******************************************************************************** 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/243/243.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 12049 1.0000 500 1205 1.0000 500 17935 1.0000 500 2018 1.0000 500 20689 1.0000 500 23199 1.0000 500 23533 1.0000 500 23577 1.0000 500 24785 1.0000 500 25214 1.0000 500 25485 1.0000 500 262474 1.0000 500 262615 1.0000 500 263650 1.0000 500 264821 1.0000 500 268118 1.0000 500 5796 1.0000 500 6961 1.0000 500 8680 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/243/243.seqs.fa -oc motifs/243 -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= 19 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= 9500 N= 19 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.257 C 0.243 G 0.232 T 0.268 Background letter frequencies (from dataset with add-one prior applied): A 0.257 C 0.243 G 0.232 T 0.268 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 12 sites = 19 llr = 175 E-value = 1.8e-004 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 3:6::393:832 pos.-specific C 7a11a6:3a236 probability G ::21:112::32 matrix T ::18:::3::2: bits 2.1 * * * 1.9 * * * 1.7 * * * 1.5 * * * * Relative 1.3 ** * * ** Entropy 1.1 ** ** * ** (13.3 bits) 0.8 ** **** ** 0.6 ** **** ** * 0.4 ******* ** * 0.2 ******* ** * 0.0 ------------ Multilevel CCATCCAACACC consensus A G A C AA sequence T G G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 2018 489 5.15e-07 GTCGATCTAT CCATCCACCAAC 17935 489 1.53e-06 AAACAAACTC CCATCCATCATC 263650 460 3.12e-06 CGATCTCCCC ACATCCACCAAC ACTCAGCTGT 1205 437 4.86e-06 TTCCCACTTT CCATCAATCATC TCCCTCCTCC 5796 314 5.69e-06 AGTCATCCAC CCCTCCATCACC CTCCCACGTG 6961 467 6.71e-06 GCTACCACAC CCTTCCAACAGC TATCTCTAAA 8680 378 1.01e-05 TTCGTGATCA CCGTCCACCACA GTCACTCCTT 262474 23 1.01e-05 CATATCGACC ACGTCCAACAGC CTTGCGTATA 262615 424 1.54e-05 TCCGCCATAT CCGTCCAGCACG AGATTTTACC 268118 415 2.00e-05 GACTCAAGTT CCAGCAAACACC AAGGTGACCA 23533 413 3.32e-05 CGACATCATT CCCTCCAGCAAA AGCAGGCTGT 264821 454 3.59e-05 AACGGCACCA ACAGCCAACAAC AACAGCCATC 25485 363 3.59e-05 TCGACCATCG ACATCAAGCAGA AGCAAGTGGT 25214 189 4.43e-05 CGTACGGACT CCTTCCATCCGC AACATGAAAG 23199 192 6.20e-05 GGCGCAAGCG CCATCAAACCAG GTCGAAAATT 24785 469 7.18e-05 GGGAATATTT CCGTCAACCCTC CACCCTTTTC 20689 16 9.72e-05 TTCTTCATCG CCATCGGCCACC TCGTCGTCAG 12049 422 1.04e-04 CTCATCCTCG ACATCCGGCAGA GTAACTCACG 23577 52 1.24e-04 TTGTGCATCA CCACCAATCACG TCGTCTCACC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 2018 5.1e-07 488_[+1] 17935 1.5e-06 488_[+1] 263650 3.1e-06 459_[+1]_29 1205 4.9e-06 436_[+1]_52 5796 5.7e-06 313_[+1]_175 6961 6.7e-06 466_[+1]_22 8680 1e-05 377_[+1]_111 262474 1e-05 22_[+1]_466 262615 1.5e-05 423_[+1]_65 268118 2e-05 414_[+1]_74 23533 3.3e-05 412_[+1]_76 264821 3.6e-05 453_[+1]_35 25485 3.6e-05 362_[+1]_126 25214 4.4e-05 188_[+1]_300 23199 6.2e-05 191_[+1]_297 24785 7.2e-05 468_[+1]_20 20689 9.7e-05 15_[+1]_473 12049 0.0001 421_[+1]_67 23577 0.00012 51_[+1]_437 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=12 seqs=19 2018 ( 489) CCATCCACCAAC 1 17935 ( 489) CCATCCATCATC 1 263650 ( 460) ACATCCACCAAC 1 1205 ( 437) CCATCAATCATC 1 5796 ( 314) CCCTCCATCACC 1 6961 ( 467) CCTTCCAACAGC 1 8680 ( 378) CCGTCCACCACA 1 262474 ( 23) ACGTCCAACAGC 1 262615 ( 424) CCGTCCAGCACG 1 268118 ( 415) CCAGCAAACACC 1 23533 ( 413) CCCTCCAGCAAA 1 264821 ( 454) ACAGCCAACAAC 1 25485 ( 363) ACATCAAGCAGA 1 25214 ( 189) CCTTCCATCCGC 1 23199 ( 192) CCATCAAACCAG 1 24785 ( 469) CCGTCAACCCTC 1 20689 ( 16) CCATCGGCCACC 1 12049 ( 422) ACATCCGGCAGA 1 23577 ( 52) CCACCAATCACG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 9291 bayes= 8.93074 E= 1.8e-004 4 160 -1089 -1089 -1089 204 -1089 -1089 117 -121 -14 -135 -1089 -220 -114 165 -1089 204 -1089 -1089 30 138 -214 -1089 180 -1089 -114 -1089 4 12 -14 -3 -1089 204 -1089 -1089 171 -62 -1089 -1089 4 38 18 -76 -29 138 -56 -1089 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 19 E= 1.8e-004 0.263158 0.736842 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.578947 0.105263 0.210526 0.105263 0.000000 0.052632 0.105263 0.842105 0.000000 1.000000 0.000000 0.000000 0.315789 0.631579 0.052632 0.000000 0.894737 0.000000 0.105263 0.000000 0.263158 0.263158 0.210526 0.263158 0.000000 1.000000 0.000000 0.000000 0.842105 0.157895 0.000000 0.000000 0.263158 0.315789 0.263158 0.157895 0.210526 0.631579 0.157895 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [CA]C[AG]TC[CA]A[ACTG]CA[CAG][CA] -------------------------------------------------------------------------------- Time 3.21 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 12 sites = 16 llr = 156 E-value = 1.4e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A 2:31:36::::1 pos.-specific C 1:::23:::::: probability G 6a:283119719 matrix T 1:771239139: bits 2.1 * 1.9 * 1.7 * * * 1.5 * ** ** Relative 1.3 * ** ** Entropy 1.1 ** * ***** (14.1 bits) 0.8 **** ****** 0.6 ***** ****** 0.4 ***** ****** 0.2 ***** ****** 0.0 ------------ Multilevel GGTTGGATGGTG consensus A AT T sequence C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 6961 205 2.07e-07 TTCGACTGAT GGTTGTATGGTG AAGCAATGGC 25214 352 8.32e-07 GGATTGGAGG AGTTGGATGGTG CTCGTCATGG 23533 101 1.20e-06 TCTTGAGGAC AGTTGCATGGTG TAGAGTGGTT 17935 291 1.46e-06 GTGTAGAAGG AGTTGAATGGTG TAGTAGTAGA 262474 216 2.02e-06 ACGGACGAGA GGATGCATGTTG TTCGACGGTT 264821 78 8.52e-06 GGTTGAGGAT GGATCGATGTTG CCACCCAAGT 268118 134 1.09e-05 GTGTACTTCT GGTTGGTTGGGG AAGGGGGGAG 262615 252 1.09e-05 CAAGTACGTC GGATCCATGTTG TATGCTACTC 23199 143 1.09e-05 TTGTGTATGG GGTTGGTGGGTG GTAGGTTGGC 24785 331 1.57e-05 GTTTCAACCA CGATGAATGTTG TAGCTGCTTC 20689 237 2.02e-05 CGTAGTTTTT GGTGCTTTGGTG GAGGTACAAG 263650 288 3.65e-05 AGATGAGAGG GGAGGGATTGTG TGGGTGTGCA 2018 39 3.89e-05 ACTCTTCAAT GGTAGAATGGTA AAAGTGACGA 23577 4 4.19e-05 ACT GGTGTCTTGGTG GTCCTCTTTG 25485 397 5.85e-05 TGGACATTTT TGTTGTGTGGTG GTAGAGCGCA 12049 148 6.61e-05 TTATACATTG CGTAGATTGTTG CGTTTGACCC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 6961 2.1e-07 204_[+2]_284 25214 8.3e-07 351_[+2]_137 23533 1.2e-06 100_[+2]_388 17935 1.5e-06 290_[+2]_198 262474 2e-06 215_[+2]_273 264821 8.5e-06 77_[+2]_411 268118 1.1e-05 133_[+2]_355 262615 1.1e-05 251_[+2]_237 23199 1.1e-05 142_[+2]_346 24785 1.6e-05 330_[+2]_158 20689 2e-05 236_[+2]_252 263650 3.7e-05 287_[+2]_201 2018 3.9e-05 38_[+2]_450 23577 4.2e-05 3_[+2]_485 25485 5.9e-05 396_[+2]_92 12049 6.6e-05 147_[+2]_341 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=12 seqs=16 6961 ( 205) GGTTGTATGGTG 1 25214 ( 352) AGTTGGATGGTG 1 23533 ( 101) AGTTGCATGGTG 1 17935 ( 291) AGTTGAATGGTG 1 262474 ( 216) GGATGCATGTTG 1 264821 ( 78) GGATCGATGTTG 1 268118 ( 134) GGTTGGTTGGGG 1 262615 ( 252) GGATCCATGTTG 1 23199 ( 143) GGTTGGTGGGTG 1 24785 ( 331) CGATGAATGTTG 1 20689 ( 237) GGTGCTTTGGTG 1 263650 ( 288) GGAGGGATTGTG 1 2018 ( 39) GGTAGAATGGTA 1 23577 ( 4) GGTGTCTTGGTG 1 25485 ( 397) TGTTGTGTGGTG 1 12049 ( 148) CGTAGATTGTTG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 9291 bayes= 9.91709 E= 1.4e-001 -45 -96 143 -210 -1064 -1064 210 -1064 28 -1064 -1064 136 -104 -1064 -31 136 -1064 -37 169 -210 -4 4 43 -51 128 -1064 -189 22 -1064 -1064 -189 181 -1064 -1064 201 -210 -1064 -1064 156 22 -1064 -1064 -189 181 -204 -1064 201 -1064 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 16 E= 1.4e-001 0.187500 0.125000 0.625000 0.062500 0.000000 0.000000 1.000000 0.000000 0.312500 0.000000 0.000000 0.687500 0.125000 0.000000 0.187500 0.687500 0.000000 0.187500 0.750000 0.062500 0.250000 0.250000 0.312500 0.187500 0.625000 0.000000 0.062500 0.312500 0.000000 0.000000 0.062500 0.937500 0.000000 0.000000 0.937500 0.062500 0.000000 0.000000 0.687500 0.312500 0.000000 0.000000 0.062500 0.937500 0.062500 0.000000 0.937500 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- GG[TA]TG[GAC][AT]TG[GT]TG -------------------------------------------------------------------------------- Time 6.34 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 18 sites = 10 llr = 142 E-value = 1.9e-003 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A :51:2316:18:2592:5 pos.-specific C :3215411:::::3:1:: probability G a2693253a9:a821795 matrix T ::1::13:::2:::::1: bits 2.1 * * * 1.9 * * * 1.7 * * ** * * 1.5 * * ** * * * Relative 1.3 * * ***** * * Entropy 1.1 * * ***** * ** (20.5 bits) 0.8 * * ***** **** 0.6 ** ** *********** 0.4 ***** ************ 0.2 ****************** 0.0 ------------------ Multilevel GAGGCCGAGGAGGAAGGA consensus CC GATG T AC A G sequence G AG G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------------ 25214 321 9.95e-11 GACGGAGAGC GAGGCCTAGGAGGAAGGG ATGGGATTGG 17935 14 6.62e-09 AATGATCAAG GCCGCAGAGGAGGCAGGA GCATGCTGTG 24785 189 1.42e-08 CGAAGAAACC GAAGGCGAGGAGGGAGGG AACAACAGTA 264821 31 3.48e-08 TGCGGCATCA GCGGCCTGGGAGGAACGA CCGTACGTGA 8680 314 1.32e-07 CAACAGTCGT GATGCCAAGGAGGAAAGG GACTGGCATA 6961 302 1.84e-07 CTGTCTAGTG GGGGAACAGGAGAAAGGA ATGGAGAGGG 263650 194 6.69e-07 CTCGTATGAA GAGCAGGGGAAGGAAGGA GTCGTAATGA 23533 10 6.69e-07 TGGATGGTT GGCGGTGAGGAGGGGGGG CTCTCCGTTG 5796 451 7.13e-07 GAAAAGTCAG GCGGCAGCGGTGGCAGTG GATGAGGCGG 23199 214 8.07e-07 GTCGAAAATT GAGGGGTGGGTGACAAGA CAACCACGGT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 25214 1e-10 320_[+3]_162 17935 6.6e-09 13_[+3]_469 24785 1.4e-08 188_[+3]_294 264821 3.5e-08 30_[+3]_452 8680 1.3e-07 313_[+3]_169 6961 1.8e-07 301_[+3]_181 263650 6.7e-07 193_[+3]_289 23533 6.7e-07 9_[+3]_473 5796 7.1e-07 450_[+3]_32 23199 8.1e-07 213_[+3]_269 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=18 seqs=10 25214 ( 321) GAGGCCTAGGAGGAAGGG 1 17935 ( 14) GCCGCAGAGGAGGCAGGA 1 24785 ( 189) GAAGGCGAGGAGGGAGGG 1 264821 ( 31) GCGGCCTGGGAGGAACGA 1 8680 ( 314) GATGCCAAGGAGGAAAGG 1 6961 ( 302) GGGGAACAGGAGAAAGGA 1 263650 ( 194) GAGCAGGGGAAGGAAGGA 1 23533 ( 10) GGCGGTGAGGAGGGGGGG 1 5796 ( 451) GCGGCAGCGGTGGCAGTG 1 23199 ( 214) GAGGGGTGGGTGACAAGA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 18 n= 9177 bayes= 10.7845 E= 1.9e-003 -997 -997 210 -997 96 30 -22 -997 -136 -28 137 -142 -997 -128 195 -997 -36 104 37 -997 22 72 -22 -142 -136 -128 110 16 122 -128 37 -997 -997 -997 210 -997 -136 -997 195 -997 164 -997 -997 -42 -997 -997 210 -997 -36 -997 178 -997 96 30 -22 -997 181 -997 -121 -997 -36 -128 159 -997 -997 -997 195 -142 96 -997 110 -997 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 18 nsites= 10 E= 1.9e-003 0.000000 0.000000 1.000000 0.000000 0.500000 0.300000 0.200000 0.000000 0.100000 0.200000 0.600000 0.100000 0.000000 0.100000 0.900000 0.000000 0.200000 0.500000 0.300000 0.000000 0.300000 0.400000 0.200000 0.100000 0.100000 0.100000 0.500000 0.300000 0.600000 0.100000 0.300000 0.000000 0.000000 0.000000 1.000000 0.000000 0.100000 0.000000 0.900000 0.000000 0.800000 0.000000 0.000000 0.200000 0.000000 0.000000 1.000000 0.000000 0.200000 0.000000 0.800000 0.000000 0.500000 0.300000 0.200000 0.000000 0.900000 0.000000 0.100000 0.000000 0.200000 0.100000 0.700000 0.000000 0.000000 0.000000 0.900000 0.100000 0.500000 0.000000 0.500000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- G[ACG][GC]G[CGA][CAG][GT][AG]GG[AT]G[GA][ACG]A[GA]G[AG] -------------------------------------------------------------------------------- Time 9.63 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 12049 2.63e-02 147_[+2(6.61e-05)]_341 1205 3.14e-02 436_[+1(4.86e-06)]_52 17935 6.73e-10 13_[+3(6.62e-09)]_153_\ [+2(7.04e-05)]_94_[+2(1.46e-06)]_186_[+1(1.53e-06)] 2018 9.05e-05 38_[+2(3.89e-05)]_438_\ [+1(5.15e-07)] 20689 1.86e-03 15_[+1(9.72e-05)]_209_\ [+2(2.02e-05)]_252 23199 9.64e-06 100_[+2(4.49e-05)]_30_\ [+2(1.09e-05)]_37_[+1(6.20e-05)]_10_[+3(8.07e-07)]_269 23533 6.49e-07 9_[+3(6.69e-07)]_73_[+2(1.20e-06)]_\ 57_[+2(6.22e-05)]_10_[+3(7.60e-05)]_203_[+1(3.32e-05)]_76 23577 3.62e-02 3_[+2(4.19e-05)]_485 24785 4.03e-07 188_[+3(1.42e-08)]_124_\ [+2(1.57e-05)]_126_[+1(7.18e-05)]_20 25214 1.83e-10 188_[+1(4.43e-05)]_90_\ [+3(9.88e-06)]_12_[+3(9.95e-11)]_13_[+2(8.32e-07)]_137 25485 1.84e-02 362_[+1(3.59e-05)]_22_\ [+2(5.85e-05)]_92 262474 2.76e-04 22_[+1(1.01e-05)]_181_\ [+2(2.02e-06)]_273 262615 1.55e-03 251_[+2(1.09e-05)]_160_\ [+1(1.54e-05)]_65 263650 1.67e-06 193_[+3(6.69e-07)]_76_\ [+2(3.65e-05)]_160_[+1(3.12e-06)]_29 264821 2.83e-07 30_[+3(3.48e-08)]_29_[+2(8.52e-06)]_\ 127_[+2(7.48e-05)]_225_[+1(3.59e-05)]_1_[+1(8.61e-05)]_22 268118 8.50e-04 133_[+2(1.09e-05)]_269_\ [+1(2.00e-05)]_74 5796 5.12e-05 186_[+3(9.80e-05)]_109_\ [+1(5.69e-06)]_125_[+3(7.13e-07)]_32 6961 9.40e-09 204_[+2(2.07e-07)]_85_\ [+3(1.84e-07)]_147_[+1(6.71e-06)]_22 8680 3.64e-05 313_[+3(1.32e-07)]_46_\ [+1(1.01e-05)]_111 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************