******************************************************************************** MEME - Motif discovery tool ******************************************************************************** MEME version 5.5.1 (Release date: Sun Jan 29 10:33:12 2023 -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= for_MEME.txt CONTROL SEQUENCES= --none-- ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ prom0 1.0000 100 prom1 1.0000 100 prom2 1.0000 100 prom3 1.0000 100 prom4 1.0000 100 prom5 1.0000 100 prom6 1.0000 100 prom7 1.0000 100 prom8 1.0000 100 prom9 1.0000 100 prom10 1.0000 100 prom11 1.0000 100 prom12 1.0000 100 prom13 1.0000 100 prom14 1.0000 100 prom15 1.0000 100 prom16 1.0000 100 prom17 1.0000 100 prom18 1.0000 100 prom19 1.0000 100 prom20 1.0000 100 prom21 1.0000 100 prom22 1.0000 100 prom23 1.0000 100 prom24 1.0000 100 prom25 1.0000 100 prom26 1.0000 100 prom27 1.0000 100 prom28 1.0000 100 prom29 1.0000 100 prom30 1.0000 100 prom31 1.0000 100 prom32 1.0000 100 prom33 1.0000 100 prom34 1.0000 100 prom35 1.0000 100 prom36 1.0000 100 prom37 1.0000 100 prom38 1.0000 100 prom39 1.0000 100 prom40 1.0000 100 prom41 1.0000 100 prom42 1.0000 100 prom43 1.0000 100 prom44 1.0000 100 prom45 1.0000 100 prom46 1.0000 100 prom47 1.0000 100 prom48 1.0000 100 prom49 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 for_MEME.txt -dna -nmotifs 3 -minw 6 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= 6 maxw= 50 nsites: minsites= 2 maxsites= 50 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= 5000 N= 50 sample: seed= 0 hsfrac= 0 searchsize= 5000 norand= no csites= 1000 Letter frequencies in dataset: A 0.204 C 0.312 G 0.265 T 0.219 Background letter frequencies (from file dataset with add-one prior applied): A 0.204 C 0.312 G 0.265 T 0.219 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF TGATTTDHHTTGYAAVMBCAKHCWTTDTHTGGTRHAATT MEME-1 width = 39 sites = 4 llr = 139 E-value = 7.6e-002 ******************************************************************************** -------------------------------------------------------------------------------- Motif TGATTTDHHTTGYAAVMBCAKHCWTTDTHTGGTRHAATT MEME-1 Description -------------------------------------------------------------------------------- Simplified A ::8:::333::::8855::8:3:533533::3:538a:: pos.-specific C 3::::::5533:5::355a3:38:::::3:::::5:::: probability G :83:::3::::a::33:3::5:::::3:::88:5:3:3: matrix T 83:aaa53388:53:::3::553588385a3:a:3::8a bits 2.3 *** * * * * 2.1 *** * * * * 1.8 *** * * * * * 1.6 *** * * * * * * Relative 1.4 **** * ** ** ** * * * **** Entropy 1.1 ****** *** ** *** *** * ***** **** (50.0 bits) 0.9 ****** ****** * *** **** * ***** **** 0.7 ******* ****** * **************** **** 0.5 *************************************** 0.2 *************************************** 0.0 --------------------------------------- Multilevel TGATTTTCCTTGCAAAACCAGTCATTATTTGGTACAATT consensus CTG AAACC TTGCCG CTATTAAGAA TA GAG G sequence GTT G T C T C T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGATTTDHHTTGYAAVMBCAKHCWTTDTHTGGTRHAATT MEME-1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------------------------- prom12 17 4.94e-19 CCCAACCCCT TGATTTACCTTGCAAAACCAGCCATTTTCTGGTAAAATT TCCCCCAGTT prom46 57 3.77e-17 TCTCCCGGCT TTATTTTTCTTGCAAAATCATACAAAATTTTGTATGATT CGCCG prom18 18 4.03e-16 TTGGTAGGTG CGATTTTATCCGTAACCGCAGTCTTTAAATGGTGCAATT ACGTCTGGTT prom48 17 3.98e-15 GCCGATCCAA TGGTTTGCATTGTTGGCCCCTTTTTTGTTTGATGCAAGT AAATTGTTCA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGATTTDHHTTGYAAVMBCAKHCWTTDTHTGGTRHAATT MEME-1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- prom12 4.9e-19 16_[+1]_45 prom46 3.8e-17 56_[+1]_5 prom18 4e-16 17_[+1]_44 prom48 4e-15 16_[+1]_45 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGATTTDHHTTGYAAVMBCAKHCWTTDTHTGGTRHAATT MEME-1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF TGATTTDHHTTGYAAVMBCAKHCWTTDTHTGGTRHAATT width=39 seqs=4 prom12 ( 17) TGATTTACCTTGCAAAACCAGCCATTTTCTGGTAAAATT 1 prom46 ( 57) TTATTTTTCTTGCAAAATCATACAAAATTTTGTATGATT 1 prom18 ( 18) CGATTTTATCCGTAACCGCAGTCTTTAAATGGTGCAATT 1 prom48 ( 17) TGGTTTGCATTGTTGGCCCCTTTTTTGTTTGATGCAAGT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGATTTDHHTTGYAAVMBCAKHCWTTDTHTGGTRHAATT MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 39 n= 3100 bayes= 8.7467 E= 7.6e-002 -865 -32 -865 177 -865 -865 150 19 188 -865 -8 -865 -865 -865 -865 219 -865 -865 -865 219 -865 -865 -865 219 30 -865 -8 119 30 68 -865 19 30 68 -865 19 -865 -32 -865 177 -865 -32 -865 177 -865 -865 191 -865 -865 68 -865 119 188 -865 -865 19 188 -865 -8 -865 129 -32 -8 -865 129 68 -865 -865 -865 68 -8 19 -865 168 -865 -865 188 -32 -865 -865 -865 -865 91 119 30 -32 -865 119 -865 126 -865 19 129 -865 -865 119 30 -865 -865 177 30 -865 -865 177 129 -865 -8 19 30 -865 -865 177 30 -32 -865 119 -865 -865 -865 219 -865 -865 150 19 30 -865 150 -865 -865 -865 -865 219 129 -865 91 -865 30 68 -865 19 188 -865 -8 -865 229 -865 -865 -865 -865 -865 -8 177 -865 -865 -865 219 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGATTTDHHTTGYAAVMBCAKHCWTTDTHTGGTRHAATT MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 39 nsites= 4 E= 7.6e-002 0.000000 0.250000 0.000000 0.750000 0.000000 0.000000 0.750000 0.250000 0.750000 0.000000 0.250000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.250000 0.000000 0.250000 0.500000 0.250000 0.500000 0.000000 0.250000 0.250000 0.500000 0.000000 0.250000 0.000000 0.250000 0.000000 0.750000 0.000000 0.250000 0.000000 0.750000 0.000000 0.000000 1.000000 0.000000 0.000000 0.500000 0.000000 0.500000 0.750000 0.000000 0.000000 0.250000 0.750000 0.000000 0.250000 0.000000 0.500000 0.250000 0.250000 0.000000 0.500000 0.500000 0.000000 0.000000 0.000000 0.500000 0.250000 0.250000 0.000000 1.000000 0.000000 0.000000 0.750000 0.250000 0.000000 0.000000 0.000000 0.000000 0.500000 0.500000 0.250000 0.250000 0.000000 0.500000 0.000000 0.750000 0.000000 0.250000 0.500000 0.000000 0.000000 0.500000 0.250000 0.000000 0.000000 0.750000 0.250000 0.000000 0.000000 0.750000 0.500000 0.000000 0.250000 0.250000 0.250000 0.000000 0.000000 0.750000 0.250000 0.250000 0.000000 0.500000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.750000 0.250000 0.250000 0.000000 0.750000 0.000000 0.000000 0.000000 0.000000 1.000000 0.500000 0.000000 0.500000 0.000000 0.250000 0.500000 0.000000 0.250000 0.750000 0.000000 0.250000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.250000 0.750000 0.000000 0.000000 0.000000 1.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGATTTDHHTTGYAAVMBCAKHCWTTDTHTGGTRHAATT MEME-1 regular expression -------------------------------------------------------------------------------- [TC][GT][AG]TTT[TAG][CAT][CAT][TC][TC]G[CT][AT][AG][ACG][AC][CGT]C[AC][GT][TAC][CT][AT][TA][TA][AGT][TA][TAC]T[GT][GA]T[AG][CAT][AG]A[TG]T -------------------------------------------------------------------------------- Time 2.35 secs. ******************************************************************************** ******************************************************************************** MOTIF RCYTGCAAARGCCCC MEME-2 width = 15 sites = 5 llr = 78 E-value = 7.0e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif RCYTGCAAARGCCCC MEME-2 Description -------------------------------------------------------------------------------- Simplified A 4:::::8aa6::::: pos.-specific C :a6::a2:::2a8a8 probability G 6::2a::::48:::2 matrix T ::48::::::::2:: bits 2.3 ** 2.1 ** 1.8 * ** 1.6 * ** ** * * Relative 1.4 * ****** * * Entropy 1.1 ** *********** (22.5 bits) 0.9 *************** 0.7 *************** 0.5 *************** 0.2 *************** 0.0 --------------- Multilevel GCCTGCAAAAGCCCC consensus A TG C GC T G sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RCYTGCAAARGCCCC MEME-2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------- prom20 53 5.02e-09 ACGGGCCTTG ACCTGCAAAAGCCCC ACGCTGCGTG prom11 37 5.02e-09 GCAGGACCCA ACCTGCAAAAGCCCC TCCCCCGAAA prom0 85 4.44e-08 ATTCGTATAC GCTTGCAAAGGCTCC C prom37 37 1.35e-07 CATTTGTTGT GCTTGCCAAAGCCCG CGCTTTGCCC prom9 6 2.18e-07 AGCGC GCCGGCAAAGCCCCC AGCAGGGTCA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RCYTGCAAARGCCCC MEME-2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- prom20 5e-09 52_[+2]_33 prom11 5e-09 36_[+2]_49 prom0 4.4e-08 84_[+2]_1 prom37 1.4e-07 36_[+2]_49 prom9 2.2e-07 5_[+2]_80 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RCYTGCAAARGCCCC MEME-2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF RCYTGCAAARGCCCC width=15 seqs=5 prom20 ( 53) ACCTGCAAAAGCCCC 1 prom11 ( 37) ACCTGCAAAAGCCCC 1 prom0 ( 85) GCTTGCAAAGGCTCC 1 prom37 ( 37) GCTTGCCAAAGCCCG 1 prom9 ( 6) GCCGGCAAAGCCCCC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RCYTGCAAARGCCCC MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 4300 bayes= 9.99832 E= 7.0e+001 97 -897 118 -897 -897 168 -897 -897 -897 94 -897 87 -897 -897 -41 187 -897 -897 191 -897 -897 168 -897 -897 197 -64 -897 -897 229 -897 -897 -897 229 -897 -897 -897 156 -897 59 -897 -897 -64 159 -897 -897 168 -897 -897 -897 136 -897 -13 -897 168 -897 -897 -897 136 -41 -897 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RCYTGCAAARGCCCC MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 5 E= 7.0e+001 0.400000 0.000000 0.600000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.600000 0.000000 0.400000 0.000000 0.000000 0.200000 0.800000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.800000 0.200000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.600000 0.000000 0.400000 0.000000 0.000000 0.200000 0.800000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.800000 0.000000 0.200000 0.000000 1.000000 0.000000 0.000000 0.000000 0.800000 0.200000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RCYTGCAAARGCCCC MEME-2 regular expression -------------------------------------------------------------------------------- [GA]C[CT][TG]GC[AC]AA[AG][GC]C[CT]C[CG] -------------------------------------------------------------------------------- Time 4.45 secs. ******************************************************************************** ******************************************************************************** MOTIF AAWWKGMGA MEME-3 width = 9 sites = 8 llr = 82 E-value = 4.5e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif AAWWKGMGA MEME-3 Description -------------------------------------------------------------------------------- Simplified A aa54::5:a pos.-specific C ::::::5:: probability G ::::4a:9: matrix T ::566::1: bits 2.3 ** * 2.1 ** * 1.8 ** * * 1.6 ** * * Relative 1.4 ** * * ** Entropy 1.1 ****** ** (14.9 bits) 0.9 ********* 0.7 ********* 0.5 ********* 0.2 ********* 0.0 --------- Multilevel AAATTGAGA consensus TAG C sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAWWKGMGA MEME-3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------- prom9 43 2.47e-06 AGCGCCATCC AATTTGAGA AAATAGCCGC prom22 47 5.40e-06 TTCATGTGCC AAAATGAGA CCCAGTGAGC prom27 77 8.54e-06 TAATCGCCAC AATTTGCGA CAGATACCCA prom7 86 9.98e-06 ATCGTAAATC AAATGGAGA CGGTTC prom17 40 1.50e-05 GGACTTTACT AATATGCGA GGAATTTTTA prom38 25 1.86e-05 CGATCAGCGC AAATGGCGA GCGCTCGGGG prom30 15 2.44e-05 ATCTTGTGCA AAAAGGCGA AAGCCGCGCG prom1 78 2.87e-05 GACTCGTCCA AATTTGATA TGACCACAAC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAWWKGMGA MEME-3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- prom9 2.5e-06 42_[+3]_49 prom22 5.4e-06 46_[+3]_45 prom27 8.5e-06 76_[+3]_15 prom7 1e-05 85_[+3]_6 prom17 1.5e-05 39_[+3]_52 prom38 1.9e-05 24_[+3]_67 prom30 2.4e-05 14_[+3]_77 prom1 2.9e-05 77_[+3]_14 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAWWKGMGA MEME-3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF AAWWKGMGA width=9 seqs=8 prom9 ( 43) AATTTGAGA 1 prom22 ( 47) AAAATGAGA 1 prom27 ( 77) AATTTGCGA 1 prom7 ( 86) AAATGGAGA 1 prom17 ( 40) AATATGCGA 1 prom38 ( 25) AAATGGCGA 1 prom30 ( 15) AAAAGGCGA 1 prom1 ( 78) AATTTGATA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAWWKGMGA MEME-3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 9 n= 4600 bayes= 9.16491 E= 4.5e+001 229 -965 -965 -965 229 -965 -965 -965 129 -965 -965 119 88 -965 -965 151 -965 -965 50 151 -965 -965 191 -965 129 68 -965 -965 -965 -965 172 -81 229 -965 -965 -965 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAWWKGMGA MEME-3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 9 nsites= 8 E= 4.5e+001 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.500000 0.000000 0.000000 0.500000 0.375000 0.000000 0.000000 0.625000 0.000000 0.000000 0.375000 0.625000 0.000000 0.000000 1.000000 0.000000 0.500000 0.500000 0.000000 0.000000 0.000000 0.000000 0.875000 0.125000 1.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAWWKGMGA MEME-3 regular expression -------------------------------------------------------------------------------- AA[AT][TA][TG]G[AC]GA -------------------------------------------------------------------------------- Time 6.51 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- prom0 6.66e-05 84_[+2(4.44e-08)]_1 prom1 2.21e-03 77_[+3(2.87e-05)]_14 prom2 4.47e-01 100 prom3 3.55e-01 100 prom4 5.85e-01 100 prom5 6.42e-01 100 prom6 5.67e-01 100 prom7 1.38e-02 85_[+3(9.98e-06)]_6 prom8 4.04e-02 100 prom9 6.00e-07 5_[+2(2.18e-07)]_22_[+3(2.47e-06)]_\ 49 prom10 5.75e-01 100 prom11 3.24e-05 36_[+2(5.02e-09)]_49 prom12 3.04e-16 16_[+1(4.94e-19)]_45 prom13 6.96e-01 100 prom14 1.80e-01 100 prom15 7.34e-01 100 prom16 1.61e-01 100 prom17 9.47e-03 39_[+3(1.50e-05)]_52 prom18 1.99e-12 17_[+1(4.03e-16)]_44 prom19 5.34e-01 100 prom20 9.64e-06 52_[+2(5.02e-09)]_33 prom21 4.86e-01 100 prom22 9.80e-03 46_[+3(5.40e-06)]_45 prom23 9.99e-01 100 prom24 7.05e-01 100 prom25 5.60e-01 100 prom26 6.08e-01 100 prom27 1.84e-03 76_[+3(8.54e-06)]_15 prom28 7.20e-01 100 prom29 6.76e-01 100 prom30 1.69e-03 14_[+3(2.44e-05)]_77 prom31 1.20e-01 100 prom32 5.14e-01 100 prom33 9.85e-01 100 prom34 6.84e-01 100 prom35 5.19e-02 100 prom36 1.85e-01 100 prom37 2.68e-05 36_[+2(1.35e-07)]_49 prom38 7.86e-03 24_[+3(1.86e-05)]_67 prom39 5.74e-01 100 prom40 8.92e-01 100 prom41 9.44e-01 100 prom42 3.99e-01 100 prom43 9.87e-02 100 prom44 9.94e-01 100 prom45 8.99e-01 100 prom46 5.30e-14 56_[+1(3.77e-17)]_5 prom47 8.02e-02 100 prom48 4.92e-11 16_[+1(3.98e-15)]_45 prom49 5.24e-01 100 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (3) found. ******************************************************************************** CPU: kodomo ********************************************************************************