******************************************************************************** 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/255/255.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ bd1911 1.0000 500 ThpsCp075 1.0000 500 ThpsCp092 1.0000 500 ThpsCp142 1.0000 500 ThpsCt001 1.0000 500 ThpsCt002 1.0000 500 ThpsCt003 1.0000 500 ThpsCt004 1.0000 500 ThpsCt005 1.0000 500 ThpsCt008 1.0000 500 ThpsCt009 1.0000 500 ThpsCt010 1.0000 500 ThpsCt013 1.0000 500 ThpsCt023 1.0000 500 ThpsCt026 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/255/255.seqs.fa -oc motifs/255 -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= 15 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= 7500 N= 15 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.364 C 0.128 G 0.128 T 0.381 Background letter frequencies (from dataset with add-one prior applied): A 0.364 C 0.128 G 0.128 T 0.380 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 21 sites = 13 llr = 234 E-value = 1.4e-028 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A :::224:::425852:224:: pos.-specific C ::5:::222:81:3:888:27 probability G 82:575881::42::::::3: matrix T 285221::76:::282::653 bits 3.0 2.7 2.4 2.1 ** * Relative 1.8 * ** * *** Entropy 1.5 * ** * *** * (25.9 bits) 1.2 * * * ** * *** * 0.9 ******** *** *** * 0.6 ********************* 0.3 ********************* 0.0 --------------------- Multilevel GTTGGGGGTTCAAATCCCTTC consensus TGCA ACCCAAGGCAT AAGT sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- ThpsCt001 73 2.58e-13 GATTCTGAAA GTCGGGGGTTCGATTCCCTTC ATGCTTATTG ThpsCt008 20 3.71e-13 TAATCCGTAG GTTGGGGGTTCAAATCCCTTC ACCAGCTTGT ThpsCt023 413 7.37e-13 GAACTACGGT GTCAGGGGTTCGAATCCCTTC TTGCCCAATA ThpsCp092 229 7.37e-13 GAACTACGGT GTCAGGGGTTCGAATCCCTTC TTGCCCAATA ThpsCt010 339 1.11e-10 TAAGCCCAAG GTCGTAGGTTCAAATCCCACC AGAGCCATTT ThpsCt009 448 1.11e-10 TAAGCCCAAG GTCGTAGGTTCAAATCCCACC AGAGCCATTT ThpsCt004 16 2.75e-09 AGTTGTTCCA GGTTGGGGCACAACTCCAATT ATGGGTCTTA ThpsCt003 100 2.75e-09 AGTTGTTCCA GGTTGGGGCACAACTCCAATT ATGGGTCTTA ThpsCp142 94 1.90e-08 GATAGTAGGA TTTGAACCTACGGCACCCTGC TCCCAAAGCA ThpsCp075 182 1.90e-08 GATAGTAGGA TTTGAACCTACGGCACCCTGC TCCCAAAGCA ThpsCt002 454 2.50e-07 TGAAAAATGG GGTGGTGGTAAAATTTACTTC TAAACTTCAA ThpsCt026 59 6.70e-07 TAAATGGAAT TTCAGACGCTACAAATCCTGT ACCACGACCT bd1911 438 1.56e-06 TAAAATTTAG GTTTGGGCGTAAGATTAAAGT GGAAACCTTG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- ThpsCt001 2.6e-13 72_[+1]_407 ThpsCt008 3.7e-13 19_[+1]_460 ThpsCt023 7.4e-13 412_[+1]_67 ThpsCp092 7.4e-13 228_[+1]_251 ThpsCt010 1.1e-10 338_[+1]_141 ThpsCt009 1.1e-10 447_[+1]_32 ThpsCt004 2.7e-09 15_[+1]_464 ThpsCt003 2.7e-09 99_[+1]_380 ThpsCp142 1.9e-08 93_[+1]_386 ThpsCp075 1.9e-08 181_[+1]_298 ThpsCt002 2.5e-07 453_[+1]_26 ThpsCt026 6.7e-07 58_[+1]_421 bd1911 1.6e-06 437_[+1]_42 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=21 seqs=13 ThpsCt001 ( 73) GTCGGGGGTTCGATTCCCTTC 1 ThpsCt008 ( 20) GTTGGGGGTTCAAATCCCTTC 1 ThpsCt023 ( 413) GTCAGGGGTTCGAATCCCTTC 1 ThpsCp092 ( 229) GTCAGGGGTTCGAATCCCTTC 1 ThpsCt010 ( 339) GTCGTAGGTTCAAATCCCACC 1 ThpsCt009 ( 448) GTCGTAGGTTCAAATCCCACC 1 ThpsCt004 ( 16) GGTTGGGGCACAACTCCAATT 1 ThpsCt003 ( 100) GGTTGGGGCACAACTCCAATT 1 ThpsCp142 ( 94) TTTGAACCTACGGCACCCTGC 1 ThpsCp075 ( 182) TTTGAACCTACGGCACCCTGC 1 ThpsCt002 ( 454) GGTGGTGGTAAAATTTACTTC 1 ThpsCt026 ( 59) TTCAGACGCTACAAATCCTGT 1 bd1911 ( 438) GTTTGGGCGTAAGATTAAAGT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 7200 bayes= 10.2766 E= 1.4e-028 -1035 -1035 259 -72 -1035 -1035 85 102 -1035 185 -1035 50 -66 -1035 208 -72 -124 -1035 244 -130 8 -1035 208 -230 -1035 85 259 -1035 -1035 85 259 -1035 -1035 85 -73 86 8 -1035 -1035 69 -66 259 -1035 -1035 57 -73 159 -1035 108 -1035 85 -1035 57 126 -1035 -130 -66 -1035 -1035 102 -1035 259 -1035 -72 -124 272 -1035 -1035 -66 259 -1035 -1035 8 -1035 -1035 69 -1035 26 127 50 -1035 243 -1035 -31 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 13 E= 1.4e-028 0.000000 0.000000 0.769231 0.230769 0.000000 0.000000 0.230769 0.769231 0.000000 0.461538 0.000000 0.538462 0.230769 0.000000 0.538462 0.230769 0.153846 0.000000 0.692308 0.153846 0.384615 0.000000 0.538462 0.076923 0.000000 0.230769 0.769231 0.000000 0.000000 0.230769 0.769231 0.000000 0.000000 0.230769 0.076923 0.692308 0.384615 0.000000 0.000000 0.615385 0.230769 0.769231 0.000000 0.000000 0.538462 0.076923 0.384615 0.000000 0.769231 0.000000 0.230769 0.000000 0.538462 0.307692 0.000000 0.153846 0.230769 0.000000 0.000000 0.769231 0.000000 0.769231 0.000000 0.230769 0.153846 0.846154 0.000000 0.000000 0.230769 0.769231 0.000000 0.000000 0.384615 0.000000 0.000000 0.615385 0.000000 0.153846 0.307692 0.538462 0.000000 0.692308 0.000000 0.307692 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [GT][TG][TC][GAT]G[GA][GC][GC][TC][TA][CA][AG][AG][AC][TA][CT]C[CA][TA][TG][CT] -------------------------------------------------------------------------------- Time 1.81 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 18 sites = 8 llr = 156 E-value = 2.4e-015 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A 11:331::a1:33a:::3 pos.-specific C ::345:3::3a:8:31:: probability G 995:::6::6::::8:a8 matrix T ::34391a:::8:::9:: bits 3.0 * * 2.7 * * 2.4 ** * * 2.1 ** * * * Relative 1.8 ** * * * ** Entropy 1.5 ** ***** *** ** (28.1 bits) 1.2 *** ***** ****** 0.9 *** ****** ****** 0.6 *** ************** 0.3 ****************** 0.0 ------------------ Multilevel GGGCCTGTAGCTCAGTGG consensus CTA C C AA C A sequence TAT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------------ ThpsCt023 367 1.29e-12 AATATAGTTT GGGCTTGTAGCTCAGTGG ACTAGAGCAC ThpsCp092 183 1.29e-12 AATATAGTTT GGGCTTGTAGCTCAGTGG ACTAGAGCAC ThpsCt010 294 1.54e-12 TATAGTATAA GGCTCTGTAGCTCAGTGG TTAGAGCAGG ThpsCt009 403 1.54e-12 TATAGTATAA GGCTCTGTAGCTCAGTGG TTAGAGCAGG ThpsCt001 28 2.01e-09 GTATTTCACA AAGCATGTAGCTCAGTGG ATAGAGCATC ThpsCt004 418 2.54e-08 CAATGCGGAT GGGTAATTAACTCAGCGG TAGAGTGTCT ThpsCp142 125 3.63e-08 TCCCAAAGCA GGTACTCTACCAAACTGA GCTATATCCC ThpsCp075 213 3.63e-08 TCCCAAAGCA GGTACTCTACCAAACTGA GCTATATCCC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- ThpsCt023 1.3e-12 366_[+2]_116 ThpsCp092 1.3e-12 182_[+2]_300 ThpsCt010 1.5e-12 293_[+2]_189 ThpsCt009 1.5e-12 402_[+2]_80 ThpsCt001 2e-09 27_[+2]_455 ThpsCt004 2.5e-08 417_[+2]_65 ThpsCp142 3.6e-08 124_[+2]_358 ThpsCp075 3.6e-08 212_[+2]_270 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=18 seqs=8 ThpsCt023 ( 367) GGGCTTGTAGCTCAGTGG 1 ThpsCp092 ( 183) GGGCTTGTAGCTCAGTGG 1 ThpsCt010 ( 294) GGCTCTGTAGCTCAGTGG 1 ThpsCt009 ( 403) GGCTCTGTAGCTCAGTGG 1 ThpsCt001 ( 28) AAGCATGTAGCTCAGTGG 1 ThpsCt004 ( 418) GGGTAATTAACTCAGCGG 1 ThpsCp142 ( 125) GGTACTCTACCAAACTGA 1 ThpsCp075 ( 213) GGTACTCTACCAAACTGA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 18 n= 7245 bayes= 10.5588 E= 2.4e-015 -154 -965 278 -965 -154 -965 278 -965 -965 96 197 -60 -54 155 -965 -2 -54 196 -965 -60 -154 -965 -965 120 -965 96 229 -160 -965 -965 -965 139 146 -965 -965 -965 -154 96 229 -965 -965 296 -965 -965 -54 -965 -965 98 -54 255 -965 -965 146 -965 -965 -965 -965 96 255 -965 -965 -3 -965 120 -965 -965 297 -965 -54 -965 255 -965 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 18 nsites= 8 E= 2.4e-015 0.125000 0.000000 0.875000 0.000000 0.125000 0.000000 0.875000 0.000000 0.000000 0.250000 0.500000 0.250000 0.250000 0.375000 0.000000 0.375000 0.250000 0.500000 0.000000 0.250000 0.125000 0.000000 0.000000 0.875000 0.000000 0.250000 0.625000 0.125000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.125000 0.250000 0.625000 0.000000 0.000000 1.000000 0.000000 0.000000 0.250000 0.000000 0.000000 0.750000 0.250000 0.750000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.250000 0.750000 0.000000 0.000000 0.125000 0.000000 0.875000 0.000000 0.000000 1.000000 0.000000 0.250000 0.000000 0.750000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- GG[GCT][CTA][CAT]T[GC]TA[GC]C[TA][CA]A[GC]TG[GA] -------------------------------------------------------------------------------- Time 3.64 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 21 sites = 7 llr = 141 E-value = 2.9e-008 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A :a::91:1:6::36:a7:16: pos.-specific C 1::9:33::19:441::3636 probability G 9:a:1363a3::::6::6::4 matrix T :::1:316::1a3:3:3131: bits 3.0 * * 2.7 * * 2.4 * * * 2.1 * ** * * * Relative 1.8 * ** * * * Entropy 1.5 **** * * ** * * * (29.1 bits) 1.2 ***** * * ** *** * * 0.9 ***** * * ** *** ** * 0.6 ***** *************** 0.3 ********************* 0.0 --------------------- Multilevel GAGCACGTGACTCAGAAGCAC consensus GCG G ACT TCTCG sequence T T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- ThpsCt010 315 5.80e-13 TCAGTGGTTA GAGCAGGGGACTCATAAGCCC AAGGTCGTAG ThpsCt009 424 5.80e-13 TCAGTGGTTA GAGCAGGGGACTCATAAGCCC AAGGTCGTAG ThpsCt023 389 1.03e-11 CAGTGGACTA GAGCACGTGGCTACGAACTAC GGTGTCAGGG ThpsCp092 205 1.03e-11 CAGTGGACTA GAGCACGTGGCTACGAACTAC GGTGTCAGGG ThpsCt004 438 5.12e-09 CTCAGCGGTA GAGTGTCTGCCTTACAAGCAG AAGGTCACAG ThpsCt001 49 1.29e-08 TCAGTGGATA GAGCATCAGATTCCGATTCTG AAAGTCGGGG ThpsCt002 59 2.11e-08 GTAAGTGCAT CAGCAATTGACTTAGATGAAG CGACAAGAAC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- ThpsCt010 5.8e-13 314_[+3]_165 ThpsCt009 5.8e-13 423_[+3]_56 ThpsCt023 1e-11 388_[+3]_91 ThpsCp092 1e-11 204_[+3]_275 ThpsCt004 5.1e-09 437_[+3]_42 ThpsCt001 1.3e-08 48_[+3]_431 ThpsCt002 2.1e-08 58_[+3]_421 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=21 seqs=7 ThpsCt010 ( 315) GAGCAGGGGACTCATAAGCCC 1 ThpsCt009 ( 424) GAGCAGGGGACTCATAAGCCC 1 ThpsCt023 ( 389) GAGCACGTGGCTACGAACTAC 1 ThpsCp092 ( 205) GAGCACGTGGCTACGAACTAC 1 ThpsCt004 ( 438) GAGTGTCTGCCTTACAAGCAG 1 ThpsCt001 ( 49) GAGCATCAGATTCCGATTCTG 1 ThpsCt002 ( 59) CAGCAATTGACTTAGATGAAG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 7200 bayes= 11.2282 E= 2.9e-008 -945 16 275 -945 146 -945 -945 -945 -945 -945 297 -945 -945 274 -945 -141 124 -945 16 -945 -135 116 116 -41 -945 116 216 -141 -135 -945 116 59 -945 -945 297 -945 65 16 116 -945 -945 274 -945 -141 -945 -945 -945 139 -35 174 -945 -41 65 174 -945 -945 -945 16 216 -41 146 -945 -945 -945 97 -945 -945 -41 -945 116 216 -141 -135 216 -945 -41 65 116 -945 -141 -945 216 175 -945 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 7 E= 2.9e-008 0.000000 0.142857 0.857143 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.857143 0.000000 0.142857 0.857143 0.000000 0.142857 0.000000 0.142857 0.285714 0.285714 0.285714 0.000000 0.285714 0.571429 0.142857 0.142857 0.000000 0.285714 0.571429 0.000000 0.000000 1.000000 0.000000 0.571429 0.142857 0.285714 0.000000 0.000000 0.857143 0.000000 0.142857 0.000000 0.000000 0.000000 1.000000 0.285714 0.428571 0.000000 0.285714 0.571429 0.428571 0.000000 0.000000 0.000000 0.142857 0.571429 0.285714 1.000000 0.000000 0.000000 0.000000 0.714286 0.000000 0.000000 0.285714 0.000000 0.285714 0.571429 0.142857 0.142857 0.571429 0.000000 0.285714 0.571429 0.285714 0.000000 0.142857 0.000000 0.571429 0.428571 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- GAGCA[CGT][GC][TG]G[AG]CT[CAT][AC][GT]A[AT][GC][CT][AC][CG] -------------------------------------------------------------------------------- Time 5.41 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- bd1911 9.02e-04 109_[+3(3.38e-05)]_307_\ [+1(1.56e-06)]_42 ThpsCp075 3.22e-08 181_[+1(1.90e-08)]_10_\ [+2(3.63e-08)]_270 ThpsCp092 2.17e-24 182_[+2(1.29e-12)]_4_[+3(1.03e-11)]_\ 3_[+1(7.37e-13)]_110_[+1(1.76e-05)]_120 ThpsCp142 3.22e-08 93_[+1(1.90e-08)]_10_[+2(3.63e-08)]_\ 358 ThpsCt001 9.16e-19 27_[+2(2.01e-09)]_3_[+3(1.29e-08)]_\ 3_[+1(2.58e-13)]_374_[+1(4.99e-07)]_12 ThpsCt002 1.97e-07 58_[+3(2.11e-08)]_374_\ [+1(2.50e-07)]_26 ThpsCt003 2.33e-05 99_[+1(2.75e-09)]_380 ThpsCt004 2.99e-14 15_[+1(2.75e-09)]_381_\ [+2(2.54e-08)]_2_[+3(5.12e-09)]_42 ThpsCt005 9.17e-01 500 ThpsCt008 2.15e-08 19_[+1(3.71e-13)]_54_[+1(5.95e-05)]_\ 56_[+1(4.68e-05)]_308 ThpsCt009 2.05e-23 72_[+1(4.68e-05)]_309_\ [+2(1.54e-12)]_3_[+3(5.80e-13)]_3_[+1(1.11e-10)]_32 ThpsCt010 2.05e-23 293_[+2(1.54e-12)]_3_[+3(5.80e-13)]_\ 3_[+1(1.11e-10)]_141 ThpsCt013 7.98e-01 500 ThpsCt023 2.17e-24 366_[+2(1.29e-12)]_4_[+3(1.03e-11)]_\ 3_[+1(7.37e-13)]_67 ThpsCt026 2.15e-03 58_[+1(6.70e-07)]_421 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************