# dreme.py -p CHEN/Esrrb.pos.fasta -n CHEN/Esrrb.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/Esrrb.pos.fasta -n CHEN/Esrrb.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 RAGGTCR YGACCTY 9589 21647 908 21647 2.2e-2325 2.6e-2321 2.6e-2321 GAGGTCA TGACCTC 2341 21647 413 21647 9.3e-346 1.1e-341 GAGGTCG CGACCTC 309 21647 123 21647 5.0e-020 6.1e-016 AAGGTCG CGACCTT 630 21647 78 21647 5.1e-110 6.2e-106 AAGGTCA TGACCTT 7123 21647 304 21647 4.6e-1970 5.6e-1966 MOTIF RAGGTCR 2.6e-2321 letter-probability matrix: alength= 4 w= 7 nsites= 11301 E= 2.6e-2321 0.745775 0.000000 0.254225 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 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.914875 0.000000 0.085125 0.000000 BEST AAGGRCR YGYCCTT 3013 21647 940 21647 2.1e-274 2.5e-270 2.2e-286 AAGGACA TGTCCTT 1209 21647 326 21647 1.3e-123 1.5e-119 AAGGACG CGTCCTT 206 21647 61 21647 5.6e-020 6.6e-016 AAGGGCA TGCCCTT 1427 21647 426 21647 2.1e-131 2.4e-127 AAGGGCG CGCCCTT 339 21647 146 21647 3.2e-019 3.7e-015 MOTIF AAGGRCR 2.5e-270 letter-probability matrix: alength= 4 w= 7 nsites= 3314 E= 2.5e-270 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 0.443573 0.000000 0.556427 0.000000 0.000000 1.000000 0.000000 0.000000 0.834037 0.000000 0.165963 0.000000 BEST AAGGTKA TMACCTT 1355 21647 332 21647 3.6e-152 4.2e-148 2.1e-204 AAGGTGA TCACCTT 902 21647 256 21647 3.3e-087 3.9e-083 AAGGTTA TAACCTT 472 21647 78 21647 8.5e-071 9.8e-067 MOTIF AAGGTKA 4.2e-148 letter-probability matrix: alength= 4 w= 7 nsites= 1416 E= 4.2e-148 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 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.654661 0.345339 1.000000 0.000000 0.000000 0.000000 BEST CMCRCCC GGGYGKG 2775 21647 1702 21647 4.5e-065 5.3e-061 7.1e-066 CCCGCCC GGGCGGG 661 21647 355 21647 8.7e-023 1.0e-018 CCCACCC GGGTGGG 1249 21647 744 21647 1.7e-031 1.9e-027 CACACCC GGGTGTG 752 21647 493 21647 4.8e-014 5.6e-010 CACGCCC GGGCGTG 351 21647 192 21647 3.2e-012 3.7e-008 MOTIF CMCRCCC 5.3e-061 letter-probability matrix: alength= 4 w= 7 nsites= 3048 E= 5.3e-061 0.000000 1.000000 0.000000 0.000000 0.361877 0.638123 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.667323 0.000000 0.332677 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 RGGTCAY RTGACCY 1573 21647 796 21647 9.1e-062 1.1e-057 1.9e-1039 GGGTCAT ATGACCC 366 21647 212 21647 5.8e-011 6.7e-007 GGGTCAC GTGACCC 707 21647 330 21647 3.2e-033 3.7e-029 AGGTCAT ATGACCT 198 21647 96 21647 1.2e-009 1.4e-005 AGGTCAC GTGACCT 362 21647 166 21647 2.9e-018 3.3e-014 MOTIF RGGTCAY 1.1e-057 letter-probability matrix: alength= 4 w= 7 nsites= 1712 E= 1.1e-057 0.338201 0.000000 0.661799 0.000000 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 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.662967 0.000000 0.337033 BEST ACAAWGV BCWTTGT 1614 21647 1071 21647 1.2e-027 1.4e-023 5.6e-043 ACAAAGA TCTTTGT 309 21647 228 21647 2.5e-004 2.9e+000 ACAAAGC GCTTTGT 329 21647 210 21647 1.4e-007 1.6e-003 ACAAAGG CCTTTGT 386 21647 250 21647 3.1e-008 3.6e-004 ACAATGG CCATTGT 279 21647 178 21647 1.2e-006 1.4e-002 ACAATGA TCATTGT 184 21647 108 21647 4.8e-006 5.5e-002 ACAATGC GCATTGT 202 21647 139 21647 3.6e-004 4.2e+000 MOTIF ACAAWGV 1.4e-023 letter-probability matrix: alength= 4 w= 7 nsites= 1704 E= 1.4e-023 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 0.605634 0.000000 0.000000 0.394366 0.000000 0.000000 1.000000 0.000000 0.292254 0.313380 0.394366 0.000000 BEST CTGCRG CYGCAG 2454 21647 1818 21647 5.9e-025 6.7e-021 8.8e-024 CTGCAG CTGCAG 1565 21647 1159 21647 4.9e-016 5.6e-012 CTGCGG CCGCAG 981 21647 699 21647 1.2e-012 1.4e-008 MOTIF CTGCRG 6.7e-021 letter-probability matrix: alength= 4 w= 6 nsites= 2704 E= 6.7e-021 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 1.000000 0.000000 0.000000 0.607618 0.000000 0.392382 0.000000 0.000000 0.000000 1.000000 0.000000 BEST GGSAGGR YCCTSCC 3310 21647 2586 21647 1.8e-024 2.0e-020 1.3e-030 GGCAGGA TCCTGCC 641 21647 526 21647 3.6e-004 4.0e+000 GGCAGGG CCCTGCC 897 21647 775 21647 1.3e-003 1.4e+001 GGGAGGG CCCTCCC 1324 21647 911 21647 1.4e-019 1.6e-015 GGGAGGA TCCTCCC 764 21647 587 21647 5.5e-007 6.2e-003 MOTIF GGSAGGR 2.0e-020 letter-probability matrix: alength= 4 w= 7 nsites= 3692 E= 2.0e-020 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.420639 0.579361 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 0.385699 0.000000 0.614301 0.000000 BEST AAWGTCA TGACWTT 716 21647 391 21647 1.5e-023 1.6e-019 1.9e-030 AATGTCA TGACATT 350 21647 161 21647 1.3e-017 1.5e-013 AAAGTCA TGACTTT 375 21647 232 21647 2.8e-009 3.1e-005 MOTIF AAWGTCA 1.6e-019 letter-probability matrix: alength= 4 w= 7 nsites= 733 E= 1.6e-019 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.515689 0.000000 0.000000 0.484311 0.000000 0.000000 1.000000 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 BEST TAHAYA TRTDTA 1491 21647 1015 21647 5.4e-023 6.1e-019 1.4e-024 TACACA TGTGTA 572 21647 433 21647 5.1e-006 5.8e-002 TAAATA TATTTA 191 21647 91 21647 1.1e-009 1.3e-005 TACATA TATGTA 223 21647 122 21647 2.6e-008 2.9e-004 TATACA TGTATA 176 21647 130 21647 4.9e-003 5.4e+001 TAAACA TGTTTA 395 21647 274 21647 1.4e-006 1.5e-002 TATATA TATATA 43 21647 20 21647 2.6e-003 2.9e+001 MOTIF TAHAYA 6.1e-019 letter-probability matrix: alength= 4 w= 6 nsites= 1576 E= 6.1e-019 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.372462 0.505076 0.000000 0.122462 1.000000 0.000000 0.000000 0.000000 0.000000 0.723985 0.000000 0.276015 1.000000 0.000000 0.000000 0.000000 BEST AGGWCA TGWCCT 1800 21647 1296 21647 2.7e-021 3.0e-017 5.5e-1662 AGGTCA TGACCT 550 21647 427 21647 3.9e-005 4.3e-001 AGGACA TGTCCT 1290 21647 900 21647 6.0e-018 6.7e-014 MOTIF AGGWCA 3.0e-017 letter-probability matrix: alength= 4 w= 6 nsites= 1909 E= 3.0e-017 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.705081 0.000000 0.000000 0.294919 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 BEST CVGGAA TTCCBG 2379 21647 1812 21647 1.6e-020 1.8e-016 2.0e-033 CCGGAA TTCCGG 439 21647 325 21647 1.8e-005 2.0e-001 CAGGAA TTCCTG 1549 21647 1206 21647 7.8e-012 8.7e-008 CGGGAA TTCCCG 472 21647 333 21647 4.3e-007 4.8e-003 MOTIF CVGGAA 1.8e-016 letter-probability matrix: alength= 4 w= 6 nsites= 2534 E= 1.8e-016 0.000000 1.000000 0.000000 0.000000 0.635359 0.176796 0.187845 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 BEST CAAGGYC GRCCTTG 933 21647 586 21647 5.7e-020 6.2e-016 1.1e-1148 CAAGGTC GACCTTG 364 21647 202 21647 3.5e-012 3.8e-008 CAAGGCC GGCCTTG 584 21647 389 21647 1.4e-010 1.5e-006 MOTIF CAAGGYC 6.2e-016 letter-probability matrix: alength= 4 w= 7 nsites= 963 E= 6.2e-016 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 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.616822 0.000000 0.383178 0.000000 1.000000 0.000000 0.000000 BEST ATGBWAA TTWVCAT 721 21647 448 21647 2.7e-016 3.0e-012 4.4e-022 ATGGAAA TTTCCAT 165 21647 122 21647 6.4e-003 7.0e+001 ATGTAAA TTTACAT 74 21647 45 21647 4.9e-003 5.4e+001 ATGCTAA TTAGCAT 128 21647 76 21647 1.6e-004 1.8e+000 ATGCAAA TTTGCAT 214 21647 125 21647 7.0e-007 7.7e-003 ATGTTAA TTAACAT 70 21647 36 21647 6.1e-004 6.7e+000 ATGGTAA TTACCAT 89 21647 51 21647 8.2e-004 9.0e+000 MOTIF ATGBWAA 3.0e-012 letter-probability matrix: alength= 4 w= 7 nsites= 743 E= 3.0e-012 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 0.467026 0.340511 0.192463 0.616420 0.000000 0.000000 0.383580 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 BEST CACGTG CACGTG 354 21647 182 21647 3.3e-014 3.6e-010 4.0e-015 CACGTG CACGTG 354 21647 182 21647 3.3e-014 3.6e-010 MOTIF CACGTG 3.6e-010 letter-probability matrix: alength= 4 w= 6 nsites= 361 E= 3.6e-010 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 BEST AGGGTYA TRACCCT 558 21647 356 21647 7.6e-012 8.3e-008 1.5e-038 AGGGTCA TGACCCT 398 21647 240 21647 1.6e-010 1.7e-006 AGGGTTA TAACCCT 166 21647 119 21647 3.1e-003 3.4e+001 MOTIF AGGGTYA 8.3e-008 letter-probability matrix: alength= 4 w= 7 nsites= 581 E= 8.3e-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 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.710843 0.000000 0.289157 1.000000 0.000000 0.000000 0.000000 BEST CACMGC GCKGTG 2498 21647 2078 21647 2.8e-011 3.1e-007 2.1e-021 CACAGC GCTGTG 1975 21647 1653 21647 1.3e-008 1.4e-004 CACCGC GCGGTG 580 21647 483 21647 1.4e-003 1.6e+001 MOTIF CACMGC 3.1e-007 letter-probability matrix: alength= 4 w= 6 nsites= 2729 E= 3.1e-007 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.779040 0.220960 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 BEST CAGCRKC GMYGCTG 1400 21647 1098 21647 2.6e-010 2.9e-006 1.5e-013 CAGCGTC GACGCTG 139 21647 99 21647 5.5e-003 6.0e+001 CAGCAGC GCTGCTG 766 21647 613 21647 1.6e-005 1.7e-001 CAGCATC GATGCTG 317 21647 233 21647 1.8e-004 2.0e+000 CAGCGGC GCCGCTG 250 21647 195 21647 5.0e-003 5.4e+001 MOTIF CAGCRKC 2.9e-006 letter-probability matrix: alength= 4 w= 7 nsites= 1481 E= 2.9e-006 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.741391 0.000000 0.258609 0.000000 0.000000 0.000000 0.694126 0.305874 0.000000 1.000000 0.000000 0.000000 BEST CWTTATM KATAAWG 233 21647 124 21647 3.7e-009 4.0e-005 4.4e-008 CTTTATA TATAAAG 41 21647 20 21647 4.9e-003 5.3e+001 CTTTATC GATAAAG 95 21647 64 21647 8.4e-003 9.2e+001 CATTATC GATAATG 68 21647 28 21647 2.7e-005 2.9e-001 CATTATA TATAATG 32 21647 12 21647 1.8e-003 2.0e+001 MOTIF CWTTATM 4.0e-005 letter-probability matrix: alength= 4 w= 7 nsites= 237 E= 4.0e-005 0.000000 1.000000 0.000000 0.000000 0.426160 0.000000 0.000000 0.573840 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 0.308017 0.691983 0.000000 0.000000 BEST AACAAWA TWTTGTT 305 21647 181 21647 8.5e-009 9.2e-005 8.1e-006 AACAATA TATTGTT 86 21647 38 21647 9.5e-006 1.0e-001 AACAAAA TTTTGTT 221 21647 144 21647 3.1e-005 3.3e-001 MOTIF AACAAWA 9.2e-005 letter-probability matrix: alength= 4 w= 7 nsites= 315 E= 9.2e-005 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 1.000000 0.000000 0.000000 0.000000 0.720635 0.000000 0.000000 0.279365 1.000000 0.000000 0.000000 0.000000 BEST CGCCGCC GGCGGCG 286 21647 167 21647 1.0e-008 1.1e-004 8.5e-007 CGCCGCC GGCGGCG 286 21647 167 21647 1.0e-008 1.1e-004 MOTIF CGCCGCC 1.1e-004 letter-probability matrix: alength= 4 w= 7 nsites= 303 E= 1.1e-004 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 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 BEST AGGAHGC GCDTCCT 640 21647 465 21647 5.4e-008 5.8e-004 6.1e-018 AGGATGC GCATCCT 254 21647 181 21647 2.5e-004 2.7e+000 AGGACGC GCGTCCT 122 21647 78 21647 1.1e-003 1.2e+001 AGGAAGC GCTTCCT 269 21647 209 21647 3.3e-003 3.6e+001 MOTIF AGGAHGC 5.8e-004 letter-probability matrix: alength= 4 w= 7 nsites= 653 E= 5.8e-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 0.416539 0.188361 0.000000 0.395100 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 BEST CGCSCTC GAGSGCG 410 21647 278 21647 2.2e-007 2.4e-003 8.2e-011 CGCGCTC GAGCGCG 187 21647 120 21647 7.4e-005 8.0e-001 CGCCCTC GAGGGCG 230 21647 163 21647 4.0e-004 4.3e+000 MOTIF CGCSCTC 2.4e-003 letter-probability matrix: alength= 4 w= 7 nsites= 428 E= 2.4e-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 0.549065 0.450935 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 BEST CTRTAGC GCTAYAG 307 21647 197 21647 4.7e-007 5.1e-003 1.8e-003 CTGTAGC GCTACAG 236 21647 162 21647 1.1e-004 1.2e+000 CTATAGC GCTATAG 74 21647 36 21647 1.8e-004 2.0e+000 MOTIF CTRTAGC 5.1e-003 letter-probability matrix: alength= 4 w= 7 nsites= 310 E= 5.1e-003 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.238710 0.000000 0.761290 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 BEST CTGCATA TATGCAG 171 21647 92 21647 5.9e-007 6.4e-003 1.5e-004 CTGCATA TATGCAG 171 21647 92 21647 5.9e-007 6.4e-003 MOTIF CTGCATA 6.4e-003 letter-probability matrix: alength= 4 w= 7 nsites= 171 E= 6.4e-003 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 1.000000 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 BEST ACACACA TGTGTGT 310 21647 202 21647 9.0e-007 9.8e-003 4.5e-007 ACACACA TGTGTGT 310 21647 202 21647 9.0e-007 9.8e-003 MOTIF ACACACA 9.8e-003 letter-probability matrix: alength= 4 w= 7 nsites= 319 E= 9.8e-003 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 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 BEST AGRAAGG CCTTYCT 763 21647 592 21647 1.3e-006 1.4e-002 1.8e-031 AGAAAGG CCTTTCT 392 21647 312 21647 1.3e-003 1.4e+001 AGGAAGG CCTTCCT 380 21647 287 21647 1.6e-004 1.7e+000 MOTIF AGRAAGG 1.4e-002 letter-probability matrix: alength= 4 w= 7 nsites= 784 E= 1.4e-002 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.505102 0.000000 0.494898 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 0.000000 BEST CTRGGAA TTCCYAG 689 21647 525 21647 1.0e-006 1.1e-002 4.3e-007 CTGGGAA TTCCCAG 533 21647 412 21647 3.9e-005 4.2e-001 CTAGGAA TTCCTAG 163 21647 117 21647 3.4e-003 3.7e+001 MOTIF CTRGGAA 1.1e-002 letter-probability matrix: alength= 4 w= 7 nsites= 708 E= 1.1e-002 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.231638 0.000000 0.768362 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 # 28 motifs with E-value < 0.05 found. #elapsed time: 1865.90 seconds