******************************************************************************** MEME - Motif discovery tool ******************************************************************************** MEME version 4.11.3 (Release date: Fri Feb 19 13:23:06 2016 -0800) For further information on how to interpret these results or to get a copy of the MEME software please access http://meme-suite.org . 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-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 ******************************************************************************** DATAFILE= common/INO_up800.s 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/meme9 -mod tcm -dna -revcomp -bfile common/yeast.nc.6.freq -x_branch -nmotifs 2 -minw 8 -nostatus model: mod= tcm nmotifs= 2 evt= inf object function= E-value of product of p-values width: minw= 8 maxw= 50 width: wg= 11 ws= 1 endgaps= yes nsites: minsites= 2 maxsites= 35 wnsites= 0.8 theta: spmap= uni spfuzz= 0.5 global: substring= yes branching= yes wbranch= no bfactor= 3 heapsize= 64 em: prior= dirichlet b= 0.01 maxiter= 50 distance= 1e-05 data: n= 5600 N= 7 shuffle= -1 strands: + - sample: seed= 0 ctfrac= -1 maxwords= -1 Letter frequencies in dataset: A 0.304 C 0.196 G 0.196 T 0.304 Background letter frequencies (from common/yeast.nc.6.freq): A 0.324 C 0.176 G 0.176 T 0.324 ******************************************************************************** ******************************************************************************** MOTIF YYWNAVTTTTCACATGCMVCC MEME-1 width = 21 sites = 13 llr = 187 E-value = 2.7e-003 ******************************************************************************** -------------------------------------------------------------------------------- Motif YYWNAVTTTTCACATGCMVCC MEME-1 Description -------------------------------------------------------------------------------- Simplified A :133742::::8:a:::4422 pos.-specific C 54222222:2a:8:2175377 probability G :113:3:1:::11::83:2:1 matrix T 55521157a8:12:81:111: bits 2.5 * 2.3 * 2.0 * 1.8 * * Relative 1.5 * * ** ** Entropy 1.3 * * ***** * (20.7 bits) 1.0 * ********* ** 0.8 * * *********** ** 0.5 ** * *********** ** 0.3 ** ****************** 0.0 --------------------- Multilevel CTTAAATTTTCACATGCCACC consensus TCAGCGAC C GACAA sequence C CC G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YYWNAVTTTTCACATGCMVCC MEME-1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- --------------------- FAS1 + 87 5.92e-10 CAAACGACGG CCAAAAACTTCACATGCCGCC CAGCCAAGCA CHO1 + 632 9.34e-10 CCCTCACGCC TTTGAGCTTTCACATGGACCC ATCTAAAGAT FAS2 + 559 2.90e-09 TTTTTTATCT CCCGCGTTTTCACATGCTACC TCATTCGCCT CHO2 + 346 1.78e-08 CAGTCAATTG CCACACTTTTCTCATGCCGCA TTCATTATTC CHO1 + 603 3.36e-08 TCAAAATCAC TTTGAACGTTCACACGGCACC CTCACGCCTT INO1 - 619 5.01e-08 ATAAAATAGA CAATACTTTTCACATGCCGCA TTTAGCCGCC ACC1 + 75 5.01e-08 GTTGCGCCCG TTAAAATCTTCACATGGCCCG GCCGCGCGCG OPI3 + 629 2.48e-07 TGAGAAGCCT TTTCAATCTTCATATGCAAAC CCACACATGC OPI3 - 584 3.40e-07 TCACAACCGG TGCAACTTTCCACATGCACTC TCATTGACAC INO1 - 126 3.40e-07 TGAACATACC CTTACGCTTCCAGACGGCCAC TGGGGGAATG INO1 - 549 8.11e-07 ACATTCAACA CTTTCGATTCCGCATCCAACC CCGGAACACC CHO2 - 480 9.92e-07 GTGGAAAGAA TCTGTATTTTCATATGCCTAC TTATAAATTC INO1 - 570 1.97e-06 TACTTGGCCT CCGCATATTTCACATTCAACA CTTTCGATTC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YYWNAVTTTTCACATGCMVCC MEME-1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- FAS1 5.9e-10 86_[+1]_693 CHO1 3.4e-08 602_[+1]_8_[+1]_148 FAS2 2.9e-09 558_[+1]_221 CHO2 9.9e-07 345_[+1]_113_[-1]_300 INO1 8.1e-07 125_[-1]_402_[-1]_[-1]_28_[-1]_161 ACC1 5e-08 74_[+1]_705 OPI3 2.5e-07 583_[-1]_24_[+1]_151 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YYWNAVTTTTCACATGCMVCC MEME-1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF YYWNAVTTTTCACATGCMVCC width=21 seqs=13 FAS1 ( 87) CCAAAAACTTCACATGCCGCC 1 CHO1 ( 632) TTTGAGCTTTCACATGGACCC 1 FAS2 ( 559) CCCGCGTTTTCACATGCTACC 1 CHO2 ( 346) CCACACTTTTCTCATGCCGCA 1 CHO1 ( 603) TTTGAACGTTCACACGGCACC 1 INO1 ( 619) CAATACTTTTCACATGCCGCA 1 ACC1 ( 75) TTAAAATCTTCACATGGCCCG 1 OPI3 ( 629) TTTCAATCTTCATATGCAAAC 1 OPI3 ( 584) TGCAACTTTCCACATGCACTC 1 INO1 ( 126) CTTACGCTTCCAGACGGCCAC 1 INO1 ( 549) CTTTCGATTCCGCATCCAACC 1 CHO2 ( 480) TCTGTATTTTCATATGCCTAC 1 INO1 ( 570) CCGCATATTTCACATTCAACA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YYWNAVTTTTCACATGCMVCC MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 5460 bayes= 9.24238 E= 2.7e-003 -1035 162 -1035 51 -207 113 -119 51 -8 -19 -119 51 -8 39 81 -108 109 39 -1035 -207 25 39 81 -207 -49 39 -1035 73 -1035 39 -119 109 -1035 -1035 -1035 162 -1035 39 -1035 124 -1035 251 -1035 -1035 138 -1035 -119 -207 -1035 213 -119 -108 162 -1035 -1035 -1035 -1035 -19 -1035 138 -1035 -119 227 -207 -1035 198 81 -1035 25 162 -1035 -207 25 81 39 -207 -49 198 -1035 -207 -49 198 -119 -1035 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YYWNAVTTTTCACATGCMVCC MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 13 E= 2.7e-003 0.000000 0.538462 0.000000 0.461538 0.076923 0.384615 0.076923 0.461538 0.307692 0.153846 0.076923 0.461538 0.307692 0.230769 0.307692 0.153846 0.692308 0.230769 0.000000 0.076923 0.384615 0.230769 0.307692 0.076923 0.230769 0.230769 0.000000 0.538462 0.000000 0.230769 0.076923 0.692308 0.000000 0.000000 0.000000 1.000000 0.000000 0.230769 0.000000 0.769231 0.000000 1.000000 0.000000 0.000000 0.846154 0.000000 0.076923 0.076923 0.000000 0.769231 0.076923 0.153846 1.000000 0.000000 0.000000 0.000000 0.000000 0.153846 0.000000 0.846154 0.000000 0.076923 0.846154 0.076923 0.000000 0.692308 0.307692 0.000000 0.384615 0.538462 0.000000 0.076923 0.384615 0.307692 0.230769 0.076923 0.230769 0.692308 0.000000 0.076923 0.230769 0.692308 0.076923 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YYWNAVTTTTCACATGCMVCC MEME-1 regular expression -------------------------------------------------------------------------------- [CT][TC][TA][AGC][AC][AGC][TAC][TC]T[TC]CACATG[CG][CA][ACG][CA][CA] -------------------------------------------------------------------------------- Time 10.05 secs. ******************************************************************************** ******************************************************************************** MOTIF MGASCHCHTBKBCAYYGKCG MEME-2 width = 20 sites = 14 llr = 185 E-value = 2.7e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif MGASCHCHTBKBCAYYGKCG MEME-2 Description -------------------------------------------------------------------------------- Simplified A 6:6:12:4:12::61:::11 pos.-specific C 4324649214:47:451:82 probability G :6162:11:432111:9416 matrix T :1:::4:492542245:611 bits 2.5 2.3 * * 2.0 * * 1.8 * * Relative 1.5 * * * Entropy 1.3 * * * * * * * (19.0 bits) 1.0 ** ** * * * **** 0.8 ***** * * ** ***** 0.5 ******* ****** ***** 0.3 ******* ************ 0.0 -------------------- Multilevel AGAGCTCATCTCCACCGTCG consensus CCCCGC T GGTTTTT G C sequence A C TAG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif MGASCHCHTBKBCAYYGKCG MEME-2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- -------------------- FAS2 + 712 2.71e-09 AGGTTACACA AGACCACATCACCACTGTCG TGCTTTTCTA INO1 - 368 4.88e-09 TTGTCCATCA AGGGCACATCGGCACCGGCC TCATCGTCTT INO1 + 705 1.65e-08 GAGCAGAGAA AGCGCACCTCTGCGTTGGCG GCAATGTTAA OPI3 - 503 1.13e-07 AATTATACGG CGGCGCCATCACTACTGTCG TCCCACCTGG FAS2 - 143 1.69e-07 TCGGTATGAC CGACACCCTGTTCTACGTCG AGTTGAGCGT INO1 + 438 2.25e-07 GTGATCGGAA CGAGCTCTTTATCACCGTAG TTCTAAATAA OPI3 - 170 2.47e-07 CAGATCTGGC ACAGACCGTTGTCATCGGCG TAGCGTTGAT INO1 - 290 3.90e-07 GGGTGAGCTT CCAGGTCACGGTCTACGGCG GGCGCAGTCG OPI3 + 443 4.26e-07 GAATTGACGT ACACCTCCTGTGTATCGGGG ACTTCTCTTA OPI3 + 90 1.14e-06 TGCTTGCTTG CGACGCCTCCTCCTTTGTCA AAGGTACATT ACC1 + 137 1.23e-06 TCGAAATTCA ACCGCTCATTGCCACTCTCT CTACTGCTTG OPI3 + 345 1.43e-06 CCTCCTTCAG ATCGCTCTTGTCGACCGTCT CCAAGAGATC OPI3 - 691 2.37e-06 TCTCTTATAA AGACCCCTTATCCAGTGGTC ATTGCAGTGG INO1 - 392 2.72e-06 CGGCCGGAAG AGAGCTGTTGTTTGTTGTCC ATCAAGGGCA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif MGASCHCHTBKBCAYYGKCG MEME-2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- FAS2 1.7e-07 142_[-2]_549_[+2]_69 INO1 2.7e-06 289_[-2]_58_[-2]_4_[-2]_26_[+2]_ 247_[+2]_76 OPI3 1.1e-06 89_[+2]_60_[-2]_155_[+2]_78_[+2]_ 40_[-2]_168_[-2]_90 ACC1 1.2e-06 136_[+2]_644 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif MGASCHCHTBKBCAYYGKCG MEME-2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF MGASCHCHTBKBCAYYGKCG width=20 seqs=14 FAS2 ( 712) AGACCACATCACCACTGTCG 1 INO1 ( 368) AGGGCACATCGGCACCGGCC 1 INO1 ( 705) AGCGCACCTCTGCGTTGGCG 1 OPI3 ( 503) CGGCGCCATCACTACTGTCG 1 FAS2 ( 143) CGACACCCTGTTCTACGTCG 1 INO1 ( 438) CGAGCTCTTTATCACCGTAG 1 OPI3 ( 170) ACAGACCGTTGTCATCGGCG 1 INO1 ( 290) CCAGGTCACGGTCTACGGCG 1 OPI3 ( 443) ACACCTCCTGTGTATCGGGG 1 OPI3 ( 90) CGACGCCTCCTCCTTTGTCA 1 ACC1 ( 137) ACCGCTCATTGCCACTCTCT 1 OPI3 ( 345) ATCGCTCTTGTCGACCGTCT 1 OPI3 ( 691) AGACCCCTTATCCAGTGGTC 1 INO1 ( 392) AGAGCTGTTGTTTGTTGTCC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif MGASCHCHTBKBCAYYGKCG MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 5467 bayes= 9.21247 E= 2.7e+000 99 102 -1045 -1045 -1045 70 187 -218 99 29 -30 -1045 -1045 129 170 -1045 -118 187 29 -1045 -60 102 -1045 40 -1045 240 -130 -1045 14 29 -130 14 -1045 -30 -1045 140 -218 102 102 -60 -60 -1045 70 62 -1045 129 29 14 -1045 202 -130 -60 99 -1045 -30 -60 -118 129 -130 14 -1045 151 -1045 62 -1045 -130 240 -1045 -1045 -1045 129 82 -218 216 -130 -218 -218 29 170 -118 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif MGASCHCHTBKBCAYYGKCG MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 14 E= 2.7e+000 0.642857 0.357143 0.000000 0.000000 0.000000 0.285714 0.642857 0.071429 0.642857 0.214286 0.142857 0.000000 0.000000 0.428571 0.571429 0.000000 0.142857 0.642857 0.214286 0.000000 0.214286 0.357143 0.000000 0.428571 0.000000 0.928571 0.071429 0.000000 0.357143 0.214286 0.071429 0.357143 0.000000 0.142857 0.000000 0.857143 0.071429 0.357143 0.357143 0.214286 0.214286 0.000000 0.285714 0.500000 0.000000 0.428571 0.214286 0.357143 0.000000 0.714286 0.071429 0.214286 0.642857 0.000000 0.142857 0.214286 0.142857 0.428571 0.071429 0.357143 0.000000 0.500000 0.000000 0.500000 0.000000 0.071429 0.928571 0.000000 0.000000 0.000000 0.428571 0.571429 0.071429 0.785714 0.071429 0.071429 0.071429 0.214286 0.571429 0.142857 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif MGASCHCHTBKBCAYYGKCG MEME-2 regular expression -------------------------------------------------------------------------------- [AC][GC][AC][GC][CG][TCA]C[ATC]T[CGT][TGA][CTG][CT][AT][CT][CT]G[TG]C[GC] -------------------------------------------------------------------------------- Time 19.91 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- CHO1 1.61e-05 602_[+1(3.36e-08)]_8_[+1(9.34e-10)]_\ 148 CHO2 1.10e-04 345_[+1(1.78e-08)]_113_\ [-1(9.92e-07)]_300 FAS1 2.24e-06 27_[-2(9.98e-05)]_39_[+1(5.92e-10)]_\ 693 FAS2 4.92e-10 142_[-2(1.69e-07)]_396_\ [+1(2.90e-09)]_132_[+2(2.71e-09)]_69 ACC1 2.51e-06 74_[+1(5.01e-08)]_41_[+2(1.23e-06)]_\ 644 INO1 1.33e-08 125_[-1(3.40e-07)]_143_\ [-2(3.90e-07)]_58_[-2(4.88e-09)]_4_[-2(2.72e-06)]_26_[+2(2.25e-07)]_91_\ [-1(8.11e-07)]_[-1(1.97e-06)]_28_[-1(5.01e-08)]_65_[+2(1.65e-08)]_76 OPI3 1.20e-06 89_[+2(1.14e-06)]_60_[-2(2.47e-07)]_\ 155_[+2(1.43e-06)]_78_[+2(4.26e-07)]_40_[-2(1.13e-07)]_61_[-1(3.40e-07)]_\ 24_[+1(2.48e-07)]_41_[-2(2.37e-06)]_90 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (2) found. ******************************************************************************** CPU: Timothys-iMac.rd.unr.edu ********************************************************************************