******************************************************************************** MEME - Motif discovery tool ******************************************************************************** MEME version 4.4.0 (Release date: Tue Apr 27 10:09:30 EST 2010) 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= ../tests/lex0.s ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ cloacin-df13 1.0000 200 colicin-e1 1.0000 200 colicin-ia 1.0000 200 colicin-ib 1.0000 200 reca 1.0000 200 recn 1.0000 200 sula 1.0000 200 umu-operon 1.0000 200 uvra 1.0000 200 uvrb 1.0000 200 uvrd 1.0000 200 colicin-a 1.0000 136 lexA 1.0000 173 muc-operon 1.0000 158 hima 1.0000 200 uvrc 1.0000 200 ******************************************************************************** ******************************************************************************** COMMAND LINE SUMMARY ******************************************************************************** This information can also be useful in the event you wish to report a problem with the MEME software. command: meme ../tests/lex0.s -dna -pal model: mod= zoops nmotifs= 1 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= 16 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= 3067 N= 16 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.296 C 0.207 G 0.213 T 0.283 Background letter frequencies (from dataset with add-one prior applied): A 0.296 C 0.207 G 0.213 T 0.283 ******************************************************************************** ******************************************************************************** MOTIF 1 width = 20 sites = 14 llr = 216 E-value = 1.9e-024 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 471:::7:6172a27:a:16 pos.-specific C 119::::::1:2:12a::1: probability G :1::a31:2:1::::::911 matrix T 61:a:72a2716:7:::174 bits 2.3 * * 2.0 * * 1.8 *** ** 1.6 *** * * *** Relative 1.4 *** * * *** Entropy 1.1 *** * * *** (22.2 bits) 0.9 **** * * **** 0.7 ****** ********** 0.5 ******************** 0.2 ******************** 0.0 -------------------- Multilevel TACTGTATATATATACAGTA consensus A G C T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------------- cloacin-df13 97 5.39e-11 GTAATAATCA TACTGTGTATATATACAGTA TTTTGGTTTT umu-operon 91 7.82e-10 AAGAACAGAC TACTGTATATAAAAACAGTA TAACTTCAGG muc-operon 49 2.55e-09 ATAACAGCGA TACTGTATAAATAAACAGTT ATTTGGAAGA recn 71 4.07e-09 CCAGCCTCTT TACTGTATATAAAACCAGTT TATACTGTAC reca 71 1.95e-08 AAACACTTGA TACTGTATGAGCATACAGTA TAATTGCTTC uvrb 71 2.36e-08 TATGGTGATG AACTGTTTTTTTATCCAGTA TAATTTGTTG sula 85 7.93e-08 TCACTGGATG TACTGTACATCCATACAGTA ACTCACAGGG uvrd 102 9.28e-08 TAATCAGCAA ATCTGTATATATACCCAGCT TTTTGGCGGA lexA 76 1.00e-07 CTCACAGCAT AACTGTATATACACCCAGGG GGCGGAATGA colicin-a 34 1.17e-07 AGTATCATTT TACTGTATATAAACACATGT GAATATATAC colicin-ib 99 1.17e-07 AATAAATTAG TACTGTATATGTATCCATAT ACGTAAGCAG colicin-ia 99 1.17e-07 AATAAATTAA TACTGTATATGTATCCATAT GCGTAAGCAG colicin-e1 97 1.26e-07 GTAGCTTTTA TGCTGTATATAAAACCAGTG GTTATATGTA uvra 60 1.82e-07 TGCATTCCAA TACTGTATATTCATTCAGGT CAATTTGTGT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- cloacin-df13 5.4e-11 96_[1]_84 umu-operon 7.8e-10 90_[1]_90 muc-operon 2.6e-09 48_[1]_90 recn 4.1e-09 70_[1]_110 reca 1.9e-08 70_[1]_110 uvrb 2.4e-08 70_[1]_110 sula 7.9e-08 84_[1]_96 uvrd 9.3e-08 101_[1]_79 lexA 1e-07 75_[1]_78 colicin-a 1.2e-07 33_[1]_83 colicin-ib 1.2e-07 98_[1]_82 colicin-ia 1.2e-07 98_[1]_82 colicin-e1 1.3e-07 96_[1]_84 uvra 1.8e-07 59_[1]_121 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=20 seqs=14 cloacin-df13 ( 97) TACTGTGTATATATACAGTA 1 umu-operon ( 91) TACTGTATATAAAAACAGTA 1 muc-operon ( 49) TACTGTATAAATAAACAGTT 1 recn ( 71) TACTGTATATAAAACCAGTT 1 reca ( 71) TACTGTATGAGCATACAGTA 1 uvrb ( 71) AACTGTTTTTTTATCCAGTA 1 sula ( 85) TACTGTACATCCATACAGTA 1 uvrd ( 102) ATCTGTATATATACCCAGCT 1 lexA ( 76) AACTGTATATACACCCAGGG 1 colicin-a ( 34) TACTGTATATAAACACATGT 1 colicin-ib ( 99) TACTGTATATGTATCCATAT 1 colicin-ia ( 99) TACTGTATATGTATCCATAT 1 colicin-e1 ( 97) TGCTGTATATAAAACCAGTG 1 uvra ( 60) TACTGTATATTCATTCAGGT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 2763 bayes= 8.84392 E= 1.9e-024 27 -154 -1047 101 127 -95 -157 -140 -147 211 -1047 -1042 -1048 -1043 -1047 182 -1048 -1043 223 -1042 -305 -1043 23 133 119 -1043 -58 -67 -1048 -253 -1047 177 112 -1043 -25 -67 -105 -95 -257 133 127 -253 -99 -99 -73 -22 -1048 118 170 -1044 -257 -1043 -73 -54 -1048 126 127 27 -1048 -298 -1049 227 -1048 -1043 175 -1044 -1048 -1043 -1049 -1044 207 -140 -147 -154 -99 133 95 -1044 -157 33 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 14 E= 1.9e-024 0.357143 0.071429 0.000000 0.571429 0.714286 0.107143 0.071429 0.107143 0.107143 0.892857 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.035714 0.000000 0.250000 0.714286 0.678571 0.000000 0.142857 0.178571 0.000000 0.035714 0.000000 0.964286 0.642857 0.000000 0.178571 0.178571 0.142856 0.107141 0.035713 0.714284 0.714285 0.035714 0.107142 0.142857 0.178570 0.178570 0.000000 0.642856 0.964285 0.000000 0.035713 0.000000 0.178570 0.142856 0.000000 0.678570 0.714285 0.249999 0.000000 0.035713 0.000000 0.999999 0.000000 0.000000 0.999999 0.000000 0.000000 0.000000 0.000000 0.000000 0.892856 0.107142 0.107142 0.071428 0.107142 0.714285 0.571428 0.000000 0.071428 0.357142 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [TA]ACTG[TG]ATATATAT[AC]CAGT[AT] -------------------------------------------------------------------------------- Time 3.98 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- cloacin-df13 9.75e-09 96_[1(5.39e-11)]_84 colicin-e1 2.28e-05 96_[1(1.26e-07)]_84 colicin-ia 2.11e-05 98_[1(1.17e-07)]_82 colicin-ib 2.11e-05 98_[1(1.17e-07)]_82 reca 3.53e-06 70_[1(1.95e-08)]_110 recn 7.36e-07 70_[1(4.07e-09)]_20_[1(1.02e-06)]_70 sula 1.44e-05 84_[1(7.93e-08)]_96 umu-operon 1.42e-07 90_[1(7.82e-10)]_90 uvra 3.29e-05 59_[1(1.82e-07)]_121 uvrb 4.27e-06 70_[1(2.36e-08)]_110 uvrd 1.68e-05 101_[1(9.28e-08)]_79 colicin-a 1.37e-05 33_[1(1.17e-07)]_83 lexA 1.54e-05 54_[1(9.22e-06)]_1_[1(1.00e-07)]_78 muc-operon 3.55e-07 48_[1(2.55e-09)]_90 hima 9.65e-01 200 uvrc 9.02e-01 200 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 1 reached. ******************************************************************************** CPU: tlb-kamikaze-lt.imb.uq.edu.au ********************************************************************************