# DREME 5.5.3 # command: dreme -oc dreme_example_output_files -png -p Klf1.fna # positives: 904 from Klf1.fna (Mon Aug 16 16:20:49 PDT 2021) # negatives: 904 from shuffled positives # host: Timothys-iMac.local # when: Fri Jun 09 08:18:41 PDT 2023 MEME version 5.5.3 ALPHABET "DNA" DNA-LIKE A "Adenine" CC0000 ~ T "Thymine" 008000 C "Cytosine" 0000CC ~ G "Guanine" FFB300 N "Any base" = ACGT X = ACGT . = ACGT V "Not T" = ACG H "Not G" = ACT D "Not C" = AGT B "Not A" = CGT M "Amino" = AC R "Purine" = AG W "Weak" = AT S "Strong" = CG Y "Pyrimidine" = CT K "Keto" = GT U = T END ALPHABET strands: + - Background letter frequencies (from dataset): A 0.255 C 0.245 G 0.243 T 0.257 MOTIF CCMCRCCC DREME-1 # Word RC Word Pos Neg P-value E-value # BEST CCMCRCCC GGGYGKGG 350 40 4.9e-078 2.1e-073 # CCACACCC GGGTGTGG 175 19 2.4e-036 1.0e-031 # CCCCACCC GGGTGGGG 128 16 8.3e-025 3.5e-020 # CCCCGCCC GGGCGGGG 53 3 2.0e-013 8.6e-009 # CCACGCCC GGGCGTGG 55 4 4.1e-013 1.7e-008 letter-probability matrix: alength= 4 w= 8 nsites= 454 E= 2.1e-073 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.550661 0.449339 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.733480 0.000000 0.266520 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 MOTIF TTATCW DREME-2 # Word RC Word Pos Neg P-value E-value # BEST TTATCW WGATAA 496 243 2.9e-034 1.2e-029 # TTATCT AGATAA 352 138 1.8e-030 7.5e-026 # TTATCA TGATAA 250 124 1.3e-013 5.5e-009 letter-probability matrix: alength= 4 w= 6 nsites= 717 E= 1.2e-029 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.417015 0.000000 0.000000 0.582985 MOTIF ACRCCCW DREME-3 # Word RC Word Pos Neg P-value E-value # BEST ACRCCCW WGGGYGT 263 108 5.5e-020 2.3e-015 # ACGCCCT AGGGCGT 54 11 1.8e-008 7.6e-004 # ACGCCCA TGGGCGT 46 12 3.0e-006 1.3e-001 # ACACCCA TGGGTGT 102 51 1.0e-005 4.3e-001 # ACACCCT AGGGTGT 95 47 1.7e-005 7.3e-001 letter-probability matrix: alength= 4 w= 7 nsites= 314 E= 2.3e-015 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.678344 0.000000 0.321656 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 0.503185 0.000000 0.000000 0.496815 MOTIF TTTMTW DREME-4 # Word RC Word Pos Neg P-value E-value # BEST TTTMTW WAKAAA 607 443 3.3e-015 1.4e-010 # TTTATT AATAAA 239 132 2.7e-010 1.1e-005 # TTTCTT AAGAAA 335 234 2.0e-007 8.2e-003 # TTTCTA TAGAAA 243 159 1.3e-006 5.3e-002 # TTTATA TATAAA 151 110 3.7e-003 1.6e+002 letter-probability matrix: alength= 4 w= 6 nsites= 1166 E= 1.4e-010 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.388508 0.611492 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.391938 0.000000 0.000000 0.608062 MOTIF CWCCRCCC DREME-5 # Word RC Word Pos Neg P-value E-value # BEST CWCCRCCC GGGYGGWG 139 36 3.5e-017 1.4e-012 # CTCCACCC GGGTGGAG 77 16 1.6e-011 6.9e-007 # CACCGCCC GGGCGGTG 23 3 3.9e-005 1.6e+000 # CTCCGCCC GGGCGGAG 23 6 1.1e-003 4.5e+001 # CACCACCC GGGTGGTG 28 12 7.7e-003 3.2e+002 letter-probability matrix: alength= 4 w= 8 nsites= 158 E= 1.4e-012 0.000000 1.000000 0.000000 0.000000 0.335443 0.000000 0.000000 0.664557 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.702532 0.000000 0.297468 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 MOTIF RASAGAAA DREME-6 # Word RC Word Pos Neg P-value E-value # BEST RASAGAAA TTTCTSTY 153 52 2.0e-014 8.5e-010 # AACAGAAA TTTCTGTT 45 12 4.8e-006 2.0e-001 # AAGAGAAA TTTCTCTT 47 16 4.5e-005 1.9e+000 # GACAGAAA TTTCTGTC 32 8 7.8e-005 3.2e+000 # GAGAGAAA TTTCTCTC 39 17 2.0e-003 8.3e+001 letter-probability matrix: alength= 4 w= 8 nsites= 166 E= 8.5e-010 0.554217 0.000000 0.445783 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.475904 0.524096 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 1.000000 0.000000 0.000000 0.000000 MOTIF CMCGCCY DREME-7 # Word RC Word Pos Neg P-value E-value # BEST CMCGCCY RGGCGKG 121 35 1.5e-013 6.1e-009 # CCCGCCC GGGCGGG 48 12 1.1e-006 4.6e-002 # CACGCCT AGGCGTG 34 6 3.4e-006 1.4e-001 # CACGCCC GGGCGTG 15 1 2.5e-004 1.0e+001 # CCCGCCT AGGCGGG 36 17 5.7e-003 2.4e+002 letter-probability matrix: alength= 4 w= 7 nsites= 139 E= 6.1e-009 0.000000 1.000000 0.000000 0.000000 0.352518 0.647482 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 1.000000 0.000000 0.000000 0.000000 0.474820 0.000000 0.525180 MOTIF TTTAAAWW DREME-8 # Word RC Word Pos Neg P-value E-value # BEST TTTAAAWW WWTTTAAA 110 32 2.6e-012 1.1e-007 # TTTAAAAA TTTTTAAA 65 15 3.4e-009 1.4e-004 # TTTAAAAT ATTTTAAA 33 10 2.6e-004 1.1e+001 # TTTAAATA TATTTAAA 18 5 5.1e-003 2.1e+002 # TTTAAATT AATTTAAA 26 11 9.4e-003 3.9e+002 letter-probability matrix: alength= 4 w= 8 nsites= 120 E= 1.1e-007 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.716667 0.000000 0.000000 0.283333 0.616667 0.000000 0.000000 0.383333 MOTIF RCAGASA DREME-9 # Word RC Word Pos Neg P-value E-value # BEST RCAGASA TSTCTGY 355 231 2.9e-010 1.2e-005 # ACAGACA TGTCTGT 109 55 6.1e-006 2.5e-001 # GCAGAGA TCTCTGC 119 72 2.0e-004 8.5e+000 # GCAGACA TGTCTGC 82 51 3.3e-003 1.4e+002 # ACAGAGA TCTCTGT 121 87 7.4e-003 3.1e+002 letter-probability matrix: alength= 4 w= 7 nsites= 451 E= 1.2e-005 0.523282 0.000000 0.476718 0.000000 0.000000 1.000000 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 0.000000 0.434590 0.565410 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF CATTTCH DREME-10 # Word RC Word Pos Neg P-value E-value # BEST CATTTCH DGAAATG 187 94 8.8e-010 3.7e-005 # CATTTCC GGAAATG 94 45 9.5e-006 3.9e-001 # CATTTCA TGAAATG 68 34 3.5e-004 1.4e+001 # CATTTCT AGAAATG 43 20 2.2e-003 9.1e+001 letter-probability matrix: alength= 4 w= 7 nsites= 216 E= 3.7e-005 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 0.314815 0.476852 0.000000 0.208333 MOTIF ACASAG DREME-11 # Word RC Word Pos Neg P-value E-value # BEST ACASAG CTSTGT 450 325 1.8e-009 7.4e-005 # ACACAG CTGTGT 299 204 3.8e-007 1.6e-002 # ACAGAG CTCTGT 242 172 5.5e-005 2.3e+000 letter-probability matrix: alength= 4 w= 6 nsites= 616 E= 7.4e-005 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 0.545455 0.454545 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 MOTIF AGGAAV DREME-12 # Word RC Word Pos Neg P-value E-value # BEST AGGAAV BTTCCT 625 505 3.5e-009 1.4e-004 # AGGAAG CTTCCT 360 269 4.3e-006 1.8e-001 # AGGAAA TTTCCT 316 243 1.2e-004 5.0e+000 # AGGAAC GTTCCT 212 170 9.1e-003 3.7e+002 letter-probability matrix: alength= 4 w= 6 nsites= 1116 E= 1.4e-004 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 0.364695 0.211470 0.423835 0.000000 MOTIF CSTCCCAG DREME-13 # Word RC Word Pos Neg P-value E-value # BEST CSTCCCAG CTGGGASG 71 19 7.2e-009 2.9e-004 # CCTCCCAG CTGGGAGG 61 17 1.6e-007 6.6e-003 # CGTCCCAG CTGGGACG 12 2 6.3e-003 2.6e+002 letter-probability matrix: alength= 4 w= 8 nsites= 74 E= 2.9e-004 0.000000 1.000000 0.000000 0.000000 0.000000 0.837838 0.162162 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 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 MOTIF AHATACA DREME-14 # Word RC Word Pos Neg P-value E-value # BEST AHATACA TGTATDT 138 66 5.0e-008 2.1e-003 # ATATACA TGTATAT 45 15 5.2e-005 2.1e+000 # ACATACA TGTATGT 50 26 3.3e-003 1.4e+002 # AAATACA TGTATTT 51 27 3.7e-003 1.5e+002 letter-probability matrix: alength= 4 w= 7 nsites= 153 E= 2.1e-003 1.000000 0.000000 0.000000 0.000000 0.346405 0.352941 0.000000 0.300654 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 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF AGAGRCAG DREME-15 # Word RC Word Pos Neg P-value E-value # BEST AGAGRCAG CTGYCTCT 85 30 5.9e-008 2.4e-003 # AGAGGCAG CTGCCTCT 51 15 3.5e-006 1.4e-001 # AGAGACAG CTGTCTCT 36 16 3.5e-003 1.4e+002 letter-probability matrix: alength= 4 w= 8 nsites= 90 E= 2.4e-003 1.000000 0.000000 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 0.411111 0.000000 0.588889 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 MOTIF ACACGB DREME-16 # Word RC Word Pos Neg P-value E-value # BEST ACACGB VCGTGT 147 79 8.1e-007 3.3e-002 # ACACGG CCGTGT 61 31 8.9e-004 3.6e+001 # ACACGT ACGTGT 51 26 2.4e-003 1.0e+002 # ACACGC GCGTGT 47 26 8.2e-003 3.3e+002 letter-probability matrix: alength= 4 w= 6 nsites= 167 E= 3.3e-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 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.299401 0.371257 0.329341 # Stopping reason: E-value threshold exceeded # Running time: 433.08 seconds