******************************************************************************** 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/180/180.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 23111 1.0000 500 24034 1.0000 500 24725 1.0000 500 269322 1.0000 500 29359 1.0000 500 31113 1.0000 500 3229 1.0000 500 33228 1.0000 500 36107 1.0000 500 41256 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/180/180.seqs.fa -oc motifs/180 -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 0.251 C 0.243 G 0.248 T 0.258 Background letter frequencies (from dataset with add-one prior applied): A 0.251 C 0.243 G 0.248 T 0.258 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 21 sites = 5 llr = 97 E-value = 1.5e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A a:2:66:8:2:a::6:28a4: pos.-specific C ::8622a:868::a4282:28 probability G :::::2::2:2:2::::::42 matrix T :a:42::2:2::8::8::::: bits 2.0 ** * * * * 1.8 ** * * * * 1.6 ** * * * * 1.4 ** * * * * Relative 1.2 *** *** **** **** * Entropy 1.0 **** *** ********* * (28.1 bits) 0.8 **** *** ********* * 0.6 ******************* * 0.4 ********************* 0.2 ********************* 0.0 --------------------- Multilevel ATCCAACACCCATCATCAAAC consensus ATCC TGAG G CCAC GG sequence TG T C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 3229 319 3.99e-13 TGTCAAGCCT ATCCAACACCCATCATCAAAC AACCACCAAT 36107 479 1.04e-09 TCGAAGGAGC ATCTCACACCGATCCTAAAGC C 24034 148 1.04e-09 CCCCATCTGA ATCTTCCACCCATCATCAACG GCAGGCCACA 33228 351 1.86e-09 TTGTCTATCT ATCCAGCAGTCATCCTCCAGC TAGCAGAGAC 24725 479 5.04e-09 CCCCAAACCA ATACAACTCACAGCACCAAAC A -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 3229 4e-13 318_[+1]_161 36107 1e-09 478_[+1]_1 24034 1e-09 147_[+1]_332 33228 1.9e-09 350_[+1]_129 24725 5e-09 478_[+1]_1 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=21 seqs=5 3229 ( 319) ATCCAACACCCATCATCAAAC 1 36107 ( 479) ATCTCACACCGATCCTAAAGC 1 24034 ( 148) ATCTTCCACCCATCATCAACG 1 33228 ( 351) ATCCAGCAGTCATCCTCCAGC 1 24725 ( 479) ATACAACTCACAGCACCAAAC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 4800 bayes= 10.1572 E= 1.5e+000 199 -897 -897 -897 -897 -897 -897 195 -33 172 -897 -897 -897 130 -897 63 125 -28 -897 -37 125 -28 -31 -897 -897 204 -897 -897 167 -897 -897 -37 -897 172 -31 -897 -33 130 -897 -37 -897 172 -31 -897 199 -897 -897 -897 -897 -897 -31 163 -897 204 -897 -897 125 72 -897 -897 -897 -28 -897 163 -33 172 -897 -897 167 -28 -897 -897 199 -897 -897 -897 67 -28 69 -897 -897 172 -31 -897 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 5 E= 1.5e+000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.200000 0.800000 0.000000 0.000000 0.000000 0.600000 0.000000 0.400000 0.600000 0.200000 0.000000 0.200000 0.600000 0.200000 0.200000 0.000000 0.000000 1.000000 0.000000 0.000000 0.800000 0.000000 0.000000 0.200000 0.000000 0.800000 0.200000 0.000000 0.200000 0.600000 0.000000 0.200000 0.000000 0.800000 0.200000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.200000 0.800000 0.000000 1.000000 0.000000 0.000000 0.600000 0.400000 0.000000 0.000000 0.000000 0.200000 0.000000 0.800000 0.200000 0.800000 0.000000 0.000000 0.800000 0.200000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.400000 0.200000 0.400000 0.000000 0.000000 0.800000 0.200000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- AT[CA][CT][ACT][ACG]C[AT][CG][CAT][CG]A[TG]C[AC][TC][CA][AC]A[AGC][CG] -------------------------------------------------------------------------------- Time 0.93 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 17 sites = 6 llr = 93 E-value = 1.7e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A :a22:3:7:527:3:3a pos.-specific C a:8752a2a572a7a7: probability G :::222::::2:::::: matrix T ::::33:2:::2::::: bits 2.0 ** * * * * * 1.8 ** * * * * * 1.6 ** * * * * * 1.4 *** * * * * * Relative 1.2 *** * * * * * Entropy 1.0 *** * ** ***** (22.5 bits) 0.8 **** *********** 0.6 ***** *********** 0.4 ***** *********** 0.2 ***** *********** 0.0 ----------------- Multilevel CACCCACACACACCCCA consensus TT C A A sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ----------------- 36107 407 5.67e-09 AATTCTCCAC CACCTTCCCCCACCCCA GAATCCGTTA 24034 63 9.77e-09 CACTCCATCA CACCCCCACCCTCCCCA TTTTCGTTGC 3229 392 2.56e-08 CACACACACA CACACACACACACACAA AGATCCGTCT 24725 457 3.04e-08 GACGTTGCAC CAACCTCACAAACCCCA AACCAATACA 29359 248 1.29e-07 TGACGTGATA CACCGACTCACCCACCA GAAAATGCAA 33228 391 1.56e-07 CACGACCCGT CACGTGCACCGACCCAA CGCATCGCAA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 36107 5.7e-09 406_[+2]_77 24034 9.8e-09 62_[+2]_421 3229 2.6e-08 391_[+2]_92 24725 3e-08 456_[+2]_27 29359 1.3e-07 247_[+2]_236 33228 1.6e-07 390_[+2]_93 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=17 seqs=6 36107 ( 407) CACCTTCCCCCACCCCA 1 24034 ( 63) CACCCCCACCCTCCCCA 1 3229 ( 392) CACACACACACACACAA 1 24725 ( 457) CAACCTCACAAACCCCA 1 29359 ( 248) CACCGACTCACCCACCA 1 33228 ( 391) CACGTGCACCGACCCAA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 17 n= 4840 bayes= 10.7545 E= 1.7e+000 -923 204 -923 -923 199 -923 -923 -923 -59 178 -923 -923 -59 146 -57 -923 -923 104 -57 37 41 -54 -57 37 -923 204 -923 -923 141 -54 -923 -63 -923 204 -923 -923 99 104 -923 -923 -59 146 -57 -923 141 -54 -923 -63 -923 204 -923 -923 41 146 -923 -923 -923 204 -923 -923 41 146 -923 -923 199 -923 -923 -923 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 17 nsites= 6 E= 1.7e+000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.166667 0.833333 0.000000 0.000000 0.166667 0.666667 0.166667 0.000000 0.000000 0.500000 0.166667 0.333333 0.333333 0.166667 0.166667 0.333333 0.000000 1.000000 0.000000 0.000000 0.666667 0.166667 0.000000 0.166667 0.000000 1.000000 0.000000 0.000000 0.500000 0.500000 0.000000 0.000000 0.166667 0.666667 0.166667 0.000000 0.666667 0.166667 0.000000 0.166667 0.000000 1.000000 0.000000 0.000000 0.333333 0.666667 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.333333 0.666667 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- CACC[CT][AT]CAC[AC]CAC[CA]C[CA]A -------------------------------------------------------------------------------- Time 1.86 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 21 sites = 5 llr = 93 E-value = 1.2e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A :::a:2::88:2:264286:: pos.-specific C a8a:22:a22a224:68::a: probability G :2::22a::::6642::22:8 matrix T ::::64::::::2:2:::2:2 bits 2.0 * ** ** * * 1.8 * ** ** * * 1.6 * ** ** * * 1.4 * ** ** * * Relative 1.2 **** ***** ** ** Entropy 1.0 **** ***** *** ** (26.7 bits) 0.8 **** ***** *** ** 0.6 ***** ******* ******* 0.4 ***** *************** 0.2 ***** *************** 0.0 --------------------- Multilevel CCCATTGCAACGGCACCAACG consensus G CA CC ACGGAAGG T sequence GC CTAT T G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 29359 145 1.22e-11 CTCAAAGATT CCCATTGCAACGGCACAAACG ACATTGGCAT 36107 439 8.68e-10 CGTTATGACT CCCACAGCAACGCCACCATCG CCCTCGGCTT 41256 102 2.28e-09 CTCATACTCT CCCATGGCACCCGGAACGACG ACCGATTTGA 33228 408 3.92e-09 ACCGACCCAA CGCATCGCAACGGATACAGCG ACAGTGTTCA 269322 334 1.70e-08 TTTGTTGAGG CCCAGTGCCACATGGCCAACT AGAACGAAGC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 29359 1.2e-11 144_[+3]_335 36107 8.7e-10 438_[+3]_41 41256 2.3e-09 101_[+3]_378 33228 3.9e-09 407_[+3]_72 269322 1.7e-08 333_[+3]_146 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=21 seqs=5 29359 ( 145) CCCATTGCAACGGCACAAACG 1 36107 ( 439) CCCACAGCAACGCCACCATCG 1 41256 ( 102) CCCATGGCACCCGGAACGACG 1 33228 ( 408) CGCATCGCAACGGATACAGCG 1 269322 ( 334) CCCAGTGCCACATGGCCAACT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 4800 bayes= 10.1572 E= 1.2e+001 -897 204 -897 -897 -897 172 -31 -897 -897 204 -897 -897 199 -897 -897 -897 -897 -28 -31 122 -33 -28 -31 63 -897 -897 201 -897 -897 204 -897 -897 167 -28 -897 -897 167 -28 -897 -897 -897 204 -897 -897 -33 -28 127 -897 -897 -28 127 -37 -33 72 69 -897 125 -897 -31 -37 67 130 -897 -897 -33 172 -897 -897 167 -897 -31 -897 125 -897 -31 -37 -897 204 -897 -897 -897 -897 169 -37 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 5 E= 1.2e+001 0.000000 1.000000 0.000000 0.000000 0.000000 0.800000 0.200000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.200000 0.200000 0.600000 0.200000 0.200000 0.200000 0.400000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.800000 0.200000 0.000000 0.000000 0.800000 0.200000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.200000 0.200000 0.600000 0.000000 0.000000 0.200000 0.600000 0.200000 0.200000 0.400000 0.400000 0.000000 0.600000 0.000000 0.200000 0.200000 0.400000 0.600000 0.000000 0.000000 0.200000 0.800000 0.000000 0.000000 0.800000 0.000000 0.200000 0.000000 0.600000 0.000000 0.200000 0.200000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.800000 0.200000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- C[CG]CA[TCG][TACG]GC[AC][AC]C[GAC][GCT][CGA][AGT][CA][CA][AG][AGT]C[GT] -------------------------------------------------------------------------------- Time 2.71 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 23111 9.93e-01 500 24034 2.07e-10 62_[+2(9.77e-09)]_68_[+1(1.04e-09)]_\ 332 24725 4.82e-10 235_[+3(7.09e-05)]_200_\ [+2(3.04e-08)]_5_[+1(5.04e-09)]_1 269322 1.90e-04 333_[+3(1.70e-08)]_146 29359 1.20e-10 144_[+3(1.22e-11)]_82_\ [+2(1.29e-07)]_236 31113 2.72e-01 500 3229 8.33e-13 29_[+1(2.77e-05)]_268_\ [+1(3.99e-13)]_22_[+2(1.66e-06)]_13_[+2(2.56e-08)]_92 33228 8.97e-14 350_[+1(1.86e-09)]_19_\ [+2(1.56e-07)]_[+3(3.92e-09)]_72 36107 5.29e-16 406_[+2(5.67e-09)]_15_\ [+3(8.68e-10)]_19_[+1(1.04e-09)]_1 41256 1.14e-05 101_[+3(2.28e-09)]_378 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************