******************************************************************************** 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/295/295.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 1150 1.0000 500 22323 1.0000 500 24776 1.0000 500 260786 1.0000 500 261017 1.0000 500 261719 1.0000 500 262503 1.0000 500 264065 1.0000 500 268443 1.0000 500 270389 1.0000 500 4853 1.0000 500 5017 1.0000 500 5197 1.0000 500 6953 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/295/295.seqs.fa -oc motifs/295 -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= 14 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= 7000 N= 14 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.255 C 0.235 G 0.239 T 0.270 Background letter frequencies (from dataset with add-one prior applied): A 0.255 C 0.235 G 0.239 T 0.270 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 16 sites = 14 llr = 164 E-value = 5.3e-006 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 4:541164:194:31: pos.-specific C 395:483499:4966a probability G :1:2:1:2::1:1::: matrix T 3::44:1:1::1:14: bits 2.1 * 1.9 * 1.7 * * * 1.5 * *** * * Relative 1.3 * *** * * Entropy 1.0 ** * *** * * (16.9 bits) 0.8 ** ** *** **** 0.6 ** *** ******** 0.4 **************** 0.2 **************** 0.0 ---------------- Multilevel ACATCCACCCAACCCC consensus C CAT CA C AT sequence T G G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 5197 457 2.37e-08 TTGACCAACC TCAACCAACCACCCCC CTTCCACCCC 1150 470 4.32e-08 CTTAACTCCC TCATCCACCCAACCTC ATCATTCAGT 24776 368 3.57e-07 TAGACGAACG ACAAACAACCAACACC GACCGACAAC 4853 452 4.00e-07 TCTCATGCTG ACCGCGAACCAACCCC CGGAGACGAC 270389 87 8.63e-07 CTCGTTGTCC ACAGTCAGCCACGCCC TCGAGAAACC 268443 86 8.63e-07 CTCGTTGTCC ACAGTCAGCCACGCCC TCGAGAAACC 261017 484 1.84e-06 ATCCATCCAC CCCTCCCGCCGCCCTC G 5017 417 2.76e-06 ATCGTCCATC ACATCAACTCACCCCC ATCATCACGC 22323 422 3.47e-06 GGTCCGTCAA CCCTACCACCACCTCC TGCCTCCTCT 6953 362 4.67e-06 TCCTCGCTAG TCCTTCCACCGTCCTC ACTAGAAGAA 262503 461 4.67e-06 AAAGCAAATG AGCACCCCCCAACATC CGATGAGATC 260786 397 5.02e-06 GCTCTCTACT CCAATCTCCCAACCAC AAGCGCTGTG 261719 485 5.40e-06 CTCTCTCTCC CCCATCACCAATCACC 264065 470 8.15e-06 CCTTCACCTC TCCTTGACTCAACATC ACCCGTCCAA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 5197 2.4e-08 456_[+1]_28 1150 4.3e-08 469_[+1]_15 24776 3.6e-07 367_[+1]_117 4853 4e-07 451_[+1]_33 270389 8.6e-07 86_[+1]_398 268443 8.6e-07 85_[+1]_399 261017 1.8e-06 483_[+1]_1 5017 2.8e-06 416_[+1]_68 22323 3.5e-06 421_[+1]_63 6953 4.7e-06 361_[+1]_123 262503 4.7e-06 460_[+1]_24 260786 5e-06 396_[+1]_88 261719 5.4e-06 484_[+1] 264065 8.2e-06 469_[+1]_15 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=16 seqs=14 5197 ( 457) TCAACCAACCACCCCC 1 1150 ( 470) TCATCCACCCAACCTC 1 24776 ( 368) ACAAACAACCAACACC 1 4853 ( 452) ACCGCGAACCAACCCC 1 270389 ( 87) ACAGTCAGCCACGCCC 1 268443 ( 86) ACAGTCAGCCACGCCC 1 261017 ( 484) CCCTCCCGCCGCCCTC 1 5017 ( 417) ACATCAACTCACCCCC 1 22323 ( 422) CCCTACCACCACCTCC 1 6953 ( 362) TCCTTCCACCGTCCTC 1 262503 ( 461) AGCACCCCCCAACATC 1 260786 ( 397) CCAATCTCCCAACCAC 1 261719 ( 485) CCCATCACCAATCACC 1 264065 ( 470) TCCTTGACTCAACATC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 6790 bayes= 9.52561 E= 5.3e-006 75 28 -1045 8 -1045 198 -174 -1045 97 109 -1045 -1045 48 -1045 -16 66 -84 87 -1045 66 -184 174 -74 -1045 133 28 -1045 -192 48 87 -16 -1045 -1045 187 -1045 -92 -184 198 -1045 -1045 175 -1045 -74 -1045 75 87 -1045 -92 -1045 187 -74 -1045 16 145 -1045 -192 -184 128 -1045 40 -1045 209 -1045 -1045 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 14 E= 5.3e-006 0.428571 0.285714 0.000000 0.285714 0.000000 0.928571 0.071429 0.000000 0.500000 0.500000 0.000000 0.000000 0.357143 0.000000 0.214286 0.428571 0.142857 0.428571 0.000000 0.428571 0.071429 0.785714 0.142857 0.000000 0.642857 0.285714 0.000000 0.071429 0.357143 0.428571 0.214286 0.000000 0.000000 0.857143 0.000000 0.142857 0.071429 0.928571 0.000000 0.000000 0.857143 0.000000 0.142857 0.000000 0.428571 0.428571 0.000000 0.142857 0.000000 0.857143 0.142857 0.000000 0.285714 0.642857 0.000000 0.071429 0.071429 0.571429 0.000000 0.357143 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [ACT]C[AC][TAG][CT]C[AC][CAG]CCA[AC]C[CA][CT]C -------------------------------------------------------------------------------- Time 1.86 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 12 sites = 14 llr = 142 E-value = 9.5e-004 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A :933a8:972:6 pos.-specific C 1:11:1::::2: probability G 9146:1a11873 matrix T ::2:::::2:11 bits 2.1 * 1.9 * * 1.7 ** * * 1.5 ** * ** Relative 1.3 ** * ** * Entropy 1.0 ** **** ** (14.6 bits) 0.8 ** ********* 0.6 ** ********* 0.4 ** ********* 0.2 ** ********* 0.0 ------------ Multilevel GAGGAAGAAGGA consensus AA TACG sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 5017 335 5.12e-08 CGTGATGGTT GAGGAAGAAGGA CAACCTGTGC 270389 258 1.06e-07 TGCCAGGAAG GAAGAAGAAGGA GTATGGCGAG 268443 257 1.06e-07 TGCCAGGAAG GAAGAAGAAGGA GTATGGCGAG 24776 187 1.50e-06 ATGGTTTGGA GAGGAAGAAGCG GTTGTTGTTG 264065 117 4.78e-06 ACATCTGCCA GATGAAGAGGGA TTTTGGTTGA 261719 368 6.26e-06 ACAGTGAGGG GACAAAGAAAGA CGGTTTGTCA 1150 34 8.09e-06 TGTCGTCATT GGGAAAGAAGGA CATCATTGAC 6953 250 9.13e-06 TGAACCATTA GAAGAAGATGCG GATGGAGAAC 261017 18 1.06e-05 AATACAGGTG GATGAAGGAGCA AGGCGCGTCG 4853 264 1.77e-05 AGTTTTGTAG GAGCAAGATGGG CGGGTTCGTC 260786 73 2.22e-05 CGGCGGCGGC GACGACGATGGA AACATTCAAC 5197 380 5.59e-05 AATTGAACCC GAGAAGGAAGTG GGTGGGTGGG 262503 301 6.20e-05 ACTACACGGC GATGAGGAAAGT TATGCGCTGC 22323 60 1.10e-04 CTTATTGTTT CAAAAAGGAAGA CATTAACCGT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 5017 5.1e-08 334_[+2]_154 270389 1.1e-07 257_[+2]_231 268443 1.1e-07 256_[+2]_232 24776 1.5e-06 186_[+2]_302 264065 4.8e-06 116_[+2]_372 261719 6.3e-06 367_[+2]_121 1150 8.1e-06 33_[+2]_455 6953 9.1e-06 249_[+2]_239 261017 1.1e-05 17_[+2]_471 4853 1.8e-05 263_[+2]_225 260786 2.2e-05 72_[+2]_416 5197 5.6e-05 379_[+2]_109 262503 6.2e-05 300_[+2]_188 22323 0.00011 59_[+2]_429 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=12 seqs=14 5017 ( 335) GAGGAAGAAGGA 1 270389 ( 258) GAAGAAGAAGGA 1 268443 ( 257) GAAGAAGAAGGA 1 24776 ( 187) GAGGAAGAAGCG 1 264065 ( 117) GATGAAGAGGGA 1 261719 ( 368) GACAAAGAAAGA 1 1150 ( 34) GGGAAAGAAGGA 1 6953 ( 250) GAAGAAGATGCG 1 261017 ( 18) GATGAAGGAGCA 1 4853 ( 264) GAGCAAGATGGG 1 260786 ( 73) GACGACGATGGA 1 5197 ( 380) GAGAAGGAAGTG 1 262503 ( 301) GATGAGGAAAGT 1 22323 ( 60) CAAAAAGGAAGA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 6846 bayes= 8.93074 E= 9.5e-004 -1045 -172 196 -1045 186 -1045 -174 -1045 16 -72 58 -33 16 -172 143 -1045 197 -1045 -1045 -1045 162 -172 -74 -1045 -1045 -1045 206 -1045 175 -1045 -74 -1045 148 -1045 -174 -33 -25 -1045 172 -1045 -1045 -13 158 -192 133 -1045 26 -192 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 14 E= 9.5e-004 0.000000 0.071429 0.928571 0.000000 0.928571 0.000000 0.071429 0.000000 0.285714 0.142857 0.357143 0.214286 0.285714 0.071429 0.642857 0.000000 1.000000 0.000000 0.000000 0.000000 0.785714 0.071429 0.142857 0.000000 0.000000 0.000000 1.000000 0.000000 0.857143 0.000000 0.142857 0.000000 0.714286 0.000000 0.071429 0.214286 0.214286 0.000000 0.785714 0.000000 0.000000 0.214286 0.714286 0.071429 0.642857 0.000000 0.285714 0.071429 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- GA[GAT][GA]AAGA[AT][GA][GC][AG] -------------------------------------------------------------------------------- Time 3.64 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 21 sites = 14 llr = 177 E-value = 5.0e-004 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A :12::::1::1311:11::14 pos.-specific C 9529415351449191425:6 probability G 1:1:1:11:22::::4::411 matrix T :45159455723:7154819: bits 2.1 1.9 1.7 * * 1.5 * * * * Relative 1.3 * * * * * * * Entropy 1.0 * * * * * * * * (18.2 bits) 0.8 * * * ** *** **** 0.6 ** **** ** *** ***** 0.4 ** **** ** ********** 0.2 ********************* 0.0 --------------------- Multilevel CCTCTTCTCTCCCTCTCTCTC consensus TA C TCTGGA GTCG A sequence C TT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 1150 373 4.75e-11 CGAGCAGCCT CTTCCTCTCTCTCTCTCTCTC TACTGAATAT 262503 3 6.18e-09 TT CCTCTTTTCTTACTCGTTGTA TTGTCGCGTT 270389 65 7.30e-08 ACCCGAAGAG CTTCCTTGTGTCCTCGTTGTC CACAGTCAGC 268443 64 7.30e-08 ACCCGAAGAG CTTCCTTGTGTCCTCGTTGTC CACAGTCAGC 6953 328 2.32e-07 TCAACGGTAC CCTCGTCTCTCACTCTCCTTC TCCTCCTCGC 22323 252 2.56e-07 TTTCTGTTGG CCACTTGCCTCTCTTTTTCTA CAAAAAACAC 261017 432 4.91e-07 GCCATACTGA CCCCCCTTTTGTCTCCTTCTC CTCCTCTCCT 24776 330 6.96e-07 AGGATACAAT CCACTTCTTTCCCCCTCCGGA CAGCGGATAG 260786 185 1.56e-06 CCGTTCGGGG CCTCTCCTCTCCCTCTCCGAG CAGAGTTCGT 261719 463 3.02e-06 TGGACACTAT CTCTTTCCTCAACTCTCTCTC CCCCATCACC 5197 69 3.23e-06 AACTTTCGTT GTACCTCCTTCACACACTCTC TACCCGTCAC 4853 25 3.46e-06 GCACCGGTTG CTCCTTGACTGCCACGATCTA TGAAGGAAGA 264065 141 3.46e-06 TTGGTTGAAA CCTCCTCTCTATACTGATCTC CCAGCATCAA 5017 454 7.90e-06 CAAACCAACA CAGCTTTCTGGCATCTTTGTA AATGTTAGAG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 1150 4.7e-11 372_[+3]_107 262503 6.2e-09 2_[+3]_477 270389 7.3e-08 64_[+3]_415 268443 7.3e-08 63_[+3]_416 6953 2.3e-07 327_[+3]_152 22323 2.6e-07 251_[+3]_228 261017 4.9e-07 431_[+3]_48 24776 7e-07 329_[+3]_150 260786 1.6e-06 184_[+3]_295 261719 3e-06 462_[+3]_17 5197 3.2e-06 68_[+3]_411 4853 3.5e-06 24_[+3]_455 264065 3.5e-06 140_[+3]_339 5017 7.9e-06 453_[+3]_26 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=21 seqs=14 1150 ( 373) CTTCCTCTCTCTCTCTCTCTC 1 262503 ( 3) CCTCTTTTCTTACTCGTTGTA 1 270389 ( 65) CTTCCTTGTGTCCTCGTTGTC 1 268443 ( 64) CTTCCTTGTGTCCTCGTTGTC 1 6953 ( 328) CCTCGTCTCTCACTCTCCTTC 1 22323 ( 252) CCACTTGCCTCTCTTTTTCTA 1 261017 ( 432) CCCCCCTTTTGTCTCCTTCTC 1 24776 ( 330) CCACTTCTTTCCCCCTCCGGA 1 260786 ( 185) CCTCTCCTCTCCCTCTCCGAG 1 261719 ( 463) CTCTTTCCTCAACTCTCTCTC 1 5197 ( 69) GTACCTCCTTCACACACTCTC 1 4853 ( 25) CTCCTTGACTGCCACGATCTA 1 264065 ( 141) CCTCCTCTCTATACTGATCTC 1 5017 ( 454) CAGCTTTCTGGCATCTTTGTA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 6720 bayes= 8.90388 E= 5.0e-004 -1045 198 -174 -1045 -184 109 -1045 66 -25 -13 -174 89 -1045 198 -1045 -192 -1045 87 -174 89 -1045 -72 -1045 166 -1045 109 -74 40 -184 28 -74 89 -1045 109 -1045 89 -1045 -172 -16 140 -84 87 -16 -33 16 87 -1045 8 -84 187 -1045 -1045 -84 -72 -1045 140 -1045 187 -1045 -92 -184 -172 58 89 -84 87 -1045 66 -1045 -13 -1045 154 -1045 109 84 -192 -184 -1045 -174 166 48 128 -174 -1045 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 14 E= 5.0e-004 0.000000 0.928571 0.071429 0.000000 0.071429 0.500000 0.000000 0.428571 0.214286 0.214286 0.071429 0.500000 0.000000 0.928571 0.000000 0.071429 0.000000 0.428571 0.071429 0.500000 0.000000 0.142857 0.000000 0.857143 0.000000 0.500000 0.142857 0.357143 0.071429 0.285714 0.142857 0.500000 0.000000 0.500000 0.000000 0.500000 0.000000 0.071429 0.214286 0.714286 0.142857 0.428571 0.214286 0.214286 0.285714 0.428571 0.000000 0.285714 0.142857 0.857143 0.000000 0.000000 0.142857 0.142857 0.000000 0.714286 0.000000 0.857143 0.000000 0.142857 0.071429 0.071429 0.357143 0.500000 0.142857 0.428571 0.000000 0.428571 0.000000 0.214286 0.000000 0.785714 0.000000 0.500000 0.428571 0.071429 0.071429 0.000000 0.071429 0.857143 0.357143 0.571429 0.071429 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- C[CT][TAC]C[TC]T[CT][TC][CT][TG][CGT][CAT]CTC[TG][CT][TC][CG]T[CA] -------------------------------------------------------------------------------- Time 5.22 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 1150 1.15e-12 33_[+2(8.09e-06)]_327_\ [+3(4.75e-11)]_50_[+3(1.54e-05)]_5_[+1(4.32e-08)]_15 22323 2.03e-06 251_[+3(2.56e-07)]_149_\ [+1(3.47e-06)]_63 24776 1.32e-08 186_[+2(1.50e-06)]_131_\ [+3(6.96e-07)]_17_[+1(3.57e-07)]_117 260786 3.47e-06 72_[+2(2.22e-05)]_100_\ [+3(1.56e-06)]_191_[+1(5.02e-06)]_88 261017 2.54e-07 17_[+2(1.06e-05)]_402_\ [+3(4.91e-07)]_31_[+1(1.84e-06)]_1 261719 2.15e-06 367_[+2(6.26e-06)]_83_\ [+3(3.02e-06)]_1_[+1(5.40e-06)] 262503 5.47e-08 2_[+3(6.18e-09)]_277_[+2(6.20e-05)]_\ 148_[+1(4.67e-06)]_24 264065 2.76e-06 116_[+2(4.78e-06)]_12_\ [+3(3.46e-06)]_308_[+1(8.15e-06)]_15 268443 3.17e-10 63_[+3(7.30e-08)]_1_[+1(8.63e-07)]_\ 155_[+2(1.06e-07)]_232 270389 3.17e-10 64_[+3(7.30e-08)]_1_[+1(8.63e-07)]_\ 155_[+2(1.06e-07)]_231 4853 5.96e-07 24_[+3(3.46e-06)]_218_\ [+2(1.77e-05)]_176_[+1(4.00e-07)]_33 5017 3.59e-08 334_[+2(5.12e-08)]_70_\ [+1(2.76e-06)]_21_[+3(7.90e-06)]_26 5197 1.21e-07 68_[+3(3.23e-06)]_290_\ [+2(5.59e-05)]_65_[+1(2.37e-08)]_28 6953 2.62e-07 249_[+2(9.13e-06)]_66_\ [+3(2.32e-07)]_13_[+1(4.67e-06)]_123 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************