******************************************************************************** MEME - Motif discovery tool ******************************************************************************** MEME version 4.0.0 (Release date: 2008-07-12 05:23:09 +1000 (Sat, 12 Jul 2008)) For further information on how to interpret these results or to get a copy of the MEME software please access http://meme.nbcr.net. 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.nbcr.net. ******************************************************************************** ******************************************************************************** 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= /home/t.bailey/MEME/SVNROOT/trunk/scripts/../tests/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 /home/t.bailey/MEME/SVNROOT/trunk/scripts/../tests/common/INO_up800.s -text -mod tcm -dna -revcomp -bfile /home/t.bailey/MEME/SVNROOT/trunk/scripts/../tests/common/yeast.nc.6.freq -x_branch -nostatus -nmotifs 2 -minw 8 model: mod= tcm nmotifs= 2 evt= inf object function= E-value of product of p-values width: minw= 8 maxw= 50 minic= 0.00 width: wg= 11 ws= 1 endgaps= yes nsites: minsites= 2 maxsites= 35 wnsites= 0.8 theta: prob= 1 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 strands: + - sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.304 C 0.196 G 0.196 T 0.304 Background letter frequencies (from /home/t.bailey/MEME/SVNROOT/trunk/scripts/../tests/common/yeast.nc.6.freq): A 0.324 C 0.176 G 0.176 T 0.324 ******************************************************************************** ******************************************************************************** MOTIF 1 width = 13 sites = 10 llr = 135 E-value = 9.1e-004 ******************************************************************************** -------------------------------------------------------------------------------- Motif 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 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 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- FAS1 3.3e-09 94_[+1]_693 INO1 2.2e-06 569_[-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 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 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 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 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 1 regular expression -------------------------------------------------------------------------------- TTCACATG[CG][CA][GAC]C[CA] -------------------------------------------------------------------------------- Time 92.97 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 width = 29 sites = 26 llr = 321 E-value = 2.2e-003 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A :11:133112:1::3:12::12::52::3 pos.-specific C :3:162341:14311412123::823337 probability G 1:5221::31122:32132:3:12:33:1 matrix T 86472445678358447278389:3337: bits 2.5 2.3 2.0 1.8 * Relative 1.5 * Entropy 1.3 ** (17.8 bits) 1.0 * * * *** * 0.8 * *** * * * *** * 0.5 ***** **** ** ** ** *** *** 0.3 ***** ******** ************** 0.0 ----------------------------- Multilevel TTGTCTTTTTTCTTTTTGTTCTTCACGTC consensus CT AACG TC AC C T GTGTCA sequence C G T G CTC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- ----------------------------- INO1 + 490 3.82e-13 ATTATTGCCT TTTTCTTCGTTCCTTTTGTTCTTCACGTC CTTTTTATGA FAS2 - 185 2.64e-08 CAACATCTAA TCTTGTTCTTTCTTGCTTTTCTGGCACTC TTGACGGCTT FAS1 + 353 2.64e-08 CTCCAAACAC TTTTCCTTTTTCCTTCTATTCTGCAGGAC CAACTAAAAC ACC1 + 298 5.51e-08 TGTTCTGCTC TCTTCAATTTTCCTTTCCTTATTCTACTC TTTTTATCCC INO1 + 761 6.20e-08 ATTGGAGCTT TCGTCACCTTTTTTTGGCTTGTTCTGTTG TCGGGTTCCT FAS2 + 244 7.83e-08 TTCGCCATCA TTGTAGTCGTTGTTGTTGTCGTTGTTGTC CCAGCCGTTG ACC1 - 349 1.10e-07 AATTAGGGAA TTGGCTTTGTTGTTTTTTATCTTCAGGTA AACTGTACGA ACC1 + 731 2.36e-07 AATAACCGAT TCGTCTTCTAGCTTAATTTTTTTCCGTTC CCGAAACAGC ACC1 + 269 2.90e-07 ACTGTCACAA TTGTTATCGGTTCTACAATTGTTCTGCTC TCTTCAATTT INO1 + 93 4.81e-07 GGACGACTTG TTGTTAATGGTTTTGGCGGTTTTCATTCC CCCAGTGGCC INO1 + 637 5.85e-07 GTGAAAAGTA TTGTCTATTTTATCTTCATCCTTCTTTCC CAGAATATTG CHO2 - 63 8.56e-07 TAAGAACTTG TTTGATCATATCTTGTTGGTTTTCAGGTA GTAATTGCAG FAS1 - 442 1.03e-06 CAATACCTTT TTTTTTCTTATATTTTTAGTTTTCCCCTA TAACTTTGTT OPI3 + 277 1.24e-06 TTCTTGTAAA GCTTCCCATTTGGTGGTCCCGTTCAACTC CGTCAGGTCT INO1 + 245 1.24e-06 ATGAAACGAG TAGTGAACGTTCGTACGATCTTTCACGCA GACATGCGAC INO1 + 177 1.35e-06 ACTATTGAAC TTACTTCTCTTCCTACTGTTATTCTTCCC AGCAATCATT CHO2 + 624 1.35e-06 TTTGATTAGT TTATCTTCTTTTCTTCATTTTATCCCCTA ATTTTATACG FAS2 + 385 1.76e-06 CTTTACTATA TTTCCTAAATTTTCTCTGGTCTGCAGGCC AAAAACAACA CHO2 + 504 1.76e-06 ATACAGATTC TTTCCACTGTGTTCCCTTTTATTCCCTTC TCATGTGAAG OPI3 - 771 2.09e-06 C GCTTGACTTGCGCTATTCTTGTTGTCTTC AATTGCTGTT FAS1 + 525 2.69e-06 AAAAAGTACA TTGGGCCTTTTCATACTTGTTATCACTTA CATTACAAAG FAS2 - 108 4.38e-06 GTCGAGTTGA GCGTCTTCAACGTTCTTGTCGATGACGTC TACGTTTTCT OPI3 + 399 5.54e-06 CATTGGTGGC TAGTCCATCTTCGAATTCTTCTTCATCGC GACGGGAATT OPI3 + 529 6.45e-06 GCCGCCGTAT AATTCGACTTCCTTGTTGTTCATGCTTCC TTGATGACCA CHO1 + 738 6.95e-06 TTGTGGGTGA TTGTCATTTTTAGTTGTCTATTTGATTCA ATCAAAAAAC CHO1 - 34 6.95e-06 AGGCCATATT TTGGTGATTATTTTGCTGCTGATCAAGTG TCAAATAATA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- INO1 1.4e-06 92_[+2]_55_[+2]_39_[+2]_216_[+2]_ 118_[+2]_95_[+2]_11 FAS2 1.8e-06 107_[-2]_48_[-2]_30_[+2]_112_[+2]_387 FAS1 1e-06 352_[+2]_60_[-2]_54_[+2]_247 ACC1 2.4e-07 268_[+2]_[+2]_22_[-2]_353_[+2]_41 CHO2 1.8e-06 62_[-2]_412_[+2]_91_[+2]_148 OPI3 6.4e-06 276_[+2]_93_[+2]_101_[+2]_213_[-2]_1 CHO1 7e-06 33_[-2]_675_[+2]_34 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=29 seqs=26 INO1 ( 490) TTTTCTTCGTTCCTTTTGTTCTTCACGTC 1 FAS2 ( 185) TCTTGTTCTTTCTTGCTTTTCTGGCACTC 1 FAS1 ( 353) TTTTCCTTTTTCCTTCTATTCTGCAGGAC 1 ACC1 ( 298) TCTTCAATTTTCCTTTCCTTATTCTACTC 1 INO1 ( 761) TCGTCACCTTTTTTTGGCTTGTTCTGTTG 1 FAS2 ( 244) TTGTAGTCGTTGTTGTTGTCGTTGTTGTC 1 ACC1 ( 349) TTGGCTTTGTTGTTTTTTATCTTCAGGTA 1 ACC1 ( 731) TCGTCTTCTAGCTTAATTTTTTTCCGTTC 1 ACC1 ( 269) TTGTTATCGGTTCTACAATTGTTCTGCTC 1 INO1 ( 93) TTGTTAATGGTTTTGGCGGTTTTCATTCC 1 INO1 ( 637) TTGTCTATTTTATCTTCATCCTTCTTTCC 1 CHO2 ( 63) TTTGATCATATCTTGTTGGTTTTCAGGTA 1 FAS1 ( 442) TTTTTTCTTATATTTTTAGTTTTCCCCTA 1 OPI3 ( 277) GCTTCCCATTTGGTGGTCCCGTTCAACTC 1 INO1 ( 245) TAGTGAACGTTCGTACGATCTTTCACGCA 1 INO1 ( 177) TTACTTCTCTTCCTACTGTTATTCTTCCC 1 CHO2 ( 624) TTATCTTCTTTTCTTCATTTTATCCCCTA 1 FAS2 ( 385) TTTCCTAAATTTTCTCTGGTCTGCAGGCC 1 CHO2 ( 504) TTTCCACTGTGTTCCCTTTTATTCCCTTC 1 OPI3 ( 771) GCTTGACTTGCGCTATTCTTGTTGTCTTC 1 FAS1 ( 525) TTGGGCCTTTTCATACTTGTTATCACTTA 1 FAS2 ( 108) GCGTCTTCAACGTTCTTGTCGATGACGTC 1 OPI3 ( 399) TAGTCCATCTTCGAATTCTTCTTCATCGC 1 OPI3 ( 529) AATTCGACTTCCTTGTTGTTCATGCTTCC 1 CHO1 ( 738) TTGTCATTTTTAGTTGTCTATTTGATTCA 1 CHO1 ( 34) TTGGTGATTATTTTGCTGCTGATCAAGTG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 29 n= 5404 bayes= 8.22507 E= 2.2e-003 -307 -1134 -61 138 -149 62 -1134 92 -207 -1134 151 38 -1134 -61 -19 117 -207 172 -19 -75 -8 -19 -61 38 -8 81 -1134 25 -149 113 -1134 62 -207 -119 62 83 -75 -1134 -61 109 -1134 -61 -119 132 -149 127 13 -27 -307 62 -19 73 -307 -61 -1134 138 -27 -119 62 25 -307 113 -19 38 -207 -61 -119 117 -75 39 98 -49 -307 -119 13 109 -307 13 -1134 125 -149 81 62 -8 -75 -1134 -1134 132 -1134 -1134 -61 145 -1134 213 39 -1134 62 39 -1134 -27 -108 81 62 -27 -1134 81 98 9 -307 62 -219 101 -27 190 -119 -1134 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 29 nsites= 26 E= 2.2e-003 0.038462 0.000000 0.115385 0.846154 0.115385 0.269231 0.000000 0.615385 0.076923 0.000000 0.500000 0.423077 0.000000 0.115385 0.153846 0.730769 0.076923 0.576923 0.153846 0.192308 0.307692 0.153846 0.115385 0.423077 0.307692 0.307692 0.000000 0.384615 0.115385 0.384615 0.000000 0.500000 0.076923 0.076923 0.269231 0.576923 0.192308 0.000000 0.115385 0.692308 0.000000 0.115385 0.076923 0.807692 0.115385 0.423077 0.192308 0.269231 0.038462 0.269231 0.153846 0.538462 0.038462 0.115385 0.000000 0.846154 0.269231 0.076923 0.269231 0.384615 0.038462 0.384615 0.153846 0.423077 0.076923 0.115385 0.076923 0.730769 0.192308 0.230769 0.346154 0.230769 0.038462 0.076923 0.192308 0.692308 0.038462 0.192308 0.000000 0.769231 0.115385 0.307692 0.269231 0.307692 0.192308 0.000000 0.000000 0.807692 0.000000 0.000000 0.115385 0.884615 0.000000 0.769231 0.230769 0.000000 0.500000 0.230769 0.000000 0.269231 0.153846 0.307692 0.269231 0.269231 0.000000 0.307692 0.346154 0.346154 0.038462 0.269231 0.038462 0.653846 0.269231 0.653846 0.076923 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- T[TC][GT]TC[TA][TAC][TC][TG]TT[CT][TC]T[TAG][TC]T[GCT]TT[CTG]TT[CG][ATC][CGT][GTC][TC][CA] -------------------------------------------------------------------------------- Time 183.58 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- CHO1 1.81e-05 33_[-2(6.95e-06)]_548_[+1(3.43e-07)]_16_[+1(7.37e-08)]_85_[+2(6.95e-06)]_34 CHO2 1.30e-05 62_[-2(8.56e-07)]_262_[+1(4.16e-07)]_137_[+2(1.76e-06)]_91_[+2(1.35e-06)]_148 FAS1 4.92e-09 94_[+1(3.29e-09)]_245_[+2(2.64e-08)]_60_[-2(1.03e-06)]_54_[+2(2.69e-06)]_247 FAS2 4.93e-07 107_[-2(4.38e-06)]_48_[-2(2.64e-08)]_30_[+2(7.83e-08)]_112_[+2(1.76e-06)]_153_[+1(4.16e-07)]_221 ACC1 4.67e-07 82_[+1(1.88e-07)]_173_[+2(2.90e-07)]_[+2(5.51e-08)]_22_[-2(1.10e-07)]_353_[+2(2.36e-07)]_41 INO1 9.37e-13 92_[+2(4.81e-07)]_55_[+2(1.35e-06)]_39_[+2(1.24e-06)]_216_[+2(3.82e-13)]_51_[-1(2.24e-06)]_36_[-1(3.13e-08)]_5_[+2(5.85e-07)]_21_[+1(1.72e-07)]_61_[+2(6.20e-08)]_11 OPI3 9.38e-05 276_[+2(1.24e-06)]_93_[+2(5.54e-06)]_101_[+2(6.45e-06)]_26_[-1(2.44e-06)]_174_[-2(2.09e-06)]_1 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 2 reached. ******************************************************************************** CPU: tlb-sayonara.imb.uq.edu.au ********************************************************************************