# DREME 4.12.0 # command: dreme -v 1 -oc /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/MouseDNase/M1ScAtacSeqNEMO/BICCN_mouse_NEMO_snATAC-Seq_L5.IT_reproduciblePeaks_enhancerShort.MemeChipResults/dreme_out -png -dna -p /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/MouseDNase/M1ScAtacSeqNEMO/BICCN_mouse_NEMO_snATAC-Seq_L5.IT_reproduciblePeaks_enhancerShort.MemeChipResults/seqs-centered -n /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/MouseDNase/M1ScAtacSeqNEMO/BICCN_mouse_NEMO_snATAC-Seq_L5.IT_reproduciblePeaks_enhancerShort.MemeChipResults/control-centered # positives: 76182 from /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/MouseDNase/M1ScAtacSeqNEMO/BICCN_mouse_NEMO_snATAC-Seq_L5.IT_reproduciblePeaks_enhancerShort.MemeChipResults/seqs-centered (Wed Jan 13 22:28:03 EST 2021) # negatives: 202202 from /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/MouseDNase/M1ScAtacSeqNEMO/BICCN_mouse_NEMO_snATAC-Seq_L5.IT_reproduciblePeaks_enhancerShort.MemeChipResults/control-centered (Wed Jan 13 22:28:11 EST 2021) # host: compute-1-40.local # when: Thu Jan 14 00:59:18 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 CCATMTGB DREME-1 # Word RC Word Pos Neg P-value E-value # BEST CCATMTGB VCAKATGG 11051 15090 6.3e-651 2.9e-646 # CCATCTGT ACAGATGG 3509 4695 1.9e-203 8.7e-199 # CCATCTGG CCAGATGG 2242 3119 4.0e-117 1.8e-112 # CCATCTGC GCAGATGG 2459 3631 5.4e-109 2.4e-104 # CCATATGT ACATATGG 1323 1708 3.3e-083 1.5e-078 # CCATATGG CCATATGG 907 1005 2.4e-078 1.1e-073 # CCATATGC GCATATGG 951 1311 1.9e-051 8.8e-047 letter-probability matrix: alength= 4 w= 8 nsites= 11524 E= 2.9e-646 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 0.000000 1.000000 0.278723 0.721277 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.299115 0.276033 0.424852 MOTIF DCCYAC DREME-2 # Word RC Word Pos Neg P-value E-value # BEST DCCYAC GTRGGH 28201 58572 4.7e-359 2.2e-354 # TCCCAC GTGGGA 9374 19093 4.4e-106 2.0e-101 # ACCCAC GTGGGT 7636 15365 3.0e-092 1.4e-087 # GCCCAC GTGGGC 5767 11056 6.3e-092 2.9e-087 # TCCTAC GTAGGA 4622 9795 1.1e-037 5.2e-033 # GCCTAC GTAGGC 3055 6676 1.9e-019 8.8e-015 # ACCTAC GTAGGT 2731 6036 8.4e-016 3.8e-011 letter-probability matrix: alength= 4 w= 6 nsites= 34286 E= 2.2e-354 0.309718 0.000000 0.264160 0.426121 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.692819 0.000000 0.307181 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF AVCAKATG DREME-3 # Word RC Word Pos Neg P-value E-value # BEST AVCAKATG CATMTGBT 3887 7243 2.9e-071 1.3e-066 # AACAGATG CATCTGTT 1053 1884 3.6e-024 1.6e-019 # AACATATG CATATGTT 619 967 4.3e-024 1.9e-019 # AGCAGATG CATCTGCT 1233 2393 6.1e-019 2.7e-014 # AGCATATG CATATGCT 628 1154 1.8e-013 8.1e-009 # ACCATATG CATATGGT 124 207 4.0e-005 1.8e+000 # ACCAGATG CATCTGGT 410 897 7.3e-004 3.3e+001 letter-probability matrix: alength= 4 w= 8 nsites= 3972 E= 1.3e-066 1.000000 0.000000 0.000000 0.000000 0.409114 0.134945 0.455942 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.684290 0.315710 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 MOTIF GTGWKA DREME-4 # Word RC Word Pos Neg P-value E-value # BEST GTGWKA TMWCAC 17607 41718 8.8e-046 3.9e-041 # GTGTGA TCACAC 7419 16715 2.4e-034 1.0e-029 # GTGAGA TCTCAC 6184 14700 3.1e-014 1.4e-009 # GTGTTA TAACAC 3794 9124 1.1e-007 4.8e-003 # GTGATA TATCAC 2684 6613 5.2e-004 2.3e+001 letter-probability matrix: alength= 4 w= 6 nsites= 19984 E= 3.9e-041 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.433547 0.000000 0.000000 0.566453 0.000000 0.000000 0.675891 0.324109 1.000000 0.000000 0.000000 0.000000 MOTIF CCTTMTGK DREME-5 # Word RC Word Pos Neg P-value E-value # BEST CCTTMTGK MCAKAAGG 2395 4406 7.9e-047 3.5e-042 # CCTTCTGT ACAGAAGG 1022 1851 2.7e-022 1.2e-017 # CCTTCTGG CCAGAAGG 806 1491 2.5e-016 1.1e-011 # CCTTATGT ACATAAGG 365 678 3.9e-008 1.7e-003 # CCTTATGG CCATAAGG 231 421 4.0e-006 1.8e-001 letter-probability matrix: alength= 4 w= 8 nsites= 2438 E= 3.5e-042 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 0.000000 0.000000 1.000000 0.244873 0.755127 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.427810 0.572190 MOTIF CTADAW DREME-6 # Word RC Word Pos Neg P-value E-value # BEST CTADAW WTHTAG 22249 53639 2.6e-045 1.1e-040 # CTAAAA TTTTAG 6586 14989 4.0e-027 1.8e-022 # CTATAT ATATAG 3537 7628 4.5e-025 2.0e-020 # CTAGAT ATCTAG 2963 6970 1.4e-008 6.3e-004 # CTATAA TTATAG 3688 8870 1.7e-007 7.3e-003 # CTAGAA TTCTAG 4617 11556 2.8e-004 1.2e+001 # CTAAAT ATTTAG 4843 12234 1.4e-003 6.2e+001 letter-probability matrix: alength= 4 w= 6 nsites= 26804 E= 1.1e-040 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.444038 0.000000 0.279809 0.276153 1.000000 0.000000 0.000000 0.000000 0.572041 0.000000 0.000000 0.427959 MOTIF CDCCBCC DREME-7 # Word RC Word Pos Neg P-value E-value # BEST CDCCBCC GGVGGHG 9388 21255 1.2e-041 5.2e-037 # CGCCTCC GGAGGCG 729 1368 5.7e-014 2.5e-009 # CTCCTCC GGAGGAG 3374 7708 1.1e-013 4.9e-009 # CACCTCC GGAGGTG 1618 3605 2.9e-009 1.3e-004 # CGCCCCC GGGGGCG 707 1453 2.0e-008 8.7e-004 # CGCCGCC GGCGGCG 193 312 7.5e-008 3.3e-003 # CTCCGCC GGCGGAG 445 879 3.2e-007 1.4e-002 # CACCCCC GGGGGTG 1550 3568 1.5e-006 6.7e-002 # CTCCCCC GGGGGAG 1933 4611 4.0e-005 1.7e+000 # CACCGCC GGCGGTG 326 702 1.1e-003 4.9e+001 letter-probability matrix: alength= 4 w= 7 nsites= 10720 E= 5.2e-037 0.000000 1.000000 0.000000 0.000000 0.316325 0.000000 0.142910 0.540765 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.385168 0.082276 0.532556 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF CARTCTGB DREME-8 # Word RC Word Pos Neg P-value E-value # BEST CARTCTGB VCAGAYTG 3389 6841 2.8e-039 1.2e-034 # CAATCTGT ACAGATTG 693 1139 1.1e-022 4.9e-018 # CAATCTGG CCAGATTG 459 829 4.9e-011 2.1e-006 # CAGTCTGG CCAGACTG 634 1267 4.9e-009 2.1e-004 # CAATCTGC GCAGATTG 398 812 1.3e-005 5.4e-001 # CAGTCTGT ACAGACTG 673 1519 2.7e-004 1.2e+001 # CAGTCTGC GCAGACTG 588 1357 2.6e-003 1.1e+002 letter-probability matrix: alength= 4 w= 8 nsites= 3467 E= 1.2e-034 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.450534 0.000000 0.549466 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 0.000000 1.000000 0.000000 0.000000 0.285261 0.316700 0.398039 MOTIF GTTGCYA DREME-9 # Word RC Word Pos Neg P-value E-value # BEST GTTGCYA TRGCAAC 2927 6161 2.2e-025 9.5e-021 # GTTGCTA TAGCAAC 1347 2676 5.0e-018 2.2e-013 # GTTGCCA TGGCAAC 1625 3569 1.5e-010 6.6e-006 letter-probability matrix: alength= 4 w= 7 nsites= 3060 E= 9.5e-021 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 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.547059 0.000000 0.452941 1.000000 0.000000 0.000000 0.000000 MOTIF CGCC DREME-10 # Word RC Word Pos Neg P-value E-value # BEST CGCC GGCG 9136 21464 4.8e-025 2.1e-020 # CGCC GGCG 9136 21464 4.8e-025 2.1e-020 letter-probability matrix: alength= 4 w= 4 nsites= 10801 E= 2.1e-020 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 MOTIF CTATTTY DREME-11 # Word RC Word Pos Neg P-value E-value # BEST CTATTTY RAAATAG 4773 10634 8.1e-025 3.4e-020 # CTATTTT AAAATAG 2986 6582 1.4e-017 5.7e-013 # CTATTTC GAAATAG 1851 4193 7.2e-009 3.0e-004 letter-probability matrix: alength= 4 w= 7 nsites= 4910 E= 3.4e-020 0.000000 1.000000 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 0.000000 0.000000 0.000000 1.000000 0.000000 0.380244 0.000000 0.619756 MOTIF CAKAMG DREME-12 # Word RC Word Pos Neg P-value E-value # BEST CAKAMG CKTMTG 12886 31684 9.6e-016 4.0e-011 # CAGAAG CTTCTG 8625 21344 3.7e-009 1.6e-004 # CAGACG CGTCTG 1280 2870 3.1e-007 1.3e-002 # CATACG CGTATG 574 1278 2.8e-004 1.2e+001 # CATAAG CTTATG 2954 7402 3.7e-003 1.6e+002 letter-probability matrix: alength= 4 w= 6 nsites= 14041 E= 4.0e-011 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.743964 0.256036 1.000000 0.000000 0.000000 0.000000 0.865893 0.134107 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 MOTIF KMTATA DREME-13 # Word RC Word Pos Neg P-value E-value # BEST KMTATA TATAKM 4996 11698 1.7e-014 7.1e-010 # GATATA TATATC 1667 3857 1.5e-006 6.1e-002 # GCTATA TATAGC 1086 2487 2.8e-005 1.2e+000 # TCTATA TATAGA 1303 3037 4.7e-005 1.9e+000 # TATATA TATATA 1458 3447 1.1e-004 4.6e+000 letter-probability matrix: alength= 4 w= 6 nsites= 5343 E= 7.1e-010 0.000000 0.000000 0.490923 0.509077 0.585252 0.414748 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 1.000000 0.000000 0.000000 0.000000 MOTIF AAKCTGT DREME-14 # Word RC Word Pos Neg P-value E-value # BEST AAKCTGT ACAGMTT 3731 8610 2.5e-013 1.0e-008 # AAGCTGT ACAGCTT 2487 5647 3.9e-011 1.6e-006 # AATCTGT ACAGATT 1278 3041 5.5e-004 2.3e+001 letter-probability matrix: alength= 4 w= 7 nsites= 3804 E= 1.0e-008 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.660095 0.339905 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 0.000000 0.000000 1.000000 MOTIF AGGKGGCA DREME-15 # Word RC Word Pos Neg P-value E-value # BEST AGGKGGCA TGCCMCCT 1074 2176 4.3e-013 1.8e-008 # AGGTGGCA TGCCACCT 644 1237 3.2e-011 1.3e-006 # AGGGGGCA TGCCCCCT 431 945 6.2e-004 2.5e+001 letter-probability matrix: alength= 4 w= 8 nsites= 1079 E= 1.8e-008 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 0.399444 0.600556 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF TATTYTTR DREME-16 # Word RC Word Pos Neg P-value E-value # BEST TATTYTTR YAARAATA 2467 5569 9.5e-012 3.9e-007 # TATTCTTA TAAGAATA 450 951 4.6e-005 1.9e+000 # TATTTTTA TAAAAATA 904 2062 8.4e-005 3.4e+000 # TATTTTTG CAAAAATA 704 1641 2.2e-003 9.0e+001 # TATTCTTG CAAGAATA 445 1006 2.8e-003 1.1e+002 letter-probability matrix: alength= 4 w= 8 nsites= 2513 E= 3.9e-007 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 0.000000 0.356944 0.000000 0.643056 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.540788 0.000000 0.459212 0.000000 MOTIF CYAC DREME-17 # Word RC Word Pos Neg P-value E-value # BEST CYAC GTRG 46813 121501 3.0e-011 1.2e-006 # CCAC GTGG 33151 85577 7.3e-009 3.0e-004 # CTAC GTAG 23780 61876 9.0e-004 3.7e+001 letter-probability matrix: alength= 4 w= 4 nsites= 71408 E= 1.2e-006 0.000000 1.000000 0.000000 0.000000 0.000000 0.608181 0.000000 0.391819 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF RTGASTCA DREME-18 # Word RC Word Pos Neg P-value E-value # BEST RTGASTCA TGASTCAY 3755 8806 6.0e-011 2.3e-006 # ATGAGTCA TGACTCAT 1581 3578 7.2e-008 2.8e-003 # ATGACTCA TGAGTCAT 1571 3593 4.6e-007 1.8e-002 # GTGAGTCA TGACTCAC 1007 2327 1.3e-004 5.1e+000 # GTGACTCA TGAGTCAC 1218 2878 3.6e-004 1.4e+001 letter-probability matrix: alength= 4 w= 8 nsites= 3874 E= 2.3e-006 0.596025 0.000000 0.403975 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.528653 0.471347 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF CCAACTGB DREME-19 # Word RC Word Pos Neg P-value E-value # BEST CCAACTGB VCAGTTGG 1138 2456 5.5e-009 2.1e-004 # CCAACTGT ACAGTTGG 413 868 6.4e-005 2.4e+000 # CCAACTGG CCAGTTGG 351 754 6.7e-004 2.6e+001 # CCAACTGC GCAGTTGG 380 842 2.1e-003 7.9e+001 letter-probability matrix: alength= 4 w= 8 nsites= 1146 E= 2.1e-004 0.000000 1.000000 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 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.331588 0.306283 0.362129 MOTIF ATATGTCY DREME-20 # Word RC Word Pos Neg P-value E-value # BEST ATATGTCY RGACATAT 420 789 1.1e-008 4.2e-004 # ATATGTCT AGACATAT 293 539 4.2e-007 1.6e-002 # ATATGTCC GGACATAT 127 254 6.0e-003 2.3e+002 letter-probability matrix: alength= 4 w= 8 nsites= 420 E= 4.2e-004 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 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.302381 0.000000 0.697619 MOTIF AGAMA DREME-21 # Word RC Word Pos Neg P-value E-value # BEST AGAMA TKTCT 40138 104259 6.0e-008 2.3e-003 # AGAAA TTTCT 26962 69802 8.8e-006 3.4e-001 # AGACA TGTCT 20141 52165 3.1e-004 1.2e+001 letter-probability matrix: alength= 4 w= 5 nsites= 56289 E= 2.3e-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 0.589227 0.410773 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF CGCGS DREME-22 # Word RC Word Pos Neg P-value E-value # BEST CGCGS SCGCG 1032 2257 1.7e-007 6.3e-003 # CGCGC GCGCG 593 1247 2.2e-006 8.2e-002 # CGCGG CCGCG 662 1422 4.6e-006 1.7e-001 letter-probability matrix: alength= 4 w= 5 nsites= 1194 E= 6.3e-003 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 0.469849 0.530151 0.000000 MOTIF CTTWAAA DREME-23 # Word RC Word Pos Neg P-value E-value # BEST CTTWAAA TTTWAAG 3157 7563 5.0e-007 1.9e-002 # CTTAAAA TTTTAAG 1509 3597 2.3e-004 8.7e+000 # CTTTAAA TTTAAAG 1686 4056 3.5e-004 1.3e+001 letter-probability matrix: alength= 4 w= 7 nsites= 3234 E= 1.9e-002 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.472171 0.000000 0.000000 0.527829 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 # Stopping reason: E-value threshold exceeded # Running time: 32086.24 seconds