******************************************************************************** MEME - Motif discovery tool ******************************************************************************** MEME version 4.11.0 (Release date: Thu Nov 26 17:48:49 2015 +1000) For further information on how to interpret these results or to get a copy of the MEME software please access http://meme-suite.org . 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-suite.org . ******************************************************************************** ******************************************************************************** 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= rna_samples.fa ALPHABET= ACGU Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ ce1cg 1.0000 105 ara 1.0000 105 bglr1 1.0000 105 crp 1.0000 105 cya 1.0000 105 deop2 1.0000 105 gale 1.0000 105 ******************************************************************************** ******************************************************************************** COMMAND LINE SUMMARY ******************************************************************************** This information can also be useful in the event you wish to report a problem with the MEME software. command: meme rna_samples.fa -nmotifs 2 -rna -mod oops model: mod= oops nmotifs= 2 evt= inf object function= E-value of product of p-values width: minw= 8 maxw= 50 width: wg= 11 ws= 1 endgaps= yes nsites: minsites= 7 maxsites= 7 wnsites= 0.8 theta: 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= 735 N= 7 shuffle= -1 sample: seed= 0 ctfrac= -1 maxwords= -1 Letter frequencies in dataset: A 0.313 C 0.174 G 0.190 U 0.322 Background letter frequencies (from dataset with add-one prior applied): A 0.313 C 0.175 G 0.191 U 0.322 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 19 sites = 7 llr = 97 E-value = 7.2e-003 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A :::364:14:1::91a116 pos.-specific C ::1:1:93:4::9:7:4:: probability G :3:6:116137:11::::: matrix U a79134::431a::1:494 bits 2.5 2.3 2.0 * * 1.8 * * * Relative 1.5 * * ** * Entropy 1.3 * * * *** * (19.9 bits) 1.0 *** ** ****** * 0.8 **** ** ******* ** 0.5 ***** ** ********** 0.3 ******************* 0.0 ------------------- Multilevel UUUGAACGACGUCACACUA consensus G AUU CUG U U sequence U -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------------- ara 58 1.37e-09 ACAUUGAUUA UUUGCACGGCGUCACACUU UGCUAUGCCA gale 45 3.90e-08 AUUCCACUAA UUUAUUCCAUGUCACACUU UUCGCAUCUU deop2 10 1.66e-07 AGUGAAUUA UUUGAACCAGAUCGCAUUA CAGUGAUGCA crp 66 2.14e-07 ACUGCAUGUA UGCAAAGGACGUCACAUUA CCGUGCAGUA bglr1 79 6.30e-07 AGUUAAUAAC UGUGAGCAUGGUCAUAUUU UUAUCAAU ce1cg 64 6.75e-07 AGACUGUUUU UUUGAUCGUUUUCACAAAA AUGGAAGUCC cya 79 7.76e-07 UUUUAGACCA UUUUUUCGUCGUGAAACUA AAAAAACC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- ara 1.4e-09 57_[1]_29 gale 3.9e-08 44_[1]_42 deop2 1.7e-07 9_[1]_77 crp 2.1e-07 65_[1]_21 bglr1 6.3e-07 78_[1]_8 ce1cg 6.8e-07 63_[1]_23 cya 7.8e-07 78_[1]_8 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=19 seqs=7 ara ( 58) UUUGCACGGCGUCACACUU 1 gale ( 45) UUUAUUCCAUGUCACACUU 1 deop2 ( 10) UUUGAACCAGAUCGCAUUA 1 crp ( 66) UGCAAAGGACGUCACAUUA 1 bglr1 ( 79) UGUGAGCAUGGUCAUAUUU 1 ce1cg ( 64) UUUGAUCGUUUUCACAAAA 1 cya ( 79) UUUUUUCGUCGUGAAACUA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 19 n= 609 bayes= 6.42626 E= 7.2e-003 -945 -945 -945 163 -945 -945 58 115 -945 -29 -945 141 -13 -945 158 -117 87 -29 -945 -17 45 -945 -42 41 -945 229 -42 -945 -113 71 158 -945 45 -945 -42 41 -945 129 58 -17 -113 -945 190 -117 -945 -945 -945 163 -945 229 -42 -945 145 -945 -42 -945 -113 203 -945 -117 168 -945 -945 -945 -113 129 -945 41 -113 -945 -945 141 87 -945 -945 41 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 19 nsites= 7 E= 7.2e-003 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.285714 0.714286 0.000000 0.142857 0.000000 0.857143 0.285714 0.000000 0.571429 0.142857 0.571429 0.142857 0.000000 0.285714 0.428571 0.000000 0.142857 0.428571 0.000000 0.857143 0.142857 0.000000 0.142857 0.285714 0.571429 0.000000 0.428571 0.000000 0.142857 0.428571 0.000000 0.428571 0.285714 0.285714 0.142857 0.000000 0.714286 0.142857 0.000000 0.000000 0.000000 1.000000 0.000000 0.857143 0.142857 0.000000 0.857143 0.000000 0.142857 0.000000 0.142857 0.714286 0.000000 0.142857 1.000000 0.000000 0.000000 0.000000 0.142857 0.428571 0.000000 0.428571 0.142857 0.000000 0.000000 0.857143 0.571429 0.000000 0.000000 0.428571 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- U[UG]U[GA][AU][AU]C[GC][AU][CGU]GUCACA[CU]U[AU] -------------------------------------------------------------------------------- Time 0.13 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 9 sites = 7 llr = 54 E-value = 7.6e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A 11:6:::1a pos.-specific C :4::::71: probability G 9:43:a:1: matrix U :461a:36: bits 2.5 2.3 * 2.0 * 1.8 * * * Relative 1.5 * *** * Entropy 1.3 * *** * (11.1 bits) 1.0 * * *** * 0.8 * * *** * 0.5 ******* * 0.3 ********* 0.0 --------- Multilevel GCUAUGCUA consensus UGG U sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------- crp 13 7.14e-06 CAAAGCGAAA GCUAUGCUA AAACAGUCAG gale 75 2.50e-05 UCGCAUCUUU GUUAUGCUA UGGUUAUUUC ara 78 3.26e-05 GUCACACUUU GCUAUGCCA UAGCAUUUUU deop2 31 1.10e-04 UCGCAUUACA GUGAUGCAA ACUUGUAAGU cya 1 1.73e-04 . ACGGUGCUA CACUUGUAUG ce1cg 44 3.33e-04 AGAAUAGCGC GUGGUGUGA AAGACUGUUU bglr1 27 8.67e-04 UAAUUAUUGG GAUUUGUUA UAUAUAACUU -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- crp 7.1e-06 12_[2]_84 gale 2.5e-05 74_[2]_22 ara 3.3e-05 77_[2]_19 deop2 0.00011 30_[2]_66 cya 0.00017 [2]_96 ce1cg 0.00033 43_[2]_53 bglr1 0.00087 26_[2]_70 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=9 seqs=7 crp ( 13) GCUAUGCUA 1 gale ( 75) GUUAUGCUA 1 ara ( 78) GCUAUGCCA 1 deop2 ( 31) GUGAUGCAA 1 cya ( 1) ACGGUGCUA 1 ce1cg ( 44) GUGGUGUGA 1 bglr1 ( 27) GAUUUGUUA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 9 n= 679 bayes= 6.58496 E= 7.6e+002 -113 -945 217 -945 -113 129 -945 41 -945 -945 117 83 87 -945 58 -117 -945 -945 -945 163 -945 -945 239 -945 -945 203 -945 -17 -113 -29 -42 83 168 -945 -945 -945 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 9 nsites= 7 E= 7.6e+002 0.142857 0.000000 0.857143 0.000000 0.142857 0.428571 0.000000 0.428571 0.000000 0.000000 0.428571 0.571429 0.571429 0.000000 0.285714 0.142857 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.714286 0.000000 0.285714 0.142857 0.142857 0.142857 0.571429 1.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- G[CU][UG][AG]UG[CU]UA -------------------------------------------------------------------------------- Time 0.17 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- ce1cg 2.65e-05 63_[1(6.75e-07)]_23 ara 8.53e-09 57_[1(1.37e-09)]_1_[2(3.26e-05)]_19 bglr1 5.90e-05 78_[1(6.30e-07)]_8 crp 2.47e-07 12_[2(7.14e-06)]_44_[1(2.14e-07)]_\ 21 cya 1.65e-05 78_[1(7.76e-07)]_8 deop2 2.56e-06 9_[1(1.66e-07)]_77 gale 1.61e-07 44_[1(3.90e-08)]_11_[2(2.50e-05)]_\ 22 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (2) found. ******************************************************************************** CPU: pc ********************************************************************************