******************************************************************************** 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/145/145.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 1339 1.0000 500 29789 1.0000 500 2988 1.0000 500 37058 1.0000 500 5204 1.0000 500 8355 1.0000 500 9722 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/145/145.seqs.fa -oc motifs/145 -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= 7 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= 3500 N= 7 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.238 C 0.229 G 0.261 T 0.271 Background letter frequencies (from dataset with add-one prior applied): A 0.238 C 0.229 G 0.261 T 0.271 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 21 sites = 6 llr = 106 E-value = 1.5e-002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 25:5383:::2235::5::52 pos.-specific C 8223:2:2aa2852aa:aa:7 probability G :2::::23::::::::3:::: matrix T :2827:55::7:23::2::52 bits 2.1 ** ** ** 1.9 ** ** ** 1.7 ** ** ** 1.5 * * ** * ** ** Relative 1.3 * * * ** * ** ** Entropy 1.1 * * ** ** * ** *** (25.4 bits) 0.8 * * ** ** * ** **** 0.6 * **** ************* 0.4 * ******************* 0.2 ********************* 0.0 --------------------- Multilevel CATATATTCCTCCACCACCAC consensus CA AG AT G T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 37058 33 6.84e-12 GTAGTTCGTT CATATATTCCTCATCCACCTC TCGTAAAACA 29789 478 6.84e-12 GTAGTTCGTT CATATATTCCTCATCCACCTC TC 2988 115 1.58e-09 TTGGCGCTTC CATCTAATCCACCACCGCCAT TGGTTTCGTT 8355 467 1.68e-08 TTACACTGCC CTTCTCTGCCTCCACCTCCAA GAAAACGACA 5204 311 3.50e-08 CGCCTGGTCT CCCAAAGCCCTACACCGCCAC TCTCATCCTA 1339 451 8.40e-08 TCAAGCTACA AGTTAAAGCCCCTCCCACCTC CTCTCACCGT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 37058 6.8e-12 32_[+1]_447 29789 6.8e-12 477_[+1]_2 2988 1.6e-09 114_[+1]_365 8355 1.7e-08 466_[+1]_13 5204 3.5e-08 310_[+1]_169 1339 8.4e-08 450_[+1]_29 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=21 seqs=6 37058 ( 33) CATATATTCCTCATCCACCTC 1 29789 ( 478) CATATATTCCTCATCCACCTC 1 2988 ( 115) CATCTAATCCACCACCGCCAT 1 8355 ( 467) CTTCTCTGCCTCCACCTCCAA 1 5204 ( 311) CCCAAAGCCCTACACCGCCAC 1 1339 ( 451) AGTTAAAGCCCCTCCCACCTC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 3360 bayes= 10.2276 E= 1.5e-002 -51 186 -923 -923 107 -46 -65 -70 -923 -46 -923 162 107 54 -923 -70 49 -923 -923 130 181 -46 -923 -923 49 -923 -65 88 -923 -46 35 88 -923 212 -923 -923 -923 212 -923 -923 -51 -46 -923 130 -51 186 -923 -923 49 112 -923 -70 107 -46 -923 30 -923 212 -923 -923 -923 212 -923 -923 107 -923 35 -70 -923 212 -923 -923 -923 212 -923 -923 107 -923 -923 88 -51 154 -923 -70 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 6 E= 1.5e-002 0.166667 0.833333 0.000000 0.000000 0.500000 0.166667 0.166667 0.166667 0.000000 0.166667 0.000000 0.833333 0.500000 0.333333 0.000000 0.166667 0.333333 0.000000 0.000000 0.666667 0.833333 0.166667 0.000000 0.000000 0.333333 0.000000 0.166667 0.500000 0.000000 0.166667 0.333333 0.500000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.166667 0.166667 0.000000 0.666667 0.166667 0.833333 0.000000 0.000000 0.333333 0.500000 0.000000 0.166667 0.500000 0.166667 0.000000 0.333333 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.500000 0.000000 0.333333 0.166667 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.500000 0.000000 0.000000 0.500000 0.166667 0.666667 0.000000 0.166667 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- CAT[AC][TA]A[TA][TG]CCTC[CA][AT]CC[AG]CC[AT]C -------------------------------------------------------------------------------- Time 0.51 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 21 sites = 7 llr = 113 E-value = 1.6e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A :313:::11:::133:1:333 pos.-specific C ::7:::6::41:96739:47: probability G 171:a9171:93:::::3::7 matrix T 9::7:13176:7:1:7:73:: bits 2.1 1.9 * 1.7 * 1.5 * * * Relative 1.3 * ** * * * * * Entropy 1.1 ** *** **** **** ** (23.3 bits) 0.8 ****** ****** **** ** 0.6 ****************** ** 0.4 ********************* 0.2 ********************* 0.0 --------------------- Multilevel TGCTGGCGTTGTCCCTCTCCG consensus A A T C G AAC GAAA sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 37058 2 2.05e-11 A TACTGGCGTTGTCCCCCTCCG GTAGTTCGTT 29789 447 2.05e-11 GAAAAAAAGA TACTGGCGTTGTCCCCCTCCG GTAGTTCGTT 8355 393 1.07e-08 AATGACAAAC TGCTGGTTTTGTCACTCGACA CTGTGTTCGT 9722 204 1.33e-08 TGAGGCACCG TGGTGGCGACGGCTCTCTCCG ACGAGGATGC 1339 341 1.01e-07 TTCGTACCAT TGCTGTCGTCGGACATCGTAG GGAGCTGTCT 5204 254 2.55e-07 CGTTTGTCAG TGAAGGTGTCGTCAATATAAA TGTGACGGGA 2988 198 3.05e-07 CGAATACGGA GGCAGGGAGTCTCCCTCTTCG ACGTCGTCGG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 37058 2e-11 1_[+2]_478 29789 2e-11 446_[+2]_33 8355 1.1e-08 392_[+2]_87 9722 1.3e-08 203_[+2]_276 1339 1e-07 340_[+2]_139 5204 2.6e-07 253_[+2]_226 2988 3.1e-07 197_[+2]_282 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=21 seqs=7 37058 ( 2) TACTGGCGTTGTCCCCCTCCG 1 29789 ( 447) TACTGGCGTTGTCCCCCTCCG 1 8355 ( 393) TGCTGGTTTTGTCACTCGACA 1 9722 ( 204) TGGTGGCGACGGCTCTCTCCG 1 1339 ( 341) TGCTGTCGTCGGACATCGTAG 1 5204 ( 254) TGAAGGTGTCGTCAATATAAA 1 2988 ( 198) GGCAGGGAGTCTCCCTCTTCG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 3360 bayes= 9.51064 E= 1.6e+000 -945 -945 -87 166 26 -945 145 -945 -74 164 -87 -945 26 -945 -945 140 -945 -945 193 -945 -945 -945 171 -92 -945 132 -87 8 -74 -945 145 -92 -74 -945 -87 140 -945 90 -945 107 -945 -68 171 -945 -945 -945 13 140 -74 190 -945 -945 26 132 -945 -92 26 164 -945 -945 -945 32 -945 140 -74 190 -945 -945 -945 -945 13 140 26 90 -945 8 26 164 -945 -945 26 -945 145 -945 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 7 E= 1.6e+000 0.000000 0.000000 0.142857 0.857143 0.285714 0.000000 0.714286 0.000000 0.142857 0.714286 0.142857 0.000000 0.285714 0.000000 0.000000 0.714286 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.857143 0.142857 0.000000 0.571429 0.142857 0.285714 0.142857 0.000000 0.714286 0.142857 0.142857 0.000000 0.142857 0.714286 0.000000 0.428571 0.000000 0.571429 0.000000 0.142857 0.857143 0.000000 0.000000 0.000000 0.285714 0.714286 0.142857 0.857143 0.000000 0.000000 0.285714 0.571429 0.000000 0.142857 0.285714 0.714286 0.000000 0.000000 0.000000 0.285714 0.000000 0.714286 0.142857 0.857143 0.000000 0.000000 0.000000 0.000000 0.285714 0.714286 0.285714 0.428571 0.000000 0.285714 0.285714 0.714286 0.000000 0.000000 0.285714 0.000000 0.714286 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- T[GA]C[TA]GG[CT]GT[TC]G[TG]C[CA][CA][TC]C[TG][CAT][CA][GA] -------------------------------------------------------------------------------- Time 1.05 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 15 sites = 7 llr = 90 E-value = 1.1e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A ::6:3a1:4464:1a pos.-specific C :a:37:11114:69: probability G ::1:::::41:6::: matrix T a:37::79:3::4:: bits 2.1 * * * 1.9 ** * * 1.7 ** * * 1.5 ** * ** Relative 1.3 ** ** * ** Entropy 1.1 ** *** * ***** (18.6 bits) 0.8 ** ***** ***** 0.6 ********* ***** 0.4 ********* ***** 0.2 *************** 0.0 --------------- Multilevel TCATCATTAAAGCCA consensus TCA GTCAT sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------- 8355 364 2.62e-08 GACCCGGCAT TCTTCATTAAAACCA CAATAATGAC 29789 418 1.18e-07 AAATACTTGG TCACAATTGAAGCCA CTGGGAAAAA 2988 54 5.57e-07 CATGAAGGGT TCATCATCATCGTCA ACGATGGAGA 1339 296 6.68e-07 AGAAGGGTCC TCTTCATTGGCATCA GCGCCGTCTA 5204 17 1.08e-06 GAGTGGTTGC TCATCAATCCAGCCA ACGATGGCAT 9722 258 1.34e-06 ATCTATAACG TCGTAATTATCGTCA AGGATTTTTT 37058 418 1.96e-06 GAAAGCACAG TCACCACTGAAACAA CTGAAAGCGA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 8355 2.6e-08 363_[+3]_122 29789 1.2e-07 417_[+3]_68 2988 5.6e-07 53_[+3]_432 1339 6.7e-07 295_[+3]_190 5204 1.1e-06 16_[+3]_469 9722 1.3e-06 257_[+3]_228 37058 2e-06 417_[+3]_68 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=15 seqs=7 8355 ( 364) TCTTCATTAAAACCA 1 29789 ( 418) TCACAATTGAAGCCA 1 2988 ( 54) TCATCATCATCGTCA 1 1339 ( 296) TCTTCATTGGCATCA 1 5204 ( 17) TCATCAATCCAGCCA 1 9722 ( 258) TCGTAATTATCGTCA 1 37058 ( 418) TCACCACTGAAACAA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 3402 bayes= 8.92184 E= 1.1e+001 -945 -945 -945 188 -945 212 -945 -945 126 -945 -87 8 -945 32 -945 140 26 164 -945 -945 207 -945 -945 -945 -74 -68 -945 140 -945 -68 -945 166 85 -68 71 -945 85 -68 -87 8 126 90 -945 -945 85 -945 113 -945 -945 132 -945 66 -74 190 -945 -945 207 -945 -945 -945 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 7 E= 1.1e+001 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.571429 0.000000 0.142857 0.285714 0.000000 0.285714 0.000000 0.714286 0.285714 0.714286 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.142857 0.142857 0.000000 0.714286 0.000000 0.142857 0.000000 0.857143 0.428571 0.142857 0.428571 0.000000 0.428571 0.142857 0.142857 0.285714 0.571429 0.428571 0.000000 0.000000 0.428571 0.000000 0.571429 0.000000 0.000000 0.571429 0.000000 0.428571 0.142857 0.857143 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- TC[AT][TC][CA]ATT[AG][AT][AC][GA][CT]CA -------------------------------------------------------------------------------- Time 1.58 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 1339 2.70e-10 295_[+3(6.68e-07)]_30_\ [+2(1.01e-07)]_89_[+1(8.40e-08)]_29 29789 2.20e-18 417_[+3(1.18e-07)]_14_\ [+2(2.05e-11)]_10_[+1(6.84e-12)]_2 2988 1.55e-11 53_[+3(5.57e-07)]_46_[+1(1.58e-09)]_\ 62_[+2(3.05e-07)]_282 37058 3.25e-17 1_[+2(2.05e-11)]_10_[+1(6.84e-12)]_\ 364_[+3(1.96e-06)]_68 5204 4.42e-10 16_[+3(1.08e-06)]_222_\ [+2(2.55e-07)]_36_[+1(3.50e-08)]_169 8355 3.46e-13 363_[+3(2.62e-08)]_14_\ [+2(1.07e-08)]_53_[+1(1.68e-08)]_13 9722 5.98e-07 203_[+2(1.33e-08)]_33_\ [+3(1.34e-06)]_228 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************