******************************************************************************** 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/298/298.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 21313 1.0000 500 261186 1.0000 500 262047 1.0000 500 262261 1.0000 500 263682 1.0000 500 269333 1.0000 500 3017 1.0000 500 32329 1.0000 500 35095 1.0000 500 40473 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/298/298.seqs.fa -oc motifs/298 -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= 10 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= 5000 N= 10 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.286 C 0.211 G 0.250 T 0.253 Background letter frequencies (from dataset with add-one prior applied): A 0.286 C 0.211 G 0.250 T 0.253 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 21 sites = 7 llr = 120 E-value = 3.5e-002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A ::71:7343399:a91116:: pos.-specific C 99:7916376::a:1439:7a probability G :::1:111::1:::::1:1:: matrix T 113:1::1:1:1:::44:33: bits 2.2 * * 2.0 * * 1.8 ** * 1.6 ** * ** * * Relative 1.3 ** * * ***** * ** Entropy 1.1 ** * * ***** * ** (24.7 bits) 0.9 ***** * ***** * ** 0.7 ******* ******** * ** 0.4 ******* ******** **** 0.2 ********************* 0.0 --------------------- Multilevel CCACCACACCAACAACTCACC consensus T ACAA TC TT sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 269333 23 1.95e-10 ATCGCCATCA CCACCACTCAAACAATTCATC GCAGTGTCGT 261186 474 4.50e-10 GCGGGAAAAC CCACCAGCCCAACAACCAACC CTAAGC 35095 414 5.64e-10 CAATGGCAAG CCACCACCAAAACAACACTCC GAGAGGCTCA 263682 457 1.36e-08 TTGGACGCGA TCTGCCAACCAACAACTCACC TCCCCGAGTG 3017 47 3.02e-08 ATACATCAAG CCAACACACCGACACATCGCC AACAAACACA 40473 467 3.69e-08 ATTGGAGTCA CTTCCAAGACATCAATCCACC ACACAGCCGA 262261 333 3.69e-08 TCTCCTCTCT CCACTGCACTAACAATGCTTC TGTCCTTCCA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 269333 1.9e-10 22_[+1]_457 261186 4.5e-10 473_[+1]_6 35095 5.6e-10 413_[+1]_66 263682 1.4e-08 456_[+1]_23 3017 3e-08 46_[+1]_433 40473 3.7e-08 466_[+1]_13 262261 3.7e-08 332_[+1]_147 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=21 seqs=7 269333 ( 23) CCACCACTCAAACAATTCATC 1 261186 ( 474) CCACCAGCCCAACAACCAACC 1 35095 ( 414) CCACCACCAAAACAACACTCC 1 263682 ( 457) TCTGCCAACCAACAACTCACC 1 3017 ( 47) CCAACACACCGACACATCGCC 1 40473 ( 467) CTTCCAAGACATCAATCCACC 1 262261 ( 333) CCACTGCACTAACAATGCTTC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 4800 bayes= 10.0258 E= 3.5e-002 -945 202 -945 -82 -945 202 -945 -82 132 -945 -945 18 -100 176 -81 -945 -945 202 -945 -82 132 -56 -81 -945 0 144 -81 -945 58 44 -81 -82 0 176 -945 -945 0 144 -945 -82 158 -945 -81 -945 158 -945 -945 -82 -945 224 -945 -945 180 -945 -945 -945 158 -56 -945 -945 -100 102 -945 76 -100 44 -81 76 -100 202 -945 -945 100 -945 -81 18 -945 176 -945 18 -945 224 -945 -945 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 7 E= 3.5e-002 0.000000 0.857143 0.000000 0.142857 0.000000 0.857143 0.000000 0.142857 0.714286 0.000000 0.000000 0.285714 0.142857 0.714286 0.142857 0.000000 0.000000 0.857143 0.000000 0.142857 0.714286 0.142857 0.142857 0.000000 0.285714 0.571429 0.142857 0.000000 0.428571 0.285714 0.142857 0.142857 0.285714 0.714286 0.000000 0.000000 0.285714 0.571429 0.000000 0.142857 0.857143 0.000000 0.142857 0.000000 0.857143 0.000000 0.000000 0.142857 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.857143 0.142857 0.000000 0.000000 0.142857 0.428571 0.000000 0.428571 0.142857 0.285714 0.142857 0.428571 0.142857 0.857143 0.000000 0.000000 0.571429 0.000000 0.142857 0.285714 0.000000 0.714286 0.000000 0.285714 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- CC[AT]CCA[CA][AC][CA][CA]AACAA[CT][TC]C[AT][CT]C -------------------------------------------------------------------------------- Time 0.93 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 15 sites = 10 llr = 115 E-value = 5.8e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A :::8::8:3413::: pos.-specific C 311:132:1::3::: probability G 162:97:a4692a93 matrix T 6372::::2::2:17 bits 2.2 2.0 * * 1.8 * * 1.6 * * * ** Relative 1.3 * * * ** Entropy 1.1 ***** * *** (16.6 bits) 0.9 ****** ** *** 0.7 ******** ** *** 0.4 ******** ** *** 0.2 *********** *** 0.0 --------------- Multilevel TGTAGGAGGGGAGGT consensus CTGT CC AA C G sequence T G T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------- 40473 107 1.43e-08 AATTCACGTA CGTAGGAGGGGAGGT GGTGTGATGT 262047 146 3.25e-07 CGTCGGTCGG TGGAGGAGTGGAGGT TGAAGTGCCG 35095 248 5.29e-07 GGTTAAAAAC TGTAGCAGAGGTGGG AGAGCTCAAG 263682 173 1.36e-06 GAGGTGTTTG TTTAGCCGGAGAGGT AGAAAACCGA 261186 434 2.14e-06 GTCTTTGAAA CCTAGGAGAAGTGGT GCGCCAAGAG 262261 265 2.33e-06 AAAGGTACGA TTTTGGCGTGGCGGT GTCCATTGAT 269333 172 3.47e-06 AACTTCAGAC TGCACGAGAGGCGGT ATCTGCCGTG 32329 346 3.74e-06 ATGCAATGAA TGTAGGAGGAAGGGG TTGGATGTGA 21313 129 1.18e-05 TATCATTGTC CTGTGGAGGAGGGGG AGACGAGCAA 3017 170 1.24e-05 CCACTGACGT GGTAGCAGCGGCGTT GTTGGAGAAG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 40473 1.4e-08 106_[+2]_379 262047 3.3e-07 145_[+2]_340 35095 5.3e-07 247_[+2]_238 263682 1.4e-06 172_[+2]_313 261186 2.1e-06 433_[+2]_52 262261 2.3e-06 264_[+2]_221 269333 3.5e-06 171_[+2]_314 32329 3.7e-06 345_[+2]_140 21313 1.2e-05 128_[+2]_357 3017 1.2e-05 169_[+2]_316 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=15 seqs=10 40473 ( 107) CGTAGGAGGGGAGGT 1 262047 ( 146) TGGAGGAGTGGAGGT 1 35095 ( 248) TGTAGCAGAGGTGGG 1 263682 ( 173) TTTAGCCGGAGAGGT 1 261186 ( 434) CCTAGGAGAAGTGGT 1 262261 ( 265) TTTTGGCGTGGCGGT 1 269333 ( 172) TGCACGAGAGGCGGT 1 32329 ( 346) TGTAGGAGGAAGGGG 1 21313 ( 129) CTGTGGAGGAGGGGG 1 3017 ( 170) GGTAGCAGCGGCGTT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 4860 bayes= 9.17386 E= 5.8e-001 -997 51 -132 125 -997 -108 126 25 -997 -108 -32 147 148 -997 -997 -34 -997 -108 185 -997 -997 51 148 -997 148 -8 -997 -997 -997 -997 200 -997 7 -108 68 -34 48 -997 126 -997 -151 -997 185 -997 7 51 -32 -34 -997 -997 200 -997 -997 -997 185 -133 -997 -997 26 147 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 10 E= 5.8e-001 0.000000 0.300000 0.100000 0.600000 0.000000 0.100000 0.600000 0.300000 0.000000 0.100000 0.200000 0.700000 0.800000 0.000000 0.000000 0.200000 0.000000 0.100000 0.900000 0.000000 0.000000 0.300000 0.700000 0.000000 0.800000 0.200000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.300000 0.100000 0.400000 0.200000 0.400000 0.000000 0.600000 0.000000 0.100000 0.000000 0.900000 0.000000 0.300000 0.300000 0.200000 0.200000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.900000 0.100000 0.000000 0.000000 0.300000 0.700000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [TC][GT][TG][AT]G[GC][AC]G[GAT][GA]G[ACGT]GG[TG] -------------------------------------------------------------------------------- Time 1.86 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 12 sites = 10 llr = 102 E-value = 4.1e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A 2:1::3:8:92: pos.-specific C ::3:::::9:12 probability G 3a:a72921::: matrix T 5:6:351::178 bits 2.2 2.0 * * 1.8 * * * 1.6 * * * * Relative 1.3 * * * ** * Entropy 1.1 * ** **** * (14.7 bits) 0.9 * ** ****** 0.7 **** ****** 0.4 ************ 0.2 ************ 0.0 ------------ Multilevel TGTGGTGACATT consensus G C TA G AC sequence A G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 40473 354 6.99e-08 GTGGAGGGGG TGTGGTGACATT TTCCCCCTAG 32329 64 6.01e-06 ACAAGGCAAT GGTGGGGGCATT GAGTCAGCGT 261186 411 6.01e-06 TTGGTGGCGT TGTGGGGACACT GGTCTTTGAA 3017 285 8.46e-06 AGATATGTGA TGTGGAGAGATT GATTCAGAAT 269333 409 8.46e-06 TGATTGGCCT GGCGTTGACATC ACGTACCTCA 35095 445 9.36e-06 GAGAGGCTCA GGTGGTGACAAC AATGCCGGCA 262047 77 9.36e-06 TTATTGTAGT AGTGGTGACTTT GTAGTGTCGA 21313 71 1.33e-05 AAAAAGTCTT TGAGTAGACATT TCAAGTTGTT 262261 199 1.65e-05 CATCGTCAAT AGCGTTGGCATT GCTTTAGTTG 263682 84 3.90e-05 GCAGAAGAGA TGCGGATACAAT CAAAACGAAT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 40473 7e-08 353_[+3]_135 32329 6e-06 63_[+3]_425 261186 6e-06 410_[+3]_78 3017 8.5e-06 284_[+3]_204 269333 8.5e-06 408_[+3]_80 35095 9.4e-06 444_[+3]_44 262047 9.4e-06 76_[+3]_412 21313 1.3e-05 70_[+3]_418 262261 1.6e-05 198_[+3]_290 263682 3.9e-05 83_[+3]_405 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=12 seqs=10 40473 ( 354) TGTGGTGACATT 1 32329 ( 64) GGTGGGGGCATT 1 261186 ( 411) TGTGGGGACACT 1 3017 ( 285) TGTGGAGAGATT 1 269333 ( 409) GGCGTTGACATC 1 35095 ( 445) GGTGGTGACAAC 1 262047 ( 77) AGTGGTGACTTT 1 21313 ( 71) TGAGTAGACATT 1 262261 ( 199) AGCGTTGGCATT 1 263682 ( 84) TGCGGATACAAT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 4890 bayes= 8.93074 E= 4.1e+001 -52 -997 26 98 -997 -997 200 -997 -151 51 -997 125 -997 -997 200 -997 -997 -997 148 25 7 -997 -32 98 -997 -997 185 -133 148 -997 -32 -997 -997 209 -132 -997 165 -997 -997 -133 -52 -108 -997 147 -997 -8 -997 166 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 10 E= 4.1e+001 0.200000 0.000000 0.300000 0.500000 0.000000 0.000000 1.000000 0.000000 0.100000 0.300000 0.000000 0.600000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.700000 0.300000 0.300000 0.000000 0.200000 0.500000 0.000000 0.000000 0.900000 0.100000 0.800000 0.000000 0.200000 0.000000 0.000000 0.900000 0.100000 0.000000 0.900000 0.000000 0.000000 0.100000 0.200000 0.100000 0.000000 0.700000 0.000000 0.200000 0.000000 0.800000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [TGA]G[TC]G[GT][TAG]G[AG]CA[TA][TC] -------------------------------------------------------------------------------- Time 2.66 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 21313 4.62e-04 70_[+3(1.33e-05)]_46_[+2(1.18e-05)]_\ 357 261186 2.78e-10 59_[+3(5.43e-05)]_339_\ [+3(6.01e-06)]_11_[+2(2.14e-06)]_25_[+1(4.50e-10)]_6 262047 1.69e-05 76_[+3(9.36e-06)]_57_[+2(3.25e-07)]_\ 340 262261 4.47e-08 62_[+1(8.21e-05)]_115_\ [+3(1.65e-05)]_54_[+2(2.33e-06)]_53_[+1(3.69e-08)]_147 263682 2.39e-08 83_[+3(3.90e-05)]_77_[+2(1.36e-06)]_\ 269_[+1(1.36e-08)]_23 269333 2.75e-10 22_[+1(1.95e-10)]_128_\ [+2(3.47e-06)]_222_[+3(8.46e-06)]_80 3017 9.34e-08 46_[+1(3.02e-08)]_54_[+1(1.11e-05)]_\ 27_[+2(1.24e-05)]_100_[+3(8.46e-06)]_204 32329 1.89e-04 63_[+3(6.01e-06)]_222_\ [+3(6.93e-05)]_36_[+2(3.74e-06)]_140 35095 1.41e-10 247_[+2(5.29e-07)]_151_\ [+1(5.64e-10)]_10_[+3(9.36e-06)]_44 40473 2.45e-12 106_[+2(1.43e-08)]_181_\ [+2(3.74e-06)]_36_[+3(6.99e-08)]_101_[+1(3.69e-08)]_13 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************