******************************************************************************** MEME - Motif discovery tool ******************************************************************************** MEME version 5.4.0 (Release date: Tue Mar 9 17:38:20 2021 -0800) 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= common/crp0.s CONTROL SEQUENCES= Primary sequences shuffled preserving 3-mers ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ ce1cg 1.0000 105 ara 1.0000 105 bglr1 1.0000 105 crp 1.0000 105 cya 1.0000 105 deop2 1.0000 105 gale 1.0000 105 ilv 1.0000 105 lac 1.0000 105 male 1.0000 105 malk 1.0000 105 malt 1.0000 105 ompa 1.0000 105 tnaa 1.0000 105 uxu1 1.0000 105 pbr322 1.0000 105 trn9cat 1.0000 105 tdc 1.0000 105 ******************************************************************************** ******************************************************************************** COMMAND LINE SUMMARY ******************************************************************************** This information can also be useful in the event you wish to report a problem with the MEME software. command: meme -minsites 3 -maxsites 17 common/crp0.s -oc results/meme21 -mod anr -dna -revcomp -nmotifs 2 -objfun de -w 12 -hsfrac 0.6 -shuf 3 -nostatus -mpi model: mod= anr nmotifs= 2 evt= inf objective function: em= Differential Enrichment mHG starts= log likelihood ratio (LLR) strands: + - width: minw= 12 maxw= 12 nsites: minsites= 3 maxsites= 17 wnsites= 0.8 theta: spmap= uni spfuzz= 0.5 em: prior= dirichlet b= 0.01 maxiter= 50 distance= 1e-05 data: n= 1890 N= 18 sample: seed= 0 hsfrac= 0.6 searchsize= 1890 norand= no csites= -1 Letter frequencies in dataset: A 0.304 C 0.196 G 0.196 T 0.304 Background letter frequencies (from file dataset with add-one prior applied): A 0.304 C 0.196 G 0.196 T 0.304 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF HCAVMTCACAWW MEME-1 width = 12 sites = 17 llr = 134 p-value = 6.6e-001 E-value = 6.6e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif HCAVMTCACAWW MEME-1 Description -------------------------------------------------------------------------------- Simplified A 5:746118:944 pos.-specific C 381442919111 probability G :122:1:11:1: matrix T 21:::6::::46 bits 2.4 2.1 * 1.9 * * 1.6 * * Relative 1.4 * * * Entropy 1.2 * * ** (11.4 bits) 0.9 * * **** 0.7 ** * **** 0.5 ********** * 0.2 ********** * 0.0 ------------ Multilevel ACACATCACAAT consensus C AC TA sequence T G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif HCAVMTCACAWW MEME-1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- ------------ deop2 - 61 1.77e-07 ACACTTCGAT ACACATCACAAT TAAGGAAATC uxu1 - 18 1.52e-05 ATTGGGTTAA CCACATCACAAC AATTTCACTC bglr1 - 22 2.04e-05 GTTATATATA ACAAATCCCAAT AATTAAGTTA bglr1 + 1 2.04e-05 . ACAAATCCCAAT AACTTAATTA deop2 + 16 2.32e-05 ATTATTTGAA CCAGATCGCATT ACAGTGATGC tnaa - 72 2.66e-05 TAAATGTGAA TCGAATCACAAT CGTTCGGGGA tdc - 79 4.33e-05 GATATGTGCG ACCACTCACAAA TTAACTTTCA lac - 82 4.33e-05 GAAATTGTTA TCCGCTCACAAT TCCACACAAC malt - 15 6.45e-05 ATCTTTATTA ACAACTCACCTA AAACGACGCT lac - 10 9.21e-05 AATGAGTGAG CTAACTCACATT AATTGCGTT pbr322 - 49 1.18e-04 GTGCGGTATT TCACACCGCATA TGGTGCACTC deop2 - 78 1.89e-04 AACATCTACT CCGCAACACACT TCGATACACA male - 40 2.18e-04 CCTTGCCCCT ACGCCCCACCGT CGCTTTGTGT male + 23 2.50e-04 ATTCTGTAAC AGAGATCACACA AAGCGACGGT lac - 69 3.10e-04 GCTCACAATT CCACACAACATA CGAGCCGGAA pbr322 + 62 3.99e-04 GCGGTGTGAA ATACCGCACAGA TGCGTAAGGA pbr322 + 20 4.53e-04 CTATGCGGCA TCAGAGCAGATT GTACTGAGAG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif HCAVMTCACAWW MEME-1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- deop2 0.00019 15_[+1]_33_[-1]_5_[-1]_16 uxu1 1.5e-05 17_[-1]_76 bglr1 2e-05 [+1]_9_[-1]_72 tnaa 2.7e-05 71_[-1]_22 tdc 4.3e-05 78_[-1]_15 lac 0.00031 9_[-1]_47_[-1]_1_[-1]_12 malt 6.4e-05 14_[-1]_79 pbr322 0.00045 19_[+1]_17_[-1]_1_[+1]_32 male 0.00022 22_[+1]_5_[-1]_54 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif HCAVMTCACAWW MEME-1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF HCAVMTCACAWW width=12 seqs=17 deop2 ( 61) ACACATCACAAT 1 uxu1 ( 18) CCACATCACAAC 1 bglr1 ( 22) ACAAATCCCAAT 1 bglr1 ( 1) ACAAATCCCAAT 1 deop2 ( 16) CCAGATCGCATT 1 tnaa ( 72) TCGAATCACAAT 1 tdc ( 79) ACCACTCACAAA 1 lac ( 82) TCCGCTCACAAT 1 malt ( 15) ACAACTCACCTA 1 lac ( 10) CTAACTCACATT 1 pbr322 ( 49) TCACACCGCATA 1 deop2 ( 78) CCGCAACACACT 1 male ( 40) ACGCCCCACCGT 1 male ( 23) AGAGATCACACA 1 lac ( 69) CCACACAACATA 1 pbr322 ( 62) ATACCGCACAGA 1 pbr322 ( 20) TCAGAGCAGATT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif HCAVMTCACAWW MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 1692 bayes= 7.30945 E= 6.6e-001 63 59 -1073 -37 -1073 207 -173 -137 121 -73 -15 -1073 21 107 26 -1073 109 85 -1073 -1073 -237 -15 -73 109 -237 226 -1073 -1073 133 -73 -73 -1073 -1073 226 -173 -1073 154 -73 -1073 -1073 44 -73 -73 21 21 -173 -1073 95 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif HCAVMTCACAWW MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 17 E= 6.6e-001 0.470588 0.294118 0.000000 0.235294 0.000000 0.823529 0.058824 0.117647 0.705882 0.117647 0.176471 0.000000 0.352941 0.411765 0.235294 0.000000 0.647059 0.352941 0.000000 0.000000 0.058824 0.176471 0.117647 0.647059 0.058824 0.941176 0.000000 0.000000 0.764706 0.117647 0.117647 0.000000 0.000000 0.941176 0.058824 0.000000 0.882353 0.117647 0.000000 0.000000 0.411765 0.117647 0.117647 0.352941 0.352941 0.058824 0.000000 0.588235 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif HCAVMTCACAWW MEME-1 regular expression -------------------------------------------------------------------------------- [ACT]CA[CAG][AC]TCACA[AT][TA] -------------------------------------------------------------------------------- Time 0.22 secs. ******************************************************************************** ******************************************************************************** MOTIF ATMAMSAWRYTM MEME-2 width = 12 sites = 6 llr = 62 p-value = 4.9e-001 E-value = 4.9e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif ATMAMSAWRYTM MEME-2 Description -------------------------------------------------------------------------------- Simplified A a:5a52a55::5 pos.-specific C ::3:53:::7:5 probability G ::2::5::5::: matrix T :a:::::5:3a: bits 2.4 2.1 1.9 1.6 ** * * * Relative 1.4 ** * * * Entropy 1.2 ** * * ** (15.0 bits) 0.9 ** ** * **** 0.7 ** ********* 0.5 ************ 0.2 ************ 0.0 ------------ Multilevel ATAAAGAAACTA consensus C CC TGT C sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ATMAMSAWRYTM MEME-2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- ------------ tdc + 47 1.52e-06 TTTAATTGTA ATAACGATACTC TGGAAAGTAT bglr1 - 82 4.41e-06 TGATAAAAAT ATGACCATGCTC ACAGTTATTA male + 83 7.68e-06 AGGTTGCCGT ATAAAGAAACTA GAGTCCGTTT malk - 58 1.01e-05 TGCAAGCAAC ATCACGAAATTC CTTACATGAC tdc - 14 2.22e-05 ACCTTTAAAT ATCAACAAGTTA AAGTATAAAA ara - 87 2.58e-05 CTTATGG ATAAAAATGCTA TGGCATAGCA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ATMAMSAWRYTM MEME-2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- tdc 2.2e-05 13_[-2]_21_[+2]_47 bglr1 4.4e-06 81_[-2]_12 male 7.7e-06 82_[+2]_11 malk 1e-05 57_[-2]_36 ara 2.6e-05 86_[-2]_7 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ATMAMSAWRYTM MEME-2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF ATMAMSAWRYTM width=12 seqs=6 tdc ( 47) ATAACGATACTC 1 bglr1 ( 82) ATGACCATGCTC 1 male ( 83) ATAAAGAAACTA 1 malk ( 58) ATCACGAAATTC 1 tdc ( 14) ATCAACAAGTTA 1 ara ( 87) ATAAAAATGCTA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ATMAMSAWRYTM MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 1692 bayes= 8.58325 E= 4.9e-001 172 -923 -923 -923 -923 -923 -923 172 72 77 -23 -923 172 -923 -923 -923 72 135 -923 -923 -87 77 135 -923 172 -923 -923 -923 72 -923 -923 72 72 -923 135 -923 -923 177 -923 13 -923 -923 -923 172 72 135 -923 -923 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ATMAMSAWRYTM MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 6 E= 4.9e-001 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.500000 0.333333 0.166667 0.000000 1.000000 0.000000 0.000000 0.000000 0.500000 0.500000 0.000000 0.000000 0.166667 0.333333 0.500000 0.000000 1.000000 0.000000 0.000000 0.000000 0.500000 0.000000 0.000000 0.500000 0.500000 0.000000 0.500000 0.000000 0.000000 0.666667 0.000000 0.333333 0.000000 0.000000 0.000000 1.000000 0.500000 0.500000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ATMAMSAWRYTM MEME-2 regular expression -------------------------------------------------------------------------------- AT[AC]A[AC][GC]A[AT][AG][CT]T[AC] -------------------------------------------------------------------------------- Time 0.38 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- ce1cg 7.25e-01 105 ara 1.54e-02 86_[-2(2.58e-05)]_7 bglr1 4.34e-05 [+1(2.04e-05)]_9_[-1(2.04e-05)]_48_\ [-2(4.41e-06)]_12 crp 3.95e-01 105 cya 5.40e-01 105 deop2 2.75e-04 15_[+1(2.32e-05)]_33_[-1(1.77e-07)]_\ 33 gale 3.62e-01 105 ilv 6.56e-01 105 lac 3.34e-02 9_[-1(9.21e-05)]_60_[-1(4.33e-05)]_\ 12 male 6.23e-04 82_[+2(7.68e-06)]_11 malk 1.00e-02 57_[-2(1.01e-05)]_36 malt 4.08e-02 14_[-1(6.45e-05)]_79 ompa 5.32e-01 105 tnaa 1.69e-02 71_[-1(2.66e-05)]_22 uxu1 1.30e-02 17_[-1(1.52e-05)]_76 pbr322 1.04e-01 105 trn9cat 6.93e-01 105 tdc 3.24e-05 13_[-2(2.22e-05)]_21_[+2(1.52e-06)]_\ 20_[-1(4.33e-05)]_15 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (2) found. ******************************************************************************** CPU: Timothys-Mac-Mini.local ********************************************************************************