******************************************************************************** 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/284/284.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 10965 1.0000 500 20793 1.0000 500 21719 1.0000 500 22954 1.0000 500 23550 1.0000 500 24275 1.0000 500 269572 1.0000 500 32858 1.0000 500 4142 1.0000 500 9524 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/284/284.seqs.fa -oc motifs/284 -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 0.269 C 0.248 G 0.222 T 0.260 Background letter frequencies (from dataset with add-one prior applied): A 0.269 C 0.248 G 0.222 T 0.260 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 16 sites = 8 llr = 115 E-value = 1.1e-003 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A ::4::::3:3:13::: pos.-specific C ::3::::::4:4:::: probability G :4:495:81:a3:a:6 matrix T a64615a:94:38:a4 bits 2.2 * * 2.0 * * * ** 1.7 * * * ** 1.5 * * * * * ** Relative 1.3 * * *** * ** Entropy 1.1 ** ****** * **** (20.8 bits) 0.9 ** ****** * **** 0.7 ** ****** * **** 0.4 *********** **** 0.2 **************** 0.0 ---------------- Multilevel TTATGGTGTCGCTGTG consensus GTG T A T GA T sequence C A T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 32858 138 6.68e-09 AGAGGTATGA TTATGTTGTTGGTGTG CATCGTCGAT 20793 123 1.43e-08 ACTTTTACTC TTTTGTTGTCGCTGTT GTAACCAGTC 269572 146 1.68e-08 GTGAGTTGTT TTCGGTTGTTGCTGTG TTGTTTATAT 9524 67 2.35e-08 TCGGGCTGCG TTTGGTTGTTGTTGTG GTTTTTGACG 22954 143 2.43e-07 GGTACTCCAT TGATGGTATCGATGTG TTCGTCAACG 21719 238 4.91e-07 AATAGTGATA TGATGGTATCGGAGTT CTTCAATGAA 4142 370 6.01e-07 CGTTGCGACC TTCTTGTGTAGTTGTT TGTTTGCAAC 23550 120 6.01e-07 GTGCTGGGTC TGTGGGTGGAGCAGTG GTGCAGTCTG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 32858 6.7e-09 137_[+1]_347 20793 1.4e-08 122_[+1]_362 269572 1.7e-08 145_[+1]_339 9524 2.4e-08 66_[+1]_418 22954 2.4e-07 142_[+1]_342 21719 4.9e-07 237_[+1]_247 4142 6e-07 369_[+1]_115 23550 6e-07 119_[+1]_365 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=16 seqs=8 32858 ( 138) TTATGTTGTTGGTGTG 1 20793 ( 123) TTTTGTTGTCGCTGTT 1 269572 ( 146) TTCGGTTGTTGCTGTG 1 9524 ( 67) TTTGGTTGTTGTTGTG 1 22954 ( 143) TGATGGTATCGATGTG 1 21719 ( 238) TGATGGTATCGGAGTT 1 4142 ( 370) TTCTTGTGTAGTTGTT 1 23550 ( 120) TGTGGGTGGAGCAGTG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 4850 bayes= 9.97931 E= 1.1e-003 -965 -965 -965 194 -965 -965 75 126 48 1 -965 53 -965 -965 75 126 -965 -965 197 -106 -965 -965 117 94 -965 -965 -965 194 -11 -965 175 -965 -965 -965 -83 175 -11 60 -965 53 -965 -965 217 -965 -111 60 17 -6 -11 -965 -965 153 -965 -965 217 -965 -965 -965 -965 194 -965 -965 149 53 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 8 E= 1.1e-003 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.375000 0.625000 0.375000 0.250000 0.000000 0.375000 0.000000 0.000000 0.375000 0.625000 0.000000 0.000000 0.875000 0.125000 0.000000 0.000000 0.500000 0.500000 0.000000 0.000000 0.000000 1.000000 0.250000 0.000000 0.750000 0.000000 0.000000 0.000000 0.125000 0.875000 0.250000 0.375000 0.000000 0.375000 0.000000 0.000000 1.000000 0.000000 0.125000 0.375000 0.250000 0.250000 0.250000 0.000000 0.000000 0.750000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.625000 0.375000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- T[TG][ATC][TG]G[GT]T[GA]T[CTA]G[CGT][TA]GT[GT] -------------------------------------------------------------------------------- Time 0.95 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 12 sites = 10 llr = 107 E-value = 6.7e-002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A ::8::8:114:: pos.-specific C :::1::3::331 probability G :a1:a:397119 matrix T a:19:24:226: bits 2.2 * * 2.0 ** * 1.7 ** * * * 1.5 ** ** * * Relative 1.3 ** ** * * Entropy 1.1 ****** * * (15.5 bits) 0.9 ****** ** * 0.7 ****** ** ** 0.4 ********* ** 0.2 ************ 0.0 ------------ Multilevel TGATGATGGATG consensus TC TCC sequence G T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 21719 308 3.51e-07 TGGTGACAAC TGATGATGGTTG AGCAAACACA 9524 351 1.02e-06 GTGGATGCCA TGATGAGGTATG AATTGATGGG 32858 254 2.26e-06 TTGAACTGAT TGATGACGGGCG ATGAAGTATG 20793 56 2.83e-06 CACCAGATGA TGTTGATGGCTG ACGTTGATTT 10965 155 4.58e-06 ACATCGAGGA TGATGACGACTG ATGAAGCGCT 4142 59 6.36e-06 GTTGCTTTTG TGATGATGGACC TATCTGCTGT 23550 380 6.95e-06 CAACAAATTC TGACGACGGACG GACGGTGTTG 269572 108 9.12e-06 TTAGCCCCGA TGATGTTGTTTG GGTATAGTGC 22954 324 9.77e-06 GGTTTGGAGT TGGTGAGGGAGG AGAAGAAACG 24275 129 1.56e-05 GTAGGTGAGT TGATGTGAGCTG CTTGGTCGCG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 21719 3.5e-07 307_[+2]_181 9524 1e-06 350_[+2]_138 32858 2.3e-06 253_[+2]_235 20793 2.8e-06 55_[+2]_433 10965 4.6e-06 154_[+2]_334 4142 6.4e-06 58_[+2]_430 23550 7e-06 379_[+2]_109 269572 9.1e-06 107_[+2]_381 22954 9.8e-06 323_[+2]_165 24275 1.6e-05 128_[+2]_360 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=12 seqs=10 21719 ( 308) TGATGATGGTTG 1 9524 ( 351) TGATGAGGTATG 1 32858 ( 254) TGATGACGGGCG 1 20793 ( 56) TGTTGATGGCTG 1 10965 ( 155) TGATGACGACTG 1 4142 ( 59) TGATGATGGACC 1 23550 ( 380) TGACGACGGACG 1 269572 ( 108) TGATGTTGTTTG 1 22954 ( 324) TGGTGAGGGAGG 1 24275 ( 129) TGATGTGAGCTG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 4890 bayes= 9.18275 E= 6.7e-002 -997 -997 -997 194 -997 -997 217 -997 157 -997 -115 -138 -997 -131 -997 179 -997 -997 217 -997 157 -997 -997 -38 -997 28 43 62 -143 -997 202 -997 -143 -997 165 -38 57 28 -115 -38 -997 28 -115 120 -997 -131 202 -997 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 10 E= 6.7e-002 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.800000 0.000000 0.100000 0.100000 0.000000 0.100000 0.000000 0.900000 0.000000 0.000000 1.000000 0.000000 0.800000 0.000000 0.000000 0.200000 0.000000 0.300000 0.300000 0.400000 0.100000 0.000000 0.900000 0.000000 0.100000 0.000000 0.700000 0.200000 0.400000 0.300000 0.100000 0.200000 0.000000 0.300000 0.100000 0.600000 0.000000 0.100000 0.900000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- TGATG[AT][TCG]G[GT][ACT][TC]G -------------------------------------------------------------------------------- Time 1.96 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 21 sites = 10 llr = 137 E-value = 3.8e-002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A ::51:42223:14:71:72:9 pos.-specific C 6a128357349:47:79:8a: probability G 4:31211:2:112:2:::::1 matrix T ::16:22133:8:31213::: bits 2.2 2.0 * * 1.7 * * 1.5 * * * ** Relative 1.3 * * * * *** Entropy 1.1 ** * ** * ***** (19.8 bits) 0.9 ** * * ** ******** 0.7 ** * * ** ******** 0.4 ** ** * ************ 0.2 ******** ************ 0.0 --------------------- Multilevel CCATCACCCCCTACACCACCA consensus G GCGCAATA CTGT TA sequence TT AT G G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 20793 18 2.97e-10 CTTCTTCTGC CCATCACCCTCTACATCACCA CCACTATCAC 24275 451 1.09e-08 GATCGATTCA CCGCCAACATCTGCACCACCA AAAGAGGCTC 9524 300 4.30e-08 CATTCGGCAA GCATCACCTCCTATGCTACCA ATCTCACATG 32858 183 4.30e-08 GTCTACGACA GCGTCTGCTACTGTACCACCA ATATGCAGCA 21719 449 7.91e-08 ATCCTCCCAT CCTTCTCCTCCTCCAACTCCA GCCTCCATTT 10965 409 1.82e-07 TCACTCCACT CCCTCCTCCCCTCCGTCTCCA TTCGTCCCCT 22954 245 4.82e-07 TTCAACAACG GCACGCCTAACTCCACCAACA TTTGTGATCG 269572 306 6.02e-07 AGCAACCACA CCATGACAGTCGACACCACCG TTTTTTCTAC 23550 458 2.07e-06 GAGACGACGG GCGGCCTCGCCTCTTCCTACA TTAGAGCACA 4142 472 4.32e-06 CCTTTTTTCG CCAACGAACAGAACACCACCA GCACAACC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 20793 3e-10 17_[+3]_462 24275 1.1e-08 450_[+3]_29 9524 4.3e-08 299_[+3]_180 32858 4.3e-08 182_[+3]_297 21719 7.9e-08 448_[+3]_31 10965 1.8e-07 408_[+3]_71 22954 4.8e-07 244_[+3]_235 269572 6e-07 305_[+3]_174 23550 2.1e-06 457_[+3]_22 4142 4.3e-06 471_[+3]_8 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=21 seqs=10 20793 ( 18) CCATCACCCTCTACATCACCA 1 24275 ( 451) CCGCCAACATCTGCACCACCA 1 9524 ( 300) GCATCACCTCCTATGCTACCA 1 32858 ( 183) GCGTCTGCTACTGTACCACCA 1 21719 ( 449) CCTTCTCCTCCTCCAACTCCA 1 10965 ( 409) CCCTCCTCCCCTCCGTCTCCA 1 22954 ( 245) GCACGCCTAACTCCACCAACA 1 269572 ( 306) CCATGACAGTCGACACCACCG 1 23550 ( 458) GCGGCCTCGCCTCTTCCTACA 1 4142 ( 472) CCAACGAACAGAACACCACCA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 4800 bayes= 9.1559 E= 3.8e-002 -997 127 85 -997 -997 201 -997 -997 89 -131 43 -138 -143 -31 -115 120 -997 169 -15 -997 57 28 -115 -38 -43 101 -115 -38 -43 150 -997 -138 -43 28 -15 20 16 69 -997 20 -997 186 -115 -997 -143 -997 -115 162 57 69 -15 -997 -997 150 -997 20 138 -997 -15 -138 -143 150 -997 -38 -997 186 -997 -138 138 -997 -997 20 -43 169 -997 -997 -997 201 -997 -997 174 -997 -115 -997 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 10 E= 3.8e-002 0.000000 0.600000 0.400000 0.000000 0.000000 1.000000 0.000000 0.000000 0.500000 0.100000 0.300000 0.100000 0.100000 0.200000 0.100000 0.600000 0.000000 0.800000 0.200000 0.000000 0.400000 0.300000 0.100000 0.200000 0.200000 0.500000 0.100000 0.200000 0.200000 0.700000 0.000000 0.100000 0.200000 0.300000 0.200000 0.300000 0.300000 0.400000 0.000000 0.300000 0.000000 0.900000 0.100000 0.000000 0.100000 0.000000 0.100000 0.800000 0.400000 0.400000 0.200000 0.000000 0.000000 0.700000 0.000000 0.300000 0.700000 0.000000 0.200000 0.100000 0.100000 0.700000 0.000000 0.200000 0.000000 0.900000 0.000000 0.100000 0.700000 0.000000 0.000000 0.300000 0.200000 0.800000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.900000 0.000000 0.100000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [CG]C[AG][TC][CG][ACT][CAT][CA][CTAG][CAT]CT[ACG][CT][AG][CT]C[AT][CA]CA -------------------------------------------------------------------------------- Time 2.95 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 10965 8.92e-06 154_[+2(4.58e-06)]_242_\ [+3(1.82e-07)]_71 20793 8.48e-13 17_[+3(2.97e-10)]_17_[+2(2.83e-06)]_\ 55_[+1(1.43e-08)]_83_[+2(1.46e-05)]_267 21719 6.18e-10 237_[+1(4.91e-07)]_54_\ [+2(3.51e-07)]_129_[+3(7.91e-08)]_31 22954 3.68e-08 142_[+1(2.43e-07)]_86_\ [+3(4.82e-07)]_58_[+2(9.77e-06)]_165 23550 2.32e-07 119_[+1(6.01e-07)]_244_\ [+2(6.95e-06)]_17_[+2(6.42e-05)]_37_[+3(2.07e-06)]_22 24275 1.02e-06 128_[+2(1.56e-05)]_310_\ [+3(1.09e-08)]_29 269572 3.63e-09 107_[+2(9.12e-06)]_26_\ [+1(1.68e-08)]_144_[+3(6.02e-07)]_174 32858 3.60e-11 137_[+1(6.68e-09)]_29_\ [+3(4.30e-08)]_50_[+2(2.26e-06)]_235 4142 4.18e-07 58_[+2(6.36e-06)]_299_\ [+1(6.01e-07)]_86_[+3(4.32e-06)]_8 9524 5.56e-11 66_[+1(2.35e-08)]_5_[+2(2.28e-05)]_\ 200_[+3(4.30e-08)]_30_[+2(1.02e-06)]_138 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************