# dreme.py -p CHEN/Smad1.pos.fasta -n CHEN/Smad1.pos.shuf1.fasta -minw 3 -maxw 7 -mink 3 -maxk 7 -e 0.05 -g 100 -a 0.01 -r 1 # ( dreme.py -p CHEN/Smad1.pos.fasta -n CHEN/Smad1.pos.shuf1.fasta ) # Revision: 1663 MEME version 4.5 ALPHABET= ACGT strands: + - Background letter frequencies (from A 0.25 C 0.25 G 0.25 T 0.25 # VALUES AFTER ERASING BEST WORD # WORD RC_WORD p P n N p-value E-value BEST ACAAWGV BCWTTGT 269 1126 83 1126 2.7e-028 2.9e-024 2.9e-024 ACAAAGA TCTTTGT 53 1126 9 1126 3.4e-009 3.6e-005 ACAAAGC GCTTTGT 59 1126 19 1126 2.2e-006 2.3e-002 ACAAAGG CCTTTGT 72 1126 26 1126 1.1e-006 1.2e-002 ACAATGG CCATTGT 61 1126 10 1126 1.3e-010 1.4e-006 ACAATGA TCATTGT 33 1126 10 1126 2.7e-004 2.8e+000 ACAATGC GCATTGT 27 1126 9 1126 1.8e-003 1.9e+001 MOTIF ACAAWGV 2.9e-024 letter-probability matrix: alength= 4 w= 7 nsites= 318 E= 2.9e-024 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.597484 0.000000 0.000000 0.402516 0.000000 0.000000 1.000000 0.000000 0.279874 0.276730 0.443396 0.000000 BEST ATGYWAA TTWRCAT 157 1126 44 1126 9.8e-018 1.0e-013 7.9e-015 ATGCTAA TTAGCAT 34 1126 12 1126 7.4e-004 7.6e+000 ATGCAAA TTTGCAT 66 1126 17 1126 1.6e-008 1.7e-004 ATGTAAA TTTACAT 31 1126 9 1126 3.1e-004 3.2e+000 ATGTTAA TTAACAT 37 1126 6 1126 6.6e-007 6.9e-003 MOTIF ATGYWAA 1.0e-013 letter-probability matrix: alength= 4 w= 7 nsites= 171 E= 1.0e-013 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.596491 0.000000 0.403509 0.578947 0.000000 0.000000 0.421053 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 BEST AAGGDCA TGHCCTT 142 1126 45 1126 3.4e-014 3.5e-010 5.2e-011 AAGGACA TGTCCTT 46 1126 7 1126 1.4e-008 1.5e-004 AAGGGCA TGCCCTT 39 1126 19 1126 5.4e-003 5.6e+001 AAGGTCA TGACCTT 63 1126 19 1126 3.7e-007 3.8e-003 MOTIF AAGGDCA 3.5e-010 letter-probability matrix: alength= 4 w= 7 nsites= 151 E= 3.5e-010 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.317881 0.000000 0.258278 0.423841 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 BEST CAGCWGG CCWGCTG 130 1126 43 1126 1.9e-012 2.0e-008 1.2e-008 CAGCTGG CCAGCTG 49 1126 21 1126 4.6e-004 4.7e+000 CAGCAGG CCTGCTG 84 1126 22 1126 2.1e-010 2.2e-006 MOTIF CAGCWGG 2.0e-008 letter-probability matrix: alength= 4 w= 7 nsites= 137 E= 2.0e-008 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.642336 0.000000 0.000000 0.357664 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 BEST AAAGRM KYCTTT 354 1126 230 1126 1.5e-009 1.5e-005 1.9e-010 AAAGGA TCCTTT 98 1126 64 1126 3.5e-003 3.6e+001 AAAGGC GCCTTT 87 1126 58 1126 8.0e-003 8.2e+001 AAAGAC GTCTTT 80 1126 50 1126 4.3e-003 4.4e+001 AAAGAA TTCTTT 141 1126 85 1126 5.4e-005 5.5e-001 MOTIF AAAGRM 1.5e-005 letter-probability matrix: alength= 4 w= 6 nsites= 425 E= 1.5e-005 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.545882 0.000000 0.454118 0.000000 0.590588 0.409412 0.000000 0.000000 BEST GGGTGK MCACCC 182 1126 98 1126 4.8e-008 4.9e-004 1.7e-004 GGGTGG CCACCC 116 1126 66 1126 7.0e-005 7.1e-001 GGGTGT ACACCC 81 1126 35 1126 7.1e-006 7.2e-002 MOTIF GGGTGK 4.9e-004 letter-probability matrix: alength= 4 w= 6 nsites= 210 E= 4.9e-004 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.595238 0.404762 BEST BAGGAA TTCCTV 256 1126 166 1126 7.2e-007 7.3e-003 8.2e-004 TAGGAA TTCCTA 65 1126 37 1126 3.0e-003 3.0e+001 CAGGAA TTCCTG 125 1126 84 1126 1.8e-003 1.8e+001 GAGGAA TTCCTC 88 1126 52 1126 1.1e-003 1.1e+001 MOTIF BAGGAA 7.3e-003 letter-probability matrix: alength= 4 w= 6 nsites= 300 E= 7.3e-003 0.000000 0.460000 0.303333 0.236667 1.000000 0.000000 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 1.000000 0.000000 0.000000 0.000000 BEST ACAATAS STATTGT 42 1126 9 1126 1.3e-006 1.3e-002 7.6e-003 ACAATAG CTATTGT 25 1126 7 1126 9.8e-004 9.9e+000 ACAATAC GTATTGT 17 1126 2 1126 3.5e-004 3.5e+000 MOTIF ACAATAS 1.3e-002 letter-probability matrix: alength= 4 w= 7 nsites= 44 E= 1.3e-002 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.409091 0.590909 0.000000 BEST CCCGS SCGGG 134 1126 72 1126 3.6e-006 3.6e-002 1.7e-002 CCCGG CCGGG 76 1126 37 1126 1.1e-004 1.1e+000 CCCGC GCGGG 66 1126 38 1126 3.2e-003 3.2e+001 MOTIF CCCGS 3.6e-002 letter-probability matrix: alength= 4 w= 5 nsites= 148 E= 3.6e-002 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.479730 0.520270 0.000000 # 9 motifs with E-value < 0.05 found. #elapsed time: 38.08 seconds