******************************************************************************** MEME - Motif discovery tool ******************************************************************************** MEME version 5.5.1 (Release date: Sun Jan 29 10:33:12 2023 -0800) For further information on how to interpret these results please access https://meme-suite.org/meme. To get a copy of the MEME Suite software please access https://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 ******************************************************************************** PRIMARY SEQUENCES= TRAIN.fasta CONTROL SEQUENCES= --none-- ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ Seq1 1.0000 25 Seq2 1.0000 25 Seq3 1.0000 25 Seq4 1.0000 25 Seq5 1.0000 25 Seq6 1.0000 25 Seq7 1.0000 25 Seq8 1.0000 25 Seq9 1.0000 25 Seq10 1.0000 25 Seq11 1.0000 25 Seq12 1.0000 25 Seq13 1.0000 25 Seq14 1.0000 25 Seq15 1.0000 25 Seq16 1.0000 25 Seq17 1.0000 25 Seq18 1.0000 25 Seq19 1.0000 25 Seq20 1.0000 25 Seq21 1.0000 25 Seq22 1.0000 25 Seq23 1.0000 25 Seq24 1.0000 25 Seq25 1.0000 25 Seq26 1.0000 25 Seq27 1.0000 25 Seq28 1.0000 25 Seq29 1.0000 25 Seq30 1.0000 25 Seq31 1.0000 25 Seq32 1.0000 25 Seq33 1.0000 25 Seq34 1.0000 25 Seq35 1.0000 25 Seq36 1.0000 25 Seq37 1.0000 25 Seq38 1.0000 25 Seq39 1.0000 25 Seq40 1.0000 25 Seq41 1.0000 25 Seq42 1.0000 25 Seq43 1.0000 25 Seq44 1.0000 25 Seq45 1.0000 25 Seq46 1.0000 25 Seq47 1.0000 25 Seq48 1.0000 25 Seq49 1.0000 25 Seq50 1.0000 25 Seq51 1.0000 25 Seq52 1.0000 25 Seq53 1.0000 25 Seq54 1.0000 25 Seq55 1.0000 25 Seq56 1.0000 25 Seq57 1.0000 25 Seq58 1.0000 25 Seq59 1.0000 25 Seq60 1.0000 25 Seq61 1.0000 25 Seq62 1.0000 25 Seq63 1.0000 25 Seq64 1.0000 25 Seq65 1.0000 25 Seq66 1.0000 25 Seq67 1.0000 25 Seq68 1.0000 25 Seq69 1.0000 25 Seq70 1.0000 25 Seq71 1.0000 25 Seq72 1.0000 25 Seq73 1.0000 25 Seq74 1.0000 25 Seq75 1.0000 25 Seq76 1.0000 25 Seq77 1.0000 25 Seq78 1.0000 25 Seq79 1.0000 25 Seq80 1.0000 25 Seq81 1.0000 25 Seq82 1.0000 25 Seq83 1.0000 25 Seq84 1.0000 25 Seq85 1.0000 25 Seq86 1.0000 25 Seq87 1.0000 25 Seq88 1.0000 25 Seq89 1.0000 25 Seq90 1.0000 25 Seq91 1.0000 25 Seq92 1.0000 25 Seq93 1.0000 25 Seq94 1.0000 25 Seq95 1.0000 25 Seq96 1.0000 25 Seq97 1.0000 25 Seq98 1.0000 25 Seq99 1.0000 25 Seq100 1.0000 25 Seq101 1.0000 25 Seq102 1.0000 25 Seq103 1.0000 25 Seq104 1.0000 25 Seq105 1.0000 25 Seq106 1.0000 25 Seq107 1.0000 25 ******************************************************************************** ******************************************************************************** COMMAND LINE SUMMARY ******************************************************************************** This information can also be useful in the event you wish to report a problem with the MEME software. command: meme TRAIN.fasta -dna -nmotifs 1 -minw 5 -maxw 10 model: mod= zoops nmotifs= 1 evt= inf objective function: em= E-value of product of p-values starts= E-value of product of p-values strands: + width: minw= 5 maxw= 10 nsites: minsites= 2 maxsites= 107 wnsites= 0.8 theta: spmap= uni spfuzz= 0.5 em: prior= dirichlet b= 0.01 maxiter= 50 distance= 1e-05 trim: wg= 11 ws= 1 endgaps= yes data: n= 2675 N= 107 sample: seed= 0 hsfrac= 0 searchsize= 2675 norand= no csites= 1000 Letter frequencies in dataset: A 0.38 C 0.129 G 0.24 T 0.251 Background letter frequencies (from file dataset with add-one prior applied): A 0.38 C 0.13 G 0.24 T 0.251 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF TTTTWGGAG MEME-1 width = 9 sites = 11 llr = 103 E-value = 7.5e-003 ******************************************************************************** -------------------------------------------------------------------------------- Motif TTTTWGGAG MEME-1 Description -------------------------------------------------------------------------------- Simplified A 2:::4:1a: pos.-specific C ::::1:::: probability G 1::3:a9:a matrix T 7aa75:::: bits 2.9 2.7 2.4 2.1 ** * * Relative 1.8 ** * * Entropy 1.5 ** **** (13.6 bits) 1.2 *** **** 0.9 **** **** 0.6 ********* 0.3 ********* 0.0 --------- Multilevel TTTTTGGAG consensus GA sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTTTWGGAG MEME-1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------- Seq15 10 5.23e-06 GTAGCTAGA TTTTTGGAG AAAAATA Seq10 8 5.23e-06 TCTTTGT TTTTTGGAG ATAGTTTTA Seq7 8 5.23e-06 AGTAAAC TTTTTGGAG TAAATAATA Seq27 4 1.82e-05 ATT TTTGTGGAG AAGTAGATAA Seq2 8 2.09e-05 AATCGTT TTTTCGGAG GTCATCTTC Seq53 13 2.84e-05 TGACGAATTT TTTGAGGAG TCAT Seq3 7 2.84e-05 GGGGGT TTTGAGGAG TTTATTAAAG Seq82 11 3.64e-05 AGCACTATGA ATTTTGGAG AAATAA Seq52 11 3.64e-05 TTAAATAACG ATTTTGGAG GTCCCC Seq38 8 7.94e-05 ACGACGA GTTTAGGAG GTACGAGTA Seq32 9 1.15e-04 GAATTGAA TTTTAGAAG GTGTATTT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTTTWGGAG MEME-1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- Seq15 5.2e-06 9_[+1]_7 Seq10 5.2e-06 7_[+1]_9 Seq7 5.2e-06 7_[+1]_9 Seq27 1.8e-05 3_[+1]_13 Seq2 2.1e-05 7_[+1]_9 Seq53 2.8e-05 12_[+1]_4 Seq3 2.8e-05 6_[+1]_10 Seq82 3.6e-05 10_[+1]_6 Seq52 3.6e-05 10_[+1]_6 Seq38 7.9e-05 7_[+1]_9 Seq32 0.00011 8_[+1]_8 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTTTWGGAG MEME-1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF TTTTWGGAG width=9 seqs=11 Seq15 ( 10) TTTTTGGAG 1 Seq10 ( 8) TTTTTGGAG 1 Seq7 ( 8) TTTTTGGAG 1 Seq27 ( 4) TTTGTGGAG 1 Seq2 ( 8) TTTTCGGAG 1 Seq53 ( 13) TTTGAGGAG 1 Seq3 ( 7) TTTGAGGAG 1 Seq82 ( 11) ATTTTGGAG 1 Seq52 ( 11) ATTTTGGAG 1 Seq38 ( 8) GTTTAGGAG 1 Seq32 ( 9) TTTTAGAAG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTTTWGGAG MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 9 n= 1819 bayes= 8.39168 E= 7.5e-003 -106 -1010 -140 153 -1010 -1010 -1010 199 -1010 -1010 -1010 199 -1010 -1010 19 153 -6 -51 -1010 112 -1010 -1010 206 -1010 -206 -1010 192 -1010 140 -1010 -1010 -1010 -1010 -1010 206 -1010 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTTTWGGAG MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 9 nsites= 11 E= 7.5e-003 0.181818 0.000000 0.090909 0.727273 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.272727 0.727273 0.363636 0.090909 0.000000 0.545455 0.000000 0.000000 1.000000 0.000000 0.090909 0.000000 0.909091 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTTTWGGAG MEME-1 regular expression -------------------------------------------------------------------------------- TTT[TG][TA]GGAG -------------------------------------------------------------------------------- Time 1.06 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- Seq1 8.06e-02 25 Seq2 3.55e-04 7_[+1(2.09e-05)]_9 Seq3 4.84e-04 6_[+1(2.84e-05)]_10 Seq4 6.81e-01 25 Seq5 2.45e-01 25 Seq6 9.31e-01 25 Seq7 8.90e-05 7_[+1(5.23e-06)]_9 Seq8 4.13e-01 25 Seq9 5.84e-01 25 Seq10 8.90e-05 7_[+1(5.23e-06)]_9 Seq11 7.55e-01 25 Seq12 7.66e-01 25 Seq13 5.61e-02 25 Seq14 9.41e-01 25 Seq15 8.90e-05 9_[+1(5.23e-06)]_7 Seq16 8.16e-01 25 Seq17 5.91e-01 25 Seq18 1.62e-01 25 Seq19 7.33e-01 25 Seq20 9.10e-01 25 Seq21 4.46e-01 25 Seq22 3.02e-01 25 Seq23 3.05e-01 25 Seq24 8.58e-01 25 Seq25 3.59e-02 25 Seq26 9.40e-02 25 Seq27 3.09e-04 3_[+1(1.82e-05)]_13 Seq28 9.58e-01 25 Seq29 8.95e-01 25 Seq30 1.40e-01 25 Seq31 2.33e-01 25 Seq32 1.95e-03 25 Seq33 2.61e-02 25 Seq34 3.86e-02 25 Seq35 1.62e-01 25 Seq36 1.52e-01 25 Seq37 2.87e-02 25 Seq38 1.35e-03 7_[+1(7.94e-05)]_9 Seq39 3.10e-01 25 Seq40 8.16e-01 25 Seq41 8.24e-01 25 Seq42 9.47e-01 25 Seq43 3.10e-01 25 Seq44 9.83e-01 25 Seq45 3.11e-02 25 Seq46 2.93e-01 25 Seq47 9.80e-01 25 Seq48 2.87e-02 25 Seq49 6.20e-01 25 Seq50 1.67e-01 25 Seq51 7.81e-01 25 Seq52 6.18e-04 10_[+1(3.64e-05)]_6 Seq53 4.84e-04 12_[+1(2.84e-05)]_4 Seq54 9.98e-01 25 Seq55 4.95e-01 25 Seq56 2.39e-01 25 Seq57 2.59e-01 25 Seq58 9.06e-01 25 Seq59 9.19e-01 25 Seq60 1.23e-01 25 Seq61 9.03e-01 25 Seq62 2.59e-01 25 Seq63 5.22e-01 25 Seq64 1.79e-01 25 Seq65 6.94e-01 25 Seq66 4.77e-01 25 Seq67 4.70e-01 25 Seq68 3.77e-01 25 Seq69 8.24e-01 25 Seq70 9.83e-01 25 Seq71 2.33e-01 25 Seq72 5.22e-01 25 Seq73 4.88e-02 25 Seq74 8.90e-01 25 Seq75 1.89e-02 25 Seq76 1.85e-01 25 Seq77 5.51e-01 25 Seq78 8.90e-01 25 Seq79 4.92e-01 25 Seq80 4.77e-01 25 Seq81 9.89e-01 25 Seq82 6.18e-04 10_[+1(3.64e-05)]_6 Seq83 4.30e-01 25 Seq84 9.93e-01 25 Seq85 6.39e-01 25 Seq86 2.00e-01 25 Seq87 1.92e-01 25 Seq88 4.30e-01 25 Seq89 1.74e-01 25 Seq90 7.98e-01 25 Seq91 2.86e-01 25 Seq92 2.00e-01 25 Seq93 6.94e-01 25 Seq94 2.10e-01 25 Seq95 9.00e-02 25 Seq96 4.92e-01 25 Seq97 8.73e-01 25 Seq98 2.00e-01 25 Seq99 7.33e-01 25 Seq100 1.52e-01 25 Seq101 3.82e-01 25 Seq102 1.47e-01 25 Seq103 3.67e-01 25 Seq104 2.59e-01 25 Seq105 6.81e-01 25 Seq106 1.85e-01 25 Seq107 7.90e-01 25 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (1) found. ******************************************************************************** CPU: kodomo ********************************************************************************