******************************************************************************** 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/340/340.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 10714 1.0000 500 10715 1.0000 500 11316 1.0000 500 11403 1.0000 500 11407 1.0000 500 11604 1.0000 500 11681 1.0000 500 11726 1.0000 500 11864 1.0000 500 12124 1.0000 500 12126 1.0000 500 1324 1.0000 500 1353 1.0000 500 2034 1.0000 500 25567 1.0000 500 263745 1.0000 500 3647 1.0000 500 4223 1.0000 500 5844 1.0000 500 7300 1.0000 500 7603 1.0000 500 7608 1.0000 500 7638 1.0000 500 7686 1.0000 500 8289 1.0000 500 8608 1.0000 500 8874 1.0000 500 8892 1.0000 500 9153 1.0000 500 9260 1.0000 500 9775 1.0000 500 bd1056 1.0000 197 bd632 1.0000 500 bd633 1.0000 500 bd650 1.0000 500 bd822 1.0000 127 bd824 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/340/340.seqs.fa -oc motifs/340 -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= 37 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= 17824 N= 37 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.272 C 0.240 G 0.224 T 0.263 Background letter frequencies (from dataset with add-one prior applied): A 0.272 C 0.240 G 0.224 T 0.263 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 21 sites = 8 llr = 166 E-value = 3.9e-010 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A ::69:a19::5::a::9:::5 pos.-specific C :5::5:11415:a:3a1:aa: probability G ::::5:::5::::::::6::: matrix T a541::8:19:a::8::4::5 bits 2.2 * * ** 1.9 * * *** * ** 1.7 * * *** * ** 1.5 * * *** * ** Relative 1.3 * * * * * *** ** ** Entropy 1.1 ** *** * * ********* (30.0 bits) 0.9 ******** ************ 0.6 ********************* 0.4 ********************* 0.2 ********************* 0.0 --------------------- Multilevel TCAACATAGTATCATCAGCCA consensus TT G C C C T T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 5844 366 5.86e-13 GTTGATTGCT TCAAGATAGTCTCATCAGCCT TGCCTCTGCT 11407 112 5.86e-13 GTCGATTGCT TCAAGATAGTCTCATCAGCCT TGCCTTTGCT 11403 367 5.86e-13 GTTGATTGCT TCAAGATAGTCTCATCAGCCT TGCCTCTGCT 7638 217 7.18e-11 GAACAACAAT TTTACATACTATCATCATCCA GATGTTACTT 7608 336 7.18e-11 GCACAACAAT TTTACATACTATCATCATCCA GATTATTCTT 7603 337 7.18e-11 GGACAACAAT TTTACATACTATCATCATCCA GATTTTACTT 10715 235 2.93e-09 TTGATTGGTC TCATCACCGTATCACCAGCCT TATCAGAAGA 12126 160 4.47e-09 CAAACCACAA TTAAGAAATCCTCACCCGCCA CAATCGCCAC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 5844 5.9e-13 365_[+1]_114 11407 5.9e-13 111_[+1]_368 11403 5.9e-13 366_[+1]_113 7638 7.2e-11 216_[+1]_263 7608 7.2e-11 335_[+1]_144 7603 7.2e-11 336_[+1]_143 10715 2.9e-09 234_[+1]_245 12126 4.5e-09 159_[+1]_320 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=21 seqs=8 5844 ( 366) TCAAGATAGTCTCATCAGCCT 1 11407 ( 112) TCAAGATAGTCTCATCAGCCT 1 11403 ( 367) TCAAGATAGTCTCATCAGCCT 1 7638 ( 217) TTTACATACTATCATCATCCA 1 7608 ( 336) TTTACATACTATCATCATCCA 1 7603 ( 337) TTTACATACTATCATCATCCA 1 10715 ( 235) TCATCACCGTATCACCAGCCT 1 12126 ( 160) TTAAGAAATCCTCACCCGCCA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 17084 bayes= 11.0597 E= 3.9e-010 -965 -965 -965 192 -965 106 -965 92 120 -965 -965 51 168 -965 -965 -107 -965 106 116 -965 188 -965 -965 -965 -112 -94 -965 151 168 -94 -965 -965 -965 64 116 -107 -965 -94 -965 173 88 106 -965 -965 -965 -965 -965 192 -965 206 -965 -965 188 -965 -965 -965 -965 6 -965 151 -965 206 -965 -965 168 -94 -965 -965 -965 -965 148 51 -965 206 -965 -965 -965 206 -965 -965 88 -965 -965 92 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 8 E= 3.9e-010 0.000000 0.000000 0.000000 1.000000 0.000000 0.500000 0.000000 0.500000 0.625000 0.000000 0.000000 0.375000 0.875000 0.000000 0.000000 0.125000 0.000000 0.500000 0.500000 0.000000 1.000000 0.000000 0.000000 0.000000 0.125000 0.125000 0.000000 0.750000 0.875000 0.125000 0.000000 0.000000 0.000000 0.375000 0.500000 0.125000 0.000000 0.125000 0.000000 0.875000 0.500000 0.500000 0.000000 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 0.250000 0.000000 0.750000 0.000000 1.000000 0.000000 0.000000 0.875000 0.125000 0.000000 0.000000 0.000000 0.000000 0.625000 0.375000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.500000 0.000000 0.000000 0.500000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- T[CT][AT]A[CG]ATA[GC]T[AC]TCA[TC]CA[GT]CC[AT] -------------------------------------------------------------------------------- Time 9.83 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 21 sites = 5 llr = 131 E-value = 3.1e-009 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A :::a::2aa:2a:22a::::: pos.-specific C aaa::68::28:a8::a::a: probability G ::::a::::8:::::::aa:: matrix T :::::4::::::::8:::::a bits 2.2 *** * * **** 1.9 ***** ** ** ****** 1.7 ***** ** ** ****** 1.5 ***** *** ** ****** Relative 1.3 ***** *************** Entropy 1.1 ********************* (37.7 bits) 0.9 ********************* 0.6 ********************* 0.4 ********************* 0.2 ********************* 0.0 --------------------- Multilevel CCCAGCCAAGCACCTACGGCT consensus TA CA AA sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 5844 273 1.64e-13 TTCAAAGAGT CCCAGCCAAGCACCTACGGCT AGTCCAATTA 11403 274 1.64e-13 TTCAAAGAGT CCCAGCCAAGCACCTACGGCT AGTCCAATTA 12124 183 3.45e-13 AACAAAGAGT CCCAGTCAAGCACCTACGGCT AGTCCAATTA 11407 19 3.45e-13 AACAAAGAGT CCCAGTCAAGCACCTACGGCT AGTCCAATTA 10715 395 1.41e-11 ATCCGTCACA CCCAGCAAACAACAAACGGCT CTCAACCGCA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 5844 1.6e-13 272_[+2]_207 11403 1.6e-13 273_[+2]_206 12124 3.4e-13 182_[+2]_297 11407 3.4e-13 18_[+2]_461 10715 1.4e-11 394_[+2]_85 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=21 seqs=5 5844 ( 273) CCCAGCCAAGCACCTACGGCT 1 11403 ( 274) CCCAGCCAAGCACCTACGGCT 1 12124 ( 183) CCCAGTCAAGCACCTACGGCT 1 11407 ( 19) CCCAGTCAAGCACCTACGGCT 1 10715 ( 395) CCCAGCAAACAACAAACGGCT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 17084 bayes= 11.1722 E= 3.1e-009 -897 206 -897 -897 -897 206 -897 -897 -897 206 -897 -897 188 -897 -897 -897 -897 -897 216 -897 -897 132 -897 60 -44 173 -897 -897 188 -897 -897 -897 188 -897 -897 -897 -897 -26 183 -897 -44 173 -897 -897 188 -897 -897 -897 -897 206 -897 -897 -44 173 -897 -897 -44 -897 -897 160 188 -897 -897 -897 -897 206 -897 -897 -897 -897 216 -897 -897 -897 216 -897 -897 206 -897 -897 -897 -897 -897 192 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 5 E= 3.1e-009 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.600000 0.000000 0.400000 0.200000 0.800000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.200000 0.800000 0.000000 0.200000 0.800000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.200000 0.800000 0.000000 0.000000 0.200000 0.000000 0.000000 0.800000 1.000000 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 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- CCCAG[CT][CA]AA[GC][CA]AC[CA][TA]ACGGCT -------------------------------------------------------------------------------- Time 19.85 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 21 sites = 10 llr = 172 E-value = 2.0e-007 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A 1::1::6::93::3a62:::: pos.-specific C ::12::11::1812:::::28 probability G 81:53a36:11::1:2:1a32 matrix T 19927::3a:5294:289:5: bits 2.2 * * 1.9 * * * * 1.7 * * * * 1.5 ** * ** * * ** Relative 1.3 ** * ** ** * *** * Entropy 1.1 *** ** ** ** * *** * (24.9 bits) 0.9 *** ** *** ** * *** * 0.6 *** ****** ** ***** * 0.4 *** ****** ** ******* 0.2 ********************* 0.0 --------------------- Multilevel GTTGTGAGTATCTTAATTGTC consensus CG GT AT A GA GG sequence T C T C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 5844 15 8.12e-13 TGATCCGACG GTTGTGAGTATCTAAATTGTC TGATGCGTTG 12124 409 8.12e-13 TGATCCAACG GTTGTGAGTATCTAAATTGTC TGATGCGTTG 11403 16 8.12e-13 TGATCCGACG GTTGTGAGTATCTAAATTGTC TGATGCGTTG 7686 221 1.29e-09 TCTGCACTGT GTTTTGGTTATCTTAAATGGC CATATGCATT 9153 180 2.41e-09 TCTGAGCTGT GTTATGGTTAACTTAATTGCC CAAATGCGTT bd633 290 3.29e-08 GTCACTCCTA GTTGGGACTATCCTATTTGGG ATACTCCACA 11407 380 5.78e-08 CTTGAGGATT GTTGTGAGTGATTCAGATGTG CTGTCGTTAA 7638 153 9.56e-08 GCTTGAATTT GTCCTGCTTACCTCATTTGTC TCTATTGCCC 8892 374 1.36e-07 CACAAGTGAC TGTTGGAGTAGCTGAATTGCC ATGCTACTTT 7608 121 1.64e-07 CCGTGCCTGA ATTCGGGGTAATTTAGTGGGC GCAATCTACA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 5844 8.1e-13 14_[+3]_465 12124 8.1e-13 408_[+3]_71 11403 8.1e-13 15_[+3]_464 7686 1.3e-09 220_[+3]_259 9153 2.4e-09 179_[+3]_300 bd633 3.3e-08 289_[+3]_190 11407 5.8e-08 379_[+3]_100 7638 9.6e-08 152_[+3]_327 8892 1.4e-07 373_[+3]_106 7608 1.6e-07 120_[+3]_359 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=21 seqs=10 5844 ( 15) GTTGTGAGTATCTAAATTGTC 1 12124 ( 409) GTTGTGAGTATCTAAATTGTC 1 11403 ( 16) GTTGTGAGTATCTAAATTGTC 1 7686 ( 221) GTTTTGGTTATCTTAAATGGC 1 9153 ( 180) GTTATGGTTAACTTAATTGCC 1 bd633 ( 290) GTTGGGACTATCCTATTTGGG 1 11407 ( 380) GTTGTGAGTGATTCAGATGTG 1 7638 ( 153) GTCCTGCTTACCTCATTTGTC 1 8892 ( 374) TGTTGGAGTAGCTGAATTGCC 1 7608 ( 121) ATTCGGGGTAATTTAGTGGGC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 17084 bayes= 10.9893 E= 2.0e-007 -144 -997 183 -139 -997 -997 -116 177 -997 -126 -997 177 -144 -26 116 -40 -997 -997 42 141 -997 -997 216 -997 114 -126 42 -997 -997 -126 142 19 -997 -997 -997 192 172 -997 -116 -997 14 -126 -116 92 -997 173 -997 -40 -997 -126 -997 177 14 -26 -116 60 188 -997 -997 -997 114 -997 -16 -40 -44 -997 -997 160 -997 -997 -116 177 -997 -997 216 -997 -997 -26 42 92 -997 173 -16 -997 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 10 E= 2.0e-007 0.100000 0.000000 0.800000 0.100000 0.000000 0.000000 0.100000 0.900000 0.000000 0.100000 0.000000 0.900000 0.100000 0.200000 0.500000 0.200000 0.000000 0.000000 0.300000 0.700000 0.000000 0.000000 1.000000 0.000000 0.600000 0.100000 0.300000 0.000000 0.000000 0.100000 0.600000 0.300000 0.000000 0.000000 0.000000 1.000000 0.900000 0.000000 0.100000 0.000000 0.300000 0.100000 0.100000 0.500000 0.000000 0.800000 0.000000 0.200000 0.000000 0.100000 0.000000 0.900000 0.300000 0.200000 0.100000 0.400000 1.000000 0.000000 0.000000 0.000000 0.600000 0.000000 0.200000 0.200000 0.200000 0.000000 0.000000 0.800000 0.000000 0.000000 0.100000 0.900000 0.000000 0.000000 1.000000 0.000000 0.000000 0.200000 0.300000 0.500000 0.000000 0.800000 0.200000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- GTT[GCT][TG]G[AG][GT]TA[TA][CT]T[TAC]A[AGT][TA]TG[TGC][CG] -------------------------------------------------------------------------------- Time 29.44 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 10714 2.58e-01 437_[+2(6.48e-05)]_42 10715 3.79e-13 234_[+1(2.93e-09)]_139_\ [+2(1.41e-11)]_85 11316 5.60e-01 500 11403 2.00e-26 15_[+3(8.12e-13)]_237_\ [+2(1.64e-13)]_72_[+1(5.86e-13)]_113 11407 2.02e-21 18_[+2(3.45e-13)]_72_[+1(5.86e-13)]_\ 247_[+3(5.78e-08)]_100 11604 2.18e-01 500 11681 2.99e-01 500 11726 6.53e-01 500 11864 6.16e-01 500 12124 2.40e-17 182_[+2(3.45e-13)]_205_\ [+3(8.12e-13)]_71 12126 1.60e-05 159_[+1(4.47e-09)]_320 1324 3.89e-01 500 1353 7.38e-01 500 2034 7.75e-01 500 25567 9.76e-01 500 263745 2.13e-02 297_[+2(4.93e-05)]_182 3647 6.10e-01 500 4223 3.73e-01 500 5844 2.00e-26 14_[+3(8.12e-13)]_237_\ [+2(1.64e-13)]_72_[+1(5.86e-13)]_114 7300 7.67e-01 500 7603 2.10e-07 87_[+3(6.44e-05)]_228_\ [+1(7.18e-11)]_143 7608 7.26e-10 120_[+3(1.64e-07)]_194_\ [+1(7.18e-11)]_100_[+1(1.17e-05)]_23 7638 3.84e-10 152_[+3(9.56e-08)]_43_\ [+1(7.18e-11)]_218_[+1(8.94e-05)]_24 7686 6.56e-07 220_[+3(1.29e-09)]_259 8289 1.74e-01 500 8608 6.79e-01 500 8874 1.38e-01 500 8892 6.22e-04 373_[+3(1.36e-07)]_106 9153 4.98e-07 179_[+3(2.41e-09)]_201_\ [+1(2.61e-05)]_78 9260 6.02e-01 500 9775 7.89e-01 500 bd1056 3.67e-01 197 bd632 6.19e-01 500 bd633 7.18e-04 289_[+3(3.29e-08)]_190 bd650 5.73e-01 500 bd822 2.96e-01 127 bd824 9.44e-01 500 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************