******************************************************************************** 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/317/317.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 42920 1.0000 500 47108 1.0000 500 47706 1.0000 500 48297 1.0000 500 50239 1.0000 500 44298 1.0000 500 45639 1.0000 500 45879 1.0000 500 50363 1.0000 500 48332 1.0000 500 31979 1.0000 500 43128 1.0000 500 44614 1.0000 500 46702 1.0000 500 39652 1.0000 500 50107 1.0000 500 39214 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/317/317.seqs.fa -oc motifs/317 -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 0.271 C 0.229 G 0.222 T 0.278 Background letter frequencies (from dataset with add-one prior applied): A 0.271 C 0.229 G 0.222 T 0.278 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 20 sites = 10 llr = 141 E-value = 4.7e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 2:116853:317a82278a7 pos.-specific C ::67:144:::1:23::::: probability G 2:3::1::a561::482::2 matrix T 6a:24:13:231::1:12:1 bits 2.2 * 2.0 * * * * 1.7 * * * * 1.5 * * * * Relative 1.3 * * ** * * Entropy 1.1 * * * ** * ** (20.4 bits) 0.9 ***** * ** ***** 0.7 ******* * **** ***** 0.4 ************** ***** 0.2 ******************** 0.0 -------------------- Multilevel TTCCAAACGGGAAAGGAAAA consensus A GTT CA AT CCAGT G sequence G T T A -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------------- 50239 234 1.09e-09 AGACTAATCT TTACAACAGGGAAAGGAAAA TTGGAGGAAC 42920 443 6.79e-09 AGCACCCCAT TTCCAAAAGAGAAAAAAAAA TCGTTCTTGA 39214 37 1.60e-08 AAAGTAAGGC ATGCAACCGTGAAACGAAAG GCATGCGCAG 47108 12 7.83e-08 CAGTGGATTT GTCCTACTGATAAAGGTAAA ATGTGCTTCT 45879 331 1.04e-07 TCTGGAAGCT GTCCTAACGGTGAACGATAA AACTGGAAGG 50107 145 2.29e-07 GGAGCGAGAA TTCTTAAAGGAAACAGAAAA CCAAATTCAT 48297 384 2.92e-07 TGTAGCTTTA TTGATATTGGGAAACGAAAG TGCTGCGACT 48332 76 4.97e-07 AGAATTCGGT ATGCAAATGGTCAAGGGTAA CCTCTTTCGA 44298 186 6.16e-07 ACAGTCTGAC TTCTAGACGAGAAATGAAAT CAACGGAACT 43128 264 1.50e-06 CTCTCCGTCC TTCCACCCGTGTACGAGAAA CAGAAGGCAC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 50239 1.1e-09 233_[+1]_247 42920 6.8e-09 442_[+1]_38 39214 1.6e-08 36_[+1]_444 47108 7.8e-08 11_[+1]_469 45879 1e-07 330_[+1]_150 50107 2.3e-07 144_[+1]_336 48297 2.9e-07 383_[+1]_97 48332 5e-07 75_[+1]_405 44298 6.2e-07 185_[+1]_295 43128 1.5e-06 263_[+1]_217 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=20 seqs=10 50239 ( 234) TTACAACAGGGAAAGGAAAA 1 42920 ( 443) TTCCAAAAGAGAAAAAAAAA 1 39214 ( 37) ATGCAACCGTGAAACGAAAG 1 47108 ( 12) GTCCTACTGATAAAGGTAAA 1 45879 ( 331) GTCCTAACGGTGAACGATAA 1 50107 ( 145) TTCTTAAAGGAAACAGAAAA 1 48297 ( 384) TTGATATTGGGAAACGAAAG 1 48332 ( 76) ATGCAAATGGTCAAGGGTAA 1 44298 ( 186) TTCTAGACGAGAAATGAAAT 1 43128 ( 264) TTCCACCCGTGTACGAGAAA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 8177 bayes= 9.92548 E= 4.7e+001 -44 -997 -15 111 -997 -997 -997 185 -143 139 43 -997 -143 161 -997 -47 115 -997 -997 53 156 -119 -115 -997 88 80 -997 -147 15 80 -997 11 -997 -997 217 -997 15 -997 117 -47 -143 -997 143 11 137 -119 -115 -147 188 -997 -997 -997 156 -19 -997 -997 -44 39 85 -147 -44 -997 185 -997 137 -997 -15 -147 156 -997 -997 -47 188 -997 -997 -997 137 -997 -15 -147 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 10 E= 4.7e+001 0.200000 0.000000 0.200000 0.600000 0.000000 0.000000 0.000000 1.000000 0.100000 0.600000 0.300000 0.000000 0.100000 0.700000 0.000000 0.200000 0.600000 0.000000 0.000000 0.400000 0.800000 0.100000 0.100000 0.000000 0.500000 0.400000 0.000000 0.100000 0.300000 0.400000 0.000000 0.300000 0.000000 0.000000 1.000000 0.000000 0.300000 0.000000 0.500000 0.200000 0.100000 0.000000 0.600000 0.300000 0.700000 0.100000 0.100000 0.100000 1.000000 0.000000 0.000000 0.000000 0.800000 0.200000 0.000000 0.000000 0.200000 0.300000 0.400000 0.100000 0.200000 0.000000 0.800000 0.000000 0.700000 0.000000 0.200000 0.100000 0.800000 0.000000 0.000000 0.200000 1.000000 0.000000 0.000000 0.000000 0.700000 0.000000 0.200000 0.100000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [TAG]T[CG][CT][AT]A[AC][CAT]G[GAT][GT]AA[AC][GCA][GA][AG][AT]A[AG] -------------------------------------------------------------------------------- Time 2.77 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 18 sites = 4 llr = 76 E-value = 2.2e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A :::85:a::a3:85:::: pos.-specific C :a::3::8::5::5:5:3 probability G a:a::8:3a:3a3:a3:8 matrix T :::333:::::::::3a: bits 2.2 *** * * * 2.0 *** * ** * * * 1.7 *** * ** * * * 1.5 *** * ** * * * Relative 1.3 *** ***** * * ** Entropy 1.1 **** ***** **** ** (27.3 bits) 0.9 **** ***** **** ** 0.7 **** ************* 0.4 ****************** 0.2 ****************** 0.0 ------------------ Multilevel GCGAAGACGACGAAGCTG consensus TCT G A GC G C sequence T G T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------------ 44614 78 2.06e-11 ATGTGCAAGG GCGACGACGACGACGCTG TTGTTATTGG 46702 20 1.10e-09 TCTTTCTTCT GCGATGACGAAGAAGGTG CAGGATCAGG 45639 214 3.63e-09 AAGATTGATA GCGAATAGGACGAAGTTG AAACCATAAG 39214 200 5.29e-09 AGGAGTGACC GCGTAGACGAGGGCGCTC CGTATTTCCG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 44614 2.1e-11 77_[+2]_405 46702 1.1e-09 19_[+2]_463 45639 3.6e-09 213_[+2]_269 39214 5.3e-09 199_[+2]_283 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=18 seqs=4 44614 ( 78) GCGACGACGACGACGCTG 1 46702 ( 20) GCGATGACGAAGAAGGTG 1 45639 ( 214) GCGAATAGGACGAAGTTG 1 39214 ( 200) GCGTAGACGAGGGCGCTC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 18 n= 8211 bayes= 11.0026 E= 2.2e+002 -865 -865 217 -865 -865 212 -865 -865 -865 -865 217 -865 147 -865 -865 -15 88 13 -865 -15 -865 -865 175 -15 188 -865 -865 -865 -865 171 17 -865 -865 -865 217 -865 188 -865 -865 -865 -12 112 17 -865 -865 -865 217 -865 147 -865 17 -865 88 112 -865 -865 -865 -865 217 -865 -865 112 17 -15 -865 -865 -865 185 -865 13 175 -865 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 18 nsites= 4 E= 2.2e+002 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.750000 0.000000 0.000000 0.250000 0.500000 0.250000 0.000000 0.250000 0.000000 0.000000 0.750000 0.250000 1.000000 0.000000 0.000000 0.000000 0.000000 0.750000 0.250000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.250000 0.500000 0.250000 0.000000 0.000000 0.000000 1.000000 0.000000 0.750000 0.000000 0.250000 0.000000 0.500000 0.500000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.500000 0.250000 0.250000 0.000000 0.000000 0.000000 1.000000 0.000000 0.250000 0.750000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- GCG[AT][ACT][GT]A[CG]GA[CAG]G[AG][AC]G[CGT]T[GC] -------------------------------------------------------------------------------- Time 5.25 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 12 sites = 5 llr = 71 E-value = 2.6e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A :8:a4::a:::: pos.-specific C a24:::::a2:: probability G ::6:::a:::a: matrix T ::::6a:::8:a bits 2.2 * * * * 2.0 * * **** ** 1.7 * * **** ** 1.5 * * **** ** Relative 1.3 ** * **** ** Entropy 1.1 **** ******* (20.5 bits) 0.9 ************ 0.7 ************ 0.4 ************ 0.2 ************ 0.0 ------------ Multilevel CAGATTGACTGT consensus CC A C sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 31979 360 6.82e-08 GGCAGCCGTA CAGATTGACTGT GAAGCATTTA 48332 285 1.35e-07 CGGGACACAC CAGAATGACTGT TGCCAACAAA 42920 268 2.05e-07 GTTGGAGGCG CACATTGACTGT GACTGTGAGT 39214 13 4.42e-07 ACAGGGTCAT CAGAATGACCGT GGAAAGTAAG 46702 326 6.16e-07 TGCCTCGAAT CCCATTGACTGT GAGCACAGAG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 31979 6.8e-08 359_[+3]_129 48332 1.3e-07 284_[+3]_204 42920 2.1e-07 267_[+3]_221 39214 4.4e-07 12_[+3]_476 46702 6.2e-07 325_[+3]_163 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=12 seqs=5 31979 ( 360) CAGATTGACTGT 1 48332 ( 285) CAGAATGACTGT 1 42920 ( 268) CACATTGACTGT 1 39214 ( 13) CAGAATGACCGT 1 46702 ( 326) CCCATTGACTGT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 8313 bayes= 10.95 E= 2.6e+002 -897 212 -897 -897 156 -19 -897 -897 -897 80 143 -897 188 -897 -897 -897 56 -897 -897 111 -897 -897 -897 185 -897 -897 217 -897 188 -897 -897 -897 -897 212 -897 -897 -897 -19 -897 152 -897 -897 217 -897 -897 -897 -897 185 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 5 E= 2.6e+002 0.000000 1.000000 0.000000 0.000000 0.800000 0.200000 0.000000 0.000000 0.000000 0.400000 0.600000 0.000000 1.000000 0.000000 0.000000 0.000000 0.400000 0.000000 0.000000 0.600000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.200000 0.000000 0.800000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- C[AC][GC]A[TA]TGAC[TC]GT -------------------------------------------------------------------------------- Time 8.03 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 42920 1.93e-09 73_[+2(3.39e-05)]_176_\ [+3(2.05e-07)]_163_[+1(6.79e-09)]_38 47108 7.78e-05 11_[+1(7.83e-08)]_469 47706 5.88e-02 239_[+2(7.67e-05)]_243 48297 9.17e-04 383_[+1(2.92e-07)]_97 50239 1.42e-05 233_[+1(1.09e-09)]_247 44298 7.33e-03 185_[+1(6.16e-07)]_295 45639 3.70e-05 213_[+2(3.63e-09)]_269 45879 8.31e-04 330_[+1(1.04e-07)]_150 50363 8.46e-01 500 48332 1.53e-06 75_[+1(4.97e-07)]_189_\ [+3(1.35e-07)]_204 31979 4.16e-04 359_[+3(6.82e-08)]_129 43128 2.29e-03 263_[+1(1.50e-06)]_217 44614 5.13e-07 77_[+2(2.06e-11)]_405 46702 3.90e-08 19_[+2(1.10e-09)]_288_\ [+3(6.16e-07)]_163 39652 5.11e-01 500 50107 8.77e-04 144_[+1(2.29e-07)]_336 39214 2.47e-12 12_[+3(4.42e-07)]_12_[+1(1.60e-08)]_\ 143_[+2(5.29e-09)]_283 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************