# DREME 4.12.0 # command: dreme -v 1 -oc /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/MouseDNase/M1ScAtacSeqNEMO/BICCN_mouse_NEMO_snATAC-Seq_Sncg_reproduciblePeaks_enhancerShort.MemeChipResults/dreme_out -png -dna -p /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/MouseDNase/M1ScAtacSeqNEMO/BICCN_mouse_NEMO_snATAC-Seq_Sncg_reproduciblePeaks_enhancerShort.MemeChipResults/seqs-centered -n /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/MouseDNase/M1ScAtacSeqNEMO/BICCN_mouse_NEMO_snATAC-Seq_Sncg_reproduciblePeaks_enhancerShort.MemeChipResults/control-centered # positives: 9161 from /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/MouseDNase/M1ScAtacSeqNEMO/BICCN_mouse_NEMO_snATAC-Seq_Sncg_reproduciblePeaks_enhancerShort.MemeChipResults/seqs-centered (Wed Jan 13 22:28:01 EST 2021) # negatives: 202202 from /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/MouseDNase/M1ScAtacSeqNEMO/BICCN_mouse_NEMO_snATAC-Seq_Sncg_reproduciblePeaks_enhancerShort.MemeChipResults/control-centered (Wed Jan 13 22:28:07 EST 2021) # host: compute-1-39.local # when: Thu Jan 14 01:04:15 EST 2021 MEME version 4.12.0 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 0.273 C 0.228 G 0.227 T 0.272 MOTIF TAATDR DREME-1 # Word RC Word Pos Neg P-value E-value # BEST TAATDR YHATTA 2915 35863 1.9e-221 8.9e-217 # TAATTG CAATTA 833 7953 7.4e-100 3.4e-095 # TAATTA TAATTA 698 6093 1.5e-098 7.0e-094 # TAATGA TCATTA 813 9487 3.1e-061 1.4e-056 # TAATAA TTATTA 560 6481 6.2e-043 2.9e-038 # TAATGG CCATTA 422 5519 7.2e-023 3.3e-018 # TAATAG CTATTA 346 5245 4.3e-011 2.0e-006 letter-probability matrix: alength= 4 w= 6 nsites= 3755 E= 8.9e-217 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.231691 0.000000 0.336352 0.431957 0.565646 0.000000 0.434354 0.000000 MOTIF CGGSB DREME-2 # Word RC Word Pos Neg P-value E-value # BEST CGGSB VSCCG 2899 36727 1.9e-201 8.9e-197 # CGGGC GCCCG 651 7008 8.7e-060 4.0e-055 # CGGCT AGCCG 850 10552 8.5e-054 3.9e-049 # CGGCG CGCCG 277 2133 3.8e-048 1.7e-043 # CGGCC GGCCG 488 5222 2.0e-045 9.2e-041 # CGGGG CCCCG 683 8819 3.9e-038 1.8e-033 # CGGGT ACCCG 418 6018 3.5e-016 1.6e-011 letter-probability matrix: alength= 4 w= 5 nsites= 3564 E= 8.9e-197 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.475028 0.524972 0.000000 0.000000 0.333614 0.297980 0.368406 MOTIF GSSC DREME-3 # Word RC Word Pos Neg P-value E-value # BEST GSSC GSSC 5196 90985 2.7e-107 1.2e-102 # GCCC GGGC 4103 72114 4.0e-069 1.7e-064 # GCGC GCGC 964 12367 2.3e-055 9.8e-051 # GGCC GGCC 2107 34235 7.0e-048 3.0e-043 letter-probability matrix: alength= 4 w= 4 nsites= 8225 E= 1.2e-102 0.000000 0.000000 1.000000 0.000000 0.000000 0.404377 0.595623 0.000000 0.000000 0.502006 0.497994 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF ATTGWY DREME-4 # Word RC Word Pos Neg P-value E-value # BEST ATTGWY RWCAAT 1595 21298 2.6e-083 1.0e-078 # ATTGTT AACAAT 666 7735 1.3e-050 5.3e-046 # ATTGTC GACAAT 492 5841 2.8e-035 1.1e-030 # ATTGAT ATCAAT 358 5035 2.5e-015 1.0e-010 # ATTGAC GTCAAT 217 3831 9.6e-004 3.8e+001 letter-probability matrix: alength= 4 w= 6 nsites= 1786 E= 1.0e-078 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 1.000000 0.000000 0.323068 0.000000 0.000000 0.676932 0.000000 0.400896 0.000000 0.599104 MOTIF BCVGC DREME-5 # Word RC Word Pos Neg P-value E-value # BEST BCVGC GCBGV 6088 114572 1.4e-078 5.4e-074 # GCAGC GCTGC 2864 49743 2.9e-045 1.2e-040 # TCCGC GCGGA 446 5816 2.5e-024 9.9e-020 # CCAGC GCTGG 2593 47812 5.4e-024 2.2e-019 # TCAGC GCTGA 2755 51334 2.7e-023 1.1e-018 # GCCGC GCGGC 180 2234 3.0e-012 1.2e-007 # CCCGC GCGGG 160 2010 1.1e-010 4.2e-006 # CCGGC GCCGG 100 1237 1.5e-007 6.1e-003 # TCGGC GCCGA 138 2240 4.2e-004 1.7e+001 letter-probability matrix: alength= 4 w= 5 nsites= 10117 E= 5.4e-074 0.000000 0.308787 0.331422 0.359790 0.000000 1.000000 0.000000 0.000000 0.901255 0.067807 0.030938 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF CGS DREME-6 # Word RC Word Pos Neg P-value E-value # BEST CGS SCG 3808 68018 5.0e-054 1.9e-049 # CGC GCG 2385 40028 1.5e-045 5.5e-041 # CGG CCG 2317 40605 2.0e-032 7.4e-028 letter-probability matrix: alength= 4 w= 3 nsites= 5534 E= 1.9e-049 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.521684 0.478316 0.000000 MOTIF GGWCA DREME-7 # Word RC Word Pos Neg P-value E-value # BEST GGWCA TGWCC 2277 39300 1.4e-035 4.3e-031 # GGACA TGTCC 1653 28681 9.4e-024 2.9e-019 # GGTCA TGACC 766 12569 1.5e-015 4.4e-011 letter-probability matrix: alength= 4 w= 5 nsites= 2649 E= 4.3e-031 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.701397 0.000000 0.000000 0.298603 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF ACAAWGV DREME-8 # Word RC Word Pos Neg P-value E-value # BEST ACAAWGV BCWTTGT 840 12382 8.2e-029 2.5e-024 # ACAAAGG CCTTTGT 187 2293 4.4e-013 1.3e-008 # ACAATGG CCATTGT 72 833 8.8e-007 2.6e-002 # ACAATGA TCATTGT 106 1414 1.7e-006 5.2e-002 # ACAAAGC GCTTTGT 200 3134 3.7e-006 1.1e-001 # ACAAAGA TCTTTGT 240 4065 5.8e-005 1.7e+000 # ACAATGC GCATTGT 70 981 3.3e-004 9.8e+000 letter-probability matrix: alength= 4 w= 7 nsites= 887 E= 2.5e-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 0.719278 0.000000 0.000000 0.280722 0.000000 0.000000 1.000000 0.000000 0.393461 0.313416 0.293123 0.000000 MOTIF RCAAATKA DREME-9 # Word RC Word Pos Neg P-value E-value # BEST RCAAATKA TMATTTGY 312 3838 1.2e-020 3.5e-016 # ACAAATGA TCATTTGT 100 1149 5.7e-009 1.7e-004 # ACAAATTA TAATTTGT 62 695 1.9e-006 5.7e-002 # GCAAATTA TAATTTGC 60 718 1.7e-005 5.0e-001 # GCAAATGA TCATTTGC 94 1312 3.2e-005 9.5e-001 letter-probability matrix: alength= 4 w= 8 nsites= 315 E= 3.5e-016 0.514286 0.000000 0.485714 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 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.615873 0.384127 1.000000 0.000000 0.000000 0.000000 MOTIF GCC DREME-10 # Word RC Word Pos Neg P-value E-value # BEST GCC GGC 6678 139518 7.5e-016 2.2e-011 # GCC GGC 6678 139518 7.5e-016 2.2e-011 letter-probability matrix: alength= 4 w= 3 nsites= 11945 E= 2.2e-011 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF AGGGG DREME-11 # Word RC Word Pos Neg P-value E-value # BEST AGGGG CCCCT 1143 20604 3.9e-012 1.1e-007 # AGGGG CCCCT 1143 20604 3.9e-012 1.1e-007 letter-probability matrix: alength= 4 w= 5 nsites= 1247 E= 1.1e-007 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 MOTIF ATTRG DREME-12 # Word RC Word Pos Neg P-value E-value # BEST ATTRG CYAAT 1494 27966 3.0e-011 8.1e-007 # ATTAG CTAAT 771 13394 5.0e-011 1.4e-006 # ATTGG CCAAT 777 15609 4.4e-003 1.2e+002 letter-probability matrix: alength= 4 w= 5 nsites= 1608 E= 8.1e-007 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.495025 0.000000 0.504975 0.000000 0.000000 0.000000 1.000000 0.000000 MOTIF CGTSM DREME-13 # Word RC Word Pos Neg P-value E-value # BEST CGTSM KSACG 730 12645 1.1e-010 2.9e-006 # CGTGC GCACG 196 2726 2.2e-009 5.8e-005 # CGTGA TCACG 275 5003 1.1e-003 3.0e+001 # CGTCA TGACG 192 3438 3.1e-003 8.4e+001 # CGTCC GGACG 138 2446 7.9e-003 2.1e+002 letter-probability matrix: alength= 4 w= 5 nsites= 771 E= 2.9e-006 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 0.408560 0.591440 0.000000 0.588846 0.411154 0.000000 0.000000 MOTIF AATATTRA DREME-14 # Word RC Word Pos Neg P-value E-value # BEST AATATTRA TYAATATT 73 697 6.5e-010 1.7e-005 # AATATTAA TTAATATT 50 414 5.1e-009 1.3e-004 # AATATTGA TCAATATT 24 293 6.3e-003 1.6e+002 letter-probability matrix: alength= 4 w= 8 nsites= 73 E= 1.7e-005 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 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.684932 0.000000 0.315068 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF TTTGTTB DREME-15 # Word RC Word Pos Neg P-value E-value # BEST TTTGTTB VAACAAA 576 9930 6.0e-009 1.6e-004 # TTTGTTT AAACAAA 283 4974 1.4e-004 3.7e+000 # TTTGTTC GAACAAA 188 3179 3.2e-004 8.2e+000 # TTTGTTG CAACAAA 124 2045 1.3e-003 3.5e+001 letter-probability matrix: alength= 4 w= 7 nsites= 604 E= 1.6e-004 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 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.307947 0.206954 0.485099 MOTIF ATTG DREME-16 # Word RC Word Pos Neg P-value E-value # BEST ATTG CAAT 2241 44339 8.2e-009 2.1e-004 # ATTG CAAT 2241 44339 8.2e-009 2.1e-004 letter-probability matrix: alength= 4 w= 4 nsites= 2621 E= 2.1e-004 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 1.000000 0.000000 MOTIF TGCAGW DREME-17 # Word RC Word Pos Neg P-value E-value # BEST TGCAGW WCTGCA 1512 29565 5.0e-007 1.3e-002 # TGCAGA TCTGCA 999 18903 5.6e-007 1.4e-002 # TGCAGT ACTGCA 693 13612 1.2e-003 3.0e+001 letter-probability matrix: alength= 4 w= 6 nsites= 1661 E= 1.3e-002 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 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 0.603251 0.000000 0.000000 0.396749 MOTIF AATKACA DREME-18 # Word RC Word Pos Neg P-value E-value # BEST AATKACA TGTMATT 257 4101 6.3e-007 1.6e-002 # AATGACA TGTCATT 137 2151 1.2e-004 3.0e+000 # AATTACA TGTAATT 122 1968 7.0e-004 1.7e+001 letter-probability matrix: alength= 4 w= 7 nsites= 261 E= 1.6e-002 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.524904 0.475096 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 ATTAAT DREME-19 # Word RC Word Pos Neg P-value E-value # BEST ATTAAT ATTAAT 88 1109 1.6e-006 4.0e-002 # ATTAAT ATTAAT 88 1109 1.6e-006 4.0e-002 letter-probability matrix: alength= 4 w= 6 nsites= 88 E= 4.0e-002 1.000000 0.000000 0.000000 0.000000 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 0.000000 0.000000 0.000000 1.000000 # Stopping reason: E-value threshold exceeded # Running time: 19845.25 seconds