******************************************************************************** MEME - Motif discovery tool ******************************************************************************** MEME version 3.0 (Release date: 2001/03/05 14:24:28) For further information on how to interpret these results or to get a copy of the MEME software please access http://meme.sdsc.edu. 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.sdsc.edu. ******************************************************************************** ******************************************************************************** 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= D10Mit194.set.genbank.fasta.nref ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 20218 1.0000 2000 10657 1.0000 2000 83796 1.0000 2000 6603 1.0000 2000 ******************************************************************************** ******************************************************************************** COMMAND LINE SUMMARY ******************************************************************************** This information can also be useful in the event you wish to report a problem with the MEME software. command: meme D10Mit194.set.genbank.fasta.nref -dna -print_fasta -nmotifs 3 -maxw 25 model: mod= zoops nmotifs= 3 evt= inf object function= E-value of product of p-values width: minw= 8 maxw= 25 minic= 0.00 width: wg= 11 ws= 1 endgaps= yes nsites: minsites= 2 maxsites= 4 wnsites= 0.8 theta: prob= 1 spmap= uni spfuzz= 0.5 em: prior= dirichlet b= 0.01 maxiter= 50 distance= 1e-05 data: n= 8000 N= 4 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.255 C 0.236 G 0.252 T 0.257 Background letter frequencies (from dataset with add-one prior applied): A 0.255 C 0.236 G 0.252 T 0.257 ******************************************************************************** ******************************************************************************** MOTIF 1 width = 25 sites = 4 llr = 106 E-value = 1.2e-002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A :8:88aaa:53a8:::3:a::3::3 pos.-specific C a3::3:::::3:::5a8a:8a5aa8 probability G ::8:::::3:5::::::::3::::: matrix T ::33::::85::3a5::::::3::: bits 2.1 * * * * ** 1.9 * *** * * * ** * ** 1.7 * *** * * * ** * ** 1.5 * *** * * * ** * ** Information 1.2 ********* *** ****** *** content 1.0 ********** ********** *** (38.1 bits) 0.8 ********** ********** *** 0.6 ********** ************** 0.4 ************************* 0.2 ************************* 0.0 ------------------------- Multilevel CAGAAAAATAGAATCCCCACCCCCC consensus CTTC GTA T T A G A A sequence C T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------------------- 6603 1311 2.59e-15 GGCGCATTGA CAGAAAAATTGAATTCCCACCCCCC AATGAGGAGG 83796 1284 2.59e-15 GGAGGATTGA CAGAAAAATTGAATTCCCACCCCCC AACGAGGAGG 20218 938 6.34e-12 TTTTTGGTAA CCTTAAAATAAAATCCCCACCACCA CTTTTAAAAA 10657 1685 8.70e-12 GGCCCGCGCG CAGACAAAGACATTCCACAGCTCCC GCCCCCTCCA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 6603 2.6e-15 1310_[1]_665 83796 2.6e-15 1283_[1]_692 20218 6.3e-12 937_[1]_1038 10657 8.7e-12 1684_[1]_291 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in FASTA format -------------------------------------------------------------------------------- >6603 pos 1311 CAGAAAAATTGAATTCCCACCCCCC >83796 pos 1284 CAGAAAAATTGAATTCCCACCCCCC >20218 pos 938 CCTTAAAATAAAATCCCCACCACCA >10657 pos 1685 CAGACAAAGACATTCCACAGCTCCC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 25 n= 7904 bayes= 11.6849 E= 1.2e-002 -865 208 -865 -865 156 8 -865 -865 -865 -865 157 -4 156 -865 -865 -4 156 8 -865 -865 197 -865 -865 -865 197 -865 -865 -865 197 -865 -865 -865 -865 -865 -1 154 97 -865 -865 96 -3 8 99 -865 197 -865 -865 -865 156 -865 -865 -4 -865 -865 -865 196 -865 108 -865 96 -865 208 -865 -865 -3 166 -865 -865 -865 208 -865 -865 197 -865 -865 -865 -865 166 -1 -865 -865 208 -865 -865 -3 108 -865 -4 -865 208 -865 -865 -865 208 -865 -865 -3 166 -865 -865 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 25 n= 7904 E= 1.2e-002 0.000635 0.998096 0.000629 0.000640 0.748765 0.249966 0.000629 0.000640 0.000635 0.000589 0.748759 0.250017 0.748765 0.000589 0.000629 0.250017 0.748765 0.249966 0.000629 0.000640 0.998141 0.000589 0.000629 0.000640 0.998141 0.000589 0.000629 0.000640 0.998141 0.000589 0.000629 0.000640 0.000635 0.000589 0.250006 0.748770 0.499388 0.000589 0.000629 0.499393 0.250012 0.249966 0.499382 0.000640 0.998141 0.000589 0.000629 0.000640 0.748765 0.000589 0.000629 0.250017 0.000635 0.000589 0.000629 0.998147 0.000635 0.499343 0.000629 0.499393 0.000635 0.998096 0.000629 0.000640 0.250012 0.748719 0.000629 0.000640 0.000635 0.998096 0.000629 0.000640 0.998141 0.000589 0.000629 0.000640 0.000635 0.748719 0.250006 0.000640 0.000635 0.998096 0.000629 0.000640 0.250012 0.499343 0.000629 0.250017 0.000635 0.998096 0.000629 0.000640 0.000635 0.998096 0.000629 0.000640 0.250012 0.748719 0.000629 0.000640 -------------------------------------------------------------------------------- Time 38.44 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 width = 25 sites = 4 llr = 101 E-value = 4.5e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A ::::a::383:5:3:::a33:83:a pos.-specific C a3a8:3a33:a::5::8::::383: probability G ::::::::::::::::3:38a::8: matrix T :8:3:8:5:8:5a3aa::5:::::: bits 2.1 * * * * * 1.9 * * * * * * ** * * * 1.7 * * * * * * ** * * * 1.5 * * * * * * ** * * * Information 1.2 ******* *** * **** ****** content 1.0 ******* ***** **** ****** (36.6 bits) 0.8 ******* ***** **** ****** 0.6 ******* ********** ****** 0.4 ************************* 0.2 ************************* 0.0 ------------------------- Multilevel CTCCATCTATCATCTTCATGGACGA consensus C T C ACA T A G AA CAC sequence C T G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------------------- 6603 1000 1.62e-15 CGGGAACATG CTCCATCTATCATCTTCATGGACGA AATCGACTCC 83796 978 4.69e-15 CGAGAACATG CTCCATCCATCATCTTCATGGACGA GATTGACTCT 20218 1545 1.69e-11 TAGCTTCTCT CCCCATCAATCTTATTCAGAGCCCA CCCCTCCCCC 10657 1075 3.40e-11 AGGATCTGGT CTCTACCTCACTTTTTGAAGGAAGA AACACTTAAT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 6603 1.6e-15 999_[2]_976 83796 4.7e-15 977_[2]_998 20218 1.7e-11 1544_[2]_431 10657 3.4e-11 1074_[2]_901 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in FASTA format -------------------------------------------------------------------------------- >6603 pos 1000 CTCCATCTATCATCTTCATGGACGA >83796 pos 978 CTCCATCCATCATCTTCATGGACGA >20218 pos 1545 CCCCATCAATCTTATTCAGAGCCCA >10657 pos 1075 CTCTACCTCACTTTTTGAAGGAAGA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 25 n= 7904 bayes= 10.9476 E= 4.5e-001 -865 208 -865 -865 -865 8 -865 154 -865 208 -865 -865 -865 166 -865 -4 197 -865 -865 -865 -865 8 -865 154 -865 208 -865 -865 -3 8 -865 96 156 8 -865 -865 -3 -865 -865 154 -865 208 -865 -865 97 -865 -865 96 -865 -865 -865 196 -3 108 -865 -4 -865 -865 -865 196 -865 -865 -865 196 -865 166 -1 -865 197 -865 -865 -865 -3 -865 -1 96 -3 -865 157 -865 -865 -865 198 -865 156 8 -865 -865 -3 166 -865 -865 -865 8 157 -865 197 -865 -865 -865 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 25 n= 7904 E= 4.5e-001 0.000635 0.998096 0.000629 0.000640 0.000635 0.249966 0.000629 0.748770 0.000635 0.998096 0.000629 0.000640 0.000635 0.748719 0.000629 0.250017 0.998141 0.000589 0.000629 0.000640 0.000635 0.249966 0.000629 0.748770 0.000635 0.998096 0.000629 0.000640 0.250012 0.249966 0.000629 0.499393 0.748765 0.249966 0.000629 0.000640 0.250012 0.000589 0.000629 0.748770 0.000635 0.998096 0.000629 0.000640 0.499388 0.000589 0.000629 0.499393 0.000635 0.000589 0.000629 0.998147 0.250012 0.499343 0.000629 0.250017 0.000635 0.000589 0.000629 0.998147 0.000635 0.000589 0.000629 0.998147 0.000635 0.748719 0.250006 0.000640 0.998141 0.000589 0.000629 0.000640 0.250012 0.000589 0.250006 0.499393 0.250012 0.000589 0.748759 0.000640 0.000635 0.000589 0.998135 0.000640 0.748765 0.249966 0.000629 0.000640 0.250012 0.748719 0.000629 0.000640 0.000635 0.249966 0.748759 0.000640 0.998141 0.000589 0.000629 0.000640 -------------------------------------------------------------------------------- Time 78.29 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 width = 21 sites = 4 llr = 88 E-value = 4.8e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A :::58:::::3::::33:::: pos.-specific C 8:833::8:8:a:8a8:a5a8 probability G 3::::::3:::::3::::::: matrix T :a33:aa:a38:a:::8:5:3 bits 2.1 * * * * 1.9 * ** * ** * * * 1.7 * ** * ** * * * 1.5 * ** * ** * * * Information 1.2 *** ************** ** content 1.0 *** ***************** (31.8 bits) 0.8 *** ***************** 0.6 *** ***************** 0.4 ********************* 0.2 ********************* 0.0 --------------------- Multilevel CTCAATTCTCTCTCCCTCCCC consensus G TCC G TA G AA T T sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 10657 1511 1.45e-13 CCCAGGCGGT CTCAATTCTCTCTCCCTCCCC TTTCCGTGAC 83796 1801 7.40e-12 TGTATATGCA CTCTCTTCTCTCTCCCTCTCC AGGTCATGCA 6603 1811 1.22e-10 GTAACTTAAT GTTCATTCTCTCTCCCACCCC TAGGTCATGC 20218 606 7.57e-10 CCCAGGCCAG CTCAATTGTTACTGCATCTCT AGGATTGGAA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 10657 1.5e-13 1510_[3]_469 83796 7.4e-12 1800_[3]_179 6603 1.2e-10 1810_[3]_169 20218 7.6e-10 605_[3]_1374 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in FASTA format -------------------------------------------------------------------------------- >10657 pos 1511 CTCAATTCTCTCTCCCTCCCC >83796 pos 1801 CTCTCTTCTCTCTCCCTCTCC >6603 pos 1811 GTTCATTCTCTCTCCCACCCC >20218 pos 606 CTCAATTGTTACTGCATCTCT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 7920 bayes= 10.9506 E= 4.8e-001 -865 166 -1 -865 -865 -865 -865 196 -865 166 -865 -4 97 8 -865 -4 156 8 -865 -865 -865 -865 -865 196 -865 -865 -865 196 -865 166 -1 -865 -865 -865 -865 196 -865 166 -865 -4 -3 -865 -865 154 -865 208 -865 -865 -865 -865 -865 196 -865 166 -1 -865 -865 208 -865 -865 -3 166 -865 -865 -3 -865 -865 154 -865 208 -865 -865 -865 108 -865 96 -865 208 -865 -865 -865 166 -865 -4 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 n= 7920 E= 4.8e-001 0.000635 0.748719 0.250006 0.000640 0.000635 0.000589 0.000629 0.998147 0.000635 0.748719 0.000629 0.250017 0.499388 0.249966 0.000629 0.250017 0.748765 0.249966 0.000629 0.000640 0.000635 0.000589 0.000629 0.998147 0.000635 0.000589 0.000629 0.998147 0.000635 0.748719 0.250006 0.000640 0.000635 0.000589 0.000629 0.998147 0.000635 0.748719 0.000629 0.250017 0.250012 0.000589 0.000629 0.748770 0.000635 0.998096 0.000629 0.000640 0.000635 0.000589 0.000629 0.998147 0.000635 0.748719 0.250006 0.000640 0.000635 0.998096 0.000629 0.000640 0.250012 0.748719 0.000629 0.000640 0.250012 0.000589 0.000629 0.748770 0.000635 0.998096 0.000629 0.000640 0.000635 0.499343 0.000629 0.499393 0.000635 0.998096 0.000629 0.000640 0.000635 0.748719 0.000629 0.250017 -------------------------------------------------------------------------------- Time 117.82 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 20218 7.77e-19 605_[3(7.57e-10)]_311_[1(6.34e-12)]_582_[2(1.69e-11)]_431 10657 5.46e-22 1_[1(1.75e-07)]_[1(1.75e-07)]_[1(1.75e-07)]_[1(1.75e-07)]_[1(1.75e-07)]_[1(1.75e-07)]_[1(1.75e-07)]_[1(1.75e-07)]_[1(1.75e-07)]_[1(1.75e-07)]_[1(1.75e-07)]_7_[1(6.00e-08)]_[1(1.75e-07)]_[1(1.75e-07)]_[1(1.75e-07)]_[1(1.75e-07)]_[1(1.75e-07)]_[1(1.75e-07)]_[1(1.75e-07)]_[1(1.75e-07)]_[1(1.75e-07)]_[1(1.75e-07)]_[1(1.75e-07)]_5_[1(1.18e-07)]_[1(1.75e-07)]_[1(1.75e-07)]_[1(1.75e-07)]_[1(1.75e-07)]_4_[1(1.29e-07)]_332_[2(3.40e-11)]_383_[3(7.75e-07)]_7_[3(1.45e-13)]_56_[3(3.47e-05)]_76_[1(8.70e-12)]_291 83796 1.73e-27 977_[2(4.69e-15)]_281_[1(2.59e-15)]_492_[3(7.40e-12)]_179 6603 9.32e-27 597_[1(1.75e-07)]_[1(1.75e-07)]_[1(1.75e-07)]_327_[2(1.62e-15)]_286_[1(2.59e-15)]_475_[3(1.22e-10)]_169 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: hydra-1.lsd.ornl.gov ********************************************************************************