******************************************************************************** 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/187/187.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 10629 1.0000 500 12094 1.0000 500 1418 1.0000 500 20769 1.0000 500 21070 1.0000 500 22375 1.0000 500 24671 1.0000 500 2540 1.0000 500 261024 1.0000 500 261490 1.0000 500 261710 1.0000 500 263269 1.0000 500 270110 1.0000 500 2927 1.0000 500 32016 1.0000 500 3378 1.0000 500 34100 1.0000 500 34702 1.0000 500 35768 1.0000 500 36988 1.0000 500 3879 1.0000 500 38861 1.0000 500 40675 1.0000 500 4096 1.0000 500 4674 1.0000 500 5133 1.0000 500 6708 1.0000 500 6819 1.0000 500 7898 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/187/187.seqs.fa -oc motifs/187 -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= 29 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= 14500 N= 29 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.263 C 0.229 G 0.251 T 0.256 Background letter frequencies (from dataset with add-one prior applied): A 0.263 C 0.229 G 0.251 T 0.256 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 21 sites = 20 llr = 252 E-value = 2.4e-008 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A :3:73161263313:144313 pos.-specific C 779269188285662864258 probability G 11:1:::::2::2::2:111: matrix T 2:211:3211:3229::153: bits 2.1 1.9 1.7 * 1.5 * * Relative 1.3 * * ** * * * Entropy 1.1 ** * ** * *** * (18.2 bits) 0.8 *** ** ** * *** * 0.6 ********* * **** * 0.4 ********* ******* ** 0.2 ********************* 0.0 --------------------- Multilevel CCCACCACCACCCCTCCATCC consensus TA CA T CATGA GACATA sequence AT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 36988 476 1.18e-08 CTACCCTCTT CCCAACACCACACCTCAATAA CGAA 6708 471 1.52e-08 CAACTAACCA CCCACCACCCCTCCTCAGGTC TCGTCCAGC 2540 291 2.79e-08 GATTTGCAAC CACACCACTCCTCCTCCAACC AACAGATGCA 40675 458 3.53e-08 CAGGTAGTCA CCCATCACCAAACATCCATCA CAAGTGATCA 24671 122 3.97e-08 TATCAACAGT TCCACCACCACCGTTCACACA AATTTCACGA 3879 213 4.45e-08 CCTTGTTCCC TCCACCACCACCGTTGCCATC TTCGTCATCA 4674 316 1.80e-07 TTTCCCCTAG CACCCCTTCGCTTCTCCCTCC TACGCCCAAC 34702 459 2.94e-07 AACCACACCT CCCAACTCCTCACCTACACCC CTTCTAACAC 4096 459 3.56e-07 TAAGCATTTA CCCACCACAACCATCCCATTC ACTGACACAT 263269 154 3.56e-07 TCCCCGCGAC CATACCTCCAACTCTCACGCC ACCAAGAGCA 3378 476 4.72e-07 CTAGGAGTTA CCCCCCCCAACTTCTCAACTC AACC 12094 476 4.72e-07 TTATCTTTAT CCTCCCTCCGCACATCCCAGC AATC 35768 138 5.66e-07 TCGTTGGAGA CCCATCTTCTCCCATCCCTGC AGGCTTCAGT 22375 323 5.66e-07 TTCATTCCCC GGCGCCACCCCTCCTCCCTCC CACTGTGTTG 2927 237 8.07e-07 GTAGAGTAGA CACAACAACCCCCCTCCTCTC TCTCCTCATC 21070 258 9.59e-07 ACGGCGAATG CCCTCCCCCGACGCTGCCTTC GTTGGATGAC 6819 46 4.26e-06 TGATGGAGAA TCCAACTTCAACGATGCTTCC ACGCCGATAT 270110 470 6.48e-06 TCGTCATTGC CATCAAACAACACATCAATCC ATAAGCTCAG 34100 200 1.40e-05 AATCACAGCA GCCACAACCACCTCCGAGACA TCAAGTGCGC 261490 405 1.40e-05 TGTGCCTCGA TCCTACACCAATCACCAAAAA GCATTGAGGT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 36988 1.2e-08 475_[+1]_4 6708 1.5e-08 470_[+1]_9 2540 2.8e-08 290_[+1]_189 40675 3.5e-08 457_[+1]_22 24671 4e-08 121_[+1]_358 3879 4.5e-08 212_[+1]_267 4674 1.8e-07 315_[+1]_164 34702 2.9e-07 458_[+1]_21 4096 3.6e-07 458_[+1]_21 263269 3.6e-07 153_[+1]_326 3378 4.7e-07 475_[+1]_4 12094 4.7e-07 475_[+1]_4 35768 5.7e-07 137_[+1]_342 22375 5.7e-07 322_[+1]_157 2927 8.1e-07 236_[+1]_243 21070 9.6e-07 257_[+1]_222 6819 4.3e-06 45_[+1]_434 270110 6.5e-06 469_[+1]_10 34100 1.4e-05 199_[+1]_280 261490 1.4e-05 404_[+1]_75 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=21 seqs=20 36988 ( 476) CCCAACACCACACCTCAATAA 1 6708 ( 471) CCCACCACCCCTCCTCAGGTC 1 2540 ( 291) CACACCACTCCTCCTCCAACC 1 40675 ( 458) CCCATCACCAAACATCCATCA 1 24671 ( 122) TCCACCACCACCGTTCACACA 1 3879 ( 213) TCCACCACCACCGTTGCCATC 1 4674 ( 316) CACCCCTTCGCTTCTCCCTCC 1 34702 ( 459) CCCAACTCCTCACCTACACCC 1 4096 ( 459) CCCACCACAACCATCCCATTC 1 263269 ( 154) CATACCTCCAACTCTCACGCC 1 3378 ( 476) CCCCCCCCAACTTCTCAACTC 1 12094 ( 476) CCTCCCTCCGCACATCCCAGC 1 35768 ( 138) CCCATCTTCTCCCATCCCTGC 1 22375 ( 323) GGCGCCACCCCTCCTCCCTCC 1 2927 ( 237) CACAACAACCCCCCTCCTCTC 1 21070 ( 258) CCCTCCCCCGACGCTGCCTTC 1 6819 ( 46) TCCAACTTCAACGATGCTTCC 1 270110 ( 470) CATCAAACAACACATCAATCC 1 34100 ( 200) GCCACAACCACCTCCGAGACA 1 261490 ( 405) TCCTACACCAATCACCAAAAA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 13920 bayes= 10.9161 E= 2.4e-008 -1097 161 -133 -36 -7 161 -233 -1097 -1097 189 -1097 -77 130 -20 -233 -136 19 139 -1097 -136 -140 197 -1097 -1097 119 -120 -1097 23 -239 180 -1097 -77 -81 180 -1097 -235 106 -20 -74 -136 -7 171 -1097 -1097 -7 97 -1097 23 -239 126 -33 -36 19 126 -1097 -77 -1097 -61 -1097 173 -239 171 -33 -1097 60 139 -1097 -1097 60 80 -133 -136 19 -61 -133 81 -140 112 -133 23 -7 171 -1097 -1097 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 20 E= 2.4e-008 0.000000 0.700000 0.100000 0.200000 0.250000 0.700000 0.050000 0.000000 0.000000 0.850000 0.000000 0.150000 0.650000 0.200000 0.050000 0.100000 0.300000 0.600000 0.000000 0.100000 0.100000 0.900000 0.000000 0.000000 0.600000 0.100000 0.000000 0.300000 0.050000 0.800000 0.000000 0.150000 0.150000 0.800000 0.000000 0.050000 0.550000 0.200000 0.150000 0.100000 0.250000 0.750000 0.000000 0.000000 0.250000 0.450000 0.000000 0.300000 0.050000 0.550000 0.200000 0.200000 0.300000 0.550000 0.000000 0.150000 0.000000 0.150000 0.000000 0.850000 0.050000 0.750000 0.200000 0.000000 0.400000 0.600000 0.000000 0.000000 0.400000 0.400000 0.100000 0.100000 0.300000 0.150000 0.100000 0.450000 0.100000 0.500000 0.100000 0.300000 0.250000 0.750000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [CT][CA]C[AC][CA]C[AT]CC[AC][CA][CTA][CGT][CA]T[CG][CA][AC][TA][CT][CA] -------------------------------------------------------------------------------- Time 7.66 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 21 sites = 16 llr = 207 E-value = 3.4e-002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A :4:6:39::843211:4:::: pos.-specific C ::1111:1:::13::1311:6 probability G a19376188254568734491 matrix T :4::31:12:13131215513 bits 2.1 1.9 * 1.7 * * 1.5 * * * * Relative 1.3 * * * ** * Entropy 1.1 * * **** * * (18.6 bits) 0.8 * * * **** ** * 0.6 ***** ***** *** **** 0.4 *********** *** **** 0.2 **************** **** 0.0 --------------------- Multilevel GAGAGGAGGAGGGGGGATTGC consensus T GTA AACT CGG T sequence T G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 3879 387 2.63e-11 TCAGCTGGTG GTGAGGAGGAAAGGGGAGGGC TCTAACAATT 261024 391 1.07e-08 CCGGACTGGC GAGAGGAGGAGGCGAGAGGGC ATGTTTCGTG 22375 147 6.62e-08 CGGTGGGCAA GAGAGCAGTAGGAGGGAGTGC TGTTGGGCGT 4674 169 8.22e-08 CAACAACACA GTGGGAGGGAGGAGGGGTGGC GCCGGGGAAT 36988 112 1.02e-07 TGGACGGATT GTGAGGAGGGATCGGTTGTGC CTGCGGATGC 34702 245 2.49e-07 TGTTGTGTCT GAGAGGAGGGGAATGCGTTGT ACACTTTGGC 24671 283 2.49e-07 ATATGTAGTT GTGGCGAGGAGTGGTGCTTGC CGAGGAACGT 40675 322 4.70e-07 CAGAAACGAA GTGATGAGGAATCTGTCCGGC GGAACACTTG 20769 179 8.48e-07 GTTTGGAAAT GGCAGAGGGAAAGGGGCTTGC TTCCCTCTTG 261490 297 9.19e-07 GCGTCTGGGT GAGGTAAGTAATGTGTATGGT GTAGGAGTGA 34100 370 1.26e-06 GACAGTTTGC GAGAGTAGGAGGGAGGGTTTG GTGTTGTGAC 6819 258 1.70e-06 TTGCTTAGCG GAGAGGATGAACCGGCGGTGT GGTAGGATGA 21070 347 1.97e-06 ACGGCCTGTT GTGCTGACGAGAGTGGCTCGT TGGGAAGGTC 6708 236 2.11e-06 CCACACACGT GGGCGAAGTGAAGAGGATTGC GACGATGAAG 10629 210 2.27e-06 GGATGCGCAA GAGGGAAGGAGGTGTGAGGTT GGTTTATTTA 32016 82 2.43e-06 GCTGTTGGAT GTGATGACGATGGTGGTGGGG ATATGAGGTA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 3879 2.6e-11 386_[+2]_93 261024 1.1e-08 390_[+2]_89 22375 6.6e-08 146_[+2]_333 4674 8.2e-08 168_[+2]_311 36988 1e-07 111_[+2]_368 34702 2.5e-07 244_[+2]_235 24671 2.5e-07 282_[+2]_197 40675 4.7e-07 321_[+2]_158 20769 8.5e-07 178_[+2]_301 261490 9.2e-07 296_[+2]_183 34100 1.3e-06 369_[+2]_110 6819 1.7e-06 257_[+2]_222 21070 2e-06 346_[+2]_133 6708 2.1e-06 235_[+2]_244 10629 2.3e-06 209_[+2]_270 32016 2.4e-06 81_[+2]_398 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=21 seqs=16 3879 ( 387) GTGAGGAGGAAAGGGGAGGGC 1 261024 ( 391) GAGAGGAGGAGGCGAGAGGGC 1 22375 ( 147) GAGAGCAGTAGGAGGGAGTGC 1 4674 ( 169) GTGGGAGGGAGGAGGGGTGGC 1 36988 ( 112) GTGAGGAGGGATCGGTTGTGC 1 34702 ( 245) GAGAGGAGGGGAATGCGTTGT 1 24671 ( 283) GTGGCGAGGAGTGGTGCTTGC 1 40675 ( 322) GTGATGAGGAATCTGTCCGGC 1 20769 ( 179) GGCAGAGGGAAAGGGGCTTGC 1 261490 ( 297) GAGGTAAGTAATGTGTATGGT 1 34100 ( 370) GAGAGTAGGAGGGAGGGTTTG 1 6819 ( 258) GAGAGGATGAACCGGCGGTGT 1 21070 ( 347) GTGCTGACGAGAGTGGCTCGT 1 6708 ( 236) GGGCGAAGTGAAGAGGATTGC 1 10629 ( 210) GAGGGAAGGAGGTGTGAGGTT 1 32016 ( 82) GTGATGACGATGGTGGTGGGG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 13920 bayes= 10.5008 E= 3.4e-002 -1064 -1064 199 -1064 73 -1064 -101 77 -1064 -187 190 -1064 125 -87 -1 -1064 -1064 -187 145 -3 25 -187 116 -203 173 -1064 -101 -1064 -1064 -87 169 -203 -1064 -1064 169 -45 163 -1064 -42 -1064 73 -1064 99 -203 25 -187 58 -3 -49 12 99 -203 -107 -1064 116 29 -207 -1064 169 -103 -1064 -87 145 -45 51 12 -1 -103 -1064 -187 80 97 -1064 -187 80 97 -1064 -1064 180 -103 -1064 129 -101 29 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 16 E= 3.4e-002 0.000000 0.000000 1.000000 0.000000 0.437500 0.000000 0.125000 0.437500 0.000000 0.062500 0.937500 0.000000 0.625000 0.125000 0.250000 0.000000 0.000000 0.062500 0.687500 0.250000 0.312500 0.062500 0.562500 0.062500 0.875000 0.000000 0.125000 0.000000 0.000000 0.125000 0.812500 0.062500 0.000000 0.000000 0.812500 0.187500 0.812500 0.000000 0.187500 0.000000 0.437500 0.000000 0.500000 0.062500 0.312500 0.062500 0.375000 0.250000 0.187500 0.250000 0.500000 0.062500 0.125000 0.000000 0.562500 0.312500 0.062500 0.000000 0.812500 0.125000 0.000000 0.125000 0.687500 0.187500 0.375000 0.250000 0.250000 0.125000 0.000000 0.062500 0.437500 0.500000 0.000000 0.062500 0.437500 0.500000 0.000000 0.000000 0.875000 0.125000 0.000000 0.562500 0.125000 0.312500 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- G[AT]G[AG][GT][GA]AGGA[GA][GAT][GC][GT]GG[ACG][TG][TG]G[CT] -------------------------------------------------------------------------------- Time 14.54 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 12 sites = 24 llr = 213 E-value = 6.6e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A :3::::5::33: pos.-specific C :11:1::::3:: probability G 9:8::a2:9336 matrix T 161a9:3a1244 bits 2.1 1.9 * 1.7 * * * 1.5 * *** ** Relative 1.3 * *** ** Entropy 1.1 * *** ** (12.8 bits) 0.8 * **** ** * 0.6 * **** ** * 0.4 ****** ** * 0.2 ********* ** 0.0 ------------ Multilevel GTGTTGATGATG consensus A T CAT sequence GG T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 6819 232 1.42e-07 CATGATGACG GTGTTGATGCTG TAGGTTGCTT 22375 348 4.26e-07 CCCTCCCACT GTGTTGTTGATG CAGCCACTCC 2540 121 3.37e-06 CCGTTTTGTT GTGTTGATGGGT GATACCCTGT 263269 46 4.53e-06 GCAACGGGAG GAGTTGATGGAG GAAGCCATGT 261490 219 4.53e-06 GTGGCGTGAT GTGTTGGTGTTG GGACGAGGTG 6708 306 5.61e-06 ATGTCGGTGT GAGTTGTTGCAG GAAGTGAGAG 261024 343 6.70e-06 CGGTGGTGAG GAGTTGATGCAT GCATGCAAAG 4096 272 1.52e-05 GGCTGGTTTG GCGTTGTTGTTG GCCATTGCTA 36988 233 1.69e-05 CTGAATAAAC GACTTGATGATG GAACTGTTCT 12094 325 2.16e-05 GTGGGATATC GCGTTGTTGGTT GCTCGGTGGT 38861 93 2.69e-05 AGTTCATCTT GATTTGTTGATG ACGGCTCCAT 35768 264 2.69e-05 AGTAGGGTGT GTGTTGATTCGG TCATCGTTGA 34702 228 3.32e-05 ATCCACTTCT GTGTCGGTGTTG TGTCTGAGAG 3378 139 4.13e-05 CGTGAGCAAT GACTTGTTGGAG ATCGTTTCGA 7898 133 4.47e-05 ATCAGACGAA GATTTGTTGCGG AGAATGCGAG 20769 264 5.25e-05 CGTACACAAT GTGTTGATTTAT CCTGTCCGGG 21070 323 5.70e-05 CGTAGTGCCA TTGTTGTTGAGT TGACGGCCTG 32016 32 6.14e-05 TGGCTGGTTG GGGTTGATGGGT TGATCGCATC 24671 314 8.47e-05 CGAGGAACGT GTGGTGGTGGTG GTGCCGGCGA 1418 324 8.47e-05 GGTAGACAGA GTGTTTATGAGT ATTACGGTTG 270110 77 8.94e-05 TGATGCAATC TTGTCGATGATG GTGTGGTCAA 261710 425 1.31e-04 TCAAATGAAC GTCTTGATGAAA CCAATAAACA 4674 118 1.84e-04 TAAGCAAGAG GTGTCGCTGTAT GAAGTGCACT 10629 429 2.11e-04 TGATCCAAAC GTTTTGGTGCCT CATCTAAACC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 6819 1.4e-07 231_[+3]_257 22375 4.3e-07 347_[+3]_141 2540 3.4e-06 120_[+3]_368 263269 4.5e-06 45_[+3]_443 261490 4.5e-06 218_[+3]_270 6708 5.6e-06 305_[+3]_183 261024 6.7e-06 342_[+3]_146 4096 1.5e-05 271_[+3]_217 36988 1.7e-05 232_[+3]_256 12094 2.2e-05 324_[+3]_164 38861 2.7e-05 92_[+3]_396 35768 2.7e-05 263_[+3]_225 34702 3.3e-05 227_[+3]_261 3378 4.1e-05 138_[+3]_350 7898 4.5e-05 132_[+3]_356 20769 5.3e-05 263_[+3]_225 21070 5.7e-05 322_[+3]_166 32016 6.1e-05 31_[+3]_457 24671 8.5e-05 313_[+3]_175 1418 8.5e-05 323_[+3]_165 270110 8.9e-05 76_[+3]_412 261710 0.00013 424_[+3]_64 4674 0.00018 117_[+3]_371 10629 0.00021 428_[+3]_60 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=12 seqs=24 6819 ( 232) GTGTTGATGCTG 1 22375 ( 348) GTGTTGTTGATG 1 2540 ( 121) GTGTTGATGGGT 1 263269 ( 46) GAGTTGATGGAG 1 261490 ( 219) GTGTTGGTGTTG 1 6708 ( 306) GAGTTGTTGCAG 1 261024 ( 343) GAGTTGATGCAT 1 4096 ( 272) GCGTTGTTGTTG 1 36988 ( 233) GACTTGATGATG 1 12094 ( 325) GCGTTGTTGGTT 1 38861 ( 93) GATTTGTTGATG 1 35768 ( 264) GTGTTGATTCGG 1 34702 ( 228) GTGTCGGTGTTG 1 3378 ( 139) GACTTGTTGGAG 1 7898 ( 133) GATTTGTTGCGG 1 20769 ( 264) GTGTTGATTTAT 1 21070 ( 323) TTGTTGTTGAGT 1 32016 ( 32) GGGTTGATGGGT 1 24671 ( 314) GTGGTGGTGGTG 1 1418 ( 324) GTGTTTATGAGT 1 270110 ( 77) TTGTCGATGATG 1 261710 ( 425) GTCTTGATGAAA 1 4674 ( 118) GTGTCGCTGTAT 1 10629 ( 429) GTTTTGGTGCCT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 14181 bayes= 9.65238 E= 6.6e-001 -1123 -1123 187 -162 15 -146 -259 119 -1123 -87 158 -103 -1123 -1123 -259 190 -1123 -87 -1123 177 -1123 -1123 193 -262 80 -246 -59 38 -1123 -1123 -1123 197 -1123 -1123 187 -162 15 12 -1 -30 15 -246 -1 70 -266 -1123 121 55 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 24 E= 6.6e-001 0.000000 0.000000 0.916667 0.083333 0.291667 0.083333 0.041667 0.583333 0.000000 0.125000 0.750000 0.125000 0.000000 0.000000 0.041667 0.958333 0.000000 0.125000 0.000000 0.875000 0.000000 0.000000 0.958333 0.041667 0.458333 0.041667 0.166667 0.333333 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.916667 0.083333 0.291667 0.250000 0.250000 0.208333 0.291667 0.041667 0.250000 0.416667 0.041667 0.000000 0.583333 0.375000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- G[TA]GTTG[AT]TG[ACGT][TAG][GT] -------------------------------------------------------------------------------- Time 21.61 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 10629 5.23e-03 209_[+2(2.27e-06)]_270 12094 1.02e-04 324_[+3(2.16e-05)]_139_\ [+1(4.72e-07)]_4 1418 1.49e-01 323_[+3(8.47e-05)]_165 20769 6.94e-04 178_[+2(8.48e-07)]_64_\ [+3(5.25e-05)]_225 21070 2.22e-06 257_[+1(9.59e-07)]_44_\ [+3(5.70e-05)]_12_[+2(1.97e-06)]_133 22375 7.07e-10 146_[+2(6.62e-08)]_155_\ [+1(5.66e-07)]_4_[+3(4.26e-07)]_141 24671 2.69e-08 121_[+1(3.97e-08)]_140_\ [+2(2.49e-07)]_10_[+3(8.47e-05)]_175 2540 2.68e-06 120_[+3(3.37e-06)]_158_\ [+1(2.79e-08)]_189 261024 2.52e-06 342_[+3(6.70e-06)]_36_\ [+2(1.07e-08)]_89 261490 1.29e-06 218_[+3(4.53e-06)]_66_\ [+2(9.19e-07)]_87_[+1(1.40e-05)]_75 261710 3.69e-01 500 263269 3.37e-05 45_[+3(4.53e-06)]_96_[+1(3.56e-07)]_\ 114_[+3(6.14e-05)]_200 270110 1.96e-03 76_[+3(8.94e-05)]_381_\ [+1(6.48e-06)]_10 2927 1.16e-02 236_[+1(8.07e-07)]_6_[+1(2.95e-05)]_\ 216 32016 1.27e-03 31_[+3(6.14e-05)]_38_[+2(2.43e-06)]_\ 398 3378 2.13e-04 138_[+3(4.13e-05)]_269_\ [+1(8.95e-05)]_35_[+1(4.72e-07)]_4 34100 5.71e-05 199_[+1(1.40e-05)]_149_\ [+2(1.26e-06)]_110 34702 7.23e-08 227_[+3(3.32e-05)]_5_[+2(2.49e-07)]_\ 193_[+1(2.94e-07)]_21 35768 3.05e-04 124_[+3(9.51e-05)]_1_[+1(5.66e-07)]_\ 105_[+3(2.69e-05)]_204_[+1(9.34e-05)] 36988 8.78e-10 111_[+2(1.02e-07)]_100_\ [+3(1.69e-05)]_231_[+1(1.18e-08)]_4 3879 1.03e-10 212_[+1(4.45e-08)]_153_\ [+2(2.63e-11)]_93 38861 7.83e-02 92_[+3(2.69e-05)]_185_\ [+3(8.47e-05)]_199 40675 7.07e-07 122_[+2(6.12e-05)]_178_\ [+2(4.70e-07)]_115_[+1(3.53e-08)]_22 4096 7.96e-05 271_[+3(1.52e-05)]_175_\ [+1(3.56e-07)]_21 4674 7.75e-08 168_[+2(8.22e-08)]_126_\ [+1(1.80e-07)]_164 5133 3.78e-01 500 6708 6.65e-09 235_[+2(2.11e-06)]_49_\ [+3(5.61e-06)]_153_[+1(1.52e-08)]_9 6819 3.30e-08 45_[+1(4.26e-06)]_165_\ [+3(1.42e-07)]_14_[+2(1.70e-06)]_222 7898 2.20e-01 132_[+3(4.47e-05)]_356 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************