******************************************************************************** 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/293/293.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 10828 1.0000 500 11347 1.0000 500 21014 1.0000 500 2244 1.0000 500 24218 1.0000 500 2433 1.0000 500 24508 1.0000 500 262949 1.0000 500 263425 1.0000 500 263947 1.0000 500 2737 1.0000 500 31375 1.0000 500 35723 1.0000 500 35984 1.0000 500 36738 1.0000 500 3674 1.0000 500 5711 1.0000 500 6198 1.0000 500 7771 1.0000 500 9125 1.0000 500 9207 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/293/293.seqs.fa -oc motifs/293 -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= 21 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= 10500 N= 21 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.256 C 0.218 G 0.250 T 0.276 Background letter frequencies (from dataset with add-one prior applied): A 0.256 C 0.218 G 0.250 T 0.276 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 12 sites = 21 llr = 185 E-value = 1.6e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A ::::11::::57 pos.-specific C 15:99173:82: probability G 4::1:2:1:23: matrix T 45a::636a::3 bits 2.2 2.0 1.8 ** 1.5 *** * Relative 1.3 *** * ** Entropy 1.1 *** * ** (12.7 bits) 0.9 **** * ** * 0.7 **** **** * 0.4 *********** 0.2 ************ 0.0 ------------ Multilevel TCTCCTCTTCAA consensus GT TC GGT sequence C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 35723 58 1.57e-06 TTAGCAGCTA GCTCCTTTTCAA TTCTTGTGCG 31375 391 4.13e-06 AGATATTATG GTTCCTCTTCGT TTGTTACCGC 24508 169 4.13e-06 TCTCGCTCAA GCTCCGCTTCCA AATCTTCAAT 2244 438 4.13e-06 GGAAAAGTAA TCTCCCCTTCAA CCAATTTGCA 21014 482 4.47e-06 CGTCTTTCTC GTTCCTCTTCCT CCTAAGG 35984 163 6.12e-06 GTTACTTCGA TCTCCGCCTCCA GCTGCATCCG 11347 403 6.75e-06 GAGAGAGACA TTTCCTCTTGGA ACAATCCTCT 263425 168 1.68e-05 GTCTGATTGC TCTCCTTCTCGT AGACGATGCG 263947 131 2.29e-05 AATGAAATGC TTTCCTTGTCAA CAGGAGACAC 262949 269 2.49e-05 CACTTTCCCA GTTGCTCTTCGA GACAGCGGCT 36738 462 3.03e-05 CACAACCCTG TCTCCTCCTCCC ACCCCCCTCC 9207 415 3.26e-05 TGAATCTTCC TTTCCACTTGAA AACACCCTGC 6198 331 3.59e-05 GTAGTAACAA ATTCCGCTTCAA TCCGTCAGCT 2737 395 5.04e-05 AATGTGGTGA GTTCCTTCTGAT TGTAAATAGT 5711 33 6.00e-05 CAATGCCATG GGTCCTCCTGAA ACTGCTGATG 9125 403 8.22e-05 TAATGGCCTC CCTCCCTCTCCA AACAAACAGT 24218 135 1.02e-04 CGATGTGTTA CTTCATCCTCAT CATTTGGATA 3674 470 1.09e-04 TGCCTTGTTG TCTCCGCTCCAT CTTGCACCAA 7771 351 1.17e-04 CGGTGTGTTC TCTCTTCTTGGA GGATAATCAA 2433 420 1.63e-04 ACTCCCTACT CCTCATCGTCGA GGTGGGAAAT 10828 464 1.98e-04 TGCAAATCGT GTTGCATTTCAA TCTCATCGCT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 35723 1.6e-06 57_[+1]_431 31375 4.1e-06 390_[+1]_98 24508 4.1e-06 168_[+1]_320 2244 4.1e-06 437_[+1]_51 21014 4.5e-06 481_[+1]_7 35984 6.1e-06 162_[+1]_326 11347 6.8e-06 402_[+1]_86 263425 1.7e-05 167_[+1]_321 263947 2.3e-05 130_[+1]_358 262949 2.5e-05 268_[+1]_220 36738 3e-05 461_[+1]_27 9207 3.3e-05 414_[+1]_74 6198 3.6e-05 330_[+1]_158 2737 5e-05 394_[+1]_94 5711 6e-05 32_[+1]_456 9125 8.2e-05 402_[+1]_86 24218 0.0001 134_[+1]_354 3674 0.00011 469_[+1]_19 7771 0.00012 350_[+1]_138 2433 0.00016 419_[+1]_69 10828 0.0002 463_[+1]_25 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=12 seqs=21 35723 ( 58) GCTCCTTTTCAA 1 31375 ( 391) GTTCCTCTTCGT 1 24508 ( 169) GCTCCGCTTCCA 1 2244 ( 438) TCTCCCCTTCAA 1 21014 ( 482) GTTCCTCTTCCT 1 35984 ( 163) TCTCCGCCTCCA 1 11347 ( 403) TTTCCTCTTGGA 1 263425 ( 168) TCTCCTTCTCGT 1 263947 ( 131) TTTCCTTGTCAA 1 262949 ( 269) GTTGCTCTTCGA 1 36738 ( 462) TCTCCTCCTCCC 1 9207 ( 415) TTTCCACTTGAA 1 6198 ( 331) ATTCCGCTTCAA 1 2737 ( 395) GTTCCTTCTGAT 1 5711 ( 33) GGTCCTCCTGAA 1 9125 ( 403) CCTCCCTCTCCA 1 24218 ( 135) CTTCATCCTCAT 1 3674 ( 470) TCTCCGCTCCAT 1 7771 ( 351) TCTCTTCTTGGA 1 2433 ( 420) CCTCATCGTCGA 1 10828 ( 464) GTTGCATTTCAA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 10269 bayes= 8.93074 E= 1.6e-001 -242 -61 61 64 -1104 113 -239 79 -1104 -1104 -1104 186 -1104 205 -139 -1104 -143 197 -1104 -253 -143 -120 -39 117 -1104 171 -1104 5 -1104 61 -139 105 -1104 -219 -1104 179 -1104 180 -7 -1104 90 13 19 -1104 138 -219 -1104 5 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 21 E= 1.6e-001 0.047619 0.142857 0.380952 0.428571 0.000000 0.476190 0.047619 0.476190 0.000000 0.000000 0.000000 1.000000 0.000000 0.904762 0.095238 0.000000 0.095238 0.857143 0.000000 0.047619 0.095238 0.095238 0.190476 0.619048 0.000000 0.714286 0.000000 0.285714 0.000000 0.333333 0.095238 0.571429 0.000000 0.047619 0.000000 0.952381 0.000000 0.761905 0.238095 0.000000 0.476190 0.238095 0.285714 0.000000 0.666667 0.047619 0.000000 0.285714 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [TG][CT]TCCT[CT][TC]T[CG][AGC][AT] -------------------------------------------------------------------------------- Time 5.01 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 12 sites = 13 llr = 135 E-value = 1.2e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A 4192:731a2:8 pos.-specific C 18::7179::9: probability G 2::::2:::::2 matrix T 311831:::811 bits 2.2 2.0 * 1.8 ** * 1.5 * ** * Relative 1.3 *** *** * Entropy 1.1 **** ***** (15.0 bits) 0.9 **** ****** 0.7 *********** 0.4 *********** 0.2 ************ 0.0 ------------ Multilevel ACATCACCATCA consensus T T A A sequence G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 35723 474 1.26e-07 ATCAAGGGAT GCATCACCATCA AATATACTCA 7771 474 2.27e-07 AGCAGCAACG ACATCAACATCA TAGAACGAGC 9125 477 2.65e-07 CCTAAGGACA ACATCACCAACA GCTAGCTAAA 36738 78 3.73e-07 TCGCAACTCA TCATTACCATCA CATCCGTCAT 2244 130 4.20e-06 ATCGTGGCTT GCAACAACATCA TCAGTTGTAT 6198 190 6.60e-06 TTCCACCATC TCATCTCCAACA CAGCCGACGC 5711 283 6.60e-06 TTGAAATGCT TCATTACCATCT GTTCGAACCG 2737 233 1.37e-05 AGACGATCCA TCATCGCCATTA TCCACACCAA 263425 119 1.54e-05 AATCTCATTG GCTTCACCATCG TCGTCGTCTT 35984 95 2.60e-05 CGAGAGAGAC AAATCACAATCA TTCACGGCGA 262949 361 2.60e-05 GAGCTTATGG ACAATAACATCG GACGTGATGG 11347 271 2.60e-05 TGCCCGGATA ATATCGCCAACA CAGTTTACGG 2433 468 3.38e-05 CTTCTCGTGA CCATTCACATCA ATCTTGACGG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 35723 1.3e-07 473_[+2]_15 7771 2.3e-07 473_[+2]_15 9125 2.6e-07 476_[+2]_12 36738 3.7e-07 77_[+2]_411 2244 4.2e-06 129_[+2]_359 6198 6.6e-06 189_[+2]_299 5711 6.6e-06 282_[+2]_206 2737 1.4e-05 232_[+2]_256 263425 1.5e-05 118_[+2]_370 35984 2.6e-05 94_[+2]_394 262949 2.6e-05 360_[+2]_128 11347 2.6e-05 270_[+2]_218 2433 3.4e-05 467_[+2]_21 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=12 seqs=13 35723 ( 474) GCATCACCATCA 1 7771 ( 474) ACATCAACATCA 1 9125 ( 477) ACATCACCAACA 1 36738 ( 78) TCATTACCATCA 1 2244 ( 130) GCAACAACATCA 1 6198 ( 190) TCATCTCCAACA 1 5711 ( 283) TCATTACCATCT 1 2737 ( 233) TCATCGCCATTA 1 263425 ( 119) GCTTCACCATCG 1 35984 ( 95) AAATCACAATCA 1 262949 ( 361) ACAATAACATCG 1 11347 ( 271) ATATCGCCAACA 1 2433 ( 468) CCATTCACATCA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 10269 bayes= 10.1548 E= 1.2e+002 59 -150 -12 16 -173 195 -1035 -184 185 -1035 -1035 -184 -73 -1035 -1035 162 -1035 166 -1035 16 143 -150 -70 -184 27 166 -1035 -1035 -173 208 -1035 -1035 196 -1035 -1035 -1035 -15 -1035 -1035 148 -1035 208 -1035 -184 159 -1035 -70 -184 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 13 E= 1.2e+002 0.384615 0.076923 0.230769 0.307692 0.076923 0.846154 0.000000 0.076923 0.923077 0.000000 0.000000 0.076923 0.153846 0.000000 0.000000 0.846154 0.000000 0.692308 0.000000 0.307692 0.692308 0.076923 0.153846 0.076923 0.307692 0.692308 0.000000 0.000000 0.076923 0.923077 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.230769 0.000000 0.000000 0.769231 0.000000 0.923077 0.000000 0.076923 0.769231 0.000000 0.153846 0.076923 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [ATG]CAT[CT]A[CA]CA[TA]CA -------------------------------------------------------------------------------- Time 9.12 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 21 sites = 4 llr = 82 E-value = 3.6e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A ::::::::35:33:55::::: pos.-specific C 888:a8:a3:883a353:a8: probability G ::3::3::35::3::::a::a matrix T 33:a::a:3:3:3:3:8::3: bits 2.2 * * * * 2.0 * * * ** * 1.8 ** ** * ** * 1.5 ** ** * ** * Relative 1.3 ******** ** * **** Entropy 1.1 ******** ** * ****** (29.4 bits) 0.9 ******** *** * ****** 0.7 ******** *** * ****** 0.4 ******** *** ******** 0.2 ******** *** ******** 0.0 --------------------- Multilevel CCCTCCTCAACCACAATGCCG consensus TTG G CGTAC CCC T sequence G G T T T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 36738 478 1.88e-12 CCTCCCACCC CCCTCCTCAACCACACTGCCG TA 7771 61 1.18e-10 GGCGGGCTCT CCGTCCTCTGCCGCTCTGCCG GATTGTCAGG 2737 456 1.49e-09 TTCACCTCTT CTCTCGTCCATCCCAACGCCG TCTGCCACAC 24508 329 1.60e-09 ATTCCGAAGC TCCTCCTCGGCATCCATGCTG TACTCTGACG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 36738 1.9e-12 477_[+3]_2 7771 1.2e-10 60_[+3]_419 2737 1.5e-09 455_[+3]_24 24508 1.6e-09 328_[+3]_151 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=21 seqs=4 36738 ( 478) CCCTCCTCAACCACACTGCCG 1 7771 ( 61) CCGTCCTCTGCCGCTCTGCCG 1 2737 ( 456) CTCTCGTCCATCCCAACGCCG 1 24508 ( 329) TCCTCCTCGGCATCCATGCTG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 10080 bayes= 11.2986 E= 3.6e+002 -865 178 -865 -14 -865 178 -865 -14 -865 178 0 -865 -865 -865 -865 186 -865 219 -865 -865 -865 178 0 -865 -865 -865 -865 186 -865 219 -865 -865 -3 20 0 -14 96 -865 100 -865 -865 178 -865 -14 -3 178 -865 -865 -3 20 0 -14 -865 219 -865 -865 96 20 -865 -14 96 119 -865 -865 -865 20 -865 144 -865 -865 200 -865 -865 219 -865 -865 -865 178 -865 -14 -865 -865 200 -865 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 4 E= 3.6e+002 0.000000 0.750000 0.000000 0.250000 0.000000 0.750000 0.000000 0.250000 0.000000 0.750000 0.250000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.750000 0.250000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.250000 0.250000 0.250000 0.250000 0.500000 0.000000 0.500000 0.000000 0.000000 0.750000 0.000000 0.250000 0.250000 0.750000 0.000000 0.000000 0.250000 0.250000 0.250000 0.250000 0.000000 1.000000 0.000000 0.000000 0.500000 0.250000 0.000000 0.250000 0.500000 0.500000 0.000000 0.000000 0.000000 0.250000 0.000000 0.750000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.750000 0.000000 0.250000 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [CT][CT][CG]TC[CG]TC[ACGT][AG][CT][CA][ACGT]C[ACT][AC][TC]GC[CT]G -------------------------------------------------------------------------------- Time 13.55 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 10828 1.43e-01 500 11347 3.94e-04 270_[+2(2.60e-05)]_120_\ [+1(6.75e-06)]_86 21014 7.81e-03 481_[+1(4.47e-06)]_7 2244 3.06e-05 129_[+2(4.20e-06)]_296_\ [+1(4.13e-06)]_51 24218 1.22e-01 500 2433 2.21e-02 467_[+2(3.38e-05)]_21 24508 9.64e-08 168_[+1(4.13e-06)]_148_\ [+3(1.60e-09)]_151 262949 5.61e-03 268_[+1(2.49e-05)]_80_\ [+2(2.60e-05)]_128 263425 4.61e-04 118_[+2(1.54e-05)]_37_\ [+1(1.68e-05)]_321 263947 6.53e-02 130_[+1(2.29e-05)]_358 2737 3.33e-08 16_[+3(1.64e-06)]_195_\ [+2(1.37e-05)]_150_[+1(5.04e-05)]_49_[+3(1.49e-09)]_24 31375 2.90e-02 390_[+1(4.13e-06)]_98 35723 4.15e-06 57_[+1(1.57e-06)]_404_\ [+2(1.26e-07)]_15 35984 5.64e-04 94_[+2(2.60e-05)]_56_[+1(6.12e-06)]_\ 326 36738 1.46e-12 77_[+2(3.73e-07)]_372_\ [+1(3.03e-05)]_4_[+3(1.88e-12)]_2 3674 3.32e-01 500 5711 2.72e-03 32_[+1(6.00e-05)]_238_\ [+2(6.60e-06)]_206 6198 1.36e-04 189_[+2(6.60e-06)]_129_\ [+1(3.59e-05)]_158 7771 1.54e-10 60_[+3(1.18e-10)]_392_\ [+2(2.27e-07)]_15 9125 3.80e-04 402_[+1(8.22e-05)]_62_\ [+2(2.65e-07)]_12 9207 1.00e-01 414_[+1(3.26e-05)]_74 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************