# dreme.py -p CHEN/STAT3.pos.fasta -n CHEN/STAT3.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/STAT3.pos.fasta -n CHEN/STAT3.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 CCRGDAA TTHCYGG 691 2546 131 2546 6.8e-109 8.0e-105 8.0e-105 CCGGAAA TTTCCGG 52 2546 4 2546 4.4e-012 5.2e-008 CCAGAAA TTTCTGG 91 2546 36 2546 4.2e-007 4.9e-003 CCGGGAA TTCCCGG 186 2546 14 2546 3.9e-041 4.6e-037 CCGGTAA TTACCGG 18 2546 5 2546 5.2e-003 6.1e+001 CCAGTAA TTACTGG 82 2546 12 2546 1.7e-014 2.0e-010 CCAGGAA TTCCTGG 324 2546 64 2546 2.3e-046 2.8e-042 MOTIF CCRGDAA 8.0e-105 letter-probability matrix: alength= 4 w= 7 nsites= 755 E= 8.0e-105 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.671523 0.000000 0.328477 0.000000 0.000000 0.000000 1.000000 0.000000 0.184106 0.000000 0.684768 0.131126 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 BEST CMCRCCC GGGYGKG 481 2546 183 2546 1.9e-036 2.1e-032 8.8e-033 CCCGCCC GGGCGGG 132 2546 52 2546 8.5e-010 9.5e-006 CCCACCC GGGTGGG 224 2546 78 2546 8.9e-019 9.9e-015 CACACCC GGGTGTG 123 2546 37 2546 1.3e-012 1.4e-008 CACGCCC GGGCGTG 57 2546 24 2546 1.4e-004 1.6e+000 MOTIF CMCRCCC 2.1e-032 letter-probability matrix: alength= 4 w= 7 nsites= 559 E= 2.1e-032 0.000000 1.000000 0.000000 0.000000 0.332737 0.667263 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.638640 0.000000 0.361360 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 BEST TTCCCR YGGGAA 462 2546 192 2546 1.8e-030 2.0e-026 1.6e-060 TTCCCA TGGGAA 327 2546 149 2546 3.5e-018 3.9e-014 TTCCCG CGGGAA 148 2546 44 2546 3.9e-015 4.4e-011 MOTIF TTCCCR 2.0e-026 letter-probability matrix: alength= 4 w= 6 nsites= 512 E= 2.0e-026 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 1.000000 0.000000 0.000000 0.691406 0.000000 0.308594 0.000000 BEST CHGGAA TTCCDG 559 2546 330 2546 1.4e-017 1.5e-013 4.6e-060 CTGGAA TTCCAG 267 2546 171 2546 9.5e-007 1.0e-002 CCGGAA TTCCGG 120 2546 34 2546 4.5e-013 4.9e-009 CAGGAA TTCCTG 214 2546 137 2546 1.2e-005 1.4e-001 MOTIF CHGGAA 1.5e-013 letter-probability matrix: alength= 4 w= 6 nsites= 639 E= 1.5e-013 0.000000 1.000000 0.000000 0.000000 0.361502 0.198748 0.000000 0.439750 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 AAGGWCA TGWCCTT 175 2546 60 2546 4.0e-015 4.4e-011 4.3e-013 AAGGACA TGTCCTT 73 2546 25 2546 5.1e-007 5.6e-003 AAGGTCA TGACCTT 107 2546 36 2546 6.8e-010 7.4e-006 MOTIF AAGGWCA 4.4e-011 letter-probability matrix: alength= 4 w= 7 nsites= 185 E= 4.4e-011 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 0.400000 0.000000 0.000000 0.600000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 BEST ACAAWG CWTTGT 334 2546 182 2546 8.5e-013 9.2e-009 2.4e-009 ACAAAG CTTTGT 226 2546 123 2546 6.2e-009 6.7e-005 ACAATG CATTGT 125 2546 61 2546 1.0e-006 1.1e-002 MOTIF ACAAWG 9.2e-009 letter-probability matrix: alength= 4 w= 6 nsites= 363 E= 9.2e-009 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 0.633609 0.000000 0.000000 0.366391 0.000000 0.000000 1.000000 0.000000 BEST ATGYAAA TTTRCAT 89 2546 21 2546 1.2e-011 1.3e-007 1.7e-008 ATGCAAA TTTGCAT 62 2546 15 2546 2.4e-008 2.7e-004 ATGTAAA TTTACAT 29 2546 6 2546 5.6e-005 6.0e-001 MOTIF ATGYAAA 1.3e-007 letter-probability matrix: alength= 4 w= 7 nsites= 93 E= 1.3e-007 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 0.688172 0.000000 0.311828 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 BEST CACGTGH DCACGTG 51 2546 6 2546 2.3e-010 2.5e-006 1.4e-006 CACGTGT ACACGTG 14 2546 1 2546 4.8e-004 5.2e+000 CACGTGA TCACGTG 33 2546 3 2546 1.0e-007 1.1e-003 CACGTGC GCACGTG 19 2546 5 2546 3.2e-003 3.5e+001 MOTIF CACGTGH 2.5e-006 letter-probability matrix: alength= 4 w= 7 nsites= 52 E= 2.5e-006 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 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 0.538462 0.288462 0.000000 0.173077 BEST CBCCTCC GGAGGVG 375 2546 244 2546 1.1e-008 1.2e-004 4.8e-006 CTCCTCC GGAGGAG 167 2546 105 2546 6.8e-005 7.3e-001 CCCCTCC GGAGGGG 189 2546 122 2546 5.3e-005 5.8e-001 CGCCTCC GGAGGCG 58 2546 33 2546 5.4e-003 5.8e+001 MOTIF CBCCTCC 1.2e-004 letter-probability matrix: alength= 4 w= 7 nsites= 419 E= 1.2e-004 0.000000 1.000000 0.000000 0.000000 0.000000 0.463007 0.136038 0.400955 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 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 BEST CATTTC GAAATG 112 2546 53 2546 1.8e-006 1.9e-002 8.5e-013 CATTTC GAAATG 112 2546 53 2546 1.8e-006 1.9e-002 MOTIF CATTTC 1.9e-002 letter-probability matrix: alength= 4 w= 6 nsites= 117 E= 1.9e-002 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 BEST CASACAC GTGTSTG 88 2546 37 2546 2.2e-006 2.4e-002 7.7e-004 CACACAC GTGTGTG 34 2546 16 2546 7.4e-003 8.0e+001 CAGACAC GTGTCTG 54 2546 22 2546 1.4e-004 1.5e+000 MOTIF CASACAC 2.4e-002 letter-probability matrix: alength= 4 w= 7 nsites= 90 E= 2.4e-002 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.400000 0.600000 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 0.000000 1.000000 0.000000 0.000000 BEST CCGAGAA TTCTCGG 41 2546 9 2546 2.5e-006 2.7e-002 1.8e-001 CCGAGAA TTCTCGG 41 2546 9 2546 2.5e-006 2.7e-002 MOTIF CCGAGAA 2.7e-002 letter-probability matrix: alength= 4 w= 7 nsites= 42 E= 2.7e-002 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 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 # 12 motifs with E-value < 0.05 found. #elapsed time: 113.47 seconds