******************************************************************************** MEME - Motif discovery tool ******************************************************************************** MEME version 4.10.0 (Release date: Wed May 21 10:35:36 2014 +1000) 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= motifs/473/473.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 36794 1.0000 500 54760 1.0000 500 47725 1.0000 500 39238 1.0000 500 41562 1.0000 500 45280 1.0000 500 51953 1.0000 500 44523 1.0000 500 36443 1.0000 500 37891 1.0000 500 45159 1.0000 500 39660 1.0000 500 41358 1.0000 500 ******************************************************************************** ******************************************************************************** COMMAND LINE SUMMARY ******************************************************************************** This information can also be useful in the event you wish to report a problem with the MEME software. command: meme motifs/473/473.seqs.fa -oc motifs/473 -dna -minw 12 -maxw 21 -nmotifs 3 -maxsize 500000 model: mod= zoops nmotifs= 3 evt= inf object function= E-value of product of p-values width: minw= 12 maxw= 21 minic= 0.00 width: wg= 11 ws= 1 endgaps= yes nsites: minsites= 2 maxsites= 13 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= 6500 N= 13 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.300 C 0.223 G 0.202 T 0.275 Background letter frequencies (from dataset with add-one prior applied): A 0.300 C 0.223 G 0.202 T 0.275 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 12 sites = 13 llr = 128 E-value = 1.4e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 3:::9::12565 pos.-specific C :::a1:155222 probability G 7a:::::2:22: matrix T ::a::a9322:3 bits 2.3 * 2.1 * * 1.8 *** * 1.6 *** * Relative 1.4 ****** Entropy 1.2 ******* (14.2 bits) 0.9 ******* 0.7 ******* * 0.5 ******* * ** 0.2 ********* ** 0.0 ------------ Multilevel GGTCATTCCAAA consensus A TACCT sequence T C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 45280 351 1.46e-07 CTTTGCAAAT GGTCATTCCAAT ACGCAAATTC 39660 233 1.39e-06 ATCAAAAGTT GGTCATTCCGAC TGTTTCAGAA 51953 127 1.75e-06 TCTAATAATC GGTCATTTCACA CGAACCGGAC 54760 202 2.55e-06 ATTAGCGGTA GGTCATTTCCAC CGGATGGCTG 44523 338 4.55e-06 TTGCTATCTG GGTCATTCAACA AGGCGTTGAC 45159 78 6.90e-06 AGAAATAGAC GGTCATTCCTCT TCCAATCATT 36794 421 9.80e-06 CCCAGCATGT GGTCATTTTGAA TCGGCAGTCA 39238 74 1.47e-05 AGACATTTCA AGTCATTCAAAT CACTAACGGT 41358 57 1.91e-05 TTGCCTGCGA GGTCATTGCTGA TCGTACAATG 37891 158 2.90e-05 CTCTTATGAT AGTCCTTCCAAA GCACAGACAC 36443 205 5.30e-05 AGAGAGCGCA AGTCATTTTCGA GACAAAATGT 47725 296 7.15e-05 TTTTTATCAG AGTCATTAAAAT ATGTTAAATA 41562 354 8.38e-05 AGGACGTTTT GGTCATCGTCAC CAAAAAACGT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 45280 1.5e-07 350_[+1]_138 39660 1.4e-06 232_[+1]_256 51953 1.7e-06 126_[+1]_362 54760 2.6e-06 201_[+1]_287 44523 4.6e-06 337_[+1]_151 45159 6.9e-06 77_[+1]_411 36794 9.8e-06 420_[+1]_68 39238 1.5e-05 73_[+1]_415 41358 1.9e-05 56_[+1]_432 37891 2.9e-05 157_[+1]_331 36443 5.3e-05 204_[+1]_284 47725 7.2e-05 295_[+1]_193 41562 8.4e-05 353_[+1]_135 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=12 seqs=13 45280 ( 351) GGTCATTCCAAT 1 39660 ( 233) GGTCATTCCGAC 1 51953 ( 127) GGTCATTTCACA 1 54760 ( 202) GGTCATTTCCAC 1 44523 ( 338) GGTCATTCAACA 1 45159 ( 78) GGTCATTCCTCT 1 36794 ( 421) GGTCATTTTGAA 1 39238 ( 74) AGTCATTCAAAT 1 41358 ( 57) GGTCATTGCTGA 1 37891 ( 158) AGTCCTTCCAAA 1 36443 ( 205) AGTCATTTTCGA 1 47725 ( 296) AGTCATTAAAAT 1 41562 ( 354) GGTCATCGTCAC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 6357 bayes= 8.93074 E= 1.4e-001 4 -1035 177 -1035 -1035 -1035 231 -1035 -1035 -1035 -1035 186 -1035 217 -1035 -1035 162 -153 -1035 -1035 -1035 -1035 -1035 186 -1035 -153 -1035 175 -196 105 -39 16 -38 127 -1035 -25 62 5 -39 -84 104 5 -39 -1035 62 5 -1035 16 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 13 E= 1.4e-001 0.307692 0.000000 0.692308 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.923077 0.076923 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.076923 0.000000 0.923077 0.076923 0.461538 0.153846 0.307692 0.230769 0.538462 0.000000 0.230769 0.461538 0.230769 0.153846 0.153846 0.615385 0.230769 0.153846 0.000000 0.461538 0.230769 0.000000 0.307692 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [GA]GTCATT[CT][CAT][AC][AC][ATC] -------------------------------------------------------------------------------- Time 1.67 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 21 sites = 5 llr = 98 E-value = 1.8e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A :4:::::8::::68a2a2::: pos.-specific C :44:2:::6828:::::48:: probability G a268::a2::8:4::2::::4 matrix T :::28a::42:2:2:6:42a6 bits 2.3 * * 2.1 * * 1.8 * ** * * * 1.6 * ** * * * * Relative 1.4 * ** ** *** * * ** Entropy 1.2 * ********** ** * *** (28.3 bits) 0.9 * ************* * *** 0.7 * ************* * *** 0.5 ********************* 0.2 ********************* 0.0 --------------------- Multilevel GAGGTTGACCGCAAATACCTT consensus CCTC GTTCTGT A TT G sequence G G A -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 36794 247 7.72e-12 TGAGTCAATC GCGGTTGATCGCAAATATCTG CGAAGAATTT 41562 312 5.02e-10 TCGATACAAC GAGGTTGGCCGCAAAAAACTT GGTACAATGC 47725 97 6.03e-10 CTTTTGCAAA GCGGCTGACCCCAAAGATCTT TCTGTGCAGG 44523 351 1.24e-09 CATTCAACAA GGCGTTGACTGTGAATACCTG ATTTTGGTAA 36443 238 4.06e-09 GATGCTCGCT GACTTTGATCGCGTATACTTT CAAGACCTAA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 36794 7.7e-12 246_[+2]_233 41562 5e-10 311_[+2]_168 47725 6e-10 96_[+2]_383 44523 1.2e-09 350_[+2]_129 36443 4.1e-09 237_[+2]_242 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=21 seqs=5 36794 ( 247) GCGGTTGATCGCAAATATCTG 1 41562 ( 312) GAGGTTGGCCGCAAAAAACTT 1 47725 ( 97) GCGGCTGACCCCAAAGATCTT 1 44523 ( 351) GGCGTTGACTGTGAATACCTG 1 36443 ( 238) GACTTTGATCGCGTATACTTT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 6240 bayes= 10.536 E= 1.8e+001 -897 -897 230 -897 41 84 -2 -897 -897 84 157 -897 -897 -897 198 -46 -897 -16 -897 154 -897 -897 -897 186 -897 -897 230 -897 141 -897 -2 -897 -897 143 -897 54 -897 184 -897 -46 -897 -16 198 -897 -897 184 -897 -46 100 -897 98 -897 141 -897 -897 -46 174 -897 -897 -897 -58 -897 -2 112 174 -897 -897 -897 -58 84 -897 54 -897 184 -897 -46 -897 -897 -897 186 -897 -897 98 112 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 5 E= 1.8e+001 0.000000 0.000000 1.000000 0.000000 0.400000 0.400000 0.200000 0.000000 0.000000 0.400000 0.600000 0.000000 0.000000 0.000000 0.800000 0.200000 0.000000 0.200000 0.000000 0.800000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.800000 0.000000 0.200000 0.000000 0.000000 0.600000 0.000000 0.400000 0.000000 0.800000 0.000000 0.200000 0.000000 0.200000 0.800000 0.000000 0.000000 0.800000 0.000000 0.200000 0.600000 0.000000 0.400000 0.000000 0.800000 0.000000 0.000000 0.200000 1.000000 0.000000 0.000000 0.000000 0.200000 0.000000 0.200000 0.600000 1.000000 0.000000 0.000000 0.000000 0.200000 0.400000 0.000000 0.400000 0.000000 0.800000 0.000000 0.200000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.400000 0.600000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- G[ACG][GC][GT][TC]TG[AG][CT][CT][GC][CT][AG][AT]A[TAG]A[CTA][CT]T[TG] -------------------------------------------------------------------------------- Time 3.32 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 16 sites = 4 llr = 71 E-value = 2.8e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A ::8a:8::3aa::::: pos.-specific C a33:8:::5:::a:5: probability G ::::::a::::a:a:8 matrix T :8::33:a3:::::53 bits 2.3 * * * 2.1 * * *** 1.8 * * ** ***** 1.6 * * ** ***** Relative 1.4 * ** ** ***** * Entropy 1.2 ** ** ** ***** * (25.6 bits) 0.9 ******** ******* 0.7 ******** ******* 0.5 **************** 0.2 **************** 0.0 ---------------- Multilevel CTAACAGTCAAGCGCG consensus CC TT A TT sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 47725 177 1.38e-09 GGTCCGCCGC CTCACAGTCAAGCGTG TGTACCATTG 41562 186 4.78e-09 TATGTTTTTC CTAACTGTTAAGCGCG GCTAACAGCA 51953 58 6.66e-09 TACATTTAGG CCAATAGTCAAGCGCG AGGGGATTGT 39660 367 1.17e-08 TAGAGAGTCA CTAACAGTAAAGCGTT TTCTGCAAGT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 47725 1.4e-09 176_[+3]_308 41562 4.8e-09 185_[+3]_299 51953 6.7e-09 57_[+3]_427 39660 1.2e-08 366_[+3]_118 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=16 seqs=4 47725 ( 177) CTCACAGTCAAGCGTG 1 41562 ( 186) CTAACTGTTAAGCGCG 1 51953 ( 58) CCAATAGTCAAGCGCG 1 39660 ( 367) CTAACAGTAAAGCGTT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 6305 bayes= 10.6214 E= 2.8e+002 -865 216 -865 -865 -865 17 -865 144 132 17 -865 -865 173 -865 -865 -865 -865 175 -865 -14 132 -865 -865 -14 -865 -865 230 -865 -865 -865 -865 186 -26 116 -865 -14 173 -865 -865 -865 173 -865 -865 -865 -865 -865 230 -865 -865 216 -865 -865 -865 -865 230 -865 -865 116 -865 86 -865 -865 189 -14 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 4 E= 2.8e+002 0.000000 1.000000 0.000000 0.000000 0.000000 0.250000 0.000000 0.750000 0.750000 0.250000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.750000 0.000000 0.250000 0.750000 0.000000 0.000000 0.250000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.250000 0.500000 0.000000 0.250000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.500000 0.000000 0.500000 0.000000 0.000000 0.750000 0.250000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- C[TC][AC]A[CT][AT]GT[CAT]AAGCG[CT][GT] -------------------------------------------------------------------------------- Time 4.94 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 36794 2.10e-09 246_[+2(7.72e-12)]_153_\ [+1(9.80e-06)]_5_[+1(8.66e-05)]_51 54760 1.89e-02 201_[+1(2.55e-06)]_287 47725 3.78e-12 96_[+2(6.03e-10)]_59_[+3(1.38e-09)]_\ 103_[+1(7.15e-05)]_193 39238 3.74e-02 73_[+1(1.47e-05)]_415 41562 1.18e-11 185_[+3(4.78e-09)]_110_\ [+2(5.02e-10)]_21_[+1(8.38e-05)]_135 45280 8.60e-04 350_[+1(1.46e-07)]_138 51953 4.64e-07 57_[+3(6.66e-09)]_53_[+1(1.75e-06)]_\ 362 44523 2.72e-07 337_[+1(4.55e-06)]_1_[+2(1.24e-09)]_\ 129 36443 5.69e-06 204_[+1(5.30e-05)]_21_\ [+2(4.06e-09)]_242 37891 4.33e-02 157_[+1(2.90e-05)]_91_\ [+1(8.66e-05)]_228 45159 2.55e-02 77_[+1(6.90e-06)]_411 39660 3.97e-07 232_[+1(1.39e-06)]_122_\ [+3(1.17e-08)]_118 41358 9.56e-02 56_[+1(1.91e-05)]_432 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************