******************************************************************************** MEME - Motif discovery tool ******************************************************************************** MEME version 5.5.5 (Release date: Thu Sep 14 08:48:04 2023 +1000) For further information on how to interpret these results please access https://meme-suite.org/meme. To get a copy of the MEME Suite software please access https://meme-suite.org. ******************************************************************************** ******************************************************************************** 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 ******************************************************************************** PRIMARY SEQUENCES= promoters100_1.txt CONTROL SEQUENCES= --none-- ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 0 1.0000 100 1 1.0000 100 2 1.0000 100 3 1.0000 100 4 1.0000 100 5 1.0000 100 6 1.0000 100 7 1.0000 100 8 1.0000 100 9 1.0000 100 10 1.0000 100 11 1.0000 100 12 1.0000 100 13 1.0000 100 14 1.0000 100 15 1.0000 100 16 1.0000 100 17 1.0000 100 18 1.0000 100 19 1.0000 100 20 1.0000 100 21 1.0000 100 22 1.0000 100 23 1.0000 100 ******************************************************************************** ******************************************************************************** COMMAND LINE SUMMARY ******************************************************************************** This information can also be useful in the event you wish to report a problem with the MEME software. command: meme promoters100_1.txt -dna -oc . -nostatus -time 14400 -mod zoops -nmotifs 3 -minw 5 -maxw 50 -objfun classic -markov_order 0 model: mod= zoops nmotifs= 3 evt= inf objective function: em= E-value of product of p-values starts= E-value of product of p-values strands: + width: minw= 5 maxw= 50 nsites: minsites= 2 maxsites= 24 wnsites= 0.8 theta: spmap= uni spfuzz= 0.5 em: prior= dirichlet b= 0.01 maxiter= 50 distance= 1e-05 trim: wg= 11 ws= 1 endgaps= yes data: n= 2400 N= 24 sample: seed= 0 hsfrac= 0 searchsize= 2400 norand= no csites= 1000 Letter frequencies in dataset: A 0.18 C 0.307 G 0.333 T 0.18 Background letter frequencies (from file dataset with add-one prior applied): A 0.18 C 0.307 G 0.333 T 0.18 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF MAYSSCCBTAKNMTA MEME-1 width = 15 sites = 12 llr = 136 E-value = 3.7e-005 ******************************************************************************** -------------------------------------------------------------------------------- Motif MAYSSCCBTAKNMTA MEME-1 Description -------------------------------------------------------------------------------- Simplified A 381::::::8:33:9 pos.-specific C 73446a833:125:: probability G :::54::3:2332:1 matrix T ::51::338:631a: bits 2.5 * 2.2 * 2.0 ** 1.7 * * ** Relative 1.5 * * ** ** Entropy 1.2 * * ** ** (16.3 bits) 1.0 ** ** ** ** 0.7 *** *** *** ** 0.5 ******* *** ** 0.2 *************** 0.0 --------------- Multilevel CATGCCCCTATACTA consensus ACCCG TGC GGA sequence T T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif MAYSSCCBTAKNMTA MEME-1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------- 0 81 6.41e-08 CCCACTTCTC CACCCCCGTATTCTA CGGAT 21 80 7.85e-08 AAGCCGGGTA AATGCCCGTATAGTA GAGGGC 8 80 2.55e-07 GGCGCTCCAG CATGCCCTTAGCATA AGGGAC 16 25 6.79e-07 AGCGGAGGCG CATGCCCCCATGCTA CCCCTTCCTG 7 4 2.19e-06 AAC CATGGCCCCATTGTA GCCGAGGGGG 22 80 3.13e-06 AAGCTCCGCA CCACGCCCTATACTA GCCCTT 13 52 3.13e-06 TGACACGCTC AACCCCCTTGGTCTA TCCTGGACCC 9 54 5.14e-06 TCCACCCCGG CACGGCCTCAGGATA CCAGGGCCCC 5 66 6.51e-06 GCCCCCTTAT AATCGCTGTGGAATA GCTTCCAAAG 3 28 6.95e-06 GTACGATGCG CATGCCCTTATCTTG ACACTCTCGG 6 41 1.21e-05 CCTTTGTTTC CCCTGCTCTATGCTA CACTCTTAGA 15 39 1.29e-05 TTAGGGGTTC ACCCCCTGTACACTA AAAGGTGGCT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif MAYSSCCBTAKNMTA MEME-1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 0 6.4e-08 80_[+1]_5 21 7.9e-08 79_[+1]_6 8 2.5e-07 79_[+1]_6 16 6.8e-07 24_[+1]_61 7 2.2e-06 3_[+1]_82 22 3.1e-06 79_[+1]_6 13 3.1e-06 51_[+1]_34 9 5.1e-06 53_[+1]_32 5 6.5e-06 65_[+1]_20 3 7e-06 27_[+1]_58 6 1.2e-05 40_[+1]_45 15 1.3e-05 38_[+1]_47 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif MAYSSCCBTAKNMTA MEME-1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF MAYSSCCBTAKNMTA width=15 seqs=12 0 ( 81) CACCCCCGTATTCTA 1 21 ( 80) AATGCCCGTATAGTA 1 8 ( 80) CATGCCCTTAGCATA 1 16 ( 25) CATGCCCCCATGCTA 1 7 ( 4) CATGGCCCCATTGTA 1 22 ( 80) CCACGCCCTATACTA 1 13 ( 52) AACCCCCTTGGTCTA 1 9 ( 54) CACGGCCTCAGGATA 1 5 ( 66) AATCGCTGTGGAATA 1 3 ( 28) CATGCCCTTATCTTG 1 6 ( 41) CCCTGCTCTATGCTA 1 15 ( 39) ACCCCCTGTACACTA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif MAYSSCCBTAKNMTA MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 2064 bayes= 7.86756 E= 3.7e-005 89 112 -1023 -1023 206 -29 -1023 -1023 -111 44 -1023 147 -1023 44 59 -111 -1023 93 32 -1023 -1023 170 -1023 -1023 -1023 129 -1023 47 -1023 12 0 89 -1023 -29 -1023 205 221 -1023 -100 -1023 -1023 -188 0 169 89 -88 -41 47 47 70 -100 -111 -1023 -1023 -1023 247 235 -1023 -199 -1023 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif MAYSSCCBTAKNMTA MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 12 E= 3.7e-005 0.333333 0.666667 0.000000 0.000000 0.750000 0.250000 0.000000 0.000000 0.083333 0.416667 0.000000 0.500000 0.000000 0.416667 0.500000 0.083333 0.000000 0.583333 0.416667 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.750000 0.000000 0.250000 0.000000 0.333333 0.333333 0.333333 0.000000 0.250000 0.000000 0.750000 0.833333 0.000000 0.166667 0.000000 0.000000 0.083333 0.333333 0.583333 0.333333 0.166667 0.250000 0.250000 0.250000 0.500000 0.166667 0.083333 0.000000 0.000000 0.000000 1.000000 0.916667 0.000000 0.083333 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif MAYSSCCBTAKNMTA MEME-1 regular expression -------------------------------------------------------------------------------- [CA][AC][TC][GC][CG]C[CT][CGT][TC]A[TG][AGT][CA]TA -------------------------------------------------------------------------------- Time 1.38 secs. ******************************************************************************** ******************************************************************************** MOTIF TGSTAWACT MEME-2 width = 9 sites = 10 llr = 91 E-value = 4.0e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif TGSTAWACT MEME-2 Description -------------------------------------------------------------------------------- Simplified A ::::a3721 pos.-specific C 2:5:::37: probability G 2a5::1:1: matrix T 6::a:6::9 bits 2.5 ** 2.2 ** 2.0 ** * 1.7 ** * Relative 1.5 * ** * * Entropy 1.2 * ** * * (13.1 bits) 1.0 * **** * 0.7 ********* 0.5 ********* 0.2 ********* 0.0 --------- Multilevel TGCTATACT consensus C G ACA sequence G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGSTAWACT MEME-2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------- 20 45 1.07e-06 GTAGCATATG TGCTATACT TACTTGAGAT 7 34 3.29e-06 GGGGGTTTCT TGCTAAACT TCACCTTAGC 17 58 5.08e-06 AGCCCCCCGG TGCTATAAT GGAAGACGGC 16 48 7.58e-06 TACCCCTTCC TGCTATCCT GGGAAGGATG 11 72 1.88e-05 GGGGGCTAAG GGGTATACT GGCCCGGAGG 2 51 4.61e-05 GGGGGAGGCG GGGTATAAT CTGGCCCTGT 18 33 4.96e-05 CAGGGGGATG TGGTAAAGT CCTCTTTGGC 23 74 6.52e-05 TACACCGAGG CGGTATCCT CTTGGGAAGA 3 60 1.05e-04 CGGGCGGGTG TGCTAGCCT AAACCCTCGG 13 15 1.90e-04 CCTCGAGGCC CGGTAAACA CATCAGAAAA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGSTAWACT MEME-2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 20 1.1e-06 44_[+2]_47 7 3.3e-06 33_[+2]_58 17 5.1e-06 57_[+2]_34 16 7.6e-06 47_[+2]_44 11 1.9e-05 71_[+2]_20 2 4.6e-05 50_[+2]_41 18 5e-05 32_[+2]_59 23 6.5e-05 73_[+2]_18 3 0.00011 59_[+2]_32 13 0.00019 14_[+2]_77 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGSTAWACT MEME-2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF TGSTAWACT width=9 seqs=10 20 ( 45) TGCTATACT 1 7 ( 34) TGCTAAACT 1 17 ( 58) TGCTATAAT 1 16 ( 48) TGCTATCCT 1 11 ( 72) GGGTATACT 1 2 ( 51) GGGTATAAT 1 18 ( 33) TGGTAAAGT 1 23 ( 74) CGGTATCCT 1 3 ( 60) TGCTAGCCT 1 13 ( 15) CGGTAAACA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGSTAWACT MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 9 n= 2208 bayes= 8.03264 E= 4.0e+000 -997 -62 -73 173 -997 -997 159 -997 -997 70 59 -997 -997 -997 -997 247 247 -997 -997 -997 74 -997 -173 173 196 -3 -997 -997 15 119 -173 -997 -85 -997 -997 232 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGSTAWACT MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 9 nsites= 10 E= 4.0e+000 0.000000 0.200000 0.200000 0.600000 0.000000 0.000000 1.000000 0.000000 0.000000 0.500000 0.500000 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.300000 0.000000 0.100000 0.600000 0.700000 0.300000 0.000000 0.000000 0.200000 0.700000 0.100000 0.000000 0.100000 0.000000 0.000000 0.900000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGSTAWACT MEME-2 regular expression -------------------------------------------------------------------------------- [TCG]G[CG]TA[TA][AC][CA]T -------------------------------------------------------------------------------- Time 2.45 secs. ******************************************************************************** ******************************************************************************** MOTIF CSYTTNYYCGSAAAGC MEME-3 width = 16 sites = 6 llr = 85 E-value = 1.5e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif CSYTTNYYCGSAAAGC MEME-3 Description -------------------------------------------------------------------------------- Simplified A ::::22:22::8aa:: pos.-specific C a73::3758232::28 probability G :3:::3:::85:::7: matrix T ::7a8233::2:::22 bits 2.5 * ** 2.2 * ** 2.0 * ** 1.7 * ** *** Relative 1.5 * ** *** Entropy 1.2 * *** * *** * (20.5 bits) 1.0 * *** * ** *** * 0.7 ***** **** *** * 0.5 ***** **** ***** 0.2 ***** ********** 0.0 ---------------- Multilevel CCTTTCCCCGGAAAGC consensus GC GTT C sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CSYTTNYYCGSAAAGC MEME-3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 17 35 2.44e-08 AATTTCTTCC CGTTTATTCGCAAAGC CCCCCGGTGC 1 38 2.85e-08 TGAGGGGGAG CGTTTCCTCGGAAATC CCAGGACAAA 16 2 2.08e-07 C CCCTTCTCCCGAAAGC GGAGGCGCAT 9 77 2.08e-07 TACCAGGGCC CCCTTTCCCGTAAAGT GGAAGGGT 7 46 3.03e-07 CTAAACTTCA CCTTAGCCCGCAAACC CTTTGACCGA 5 9 4.90e-07 CCTCCTGA CCTTTGCAAGGCAAGC CCACCCCTCC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CSYTTNYYCGSAAAGC MEME-3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 17 2.4e-08 34_[+3]_50 1 2.9e-08 37_[+3]_47 16 2.1e-07 1_[+3]_83 9 2.1e-07 76_[+3]_8 7 3e-07 45_[+3]_39 5 4.9e-07 8_[+3]_76 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CSYTTNYYCGSAAAGC MEME-3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF CSYTTNYYCGSAAAGC width=16 seqs=6 17 ( 35) CGTTTATTCGCAAAGC 1 1 ( 38) CGTTTCCTCGGAAATC 1 16 ( 2) CCCTTCTCCCGAAAGC 1 9 ( 77) CCCTTTCCCGTAAAGT 1 7 ( 46) CCTTAGCCCGCAAACC 1 5 ( 9) CCTTTGCAAGGCAAGC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CSYTTNYYCGSAAAGC MEME-3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 2040 bayes= 8.06297 E= 1.5e+001 -923 170 -923 -923 -923 112 0 -923 -923 12 -923 188 -923 -923 -923 247 -11 -923 -923 221 -11 12 0 -11 -923 112 -923 88 -11 70 -923 88 -11 144 -923 -923 -923 -88 132 -923 -923 12 59 -11 221 -88 -923 -923 247 -923 -923 -923 247 -923 -923 -923 -923 -88 100 -11 -923 144 -923 -11 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CSYTTNYYCGSAAAGC MEME-3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 6 E= 1.5e+001 0.000000 1.000000 0.000000 0.000000 0.000000 0.666667 0.333333 0.000000 0.000000 0.333333 0.000000 0.666667 0.000000 0.000000 0.000000 1.000000 0.166667 0.000000 0.000000 0.833333 0.166667 0.333333 0.333333 0.166667 0.000000 0.666667 0.000000 0.333333 0.166667 0.500000 0.000000 0.333333 0.166667 0.833333 0.000000 0.000000 0.000000 0.166667 0.833333 0.000000 0.000000 0.333333 0.500000 0.166667 0.833333 0.166667 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.166667 0.666667 0.166667 0.000000 0.833333 0.000000 0.166667 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CSYTTNYYCGSAAAGC MEME-3 regular expression -------------------------------------------------------------------------------- C[CG][TC]TT[CG][CT][CT]CG[GC]AAAGC -------------------------------------------------------------------------------- Time 3.51 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 0 1.43e-04 80_[+1(6.41e-08)]_5 1 1.14e-04 37_[+3(2.85e-08)]_47 2 6.01e-02 50_[+2(4.61e-05)]_41 3 1.02e-04 27_[+1(6.95e-06)]_58 4 4.07e-01 100 5 2.59e-06 8_[+3(4.90e-07)]_41_[+1(6.51e-06)]_\ 20 6 8.43e-04 40_[+1(1.21e-05)]_45 7 5.88e-10 3_[+1(2.19e-06)]_15_[+2(3.29e-06)]_\ 3_[+3(3.03e-07)]_39 8 4.17e-04 79_[+1(2.55e-07)]_6 9 4.22e-07 53_[+1(5.14e-06)]_8_[+3(2.08e-07)]_\ 8 10 5.74e-01 100 11 1.01e-02 71_[+2(1.88e-05)]_20 12 3.39e-01 100 13 3.97e-04 51_[+1(3.13e-06)]_34 14 3.18e-01 100 15 1.11e-02 38_[+1(1.29e-05)]_47 16 3.03e-10 1_[+3(2.08e-07)]_7_[+1(6.79e-07)]_8_\ [+2(7.58e-06)]_44 17 2.02e-08 34_[+3(2.44e-08)]_7_[+2(5.08e-06)]_\ 34 18 2.02e-02 32_[+2(4.96e-05)]_59 19 9.97e-01 100 20 2.58e-03 44_[+2(1.07e-06)]_47 21 3.74e-05 79_[+1(7.85e-08)]_6 22 4.90e-04 79_[+1(3.13e-06)]_6 23 4.83e-02 73_[+2(6.52e-05)]_18 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (3) found. ******************************************************************************** CPU: noble-meme.grid.gs.washington.edu ********************************************************************************