******************************************************************************** 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/INO_up800.s CONTROL SEQUENCES= --none-- ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ CHO1 1.0000 800 CHO2 1.0000 800 FAS1 1.0000 800 FAS2 1.0000 800 ACC1 1.0000 800 INO1 1.0000 800 OPI3 1.0000 800 ******************************************************************************** ******************************************************************************** COMMAND LINE SUMMARY ******************************************************************************** This information can also be useful in the event you wish to report a problem with the MEME software. command: meme common/INO_up800.s -oc results/meme12 -mod anr -dna -revcomp -bfile common/yeast.nc.6.freq -nmotifs 2 -objfun classic -minw 8 -nostatus -mpi model: mod= anr nmotifs= 2 evt= inf objective function: em= E-value of product of p-values starts= E-value of product of p-values strands: + - width: minw= 8 maxw= 50 nsites: minsites= 2 maxsites= 35 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= 5600 N= 7 sample: seed= 0 hsfrac= 0 searchsize= 5600 norand= no csites= 1000 Letter frequencies in dataset: A 0.304 C 0.196 G 0.196 T 0.304 Background letter frequencies (from file common/yeast.nc.6.freq): A 0.324 C 0.176 G 0.176 T 0.324 Background model order: 5 ******************************************************************************** ******************************************************************************** MOTIF TTCACATGSMVCM MEME-1 width = 13 sites = 10 llr = 135 E-value = 9.1e-004 ******************************************************************************** -------------------------------------------------------------------------------- Motif TTCACATGSMVCM MEME-1 Description -------------------------------------------------------------------------------- Simplified A :::9:a:::43:4 pos.-specific C :1a:a:1:65395 probability G :::::::94:4:1 matrix T a9:1::91:1:1: bits 2.5 * * 2.3 * * 2.0 * * * * 1.8 * * * * Relative 1.5 * * ** ** * Entropy 1.3 ********* * (19.5 bits) 1.0 ********* * 0.8 ************* 0.5 ************* 0.3 ************* 0.0 ------------- Multilevel TTCACATGCCGCC consensus GAA A sequence C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTCACATGSMVCM MEME-1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- ------------- FAS1 + 95 3.29e-09 GGCCAAAAAC TTCACATGCCGCC CAGCCAAGCA INO1 - 619 3.13e-08 GACAATACTT TTCACATGCCGCA TTTAGCCGCC CHO1 + 640 7.37e-08 CCTTTGAGCT TTCACATGGACCC ATCTAAAGAT INO1 + 687 1.72e-07 ACTTATTTAA TTCACATGGAGCA GAGAAAGCGC ACC1 + 83 1.88e-07 CGTTAAAATC TTCACATGGCCCG GCCGCGCGCG CHO1 + 611 3.43e-07 ACTTTGAACG TTCACACGGCACC CTCACGCCTT FAS2 + 567 4.16e-07 CTCCCGCGTT TTCACATGCTACC TCATTCGCCT CHO2 + 354 4.16e-07 TGCCACACTT TTCTCATGCCGCA TTCATTATTC INO1 - 570 2.24e-06 CTCCGCATAT TTCACATTCAACA CTTTCGATTC OPI3 - 584 2.44e-06 GGTGCAACTT TCCACATGCACTC TCATTGACAC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTCACATGSMVCM MEME-1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- FAS1 3.3e-09 94_[+1]_693 INO1 1.7e-07 569_[-1]_36_[-1]_55_[+1]_101 CHO1 3.4e-07 610_[+1]_16_[+1]_148 ACC1 1.9e-07 82_[+1]_705 FAS2 4.2e-07 566_[+1]_221 CHO2 4.2e-07 353_[+1]_434 OPI3 2.4e-06 583_[-1]_204 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTCACATGSMVCM MEME-1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF TTCACATGSMVCM width=13 seqs=10 FAS1 ( 95) TTCACATGCCGCC 1 INO1 ( 619) TTCACATGCCGCA 1 CHO1 ( 640) TTCACATGGACCC 1 INO1 ( 687) TTCACATGGAGCA 1 ACC1 ( 83) TTCACATGGCCCG 1 CHO1 ( 611) TTCACACGGCACC 1 FAS2 ( 567) TTCACATGCTACC 1 CHO2 ( 354) TTCTCATGCCGCA 1 INO1 ( 570) TTCACATTCAACA 1 OPI3 ( 584) TCCACATGCACTC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTCACATGSMVCM MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 13 n= 5516 bayes= 9.35682 E= 9.1e-004 -997 -997 -997 162 -997 -81 -997 147 -997 251 -997 -997 147 -997 -997 -169 -997 251 -997 -997 162 -997 -997 -997 -997 -81 -997 147 -997 -997 236 -169 -997 177 119 -997 30 151 -997 -169 -11 77 119 -997 -997 236 -997 -169 30 151 -81 -997 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTCACATGSMVCM MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 13 nsites= 10 E= 9.1e-004 0.000000 0.000000 0.000000 1.000000 0.000000 0.100000 0.000000 0.900000 0.000000 1.000000 0.000000 0.000000 0.900000 0.000000 0.000000 0.100000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.100000 0.000000 0.900000 0.000000 0.000000 0.900000 0.100000 0.000000 0.600000 0.400000 0.000000 0.400000 0.500000 0.000000 0.100000 0.300000 0.300000 0.400000 0.000000 0.000000 0.900000 0.000000 0.100000 0.400000 0.500000 0.100000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTCACATGSMVCM MEME-1 regular expression -------------------------------------------------------------------------------- TTCACATG[CG][CA][GAC]C[CA] -------------------------------------------------------------------------------- Time 0.89 secs. ******************************************************************************** ******************************************************************************** MOTIF VDMBNCCMSHTSWVYACYGKC MEME-2 width = 21 sites = 12 llr = 172 E-value = 2.0e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif VDMBNCCMSHTSWVYACYGKC MEME-2 Description -------------------------------------------------------------------------------- Simplified A 345:32:5:3::33:7::::: pos.-specific C 4:3336936435:45:86::8 probability G 3324331:4:152321::a63 matrix T :3:32::2:37:5:3324:4: bits 2.5 * 2.3 * 2.0 * * 1.8 * * * * Relative 1.5 * * * * * * Entropy 1.3 * * * ***** (20.6 bits) 1.0 ** * * ***** 0.8 * * ** * ** ** ***** 0.5 * ** ******* ******** 0.3 **** **************** 0.0 --------------------- Multilevel CAAGACCACCTCTCCACCGGC consensus ATCCCG CGACGAATT T TG sequence GG TG T G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif VDMBNCCMSHTSWVYACYGKC MEME-2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- --------------------- INO1 - 369 1.17e-09 TGTTGTCCAT CAAGGGCACATCGGCACCGGC CTCATCGTCT FAS2 + 710 4.56e-09 GAAGGTTACA CAAGACCACATCACCACTGTC GTGCTTTTCT INO1 + 283 6.95e-08 AGACATGCGA CTGCGCCCGCCGTAGACCGTG ACCTGGAAGC INO1 - 536 7.72e-08 TCGATTCCGC ATCCAACCCCGGAACACCGGC ACGTATTTCA INO1 + 399 8.57e-08 GATGGACAAC AAACAACAGCTCTCTTCCGGC CGTACTTAGT INO1 - 122 1.40e-07 CATACCCTTA CGCTTCCAGACGGCCACTGGG GGAATGAAAA OPI3 - 504 2.39e-07 CGAATTATAC GGCGGCGCCATCACTACTGTC GTCCCACCTG OPI3 + 289 2.60e-07 TTCCCATTTG GTGGTCCCGTTCAACTCCGTC AGGTCTTCCA ACC1 + 217 2.60e-07 AGAAGAACAG CACTCCCAGTCGTATTCTGGC ACAGTATAGC INO1 + 703 3.58e-07 TGGAGCAGAG AAAGCGCACCTCTGCGTTGGC GGCAATGTTA OPI3 + 343 4.17e-07 AGCCTCCTTC AGATCGCTCTTGTCGACCGTC TCCAAGAGAT OPI3 + 441 4.49e-07 GGGAATTGAC GTACACCTCCTGTGTATCGGG GACTTCTCTT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif VDMBNCCMSHTSWVYACYGKC MEME-2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- INO1 8.6e-08 121_[-2]_140_[+2]_65_[-2]_9_[+2]_ 116_[-2]_146_[+2]_77 FAS2 4.6e-09 709_[+2]_70 OPI3 2.4e-07 288_[+2]_33_[+2]_77_[+2]_42_[-2]_276 ACC1 2.6e-07 216_[+2]_563 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif VDMBNCCMSHTSWVYACYGKC MEME-2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF VDMBNCCMSHTSWVYACYGKC width=21 seqs=12 INO1 ( 369) CAAGGGCACATCGGCACCGGC 1 FAS2 ( 710) CAAGACCACATCACCACTGTC 1 INO1 ( 283) CTGCGCCCGCCGTAGACCGTG 1 INO1 ( 536) ATCCAACCCCGGAACACCGGC 1 INO1 ( 399) AAACAACAGCTCTCTTCCGGC 1 INO1 ( 122) CGCTTCCAGACGGCCACTGGG 1 OPI3 ( 504) GGCGGCGCCATCACTACTGTC 1 OPI3 ( 289) GTGGTCCCGTTCAACTCCGTC 1 ACC1 ( 217) CACTCCCAGTCGTATTCTGGC 1 INO1 ( 703) AAAGCGCACCTCTGCGTTGGC 1 OPI3 ( 343) AGATCGCTCTTGTCGACCGTC 1 OPI3 ( 441) GTACACCTCCTGTGTATCGGG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif VDMBNCCMSHTSWVYACYGKC MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 5460 bayes= 9.92778 E= 2.0e+000 4 125 51 -1023 36 -1023 51 4 62 92 -8 -1023 -1023 92 125 -38 4 51 51 -96 -96 173 51 -1023 -1023 238 -107 -1023 62 92 -1023 -96 -1023 173 125 -1023 4 125 -1023 -38 -1023 51 -107 104 -1023 151 151 -1023 4 -1023 -8 62 4 125 51 -1023 -1023 151 -8 4 104 -1023 -107 -38 -1023 225 -1023 -96 -1023 173 -1023 36 -1023 -1023 251 -1023 -1023 -1023 173 36 -1023 209 51 -1023 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif VDMBNCCMSHTSWVYACYGKC MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 12 E= 2.0e+000 0.333333 0.416667 0.250000 0.000000 0.416667 0.000000 0.250000 0.333333 0.500000 0.333333 0.166667 0.000000 0.000000 0.333333 0.416667 0.250000 0.333333 0.250000 0.250000 0.166667 0.166667 0.583333 0.250000 0.000000 0.000000 0.916667 0.083333 0.000000 0.500000 0.333333 0.000000 0.166667 0.000000 0.583333 0.416667 0.000000 0.333333 0.416667 0.000000 0.250000 0.000000 0.250000 0.083333 0.666667 0.000000 0.500000 0.500000 0.000000 0.333333 0.000000 0.166667 0.500000 0.333333 0.416667 0.250000 0.000000 0.000000 0.500000 0.166667 0.333333 0.666667 0.000000 0.083333 0.250000 0.000000 0.833333 0.000000 0.166667 0.000000 0.583333 0.000000 0.416667 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.583333 0.416667 0.000000 0.750000 0.250000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif VDMBNCCMSHTSWVYACYGKC MEME-2 regular expression -------------------------------------------------------------------------------- [CAG][ATG][AC][GCT][ACG][CG]C[AC][CG][CAT][TC][CG][TA][CAG][CT][AT]C[CT]G[GT][CG] -------------------------------------------------------------------------------- Time 1.76 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- CHO1 8.42e-04 610_[+1(3.43e-07)]_16_\ [+1(7.37e-08)]_148 CHO2 4.72e-03 353_[+1(4.16e-07)]_434 FAS1 3.41e-05 94_[+1(3.29e-09)]_693 FAS2 9.42e-08 566_[+1(4.16e-07)]_130_\ [+2(4.56e-09)]_70 ACC1 2.04e-06 82_[+1(1.88e-07)]_121_\ [+2(2.60e-07)]_563 INO1 2.18e-09 121_[-2(1.40e-07)]_140_\ [+2(6.95e-08)]_65_[-2(1.17e-09)]_9_[+2(8.57e-08)]_116_[-2(7.72e-08)]_13_\ [-1(2.24e-06)]_36_[-1(3.13e-08)]_55_[+1(1.72e-07)]_3_[+2(3.58e-07)]_77 OPI3 2.07e-05 87_[+2(3.51e-05)]_180_\ [+2(2.60e-07)]_33_[+2(4.17e-07)]_77_[+2(4.49e-07)]_42_[-2(2.39e-07)]_59_\ [-1(2.44e-06)]_204 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (2) found. ******************************************************************************** CPU: Timothys-Mac-Mini.local ********************************************************************************