******************************************************************************** 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/245/245.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 20567 1.0000 500 22185 1.0000 500 24854 1.0000 500 25187 1.0000 500 25548 1.0000 500 261180 1.0000 500 262821 1.0000 500 264869 1.0000 500 268839 1.0000 500 268943 1.0000 500 269534 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/245/245.seqs.fa -oc motifs/245 -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= 11 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= 5500 N= 11 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.273 C 0.225 G 0.245 T 0.256 Background letter frequencies (from dataset with add-one prior applied): A 0.273 C 0.225 G 0.245 T 0.256 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 16 sites = 11 llr = 128 E-value = 5.2e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 155:42::5:1:656: pos.-specific C 1:2::2:12::7:22: probability G 85:a54a9:a434328 matrix T ::4:13::4:5::::2 bits 2.1 1.9 * * * 1.7 * * * 1.5 * ** * Relative 1.3 * ** * * * Entropy 1.1 * * ** * ** * (16.8 bits) 0.9 ** * ** * ** * 0.6 ** ** ** **** ** 0.4 ***** ********** 0.2 ***** ********** 0.0 ---------------- Multilevel GAAGGGGGAGTCAAAG consensus GT AT T GGGG sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 268839 7 1.17e-09 GAACAC GATGGGGGAGTCAAAG GGCCAGTGTC 261180 417 1.49e-07 AATCAAATGC GGAGGGGGAGTGAGAG AAGACGCAAA 20567 16 7.38e-07 AATACCGACG GATGGAGGTGTCGAGG CGGGTGGCGG 268943 18 1.12e-06 TGGAGAGGAA GGAGGAGGCGTGGAAG GTGACTGGAG 25187 63 1.12e-06 CGTCGGTACT GGAGTGGGTGGCAGAG GTGCCAAGGA 269534 45 2.14e-06 GTGGGTGGGT GGTGGTGGAGTGACGG AGGGGAACTG 25548 442 2.52e-06 AACGTACCAC GACGATGGAGGCACCG ATAAATCCCG 264869 224 3.73e-06 TGGCTGGGGG GAAGAGGGTGGCAGCT CTATTGGTTG 24854 199 7.33e-06 ACACTTTGCT GGAGACGGAGACGAAT GGAACCATCT 22185 272 7.79e-06 GTTGTCAGCA AACGACGGCGGCAAAG GGACAGGAGC 262821 132 1.03e-05 GCTGGCATTT CATGGTGCTGTCGAAG GCGGCTCTTC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 268839 1.2e-09 6_[+1]_478 261180 1.5e-07 416_[+1]_68 20567 7.4e-07 15_[+1]_469 268943 1.1e-06 17_[+1]_467 25187 1.1e-06 62_[+1]_422 269534 2.1e-06 44_[+1]_440 25548 2.5e-06 441_[+1]_43 264869 3.7e-06 223_[+1]_261 24854 7.3e-06 198_[+1]_286 22185 7.8e-06 271_[+1]_213 262821 1e-05 131_[+1]_353 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=16 seqs=11 268839 ( 7) GATGGGGGAGTCAAAG 1 261180 ( 417) GGAGGGGGAGTGAGAG 1 20567 ( 16) GATGGAGGTGTCGAGG 1 268943 ( 18) GGAGGAGGCGTGGAAG 1 25187 ( 63) GGAGTGGGTGGCAGAG 1 269534 ( 45) GGTGGTGGAGTGACGG 1 25548 ( 442) GACGATGGAGGCACCG 1 264869 ( 224) GAAGAGGGTGGCAGCT 1 24854 ( 199) GGAGACGGAGACGAAT 1 22185 ( 272) AACGACGGCGGCAAAG 1 262821 ( 132) CATGGTGCTGTCGAAG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 5335 bayes= 9.27461 E= 5.2e-001 -158 -131 174 -1010 100 -1010 89 -1010 74 -31 -1010 50 -1010 -1010 203 -1010 41 -1010 115 -149 -59 -31 57 9 -1010 -1010 203 -1010 -1010 -131 189 -1010 74 -31 -1010 50 -1010 -1010 203 -1010 -158 -1010 57 109 -1010 169 15 -1010 122 -1010 57 -1010 100 -31 15 -1010 122 -31 -43 -1010 -1010 -1010 174 -49 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 11 E= 5.2e-001 0.090909 0.090909 0.818182 0.000000 0.545455 0.000000 0.454545 0.000000 0.454545 0.181818 0.000000 0.363636 0.000000 0.000000 1.000000 0.000000 0.363636 0.000000 0.545455 0.090909 0.181818 0.181818 0.363636 0.272727 0.000000 0.000000 1.000000 0.000000 0.000000 0.090909 0.909091 0.000000 0.454545 0.181818 0.000000 0.363636 0.000000 0.000000 1.000000 0.000000 0.090909 0.000000 0.363636 0.545455 0.000000 0.727273 0.272727 0.000000 0.636364 0.000000 0.363636 0.000000 0.545455 0.181818 0.272727 0.000000 0.636364 0.181818 0.181818 0.000000 0.000000 0.000000 0.818182 0.181818 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- G[AG][AT]G[GA][GT]GG[AT]G[TG][CG][AG][AG]AG -------------------------------------------------------------------------------- Time 1.08 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 15 sites = 5 llr = 75 E-value = 1.0e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A ::a::::::82:442 pos.-specific C :6:a2:aa::88:28 probability G :4::68::a2:262: matrix T a:::22:::::::2: bits 2.1 * ** 1.9 * ** *** 1.7 * ** *** 1.5 * ** *** * Relative 1.3 * ** ******* * Entropy 1.1 **** ******** * (21.8 bits) 0.9 **** ******** * 0.6 ************* * 0.4 ************* * 0.2 ************* * 0.0 --------------- Multilevel TCACGGCCGACCGAC consensus G CT GAGACA sequence T G T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------- 268943 186 1.15e-08 TTTTTAGAGC TCACGGCCGACGGAC GTGACGGAGG 25548 386 2.33e-08 AGCGGTTGGT TGACCGCCGACCAAC GTGTCTCCAA 269534 220 5.15e-08 CCACTGACCA TGACGGCCGGCCGTC TGTGTTGATG 264869 359 1.21e-07 TACTCTTGTT TCACTGCCGACCGGA CTGGGAAAGA 24854 358 2.31e-07 AGCACAGAAA TCACGTCCGAACACC TTATATCGAT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 268943 1.1e-08 185_[+2]_300 25548 2.3e-08 385_[+2]_100 269534 5.1e-08 219_[+2]_266 264869 1.2e-07 358_[+2]_127 24854 2.3e-07 357_[+2]_128 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=15 seqs=5 268943 ( 186) TCACGGCCGACGGAC 1 25548 ( 386) TGACCGCCGACCAAC 1 269534 ( 220) TGACGGCCGGCCGTC 1 264869 ( 359) TCACTGCCGACCGGA 1 24854 ( 358) TCACGTCCGAACACC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 5346 bayes= 10.3127 E= 1.0e+002 -897 -897 -897 196 -897 141 70 -897 187 -897 -897 -897 -897 215 -897 -897 -897 -17 129 -36 -897 -897 170 -36 -897 215 -897 -897 -897 215 -897 -897 -897 -897 202 -897 155 -897 -29 -897 -45 182 -897 -897 -897 182 -29 -897 55 -897 129 -897 55 -17 -29 -36 -45 182 -897 -897 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 5 E= 1.0e+002 0.000000 0.000000 0.000000 1.000000 0.000000 0.600000 0.400000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.200000 0.600000 0.200000 0.000000 0.000000 0.800000 0.200000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.800000 0.000000 0.200000 0.000000 0.200000 0.800000 0.000000 0.000000 0.000000 0.800000 0.200000 0.000000 0.400000 0.000000 0.600000 0.000000 0.400000 0.200000 0.200000 0.200000 0.200000 0.800000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- T[CG]AC[GCT][GT]CCG[AG][CA][CG][GA][ACGT][CA] -------------------------------------------------------------------------------- Time 2.06 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 15 sites = 7 llr = 94 E-value = 1.5e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A ::::16:a9134993 pos.-specific C 3:919:7::9:::17 probability G :1:::1::1:7:1:: matrix T 7919:33::::6::: bits 2.1 1.9 * 1.7 * 1.5 *** * * Relative 1.3 **** **** *** Entropy 1.1 ***** ***** *** (19.3 bits) 0.9 ***** ********* 0.6 *************** 0.4 *************** 0.2 *************** 0.0 --------------- Multilevel TTCTCACAACGTAAC consensus C TT AA A sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------- 261180 273 1.90e-09 ACAGATCAAC TTCTCACAACGAAAC CTCGGATACA 20567 421 5.43e-08 TTGTCTTCTA TTCTCGTAACGTAAC AGAAGACGAG 268839 102 3.51e-07 GTGCTGTCGA TTCCAACAACGAAAC TAGTGCATCT 25548 425 3.81e-07 CAACAGCGCA TGCTCTCAACGTACC ACGACGATGG 24854 458 5.02e-07 CCTCCCGTTG CTCTCATAACAAAAA TTTCGCTCCT 268943 403 6.72e-07 TGACACCTGC TTTTCACAGCATAAC CTTGATTGGA 262821 380 2.28e-06 GACTGTCATA CTCTCTCAAAGTGAA CCAAGAGTTT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 261180 1.9e-09 272_[+3]_213 20567 5.4e-08 420_[+3]_65 268839 3.5e-07 101_[+3]_384 25548 3.8e-07 424_[+3]_61 24854 5e-07 457_[+3]_28 268943 6.7e-07 402_[+3]_83 262821 2.3e-06 379_[+3]_106 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=15 seqs=7 261180 ( 273) TTCTCACAACGAAAC 1 20567 ( 421) TTCTCGTAACGTAAC 1 268839 ( 102) TTCCAACAACGAAAC 1 25548 ( 425) TGCTCTCAACGTACC 1 24854 ( 458) CTCTCATAACAAAAA 1 268943 ( 403) TTTTCACAGCATAAC 1 262821 ( 380) CTCTCTCAAAGTGAA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 5346 bayes= 10.1814 E= 1.5e+002 -945 34 -945 148 -945 -945 -78 174 -945 193 -945 -84 -945 -66 -945 174 -93 193 -945 -945 107 -945 -78 16 -945 166 -945 16 187 -945 -945 -945 165 -945 -78 -945 -93 193 -945 -945 7 -945 154 -945 65 -945 -945 116 165 -945 -78 -945 165 -66 -945 -945 7 166 -945 -945 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 7 E= 1.5e+002 0.000000 0.285714 0.000000 0.714286 0.000000 0.000000 0.142857 0.857143 0.000000 0.857143 0.000000 0.142857 0.000000 0.142857 0.000000 0.857143 0.142857 0.857143 0.000000 0.000000 0.571429 0.000000 0.142857 0.285714 0.000000 0.714286 0.000000 0.285714 1.000000 0.000000 0.000000 0.000000 0.857143 0.000000 0.142857 0.000000 0.142857 0.857143 0.000000 0.000000 0.285714 0.000000 0.714286 0.000000 0.428571 0.000000 0.000000 0.571429 0.857143 0.000000 0.142857 0.000000 0.857143 0.142857 0.000000 0.000000 0.285714 0.714286 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [TC]TCTC[AT][CT]AAC[GA][TA]AA[CA] -------------------------------------------------------------------------------- Time 3.04 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 20567 6.15e-07 15_[+1(7.38e-07)]_389_\ [+3(5.43e-08)]_65 22185 4.75e-02 271_[+1(7.79e-06)]_213 24854 2.82e-08 198_[+1(7.33e-06)]_143_\ [+2(2.31e-07)]_85_[+3(5.02e-07)]_28 25187 6.25e-03 62_[+1(1.12e-06)]_422 25548 9.84e-10 385_[+2(2.33e-08)]_24_\ [+3(3.81e-07)]_2_[+1(2.52e-06)]_43 261180 1.97e-08 272_[+3(1.90e-09)]_129_\ [+1(1.49e-07)]_68 262821 2.38e-04 131_[+1(1.03e-05)]_232_\ [+3(2.28e-06)]_106 264869 1.23e-05 223_[+1(3.73e-06)]_119_\ [+2(1.21e-07)]_127 268839 2.68e-08 6_[+1(1.17e-09)]_79_[+3(3.51e-07)]_\ 106_[+1(1.40e-05)]_74_[+1(5.37e-05)]_59_[+1(2.74e-06)]_97 268943 4.06e-10 17_[+1(1.12e-06)]_152_\ [+2(1.15e-08)]_1_[+2(6.15e-05)]_186_[+3(6.72e-07)]_83 269534 1.54e-06 44_[+1(2.14e-06)]_159_\ [+2(5.15e-08)]_266 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************