******************************************************************************** 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/182/182.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 3171 1.0000 500 9547 1.0000 500 42957 1.0000 500 43202 1.0000 500 46372 1.0000 500 21535 1.0000 500 37571 1.0000 500 14212 1.0000 500 14572 1.0000 500 14927 1.0000 500 7018 1.0000 500 29658 1.0000 500 29660 1.0000 500 29711 1.0000 500 43498 1.0000 500 30436 1.0000 500 51242 1.0000 500 50014 1.0000 500 10209 1.0000 500 19093 1.0000 500 34457 1.0000 500 19705 1.0000 500 19901 1.0000 500 45476 1.0000 500 45580 1.0000 500 27190 1.0000 500 27518 1.0000 500 46109 1.0000 500 36198 1.0000 500 44243 1.0000 500 48364 1.0000 500 40425 1.0000 500 54465 1.0000 500 45287 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/182/182.seqs.fa -oc motifs/182 -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= 34 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= 17000 N= 34 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.259 C 0.248 G 0.227 T 0.265 Background letter frequencies (from dataset with add-one prior applied): A 0.259 C 0.248 G 0.227 T 0.265 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 12 sites = 19 llr = 192 E-value = 1.1e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 162::8:6:::8 pos.-specific C 625:3:a1:151 probability G 4:1:62::a:51 matrix T :23a1::4:9:: bits 2.1 * 1.9 * * * 1.7 * * ** 1.5 * * ** Relative 1.3 * ** ** * Entropy 1.1 * ** **** (14.5 bits) 0.9 * **** **** 0.6 ** ********* 0.4 ** ********* 0.2 ************ 0.0 ------------ Multilevel CACTGACAGTGA consensus GCT CG T C sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 27190 416 5.64e-08 GATTCGCAGT CACTGACAGTGA ATGGATCTCT 54465 288 1.70e-07 ACTCGTTTAT GACTGACAGTGA CGCCAATCCG 43498 140 7.66e-07 CACTCACTGT CACTCACAGTCA CTCACAGTCA 19093 220 2.10e-06 TTCGAACAGT GATTGACTGTGA ATCCTTGTGG 50014 134 2.38e-06 ACACATGTGA CACTGGCTGTGA ATAGGTGTAC 46109 296 3.99e-06 AACCCCGTGA GAATGACTGTGA CTTTTGACCA 34457 441 4.99e-06 GTCCATTCAA CATTCACTGTCA GCCTAGCTCC 45580 261 6.07e-06 CCCTGCCTGT CTCTCACAGTCA GTTTCAAGTC 45287 445 6.64e-06 CGCTTTTCAA CAGTCACAGTCA GTTGCGAAAA 36198 295 9.89e-06 GTTCGACAGG GACTGACTGTGG GCTATCTAGG 21535 222 1.73e-05 CTTCCGGGTT CTTTGGCAGTCA TTTTTCGGTC 29711 67 2.01e-05 CACGGAGTTG CCGTGGCAGTGA GGCTGTTTTA 43202 224 2.16e-05 TAACAGAAAG CAATGACCGTCA ACGACAAGCA 48364 93 2.50e-05 CCAGACGGTT GTCTCGCAGTCA AGTTGGTGTC 14572 33 2.85e-05 ATACACCTCA CATTGACTGCGA ATCCGATCTC 44243 311 3.06e-05 AGACTAGCGG CAATGACAGTCC AACAAACAAC 10209 155 3.06e-05 GAAAACAAGA GCCTTACAGTCA AAAGAGAGGA 29658 131 3.06e-05 TGACTCCCAA ACTTGACAGTGA ATAGGGGACA 7018 447 4.21e-05 CGGTACTCAA GCCTCACTGTGG GTGCTTTCAT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 27190 5.6e-08 415_[+1]_73 54465 1.7e-07 287_[+1]_201 43498 7.7e-07 139_[+1]_349 19093 2.1e-06 219_[+1]_269 50014 2.4e-06 133_[+1]_355 46109 4e-06 295_[+1]_193 34457 5e-06 440_[+1]_48 45580 6.1e-06 260_[+1]_228 45287 6.6e-06 444_[+1]_44 36198 9.9e-06 294_[+1]_194 21535 1.7e-05 221_[+1]_267 29711 2e-05 66_[+1]_422 43202 2.2e-05 223_[+1]_265 48364 2.5e-05 92_[+1]_396 14572 2.9e-05 32_[+1]_456 44243 3.1e-05 310_[+1]_178 10209 3.1e-05 154_[+1]_334 29658 3.1e-05 130_[+1]_358 7018 4.2e-05 446_[+1]_42 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=12 seqs=19 27190 ( 416) CACTGACAGTGA 1 54465 ( 288) GACTGACAGTGA 1 43498 ( 140) CACTCACAGTCA 1 19093 ( 220) GATTGACTGTGA 1 50014 ( 134) CACTGGCTGTGA 1 46109 ( 296) GAATGACTGTGA 1 34457 ( 441) CATTCACTGTCA 1 45580 ( 261) CTCTCACAGTCA 1 45287 ( 445) CAGTCACAGTCA 1 36198 ( 295) GACTGACTGTGG 1 21535 ( 222) CTTTGGCAGTCA 1 29711 ( 67) CCGTGGCAGTGA 1 43202 ( 224) CAATGACCGTCA 1 48364 ( 93) GTCTCGCAGTCA 1 14572 ( 33) CATTGACTGCGA 1 44243 ( 311) CAATGACAGTCC 1 10209 ( 155) GCCTTACAGTCA 1 29658 ( 131) ACTTGACAGTGA 1 7018 ( 447) GCCTCACTGTGG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 16626 bayes= 10.6698 E= 1.1e+000 -230 122 70 -1089 129 -24 -1089 -75 -71 93 -111 -1 -1089 -1089 -1089 191 -1089 35 147 -233 161 -1089 -11 -1089 -1089 201 -1089 -1089 116 -224 -1089 47 -1089 -1089 214 -1089 -1089 -224 -1089 184 -1089 93 121 -1089 170 -224 -111 -1089 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 19 E= 1.1e+000 0.052632 0.578947 0.368421 0.000000 0.631579 0.210526 0.000000 0.157895 0.157895 0.473684 0.105263 0.263158 0.000000 0.000000 0.000000 1.000000 0.000000 0.315789 0.631579 0.052632 0.789474 0.000000 0.210526 0.000000 0.000000 1.000000 0.000000 0.000000 0.578947 0.052632 0.000000 0.368421 0.000000 0.000000 1.000000 0.000000 0.000000 0.052632 0.000000 0.947368 0.000000 0.473684 0.526316 0.000000 0.842105 0.052632 0.105263 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [CG][AC][CT]T[GC][AG]C[AT]GT[GC]A -------------------------------------------------------------------------------- Time 10.23 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 16 sites = 12 llr = 152 E-value = 2.5e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A :15881::412::311 pos.-specific C a:5224a::8132369 probability G :9::11:a2:83813: matrix T :::::4::42:4:4:: bits 2.1 * 1.9 * ** 1.7 ** ** 1.5 ** ** * * Relative 1.3 ** * ** * * Entropy 1.1 **** ** * * * (18.3 bits) 0.9 ***** ** ** * ** 0.6 ***** ** ** * ** 0.4 ************* ** 0.2 **************** 0.0 ---------------- Multilevel CGAAACCGACGTGTCC consensus C T T C AG sequence G C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 14927 339 1.18e-09 AAGTGGCCTC CGAAACCGACGTGTCC TTTCGGCAGT 54465 357 2.99e-08 ACGACCGGCA CGCAACCGGCGCGTGC CCAATTTTGA 48364 68 1.41e-07 ACGCTACCTT CGAAAACGTCGCGTGC CAGACGGTTG 36198 437 1.61e-07 CGAAGCAGTT CGCAACCGTTGGGACC AAGAAGAAAG 9547 351 3.19e-07 GAGAGTGGCG CGAAATCGACAGGCGC GCGTTTGCAC 14212 356 3.79e-07 AAGCCATGGC CGAACTCGACATGTCC AAACAAACCG 19901 272 8.34e-07 TCGTACCGGT CGCCGCCGACGTGCCC TTTCCGCCAT 46372 432 1.61e-06 AAGGCGATGT CGCAAGCGGAGCGTCC GCGACTACCA 27190 485 1.98e-06 TCTCATTCTT CGAAATCGATCGGACC 29660 343 2.57e-06 CCTTCCCGAG CAAAATCGTCGTCCGC TCTTTTCCGC 51242 367 3.31e-06 CAGCACACGG CGCCATCGTCGCGGCA AAGCCACGGT 37571 20 3.31e-06 TTGGTGGAGT CGCACCCGTCGTCAAC GCGGCGGGAA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 14927 1.2e-09 338_[+2]_146 54465 3e-08 356_[+2]_128 48364 1.4e-07 67_[+2]_417 36198 1.6e-07 436_[+2]_48 9547 3.2e-07 350_[+2]_134 14212 3.8e-07 355_[+2]_129 19901 8.3e-07 271_[+2]_213 46372 1.6e-06 431_[+2]_53 27190 2e-06 484_[+2] 29660 2.6e-06 342_[+2]_142 51242 3.3e-06 366_[+2]_118 37571 3.3e-06 19_[+2]_465 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=16 seqs=12 14927 ( 339) CGAAACCGACGTGTCC 1 54465 ( 357) CGCAACCGGCGCGTGC 1 48364 ( 68) CGAAAACGTCGCGTGC 1 36198 ( 437) CGCAACCGTTGGGACC 1 9547 ( 351) CGAAATCGACAGGCGC 1 14212 ( 356) CGAACTCGACATGTCC 1 19901 ( 272) CGCCGCCGACGTGCCC 1 46372 ( 432) CGCAAGCGGAGCGTCC 1 27190 ( 485) CGAAATCGATCGGACC 1 29660 ( 343) CAAAATCGTCGTCCGC 1 51242 ( 367) CGCCATCGTCGCGGCA 1 37571 ( 20) CGCACCCGTCGTCAAC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 16490 bayes= 10.871 E= 2.5e+001 -1023 201 -1023 -1023 -163 -1023 201 -1023 95 101 -1023 -1023 168 -58 -1023 -1023 153 -58 -145 -1023 -163 75 -145 65 -1023 201 -1023 -1023 -1023 -1023 214 -1023 69 -1023 -45 65 -163 159 -1023 -67 -64 -157 172 -1023 -1023 42 14 65 -1023 -58 187 -1023 -5 1 -145 65 -163 123 55 -1023 -163 188 -1023 -1023 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 12 E= 2.5e+001 0.000000 1.000000 0.000000 0.000000 0.083333 0.000000 0.916667 0.000000 0.500000 0.500000 0.000000 0.000000 0.833333 0.166667 0.000000 0.000000 0.750000 0.166667 0.083333 0.000000 0.083333 0.416667 0.083333 0.416667 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.416667 0.000000 0.166667 0.416667 0.083333 0.750000 0.000000 0.166667 0.166667 0.083333 0.750000 0.000000 0.000000 0.333333 0.250000 0.416667 0.000000 0.166667 0.833333 0.000000 0.250000 0.250000 0.083333 0.416667 0.083333 0.583333 0.333333 0.000000 0.083333 0.916667 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- CG[AC]AA[CT]CG[AT]CG[TCG]G[TAC][CG]C -------------------------------------------------------------------------------- Time 20.02 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 19 sites = 4 llr = 83 E-value = 7.0e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A :::::::a3:::385a33: pos.-specific C :a::a:::8:::::::83: probability G a:88:aa::aa58:3:::a matrix T ::33:::::::5:33::5: bits 2.1 * ** ** * 1.9 ** **** ** * * 1.7 ** **** ** * * 1.5 ** **** ** * * Relative 1.3 *********** * ** * Entropy 1.1 ************** ** * (30.0 bits) 0.9 ************** ** * 0.6 ************** ** * 0.4 ******************* 0.2 ******************* 0.0 ------------------- Multilevel GCGGCGGACGGGGAAACTG consensus TT A TATG AA sequence T C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------------- 50014 259 4.20e-11 CTCCCGACAA GCGGCGGACGGTGAGACAG CGGGTTTGAT 10209 465 7.78e-11 TTGCACCATG GCGGCGGACGGGGAAAACG GTGGCGGAAT 30436 208 5.36e-10 TCTGGTTATG GCGTCGGACGGTAATACTG ACTTGACTTG 3171 312 5.78e-10 AGGTTCGGCA GCTGCGGAAGGGGTAACTG CTAACGGGTC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 50014 4.2e-11 258_[+3]_223 10209 7.8e-11 464_[+3]_17 30436 5.4e-10 207_[+3]_274 3171 5.8e-10 311_[+3]_170 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=19 seqs=4 50014 ( 259) GCGGCGGACGGTGAGACAG 1 10209 ( 465) GCGGCGGACGGGGAAAACG 1 30436 ( 208) GCGTCGGACGGTAATACTG 1 3171 ( 312) GCTGCGGAAGGGGTAACTG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 19 n= 16388 bayes= 12 E= 7.0e+001 -865 -865 213 -865 -865 201 -865 -865 -865 -865 172 -9 -865 -865 172 -9 -865 201 -865 -865 -865 -865 213 -865 -865 -865 213 -865 195 -865 -865 -865 -5 159 -865 -865 -865 -865 213 -865 -865 -865 213 -865 -865 -865 114 91 -5 -865 172 -865 153 -865 -865 -9 95 -865 14 -9 195 -865 -865 -865 -5 159 -865 -865 -5 1 -865 91 -865 -865 213 -865 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 19 nsites= 4 E= 7.0e+001 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.750000 0.250000 0.000000 0.000000 0.750000 0.250000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.250000 0.750000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.500000 0.500000 0.250000 0.000000 0.750000 0.000000 0.750000 0.000000 0.000000 0.250000 0.500000 0.000000 0.250000 0.250000 1.000000 0.000000 0.000000 0.000000 0.250000 0.750000 0.000000 0.000000 0.250000 0.250000 0.000000 0.500000 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- GC[GT][GT]CGGA[CA]GG[GT][GA][AT][AGT]A[CA][TAC]G -------------------------------------------------------------------------------- Time 29.20 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 3171 4.08e-06 217_[+3(3.08e-05)]_75_\ [+3(5.78e-10)]_170 9547 1.86e-03 350_[+2(3.19e-07)]_134 42957 2.31e-01 500 43202 4.65e-02 223_[+1(2.16e-05)]_265 46372 1.71e-02 431_[+2(1.61e-06)]_53 21535 2.92e-02 221_[+1(1.73e-05)]_267 37571 3.63e-03 19_[+2(3.31e-06)]_465 14212 1.21e-03 355_[+2(3.79e-07)]_129 14572 4.09e-02 32_[+1(2.85e-05)]_456 14927 2.83e-05 338_[+2(1.18e-09)]_146 7018 3.03e-02 446_[+1(4.21e-05)]_42 29658 1.06e-01 130_[+1(3.06e-05)]_358 29660 3.36e-02 342_[+2(2.57e-06)]_142 29711 1.04e-03 66_[+1(2.01e-05)]_88_[+2(2.74e-05)]_\ 318 43498 9.39e-03 139_[+1(7.66e-07)]_349 30436 7.05e-07 207_[+3(5.36e-10)]_274 51242 1.98e-02 366_[+2(3.31e-06)]_118 50014 1.99e-09 133_[+1(2.38e-06)]_113_\ [+3(4.20e-11)]_223 10209 4.73e-08 154_[+1(3.06e-05)]_298_\ [+3(7.78e-11)]_17 19093 2.42e-03 219_[+1(2.10e-06)]_21_\ [+1(1.07e-05)]_236 34457 1.60e-02 440_[+1(4.99e-06)]_48 19705 9.44e-01 500 19901 1.22e-03 214_[+2(7.85e-05)]_41_\ [+2(8.34e-07)]_213 45476 9.84e-01 500 45580 8.83e-04 133_[+2(2.27e-05)]_4_[+2(3.49e-05)]_\ 91_[+1(6.07e-06)]_5_[+1(6.54e-05)]_211 27190 3.13e-06 415_[+1(5.64e-08)]_57_\ [+2(1.98e-06)] 27518 8.76e-01 500 46109 2.74e-02 295_[+1(3.99e-06)]_193 36198 1.53e-05 67_[+1(6.54e-05)]_215_\ [+1(9.89e-06)]_130_[+2(1.61e-07)]_48 44243 9.39e-02 310_[+1(3.06e-05)]_178 48364 6.03e-05 67_[+2(1.41e-07)]_9_[+1(2.50e-05)]_\ 396 40425 8.23e-01 500 54465 2.56e-07 287_[+1(1.70e-07)]_57_\ [+2(2.99e-08)]_128 45287 3.46e-02 444_[+1(6.64e-06)]_44 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************