# dreme.py -p CHEN/nMyc.pos.fasta -n CHEN/nMyc.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/nMyc.pos.fasta -n CHEN/nMyc.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 CACGTG CACGTG 1389 7182 135 7182 1.9e-289 2.3e-285 2.3e-285 CACGTG CACGTG 1389 7182 135 7182 1.9e-289 2.3e-285 MOTIF CACGTG 2.3e-285 letter-probability matrix: alength= 4 w= 6 nsites= 1485 E= 2.3e-285 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 GGAAR YTTCC 3193 7182 2152 7182 1.1e-072 1.3e-068 3.3e-070 GGAAA TTTCC 1288 7182 830 7182 1.9e-027 2.3e-023 GGAAG CTTCC 2438 7182 1529 7182 4.0e-065 4.7e-061 MOTIF GGAAR 1.3e-068 letter-probability matrix: alength= 4 w= 5 nsites= 4545 E= 1.3e-068 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 0.320572 0.000000 0.679428 0.000000 BEST CBCCKCC GGMGGVG 2412 7182 1590 7182 2.8e-053 3.1e-049 6.0e-052 CTCCTCC GGAGGAG 452 7182 213 7182 6.5e-022 7.4e-018 CCCCTCC GGAGGGG 529 7182 334 7182 4.0e-012 4.6e-008 CGCCTCC GGAGGCG 422 7182 269 7182 1.3e-009 1.5e-005 CTCCGCC GGCGGAG 491 7182 271 7182 1.1e-016 1.3e-012 CCCCGCC GGCGGGG 677 7182 423 7182 7.9e-016 9.0e-012 CGCCGCC GGCGGCG 624 7182 417 7182 1.5e-011 1.7e-007 MOTIF CBCCKCC 3.1e-049 letter-probability matrix: alength= 4 w= 7 nsites= 3069 E= 3.1e-049 0.000000 1.000000 0.000000 0.000000 0.000000 0.386445 0.321277 0.292278 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.576735 0.423265 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 BEST CAYGCK MGCRTG 2055 7182 1348 7182 3.5e-044 3.9e-040 6.4e-043 CACGCT AGCGTG 497 7182 357 7182 4.5e-007 5.0e-003 CATGCT AGCATG 391 7182 284 7182 1.4e-005 1.6e-001 CATGCG CGCATG 422 7182 274 7182 5.0e-009 5.6e-005 CACGCG CGCGTG 1041 7182 577 7182 4.8e-035 5.4e-031 MOTIF CAYGCK 3.9e-040 letter-probability matrix: alength= 4 w= 6 nsites= 2474 E= 3.9e-040 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.671787 0.000000 0.328213 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.639046 0.360954 BEST CACATGG CCATGTG 308 7182 79 7182 3.8e-034 4.1e-030 6.5e-033 CACATGG CCATGTG 308 7182 79 7182 3.8e-034 4.1e-030 MOTIF CACATGG 4.1e-030 letter-probability matrix: alength= 4 w= 7 nsites= 317 E= 4.1e-030 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 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 BEST ATGGCG CGCCAT 445 7182 191 7182 1.3e-025 1.4e-021 9.0e-039 ATGGCG CGCCAT 445 7182 191 7182 1.3e-025 1.4e-021 MOTIF ATGGCG 1.4e-021 letter-probability matrix: alength= 4 w= 6 nsites= 461 E= 1.4e-021 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 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 BEST CYGGGA TCCCRG 1170 7182 812 7182 2.4e-018 2.7e-014 8.1e-025 CTGGGA TCCCAG 593 7182 433 7182 1.2e-007 1.4e-003 CCGGGA TCCCGG 621 7182 404 7182 1.1e-012 1.2e-008 MOTIF CYGGGA 2.7e-014 letter-probability matrix: alength= 4 w= 6 nsites= 1275 E= 2.7e-014 0.000000 1.000000 0.000000 0.000000 0.000000 0.508235 0.000000 0.491765 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 0.000000 BEST CACGAGG CCTCGTG 277 7182 114 7182 1.8e-017 1.9e-013 4.3e-015 CACGAGG CCTCGTG 277 7182 114 7182 1.8e-017 1.9e-013 MOTIF CACGAGG 1.9e-013 letter-probability matrix: alength= 4 w= 7 nsites= 282 E= 1.9e-013 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 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 GGMGGGA TCCCKCC 453 7182 260 7182 5.9e-014 6.5e-010 5.3e-025 GGAGGGA TCCCTCC 190 7182 108 7182 9.2e-007 1.0e-002 GGCGGGA TCCCGCC 269 7182 156 7182 1.5e-008 1.6e-004 MOTIF GGMGGGA 6.5e-010 letter-probability matrix: alength= 4 w= 7 nsites= 470 E= 6.5e-010 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.421277 0.578723 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 0.000000 BEST KACGTCA TGACGTM 142 7182 48 7182 2.0e-012 2.2e-008 3.7e-009 GACGTCA TGACGTC 99 7182 33 7182 3.2e-009 3.5e-005 TACGTCA TGACGTA 46 7182 15 7182 4.3e-005 4.7e-001 MOTIF KACGTCA 2.2e-008 letter-probability matrix: alength= 4 w= 7 nsites= 146 E= 2.2e-008 0.000000 0.000000 0.684932 0.315068 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 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 BEST CCACSCC GGSGTGG 574 7182 372 7182 5.8e-012 6.3e-008 3.7e-012 CCACGCC GGCGTGG 316 7182 182 7182 5.3e-010 5.8e-006 CCACCCC GGGGTGG 264 7182 195 7182 6.2e-004 6.7e+000 MOTIF CCACSCC 6.3e-008 letter-probability matrix: alength= 4 w= 7 nsites= 617 E= 6.3e-008 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 0.448947 0.551053 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 BEST GATGHAA TTDCATC 177 7182 73 7182 1.3e-011 1.4e-007 2.1e-007 GATGAAA TTTCATC 48 7182 22 7182 1.2e-003 1.4e+001 GATGCAA TTGCATC 95 7182 42 7182 3.1e-006 3.4e-002 GATGTAA TTACATC 36 7182 9 7182 3.2e-005 3.5e-001 MOTIF GATGHAA 1.4e-007 letter-probability matrix: alength= 4 w= 7 nsites= 181 E= 1.4e-007 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.270718 0.530387 0.000000 0.198895 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 BEST ABAAA TTTVT 1551 7182 1243 7182 4.7e-011 5.1e-007 1.1e-009 ACAAA TTTGT 680 7182 564 7182 3.2e-004 3.5e+000 ATAAA TTTAT 243 7182 171 7182 1.9e-004 2.1e+000 AGAAA TTTCT 806 7182 628 7182 4.1e-007 4.4e-003 MOTIF ABAAA 5.1e-007 letter-probability matrix: alength= 4 w= 5 nsites= 1875 E= 5.1e-007 1.000000 0.000000 0.000000 0.000000 0.000000 0.398933 0.467200 0.133867 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 BEST TTCCB VGGAA 1295 7182 1021 7182 2.8e-010 3.0e-006 2.4e-065 TTCCT AGGAA 484 7182 360 7182 6.2e-006 6.6e-002 TTCCG CGGAA 442 7182 346 7182 2.5e-004 2.6e+000 TTCCC GGGAA 472 7182 370 7182 1.6e-004 1.8e+000 MOTIF TTCCB 3.0e-006 letter-probability matrix: alength= 4 w= 5 nsites= 1456 E= 3.0e-006 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 0.335165 0.317995 0.346841 BEST TTTWAAW WTTWAAA 73 7182 18 7182 2.3e-009 2.4e-005 3.4e-006 TTTAAAA TTTTAAA 33 7182 12 7182 1.2e-003 1.3e+001 TTTAAAT ATTTAAA 31 7182 5 7182 6.3e-006 6.6e-002 TTTTAAT ATTAAAA 17 7182 4 7182 3.6e-003 3.8e+001 MOTIF TTTWAAW 2.4e-005 letter-probability matrix: alength= 4 w= 7 nsites= 75 E= 2.4e-005 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.520000 0.000000 0.000000 0.480000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.400000 0.000000 0.000000 0.600000 BEST CTRCAGC GCTGYAG 410 7182 262 7182 2.8e-009 2.9e-005 9.0e-006 CTACAGC GCTGTAG 87 7182 39 7182 1.1e-005 1.1e-001 CTGCAGC GCTGCAG 330 7182 224 7182 2.5e-006 2.7e-002 MOTIF CTRCAGC 2.9e-005 letter-probability matrix: alength= 4 w= 7 nsites= 428 E= 2.9e-005 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.205607 0.000000 0.794393 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 0.000000 1.000000 0.000000 0.000000 BEST AAGATGG CCATCTT 91 7182 30 7182 1.1e-008 1.1e-004 1.0e-025 AAGATGG CCATCTT 91 7182 30 7182 1.1e-008 1.1e-004 MOTIF AAGATGG 1.1e-004 letter-probability matrix: alength= 4 w= 7 nsites= 94 E= 1.1e-004 1.000000 0.000000 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 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 BEST AGGTAAR YTTACCT 95 7182 38 7182 3.7e-007 3.9e-003 2.9e-003 AGGTAAA TTTACCT 30 7182 9 7182 5.2e-004 5.5e+000 AGGTAAG CTTACCT 65 7182 29 7182 1.2e-004 1.3e+000 MOTIF AGGTAAR 3.9e-003 letter-probability matrix: alength= 4 w= 7 nsites= 95 E= 3.9e-003 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 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.315789 0.000000 0.684211 0.000000 BEST BCACATG CATGTGV 205 7182 120 7182 1.1e-006 1.1e-002 3.0e-031 CCACATG CATGTGG 79 7182 42 7182 4.7e-004 4.9e+000 GCACATG CATGTGC 81 7182 48 7182 2.2e-003 2.3e+001 TCACATG CATGTGA 61 7182 36 7182 7.0e-003 7.4e+001 MOTIF BCACATG 1.1e-002 letter-probability matrix: alength= 4 w= 7 nsites= 210 E= 1.1e-002 0.000000 0.352381 0.352381 0.295238 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 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 BEST ACCCRGA TCYGGGT 206 7182 121 7182 1.2e-006 1.2e-002 1.9e-008 ACCCGGA TCCGGGT 94 7182 49 7182 9.7e-005 1.0e+000 ACCCAGA TCTGGGT 114 7182 72 7182 1.2e-003 1.3e+001 MOTIF ACCCRGA 1.2e-002 letter-probability matrix: alength= 4 w= 7 nsites= 208 E= 1.2e-002 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.552885 0.000000 0.447115 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 # 20 motifs with E-value < 0.05 found. #elapsed time: 520.15 seconds