******************************************************************************** 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/116/116.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 46530 1.0000 500 47780 1.0000 500 29042 1.0000 500 40950 1.0000 500 31147 1.0000 500 768 1.0000 500 44737 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/116/116.seqs.fa -oc motifs/116 -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= 7 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= 3500 N= 7 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.271 C 0.249 G 0.227 T 0.253 Background letter frequencies (from dataset with add-one prior applied): A 0.271 C 0.249 G 0.227 T 0.253 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 20 sites = 7 llr = 107 E-value = 3.6e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A :7::1:333:::14:1931: pos.-specific C 4:a::34::::19:37111: probability G :1::1314::9::::1:::7 matrix T 61:a74137a19:67::673 bits 2.1 1.9 ** * 1.7 ** * 1.5 ** **** Relative 1.3 ** **** * * Entropy 1.1 * ** ***** * * * (22.0 bits) 0.9 ***** ********* ** 0.6 ***** ************ 0.4 ****** ************* 0.2 ******************** 0.0 -------------------- Multilevel TACTTTCGTTGTCTTCATTG consensus C CAAA AC A T sequence G T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------------- 44737 461 1.16e-10 TCCCTGTCAC TACTTTCGTTGTCTTCATCG TTCCTTTCCA 768 212 3.76e-10 AGAAACGGTT CACTTCAATTGTCATCATTG ACACAGTCAT 31147 284 1.83e-08 GTGACCGACC TACTTTCATTGTCTTCACAT CACTTTCTAG 46530 6 3.79e-08 CCATA TACTTGAGATGTCTCAAATG ACTTTATAAT 47780 326 2.51e-07 TACGATTTCT TTCTACGTTTGTCATCAATT AACAAATCGC 29042 190 3.97e-07 TGTCCGAATC CGCTGGTTTTGTCACGATTG ACACTGATAT 40950 460 5.71e-07 TCTCCACGTT CACTTTCGATTCATTCCTTG GTTCAATCCT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 44737 1.2e-10 460_[+1]_20 768 3.8e-10 211_[+1]_269 31147 1.8e-08 283_[+1]_197 46530 3.8e-08 5_[+1]_475 47780 2.5e-07 325_[+1]_155 29042 4e-07 189_[+1]_291 40950 5.7e-07 459_[+1]_21 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=20 seqs=7 44737 ( 461) TACTTTCGTTGTCTTCATCG 1 768 ( 212) CACTTCAATTGTCATCATTG 1 31147 ( 284) TACTTTCATTGTCTTCACAT 1 46530 ( 6) TACTTGAGATGTCTCAAATG 1 47780 ( 326) TTCTACGTTTGTCATCAATT 1 29042 ( 190) CGCTGGTTTTGTCACGATTG 1 40950 ( 460) CACTTTCGATTCATTCCTTG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 3367 bayes= 8.90689 E= 3.6e+001 -945 78 -945 118 140 -945 -67 -82 -945 200 -945 -945 -945 -945 -945 198 -92 -945 -67 150 -945 20 33 76 8 78 -67 -82 8 -945 91 18 8 -945 -945 150 -945 -945 -945 198 -945 -945 191 -82 -945 -80 -945 176 -92 178 -945 -945 66 -945 -945 118 -945 20 -945 150 -92 152 -67 -945 166 -80 -945 -945 8 -80 -945 118 -92 -80 -945 150 -945 -945 165 18 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 7 E= 3.6e+001 0.000000 0.428571 0.000000 0.571429 0.714286 0.000000 0.142857 0.142857 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.142857 0.000000 0.142857 0.714286 0.000000 0.285714 0.285714 0.428571 0.285714 0.428571 0.142857 0.142857 0.285714 0.000000 0.428571 0.285714 0.285714 0.000000 0.000000 0.714286 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.857143 0.142857 0.000000 0.142857 0.000000 0.857143 0.142857 0.857143 0.000000 0.000000 0.428571 0.000000 0.000000 0.571429 0.000000 0.285714 0.000000 0.714286 0.142857 0.714286 0.142857 0.000000 0.857143 0.142857 0.000000 0.000000 0.285714 0.142857 0.000000 0.571429 0.142857 0.142857 0.000000 0.714286 0.000000 0.000000 0.714286 0.285714 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [TC]ACTT[TCG][CA][GAT][TA]TGTC[TA][TC]CA[TA]T[GT] -------------------------------------------------------------------------------- Time 0.43 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 21 sites = 7 llr = 110 E-value = 6.3e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A 1:a34:7:341:441:1714: pos.-specific C :9:64114:4991:1a4:94: probability G :1:1:9:4:1::41::43::a matrix T 9:::1:117::1:47::::1: bits 2.1 * 1.9 * * * 1.7 * * * 1.5 ** * ** * * * Relative 1.3 *** * ** * * * Entropy 1.1 *** * * ** * ** * (22.8 bits) 0.9 *** ** * ** ** ** * 0.6 **** **** *** ***** * 0.4 ********************* 0.2 ********************* 0.0 --------------------- Multilevel TCACAGACTACCAATCCACAG consensus AC GAC GT GG C sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 29042 348 1.82e-10 GCGAATCCTG TCACAGAGTACCGTTCCACTG TCGCAGTAAG 31147 356 4.91e-09 TGAGTAGACG TCAACGCGTACCGATCCGCAG TCCGAGGCAC 46530 309 6.53e-09 CGACTCAAAG TCAGCGACTCCCAGTCAACCG GTTTGTTCGG 40950 319 1.90e-08 CCGACGTCAG TGACCGACAACCGAACGACAG GGCGGTGTGG 47780 403 1.29e-07 TAGTCCGGTG TCAAAGTCACCTCTTCCACCG GCATGCTCCG 44737 388 1.39e-07 TTTTTCAAGG TCACACAGTCACAATCGGACG AAACGTCGGG 768 327 1.67e-07 ATACATCATC ACACTGATTGCCATCCGACAG AGTTGTCACA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 29042 1.8e-10 347_[+2]_132 31147 4.9e-09 355_[+2]_124 46530 6.5e-09 308_[+2]_171 40950 1.9e-08 318_[+2]_161 47780 1.3e-07 402_[+2]_77 44737 1.4e-07 387_[+2]_92 768 1.7e-07 326_[+2]_153 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=21 seqs=7 29042 ( 348) TCACAGAGTACCGTTCCACTG 1 31147 ( 356) TCAACGCGTACCGATCCGCAG 1 46530 ( 309) TCAGCGACTCCCAGTCAACCG 1 40950 ( 319) TGACCGACAACCGAACGACAG 1 47780 ( 403) TCAAAGTCACCTCTTCCACCG 1 44737 ( 388) TCACACAGTCACAATCGGACG 1 768 ( 327) ACACTGATTGCCATCCGACAG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 3360 bayes= 8.90388 E= 6.3e+000 -92 -945 -945 176 -945 178 -67 -945 188 -945 -945 -945 8 120 -67 -945 66 78 -945 -82 -945 -80 191 -945 140 -80 -945 -82 -945 78 91 -82 8 -945 -945 150 66 78 -67 -945 -92 178 -945 -945 -945 178 -945 -82 66 -80 91 -945 66 -945 -67 76 -92 -80 -945 150 -945 200 -945 -945 -92 78 91 -945 140 -945 33 -945 -92 178 -945 -945 66 78 -945 -82 -945 -945 214 -945 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 7 E= 6.3e+000 0.142857 0.000000 0.000000 0.857143 0.000000 0.857143 0.142857 0.000000 1.000000 0.000000 0.000000 0.000000 0.285714 0.571429 0.142857 0.000000 0.428571 0.428571 0.000000 0.142857 0.000000 0.142857 0.857143 0.000000 0.714286 0.142857 0.000000 0.142857 0.000000 0.428571 0.428571 0.142857 0.285714 0.000000 0.000000 0.714286 0.428571 0.428571 0.142857 0.000000 0.142857 0.857143 0.000000 0.000000 0.000000 0.857143 0.000000 0.142857 0.428571 0.142857 0.428571 0.000000 0.428571 0.000000 0.142857 0.428571 0.142857 0.142857 0.000000 0.714286 0.000000 1.000000 0.000000 0.000000 0.142857 0.428571 0.428571 0.000000 0.714286 0.000000 0.285714 0.000000 0.142857 0.857143 0.000000 0.000000 0.428571 0.428571 0.000000 0.142857 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- TCA[CA][AC]GA[CG][TA][AC]CC[AG][AT]TC[CG][AG]C[AC]G -------------------------------------------------------------------------------- Time 0.85 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 19 sites = 4 llr = 73 E-value = 9.7e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A 3a::::3a::53535:aa: pos.-specific C ::aa:8:::::3:::3::a probability G ::::a38:88535538::: matrix T 8:::::::33:3:33:::: bits 2.1 * 1.9 **** * *** 1.7 **** * *** 1.5 **** * *** Relative 1.3 ********* **** Entropy 1.1 *********** * **** (26.2 bits) 0.9 *********** * **** 0.6 *********** ** **** 0.4 *********** ******* 0.2 *********** ******* 0.0 ------------------- Multilevel TACCGCGAGGAAAGAGAAC consensus A GA TTGCGAGC sequence G TT T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------------- 46530 473 1.64e-09 TCCCACTCTA AACCGGGAGGGTGGAGAAC ACATACACC 40950 118 2.20e-09 ACAGGAAAAG TACCGCGAGTACATAGAAC TTCGTTCGTA 44737 120 4.57e-09 GCGGAGCGCC TACCGCAAGGAGAAGGAAC AGGAAGCCCT 47780 444 4.57e-09 TCGACCACAA TACCGCGATGGAGGTCAAC GTTTCACTTT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 46530 1.6e-09 472_[+3]_9 40950 2.2e-09 117_[+3]_364 44737 4.6e-09 119_[+3]_362 47780 4.6e-09 443_[+3]_38 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=19 seqs=4 46530 ( 473) AACCGGGAGGGTGGAGAAC 1 40950 ( 118) TACCGCGAGTACATAGAAC 1 44737 ( 120) TACCGCAAGGAGAAGGAAC 1 47780 ( 444) TACCGCGATGGAGGTCAAC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 19 n= 3374 bayes= 9.71853 E= 9.7e+002 -12 -865 -865 157 188 -865 -865 -865 -865 200 -865 -865 -865 200 -865 -865 -865 -865 214 -865 -865 159 14 -865 -12 -865 172 -865 188 -865 -865 -865 -865 -865 172 -2 -865 -865 172 -2 88 -865 114 -865 -12 0 14 -2 88 -865 114 -865 -12 -865 114 -2 88 -865 14 -2 -865 0 172 -865 188 -865 -865 -865 188 -865 -865 -865 -865 200 -865 -865 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 19 nsites= 4 E= 9.7e+002 0.250000 0.000000 0.000000 0.750000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.750000 0.250000 0.000000 0.250000 0.000000 0.750000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.750000 0.250000 0.000000 0.000000 0.750000 0.250000 0.500000 0.000000 0.500000 0.000000 0.250000 0.250000 0.250000 0.250000 0.500000 0.000000 0.500000 0.000000 0.250000 0.000000 0.500000 0.250000 0.500000 0.000000 0.250000 0.250000 0.000000 0.250000 0.750000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [TA]ACCG[CG][GA]A[GT][GT][AG][ACGT][AG][GAT][AGT][GC]AAC -------------------------------------------------------------------------------- Time 1.28 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 46530 3.36e-14 5_[+1(3.79e-08)]_283_[+2(6.53e-09)]_\ 67_[+2(8.07e-05)]_55_[+3(1.64e-09)]_9 47780 8.87e-12 325_[+1(2.51e-07)]_57_\ [+2(1.29e-07)]_20_[+3(4.57e-09)]_38 29042 2.16e-09 189_[+1(3.97e-07)]_138_\ [+2(1.82e-10)]_132 40950 1.58e-12 117_[+3(2.20e-09)]_182_\ [+2(1.90e-08)]_120_[+1(5.71e-07)]_21 31147 3.77e-09 283_[+1(1.83e-08)]_52_\ [+2(4.91e-09)]_124 768 4.59e-09 211_[+1(3.76e-10)]_95_\ [+2(1.67e-07)]_153 44737 6.68e-15 119_[+3(4.57e-09)]_249_\ [+2(1.39e-07)]_52_[+1(1.16e-10)]_20 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************