******************************************************************************** MEME - Motif discovery tool ******************************************************************************** MEME version 4.12.0 (Release date: Tue Jun 27 16:22:50 2017 -0700) 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= common/Puf3p-20.s ALPHABET= ACGU Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ sacCer3_chrII_556467_556 1.0000 100 sacCer3_chrIX_312444_312 1.0000 100 sacCer3_chrXIV_443327_44 1.0000 100 sacCer3_chrVII_905741_90 1.0000 100 sacCer3_chrXI_356613_356 1.0000 100 sacCer3_chrI_93336_93436 1.0000 100 sacCer3_chrIV_309697_309 1.0000 100 sacCer3_chrXVI_564127_56 1.0000 100 sacCer3_chrXIII_123147_1 1.0000 100 sacCer3_chrVII_559616_55 1.0000 100 sacCer3_chrVII_395909_39 1.0000 100 sacCer3_chrXI_569507_569 1.0000 100 sacCer3_chrIV_600891_600 1.0000 100 sacCer3_chrII_531780_531 1.0000 100 sacCer3_chrXVI_522715_52 1.0000 100 sacCer3_chrIV_1170148_11 1.0000 100 sacCer3_chrXI_141677_141 1.0000 100 sacCer3_chrIV_1233184_12 1.0000 100 sacCer3_chrXIV_582075_58 1.0000 100 sacCer3_chrIV_915979_916 1.0000 100 ******************************************************************************** ******************************************************************************** COMMAND LINE SUMMARY ******************************************************************************** This information can also be useful in the event you wish to report a problem with the MEME software. command: meme -oc results/motif.meme.puf3p -nostatus -rna -nmotifs 3 common/Puf3p-20.s model: mod= zoops nmotifs= 3 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= 2 maxsites= 20 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= 2000 N= 20 shuffle= -1 sample: seed= 0 ctfrac= -1 maxwords= -1 Letter frequencies in dataset: A 0.295 C 0.191 G 0.137 U 0.377 Background letter frequencies (from dataset with add-one prior applied): A 0.295 C 0.191 G 0.137 U 0.377 ******************************************************************************** ******************************************************************************** MOTIF RAYKKURCMARCMCMRCWKYACC MEME-1 width = 23 sites = 3 llr = 77 E-value = 3.9e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif RAYKKURCMARCMCMRCWKYACC MEME-1 Description -------------------------------------------------------------------------------- Simplified A 3a::::3:3a3:7:73:7::7:: pos.-specific C ::3::::a7::a3a3:a::7:aa probability G 7::77:7:::7::::7::7:3:: matrix U ::733a:::::::::::333::: bits 2.9 2.6 2.3 * * * * ** 2.0 * * * * ** Relative 1.7 ** ** *** * ** ** Entropy 1.4 ** ***** *** * ** * ** (37.2 bits) 1.1 ** ************** ***** 0.9 *********************** 0.6 *********************** 0.3 *********************** 0.0 ----------------------- Multilevel GAUGGUGCCAGCACAGCAGCACC consensus A CUU A A A C CA UUUG sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RAYKKURCMARCMCMRCWKYACC MEME-1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ----------------------- sacCer3_chrI_93336_93436 61 1.21e-13 CCUCAUUUAA GAUGUUGCAAGCCCAGCAGCACC CAGCCCAUCG sacCer3_chrIV_600891_600 67 2.48e-13 AGAAUCCGAC AACGGUACCAGCACAGCUGCACC AACUGAAACC sacCer3_chrXIV_582075_58 65 1.35e-11 UUAAAUAAGA GAUUGUGCCAACACCACAUUGCC UUGAACGCCA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RAYKKURCMARCMCMRCWKYACC MEME-1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- sacCer3_chrI_93336_93436 1.2e-13 60_[1]_17 sacCer3_chrIV_600891_600 2.5e-13 66_[1]_11 sacCer3_chrXIV_582075_58 1.4e-11 64_[1]_13 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RAYKKURCMARCMCMRCWKYACC MEME-1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF RAYKKURCMARCMCMRCWKYACC width=23 seqs=3 sacCer3_chrI_93336_93436 ( 61) GAUGUUGCAAGCCCAGCAGCACC 1 sacCer3_chrIV_600891_600 ( 67) AACGGUACCAGCACAGCUGCACC 1 sacCer3_chrXIV_582075_58 ( 65) GAUUGUGCCAACACCACAUUGCC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RAYKKURCMARCMCMRCWKYACC MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 23 n= 1560 bayes= 8.67781 E= 3.9e+000 17 -823 228 -823 176 -823 -823 -823 -823 80 -823 82 -823 -823 228 -18 -823 -823 228 -18 -823 -823 -823 141 17 -823 228 -823 -823 238 -823 -823 17 180 -823 -823 176 -823 -823 -823 17 -823 228 -823 -823 238 -823 -823 117 80 -823 -823 -823 238 -823 -823 117 80 -823 -823 17 -823 228 -823 -823 238 -823 -823 117 -823 -823 -18 -823 -823 228 -18 -823 180 -823 -18 117 -823 128 -823 -823 238 -823 -823 -823 238 -823 -823 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RAYKKURCMARCMCMRCWKYACC MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 23 nsites= 3 E= 3.9e+000 0.333333 0.000000 0.666667 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.333333 0.000000 0.666667 0.000000 0.000000 0.666667 0.333333 0.000000 0.000000 0.666667 0.333333 0.000000 0.000000 0.000000 1.000000 0.333333 0.000000 0.666667 0.000000 0.000000 1.000000 0.000000 0.000000 0.333333 0.666667 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.333333 0.000000 0.666667 0.000000 0.000000 1.000000 0.000000 0.000000 0.666667 0.333333 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.666667 0.333333 0.000000 0.000000 0.333333 0.000000 0.666667 0.000000 0.000000 1.000000 0.000000 0.000000 0.666667 0.000000 0.000000 0.333333 0.000000 0.000000 0.666667 0.333333 0.000000 0.666667 0.000000 0.333333 0.666667 0.000000 0.333333 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RAYKKURCMARCMCMRCWKYACC MEME-1 regular expression -------------------------------------------------------------------------------- [GA]A[UC][GU][GU]U[GA]C[CA]A[GA]C[AC]C[AC][GA]C[AU][GU][CU][AG]CC -------------------------------------------------------------------------------- Time 0.66 secs. ******************************************************************************** ******************************************************************************** MOTIF UGGGUCAG MEME-2 width = 8 sites = 4 llr = 43 E-value = 4.1e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif UGGGUCAG MEME-2 Description -------------------------------------------------------------------------------- Simplified A ::::::8: pos.-specific C :3:3:a:: probability G :8a83:3a matrix U a:::8::: bits 2.9 * * 2.6 * * 2.3 * * * 2.0 *** * * Relative 1.7 *** * * Entropy 1.4 **** * * (15.6 bits) 1.1 **** *** 0.9 ******** 0.6 ******** 0.3 ******** 0.0 -------- Multilevel UGGGUCAG consensus C CG G sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif UGGGUCAG MEME-2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- sacCer3_chrXIV_582075_58 26 3.85e-06 UCCAUUACUU UGGGGCAG CUAGUGAAAA sacCer3_chrXI_141677_141 77 5.16e-06 GGGCAUAAUU UGGGUCGG UUCAUUUUUU sacCer3_chrIV_600891_600 24 1.35e-05 CCACUUCCUC UGGCUCAG UAACUAUCAC sacCer3_chrXVI_564127_56 4 1.35e-05 AAA UCGGUCAG ACUGGUAAGG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif UGGGUCAG MEME-2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- sacCer3_chrXIV_582075_58 3.8e-06 25_[2]_67 sacCer3_chrXI_141677_141 5.2e-06 76_[2]_16 sacCer3_chrIV_600891_600 1.3e-05 23_[2]_69 sacCer3_chrXVI_564127_56 1.3e-05 3_[2]_89 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif UGGGUCAG MEME-2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF UGGGUCAG width=8 seqs=4 sacCer3_chrXIV_582075_58 ( 26) UGGGGCAG 1 sacCer3_chrXI_141677_141 ( 77) UGGGUCGG 1 sacCer3_chrIV_600891_600 ( 24) UGGCUCAG 1 sacCer3_chrXVI_564127_56 ( 4) UCGGUCAG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif UGGGUCAG MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 1860 bayes= 8.85798 E= 4.1e+001 -865 -865 -865 141 -865 39 245 -865 -865 -865 287 -865 -865 39 245 -865 -865 -865 87 99 -865 238 -865 -865 134 -865 87 -865 -865 -865 287 -865 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif UGGGUCAG MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 4 E= 4.1e+001 0.000000 0.000000 0.000000 1.000000 0.000000 0.250000 0.750000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.250000 0.750000 0.000000 0.000000 0.000000 0.250000 0.750000 0.000000 1.000000 0.000000 0.000000 0.750000 0.000000 0.250000 0.000000 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif UGGGUCAG MEME-2 regular expression -------------------------------------------------------------------------------- U[GC]G[GC][UG]C[AG]G -------------------------------------------------------------------------------- Time 1.26 secs. ******************************************************************************** ******************************************************************************** MOTIF CUCCAAAAASC MEME-3 width = 11 sites = 6 llr = 66 E-value = 1.1e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif CUCCAAAAASC MEME-3 Description -------------------------------------------------------------------------------- Simplified A ::::a7a75:: pos.-specific C 8:8a::::278 probability G :22::2:3232 matrix U 28:::2::2:: bits 2.9 2.6 2.3 * 2.0 * Relative 1.7 *** * ** Entropy 1.4 * *** * ** (15.8 bits) 1.1 * *** ** ** 0.9 ***** ** ** 0.6 ******** ** 0.3 *********** 0.0 ----------- Multilevel CUCCAAAAACC consensus G G sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CUCCAAAAASC MEME-3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ----------- sacCer3_chrXVI_522715_52 7 6.84e-07 CAAACA CUCCAAAAAGC UUGAAUAGCA sacCer3_chrXI_141677_141 60 1.25e-06 UCAUUUCUGU CUCCAAAGGGC AUAAUUUGGG sacCer3_chrIV_600891_600 53 5.65e-06 UCUUCUGAAG CUCCAGAAUCC GACAACGGUA sacCer3_chrVII_905741_90 66 7.74e-06 UAUACGCGCU CUCCAUAACCC GUAACUUUUU sacCer3_chrVII_559616_55 65 8.67e-06 AUUUUAUUGG CUGCAAAAACG UGACUUAUGU sacCer3_chrI_93336_93436 34 1.09e-05 GUGGAUACUC UGCCAAAGACC AUUUUCCCUC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CUCCAAAAASC MEME-3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- sacCer3_chrXVI_522715_52 6.8e-07 6_[3]_83 sacCer3_chrXI_141677_141 1.3e-06 59_[3]_30 sacCer3_chrIV_600891_600 5.6e-06 52_[3]_37 sacCer3_chrVII_905741_90 7.7e-06 65_[3]_24 sacCer3_chrVII_559616_55 8.7e-06 64_[3]_25 sacCer3_chrI_93336_93436 1.1e-05 33_[3]_56 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CUCCAAAAASC MEME-3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF CUCCAAAAASC width=11 seqs=6 sacCer3_chrXVI_522715_52 ( 7) CUCCAAAAAGC 1 sacCer3_chrXI_141677_141 ( 60) CUCCAAAGGGC 1 sacCer3_chrIV_600891_600 ( 53) CUCCAGAAUCC 1 sacCer3_chrVII_905741_90 ( 66) CUCCAUAACCC 1 sacCer3_chrVII_559616_55 ( 65) CUGCAAAAACG 1 sacCer3_chrI_93336_93436 ( 34) UGCCAAAGACC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CUCCAAAAASC MEME-3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 11 n= 1800 bayes= 8.67275 E= 1.1e+002 -923 212 -923 -117 -923 -923 29 114 -923 212 29 -923 -923 239 -923 -923 176 -923 -923 -923 117 -923 29 -117 176 -923 -923 -923 117 -923 128 -923 76 -20 29 -117 -923 180 128 -923 -923 212 29 -923 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CUCCAAAAASC MEME-3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 11 nsites= 6 E= 1.1e+002 0.000000 0.833333 0.000000 0.166667 0.000000 0.000000 0.166667 0.833333 0.000000 0.833333 0.166667 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.666667 0.000000 0.166667 0.166667 1.000000 0.000000 0.000000 0.000000 0.666667 0.000000 0.333333 0.000000 0.500000 0.166667 0.166667 0.166667 0.000000 0.666667 0.333333 0.000000 0.000000 0.833333 0.166667 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CUCCAAAAASC MEME-3 regular expression -------------------------------------------------------------------------------- CUCCAAA[AG]A[CG]C -------------------------------------------------------------------------------- Time 1.82 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- sacCer3_chrII_556467_556 8.73e-01 100 sacCer3_chrIX_312444_312 8.63e-01 100 sacCer3_chrXIV_443327_44 9.80e-01 100 sacCer3_chrVII_905741_90 3.26e-03 65_[3(7.74e-06)]_24 sacCer3_chrXI_356613_356 7.71e-01 100 sacCer3_chrI_93336_93436 2.97e-12 33_[3(1.09e-05)]_16_[1(1.21e-13)]_\ 17 sacCer3_chrIV_309697_309 8.62e-01 100 sacCer3_chrXVI_564127_56 1.23e-02 3_[2(1.35e-05)]_89 sacCer3_chrXIII_123147_1 8.76e-01 100 sacCer3_chrVII_559616_55 5.02e-03 64_[3(8.67e-06)]_25 sacCer3_chrVII_395909_39 9.94e-01 100 sacCer3_chrXI_569507_569 2.24e-01 100 sacCer3_chrIV_600891_600 9.83e-15 23_[2(1.35e-05)]_21_[3(5.65e-06)]_3_\ [1(2.48e-13)]_11 sacCer3_chrII_531780_531 4.95e-02 32_[1(4.39e-05)]_45 sacCer3_chrXVI_522715_52 1.32e-03 6_[3(6.84e-07)]_83 sacCer3_chrIV_1170148_11 9.87e-01 100 sacCer3_chrXI_141677_141 7.48e-06 59_[3(1.25e-06)]_6_[2(5.16e-06)]_16 sacCer3_chrIV_1233184_12 7.91e-01 100 sacCer3_chrXIV_582075_58 6.03e-11 25_[2(3.85e-06)]_31_[1(1.35e-11)]_\ 13 sacCer3_chrIV_915979_916 9.93e-01 100 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (3) found. ******************************************************************************** CPU: sh-ln04.stanford.edu ********************************************************************************