******************************************************************************** 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/400/400.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 9223 1.0000 500 13975 1.0000 500 28797 1.0000 500 3834 1.0000 500 14549 1.0000 500 1174 1.0000 500 49097 1.0000 500 5934 1.0000 500 5951 1.0000 500 34716 1.0000 500 45561 1.0000 500 46233 1.0000 500 42660 1.0000 500 48708 1.0000 500 32274 1.0000 500 48941 1.0000 500 47335 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/400/400.seqs.fa -oc motifs/400 -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 0.275 C 0.251 G 0.212 T 0.262 Background letter frequencies (from dataset with add-one prior applied): A 0.275 C 0.251 G 0.212 T 0.262 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 12 sites = 10 llr = 115 E-value = 5.9e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A ::9:189:a159 pos.-specific C 76::7::a::31 probability G 341:22:::92: matrix T :::a::1::::: bits 2.2 2.0 * * 1.8 * *** 1.6 * *** Relative 1.3 ** **** * Entropy 1.1 **** ***** * (16.6 bits) 0.9 ********** * 0.7 ********** * 0.4 ************ 0.2 ************ 0.0 ------------ Multilevel CCATCAACAGAA consensus GG GG C sequence G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 3834 424 9.54e-08 GACGGAGGTC CCATCAACAGAA TGGTATCCAA 14549 71 4.90e-07 CTTTGTCCAA CGATCAACAGCA TCCTGTACAC 5951 219 6.21e-07 CGCTTGTCGA CGATCAACAGGA TAGCGACTCC 5934 165 8.48e-07 ACAGTTTACA GCATCAACAGCA AATTTGCCAG 45561 474 1.10e-06 TCAATCACAA CGATGAACAGAA CCAAAGCTGA 28797 373 4.08e-06 CACTGTCTTC GCATAAACAGAA CTCCCAGTCC 48941 223 6.18e-06 TCGTCTCAGT CCATCGACAGAC GAAACAACAG 46233 149 8.08e-06 TGCTTAAGCT CCATGAACAAAA AGTGTTGTGC 1174 381 8.08e-06 AACTACAGCG GGGTCAACAGGA CTATAGATGA 9223 365 8.74e-06 GAGAACAACG CCATCGTCAGCA ACAGCTCCCG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 3834 9.5e-08 423_[+1]_65 14549 4.9e-07 70_[+1]_418 5951 6.2e-07 218_[+1]_270 5934 8.5e-07 164_[+1]_324 45561 1.1e-06 473_[+1]_15 28797 4.1e-06 372_[+1]_116 48941 6.2e-06 222_[+1]_266 46233 8.1e-06 148_[+1]_340 1174 8.1e-06 380_[+1]_108 9223 8.7e-06 364_[+1]_124 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=12 seqs=10 3834 ( 424) CCATCAACAGAA 1 14549 ( 71) CGATCAACAGCA 1 5951 ( 219) CGATCAACAGGA 1 5934 ( 165) GCATCAACAGCA 1 45561 ( 474) CGATGAACAGAA 1 28797 ( 373) GCATAAACAGAA 1 48941 ( 223) CCATCGACAGAC 1 46233 ( 149) CCATGAACAAAA 1 1174 ( 381) GGGTCAACAGGA 1 9223 ( 365) CCATCGTCAGCA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 8313 bayes= 9.94931 E= 5.9e+000 -997 148 50 -997 -997 126 92 -997 171 -997 -108 -997 -997 -997 -997 193 -146 148 -8 -997 154 -997 -8 -997 171 -997 -997 -139 -997 200 -997 -997 186 -997 -997 -997 -146 -997 209 -997 86 26 -8 -997 171 -132 -997 -997 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 10 E= 5.9e+000 0.000000 0.700000 0.300000 0.000000 0.000000 0.600000 0.400000 0.000000 0.900000 0.000000 0.100000 0.000000 0.000000 0.000000 0.000000 1.000000 0.100000 0.700000 0.200000 0.000000 0.800000 0.000000 0.200000 0.000000 0.900000 0.000000 0.000000 0.100000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.100000 0.000000 0.900000 0.000000 0.500000 0.300000 0.200000 0.000000 0.900000 0.100000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [CG][CG]AT[CG][AG]ACAG[ACG]A -------------------------------------------------------------------------------- Time 3.08 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 16 sites = 5 llr = 79 E-value = 1.9e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A ::2:::a:::a6:2:: pos.-specific C :a:4:2:4:2:::2:6 probability G ::86:8::a8:22224 matrix T a:::a::6:::2848: bits 2.2 * 2.0 ** * * 1.8 ** * * * * 1.6 ** *** *** Relative 1.3 *** *** *** * * Entropy 1.1 ******* *** * ** (22.7 bits) 0.9 *********** * ** 0.7 ************* ** 0.4 ************* ** 0.2 ************* ** 0.0 ---------------- Multilevel TCGGTGATGGAATTTC consensus AC C C C GGAGG sequence T C G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 5934 321 2.11e-09 TAAGGGTGTG TCGGTGATGGAGTTTC GGACAGAGGA 47335 469 3.65e-08 TTCTGTGACG TCAGTGATGGATTTTC TTTCTTCTCT 3834 282 5.47e-08 TGGACCGCCA TCGCTGACGGAAGATG TTGGTAAGAG 32274 182 6.45e-08 ATGTCGCGCG TCGCTGACGCAATGTG TCTTTATATG 48708 113 7.44e-08 ATTGCTATTA TCGGTCATGGAATCGC TTACGGTGAA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 5934 2.1e-09 320_[+2]_164 47335 3.6e-08 468_[+2]_16 3834 5.5e-08 281_[+2]_203 32274 6.4e-08 181_[+2]_303 48708 7.4e-08 112_[+2]_372 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=16 seqs=5 5934 ( 321) TCGGTGATGGAGTTTC 1 47335 ( 469) TCAGTGATGGATTTTC 1 3834 ( 282) TCGCTGACGGAAGATG 1 32274 ( 182) TCGCTGACGCAATGTG 1 48708 ( 113) TCGGTCATGGAATCGC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 8245 bayes= 10.9382 E= 1.9e+003 -897 -897 -897 193 -897 199 -897 -897 -46 -897 192 -897 -897 67 150 -897 -897 -897 -897 193 -897 -32 192 -897 186 -897 -897 -897 -897 67 -897 119 -897 -897 224 -897 -897 -32 192 -897 186 -897 -897 -897 112 -897 -8 -39 -897 -897 -8 161 -46 -32 -8 61 -897 -897 -8 161 -897 126 92 -897 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 5 E= 1.9e+003 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.200000 0.000000 0.800000 0.000000 0.000000 0.400000 0.600000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.200000 0.800000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.400000 0.000000 0.600000 0.000000 0.000000 1.000000 0.000000 0.000000 0.200000 0.800000 0.000000 1.000000 0.000000 0.000000 0.000000 0.600000 0.000000 0.200000 0.200000 0.000000 0.000000 0.200000 0.800000 0.200000 0.200000 0.200000 0.400000 0.000000 0.000000 0.200000 0.800000 0.000000 0.600000 0.400000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- TC[GA][GC]T[GC]A[TC]G[GC]A[AGT][TG][TACG][TG][CG] -------------------------------------------------------------------------------- Time 5.91 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 12 sites = 5 llr = 69 E-value = 8.8e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A ::a:6:4:4a6: pos.-specific C :::a2::::::: probability G aa::2a:86:4a matrix T ::::::62:::: bits 2.2 ** * * 2.0 ** * * * 1.8 **** * * * 1.6 **** * * * * Relative 1.3 **** * * * * Entropy 1.1 **** * ***** (19.8 bits) 0.9 **** ******* 0.7 ************ 0.4 ************ 0.2 ************ 0.0 ------------ Multilevel GGACAGTGGAAG consensus C ATA G sequence G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 5934 337 9.63e-08 ATGGAGTTTC GGACAGAGGAAG CTCTGTTAAA 48708 378 3.27e-07 AATTTCGGTC GGACAGAGAAAG TCTCTGCCTG 3834 455 3.51e-07 AAATTAATCA GGACCGTGGAGG TGTAGTCTTT 45561 313 5.44e-07 TTGGGAAAGC GGACAGTTGAAG CACAGACAAC 14549 255 6.36e-07 GGCAGACAGC GGACGGTGAAGG AAACCAAGCT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 5934 9.6e-08 336_[+3]_152 48708 3.3e-07 377_[+3]_111 3834 3.5e-07 454_[+3]_34 45561 5.4e-07 312_[+3]_176 14549 6.4e-07 254_[+3]_234 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=12 seqs=5 5934 ( 337) GGACAGAGGAAG 1 48708 ( 378) GGACAGAGAAAG 1 3834 ( 455) GGACCGTGGAGG 1 45561 ( 313) GGACAGTTGAAG 1 14549 ( 255) GGACGGTGAAGG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 8313 bayes= 10.95 E= 8.8e+002 -897 -897 224 -897 -897 -897 224 -897 186 -897 -897 -897 -897 199 -897 -897 112 -32 -8 -897 -897 -897 224 -897 54 -897 -897 119 -897 -897 192 -39 54 -897 150 -897 186 -897 -897 -897 112 -897 92 -897 -897 -897 224 -897 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 5 E= 8.8e+002 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.600000 0.200000 0.200000 0.000000 0.000000 0.000000 1.000000 0.000000 0.400000 0.000000 0.000000 0.600000 0.000000 0.000000 0.800000 0.200000 0.400000 0.000000 0.600000 0.000000 1.000000 0.000000 0.000000 0.000000 0.600000 0.000000 0.400000 0.000000 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- GGAC[ACG]G[TA][GT][GA]A[AG]G -------------------------------------------------------------------------------- Time 8.43 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 9223 1.98e-02 364_[+1(8.74e-06)]_124 13975 3.35e-01 500 28797 6.86e-03 372_[+1(4.08e-06)]_116 3834 9.67e-11 190_[+3(2.91e-05)]_79_\ [+2(5.47e-08)]_126_[+1(9.54e-08)]_19_[+3(3.51e-07)]_34 14549 3.54e-06 70_[+1(4.90e-07)]_172_\ [+3(6.36e-07)]_234 1174 2.87e-02 380_[+1(8.08e-06)]_108 49097 1.93e-01 500 5934 1.06e-11 164_[+1(8.48e-07)]_144_\ [+2(2.11e-09)]_[+3(9.63e-08)]_152 5951 4.76e-03 218_[+1(6.21e-07)]_270 34716 5.61e-01 500 45561 1.41e-05 312_[+3(5.44e-07)]_149_\ [+1(1.10e-06)]_15 46233 5.91e-02 148_[+1(8.08e-06)]_340 42660 2.56e-01 321_[+2(8.03e-05)]_163 48708 6.17e-07 112_[+2(7.44e-08)]_249_\ [+3(3.27e-07)]_66_[+3(2.31e-05)]_33 32274 1.37e-03 181_[+2(6.45e-08)]_303 48941 1.23e-02 222_[+1(6.18e-06)]_266 47335 6.09e-04 468_[+2(3.65e-08)]_16 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************