******************************************************************************** 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/9/9.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 27877 1.0000 500 46560 1.0000 500 46563 1.0000 500 47789 1.0000 500 39908 1.0000 500 49555 1.0000 500 51761 1.0000 500 11631 1.0000 500 48378 1.0000 500 45027 1.0000 500 39869 1.0000 500 36633 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/9/9.seqs.fa -oc motifs/9 -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= 12 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= 6000 N= 12 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.291 C 0.226 G 0.209 T 0.273 Background letter frequencies (from dataset with add-one prior applied): A 0.291 C 0.226 G 0.210 T 0.273 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 21 sites = 5 llr = 101 E-value = 9.3e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A :::2::226::a:42:66::: pos.-specific C a42:2::2::::::6a::4a2 probability G :6:8::462a::a:2:4:::8 matrix T ::8:8a4:2:a::6:::46:: bits 2.3 * * * * * 2.0 * * * * * 1.8 * * **** * * 1.6 * * **** * ** Relative 1.4 * * * **** * ** Entropy 1.1 ****** **** * ** (29.3 bits) 0.9 ****** ***** ****** 0.7 ****** * ************ 0.5 ********************* 0.2 ********************* 0.0 --------------------- Multilevel CGTGTTGGAGTAGTCCAATCG consensus CCAC TAG AA GTC C sequence ACT G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 46563 230 2.03e-12 TGGAAATGAC CGTGTTGGAGTAGACCGATCG TGCCCAGACT 46560 237 2.03e-12 TGGAAATGAC CGTGTTGGAGTAGACCGATCG TGCCCAGACT 39908 12 4.90e-10 CAAATGCATC CGTGTTAATGTAGTCCATTCG AAATTCTATT 48378 159 1.99e-09 GACCTCATTT CCTGCTTCGGTAGTGCATCCG ATCAACGAGG 47789 151 3.69e-09 ACAGTTTGTA CCCATTTGAGTAGTACAACCC TGCAATTGGC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 46563 2e-12 229_[+1]_250 46560 2e-12 236_[+1]_243 39908 4.9e-10 11_[+1]_468 48378 2e-09 158_[+1]_321 47789 3.7e-09 150_[+1]_329 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=21 seqs=5 46563 ( 230) CGTGTTGGAGTAGACCGATCG 1 46560 ( 237) CGTGTTGGAGTAGACCGATCG 1 39908 ( 12) CGTGTTAATGTAGTCCATTCG 1 48378 ( 159) CCTGCTTCGGTAGTGCATCCG 1 47789 ( 151) CCCATTTGAGTAGTACAACCC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 5760 bayes= 10.4204 E= 9.3e-001 -897 214 -897 -897 -897 82 152 -897 -897 -18 -897 155 -54 -897 193 -897 -897 -18 -897 155 -897 -897 -897 187 -54 -897 93 55 -54 -18 152 -897 104 -897 -7 -45 -897 -897 225 -897 -897 -897 -897 187 178 -897 -897 -897 -897 -897 225 -897 46 -897 -897 114 -54 140 -7 -897 -897 214 -897 -897 104 -897 93 -897 104 -897 -897 55 -897 82 -897 114 -897 214 -897 -897 -897 -18 193 -897 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 5 E= 9.3e-001 0.000000 1.000000 0.000000 0.000000 0.000000 0.400000 0.600000 0.000000 0.000000 0.200000 0.000000 0.800000 0.200000 0.000000 0.800000 0.000000 0.000000 0.200000 0.000000 0.800000 0.000000 0.000000 0.000000 1.000000 0.200000 0.000000 0.400000 0.400000 0.200000 0.200000 0.600000 0.000000 0.600000 0.000000 0.200000 0.200000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.400000 0.000000 0.000000 0.600000 0.200000 0.600000 0.200000 0.000000 0.000000 1.000000 0.000000 0.000000 0.600000 0.000000 0.400000 0.000000 0.600000 0.000000 0.000000 0.400000 0.000000 0.400000 0.000000 0.600000 0.000000 1.000000 0.000000 0.000000 0.000000 0.200000 0.800000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- C[GC][TC][GA][TC]T[GTA][GAC][AGT]GTAG[TA][CAG]C[AG][AT][TC]C[GC] -------------------------------------------------------------------------------- Time 1.25 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 15 sites = 8 llr = 106 E-value = 3.1e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A :13:8:435::::94 pos.-specific C :3:3:1665:6:a:6 probability G :46839:1:::::1: matrix T a31::::::a4a::: bits 2.3 * 2.0 * 1.8 * * * ** 1.6 * * * ** Relative 1.4 * * * * *** Entropy 1.1 * **** ****** (19.1 bits) 0.9 * ***** ******* 0.7 * ************* 0.5 * ************* 0.2 *************** 0.0 --------------- Multilevel TGGGAGCCATCTCAC consensus CACG AAC T A sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------- 46563 195 4.09e-09 CCAGATGCTT TGGGAGACCTCTCAC AGAAGATTGA 46560 200 4.09e-09 CCAGATGCTT TGGGAGACCTCTCAC TCTGAAGATT 11631 144 3.24e-08 AGAGGCAAAC TTGGAGCCATCTCAA ATTACAAGTC 39869 47 4.49e-07 ACAACTATTG TTGGAGCAATTTCAA TATAGCAGGT 47789 387 8.82e-07 TTTTTACGCT TGTGACCCATCTCAC AGAATGACCG 36633 7 2.06e-06 TACCAA TAACAGCGCTCTCAC GGTCGCGGTC 45027 47 2.16e-06 ATTTTCGATT TCAGGGCAATTTCAA TGAATGATGC 49555 420 2.16e-06 GTTTCTTCGT TCGCGGACCTTTCGC TGTGCGCGTC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 46563 4.1e-09 194_[+2]_291 46560 4.1e-09 199_[+2]_286 11631 3.2e-08 143_[+2]_342 39869 4.5e-07 46_[+2]_439 47789 8.8e-07 386_[+2]_99 36633 2.1e-06 6_[+2]_479 45027 2.2e-06 46_[+2]_439 49555 2.2e-06 419_[+2]_66 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=15 seqs=8 46563 ( 195) TGGGAGACCTCTCAC 1 46560 ( 200) TGGGAGACCTCTCAC 1 11631 ( 144) TTGGAGCCATCTCAA 1 39869 ( 47) TTGGAGCAATTTCAA 1 47789 ( 387) TGTGACCCATCTCAC 1 36633 ( 7) TAACAGCGCTCTCAC 1 45027 ( 47) TCAGGGCAATTTCAA 1 49555 ( 420) TCGCGGACCTTTCGC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 5832 bayes= 10.2456 E= 3.1e+000 -965 -965 -965 187 -122 14 84 -13 -22 -965 158 -112 -965 14 184 -965 136 -965 25 -965 -965 -86 206 -965 36 146 -965 -965 -22 146 -74 -965 78 114 -965 -965 -965 -965 -965 187 -965 146 -965 46 -965 -965 -965 187 -965 214 -965 -965 159 -965 -74 -965 36 146 -965 -965 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 8 E= 3.1e+000 0.000000 0.000000 0.000000 1.000000 0.125000 0.250000 0.375000 0.250000 0.250000 0.000000 0.625000 0.125000 0.000000 0.250000 0.750000 0.000000 0.750000 0.000000 0.250000 0.000000 0.000000 0.125000 0.875000 0.000000 0.375000 0.625000 0.000000 0.000000 0.250000 0.625000 0.125000 0.000000 0.500000 0.500000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.625000 0.000000 0.375000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.875000 0.000000 0.125000 0.000000 0.375000 0.625000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- T[GCT][GA][GC][AG]G[CA][CA][AC]T[CT]TCA[CA] -------------------------------------------------------------------------------- Time 2.67 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 21 sites = 4 llr = 88 E-value = 5.2e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A ::3:::a5:3:8:::8::3:: pos.-specific C :::::::3:3:33::38:::: probability G :3:aa::3::a:88::338:: matrix T a88::a::a5:::3a::8:aa bits 2.3 ** * 2.0 ** * 1.8 * **** * * * ** 1.6 * **** * * * ** Relative 1.4 * **** * * *** * *** Entropy 1.1 ******* * *********** (31.6 bits) 0.9 ******* * *********** 0.7 ******* * *********** 0.5 ********************* 0.2 ********************* 0.0 --------------------- Multilevel TTTGGTAATTGAGGTACTGTT consensus GA C A CCT CGGA sequence G C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 46563 365 3.20e-13 ATACCAAGGA TTTGGTAATTGAGGTACTGTT TGATGTTACA 46560 363 1.06e-12 ATACCAAGGA TTTGGTAATCGAGGTACTGTT TGAATGTTAC 39869 337 5.17e-10 AGACCCAGCT TGTGGTACTAGCCTTACTGTT GATAGATGAA 39908 218 5.93e-10 CATCTCTCGT TTAGGTAGTTGAGGTCGGATT TCAAAAAGGG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 46563 3.2e-13 364_[+3]_115 46560 1.1e-12 362_[+3]_117 39869 5.2e-10 336_[+3]_143 39908 5.9e-10 217_[+3]_262 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=21 seqs=4 46563 ( 365) TTTGGTAATTGAGGTACTGTT 1 46560 ( 363) TTTGGTAATCGAGGTACTGTT 1 39869 ( 337) TGTGGTACTAGCCTTACTGTT 1 39908 ( 218) TTAGGTAGTTGAGGTCGGATT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 5760 bayes= 10.4909 E= 5.2e+000 -865 -865 -865 187 -865 -865 25 146 -22 -865 -865 146 -865 -865 225 -865 -865 -865 225 -865 -865 -865 -865 187 178 -865 -865 -865 78 14 25 -865 -865 -865 -865 187 -22 14 -865 87 -865 -865 225 -865 136 14 -865 -865 -865 14 184 -865 -865 -865 184 -13 -865 -865 -865 187 136 14 -865 -865 -865 173 25 -865 -865 -865 25 146 -22 -865 184 -865 -865 -865 -865 187 -865 -865 -865 187 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 4 E= 5.2e+000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.250000 0.750000 0.250000 0.000000 0.000000 0.750000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.500000 0.250000 0.250000 0.000000 0.000000 0.000000 0.000000 1.000000 0.250000 0.250000 0.000000 0.500000 0.000000 0.000000 1.000000 0.000000 0.750000 0.250000 0.000000 0.000000 0.000000 0.250000 0.750000 0.000000 0.000000 0.000000 0.750000 0.250000 0.000000 0.000000 0.000000 1.000000 0.750000 0.250000 0.000000 0.000000 0.000000 0.750000 0.250000 0.000000 0.000000 0.000000 0.250000 0.750000 0.250000 0.000000 0.750000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- T[TG][TA]GGTA[ACG]T[TAC]G[AC][GC][GT]T[AC][CG][TG][GA]TT -------------------------------------------------------------------------------- Time 3.91 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 27877 7.18e-01 500 46560 1.56e-21 199_[+2(4.09e-09)]_22_\ [+1(2.03e-12)]_105_[+3(1.06e-12)]_117 46563 4.91e-22 194_[+2(4.09e-09)]_20_\ [+1(2.03e-12)]_114_[+3(3.20e-13)]_115 47789 1.39e-07 150_[+1(3.69e-09)]_215_\ [+2(8.82e-07)]_99 39908 2.52e-11 11_[+1(4.90e-10)]_185_\ [+3(5.93e-10)]_262 49555 1.04e-02 419_[+2(2.16e-06)]_66 51761 8.70e-01 500 11631 6.03e-04 143_[+2(3.24e-08)]_342 48378 4.43e-05 158_[+1(1.99e-09)]_321 45027 7.63e-03 46_[+2(2.16e-06)]_439 39869 9.83e-09 46_[+2(4.49e-07)]_275_\ [+3(5.17e-10)]_143 36633 4.08e-03 6_[+2(2.06e-06)]_303_[+2(6.05e-05)]_\ 161 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************