******************************************************************************** MEME - Motif discovery tool ******************************************************************************** MEME version 4.3.0 (Release date: Sat Sep 26 01:51:56 PDT 2009) 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= SHEFN_motiv/meme.fasta ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ Sfri_0493 1.0000 100 Sfri_1138 1.0000 100 Sfri_1141 1.0000 100 Sfri_1452 1.0000 100 Sfri_2598 1.0000 100 Sfri_3070 1.0000 60 Sfri_3357 1.0000 100 Sfri_3716 1.0000 140 ******************************************************************************** ******************************************************************************** COMMAND LINE SUMMARY ******************************************************************************** This information can also be useful in the event you wish to report a problem with the MEME software. command: meme SHEFN_motiv/meme.fasta -mod zoops -nmotifs 3 -prior dirichlet -revcomp -nostatus -dna -oc SHEFN_motiv/ model: mod= zoops nmotifs= 3 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= 8 wnsites= 0.8 theta: prob= 1 spmap= uni spfuzz= 0.5 global: substring= yes branching= no wbranch= no em: prior= dirichlet b= 0.01 maxiter= 50 distance= 1e-05 data: n= 800 N= 8 strands: + - sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.306 C 0.194 G 0.194 T 0.306 Background letter frequencies (from dataset with add-one prior applied): A 0.306 C 0.194 G 0.194 T 0.306 ******************************************************************************** ******************************************************************************** MOTIF 1 width = 21 sites = 8 llr = 110 E-value = 7.9e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 16:3346158111:5:549a: pos.-specific C :::64::3::545a41:1::: probability G ::8:4:4:131:4::::1::: matrix T 9431:6:64:35::19541:a bits 2.4 * 2.1 * 1.9 * 1.7 * ** Relative 1.4 * * ** Entropy 1.2 * * * * *** (19.9 bits) 0.9 * * * * ** * *** 0.7 ******* * ** ** *** 0.5 ***************** *** 0.2 ***************** *** 0.0 --------------------- Multilevel TAGCCTATAACTCCATAAAAT consensus TTAGAGCTGTCG C TT sequence A -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- --------------------- Sfri_3357 + 37 8.30e-11 AATAAAACAC TTGCCTATAACCCCCTAAAAT CTGTTAAAAT Sfri_1452 + 48 4.67e-08 CACAAACTGG TAGAATATTGCCGCATAAAAT TCCATAAAAC Sfri_1141 + 35 7.26e-08 AGGTGATTTG TAGTGTGCAATTCCCTATAAT AGCGCCAATT Sfri_2598 + 8 1.34e-07 CCACGTC TAGCAAATGACACCCTTCAAT ACGCCTGCTA Sfri_3070 + 4 1.96e-07 TTT TAGCCAATTAGTGCATTTTAT ATTGGATTTT Sfri_3716 + 23 3.02e-07 CACCTCCTTT TATCGTGCAAACGCATTGAAT GCAGGTAAAA Sfri_0493 + 57 1.80e-06 TTGACTCTGT TTTACTAAAGCTCCTTAAAAT CAAACTAGCG Sfri_1138 + 61 2.85e-06 CATCAATTGG ATGCGAGTTATTACACTTAAT TAATATGTAA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- Sfri_3357 8.3e-11 36_[+1]_43 Sfri_1452 4.7e-08 47_[+1]_32 Sfri_1141 7.3e-08 34_[+1]_45 Sfri_2598 1.3e-07 7_[+1]_72 Sfri_3070 2e-07 3_[+1]_36 Sfri_3716 3e-07 22_[+1]_97 Sfri_0493 1.8e-06 56_[+1]_23 Sfri_1138 2.9e-06 60_[+1]_19 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=21 seqs=8 Sfri_3357 ( 37) TTGCCTATAACCCCCTAAAAT 1 Sfri_1452 ( 48) TAGAATATTGCCGCATAAAAT 1 Sfri_1141 ( 35) TAGTGTGCAATTCCCTATAAT 1 Sfri_2598 ( 8) TAGCAAATGACACCCTTCAAT 1 Sfri_3070 ( 4) TAGCCAATTAGTGCATTTTAT 1 Sfri_3716 ( 23) TATCGTGCAAACGCATTGAAT 1 Sfri_0493 ( 57) TTTACTAAAGCTCCTTAAAAT 1 Sfri_1138 ( 61) ATGCGAGTTATTACACTTAAT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 640 bayes= 7.04803 E= 7.9e+000 -129 -965 -965 151 103 -965 -965 29 -965 -965 195 -29 -29 169 -965 -129 -29 95 95 -965 29 -965 -965 103 103 -965 95 -965 -129 37 -965 103 71 -965 -63 29 129 -965 37 -965 -129 136 -63 -29 -129 95 -965 71 -129 136 95 -965 -965 236 -965 -965 71 95 -965 -129 -965 -63 -965 151 71 -965 -965 71 29 -63 -63 29 151 -965 -965 -129 171 -965 -965 -965 -965 -965 -965 171 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 8 E= 7.9e+000 0.125000 0.000000 0.000000 0.875000 0.625000 0.000000 0.000000 0.375000 0.000000 0.000000 0.750000 0.250000 0.250000 0.625000 0.000000 0.125000 0.250000 0.375000 0.375000 0.000000 0.375000 0.000000 0.000000 0.625000 0.625000 0.000000 0.375000 0.000000 0.125000 0.250000 0.000000 0.625000 0.500000 0.000000 0.125000 0.375000 0.750000 0.000000 0.250000 0.000000 0.125000 0.500000 0.125000 0.250000 0.125000 0.375000 0.000000 0.500000 0.125000 0.500000 0.375000 0.000000 0.000000 1.000000 0.000000 0.000000 0.500000 0.375000 0.000000 0.125000 0.000000 0.125000 0.000000 0.875000 0.500000 0.000000 0.000000 0.500000 0.375000 0.125000 0.125000 0.375000 0.875000 0.000000 0.000000 0.125000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- T[AT][GT][CA][CGA][TA][AG][TC][AT][AG][CT][TC][CG]C[AC]T[AT][AT]AAT -------------------------------------------------------------------------------- Time 0.37 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 width = 31 sites = 3 llr = 87 E-value = 7.6e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A aa3a:33:::::a:7:aa333373::::a:a pos.-specific C ::7:a33:7:37:7:3::3::3:3a77::a: probability G :::::::a3a33::::::373:3:::::::: matrix T :::::33:::3::337::::33:3:33a::: bits 2.4 * * * * * 2.1 * * * * * 1.9 * * * * * 1.7 ** ** * * * ** * **** Relative 1.4 ** ** *** ** ** * **** Entropy 1.2 ***** *** *** ** * ******* (41.9 bits) 0.9 ***** *** *** *** * * ******* 0.7 ***** *** ******* * * ******* 0.5 ***** ************* * ******* 0.2 ******************************* 0.0 ------------------------------- Multilevel AACACAAGCGCCACATAAAGAAAACCCTACA consensus A CC G GG TTC CAGCGC TT sequence TT T G TT T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- ------------------------------- Sfri_3716 + 92 3.18e-14 CTACCTAAGG AACACTCGCGGCATATAAGAATATCCCTACA CAGAGGCTGT Sfri_2598 + 67 3.46e-14 AATTGACTTC AACACCTGCGTCACTCAAAGGAAACTCTACA GCC Sfri_1138 - 1 1.26e-13 TAACGCTAAT AAAACAAGGGCGACATAACGTCGCCCTTACA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- Sfri_3716 3.2e-14 91_[+2]_18 Sfri_2598 3.5e-14 66_[+2]_3 Sfri_1138 1.3e-13 [-2]_69 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=31 seqs=3 Sfri_3716 ( 92) AACACTCGCGGCATATAAGAATATCCCTACA 1 Sfri_2598 ( 67) AACACCTGCGTCACTCAAAGGAAACTCTACA 1 Sfri_1138 ( 1) AAAACAAGGGCGACATAACGTCGCCCTTACA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 31 n= 560 bayes= 6.30378 E= 7.6e+003 171 -823 -823 -823 171 -823 -823 -823 12 178 -823 -823 171 -823 -823 -823 -823 236 -823 -823 12 78 -823 12 12 78 -823 12 -823 -823 236 -823 -823 178 78 -823 -823 -823 236 -823 -823 78 78 12 -823 178 78 -823 171 -823 -823 -823 -823 178 -823 12 112 -823 -823 12 -823 78 -823 112 171 -823 -823 -823 171 -823 -823 -823 12 78 78 -823 12 -823 178 -823 12 -823 78 12 12 78 -823 12 112 -823 78 -823 12 78 -823 12 -823 236 -823 -823 -823 178 -823 12 -823 178 -823 12 -823 -823 -823 171 171 -823 -823 -823 -823 236 -823 -823 171 -823 -823 -823 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 31 nsites= 3 E= 7.6e+003 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.333333 0.666667 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.333333 0.333333 0.000000 0.333333 0.333333 0.333333 0.000000 0.333333 0.000000 0.000000 1.000000 0.000000 0.000000 0.666667 0.333333 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.333333 0.333333 0.333333 0.000000 0.666667 0.333333 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.666667 0.000000 0.333333 0.666667 0.000000 0.000000 0.333333 0.000000 0.333333 0.000000 0.666667 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.333333 0.333333 0.333333 0.000000 0.333333 0.000000 0.666667 0.000000 0.333333 0.000000 0.333333 0.333333 0.333333 0.333333 0.000000 0.333333 0.666667 0.000000 0.333333 0.000000 0.333333 0.333333 0.000000 0.333333 0.000000 1.000000 0.000000 0.000000 0.000000 0.666667 0.000000 0.333333 0.000000 0.666667 0.000000 0.333333 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- AA[CA]AC[ACT][ACT]G[CG]G[CGT][CG]A[CT][AT][TC]AA[ACG][GA][AGT][ACT][AG][ACT]C[CT][CT]TACA -------------------------------------------------------------------------------- Time 0.56 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 width = 10 sites = 5 llr = 51 E-value = 1.2e+004 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A :::2:::a2: pos.-specific C ::a4:8:::: probability G 68:2a:::4: matrix T 42:2:2a:4a bits 2.4 * * 2.1 * * 1.9 * * 1.7 * * ** * Relative 1.4 ** **** * Entropy 1.2 *** **** * (14.6 bits) 0.9 *** **** * 0.7 *** **** * 0.5 *** ****** 0.2 ********** 0.0 ---------- Multilevel GGCCGCTAGT consensus TT A T T sequence G A T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- ---------- Sfri_3716 - 52 1.99e-06 AGGATTTTAT GGCGGCTATT TTACCTGCAT Sfri_0493 - 81 7.48e-06 GTAGGTACAG GTCCGCTAGT TTGATTTTAA Sfri_1452 - 30 1.04e-05 TACCAGTTTG TGCTGCTAGT CGGAAGCCAT Sfri_2598 - 40 1.34e-05 ATTGTCGATC GGCCGTTATT CTAGCAGGCG Sfri_3357 + 90 2.94e-05 CACAAGACGT TGCAGCTAAT A -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- Sfri_3716 2e-06 51_[-3]_79 Sfri_0493 7.5e-06 80_[-3]_10 Sfri_1452 1e-05 29_[-3]_61 Sfri_2598 1.3e-05 39_[-3]_51 Sfri_3357 2.9e-05 89_[+3]_1 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=10 seqs=5 Sfri_3716 ( 52) GGCGGCTATT 1 Sfri_0493 ( 81) GTCCGCTAGT 1 Sfri_1452 ( 30) TGCTGCTAGT 1 Sfri_2598 ( 40) GGCCGTTATT 1 Sfri_3357 ( 90) TGCAGCTAAT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 10 n= 728 bayes= 6.60553 E= 1.2e+004 -897 -897 163 39 -897 -897 204 -61 -897 236 -897 -897 -61 104 4 -61 -897 -897 236 -897 -897 204 -897 -61 -897 -897 -897 171 171 -897 -897 -897 -61 -897 104 39 -897 -897 -897 171 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 10 nsites= 5 E= 1.2e+004 0.000000 0.000000 0.600000 0.400000 0.000000 0.000000 0.800000 0.200000 0.000000 1.000000 0.000000 0.000000 0.200000 0.400000 0.200000 0.200000 0.000000 0.000000 1.000000 0.000000 0.000000 0.800000 0.000000 0.200000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.200000 0.000000 0.400000 0.400000 0.000000 0.000000 0.000000 1.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [GT][GT]C[CAGTA]G[CT]TA[GTA]T -------------------------------------------------------------------------------- Time 0.71 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- Sfri_0493 3.72e-07 56_[+1(1.80e-06)]_3_[-3(7.48e-06)]_10 Sfri_1138 1.95e-12 [-2(1.26e-13)]_29_[+1(2.85e-06)]_19 Sfri_1141 4.01e-05 34_[+1(7.26e-08)]_45 Sfri_1452 2.40e-06 29_[-3(1.04e-05)]_8_[+1(4.67e-08)]_32 Sfri_2598 2.43e-16 7_[+1(1.34e-07)]_11_[-3(1.34e-05)]_17_[+2(3.46e-14)]_3 Sfri_3070 4.47e-04 3_[+1(1.96e-07)]_36 Sfri_3357 2.84e-09 36_[+1(8.30e-11)]_32_[+3(2.94e-05)]_1 Sfri_3716 2.54e-16 22_[+1(3.02e-07)]_8_[-3(1.99e-06)]_30_[+2(3.18e-14)]_18 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: kodomo.fbb.msu.ru ********************************************************************************