC TAAATAAACCAACCTCACAC CTCCTTCCCT 21141 182 9.02e-06 TGCAAACAGC CAAAACTGCCGATCAAAGAG ACGTGTCAAA 7886 325 9.84e-06 ACATTAGAAT CAACAAATATCAACACCAAC ACAAGCTACA 1926 461 9.84e-06 ATCCAAAATC CAACTCCTCCCTTCTCCCCT GCCGCAAACC 11614 480 9.84e-06 CATCACCTAC CGAACCAGCCATCCATACAT C 8860 75 1.17e-05 TGTGTTCACT AACCACCGACAACAATCCAC CCCTACGTTT 31661 197 1.51e-05 GGTAGAAACT CAACGCCAAACATCGCAACC TCGTCAAAAA 22245 345 1.64e-05 GTGAATCTTT CACCACAACGAACTGCTCAT TGTCAACAAT 8349 234 3.09e-05 GCGATGCTAC CAAACCAACGGATGACACCG AAATGACTCC 25650 478 3.59e-05 GCGACGACTC CATCACTTTCCACATTCGAT CAC 21355 220 7.35e-05 ATGGGTGTAG TAACGATGCCAGCAATCAAT ACTGAGAGAC 262610 442 1.80e-04 TGCTCACTCT CCTCCAAACACATCTCCACG TTGCTACACT 1428 82 1.80e-04 TAAAGTAGTC CACACCATACGATAAATAAA GAAACAAAAT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 20641 5.7e-09 394_[+2]_86 35690 4.8e-08 433_[+2]_47 3032 1.2e-07 420_[+2]_60 2087 2.3e-07 342_[+2]_138 38191 2.6e-07 435_[+2]_45 5828 5.4e-07 108_[+2]_372 25797 6e-07 452_[+2]_28 22993 9.4e-07 109_[+2]_371 38294 2e-06 236_[+2]_244 6209 4.8e-06 141_[+2]_339 268024 4.8e-06 352_[+2]_128 263509 4.8e-06 468_[+2]_12 10628 4.8e-06 388_[+2]_92 21141 9e-06 181_[+2]_299 7886 9.8e-06 324_[+2]_156 1926 9.8e-06 460_[+2]_20 11614 9.8e-06 479_[+2]_1 8860 1.2e-05 74_[+2]_406 31661 1.5e-05 196_[+2]_284 22245 1.6e-05 344_[+2]_136 8349 3.1e-05 233_[+2]_247 25650 3.6e-05 477_[+2]_3 21355 7.3e-05 219_[+2]_261 262610 0.00018 441_[+2]_39 1428 0.00018 81_[+2]_399 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=20 seqs=25 20641 ( 395) CATCACATCACACCACAAAC 1 35690 ( 434) CACCCCAGCACATCACACAA 1 3032 ( 421) CAACACAGCACTCAACGCAC 1 2087 ( 343) CAACACAGTGAACAAAACAC 1 38191 ( 436) CAACACAACATACCACCCCT 1 5828 ( 109) CAACTCAGCCAACGTCTAAC 1 25797 ( 453) CAACACAGTAGAGCACAAAT 1 22993 ( 110) CAACGCCTTCCAACACCAAC 1 38294 ( 237) CACCTGTGCCAACCATCCAC 1 6209 ( 142) CAACACTGCCGGCTACACCA 1 268024 ( 353) CAACCAATTCCACCGTGCAC 1 263509 ( 469) TCTCGCTGCCGACCACACAC 1 10628 ( 389) TAAATAAACCAACCTCACAC 1 21141 ( 182) CAAAACTGCCGATCAAAGAG 1 7886 ( 325) CAACAAATATCAACACCAAC 1 1926 ( 461) CAACTCCTCCCTTCTCCCCT 1 11614 ( 480) CGAACCAGCCATCCATACAT 1 8860 ( 75) AACCACCGACAACAATCCAC 1 31661 ( 197) CAACGCCAAACATCGCAACC 1 22245 ( 345) CACCACAACGAACTGCTCAT 1 8349 ( 234) CAAACCAACGGATGACACCG 1 25650 ( 478) CATCACTTTCCACATTCGAT 1 21355 ( 220) TAACGATGCCAGCAATCAAT 1 262610 ( 442) CCTCCAAACACATCTCCACG 1 1428 ( 82) CACACCATACGATAAATAAA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 12506 bayes= 9.45447 E= 8.0e-003 -266 184 -1129 -117 180 -155 -259 -1129 134 -23 -1129 -76 -34 177 -1129 -1129 80 3 -60 -76 -34 169 -259 -1129 125 -55 -1129 -17 -8 -1129 99 5 -66 145 -1129 -44 15 125 -101 -275 34 77 -1 -275 166 -1129 -159 -117 -166 135 -259 5 -8 135 -159 -176 143 -1129 -101 -44 -107 145 -1129 -17 80 62 -159 -117 51 125 -159 -1129 159 3 -1129 -1129 -107 103 -101 5 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 25 E= 8.0e-003 0.040000 0.840000 0.000000 0.120000 0.880000 0.080000 0.040000 0.000000 0.640000 0.200000 0.000000 0.160000 0.200000 0.800000 0.000000 0.000000 0.440000 0.240000 0.160000 0.160000 0.200000 0.760000 0.040000 0.000000 0.600000 0.160000 0.000000 0.240000 0.240000 0.000000 0.480000 0.280000 0.160000 0.640000 0.000000 0.200000 0.280000 0.560000 0.120000 0.040000 0.320000 0.400000 0.240000 0.040000 0.800000 0.000000 0.080000 0.120000 0.080000 0.600000 0.040000 0.280000 0.240000 0.600000 0.080000 0.080000 0.680000 0.000000 0.120000 0.200000 0.120000 0.640000 0.000000 0.240000 0.440000 0.360000 0.080000 0.120000 0.360000 0.560000 0.080000 0.000000 0.760000 0.240000 0.000000 0.000000 0.120000 0.480000 0.120000 0.280000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- CA[AC][CA][AC][CA][AT][GTA][CT][CA][CAG]A[CT][CA][AT][CT][AC][CA][AC][CT] -------------------------------------------------------------------------------- Time 11.33 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 15 sites = 21 llr = 214 E-value = 5.2e-004 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A :9::4:1a:2a212: pos.-specific C 2::117::2:::::2 probability G 8:292:8:58:5744 matrix T ::8:33::2::2233 bits 2.1 1.9 * 1.7 * * 1.5 * * * * Relative 1.3 **** ** ** Entropy 1.0 **** ** ** (14.7 bits) 0.8 **** *** ** * 0.6 **** *** ** * 0.4 **** *** ** ** 0.2 *************** 0.0 --------------- Multilevel GATGACGAGGAGGGG consensus C TT CA ATTT sequence T T A -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------- 10628 370 7.90e-08 ACACCACCTA GATGACGAGGAAGAT ATCCTAAATA 31661 359 1.58e-07 TCAGTTATAG GAGGACGAGGAAGGG CCGTCAGGTG 25650 118 5.38e-07 CATGGATAGG GATGTCGAGGATGAC GGTGCACATC 25797 353 1.03e-06 AGGCAACAAC GATGACGAGAAGTGC AGCCGCATAA 262610 201 1.17e-06 CTACGGCGGC GAGGGCGATGAGGGT AAAGAGCTTC 2087 187 2.10e-06 GGTAGGGGGA GATGATGATGAGTGC ACCTCCTGAA 5828 401 2.32e-06 AATGATGTTC CATGACGAAGAGGTG ATTGGCAGCA 1926 108 2.59e-06 AAAGGCGGAG GAGGCCGAGGATGTG GAGTTGGGAG 20641 71 3.56e-06 ACAAGTAAGG GATGGCAAGAAGGGT AGCTAAAGCA 262819 253 7.68e-06 AAATGAGAAT GATCACGAGGATATG AAGAAGAGTA 3032 168 1.09e-05 ATTATCTGCA GATGTCAACGAGAGT CTGACTTTGT 22993 300 1.09e-05 TCTTCTTTGT CATGGTGATGAGTTG TGGATTGTGT 8860 364 1.29e-05 TGGGGCGTTC GATGACGACAGAGGG GCGTTGTATG 263509 200 1.29e-05 GTTGTAATCA GATGTTAATGAAGAG ATTGATCGAC 7886 460 1.40e-05 GATCATCATT CATCAGGAGGAGGGG GCGAATCAAC 6209 341 1.78e-05 TAGAGGTTGC CGTGGCGAGGAGGAT GGAGATGCAC 21355 147 2.08e-05 TTTGAGTATA GCTGTCGACGATGTC CGTGTTGCAA 8349 89 2.23e-05 TAAGTCCACA GATCTTGACGAGTAT TGACTCAATC 11614 129 2.59e-05 GGCGACGGGA GATGCCGACAAAGGA TGAGGCACGT 38294 387 4.51e-05 AGTGTTGTTG CATGATTATGATGTG ATGTTTTCAT 22245 426 1.04e-04 ACCGCAGAGA GAGGTTGAGAACTTT ACTCCATTGC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 10628 7.9e-08 369_[+3]_116 31661 1.6e-07 358_[+3]_127 25650 5.4e-07 117_[+3]_368 25797 1e-06 352_[+3]_133 262610 1.2e-06 200_[+3]_285 2087 2.1e-06 186_[+3]_299 5828 2.3e-06 400_[+3]_85 1926 2.6e-06 107_[+3]_378 20641 3.6e-06 70_[+3]_415 262819 7.7e-06 252_[+3]_233 3032 1.1e-05 167_[+3]_318 22993 1.1e-05 299_[+3]_186 8860 1.3e-05 363_[+3]_122 263509 1.3e-05 199_[+3]_286 7886 1.4e-05 459_[+3]_26 6209 1.8e-05 340_[+3]_145 21355 2.1e-05 146_[+3]_339 8349 2.2e-05 88_[+3]_397 11614 2.6e-05 128_[+3]_357 38294 4.5e-05 386_[+3]_99 22245 0.0001 425_[+3]_60 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=15 seqs=21 10628 ( 370) GATGACGAGGAAGAT 1 31661 ( 359) GAGGACGAGGAAGGG 1 25650 ( 118) GATGTCGAGGATGAC 1 25797 ( 353) GATGACGAGAAGTGC 1 262610 ( 201) GAGGGCGATGAGGGT 1 2087 ( 187) GATGATGATGAGTGC 1 5828 ( 401) CATGACGAAGAGGTG 1 1926 ( 108) GAGGCCGAGGATGTG 1 20641 ( 71) GATGGCAAGAAGGGT 1 262819 ( 253) GATCACGAGGATATG 1 3032 ( 168) GATGTCAACGAGAGT 1 22993 ( 300) CATGGTGATGAGTTG 1 8860 ( 364) GATGACGACAGAGGG 1 263509 ( 200) GATGTTAATGAAGAG 1 7886 ( 460) CATCAGGAGGAGGGG 1 6209 ( 341) CGTGGCGAGGAGGAT 1 21355 ( 147) GCTGTCGACGATGTC 1 8349 ( 89) GATCTTGACGAGTAT 1 11614 ( 129) GATGCCGACAAAGGA 1 38294 ( 387) CATGATTATGATGTG 1 22245 ( 426) GAGGTTGAGAACTTT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 12636 bayes= 9.53585 E= 5.2e-004 -1104 2 166 -1104 184 -230 -234 -1104 -1104 -1104 -34 158 -1104 -72 183 -1104 76 -130 -34 8 -1104 150 -234 8 -82 -1104 174 -250 198 -1104 -1104 -1104 -241 2 98 -18 -9 -1104 166 -1104 191 -1104 -234 -1104 -9 -230 98 -18 -141 -1104 146 -18 -9 -1104 83 30 -241 -30 83 30 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 21 E= 5.2e-004 0.000000 0.238095 0.761905 0.000000 0.904762 0.047619 0.047619 0.000000 0.000000 0.000000 0.190476 0.809524 0.000000 0.142857 0.857143 0.000000 0.428571 0.095238 0.190476 0.285714 0.000000 0.666667 0.047619 0.285714 0.142857 0.000000 0.809524 0.047619 1.000000 0.000000 0.000000 0.000000 0.047619 0.238095 0.476190 0.238095 0.238095 0.000000 0.761905 0.000000 0.952381 0.000000 0.047619 0.000000 0.238095 0.047619 0.476190 0.238095 0.095238 0.000000 0.666667 0.238095 0.238095 0.000000 0.428571 0.333333 0.047619 0.190476 0.428571 0.333333 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [GC]ATG[AT][CT]GA[GCT][GA]A[GAT][GT][GTA][GT] -------------------------------------------------------------------------------- Time 16.96 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 10628 1.25e-08 245_[+1(9.35e-07)]_112_\ [+3(7.90e-08)]_4_[+2(4.78e-06)]_92 11614 1.69e-05 128_[+3(2.59e-05)]_94_\ [+1(4.05e-06)]_230_[+2(9.84e-06)]_1 1428 3.38e-02 224_[+1(2.70e-05)]_264 1926 1.69e-06 23_[+1(3.04e-06)]_72_[+3(2.59e-06)]_\ 29_[+1(4.46e-05)]_61_[+1(5.56e-05)]_224_[+2(9.84e-06)]_20 20641 8.97e-07 70_[+3(3.56e-06)]_126_\ [+2(8.99e-05)]_163_[+2(5.65e-09)]_86 2087 2.38e-08 172_[+1(1.44e-06)]_2_[+3(2.10e-06)]_\ 141_[+2(2.34e-07)]_138 21141 7.29e-04 181_[+2(9.02e-06)]_105_\ [+1(5.11e-06)]_182 21355 6.71e-04 49_[+1(4.90e-05)]_85_[+3(2.08e-05)]_\ 58_[+2(7.35e-05)]_261 22245 7.31e-04 233_[+1(4.90e-05)]_32_\ [+2(9.61e-05)]_47_[+2(1.64e-05)]_136 22993 1.19e-06 7_[+1(5.11e-06)]_90_[+2(9.44e-07)]_\ 170_[+3(1.09e-05)]_186 25650 2.00e-05 30_[+1(6.56e-05)]_75_[+3(5.38e-07)]_\ 345_[+2(3.59e-05)]_3 25797 1.63e-06 352_[+3(1.03e-06)]_85_\ [+2(6.04e-07)]_28 262610 8.34e-05 200_[+3(1.17e-06)]_26_\ [+1(3.18e-05)]_247 262819 9.64e-04 252_[+3(7.68e-06)]_46_\ [+1(7.34e-06)]_175 263509 1.13e-04 199_[+3(1.29e-05)]_41_\ [+3(9.31e-05)]_198_[+2(4.78e-06)]_12 268024 1.49e-03 293_[+1(2.00e-05)]_47_\ [+2(4.78e-06)]_128 3032 1.45e-06 167_[+3(1.09e-05)]_96_\ [+1(4.90e-05)]_130_[+2(1.24e-07)]_60 31661 1.10e-05 196_[+2(1.51e-05)]_142_\ [+3(1.58e-07)]_16_[+3(4.78e-06)]_96 35690 1.30e-04 433_[+2(4.82e-08)]_47 38191 3.24e-05 6_[+1(3.52e-05)]_259_[+2(2.64e-05)]_\ 138_[+2(2.65e-07)]_45 38294 1.47e-07 175_[+1(5.86e-08)]_49_\ [+2(1.98e-06)]_130_[+3(4.51e-05)]_99 5828 2.88e-07 108_[+2(5.39e-07)]_272_\ [+3(2.32e-06)]_16_[+1(8.72e-06)]_57 6209 2.62e-05 141_[+2(4.78e-06)]_179_\ [+3(1.78e-05)]_17_[+1(2.00e-05)]_116 7886 1.55e-05 40_[+1(6.77e-06)]_272_\ [+2(9.84e-06)]_115_[+3(1.40e-05)]_26 8349 7.23e-03 88_[+3(2.23e-05)]_130_\ [+2(3.09e-05)]_247 8860 2.09e-05 74_[+2(1.17e-05)]_252_\ [+1(8.72e-06)]_5_[+3(1.29e-05)]_122 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************