******************************************************************************** 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/150/150.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 1744 1.0000 500 19622 1.0000 500 23070 1.0000 500 23467 1.0000 500 261864 1.0000 500 262704 1.0000 500 263934 1.0000 500 2717 1.0000 500 4679 1.0000 500 4916 1.0000 500 7424 1.0000 500 7707 1.0000 500 8148 1.0000 500 9691 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/150/150.seqs.fa -oc motifs/150 -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= 14 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= 7000 N= 14 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.259 C 0.228 G 0.253 T 0.260 Background letter frequencies (from dataset with add-one prior applied): A 0.259 C 0.228 G 0.253 T 0.260 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 21 sites = 7 llr = 119 E-value = 1.6e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A :11::4::46::::13:::1: pos.-specific C a443943941a7a191919:9 probability G :1::11:::1:::1::131:1 matrix T :347::7111:3:7:6:6:9: bits 2.1 * * * 1.9 * * * 1.7 * * * 1.5 * * * * * * * * * Relative 1.3 * * * *** * * *** Entropy 1.1 * ** ** *** * * *** (24.6 bits) 0.9 * ** ** ***** * *** 0.6 * ******* *********** 0.4 * ******* *********** 0.2 ********************* 0.0 --------------------- Multilevel CCCTCATCAACCCTCTCTCTC consensus TTC CC C T A G sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 19622 393 4.44e-10 CTCGATAAAC CTCTCACCAACCCTCACCCTC CAATTGGTAC 4916 394 7.60e-10 TCACTCCATT CCCTCATCCACTCTATCGCTC AATTTGATCA 23070 467 1.11e-09 TCCATCTCCT CTTTCCTCTACCCGCTCGCTC GGAGAACAGC 23467 399 7.41e-09 AGGAACACTG CCCTCGTTCGCCCTCCCTCTC CTCTGACGTT 263934 390 1.05e-08 GACCGACCGA CGTCCCTCCTCCCTCACTCTG CCTGCATTGC 4679 426 1.54e-08 CCGAGCCGAG CAACGATCAACTCTCTCTCTC CTCCCCGAAC 261864 458 1.34e-07 CTTAAAAATC CCTTCCCCACCCCCCTGTGAC CATCGTGTGC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 19622 4.4e-10 392_[+1]_87 4916 7.6e-10 393_[+1]_86 23070 1.1e-09 466_[+1]_13 23467 7.4e-09 398_[+1]_81 263934 1e-08 389_[+1]_90 4679 1.5e-08 425_[+1]_54 261864 1.3e-07 457_[+1]_22 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=21 seqs=7 19622 ( 393) CTCTCACCAACCCTCACCCTC 1 4916 ( 394) CCCTCATCCACTCTATCGCTC 1 23070 ( 467) CTTTCCTCTACCCGCTCGCTC 1 23467 ( 399) CCCTCGTTCGCCCTCCCTCTC 1 263934 ( 390) CGTCCCTCCTCCCTCACTCTG 1 4679 ( 426) CAACGATCAACTCTCTCTCTC 1 261864 ( 458) CCTTCCCCACCCCCCTGTGAC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 6720 bayes= 9.7491 E= 1.6e-001 -945 213 -945 -945 -86 91 -82 14 -86 91 -945 72 -945 33 -945 146 -945 191 -82 -945 73 91 -82 -945 -945 33 -945 146 -945 191 -945 -86 73 91 -945 -86 114 -67 -82 -86 -945 213 -945 -945 -945 165 -945 14 -945 213 -945 -945 -945 -67 -82 146 -86 191 -945 -945 14 -67 -945 113 -945 191 -82 -945 -945 -67 17 113 -945 191 -82 -945 -86 -945 -945 172 -945 191 -82 -945 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 7 E= 1.6e-001 0.000000 1.000000 0.000000 0.000000 0.142857 0.428571 0.142857 0.285714 0.142857 0.428571 0.000000 0.428571 0.000000 0.285714 0.000000 0.714286 0.000000 0.857143 0.142857 0.000000 0.428571 0.428571 0.142857 0.000000 0.000000 0.285714 0.000000 0.714286 0.000000 0.857143 0.000000 0.142857 0.428571 0.428571 0.000000 0.142857 0.571429 0.142857 0.142857 0.142857 0.000000 1.000000 0.000000 0.000000 0.000000 0.714286 0.000000 0.285714 0.000000 1.000000 0.000000 0.000000 0.000000 0.142857 0.142857 0.714286 0.142857 0.857143 0.000000 0.000000 0.285714 0.142857 0.000000 0.571429 0.000000 0.857143 0.142857 0.000000 0.000000 0.142857 0.285714 0.571429 0.000000 0.857143 0.142857 0.000000 0.142857 0.000000 0.000000 0.857143 0.000000 0.857143 0.142857 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- C[CT][CT][TC]C[AC][TC]C[AC]AC[CT]CTC[TA]C[TG]CTC -------------------------------------------------------------------------------- Time 2.25 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 21 sites = 10 llr = 145 E-value = 7.3e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A :6:13:512::52:5:228:: pos.-specific C 111:2::1:35:6:29:::13 probability G 82964a548753193:87197 matrix T 11:31::4:::211:1:11:: bits 2.1 1.9 * 1.7 * * 1.5 * * * * * Relative 1.3 * * * * ** * Entropy 1.1 * * ** *** * ** *** (20.9 bits) 0.9 * * ** *** * ****** 0.6 * ** ** *** * ****** 0.4 **** ** ************* 0.2 ********************* 0.0 --------------------- Multilevel GAGGGGAGGGCACGACGGAGG consensus G TA GTACGGA G AA C sequence C T C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 7707 173 7.91e-11 GCTGTGGAGC GAGTCGAGGGGACGACGGAGG GACGGAATAG 1744 429 3.57e-09 CAGTGGAAGG GAGGAGACAGCACGGCGGAGG AGGTAAGTTG 4679 204 1.89e-08 TGGTCGATTG GAGGGGGGGCGAGGACGGACG ACACCGAGAT 7424 409 2.09e-08 TGTGTGGCAT GAGGAGAGAGGACGCTGGAGG TTGTGAGGAT 2717 180 1.17e-07 TCGGTCAAGA GGCGCGATGCCGCGACAGAGG ATGGCTGATT 263934 151 2.19e-07 GCGAAGACAT TAGAGGATGCCAAGGCGGAGC ACGTCATTTC 8148 80 2.36e-07 GGAATGAGTT GAGTGGGAGGGTCGCCGATGG TGATGGAGAT 4916 42 4.47e-07 GTATTTCATG GCGGTGGTGGCTAGACGTAGC TCTGGTTCTG 23467 431 4.47e-07 TCTGACGTTG GTGTAGGTGGCGTTGCGGAGG CTTAGCTTGA 23070 247 1.08e-06 AGATGGAGCC CGGGGGGGGGGGCGACAAGGC TTTTTACCTA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 7707 7.9e-11 172_[+2]_307 1744 3.6e-09 428_[+2]_51 4679 1.9e-08 203_[+2]_276 7424 2.1e-08 408_[+2]_71 2717 1.2e-07 179_[+2]_300 263934 2.2e-07 150_[+2]_329 8148 2.4e-07 79_[+2]_400 4916 4.5e-07 41_[+2]_438 23467 4.5e-07 430_[+2]_49 23070 1.1e-06 246_[+2]_233 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=21 seqs=10 7707 ( 173) GAGTCGAGGGGACGACGGAGG 1 1744 ( 429) GAGGAGACAGCACGGCGGAGG 1 4679 ( 204) GAGGGGGGGCGAGGACGGACG 1 7424 ( 409) GAGGAGAGAGGACGCTGGAGG 1 2717 ( 180) GGCGCGATGCCGCGACAGAGG 1 263934 ( 151) TAGAGGATGCCAAGGCGGAGC 1 8148 ( 80) GAGTGGGAGGGTCGCCGATGG 1 4916 ( 42) GCGGTGGTGGCTAGACGTAGC 1 23467 ( 431) GTGTAGGTGGCGTTGCGGAGG 1 23070 ( 247) CGGGGGGGGGGGCGACAAGGC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 6720 bayes= 9.64205 E= 7.3e-001 -997 -119 166 -138 121 -119 -34 -138 -997 -119 183 -997 -137 -997 124 21 21 -19 66 -138 -997 -997 198 -997 95 -997 98 -997 -137 -119 66 62 -37 -997 166 -997 -997 40 147 -997 -997 113 98 -997 95 -997 24 -38 -37 140 -134 -138 -997 -997 183 -138 95 -19 24 -997 -997 198 -997 -138 -37 -997 166 -997 -37 -997 147 -138 163 -997 -134 -138 -997 -119 183 -997 -997 40 147 -997 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 10 E= 7.3e-001 0.000000 0.100000 0.800000 0.100000 0.600000 0.100000 0.200000 0.100000 0.000000 0.100000 0.900000 0.000000 0.100000 0.000000 0.600000 0.300000 0.300000 0.200000 0.400000 0.100000 0.000000 0.000000 1.000000 0.000000 0.500000 0.000000 0.500000 0.000000 0.100000 0.100000 0.400000 0.400000 0.200000 0.000000 0.800000 0.000000 0.000000 0.300000 0.700000 0.000000 0.000000 0.500000 0.500000 0.000000 0.500000 0.000000 0.300000 0.200000 0.200000 0.600000 0.100000 0.100000 0.000000 0.000000 0.900000 0.100000 0.500000 0.200000 0.300000 0.000000 0.000000 0.900000 0.000000 0.100000 0.200000 0.000000 0.800000 0.000000 0.200000 0.000000 0.700000 0.100000 0.800000 0.000000 0.100000 0.100000 0.000000 0.100000 0.900000 0.000000 0.000000 0.300000 0.700000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- G[AG]G[GT][GAC]G[AG][GT][GA][GC][CG][AGT][CA]G[AGC]C[GA][GA]AG[GC] -------------------------------------------------------------------------------- Time 4.40 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 21 sites = 8 llr = 131 E-value = 6.8e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A :1:3::::1::1:311::::5 pos.-specific C ::1::::14::::1:6::::: probability G 14919418563:a643933a5 matrix T 95:61691:489::5:188:: bits 2.1 1.9 * * 1.7 * * 1.5 * * * * ** * * Relative 1.3 * * * * ** * * Entropy 1.1 * * *** **** ***** (23.7 bits) 0.9 * * **** **** ****** 0.6 ********************* 0.4 ********************* 0.2 ********************* 0.0 --------------------- Multilevel TTGTGTTGGGTTGGTCGTTGA consensus G A G CTG AGG GG G sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 2717 273 1.23e-09 TGTGGTGTCT TGGTGTTGCGTTGAGAGTTGA GAAGAATAGT 8148 254 4.98e-09 TGCAACGGCC TGGTGTTCGTTTGATCGTGGA GGTGGGTATT 4679 165 9.63e-09 TGGTTTCTGT TTCTGGTGGTGTGGTCGGTGG TGGAACTGTG 1744 247 1.15e-08 CCAGAGGAGG TTGTTGTGCGTTGCTGGTTGA GGTGAGAGAT 7707 149 1.62e-08 TTCATTCATC GTGTGTTGCGTTGGGCTGTGG AGCGAGTCGA 261864 198 1.91e-08 ATCGTACTGC TGGAGTTGAGGAGGTCGTTGG ACGTGAGAGT 262704 139 3.28e-08 TCTCGCTCTG TTGGGGGTGGTTGGGCGTTGG TGATGGCTGA 7424 10 3.53e-08 GGGTATAGA TAGAGTTGGTTTGGAGGTGGA ATCTCGCGTT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 2717 1.2e-09 272_[+3]_207 8148 5e-09 253_[+3]_226 4679 9.6e-09 164_[+3]_315 1744 1.1e-08 246_[+3]_233 7707 1.6e-08 148_[+3]_331 261864 1.9e-08 197_[+3]_282 262704 3.3e-08 138_[+3]_341 7424 3.5e-08 9_[+3]_470 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=21 seqs=8 2717 ( 273) TGGTGTTGCGTTGAGAGTTGA 1 8148 ( 254) TGGTGTTCGTTTGATCGTGGA 1 4679 ( 165) TTCTGGTGGTGTGGTCGGTGG 1 1744 ( 247) TTGTTGTGCGTTGCTGGTTGA 1 7707 ( 149) GTGTGTTGCGTTGGGCTGTGG 1 261864 ( 198) TGGAGTTGAGGAGGTCGTTGG 1 262704 ( 139) TTGGGGGTGGTTGGGCGTTGG 1 7424 ( 10) TAGAGTTGGTTTGGAGGTGGA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 6720 bayes= 9.71253 E= 6.8e+000 -965 -965 -102 175 -105 -965 57 94 -965 -86 179 -965 -5 -965 -102 126 -965 -965 179 -105 -965 -965 57 126 -965 -965 -102 175 -965 -86 157 -105 -105 72 98 -965 -965 -965 130 53 -965 -965 -2 153 -105 -965 -965 175 -965 -965 198 -965 -5 -86 130 -965 -105 -965 57 94 -105 145 -2 -965 -965 -965 179 -105 -965 -965 -2 153 -965 -965 -2 153 -965 -965 198 -965 95 -965 98 -965 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 8 E= 6.8e+000 0.000000 0.000000 0.125000 0.875000 0.125000 0.000000 0.375000 0.500000 0.000000 0.125000 0.875000 0.000000 0.250000 0.000000 0.125000 0.625000 0.000000 0.000000 0.875000 0.125000 0.000000 0.000000 0.375000 0.625000 0.000000 0.000000 0.125000 0.875000 0.000000 0.125000 0.750000 0.125000 0.125000 0.375000 0.500000 0.000000 0.000000 0.000000 0.625000 0.375000 0.000000 0.000000 0.250000 0.750000 0.125000 0.000000 0.000000 0.875000 0.000000 0.000000 1.000000 0.000000 0.250000 0.125000 0.625000 0.000000 0.125000 0.000000 0.375000 0.500000 0.125000 0.625000 0.250000 0.000000 0.000000 0.000000 0.875000 0.125000 0.000000 0.000000 0.250000 0.750000 0.000000 0.000000 0.250000 0.750000 0.000000 0.000000 1.000000 0.000000 0.500000 0.000000 0.500000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- T[TG]G[TA]G[TG]TG[GC][GT][TG]TG[GA][TG][CG]G[TG][TG]G[AG] -------------------------------------------------------------------------------- Time 6.42 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 1744 2.46e-09 246_[+3(1.15e-08)]_161_\ [+2(3.57e-09)]_51 19622 9.15e-06 392_[+1(4.44e-10)]_87 23070 3.96e-08 246_[+2(1.08e-06)]_199_\ [+1(1.11e-09)]_13 23467 4.54e-08 281_[+1(2.54e-05)]_96_\ [+1(7.41e-09)]_11_[+2(4.47e-07)]_49 261864 3.79e-08 197_[+3(1.91e-08)]_239_\ [+1(1.34e-07)]_22 262704 2.16e-05 138_[+3(3.28e-08)]_341 263934 7.00e-08 150_[+2(2.19e-07)]_218_\ [+1(1.05e-08)]_90 2717 1.85e-09 179_[+2(1.17e-07)]_19_\ [+3(8.11e-05)]_32_[+3(1.23e-09)]_207 4679 2.09e-13 164_[+3(9.63e-09)]_18_\ [+2(1.89e-08)]_201_[+1(1.54e-08)]_54 4916 1.39e-08 41_[+2(4.47e-07)]_331_\ [+1(7.60e-10)]_86 7424 4.36e-08 9_[+3(3.53e-08)]_378_[+2(2.09e-08)]_\ 71 7707 7.53e-11 148_[+3(1.62e-08)]_3_[+2(7.91e-11)]_\ 307 8148 5.40e-08 79_[+2(2.36e-07)]_114_\ [+2(3.63e-05)]_18_[+3(4.98e-09)]_226 9691 2.20e-01 500 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************