******************************************************************************** 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/112/112.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 1463 1.0000 500 16777 1.0000 500 20795 1.0000 500 20927 1.0000 500 21102 1.0000 500 22368 1.0000 500 23116 1.0000 500 24826 1.0000 500 25054 1.0000 500 25073 1.0000 500 25136 1.0000 500 270029 1.0000 500 31034 1.0000 500 32691 1.0000 500 35135 1.0000 500 35541 1.0000 500 39973 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/112/112.seqs.fa -oc motifs/112 -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= 17 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= 8500 N= 17 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.253 C 0.238 G 0.245 T 0.264 Background letter frequencies (from dataset with add-one prior applied): A 0.253 C 0.238 G 0.245 T 0.264 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 15 sites = 16 llr = 181 E-value = 3.5e-007 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A :1:41181:6327:: pos.-specific C :::31213::3::1: probability G 31a1:7::a3:81:9 matrix T 89:38:26:25:291 bits 2.1 * * 1.9 * * 1.7 * * * 1.5 * * ** Relative 1.2 ** * * ** Entropy 1.0 *** * * * ** (16.3 bits) 0.8 *** ***** **** 0.6 *** ****** **** 0.4 *** *********** 0.2 *************** 0.0 --------------- Multilevel TTGATGATGATGATG consensus G T C GA sequence C C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------- 25073 128 3.65e-09 TCTGTTGTTG TTGCTGATGATGATG CTGATGCTGC 39973 146 1.84e-08 GTTGAGGCGG TTGCTGATGGTGATG AACGAAGATG 23116 272 3.50e-07 GGAGGGTGGA TTGATGATGATATTG GTGTTGATAA 35135 184 4.39e-07 CAATCTTATC TTGTTGACGACGGTG AACCAAACAA 21102 119 6.27e-07 CTTTCTGGCT GTGACGATGACGATG TATTGGTGTT 32691 472 1.44e-06 ATTGGATTGG TTGATCACGATGATT GTGTGAGGCA 22368 366 1.44e-06 GTTCGTGGCA TTGTTGTCGTAGATG TGCGAAGCCT 20795 13 1.59e-06 GTTGGTGTTG TTGTTGTTGTTGTTG AGCTCCTACA 25054 271 1.92e-06 ATGGGAGGGT TTGCTCACGACAATG GTTTGACAAA 25136 76 2.30e-06 ATCGCTTGCC GTGATGATGATGTTT GTGCAGCATG 20927 120 5.37e-06 ACGTGTTGAG TTGTTAATGGTGACG CTTGAAACGA 31034 117 6.75e-06 CGCGGCACAC TTGCAGACGGAAATG GTGCATCATC 24826 467 1.12e-05 ATCGTACGTC GAGACGATGGTGATG ACATATCAAT 35541 35 1.56e-05 TTTTTTATCA TGGATGAAGTCGATG CAGCATTGGA 16777 302 1.99e-05 TGTGGGAGGT TTGTACTTGAAGGTG GGAAGCATTG 1463 28 2.98e-05 GTCCGTCCCA GTGGTACTGAAGATG CGGTGCGTGT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 25073 3.7e-09 127_[+1]_358 39973 1.8e-08 145_[+1]_340 23116 3.5e-07 271_[+1]_214 35135 4.4e-07 183_[+1]_302 21102 6.3e-07 118_[+1]_367 32691 1.4e-06 471_[+1]_14 22368 1.4e-06 365_[+1]_120 20795 1.6e-06 12_[+1]_473 25054 1.9e-06 270_[+1]_215 25136 2.3e-06 75_[+1]_410 20927 5.4e-06 119_[+1]_366 31034 6.8e-06 116_[+1]_369 24826 1.1e-05 466_[+1]_19 35541 1.6e-05 34_[+1]_451 16777 2e-05 301_[+1]_184 1463 3e-05 27_[+1]_458 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=15 seqs=16 25073 ( 128) TTGCTGATGATGATG 1 39973 ( 146) TTGCTGATGGTGATG 1 23116 ( 272) TTGATGATGATATTG 1 35135 ( 184) TTGTTGACGACGGTG 1 21102 ( 119) GTGACGATGACGATG 1 32691 ( 472) TTGATCACGATGATT 1 22368 ( 366) TTGTTGTCGTAGATG 1 20795 ( 13) TTGTTGTTGTTGTTG 1 25054 ( 271) TTGCTCACGACAATG 1 25136 ( 76) GTGATGATGATGTTT 1 20927 ( 120) TTGTTAATGGTGACG 1 31034 ( 117) TTGCAGACGGAAATG 1 24826 ( 467) GAGACGATGGTGATG 1 35541 ( 35) TGGATGAAGTCGATG 1 16777 ( 302) TTGTACTTGAAGGTG 1 1463 ( 28) GTGGTACTGAAGATG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 8262 bayes= 9.00948 E= 3.5e-007 -1064 -1064 3 150 -201 -1064 -197 173 -1064 -1064 203 -1064 57 7 -197 24 -102 -93 -1064 150 -102 -34 149 -1064 157 -192 -1064 -49 -201 40 -1064 124 -1064 -1064 203 -1064 115 -1064 3 -49 -2 7 -1064 92 -43 -1064 173 -1064 144 -1064 -97 -49 -1064 -192 -1064 183 -1064 -1064 183 -108 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 16 E= 3.5e-007 0.000000 0.000000 0.250000 0.750000 0.062500 0.000000 0.062500 0.875000 0.000000 0.000000 1.000000 0.000000 0.375000 0.250000 0.062500 0.312500 0.125000 0.125000 0.000000 0.750000 0.125000 0.187500 0.687500 0.000000 0.750000 0.062500 0.000000 0.187500 0.062500 0.312500 0.000000 0.625000 0.000000 0.000000 1.000000 0.000000 0.562500 0.000000 0.250000 0.187500 0.250000 0.250000 0.000000 0.500000 0.187500 0.000000 0.812500 0.000000 0.687500 0.000000 0.125000 0.187500 0.000000 0.062500 0.000000 0.937500 0.000000 0.000000 0.875000 0.125000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [TG]TG[ATC]TGA[TC]G[AG][TAC]GATG -------------------------------------------------------------------------------- Time 3.43 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 15 sites = 17 llr = 172 E-value = 1.7e-002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A :41194::418:28: pos.-specific C 6179:57229:8427 probability G 12::11:8111:4:: matrix T 432::13:4:221:3 bits 2.1 1.9 1.7 * 1.5 ** * * Relative 1.2 ** ** * * ** Entropy 1.0 *** ** *** ** (14.6 bits) 0.8 * *** ** *** ** 0.6 * *** ** *** ** 0.4 * ****** *** ** 0.2 * ************* 0.0 --------------- Multilevel CACCACCGACACCAC consensus TTT AT T TGCT sequence G A -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------- 270029 135 5.24e-09 CCACACCGAC CACCAACGACACGAC AGAACTCTGA 24826 358 3.23e-07 GAAGATGCAA CACCACTGTCACCAT GCCACCGTTG 22368 451 4.29e-07 TCGGAAAGTT CACCACCGCCACACC ACGACTGACG 21102 450 1.19e-06 TGGACCAATC TGCCAACCTCACGAC TCCAACGGCA 20927 428 2.86e-06 CCTCCTCGCC CTCCAATCCCACCAC ATCCCACCCA 1463 402 3.17e-06 CACCGACCCC TCCCAACGGCACGAC TTCCTCCTCC 20795 204 4.27e-06 GTACTAGTAG TGCCACTGTCACTAC AGTTGTTGCC 25073 479 6.29e-06 GTTGTTGCTG CTTCACCGTCATACC AGCATAC 16777 226 6.86e-06 CCCAAGGCAT CACCACCGCCTTGAT AAGGATTTGT 31034 234 8.21e-06 TGCCACACCT CACCAGCGACGCCAC ACGAGTTTTA 25136 215 8.21e-06 TCATCTTCAA CGTCAACGACATACC ACACGTCACA 23116 25 9.77e-06 GTTGCGAAAA TTCCACCGTCTTCAT CCCGTCGTCC 39973 478 1.88e-05 GGTAACCCTT TCCAAACCACACCAC ACAAAGCA 32691 257 2.36e-05 CCGTCAGGAG CATCACTGAGACGAT TGAGCGTTGA 25054 132 4.17e-05 TGCTCACTGC CTTCGTCGTCACCAC CACTCATTTG 35135 474 8.80e-05 GATGTATACG TTACACTGACTCACC CCTACTGTAC 35541 474 1.94e-04 TATTTTTAGT GGCAAACGAAACGAT GAAATTCTGC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 270029 5.2e-09 134_[+2]_351 24826 3.2e-07 357_[+2]_128 22368 4.3e-07 450_[+2]_35 21102 1.2e-06 449_[+2]_36 20927 2.9e-06 427_[+2]_58 1463 3.2e-06 401_[+2]_84 20795 4.3e-06 203_[+2]_282 25073 6.3e-06 478_[+2]_7 16777 6.9e-06 225_[+2]_260 31034 8.2e-06 233_[+2]_252 25136 8.2e-06 214_[+2]_271 23116 9.8e-06 24_[+2]_461 39973 1.9e-05 477_[+2]_8 32691 2.4e-05 256_[+2]_229 25054 4.2e-05 131_[+2]_354 35135 8.8e-05 473_[+2]_12 35541 0.00019 473_[+2]_12 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=15 seqs=17 270029 ( 135) CACCAACGACACGAC 1 24826 ( 358) CACCACTGTCACCAT 1 22368 ( 451) CACCACCGCCACACC 1 21102 ( 450) TGCCAACCTCACGAC 1 20927 ( 428) CTCCAATCCCACCAC 1 1463 ( 402) TCCCAACGGCACGAC 1 20795 ( 204) TGCCACTGTCACTAC 1 25073 ( 479) CTTCACCGTCATACC 1 16777 ( 226) CACCACCGCCTTGAT 1 31034 ( 234) CACCAGCGACGCCAC 1 25136 ( 215) CGTCAACGACATACC 1 23116 ( 25) TTCCACCGTCTTCAT 1 39973 ( 478) TCCAAACCACACCAC 1 32691 ( 257) CATCACTGAGACGAT 1 25054 ( 132) CTTCGTCGTCACCAC 1 35135 ( 474) TTACACTGACTCACC 1 35541 ( 474) GGCAAACGAAACGAT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 8262 bayes= 8.92184 E= 1.7e-002 -1073 131 -206 42 48 -101 -6 15 -210 157 -1073 -17 -110 189 -1073 -1073 190 -1073 -206 -1073 70 99 -206 -216 -1073 157 -1073 15 -1073 -43 175 -1073 70 -43 -206 42 -210 189 -206 -1073 160 -1073 -206 -58 -1073 169 -1073 -17 -10 57 52 -216 160 -1 -1073 -1073 -1073 157 -1073 15 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 17 E= 1.7e-002 0.000000 0.588235 0.058824 0.352941 0.352941 0.117647 0.235294 0.294118 0.058824 0.705882 0.000000 0.235294 0.117647 0.882353 0.000000 0.000000 0.941176 0.000000 0.058824 0.000000 0.411765 0.470588 0.058824 0.058824 0.000000 0.705882 0.000000 0.294118 0.000000 0.176471 0.823529 0.000000 0.411765 0.176471 0.058824 0.352941 0.058824 0.882353 0.058824 0.000000 0.764706 0.000000 0.058824 0.176471 0.000000 0.764706 0.000000 0.235294 0.235294 0.352941 0.352941 0.058824 0.764706 0.235294 0.000000 0.000000 0.000000 0.705882 0.000000 0.294118 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [CT][ATG][CT]CA[CA][CT]G[AT]CA[CT][CGA][AC][CT] -------------------------------------------------------------------------------- Time 7.12 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 18 sites = 7 llr = 115 E-value = 3.4e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A :744:4a:a9:a61a41a pos.-specific C a11:6::a:17:37::9: probability G ::3344::::3:1::6:: matrix T :113:1:::::::1:::: bits 2.1 * *** * * * 1.9 * *** * * * 1.7 * *** * * * 1.5 * **** * * ** Relative 1.2 * ****** * ** Entropy 1.0 * * ****** **** (23.7 bits) 0.8 ** * ****** ***** 0.6 ** ************** 0.4 ** *************** 0.2 ****************** 0.0 ------------------ Multilevel CAAACAACAACAACAGCA consensus GGGG G C A sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------------ 35135 202 7.30e-11 GACGGTGAAC CAAACAACAACAACAACA ACAATATGGA 20927 388 4.83e-09 AAATTAGTAA CAGAGGACAAGACCAGCA CCACCCCACC 25136 352 1.34e-08 TCTTCACTCC CAAACAACAACAGTAGCA ACAACCTATG 39973 429 1.60e-08 AATATGTGGA CACGGTACAACAACAACA CGCCGGACAC 270029 468 2.11e-08 ATCAACATGT CCTTCAACAACAACAACA ATCGCTCCAC 21102 319 5.72e-08 GTTGCAAAAA CAGGGGACAACAAAAGAA AGTTATGGCC 25073 44 9.99e-08 CATCGTTACC CTATCGACACGACCAGCA TCGTGATGGT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 35135 7.3e-11 201_[+3]_281 20927 4.8e-09 387_[+3]_95 25136 1.3e-08 351_[+3]_131 39973 1.6e-08 428_[+3]_54 270029 2.1e-08 467_[+3]_15 21102 5.7e-08 318_[+3]_164 25073 1e-07 43_[+3]_439 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=18 seqs=7 35135 ( 202) CAAACAACAACAACAACA 1 20927 ( 388) CAGAGGACAAGACCAGCA 1 25136 ( 352) CAAACAACAACAGTAGCA 1 39973 ( 429) CACGGTACAACAACAACA 1 270029 ( 468) CCTTCAACAACAACAACA 1 21102 ( 319) CAGGGGACAACAAAAGAA 1 25073 ( 44) CTATCGACACGACCAGCA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 18 n= 8211 bayes= 11.4179 E= 3.4e-001 -945 207 -945 -945 150 -73 -945 -89 76 -73 22 -89 76 -945 22 11 -945 127 80 -945 76 -945 80 -89 198 -945 -945 -945 -945 207 -945 -945 198 -945 -945 -945 176 -73 -945 -945 -945 159 22 -945 198 -945 -945 -945 117 27 -78 -945 -82 159 -945 -89 198 -945 -945 -945 76 -945 122 -945 -82 185 -945 -945 198 -945 -945 -945 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 18 nsites= 7 E= 3.4e-001 0.000000 1.000000 0.000000 0.000000 0.714286 0.142857 0.000000 0.142857 0.428571 0.142857 0.285714 0.142857 0.428571 0.000000 0.285714 0.285714 0.000000 0.571429 0.428571 0.000000 0.428571 0.000000 0.428571 0.142857 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.857143 0.142857 0.000000 0.000000 0.000000 0.714286 0.285714 0.000000 1.000000 0.000000 0.000000 0.000000 0.571429 0.285714 0.142857 0.000000 0.142857 0.714286 0.000000 0.142857 1.000000 0.000000 0.000000 0.000000 0.428571 0.000000 0.571429 0.000000 0.142857 0.857143 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- CA[AG][AGT][CG][AG]ACAA[CG]A[AC]CA[GA]CA -------------------------------------------------------------------------------- Time 10.39 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 1463 1.38e-03 27_[+1(2.98e-05)]_359_\ [+2(3.17e-06)]_84 16777 7.23e-04 225_[+2(6.86e-06)]_61_\ [+1(1.99e-05)]_184 20795 1.66e-04 9_[+1(1.59e-06)]_99_[+1(1.59e-06)]_\ 36_[+2(9.33e-05)]_14_[+2(4.27e-06)]_121_[+1(6.22e-05)]_146 20927 2.97e-09 119_[+1(5.37e-06)]_253_\ [+3(4.83e-09)]_22_[+2(2.86e-06)]_58 21102 1.78e-09 118_[+1(6.27e-07)]_185_\ [+3(5.72e-08)]_113_[+2(1.19e-06)]_36 22368 1.31e-05 365_[+1(1.44e-06)]_70_\ [+2(4.29e-07)]_35 23116 7.64e-06 24_[+2(9.77e-06)]_232_\ [+1(3.50e-07)]_214 24826 2.65e-05 357_[+2(3.23e-07)]_94_\ [+1(1.12e-05)]_19 25054 3.20e-04 131_[+2(4.17e-05)]_124_\ [+1(1.92e-06)]_215 25073 1.18e-10 43_[+3(9.99e-08)]_66_[+1(3.65e-09)]_\ 336_[+2(6.29e-06)]_7 25136 9.24e-09 75_[+1(2.30e-06)]_124_\ [+2(8.21e-06)]_122_[+3(1.34e-08)]_131 270029 5.78e-09 134_[+2(5.24e-09)]_50_\ [+2(4.45e-05)]_253_[+3(2.11e-08)]_15 31034 4.46e-04 116_[+1(6.75e-06)]_102_\ [+2(8.21e-06)]_252 32691 5.01e-04 256_[+2(2.36e-05)]_200_\ [+1(1.44e-06)]_14 35135 1.40e-10 183_[+1(4.39e-07)]_3_[+3(7.30e-11)]_\ 155_[+1(3.88e-05)]_84_[+2(8.80e-05)]_12 35541 8.97e-03 34_[+1(1.56e-05)]_451 39973 2.67e-10 145_[+1(1.84e-08)]_268_\ [+3(1.60e-08)]_31_[+2(1.88e-05)]_8 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************