******************************************************************************** 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/341/341.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 9078 1.0000 500 37072 1.0000 500 37226 1.0000 500 47157 1.0000 500 37960 1.0000 500 11022 1.0000 500 49265 1.0000 500 54365 1.0000 500 49830 1.0000 500 44278 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/341/341.seqs.fa -oc motifs/341 -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= 10 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= 5000 N= 10 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.253 C 0.249 G 0.222 T 0.277 Background letter frequencies (from dataset with add-one prior applied): A 0.253 C 0.249 G 0.222 T 0.277 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 12 sites = 9 llr = 93 E-value = 2.3e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A ::711:::8:82 pos.-specific C :::42:2::a:: probability G 2921:91a2:28 matrix T 8113717::::: bits 2.2 * 2.0 * * 1.7 * * * * 1.5 * * * * Relative 1.3 * * ***** Entropy 1.1 ** * ***** (14.9 bits) 0.9 *** * ***** 0.7 *** ******** 0.4 *** ******** 0.2 ************ 0.0 ------------ Multilevel TGACTGTGACAG consensus G GTC C G GA sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 37072 387 1.09e-07 AAATTTTTAA TGATTGTGACAG ATCCGCGCCA 44278 117 2.03e-07 GATCTGACAC TGACCGTGACAG TGAGTCAAAC 54365 430 2.60e-06 AAAATCGCAA TGAATGCGACAG GCGCTAGGTT 37960 332 3.48e-06 AGCAATCTAC TGGTTGTGGCAG CACTGCGTTC 9078 412 1.36e-05 AGTGCCGCGG TGATTGCGACGA CGCTACCGGG 47157 258 1.55e-05 GTATGGTCAC TGACATTGACAG TGATTTGACT 11022 397 2.34e-05 TGGGGGAAAA TGACCGTGGCGA CGGCTCTCGT 49265 152 2.88e-05 TTCTTGATGT GGGGTGGGACAG CGAGTGGGAC 37226 285 4.01e-05 GGATTGTCTG GTTCTGTGACAG AACGGCAATA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 37072 1.1e-07 386_[+1]_102 44278 2e-07 116_[+1]_372 54365 2.6e-06 429_[+1]_59 37960 3.5e-06 331_[+1]_157 9078 1.4e-05 411_[+1]_77 47157 1.5e-05 257_[+1]_231 11022 2.3e-05 396_[+1]_92 49265 2.9e-05 151_[+1]_337 37226 4e-05 284_[+1]_204 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=12 seqs=9 37072 ( 387) TGATTGTGACAG 1 44278 ( 117) TGACCGTGACAG 1 54365 ( 430) TGAATGCGACAG 1 37960 ( 332) TGGTTGTGGCAG 1 9078 ( 412) TGATTGCGACGA 1 47157 ( 258) TGACATTGACAG 1 11022 ( 397) TGACCGTGGCGA 1 49265 ( 152) GGGGTGGGACAG 1 37226 ( 285) GTTCTGTGACAG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 4890 bayes= 9.21757 E= 2.3e+002 -982 -982 0 149 -982 -982 200 -131 140 -982 0 -131 -118 84 -100 27 -118 -16 -982 127 -982 -982 200 -131 -982 -16 -100 127 -982 -982 217 -982 162 -982 0 -982 -982 201 -982 -982 162 -982 0 -982 -18 -982 181 -982 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 9 E= 2.3e+002 0.000000 0.000000 0.222222 0.777778 0.000000 0.000000 0.888889 0.111111 0.666667 0.000000 0.222222 0.111111 0.111111 0.444444 0.111111 0.333333 0.111111 0.222222 0.000000 0.666667 0.000000 0.000000 0.888889 0.111111 0.000000 0.222222 0.111111 0.666667 0.000000 0.000000 1.000000 0.000000 0.777778 0.000000 0.222222 0.000000 0.000000 1.000000 0.000000 0.000000 0.777778 0.000000 0.222222 0.000000 0.222222 0.000000 0.777778 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [TG]G[AG][CT][TC]G[TC]G[AG]C[AG][GA] -------------------------------------------------------------------------------- Time 0.95 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 21 sites = 6 llr = 101 E-value = 1.2e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A 37a2:::3:2:8535:52:a2 pos.-specific C 7::2a28:::2::333288:: probability G :3:::2252882:2272:2:8 matrix T :::7:7:28:::52::2:::: bits 2.2 2.0 * * * 1.7 * * * 1.5 * * ** ** Relative 1.3 * * * **** * **** Entropy 1.1 *** * * **** * **** (24.3 bits) 0.9 *** * * ***** * **** 0.7 ************* ** **** 0.4 ************* ** **** 0.2 ************* ******* 0.0 --------------------- Multilevel CAATCTCGTGGAAAAGACCAG consensus AG A TCCC sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 11022 210 1.51e-10 ATAGTCTCGA AGATCTCGTGGAAGCGACCAG TGTTCATTCT 44278 152 1.46e-09 AAAACGTGTT CGACCTCGGGGATCCGACCAG ATCAATTGTC 47157 111 7.60e-09 GGAAAATCAA CAATCTCATGCAAAAGCCCAA GCACAAGGAC 37226 310 1.46e-08 GGCAATAAAA CAATCCGTTGGGTAAGACCAG TGGCATTGTT 9078 212 4.15e-08 AGGATGATAT CAATCTCGTGGATTGCGAGAG TCCTCGAGTC 37072 246 5.94e-08 GGGTAGCATC AAAACGCATAGAACACTCCAG ATCGTCAGGG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 11022 1.5e-10 209_[+2]_270 44278 1.5e-09 151_[+2]_328 47157 7.6e-09 110_[+2]_369 37226 1.5e-08 309_[+2]_170 9078 4.1e-08 211_[+2]_268 37072 5.9e-08 245_[+2]_234 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=21 seqs=6 11022 ( 210) AGATCTCGTGGAAGCGACCAG 1 44278 ( 152) CGACCTCGGGGATCCGACCAG 1 47157 ( 111) CAATCTCATGCAAAAGCCCAA 1 37226 ( 310) CAATCCGTTGGGTAAGACCAG 1 9078 ( 212) CAATCTCGTGGATTGCGAGAG 1 37072 ( 246) AAAACGCATAGAACACTCCAG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 4800 bayes= 10.7426 E= 1.2e+002 40 142 -923 -923 140 -923 58 -923 198 -923 -923 -923 -60 -58 -923 127 -923 201 -923 -923 -923 -58 -41 127 -923 174 -41 -923 40 -923 117 -73 -923 -923 -41 159 -60 -923 191 -923 -923 -58 191 -923 172 -923 -41 -923 98 -923 -923 85 40 42 -41 -73 98 42 -41 -923 -923 42 158 -923 98 -58 -41 -73 -60 174 -923 -923 -923 174 -41 -923 198 -923 -923 -923 -60 -923 191 -923 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 6 E= 1.2e+002 0.333333 0.666667 0.000000 0.000000 0.666667 0.000000 0.333333 0.000000 1.000000 0.000000 0.000000 0.000000 0.166667 0.166667 0.000000 0.666667 0.000000 1.000000 0.000000 0.000000 0.000000 0.166667 0.166667 0.666667 0.000000 0.833333 0.166667 0.000000 0.333333 0.000000 0.500000 0.166667 0.000000 0.000000 0.166667 0.833333 0.166667 0.000000 0.833333 0.000000 0.000000 0.166667 0.833333 0.000000 0.833333 0.000000 0.166667 0.000000 0.500000 0.000000 0.000000 0.500000 0.333333 0.333333 0.166667 0.166667 0.500000 0.333333 0.166667 0.000000 0.000000 0.333333 0.666667 0.000000 0.500000 0.166667 0.166667 0.166667 0.166667 0.833333 0.000000 0.000000 0.000000 0.833333 0.166667 0.000000 1.000000 0.000000 0.000000 0.000000 0.166667 0.000000 0.833333 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [CA][AG]ATCTC[GA]TGGA[AT][AC][AC][GC]ACCAG -------------------------------------------------------------------------------- Time 1.84 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 16 sites = 5 llr = 75 E-value = 7.0e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A :2:8:4::6:2::::: pos.-specific C 68::82:8:28:::2: probability G ::a2228:28:a::4a matrix T 4::::2222:::aa4: bits 2.2 * * * 2.0 * *** * 1.7 * *** * 1.5 * * *** * Relative 1.3 **** ** ***** * Entropy 1.1 **** ** ***** * (21.6 bits) 0.9 ***** ** ***** * 0.7 ***** ******** * 0.4 ***** ********** 0.2 ***** ********** 0.0 ---------------- Multilevel CCGACAGCAGCGTTGG consensus TA GGCTTGCA T sequence G T C T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 11022 300 5.54e-09 GCTGACCGCT TCGACTGCAGCGTTTG CTCCTCGCCA 44278 393 2.81e-08 CCACGCTTTC TCGACCGCACCGTTGG CATATCCTTT 37226 464 8.49e-08 TGTGAATGGC CCGACAGTTGCGTTCG AGAATCATCC 9078 429 8.49e-08 GACGACGCTA CCGGGAGCGGCGTTGG CCGAGATTGT 37960 24 3.74e-07 TGTTGCGAGG CAGACGTCAGAGTTTG TTCCTAGCTC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 11022 5.5e-09 299_[+3]_185 44278 2.8e-08 392_[+3]_92 37226 8.5e-08 463_[+3]_21 9078 8.5e-08 428_[+3]_56 37960 3.7e-07 23_[+3]_461 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=16 seqs=5 11022 ( 300) TCGACTGCAGCGTTTG 1 44278 ( 393) TCGACCGCACCGTTGG 1 37226 ( 464) CCGACAGTTGCGTTCG 1 9078 ( 429) CCGGGAGCGGCGTTGG 1 37960 ( 24) CAGACGTCAGAGTTTG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 4850 bayes= 10.1721 E= 7.0e+002 -897 127 -897 53 -34 168 -897 -897 -897 -897 217 -897 166 -897 -15 -897 -897 168 -15 -897 66 -31 -15 -47 -897 -897 185 -47 -897 168 -897 -47 125 -897 -15 -47 -897 -31 185 -897 -34 168 -897 -897 -897 -897 217 -897 -897 -897 -897 185 -897 -897 -897 185 -897 -31 85 53 -897 -897 217 -897 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 5 E= 7.0e+002 0.000000 0.600000 0.000000 0.400000 0.200000 0.800000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.800000 0.000000 0.200000 0.000000 0.000000 0.800000 0.200000 0.000000 0.400000 0.200000 0.200000 0.200000 0.000000 0.000000 0.800000 0.200000 0.000000 0.800000 0.000000 0.200000 0.600000 0.000000 0.200000 0.200000 0.000000 0.200000 0.800000 0.000000 0.200000 0.800000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.200000 0.400000 0.400000 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [CT][CA]G[AG][CG][ACGT][GT][CT][AGT][GC][CA]GTT[GTC]G -------------------------------------------------------------------------------- Time 2.69 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 9078 1.97e-09 211_[+2(4.15e-08)]_150_\ [+2(2.17e-05)]_8_[+1(1.36e-05)]_5_[+3(8.49e-08)]_56 37072 2.61e-07 245_[+2(5.94e-08)]_120_\ [+1(1.09e-07)]_102 37226 2.03e-09 284_[+1(4.01e-05)]_13_\ [+2(1.46e-08)]_133_[+3(8.49e-08)]_21 47157 2.97e-06 110_[+2(7.60e-09)]_126_\ [+1(1.55e-05)]_231 37960 1.29e-05 23_[+3(3.74e-07)]_292_\ [+1(3.48e-06)]_157 11022 1.34e-12 209_[+2(1.51e-10)]_69_\ [+3(5.54e-09)]_81_[+1(2.34e-05)]_92 49265 1.40e-01 151_[+1(2.88e-05)]_337 54365 1.25e-03 429_[+1(2.60e-06)]_59 49830 9.84e-01 500 44278 6.01e-13 116_[+1(2.03e-07)]_23_\ [+2(1.46e-09)]_220_[+3(2.81e-08)]_92 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************