# DREME 4.12.0 # command: dreme -v 1 -oc /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/MouseDNase/M1ScAtacSeqNEMO/BICCN_mouse_NEMO_snATAC-Seq_L5.PT_reproduciblePeaks_enhancerShort.MemeChipResults/dreme_out -png -dna -p /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/MouseDNase/M1ScAtacSeqNEMO/BICCN_mouse_NEMO_snATAC-Seq_L5.PT_reproduciblePeaks_enhancerShort.MemeChipResults/seqs-centered -n /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/MouseDNase/M1ScAtacSeqNEMO/BICCN_mouse_NEMO_snATAC-Seq_L5.PT_reproduciblePeaks_enhancerShort.MemeChipResults/control-centered # positives: 47035 from /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/MouseDNase/M1ScAtacSeqNEMO/BICCN_mouse_NEMO_snATAC-Seq_L5.PT_reproduciblePeaks_enhancerShort.MemeChipResults/seqs-centered (Wed Jan 13 22:28:02 EST 2021) # negatives: 202202 from /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/MouseDNase/M1ScAtacSeqNEMO/BICCN_mouse_NEMO_snATAC-Seq_L5.PT_reproduciblePeaks_enhancerShort.MemeChipResults/control-centered (Wed Jan 13 22:28:10 EST 2021) # host: compute-1-40.local # when: Thu Jan 14 01:01:04 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 TGHATAW DREME-1 # Word RC Word Pos Neg P-value E-value # BEST TGHATAW WTATDCA 7007 21005 6.3e-161 2.9e-156 # TGAATAT ATATTCA 1622 4294 2.8e-059 1.3e-054 # TGCATAT ATATGCA 1679 4564 1.2e-055 5.8e-051 # TGCATAA TTATGCA 1503 4123 3.7e-048 1.7e-043 # TGAATAA TTATTCA 1330 4209 5.1e-022 2.4e-017 # TGTATAA TTATACA 906 2819 6.4e-017 3.0e-012 # TGTATAT ATATACA 947 3028 3.3e-015 1.5e-010 letter-probability matrix: alength= 4 w= 7 nsites= 7990 E= 2.9e-156 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.370338 0.396496 0.000000 0.233166 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.476095 0.000000 0.000000 0.523905 MOTIF ATDTAW DREME-2 # Word RC Word Pos Neg P-value E-value # BEST ATDTAW WTAHAT 14091 51264 2.8e-091 1.3e-086 # ATTTAA TTAAAT 4194 14281 6.3e-042 2.9e-037 # ATGTAT ATACAT 2665 8628 1.2e-037 5.5e-033 # ATATAT ATATAT 1519 4541 1.4e-033 6.3e-029 # ATATAA TTATAT 2684 9480 7.5e-020 3.4e-015 # ATGTAA TTACAT 3394 12351 1.1e-018 5.1e-014 # ATTTAT ATAAAT 3854 14340 1.8e-016 8.1e-012 letter-probability matrix: alength= 4 w= 6 nsites= 18072 E= 1.3e-086 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.211764 0.000000 0.341965 0.446270 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.564852 0.000000 0.000000 0.435148 MOTIF TGAMTYA DREME-3 # Word RC Word Pos Neg P-value E-value # BEST TGAMTYA TRAKTCA 6284 20628 4.0e-084 1.8e-079 # TGACTCA TGAGTCA 3661 11596 2.3e-059 1.0e-054 # TGAATCA TGATTCA 1601 5363 2.0e-018 9.1e-014 # TGAATTA TAATTCA 771 2522 3.9e-011 1.7e-006 # TGACTTA TAAGTCA 505 1860 1.2e-003 5.5e+001 letter-probability matrix: alength= 4 w= 7 nsites= 6762 E= 1.8e-079 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.358917 0.641083 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.809524 0.000000 0.190476 1.000000 0.000000 0.000000 0.000000 MOTIF TGCMAA DREME-4 # Word RC Word Pos Neg P-value E-value # BEST TGCMAA TTKGCA 9701 34871 6.2e-065 2.7e-060 # TGCCAA TTGGCA 5781 19477 8.1e-064 3.6e-059 # TGCAAA TTTGCA 4421 16911 4.4e-013 2.0e-008 letter-probability matrix: alength= 4 w= 6 nsites= 10838 E= 2.7e-060 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.429230 0.570770 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF ATATR DREME-5 # Word RC Word Pos Neg P-value E-value # BEST ATATR YATAT 7373 26882 1.0e-040 4.4e-036 # ATATG CATAT 5952 21575 2.2e-034 9.8e-030 # ATATA TATAT 2238 8191 6.0e-012 2.6e-007 letter-probability matrix: alength= 4 w= 5 nsites= 8193 E= 4.4e-036 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 0.248627 0.000000 0.751373 0.000000 MOTIF TTTWAR DREME-6 # Word RC Word Pos Neg P-value E-value # BEST TTTWAR YTWAAA 9533 35722 4.0e-039 1.7e-034 # TTTTAA TTAAAA 4618 17203 2.1e-019 9.4e-015 # TTTTAG CTAAAA 3940 14865 3.7e-014 1.6e-009 # TTTAAA TTTAAA 2054 7394 5.1e-013 2.2e-008 # TTTAAG CTTAAA 2431 8957 5.3e-012 2.3e-007 letter-probability matrix: alength= 4 w= 6 nsites= 10844 E= 1.7e-034 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.264478 0.000000 0.000000 0.735522 1.000000 0.000000 0.000000 0.000000 0.446975 0.000000 0.553025 0.000000 MOTIF KYATA DREME-7 # Word RC Word Pos Neg P-value E-value # BEST KYATA TATRM 13007 51421 3.1e-023 1.3e-018 # GCATA TATGC 4355 16683 1.3e-012 5.5e-008 # TTATA TATAA 3752 14626 1.9e-008 8.3e-004 # GTATA TATAC 2217 8375 2.4e-008 1.1e-003 # TCATA TATGA 5047 20374 1.4e-005 6.0e-001 letter-probability matrix: alength= 4 w= 5 nsites= 15438 E= 1.3e-018 0.000000 0.000000 0.422270 0.577730 0.000000 0.648076 0.000000 0.351924 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 ARATTY DREME-8 # Word RC Word Pos Neg P-value E-value # BEST ARATTY RAATYT 9064 35588 1.6e-017 6.6e-013 # AAATTC GAATTT 2824 10617 6.7e-011 2.9e-006 # AGATTC GAATCT 2844 10996 1.5e-007 6.2e-003 # AAATTT AAATTT 1202 4571 8.2e-005 3.5e+000 # AGATTT AAATCT 2970 12175 8.7e-003 3.7e+002 letter-probability matrix: alength= 4 w= 6 nsites= 10185 E= 6.6e-013 1.000000 0.000000 0.000000 0.000000 0.410997 0.000000 0.589003 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 0.576632 0.000000 0.423368 MOTIF CCGCSY DREME-9 # Word RC Word Pos Neg P-value E-value # BEST CCGCSY RSGCGG 2150 7527 2.3e-017 9.6e-013 # CCGCCC GGGCGG 1025 3458 9.5e-012 4.0e-007 # CCGCGC GCGCGG 231 654 7.7e-008 3.3e-003 # CCGCCT AGGCGG 905 3302 7.6e-006 3.2e-001 # CCGCGT ACGCGG 162 552 6.0e-003 2.5e+002 letter-probability matrix: alength= 4 w= 6 nsites= 2487 E= 9.6e-013 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 0.822678 0.177322 0.000000 0.000000 0.563731 0.000000 0.436269 MOTIF KRCGY DREME-10 # Word RC Word Pos Neg P-value E-value # BEST KRCGY RCGYM 8914 35088 2.2e-016 9.1e-012 # TGCGC GCGCA 1617 6101 1.5e-006 6.3e-002 # GGCGC GCGCC 1673 6372 5.0e-006 2.1e-001 # TACGT ACGTA 1148 4266 6.6e-006 2.8e-001 # GGCGT ACGCC 1873 7291 5.7e-005 2.4e+000 # GACGT ACGTC 1449 5571 7.6e-005 3.2e+000 # TGCGT ACGCA 2172 8564 1.4e-004 5.7e+000 # GACGC GCGTC 1450 5692 9.8e-004 4.1e+001 # TACGC GCGTA 901 3527 6.3e-003 2.6e+002 letter-probability matrix: alength= 4 w= 5 nsites= 10597 E= 9.1e-012 0.000000 0.000000 0.523073 0.476927 0.382655 0.000000 0.617345 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.438332 0.000000 0.561668 MOTIF RAGCCAA DREME-11 # Word RC Word Pos Neg P-value E-value # BEST RAGCCAA TTGGCTY 2404 8815 1.7e-012 6.7e-008 # GAGCCAA TTGGCTC 1213 4349 1.5e-008 5.8e-004 # AAGCCAA TTGGCTT 1215 4552 1.1e-005 4.4e-001 letter-probability matrix: alength= 4 w= 7 nsites= 2458 E= 6.7e-008 0.499186 0.000000 0.500814 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 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF ATSTYA DREME-12 # Word RC Word Pos Neg P-value E-value # BEST ATSTYA TRASAT 7308 29021 3.8e-011 1.5e-006 # ATGTCA TGACAT 2470 9587 2.2e-006 8.8e-002 # ATCTCA TGAGAT 2556 10193 2.8e-004 1.1e+001 # ATCTTA TAAGAT 1254 4869 6.6e-004 2.6e+001 # ATGTTA TAACAT 1569 6284 5.9e-003 2.3e+002 letter-probability matrix: alength= 4 w= 6 nsites= 7934 E= 1.5e-006 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.485631 0.514369 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.643685 0.000000 0.356315 1.000000 0.000000 0.000000 0.000000 MOTIF GAACATD DREME-13 # Word RC Word Pos Neg P-value E-value # BEST GAACATD HATGTTC 2265 8440 5.8e-010 2.3e-005 # GAACATT AATGTTC 1015 3634 1.7e-007 6.7e-003 # GAACATA TATGTTC 461 1718 3.7e-003 1.5e+002 # GAACATG CATGTTC 826 3198 3.9e-003 1.5e+002 letter-probability matrix: alength= 4 w= 7 nsites= 2328 E= 2.3e-005 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.200601 0.000000 0.359107 0.440292 MOTIF AATKCA DREME-14 # Word RC Word Pos Neg P-value E-value # BEST AATKCA TGMATT 4125 16040 1.5e-009 5.8e-005 # AATGCA TGCATT 2735 10647 1.3e-006 5.0e-002 # AATTCA TGAATT 1462 5714 5.7e-004 2.2e+001 letter-probability matrix: alength= 4 w= 6 nsites= 4296 E= 5.8e-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 0.000000 0.000000 0.652467 0.347533 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF TGCCAGAR DREME-15 # Word RC Word Pos Neg P-value E-value # BEST TGCCAGAR YTCTGGCA 910 3131 2.8e-009 1.1e-004 # TGCCAGAA TTCTGGCA 435 1444 2.0e-006 7.8e-002 # TGCCAGAG CTCTGGCA 483 1695 5.7e-005 2.3e+000 letter-probability matrix: alength= 4 w= 8 nsites= 927 E= 1.1e-004 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 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 0.474649 0.000000 0.525351 0.000000 MOTIF AACYT DREME-16 # Word RC Word Pos Neg P-value E-value # BEST AACYT ARGTT 11952 48848 7.0e-009 2.7e-004 # AACCT AGGTT 5784 23584 6.8e-005 2.7e+000 # AACTT AAGTT 6922 28458 1.7e-004 6.8e+000 letter-probability matrix: alength= 4 w= 5 nsites= 13662 E= 2.7e-004 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 0.453155 0.000000 0.546845 0.000000 0.000000 0.000000 1.000000 MOTIF ATSTA DREME-17 # Word RC Word Pos Neg P-value E-value # BEST ATSTA TASAT 7521 30509 5.6e-007 2.2e-002 # ATGTA TACAT 3530 14155 7.1e-005 2.7e+000 # ATCTA TAGAT 4461 18127 2.2e-004 8.6e+000 letter-probability matrix: alength= 4 w= 5 nsites= 8265 E= 2.2e-002 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.562855 0.437145 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 MOTIF ATGGAAAW DREME-18 # Word RC Word Pos Neg P-value E-value # BEST ATGGAAAW WTTTCCAT 695 2379 1.1e-007 4.0e-003 # ATGGAAAT ATTTCCAT 363 1156 6.3e-007 2.4e-002 # ATGGAAAA TTTTCCAT 335 1236 7.6e-003 2.9e+002 letter-probability matrix: alength= 4 w= 8 nsites= 698 E= 4.0e-003 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 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 0.479943 0.000000 0.000000 0.520057 # Stopping reason: E-value threshold exceeded # Running time: 26565.31 seconds