******************************************************************************** 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/420/420.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 32342 1.0000 500 36289 1.0000 500 38097 1.0000 500 48394 1.0000 500 43494 1.0000 500 43495 1.0000 500 35518 1.0000 500 39159 1.0000 500 39265 1.0000 500 49427 1.0000 500 46486 1.0000 500 46677 1.0000 500 39943 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/420/420.seqs.fa -oc motifs/420 -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= 13 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= 6500 N= 13 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.276 C 0.231 G 0.222 T 0.270 Background letter frequencies (from dataset with add-one prior applied): A 0.276 C 0.231 G 0.222 T 0.270 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 12 sites = 7 llr = 86 E-value = 6.5e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A :3::7:6:::a: pos.-specific C 34:61a:::a:: probability G 3:::1::a:::a matrix T 43a4::4:a::: bits 2.2 * * * * 2.0 * * ***** 1.7 * * ***** 1.5 * * ***** Relative 1.3 * * ***** Entropy 1.1 ** * ***** (17.8 bits) 0.9 ********** 0.7 ********** 0.4 ************ 0.2 ************ 0.0 ------------ Multilevel TCTCACAGTCAG consensus CA T T sequence GT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 39159 413 2.12e-07 TATAGTTATC TCTCACTGTCAG GTTAAATGTT 39943 384 3.76e-07 CGAGAGCGAG CCTCACTGTCAG ACCTACTAGC 46677 254 5.13e-07 CGCGACTGTA TTTCACAGTCAG CGTCAACCAC 36289 314 5.13e-07 AATCAGCGGA TATCACAGTCAG TCTCTCTTAC 49427 270 1.98e-06 TCTACATGCA GTTTACAGTCAG CCTGGCGTGA 38097 409 4.07e-06 AGTGTCTTTC GCTTGCTGTCAG GCCCACGTCT 48394 342 5.50e-06 CGCGTACCTC CATTCCAGTCAG CTACACTCCA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 39159 2.1e-07 412_[+1]_76 39943 3.8e-07 383_[+1]_105 46677 5.1e-07 253_[+1]_235 36289 5.1e-07 313_[+1]_175 49427 2e-06 269_[+1]_219 38097 4.1e-06 408_[+1]_80 48394 5.5e-06 341_[+1]_147 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=12 seqs=7 39159 ( 413) TCTCACTGTCAG 1 39943 ( 384) CCTCACTGTCAG 1 46677 ( 254) TTTCACAGTCAG 1 36289 ( 314) TATCACAGTCAG 1 49427 ( 270) GTTTACAGTCAG 1 38097 ( 409) GCTTGCTGTCAG 1 48394 ( 342) CATTCCAGTCAG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 6357 bayes= 10.4315 E= 6.5e+001 -945 30 36 66 5 89 -945 8 -945 -945 -945 189 -945 130 -945 66 137 -69 -63 -945 -945 211 -945 -945 105 -945 -945 66 -945 -945 217 -945 -945 -945 -945 189 -945 211 -945 -945 185 -945 -945 -945 -945 -945 217 -945 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 7 E= 6.5e+001 0.000000 0.285714 0.285714 0.428571 0.285714 0.428571 0.000000 0.285714 0.000000 0.000000 0.000000 1.000000 0.000000 0.571429 0.000000 0.428571 0.714286 0.142857 0.142857 0.000000 0.000000 1.000000 0.000000 0.000000 0.571429 0.000000 0.000000 0.428571 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [TCG][CAT]T[CT]AC[AT]GTCAG -------------------------------------------------------------------------------- Time 1.52 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 20 sites = 8 llr = 119 E-value = 4.7e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A 16a43531333::a3::399 pos.-specific C 9::355::14:33::::5:: probability G :1:41:::1:8:6:::9::1 matrix T :3::1:8954:81:8a131: bits 2.2 2.0 * * * 1.7 * * * 1.5 * * * ** Relative 1.3 * * * * * ** ** Entropy 1.1 * * *** ** **** ** (21.5 bits) 0.9 * * *** ******* ** 0.7 *** *** ******* ** 0.4 **** *** *********** 0.2 ******************** 0.0 -------------------- Multilevel CAAACATTTCGTGATTGCAA consensus T GACA ATACC A A sequence C A T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------------- 43494 358 2.63e-11 ATCTTCCGGA CAAGCCTTTCGTGATTGTAA TCACGACGTG 43495 358 8.48e-11 ATGGCGAGGG CAAGCCTTCCGTGATTGCAA TGCTTTCGGA 46677 384 2.27e-08 CTCGACTACT CAAAGCATATGTGATTGTAA GCAACATCCA 38097 97 1.36e-07 ACTTAATATC CAACACTTATGCCAATGAAA TTATGAGTAC 32342 459 1.46e-07 ATCGTTTTAG CAAGCATAGAATCATTGCAA CTTGCAGATC 48394 85 3.46e-07 CAAGGGTAAG CGAAAAATTTATGAATGAAA AGCTCGGACT 39943 175 5.17e-07 TCACATGGCA CTACTATTTAGTGATTTCTA TATATCGTGG 39159 235 5.45e-07 GAGGGGATTT ATAACATTTCGCTATTGCAG TATCCACAAA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 43494 2.6e-11 357_[+2]_123 43495 8.5e-11 357_[+2]_123 46677 2.3e-08 383_[+2]_97 38097 1.4e-07 96_[+2]_384 32342 1.5e-07 458_[+2]_22 48394 3.5e-07 84_[+2]_396 39943 5.2e-07 174_[+2]_306 39159 5.5e-07 234_[+2]_246 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=20 seqs=8 43494 ( 358) CAAGCCTTTCGTGATTGTAA 1 43495 ( 358) CAAGCCTTCCGTGATTGCAA 1 46677 ( 384) CAAAGCATATGTGATTGTAA 1 38097 ( 97) CAACACTTATGCCAATGAAA 1 32342 ( 459) CAAGCATAGAATCATTGCAA 1 48394 ( 85) CGAAAAATTTATGAATGAAA 1 39943 ( 175) CTACTATTTAGTGATTTCTA 1 39159 ( 235) ATAACATTTCGCTATTGCAG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 6253 bayes= 9.60849 E= 4.7e+002 -114 192 -965 -965 118 -965 -83 -11 185 -965 -965 -965 44 11 76 -965 -14 111 -83 -111 85 111 -965 -965 -14 -965 -965 147 -114 -965 -965 169 -14 -89 -83 89 -14 70 -965 47 -14 -965 176 -965 -965 11 -965 147 -965 11 149 -111 185 -965 -965 -965 -14 -965 -965 147 -965 -965 -965 189 -965 -965 198 -111 -14 111 -965 -11 166 -965 -965 -111 166 -965 -83 -965 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 8 E= 4.7e+002 0.125000 0.875000 0.000000 0.000000 0.625000 0.000000 0.125000 0.250000 1.000000 0.000000 0.000000 0.000000 0.375000 0.250000 0.375000 0.000000 0.250000 0.500000 0.125000 0.125000 0.500000 0.500000 0.000000 0.000000 0.250000 0.000000 0.000000 0.750000 0.125000 0.000000 0.000000 0.875000 0.250000 0.125000 0.125000 0.500000 0.250000 0.375000 0.000000 0.375000 0.250000 0.000000 0.750000 0.000000 0.000000 0.250000 0.000000 0.750000 0.000000 0.250000 0.625000 0.125000 1.000000 0.000000 0.000000 0.000000 0.250000 0.000000 0.000000 0.750000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.875000 0.125000 0.250000 0.500000 0.000000 0.250000 0.875000 0.000000 0.000000 0.125000 0.875000 0.000000 0.125000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- C[AT]A[AGC][CA][AC][TA]T[TA][CTA][GA][TC][GC]A[TA]TG[CAT]AA -------------------------------------------------------------------------------- Time 3.01 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 16 sites = 7 llr = 94 E-value = 7.0e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A 7113::4::7:497:: pos.-specific C 1:37::1:1::3:3:6 probability G 191:a31a9:a1:::: matrix T ::4::73::3:11:a4 bits 2.2 * * * 2.0 * * * * 1.7 * * * * 1.5 * * ** * * Relative 1.3 * * ** * * * Entropy 1.1 * *** **** **** (19.3 bits) 0.9 ** *** **** **** 0.7 ** *** **** **** 0.4 ** *** **** **** 0.2 ****** ********* 0.0 ---------------- Multilevel AGTCGTAGGAGAAATC consensus CA GT T C C T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 39943 126 5.15e-09 TCGTTTTGCG AGTCGTCGGAGAAATC GCGAAACAAA 46677 413 4.95e-08 AGCAACATCC AGTCGGAGGAGGAATT CCTCTCACAA 43495 247 9.19e-08 GGATATATAT GGACGTAGGAGAAATC AAAAGTACGA 39265 387 2.15e-07 CGGTAGCAGT AGCAGTAGCAGAAATC AATAGCAGAA 39159 94 9.87e-07 TTGACTGTGA AGTAGTTGGTGTACTT TGAGCGACCT 36289 389 1.43e-06 ACTGGAAAAT AAGCGTTGGTGCACTC TTTTGCTGGG 35518 461 2.17e-06 TGGTCGCAAA CGCCGGGGGAGCTATT TCCTTGTCAC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 39943 5.2e-09 125_[+3]_359 46677 5e-08 412_[+3]_72 43495 9.2e-08 246_[+3]_238 39265 2.2e-07 386_[+3]_98 39159 9.9e-07 93_[+3]_391 36289 1.4e-06 388_[+3]_96 35518 2.2e-06 460_[+3]_24 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=16 seqs=7 39943 ( 126) AGTCGTCGGAGAAATC 1 46677 ( 413) AGTCGGAGGAGGAATT 1 43495 ( 247) GGACGTAGGAGAAATC 1 39265 ( 387) AGCAGTAGCAGAAATC 1 39159 ( 94) AGTAGTTGGTGTACTT 1 36289 ( 389) AAGCGTTGGTGCACTC 1 35518 ( 461) CGCCGGGGGAGCTATT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 6305 bayes= 10.4196 E= 7.0e+002 137 -69 -63 -945 -95 -945 195 -945 -95 30 -63 66 5 162 -945 -945 -945 -945 217 -945 -945 -945 36 140 63 -69 -63 8 -945 -945 217 -945 -945 -69 195 -945 137 -945 -945 8 -945 -945 217 -945 63 30 -63 -92 163 -945 -945 -92 137 30 -945 -945 -945 -945 -945 189 -945 130 -945 66 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 7 E= 7.0e+002 0.714286 0.142857 0.142857 0.000000 0.142857 0.000000 0.857143 0.000000 0.142857 0.285714 0.142857 0.428571 0.285714 0.714286 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.285714 0.714286 0.428571 0.142857 0.142857 0.285714 0.000000 0.000000 1.000000 0.000000 0.000000 0.142857 0.857143 0.000000 0.714286 0.000000 0.000000 0.285714 0.000000 0.000000 1.000000 0.000000 0.428571 0.285714 0.142857 0.142857 0.857143 0.000000 0.000000 0.142857 0.714286 0.285714 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.571429 0.000000 0.428571 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- AG[TC][CA]G[TG][AT]GG[AT]G[AC]A[AC]T[CT] -------------------------------------------------------------------------------- Time 4.51 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 32342 9.97e-04 241_[+2(9.93e-05)]_197_\ [+2(1.46e-07)]_22 36289 2.01e-05 313_[+1(5.13e-07)]_63_\ [+3(1.43e-06)]_96 38097 1.83e-05 96_[+2(1.36e-07)]_292_\ [+1(4.07e-06)]_80 48394 4.66e-05 84_[+2(3.46e-07)]_237_\ [+1(5.50e-06)]_147 43494 5.47e-07 357_[+2(2.63e-11)]_123 43495 3.52e-10 246_[+3(9.19e-08)]_95_\ [+2(8.48e-11)]_123 35518 1.67e-02 460_[+3(2.17e-06)]_24 39159 4.43e-09 38_[+1(1.14e-05)]_43_[+3(9.87e-07)]_\ 125_[+2(5.45e-07)]_158_[+1(2.12e-07)]_76 39265 4.69e-03 386_[+3(2.15e-07)]_18_\ [+3(5.02e-05)]_64 49427 2.11e-03 269_[+1(1.98e-06)]_219 46486 6.79e-01 500 46677 3.24e-11 253_[+1(5.13e-07)]_118_\ [+2(2.27e-08)]_9_[+3(4.95e-08)]_72 39943 5.42e-11 125_[+3(5.15e-09)]_33_\ [+2(5.17e-07)]_189_[+1(3.76e-07)]_105 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************