******************************************************************************** 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/390/390.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 1160 1.0000 500 21779 1.0000 500 24963 1.0000 500 25805 1.0000 500 268858 1.0000 500 269163 1.0000 500 269655 1.0000 500 270227 1.0000 500 33772 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/390/390.seqs.fa -oc motifs/390 -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= 9 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= 4500 N= 9 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.265 C 0.232 G 0.246 T 0.258 Background letter frequencies (from dataset with add-one prior applied): A 0.265 C 0.232 G 0.246 T 0.258 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 21 sites = 7 llr = 124 E-value = 1.3e-002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A ::1476:1::::::::::::: pos.-specific C :1:4:1:1:::::1::1:::: probability G a13::3666494699:7a:9a matrix T :7613:4146164:1a1:a1: bits 2.1 * * * 1.9 * * ** * 1.7 * * ** * 1.5 * * *** **** Relative 1.3 * * *** **** Entropy 1.1 * * * ******** **** (25.6 bits) 0.8 ** * * ************* 0.6 ******* ************* 0.4 ********************* 0.2 ********************* 0.0 --------------------- Multilevel GTTAAAGGGTGTGGGTGGTGG consensus GCTGT TG GT sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 270227 179 6.34e-11 ATTCGAAACT GTGAAATGGTGGTGGTGGTGG TTGTTTGTTT 269655 45 6.34e-11 ATTCGAAACT GTGAAATGGTGGTGGTGGTGG TTGTTTGTTT 1160 20 1.41e-10 TAGTATCACA GCTCAAGGGTGGTGGTGGTGG TGGAGGTAGA 268858 106 1.89e-10 ATCAACAGGG GTTCAGGCGGGTGGGTGGTGG GCTTGTGTTG 24963 391 1.97e-08 TCGCATTAAA GTACTATTTGGTGGGTTGTGG CGGGAAGCTC 33772 453 7.25e-08 GGGTGACAAG GGTAACGATGTTGGGTCGTGG AGAGAGGTGT 25805 255 7.53e-08 ACAATTGTGT GTTTTGGGTTGTGCTTGGTTG ATTTTATCAC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 270227 6.3e-11 178_[+1]_301 269655 6.3e-11 44_[+1]_435 1160 1.4e-10 19_[+1]_460 268858 1.9e-10 105_[+1]_374 24963 2e-08 390_[+1]_89 33772 7.3e-08 452_[+1]_27 25805 7.5e-08 254_[+1]_225 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=21 seqs=7 270227 ( 179) GTGAAATGGTGGTGGTGGTGG 1 269655 ( 45) GTGAAATGGTGGTGGTGGTGG 1 1160 ( 20) GCTCAAGGGTGGTGGTGGTGG 1 268858 ( 106) GTTCAGGCGGGTGGGTGGTGG 1 24963 ( 391) GTACTATTTGGTGGGTTGTGG 1 33772 ( 453) GGTAACGATGTTGGGTCGTGG 1 25805 ( 255) GTTTTGGGTTGTGCTTGGTTG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 4320 bayes= 9.11073 E= 1.3e-002 -945 -945 202 -945 -945 -70 -78 147 -89 -945 22 115 69 89 -945 -85 143 -945 -945 15 111 -70 22 -945 -945 -945 121 73 -89 -70 121 -85 -945 -945 121 73 -945 -945 80 115 -945 -945 180 -85 -945 -945 80 115 -945 -945 121 73 -945 -70 180 -945 -945 -945 180 -85 -945 -945 -945 196 -945 -70 154 -85 -945 -945 202 -945 -945 -945 -945 196 -945 -945 180 -85 -945 -945 202 -945 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 7 E= 1.3e-002 0.000000 0.000000 1.000000 0.000000 0.000000 0.142857 0.142857 0.714286 0.142857 0.000000 0.285714 0.571429 0.428571 0.428571 0.000000 0.142857 0.714286 0.000000 0.000000 0.285714 0.571429 0.142857 0.285714 0.000000 0.000000 0.000000 0.571429 0.428571 0.142857 0.142857 0.571429 0.142857 0.000000 0.000000 0.571429 0.428571 0.000000 0.000000 0.428571 0.571429 0.000000 0.000000 0.857143 0.142857 0.000000 0.000000 0.428571 0.571429 0.000000 0.000000 0.571429 0.428571 0.000000 0.142857 0.857143 0.000000 0.000000 0.000000 0.857143 0.142857 0.000000 0.000000 0.000000 1.000000 0.000000 0.142857 0.714286 0.142857 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.857143 0.142857 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- GT[TG][AC][AT][AG][GT]G[GT][TG]G[TG][GT]GGTGGTGG -------------------------------------------------------------------------------- Time 0.79 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 20 sites = 8 llr = 124 E-value = 6.6e-002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A 9454:a6:93:41:8::5:: pos.-specific C 1:35a:4a:88398:64515 probability G :33:::::::13:3:1::3: matrix T :4:1::::1:11::336:65 bits 2.1 * * 1.9 ** * 1.7 ** * 1.5 * ** ** * Relative 1.3 * ** *** ** Entropy 1.1 * ******* *** ** * (22.3 bits) 0.8 * ******* ****** * 0.6 * ******** ******** 0.4 *********** ******** 0.2 *********** ******** 0.0 -------------------- Multilevel AAACCAACACCACCACTATC consensus TCA C A C GTTCCGT sequence GG G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------------- 24963 478 3.83e-11 CCTCTCCTCC ATAACAACACCACCACTATT ATC 269163 105 6.90e-09 CATCAAGCTG ATACCAACAACCCCATCATT GTGTTAGAAA 269655 459 8.69e-09 CTCCTCCTCG AACCCACCACCTCCTCTCTC ACCATACACC 33772 238 4.26e-08 AACAACGAGG AACACACCTCCACCTCTCTC TCCACCACAA 25805 463 1.02e-07 ACCGGTAGGC CTAACAACACCAACACTAGT TGCCTTCAAA 270227 111 1.25e-07 ATTCTGAGCT AGGCCACCACTGCCATTCGT CTTTCGTCTG 268858 448 1.53e-07 TCGGCCACGC AAGCCAACACCGCGAGCACC AACGACCCAA 21779 85 2.78e-07 TTAGGCTCTC AGATCAACAAGCCGACCCTC AGATTGAAAT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 24963 3.8e-11 477_[+2]_3 269163 6.9e-09 104_[+2]_376 269655 8.7e-09 458_[+2]_22 33772 4.3e-08 237_[+2]_243 25805 1e-07 462_[+2]_18 270227 1.3e-07 110_[+2]_370 268858 1.5e-07 447_[+2]_33 21779 2.8e-07 84_[+2]_396 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=20 seqs=8 24963 ( 478) ATAACAACACCACCACTATT 1 269163 ( 105) ATACCAACAACCCCATCATT 1 269655 ( 459) AACCCACCACCTCCTCTCTC 1 33772 ( 238) AACACACCTCCACCTCTCTC 1 25805 ( 463) CTAACAACACCAACACTAGT 1 270227 ( 111) AGGCCACCACTGCCATTCGT 1 268858 ( 448) AAGCCAACACCGCGAGCACC 1 21779 ( 85) AGATCAACAAGCCGACCCTC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 4329 bayes= 9.07715 E= 6.6e-002 172 -89 -965 -965 50 -965 2 54 92 11 2 -965 50 111 -965 -104 -965 211 -965 -965 192 -965 -965 -965 124 69 -965 -965 -965 211 -965 -965 172 -965 -965 -104 -8 169 -965 -965 -965 169 -98 -104 50 11 2 -104 -108 192 -965 -965 -965 169 2 -965 150 -965 -965 -4 -965 143 -98 -4 -965 69 -965 128 92 111 -965 -965 -965 -89 2 128 -965 111 -965 96 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 8 E= 6.6e-002 0.875000 0.125000 0.000000 0.000000 0.375000 0.000000 0.250000 0.375000 0.500000 0.250000 0.250000 0.000000 0.375000 0.500000 0.000000 0.125000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.625000 0.375000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.875000 0.000000 0.000000 0.125000 0.250000 0.750000 0.000000 0.000000 0.000000 0.750000 0.125000 0.125000 0.375000 0.250000 0.250000 0.125000 0.125000 0.875000 0.000000 0.000000 0.000000 0.750000 0.250000 0.000000 0.750000 0.000000 0.000000 0.250000 0.000000 0.625000 0.125000 0.250000 0.000000 0.375000 0.000000 0.625000 0.500000 0.500000 0.000000 0.000000 0.000000 0.125000 0.250000 0.625000 0.000000 0.500000 0.000000 0.500000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- A[ATG][ACG][CA]CA[AC]CA[CA]C[ACG]C[CG][AT][CT][TC][AC][TG][CT] -------------------------------------------------------------------------------- Time 1.53 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 20 sites = 8 llr = 120 E-value = 1.5e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A 1:34::::115::::3:819 pos.-specific C 536153a196:98541919: probability G :81115:::::13:6::::: matrix T 4::443:9:35::5:611:1 bits 2.1 * 1.9 * 1.7 * 1.5 *** * * ** Relative 1.3 * *** ** * ** Entropy 1.1 * *** **** * ** (21.7 bits) 0.8 ** ********* **** 0.6 *** **************** 0.4 *** **************** 0.2 ******************** 0.0 -------------------- Multilevel CGCACGCTCCACCCGTCACA consensus TCATTC TT GTCA sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------------- 270227 411 3.80e-10 CAGATCGGAT TGCTTGCTCCACGTGTCACA ATAGGGGTAA 269655 277 3.80e-10 CAGATCGGAT TGCTTGCTCCACGTGTCACA ATAGGGGTAA 33772 34 1.80e-08 GCCAAAGCGT CGCGTCCTCCTCCCCTCACT CGGAAATCGC 21779 355 2.67e-08 CCCCGCCAAG CGCACGCCCCACCCGACTCA CACCCCGGCC 1160 471 1.52e-07 TTCCACGTTC CGCTCCCTCTTCCTGATCCA CTGGTAAACA 269163 326 3.22e-07 ACACCACACA ACAACTCTCTTGCCGTCACA GCCACCTCCA 268858 347 3.22e-07 TATATAAATT TGACCTCTCAACCCCTCAAA ATCGTTGGAG 25805 347 6.18e-07 CGATCGGCGG CCGAGGCTACTCCTCCCACA GGACGAATGC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 270227 3.8e-10 410_[+3]_70 269655 3.8e-10 276_[+3]_204 33772 1.8e-08 33_[+3]_447 21779 2.7e-08 354_[+3]_126 1160 1.5e-07 470_[+3]_10 269163 3.2e-07 325_[+3]_155 268858 3.2e-07 346_[+3]_134 25805 6.2e-07 346_[+3]_134 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=20 seqs=8 270227 ( 411) TGCTTGCTCCACGTGTCACA 1 269655 ( 277) TGCTTGCTCCACGTGTCACA 1 33772 ( 34) CGCGTCCTCCTCCCCTCACT 1 21779 ( 355) CGCACGCCCCACCCGACTCA 1 1160 ( 471) CGCTCCCTCTTCCTGATCCA 1 269163 ( 326) ACAACTCTCTTGCCGTCACA 1 268858 ( 347) TGACCTCTCAACCCCTCAAA 1 25805 ( 347) CCGAGGCTACTCCTCCCACA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 4329 bayes= 9.81518 E= 1.5e-001 -108 111 -965 54 -965 11 161 -965 -8 143 -98 -965 50 -89 -98 54 -965 111 -98 54 -965 11 102 -4 -965 211 -965 -965 -965 -89 -965 176 -108 192 -965 -965 -108 143 -965 -4 92 -965 -965 96 -965 192 -98 -965 -965 169 2 -965 -965 111 -965 96 -965 69 134 -965 -8 -89 -965 128 -965 192 -965 -104 150 -89 -965 -104 -108 192 -965 -965 172 -965 -965 -104 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 8 E= 1.5e-001 0.125000 0.500000 0.000000 0.375000 0.000000 0.250000 0.750000 0.000000 0.250000 0.625000 0.125000 0.000000 0.375000 0.125000 0.125000 0.375000 0.000000 0.500000 0.125000 0.375000 0.000000 0.250000 0.500000 0.250000 0.000000 1.000000 0.000000 0.000000 0.000000 0.125000 0.000000 0.875000 0.125000 0.875000 0.000000 0.000000 0.125000 0.625000 0.000000 0.250000 0.500000 0.000000 0.000000 0.500000 0.000000 0.875000 0.125000 0.000000 0.000000 0.750000 0.250000 0.000000 0.000000 0.500000 0.000000 0.500000 0.000000 0.375000 0.625000 0.000000 0.250000 0.125000 0.000000 0.625000 0.000000 0.875000 0.000000 0.125000 0.750000 0.125000 0.000000 0.125000 0.125000 0.875000 0.000000 0.000000 0.875000 0.000000 0.000000 0.125000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [CT][GC][CA][AT][CT][GCT]CTC[CT][AT]C[CG][CT][GC][TA]CACA -------------------------------------------------------------------------------- Time 2.25 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 1160 1.79e-09 19_[+1(1.41e-10)]_200_\ [+1(9.13e-05)]_209_[+3(1.52e-07)]_10 21779 1.70e-07 84_[+2(2.78e-07)]_250_\ [+3(2.67e-08)]_126 24963 5.34e-11 390_[+1(1.97e-08)]_66_\ [+2(3.83e-11)]_3 25805 2.25e-10 254_[+1(7.53e-08)]_71_\ [+3(6.18e-07)]_44_[+2(7.71e-05)]_32_[+2(1.02e-07)]_18 268858 6.52e-13 105_[+1(1.89e-10)]_220_\ [+3(3.22e-07)]_81_[+2(1.53e-07)]_33 269163 1.29e-07 104_[+2(6.90e-09)]_201_\ [+3(3.22e-07)]_155 269655 2.48e-17 44_[+1(6.34e-11)]_211_\ [+3(3.80e-10)]_162_[+2(8.69e-09)]_22 270227 3.18e-16 110_[+2(1.25e-07)]_48_\ [+1(6.34e-11)]_211_[+3(3.80e-10)]_70 33772 3.52e-12 33_[+3(1.80e-08)]_184_\ [+2(4.26e-08)]_195_[+1(7.25e-08)]_27 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************