******************************************************************************** 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/294/294.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 11825 1.0000 500 1373 1.0000 500 2094 1.0000 500 23290 1.0000 500 25443 1.0000 500 261027 1.0000 500 261769 1.0000 500 262079 1.0000 500 263386 1.0000 500 263766 1.0000 500 3118 1.0000 500 3189 1.0000 500 3190 1.0000 500 33699 1.0000 500 34233 1.0000 500 3868 1.0000 500 4543 1.0000 500 7368 1.0000 500 7928 1.0000 500 bd1092 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/294/294.seqs.fa -oc motifs/294 -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= 20 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= 10000 N= 20 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.267 C 0.249 G 0.226 T 0.257 Background letter frequencies (from dataset with add-one prior applied): A 0.267 C 0.249 G 0.226 T 0.257 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 14 sites = 12 llr = 146 E-value = 3.3e-003 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A :3:3::::3:::11 pos.-specific C 5:76::8::a:11: probability G 53:2a:392:9569 matrix T :43::a:16:143: bits 2.1 * 1.9 ** * 1.7 ** * ** * 1.5 ** * ** * Relative 1.3 **** ** * Entropy 1.1 * * **** ** * (17.5 bits) 0.9 * * **** ** * 0.6 * ********** * 0.4 ************** 0.2 ************** 0.0 -------------- Multilevel CTCCGTCGTCGGGG consensus GGTA G A TT sequence A -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------- 3868 78 4.20e-08 TGCCGCTGTC GTCAGTCGTCGGGG TGGTGACACG 7928 234 7.07e-08 GGAACCGGTT GTCCGTCGGCGGGG TGGCAACCAC 3189 80 8.65e-08 TCCACCAAGA CGCCGTCGTCGGTG TAACCGGTCG 23290 401 8.65e-08 ACCGTCTTGT CGTCGTCGTCGTGG TGAACCAAAT bd1092 254 4.74e-07 CGGTCCTTGA GGCCGTGGACGTGG TTAACGAGTG 7368 178 1.03e-06 CGGTCGAGTA CACGGTCGACGTGG TCATCCACCT 33699 79 1.57e-06 GGGCTTGAGT GGCGGTGGGCGGGG GGGACATTCC 262079 145 1.70e-06 ATGCCGATCG GATAGTCGTCGTTG ATAATGGTTC 1373 39 3.31e-06 TCGGAAAGAA CTTCGTCGTCTGTG CCTCGAGACG 2094 274 6.17e-06 ATGAGACTCT CTTCGTCTTCGCGG CGACGGCGAC 3190 403 6.50e-06 CAAGTATACT GTCAGTGGACGTCG TTTTGAGGGA 261027 94 6.82e-06 AAACATCAAT CACCGTCGTCGGAA ACGAAGAATC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 3868 4.2e-08 77_[+1]_409 7928 7.1e-08 233_[+1]_253 3189 8.6e-08 79_[+1]_407 23290 8.6e-08 400_[+1]_86 bd1092 4.7e-07 253_[+1]_233 7368 1e-06 177_[+1]_309 33699 1.6e-06 78_[+1]_408 262079 1.7e-06 144_[+1]_342 1373 3.3e-06 38_[+1]_448 2094 6.2e-06 273_[+1]_213 3190 6.5e-06 402_[+1]_84 261027 6.8e-06 93_[+1]_393 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=14 seqs=12 3868 ( 78) GTCAGTCGTCGGGG 1 7928 ( 234) GTCCGTCGGCGGGG 1 3189 ( 80) CGCCGTCGTCGGTG 1 23290 ( 401) CGTCGTCGTCGTGG 1 bd1092 ( 254) GGCCGTGGACGTGG 1 7368 ( 178) CACGGTCGACGTGG 1 33699 ( 79) GGCGGTGGGCGGGG 1 262079 ( 145) GATAGTCGTCGTTG 1 1373 ( 39) CTTCGTCGTCTGTG 1 2094 ( 274) CTTCGTCTTCGCGG 1 3190 ( 403) GTCAGTGGACGTCG 1 261027 ( 94) CACCGTCGTCGGAA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 14 n= 9740 bayes= 10.1109 E= 3.3e-003 -1023 100 114 -1023 -10 -1023 56 69 -1023 142 -1023 37 -10 123 -44 -1023 -1023 -1023 214 -1023 -1023 -1023 -1023 196 -1023 159 14 -1023 -1023 -1023 202 -162 -10 -1023 -44 118 -1023 200 -1023 -1023 -1023 -1023 202 -162 -1023 -158 114 69 -168 -158 137 -4 -168 -1023 202 -1023 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 14 nsites= 12 E= 3.3e-003 0.000000 0.500000 0.500000 0.000000 0.250000 0.000000 0.333333 0.416667 0.000000 0.666667 0.000000 0.333333 0.250000 0.583333 0.166667 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.750000 0.250000 0.000000 0.000000 0.000000 0.916667 0.083333 0.250000 0.000000 0.166667 0.583333 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.916667 0.083333 0.000000 0.083333 0.500000 0.416667 0.083333 0.083333 0.583333 0.250000 0.083333 0.000000 0.916667 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [CG][TGA][CT][CA]GT[CG]G[TA]CG[GT][GT]G -------------------------------------------------------------------------------- Time 4.15 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 12 sites = 15 llr = 156 E-value = 1.3e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A :82:7548::6: pos.-specific C :::::::::::: probability G 7:77256297:a matrix T 32131:::134: bits 2.1 * 1.9 * 1.7 * * 1.5 * * Relative 1.3 ** * ** * Entropy 1.1 **** ***** * (15.0 bits) 0.9 ************ 0.6 ************ 0.4 ************ 0.2 ************ 0.0 ------------ Multilevel GAGGAAGAGGAG consensus TTATGGAG TT sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 263386 312 7.54e-08 AGAAGGAGGA GAGGAAGAGGAG AAAGCGGTAT 23290 224 7.54e-08 GAGTTTGGTG GAGGAGGAGGAG ATTTATAGGT 7928 11 1.48e-07 GAGTTGATAG GAGGAGGAGGTG TGCAGTTCAC 2094 380 7.27e-07 GGCCAAGCAA GAGGAAGAGTTG TCGCGAGACT 3190 378 4.03e-06 TTGTGTGGCG GAGGTGGAGGAG CGACAAGTAT 3189 233 4.03e-06 CGGAGGGAGC GAGGGGGGGGAG TTTTCGAGCA 3868 265 8.74e-06 GGCTGGGCAC GAAGAAGGGGTG GAAAAATGTA 33699 105 9.84e-06 GACATTCCAC GTGGAGAGGGAG TTTTCTCCTG 34233 118 1.20e-05 TATCTTCGTC TAGTAAGAGTTG AGCCTTGATC 262079 271 1.32e-05 GAAGCTGGCT GAATAGAAGGTG ATAACCCAGA 4543 222 1.38e-05 CTATCTCACA TAGGGAAAGTAG CACCAGCACC 1373 63 2.34e-05 CCTCGAGACG TATGAGAAGGAG TACGACGAGA 11825 1 3.32e-05 . GAGTAAAATGTG ACGGTGACAT 7368 152 3.51e-05 AAAGTCCATA GTAGGAGAGTAG TACACGGTCG 261769 228 3.96e-05 CGTATACGAA TTGTAAAAGTAG GAATCTTCGT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 263386 7.5e-08 311_[+2]_177 23290 7.5e-08 223_[+2]_265 7928 1.5e-07 10_[+2]_478 2094 7.3e-07 379_[+2]_109 3190 4e-06 377_[+2]_111 3189 4e-06 232_[+2]_256 3868 8.7e-06 264_[+2]_224 33699 9.8e-06 104_[+2]_384 34233 1.2e-05 117_[+2]_371 262079 1.3e-05 270_[+2]_218 4543 1.4e-05 221_[+2]_267 1373 2.3e-05 62_[+2]_426 11825 3.3e-05 [+2]_488 7368 3.5e-05 151_[+2]_337 261769 4e-05 227_[+2]_261 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=12 seqs=15 263386 ( 312) GAGGAAGAGGAG 1 23290 ( 224) GAGGAGGAGGAG 1 7928 ( 11) GAGGAGGAGGTG 1 2094 ( 380) GAGGAAGAGTTG 1 3190 ( 378) GAGGTGGAGGAG 1 3189 ( 233) GAGGGGGGGGAG 1 3868 ( 265) GAAGAAGGGGTG 1 33699 ( 105) GTGGAGAGGGAG 1 34233 ( 118) TAGTAAGAGTTG 1 262079 ( 271) GAATAGAAGGTG 1 4543 ( 222) TAGGGAAAGTAG 1 1373 ( 63) TATGAGAAGGAG 1 11825 ( 1) GAGTAAAATGTG 1 7368 ( 152) GTAGGAGAGTAG 1 261769 ( 228) TTGTAAAAGTAG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 9780 bayes= 10.0216 E= 1.3e-001 -1055 -1055 170 5 158 -1055 -1055 -36 -42 -1055 170 -195 -1055 -1055 170 5 146 -1055 -18 -195 100 -1055 104 -1055 58 -1055 141 -1055 158 -1055 -18 -1055 -1055 -1055 204 -195 -1055 -1055 156 37 117 -1055 -1055 64 -1055 -1055 214 -1055 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 15 E= 1.3e-001 0.000000 0.000000 0.733333 0.266667 0.800000 0.000000 0.000000 0.200000 0.200000 0.000000 0.733333 0.066667 0.000000 0.000000 0.733333 0.266667 0.733333 0.000000 0.200000 0.066667 0.533333 0.000000 0.466667 0.000000 0.400000 0.000000 0.600000 0.000000 0.800000 0.000000 0.200000 0.000000 0.000000 0.000000 0.933333 0.066667 0.000000 0.000000 0.666667 0.333333 0.600000 0.000000 0.000000 0.400000 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [GT][AT][GA][GT][AG][AG][GA][AG]G[GT][AT]G -------------------------------------------------------------------------------- Time 8.30 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 16 sites = 13 llr = 154 E-value = 5.3e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A :25:25:451271283 pos.-specific C 97:a8284:88:9726 probability G 11:::2:221:2:::: matrix T ::5:::213::2:2:1 bits 2.1 1.9 * 1.7 * * 1.5 * * * Relative 1.3 * ** * ** * * Entropy 1.1 * ** * ** * * (17.1 bits) 0.9 ***** * ****** 0.6 ***** * ******* 0.4 ******* ******** 0.2 **************** 0.0 ---------------- Multilevel CCTCCACAACCACCAC consensus AA C CT A sequence G G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 33699 462 9.27e-10 ACCAGCCCTT CCACCACCACCACCAC CACCACTCCT 3189 418 2.62e-08 ACTTGTCGCT CCTCCACCTCCGCCAC ACAACGCCAT 263386 168 4.06e-08 GACGACGACT CCACCATAACCACCAC GGTGAATCTT 7368 193 2.42e-07 TCGACGTGGT CATCCACCTCCACAAC ACGGTCGACC 34233 385 8.89e-07 CCAACCCAAC GCACCACAACCACAAC TTTCTCACTC 262079 468 9.77e-07 CTCGAATTTC CCACCCCTTCCTCCAC CGTTGCCACT 25443 218 1.53e-06 TGAACAACTT CCTCCCCGACCACTCC CTCTTATCCA 23290 59 1.80e-06 TCAATGAACT CCTCCGTCTCCTCCAA TTGTAAATTC 4543 461 3.88e-06 TCGTCATTTC CGACCGCCGCCACTAA CCGACACCAC 3868 432 6.37e-06 ATCTATTGGA CAACCACAACCAACCA CCCCCTCCGT bd1092 279 8.81e-06 TAACGAGTGA CATCACCAGACACCAC GCAGCCCGCC 7928 404 9.96e-06 TCTCGCAGTG CCTCCACGAGAACCAT CAGATTTGAT 3118 431 9.96e-06 GTCATTCGTC CCTCAGCAGCAGCCAA CCTCTTTTCC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 33699 9.3e-10 461_[+3]_23 3189 2.6e-08 417_[+3]_67 263386 4.1e-08 167_[+3]_317 7368 2.4e-07 192_[+3]_292 34233 8.9e-07 384_[+3]_100 262079 9.8e-07 467_[+3]_17 25443 1.5e-06 217_[+3]_267 23290 1.8e-06 58_[+3]_426 4543 3.9e-06 460_[+3]_24 3868 6.4e-06 431_[+3]_53 bd1092 8.8e-06 278_[+3]_206 7928 1e-05 403_[+3]_81 3118 1e-05 430_[+3]_54 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=16 seqs=13 33699 ( 462) CCACCACCACCACCAC 1 3189 ( 418) CCTCCACCTCCGCCAC 1 263386 ( 168) CCACCATAACCACCAC 1 7368 ( 193) CATCCACCTCCACAAC 1 34233 ( 385) GCACCACAACCACAAC 1 262079 ( 468) CCACCCCTTCCTCCAC 1 25443 ( 218) CCTCCCCGACCACTCC 1 23290 ( 59) CCTCCGTCTCCTCCAA 1 4543 ( 461) CGACCGCCGCCACTAA 1 3868 ( 432) CAACCACAACCAACCA 1 bd1092 ( 279) CATCACCAGACACCAC 1 7928 ( 404) CCTCCACGAGAACCAT 1 3118 ( 431) CCTCAGCAGCAGCCAA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 9700 bayes= 10.0725 E= 5.3e-001 -1035 189 -155 -1035 -21 147 -155 -1035 79 -1035 -1035 106 -1035 200 -1035 -1035 -80 176 -1035 -1035 101 -11 3 -1035 -1035 176 -1035 -74 53 63 -56 -174 79 -1035 3 26 -179 176 -155 -1035 -80 176 -1035 -1035 137 -1035 -56 -74 -179 189 -1035 -1035 -80 147 -1035 -74 166 -70 -1035 -1035 20 130 -1035 -174 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 13 E= 5.3e-001 0.000000 0.923077 0.076923 0.000000 0.230769 0.692308 0.076923 0.000000 0.461538 0.000000 0.000000 0.538462 0.000000 1.000000 0.000000 0.000000 0.153846 0.846154 0.000000 0.000000 0.538462 0.230769 0.230769 0.000000 0.000000 0.846154 0.000000 0.153846 0.384615 0.384615 0.153846 0.076923 0.461538 0.000000 0.230769 0.307692 0.076923 0.846154 0.076923 0.000000 0.153846 0.846154 0.000000 0.000000 0.692308 0.000000 0.153846 0.153846 0.076923 0.923077 0.000000 0.000000 0.153846 0.692308 0.000000 0.153846 0.846154 0.153846 0.000000 0.000000 0.307692 0.615385 0.000000 0.076923 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- C[CA][TA]CC[ACG]C[AC][ATG]CCACCA[CA] -------------------------------------------------------------------------------- Time 11.97 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 11825 9.57e-02 [+2(3.32e-05)]_488 1373 5.21e-04 38_[+1(3.31e-06)]_10_[+2(2.34e-05)]_\ 426 2094 9.09e-05 273_[+1(6.17e-06)]_92_\ [+2(7.27e-07)]_109 23290 5.45e-10 58_[+3(1.80e-06)]_149_\ [+2(7.54e-08)]_165_[+1(8.65e-08)]_86 25443 1.26e-02 217_[+3(1.53e-06)]_267 261027 3.37e-02 93_[+1(6.82e-06)]_393 261769 9.38e-02 227_[+2(3.96e-05)]_261 262079 5.49e-07 144_[+1(1.70e-06)]_112_\ [+2(1.32e-05)]_185_[+3(9.77e-07)]_17 263386 6.92e-08 139_[+3(2.06e-05)]_12_\ [+3(4.06e-08)]_23_[+3(3.21e-05)]_65_[+2(3.32e-05)]_12_[+2(7.54e-08)]_177 263766 6.56e-01 500 3118 3.89e-02 430_[+3(9.96e-06)]_54 3189 4.30e-10 79_[+1(8.65e-08)]_139_\ [+2(4.03e-06)]_173_[+3(2.62e-08)]_67 3190 3.89e-04 377_[+2(4.03e-06)]_13_\ [+1(6.50e-06)]_18_[+2(6.41e-05)]_54 33699 6.54e-10 78_[+1(1.57e-06)]_12_[+2(9.84e-06)]_\ 345_[+3(9.27e-10)]_23 34233 1.49e-04 117_[+2(1.20e-05)]_255_\ [+3(8.89e-07)]_100 3868 7.14e-08 77_[+1(4.20e-08)]_173_\ [+2(8.74e-06)]_155_[+3(6.37e-06)]_4_[+1(2.07e-05)]_35 4543 1.84e-04 221_[+2(1.38e-05)]_227_\ [+3(3.88e-06)]_6_[+3(4.00e-05)]_2 7368 2.37e-07 151_[+2(3.51e-05)]_14_\ [+1(1.03e-06)]_1_[+3(2.42e-07)]_239_[+3(5.13e-05)]_37 7928 4.11e-09 10_[+2(1.48e-07)]_185_\ [+1(4.91e-05)]_12_[+1(7.07e-08)]_156_[+3(9.96e-06)]_81 bd1092 8.82e-05 253_[+1(4.74e-07)]_11_\ [+3(8.81e-06)]_206 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************