******************************************************************************** MEME - Motif discovery tool ******************************************************************************** MEME version 3.0 (Release date: 2004/07/26 08:17:15) For further information on how to interpret these results or to get a copy of the MEME software please access http://meme.sdsc.edu. This file may be used as input to the MAST algorithm for searching sequence databases for matches to groups of motifs. MAST is available for interactive use and downloading at http://meme.sdsc.edu. ******************************************************************************** ******************************************************************************** REFERENCE ******************************************************************************** If you use this program in your research, please cite: Timothy L. Bailey and Charles Elkan, "Fitting a mixture model by expectation maximization to discover motifs in biopolymers", Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology, pp. 28-36, AAAI Press, Menlo Park, California, 1994. ******************************************************************************** ******************************************************************************** TRAINING SET ******************************************************************************** DATAFILE= all_X_B.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ CfBhoxB1 1.0000 501 CfBhoxB2 1.0000 501 CfBhoxB3 1.0000 501 CfBhoxB4 1.0000 501 CfBhoxB5 1.0000 501 CfBhoxB6 1.0000 501 CfBhoxB7 1.0000 501 CfBhoxB8 1.0000 501 CfBhoxB9 1.0000 501 CfBhoxB13 1.0000 501 HsBhoxB1 1.0000 501 HsBhoxB2 1.0000 501 HsBhoxB3 1.0000 501 HsBhoxB4 1.0000 501 HsBhoxB5 1.0000 501 HsBhoxB6 1.0000 501 HsBhoxB7 1.0000 501 HsBhoxB8 1.0000 501 HsBhoxB9 1.0000 501 ******************************************************************************** ******************************************************************************** COMMAND LINE SUMMARY ******************************************************************************** This information can also be useful in the event you wish to report a problem with the MEME software. command: meme all_X_B.fa -dna -mod zoops -minw 10 -maxw 10 -wg 11 -ws 1 -nmotifs 10 -evt 1e+07 -revcomp -maxiter 50 -distance 0.001 -prior dirichlet -b 0.01 -maxsize 1000000 model: mod= zoops nmotifs= 10 evt= 1e+07 object function= E-value of product of p-values width: minw= 10 maxw= 10 minic= 0.00 width: wg= 11 ws= 1 endgaps= yes nsites: minsites= 2 maxsites= 19 wnsites= 0.8 theta: prob= 1 spmap= uni spfuzz= 0.5 em: prior= dirichlet b= 0.01 maxiter= 50 distance= 0.001 data: n= 9519 N= 19 strands: + - sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.223 C 0.277 G 0.277 T 0.223 Background letter frequencies (from dataset with add-one prior applied): A 0.223 C 0.277 G 0.277 T 0.223 ******************************************************************************** ******************************************************************************** MOTIF 1 width = 10 sites = 19 llr = 204 E-value = 8.0e-012 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A ::2:3::::: pos.-specific C :::2:::::: probability G aa8839a9aa matrix T ::::51:1:: bits 2.2 1.9 ** * ** 1.7 ** * ** 1.5 ** ***** Information 1.3 **** ***** content 1.1 **** ***** (15.5 bits) 0.9 **** ***** 0.6 ********** 0.4 ********** 0.2 ********** 0.0 ---------- Multilevel GGGGTGGGGG consensus A sequence G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- ---------- HsBhoxB8 + 193 2.14e-06 TTTTGTTTGG GGGGTGGGGG GTGGGGGGAG HsBhoxB6 + 62 2.14e-06 AATCCTGCGT GGGGTGGGGG AGAGACATAT HsBhoxB5 - 344 2.14e-06 GGTTGGAAGG GGGGTGGGGG GGCGTTAGGG CfBhoxB8 + 192 2.14e-06 TTTTGTTTGG GGGGTGGGGG GTGGGGGGAG CfBhoxB3 + 239 2.14e-06 TGAAGATGTT GGGGTGGGGG AGAAGAAGAA HsBhoxB4 + 270 4.28e-06 GTGGGTGGGT GGGGAGGGGG AAGGGAAGAA HsBhoxB2 - 477 4.28e-06 TTCAATGGTG GGGGAGGGGG CTGCTGGGGG CfBhoxB2 - 477 4.28e-06 TTCAATGGTG GGGGAGGGGG CCTGCTGGGG HsBhoxB3 + 391 6.94e-06 GAGGGGAGGT GGGGGGGGGG GGGTCCGGCG CfBhoxB13 - 79 6.94e-06 CCAGCTGGGG GGGGGGGGGG CGGAAAAGAA CfBhoxB5 - 361 6.94e-06 CCAAATATGG GGGGGGGGGG TTGGAAGGGG HsBhoxB1 - 347 8.67e-06 AAGGGGGTAG GGAGTGGGGG TGAGGGGGCA CfBhoxB1 - 346 8.67e-06 AAGGGGGTAG GGAGTGGGGG TGGAGGGGCG HsBhoxB7 - 225 1.08e-05 CTGTGGATTG GGGCTGGGGG CTCAAGGGCC CfBhoxB7 - 225 1.08e-05 CTGCGGATTG GGGCTGGGGG CTCAAGGGCC HsBhoxB9 + 86 1.47e-05 TCCTGCAGCG GGAGGGGGGG ACCGGGCGGC CfBhoxB4 + 55 1.68e-05 CGGTGAGGCG GGGCAGGGGG CTGGAAGAGA CfBhoxB6 + 82 2.81e-05 TTAATCACTG GGGGATGGGG TGGTCTCAAT CfBhoxB9 + 88 3.24e-05 TGCAAAAAGA GGGGGGGTGG CGGGCGGCCG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- HsBhoxB8 2.1e-06 192_[+1]_299 HsBhoxB6 2.1e-06 61_[+1]_430 HsBhoxB5 2.1e-06 343_[-1]_148 CfBhoxB8 2.1e-06 191_[+1]_300 CfBhoxB3 2.1e-06 238_[+1]_253 HsBhoxB4 4.3e-06 269_[+1]_222 HsBhoxB2 4.3e-06 476_[-1]_15 CfBhoxB2 4.3e-06 476_[-1]_15 HsBhoxB3 6.9e-06 390_[+1]_101 CfBhoxB13 6.9e-06 78_[-1]_413 CfBhoxB5 6.9e-06 360_[-1]_131 HsBhoxB1 8.7e-06 346_[-1]_145 CfBhoxB1 8.7e-06 345_[-1]_146 HsBhoxB7 1.1e-05 224_[-1]_267 CfBhoxB7 1.1e-05 224_[-1]_267 HsBhoxB9 1.5e-05 85_[+1]_406 CfBhoxB4 1.7e-05 54_[+1]_437 CfBhoxB6 2.8e-05 81_[+1]_410 CfBhoxB9 3.2e-05 87_[+1]_404 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=10 seqs=19 HsBhoxB8 ( 193) GGGGTGGGGG 1 HsBhoxB6 ( 62) GGGGTGGGGG 1 HsBhoxB5 ( 344) GGGGTGGGGG 1 CfBhoxB8 ( 192) GGGGTGGGGG 1 CfBhoxB3 ( 239) GGGGTGGGGG 1 HsBhoxB4 ( 270) GGGGAGGGGG 1 HsBhoxB2 ( 477) GGGGAGGGGG 1 CfBhoxB2 ( 477) GGGGAGGGGG 1 HsBhoxB3 ( 391) GGGGGGGGGG 1 CfBhoxB13 ( 79) GGGGGGGGGG 1 CfBhoxB5 ( 361) GGGGGGGGGG 1 HsBhoxB1 ( 347) GGAGTGGGGG 1 CfBhoxB1 ( 346) GGAGTGGGGG 1 HsBhoxB7 ( 225) GGGCTGGGGG 1 CfBhoxB7 ( 225) GGGCTGGGGG 1 HsBhoxB9 ( 86) GGAGGGGGGG 1 CfBhoxB4 ( 55) GGGCAGGGGG 1 CfBhoxB6 ( 82) GGGGATGGGG 1 CfBhoxB9 ( 88) GGGGGGGTGG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 10 n= 9348 bayes= 9.13477 E= 8.0e-012 -1089 -1089 185 -1089 -1089 -1089 185 -1089 -50 -1089 160 -1089 -1089 -81 160 -1089 24 -1089 -7 109 -1089 -1089 177 -208 -1089 -1089 185 -1089 -1089 -1089 177 -208 -1089 -1089 185 -1089 -1089 -1089 185 -1089 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 10 nsites= 19 E= 8.0e-012 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.157895 0.000000 0.842105 0.000000 0.000000 0.157895 0.842105 0.000000 0.263158 0.000000 0.263158 0.473684 0.000000 0.000000 0.947368 0.052632 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.947368 0.052632 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- Time 4.98 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 width = 10 sites = 19 llr = 196 E-value = 1.9e-009 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A 585a3aaa16 pos.-specific C ::5:::::34 probability G 3::::::::: matrix T 22::7:::6: bits 2.2 * *** 1.9 * *** 1.7 * *** 1.5 * * *** Information 1.3 * ***** content 1.1 ******* * (14.9 bits) 0.9 ********* 0.6 ********** 0.4 ********** 0.2 ********** 0.0 ---------- Multilevel AAAATAAATA consensus GTC A CC sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- ---------- HsBhoxB7 - 135 3.04e-07 AGTGGAAGGG AAAATAAATA ACCTCGGGGC HsBhoxB3 - 156 3.04e-07 AAAAAATAAA AAAATAAATA AAGACTATAT CfBhoxB7 - 135 3.04e-07 AGTAGGAGGG AAAATAAATA ACCTCTGAGC CfBhoxB9 - 243 3.06e-06 CGTCAGCTCC AACATAAATC AATCGGGCGA HsBhoxB8 - 180 3.74e-06 CCACCCCCCA AACAAAAATA TACCACCACT HsBhoxB6 - 79 3.74e-06 CCCGGGTGAT TAAATAAATA TGTCTCTCCC CfBhoxB8 - 179 3.74e-06 CCACCCCCCA AACAAAAATA TACCGCCACT CfBhoxB6 - 65 3.74e-06 CCCCAGTGAT TAAATAAATA TATCCCTCCC HsBhoxB9 - 243 8.31e-06 CGTCAGCTCC GACATAAATC AATCGGGCGA CfBhoxB13 - 46 1.00e-05 GGCCGAGGGA AAAAAAAACA GGGGGCCATC HsBhoxB2 + 407 1.47e-05 ATCGCTCCAT TACATAAATC GGGGGGGGTG HsBhoxB5 + 432 1.64e-05 TCATTAATAC ATCATAAATC GTGAAGCACA CfBhoxB5 + 432 1.64e-05 TCATTAATAC ATCATAAATC GTGAAGCACA HsBhoxB4 + 293 1.84e-05 GGAAGAAGGG GAAATAAACC TCTTTGGCTG CfBhoxB4 + 293 1.84e-05 GAAGAAGGGG GAAATAAACC TCTTTGGCTG CfBhoxB3 + 137 1.84e-05 TTTTGAAGTG GAAATAAAAA CTGGTGGGCT CfBhoxB2 + 321 2.07e-05 CCCAAAATTT AAAAAAAAAA AAANNNNNNN HsBhoxB1 - 187 5.20e-05 ACATGGAAGC GTCAAAAACA TCTTTCTTCA CfBhoxB1 - 186 5.20e-05 ACGTGGAAGC GTCAAAAACA TCTTTCTTCA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- HsBhoxB7 3e-07 134_[-2]_357 HsBhoxB3 3e-07 155_[-2]_336 CfBhoxB7 3e-07 134_[-2]_357 CfBhoxB9 3.1e-06 242_[-2]_249 HsBhoxB8 3.7e-06 179_[-2]_312 HsBhoxB6 3.7e-06 78_[-2]_413 CfBhoxB8 3.7e-06 178_[-2]_313 CfBhoxB6 3.7e-06 64_[-2]_427 HsBhoxB9 8.3e-06 242_[-2]_249 CfBhoxB13 1e-05 45_[-2]_446 HsBhoxB2 1.5e-05 406_[+2]_85 HsBhoxB5 1.6e-05 431_[+2]_60 CfBhoxB5 1.6e-05 431_[+2]_60 HsBhoxB4 1.8e-05 292_[+2]_199 CfBhoxB4 1.8e-05 292_[+2]_199 CfBhoxB3 1.8e-05 136_[+2]_355 CfBhoxB2 2.1e-05 320_[+2]_171 HsBhoxB1 5.2e-05 186_[-2]_305 CfBhoxB1 5.2e-05 185_[-2]_306 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=10 seqs=19 HsBhoxB7 ( 135) AAAATAAATA 1 HsBhoxB3 ( 156) AAAATAAATA 1 CfBhoxB7 ( 135) AAAATAAATA 1 CfBhoxB9 ( 243) AACATAAATC 1 HsBhoxB8 ( 180) AACAAAAATA 1 HsBhoxB6 ( 79) TAAATAAATA 1 CfBhoxB8 ( 179) AACAAAAATA 1 CfBhoxB6 ( 65) TAAATAAATA 1 HsBhoxB9 ( 243) GACATAAATC 1 CfBhoxB13 ( 46) AAAAAAAACA 1 HsBhoxB2 ( 407) TACATAAATC 1 HsBhoxB5 ( 432) ATCATAAATC 1 CfBhoxB5 ( 432) ATCATAAATC 1 HsBhoxB4 ( 293) GAAATAAACC 1 CfBhoxB4 ( 293) GAAATAAACC 1 CfBhoxB3 ( 137) GAAATAAAAA 1 CfBhoxB2 ( 321) AAAAAAAAAA 1 HsBhoxB1 ( 187) GTCAAAAACA 1 CfBhoxB1 ( 186) GTCAAAAACA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 10 n= 9348 bayes= 10.7566 E= 1.9e-009 124 -1089 19 -50 182 -1089 -1089 -8 124 77 -1089 -1089 216 -1089 -1089 -1089 50 -1089 -1089 162 216 -1089 -1089 -1089 216 -1089 -1089 -1089 216 -1089 -1089 -1089 -108 -7 -1089 150 150 41 -1089 -1089 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 10 nsites= 19 E= 1.9e-009 0.526316 0.000000 0.315789 0.157895 0.789474 0.000000 0.000000 0.210526 0.526316 0.473684 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.315789 0.000000 0.000000 0.684211 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.105263 0.263158 0.000000 0.631579 0.631579 0.368421 0.000000 0.000000 -------------------------------------------------------------------------------- Time 9.89 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 width = 10 sites = 13 llr = 149 E-value = 4.5e-005 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A 88:::2:1:: pos.-specific C 2241::::aa probability G ::2::::::: matrix T ::49a8a9:: bits 2.2 * * 1.9 * * ** 1.7 ** **** 1.5 ** ******* Information 1.3 ** ******* content 1.1 ** ******* (16.5 bits) 0.9 ** ******* 0.6 ** ******* 0.4 ********** 0.2 ********** 0.0 ---------- Multilevel AACTTTTTCC consensus T sequence G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- ---------- HsBhoxB7 + 298 4.69e-07 AACGCCACAC AATTTTTTCC ACATTACCGG CfBhoxB7 + 298 4.69e-07 AACGCCACAC AATTTTTTCC ACATTACCGG HsBhoxB6 + 42 1.05e-06 AAACACAATT AACTTTTTCC AATCCTGCGT HsBhoxB1 + 132 1.05e-06 ATATTCTCCT AACTTTTTCC CCCTCTCCCT CfBhoxB6 + 29 1.05e-06 AAACACAATT AACTTTTTCC TATCCTGCGT HsBhoxB9 - 278 1.63e-06 TGATTGGTCA AAGTTTTTCC GACTGCCTGA CfBhoxB9 - 278 1.63e-06 TGATTGGTCA AAGTTTTTCC GACTGCCTGA HsBhoxB4 - 458 2.10e-06 AATATACTAA AATTTATTCC GACCCCTGAC CfBhoxB4 - 458 2.10e-06 AATATACTAA AATTTATTCC GACCCCTGAC CfBhoxB1 + 131 8.96e-06 ATATTCCTCT AACTTTTACC CCCTCTCCCT HsBhoxB2 - 69 9.69e-06 AAGCTAGAGG AACCTTTTCC TCATCCCCTT HsBhoxB5 + 192 1.29e-05 TCCCCCTTCT CCTTTTTTCC CCCTCTCTCG CfBhoxB5 + 191 2.04e-05 TCCCCCTTCT CCGTTTTTCC CCCTCTCTCA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- HsBhoxB7 4.7e-07 297_[+3]_194 CfBhoxB7 4.7e-07 297_[+3]_194 HsBhoxB6 1.1e-06 41_[+3]_450 HsBhoxB1 1.1e-06 131_[+3]_360 CfBhoxB6 1.1e-06 28_[+3]_463 HsBhoxB9 1.6e-06 277_[-3]_214 CfBhoxB9 1.6e-06 277_[-3]_214 HsBhoxB4 2.1e-06 457_[-3]_34 CfBhoxB4 2.1e-06 457_[-3]_34 CfBhoxB1 9e-06 130_[+3]_361 HsBhoxB2 9.7e-06 68_[-3]_423 HsBhoxB5 1.3e-05 191_[+3]_300 CfBhoxB5 2e-05 190_[+3]_301 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=10 seqs=13 HsBhoxB7 ( 298) AATTTTTTCC 1 CfBhoxB7 ( 298) AATTTTTTCC 1 HsBhoxB6 ( 42) AACTTTTTCC 1 HsBhoxB1 ( 132) AACTTTTTCC 1 CfBhoxB6 ( 29) AACTTTTTCC 1 HsBhoxB9 ( 278) AAGTTTTTCC 1 CfBhoxB9 ( 278) AAGTTTTTCC 1 HsBhoxB4 ( 458) AATTTATTCC 1 CfBhoxB4 ( 458) AATTTATTCC 1 CfBhoxB1 ( 131) AACTTTTACC 1 HsBhoxB2 ( 69) AACCTTTTCC 1 HsBhoxB5 ( 192) CCTTTTTTCC 1 CfBhoxB5 ( 191) CCGTTTTTCC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 10 n= 9348 bayes= 10.0191 E= 4.5e-005 192 -85 -1035 -1035 192 -85 -1035 -1035 -1035 47 -26 79 -1035 -185 -1035 205 -1035 -1035 -1035 216 -53 -1035 -1035 192 -1035 -1035 -1035 216 -153 -1035 -1035 205 -1035 185 -1035 -1035 -1035 185 -1035 -1035 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 10 nsites= 13 E= 4.5e-005 0.846154 0.153846 0.000000 0.000000 0.846154 0.153846 0.000000 0.000000 0.000000 0.384615 0.230769 0.384615 0.000000 0.076923 0.000000 0.923077 0.000000 0.000000 0.000000 1.000000 0.153846 0.000000 0.000000 0.846154 0.000000 0.000000 0.000000 1.000000 0.076923 0.000000 0.000000 0.923077 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- Time 14.95 secs. ******************************************************************************** ******************************************************************************** MOTIF 4 width = 10 sites = 19 llr = 187 E-value = 1.5e-004 ******************************************************************************** -------------------------------------------------------------------------------- Motif 4 Description -------------------------------------------------------------------------------- Simplified A 1::::a:346 pos.-specific C ::1::::::1 probability G 499aa:a763 matrix T 51:::::::: bits 2.2 * 1.9 **** 1.7 **** 1.5 * **** Information 1.3 ****** content 1.1 ******** (14.2 bits) 0.9 ********* 0.6 ********** 0.4 ********** 0.2 ********** 0.0 ---------- Multilevel TGGGGAGGGA consensus G AAG sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 4 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- ---------- CfBhoxB4 + 267 1.39e-06 GGTGGGTGGG TGGGGAGGGA GAAAGAGAAG HsBhoxB7 - 162 2.51e-06 AGGCGAGATT TGGGGAGGAA GAGATTGAGT CfBhoxB7 - 162 2.51e-06 AGGCGAGATT TGGGGAGGAA TGGATTGAGT HsBhoxB6 + 196 5.35e-06 GTTGTGTTGT TGGGGAGAGA GNNNNNNNNN HsBhoxB2 + 109 5.35e-06 ACGGAGGCAT TGGGGAGAGA GCATGTGAGG CfBhoxB13 + 432 5.35e-06 GGGGCCTGGG TGGGGAGAGA CGGCTGGGTG CfBhoxB6 + 48 1.07e-05 CTATCCTGCG TGGGGAGGGG AGGGATATAT HsBhoxB5 - 178 1.33e-05 AAAAGGAGAA GGGGGAGAAA CAGAGAGAAG HsBhoxB3 + 33 1.33e-05 ATCCCAGAGT TGGGGAGGAG AGATAGGGAG CfBhoxB5 - 177 1.33e-05 AAACGGAGAA GGGGGAGAAA CAGGGAGAAG CfBhoxB2 + 80 1.82e-05 AGGGAGGCAT TGGGGAGAGG GAGTATAGGA CfBhoxB3 + 18 2.21e-05 TGGGTAGGGA GGGGGAGGAG GAGAGCTCAG CfBhoxB1 + 103 2.21e-05 GGGGGTTGGG AGGGGAGGAA AGTCTTGAAT HsBhoxB8 + 206 3.64e-05 GTGGGGGGTG GGGGGAGGGC GAGCGAGCCG CfBhoxB8 + 205 3.64e-05 GTGGGGGGTG GGGGGAGGGC GAGCGAGCCG HsBhoxB9 - 24 3.92e-05 GCGGAGGAGA GGCGGAGGGA AGCGGCGGGC CfBhoxB9 - 23 3.92e-05 GCGGAGGAGA GGCGGAGGGA AAGCAGCGGG HsBhoxB1 + 99 4.49e-05 GCCTTGGGGG TTGGGAGGGA AGGAAAGTCT HsBhoxB4 + 16 4.95e-05 CCTCCCGCCG AGGGGAGGAG ACTGGGGCCT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 4 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- CfBhoxB4 1.4e-06 266_[+4]_225 HsBhoxB7 2.5e-06 161_[-4]_330 CfBhoxB7 2.5e-06 161_[-4]_330 HsBhoxB6 5.3e-06 195_[+4]_296 HsBhoxB2 5.3e-06 108_[+4]_383 CfBhoxB13 5.3e-06 431_[+4]_60 CfBhoxB6 1.1e-05 47_[+4]_444 HsBhoxB5 1.3e-05 177_[-4]_314 HsBhoxB3 1.3e-05 32_[+4]_459 CfBhoxB5 1.3e-05 176_[-4]_315 CfBhoxB2 1.8e-05 79_[+4]_412 CfBhoxB3 2.2e-05 17_[+4]_474 CfBhoxB1 2.2e-05 102_[+4]_389 HsBhoxB8 3.6e-05 205_[+4]_286 CfBhoxB8 3.6e-05 204_[+4]_287 HsBhoxB9 3.9e-05 23_[-4]_468 CfBhoxB9 3.9e-05 22_[-4]_469 HsBhoxB1 4.5e-05 98_[+4]_393 HsBhoxB4 4.9e-05 15_[+4]_476 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 4 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 4 width=10 seqs=19 CfBhoxB4 ( 267) TGGGGAGGGA 1 HsBhoxB7 ( 162) TGGGGAGGAA 1 CfBhoxB7 ( 162) TGGGGAGGAA 1 HsBhoxB6 ( 196) TGGGGAGAGA 1 HsBhoxB2 ( 109) TGGGGAGAGA 1 CfBhoxB13 ( 432) TGGGGAGAGA 1 CfBhoxB6 ( 48) TGGGGAGGGG 1 HsBhoxB5 ( 178) GGGGGAGAAA 1 HsBhoxB3 ( 33) TGGGGAGGAG 1 CfBhoxB5 ( 177) GGGGGAGAAA 1 CfBhoxB2 ( 80) TGGGGAGAGG 1 CfBhoxB3 ( 18) GGGGGAGGAG 1 CfBhoxB1 ( 103) AGGGGAGGAA 1 HsBhoxB8 ( 206) GGGGGAGGGC 1 CfBhoxB8 ( 205) GGGGGAGGGC 1 HsBhoxB9 ( 24) GGCGGAGGGA 1 CfBhoxB9 ( 23) GGCGGAGGGA 1 HsBhoxB1 ( 99) TTGGGAGGGA 1 HsBhoxB4 ( 16) AGGGGAGGAG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 4 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 10 n= 9348 bayes= 8.93958 E= 1.5e-004 -108 -1089 41 124 -1089 -1089 177 -208 -1089 -139 169 -1089 -1089 -1089 185 -1089 -1089 -1089 185 -1089 216 -1089 -1089 -1089 -1089 -1089 185 -1089 50 -1089 130 -1089 92 -1089 106 -1089 150 -139 -7 -1089 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 4 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 10 nsites= 19 E= 1.5e-004 0.105263 0.000000 0.368421 0.526316 0.000000 0.000000 0.947368 0.052632 0.000000 0.105263 0.894737 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 0.000000 0.000000 1.000000 0.000000 0.315789 0.000000 0.684211 0.000000 0.421053 0.000000 0.578947 0.000000 0.631579 0.105263 0.263158 0.000000 -------------------------------------------------------------------------------- Time 19.63 secs. ******************************************************************************** ******************************************************************************** MOTIF 5 width = 10 sites = 14 llr = 147 E-value = 2.4e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif 5 Description -------------------------------------------------------------------------------- Simplified A 1:1:a::::: pos.-specific C :397:::::9 probability G 67:1:::aa: matrix T 3::1:aa::1 bits 2.2 *** 1.9 ***** 1.7 ***** 1.5 ***** Information 1.3 * ****** content 1.1 ** ****** (15.2 bits) 0.9 ** ****** 0.6 ********** 0.4 ********** 0.2 ********** 0.0 ---------- Multilevel GGCCATTGGC consensus TC sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 5 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- ---------- HsBhoxB7 + 338 1.39e-06 GAGACGGCCC GGCCATTGGC GGAGGGGACG HsBhoxB4 + 364 1.39e-06 CAGGCGGGGC GGCCATTGGC TCGGAGGATC CfBhoxB7 + 338 1.39e-06 GAGGCTGCCG GGCCATTGGC GGAGGGCGCG CfBhoxB4 + 364 1.39e-06 CAGGCGGGGC GGCCATTGGC TCCGAGGATC HsBhoxB1 + 310 3.89e-06 GGCCCGCTTA GCCCATTGGC CTGGGAGAGA CfBhoxB1 + 309 3.89e-06 GGCCCGCTGC GCCCATTGGC CTGGGAGAGA HsBhoxB3 - 432 9.48e-06 CCTCAGGACC GGACATTGGC AACCCTGGGG CfBhoxB3 - 432 9.48e-06 CCTCACGACC GGACATTGGC ACCCGCGGGG HsBhoxB6 + 316 1.36e-05 TTCCTGCCTC TGCCATTGGT CAGTGTTGGA CfBhoxB6 + 316 1.36e-05 TTCCTGCCTC TGCCATTGGT CAGTGTTGGA HsBhoxB8 - 20 2.53e-05 AGACCCCGCA TCCTATTGGC TTCTTCGTAC HsBhoxB2 + 234 2.53e-05 GGCCCAGACG AGCGATTGGC GGAGGCCGGT CfBhoxB8 - 19 2.53e-05 AGCCCCCGCA TCCTATTGGC TTCTCCGTAC CfBhoxB2 + 192 2.53e-05 GGCCCAGACA AGCGATTGGC CGAGGCCAGT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 5 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- HsBhoxB7 1.4e-06 337_[+5]_154 HsBhoxB4 1.4e-06 363_[+5]_128 CfBhoxB7 1.4e-06 337_[+5]_154 CfBhoxB4 1.4e-06 363_[+5]_128 HsBhoxB1 3.9e-06 309_[+5]_182 CfBhoxB1 3.9e-06 308_[+5]_183 HsBhoxB3 9.5e-06 431_[-5]_60 CfBhoxB3 9.5e-06 431_[-5]_60 HsBhoxB6 1.4e-05 315_[+5]_176 CfBhoxB6 1.4e-05 315_[+5]_176 HsBhoxB8 2.5e-05 19_[-5]_472 HsBhoxB2 2.5e-05 233_[+5]_258 CfBhoxB8 2.5e-05 18_[-5]_473 CfBhoxB2 2.5e-05 191_[+5]_300 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 5 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 5 width=10 seqs=14 HsBhoxB7 ( 338) GGCCATTGGC 1 HsBhoxB4 ( 364) GGCCATTGGC 1 CfBhoxB7 ( 338) GGCCATTGGC 1 CfBhoxB4 ( 364) GGCCATTGGC 1 HsBhoxB1 ( 310) GCCCATTGGC 1 CfBhoxB1 ( 309) GCCCATTGGC 1 HsBhoxB3 ( 432) GGACATTGGC 1 CfBhoxB3 ( 432) GGACATTGGC 1 HsBhoxB6 ( 316) TGCCATTGGT 1 CfBhoxB6 ( 316) TGCCATTGGT 1 HsBhoxB8 ( 20) TCCTATTGGC 1 HsBhoxB2 ( 234) AGCGATTGGC 1 CfBhoxB8 ( 19) TCCTATTGGC 1 CfBhoxB2 ( 192) AGCGATTGGC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 5 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 10 n= 9348 bayes= 9.98739 E= 2.4e+000 -64 -1045 104 36 -1045 4 137 -1045 -64 163 -1045 -1045 -1045 137 -95 -64 216 -1045 -1045 -1045 -1045 -1045 -1045 216 -1045 -1045 -1045 216 -1045 -1045 185 -1045 -1045 -1045 185 -1045 -1045 163 -1045 -64 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 5 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 10 nsites= 14 E= 2.4e+000 0.142857 0.000000 0.571429 0.285714 0.000000 0.285714 0.714286 0.000000 0.142857 0.857143 0.000000 0.000000 0.000000 0.714286 0.142857 0.142857 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 0.000000 0.000000 1.000000 0.000000 0.000000 0.857143 0.000000 0.142857 -------------------------------------------------------------------------------- Time 23.39 secs. ******************************************************************************** ******************************************************************************** MOTIF 6 width = 10 sites = 12 llr = 137 E-value = 1.5e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 6 Description -------------------------------------------------------------------------------- Simplified A 78:aa7:3a: pos.-specific C :1a::227:: probability G :1:::::::: matrix T 3::::28::a bits 2.2 ** ** 1.9 *** ** 1.7 *** ** 1.5 *** * ** Information 1.3 ***** * ** content 1.1 ***** **** (16.4 bits) 0.9 ********** 0.6 ********** 0.4 ********** 0.2 ********** 0.0 ---------- Multilevel AACAAATCAT consensus T A sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 6 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- ---------- HsBhoxB6 + 448 4.69e-07 TATAAAACAC AACAAATCAT AAACCCGGCG CfBhoxB6 + 448 4.69e-07 TATAAAACAC AACAAATCAT AAACCCGGCG HsBhoxB7 + 480 1.32e-06 CGTCCCTGCC TACAAATCAT CCGGCCAAAT CfBhoxB7 + 480 1.32e-06 CGTCCCTGCC TACAAATCAT CCGGCCAAAT HsBhoxB5 - 253 1.69e-06 GCTCTATGGT TACAAATAAT GACGATCCGA CfBhoxB5 - 252 1.69e-06 GCTCTATGGT TACAAATAAT GACGATCCGA HsBhoxB8 + 83 2.75e-06 CAAAATATGA AACAACTCAT TTGCAGGGAA CfBhoxB8 + 82 2.75e-06 CAAAATATGA AACAACTCAT TTGCAGGGAA HsBhoxB2 + 196 9.70e-06 AATCAATTAA ACCAAATAAT GCTCTCTGTT CfBhoxB2 + 154 9.70e-06 AATCAATTAA AGCAAATAAT GCTCTCTGTT HsBhoxB9 + 173 1.14e-05 ATCAGCATAA AACAATCCAT CCTCGATATG CfBhoxB9 + 173 1.14e-05 ATCAGCATAA AACAATCCAT CCTCGATATG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 6 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- HsBhoxB6 4.7e-07 447_[+6]_44 CfBhoxB6 4.7e-07 447_[+6]_44 HsBhoxB7 1.3e-06 479_[+6]_12 CfBhoxB7 1.3e-06 479_[+6]_12 HsBhoxB5 1.7e-06 252_[-6]_239 CfBhoxB5 1.7e-06 251_[-6]_240 HsBhoxB8 2.7e-06 82_[+6]_409 CfBhoxB8 2.7e-06 81_[+6]_410 HsBhoxB2 9.7e-06 195_[+6]_296 CfBhoxB2 9.7e-06 153_[+6]_338 HsBhoxB9 1.1e-05 172_[+6]_319 CfBhoxB9 1.1e-05 172_[+6]_319 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 6 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 6 width=10 seqs=12 HsBhoxB6 ( 448) AACAAATCAT 1 CfBhoxB6 ( 448) AACAAATCAT 1 HsBhoxB7 ( 480) TACAAATCAT 1 CfBhoxB7 ( 480) TACAAATCAT 1 HsBhoxB5 ( 253) TACAAATAAT 1 CfBhoxB5 ( 252) TACAAATAAT 1 HsBhoxB8 ( 83) AACAACTCAT 1 CfBhoxB8 ( 82) AACAACTCAT 1 HsBhoxB2 ( 196) ACCAAATAAT 1 CfBhoxB2 ( 154) AGCAAATAAT 1 HsBhoxB9 ( 173) AACAATCCAT 1 CfBhoxB9 ( 173) AACAATCCAT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 6 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 10 n= 9348 bayes= 10.0516 E= 1.5e-001 158 -1023 -1023 58 190 -173 -173 -1023 -1023 185 -1023 -1023 216 -1023 -1023 -1023 216 -1023 -1023 -1023 158 -73 -1023 -42 -1023 -73 -1023 190 58 127 -1023 -1023 216 -1023 -1023 -1023 -1023 -1023 -1023 216 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 6 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 10 nsites= 12 E= 1.5e-001 0.666667 0.000000 0.000000 0.333333 0.833333 0.083333 0.083333 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 0.666667 0.166667 0.000000 0.166667 0.000000 0.166667 0.000000 0.833333 0.333333 0.666667 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 -------------------------------------------------------------------------------- Time 27.04 secs. ******************************************************************************** ******************************************************************************** MOTIF 7 width = 10 sites = 8 llr = 99 E-value = 8.9e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 7 Description -------------------------------------------------------------------------------- Simplified A a:::a:::6a pos.-specific C :::::::a:: probability G ::8a::4:4: matrix T :a3::a6::: bits 2.2 ** ** * 1.9 ** *** * * 1.7 ** *** * * 1.5 ** *** * * Information 1.3 ** *** * * content 1.1 ********** (17.8 bits) 0.9 ********** 0.6 ********** 0.4 ********** 0.2 ********** 0.0 ---------- Multilevel ATGGATTCAA consensus T G G sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 7 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- ---------- HsBhoxB8 + 43 2.03e-06 GGGGTCTCTA ATGGATGCAA ATGATCATGA HsBhoxB3 + 286 2.03e-06 AGTTCCTAAG ATGGATTCGA GCCCCAGTCC HsBhoxB1 + 404 2.03e-06 GGGTCAGGCC ATGGATTCGA GCCCCAGCGC CfBhoxB8 + 42 2.03e-06 GGGGGCTCTA ATGGATGCAA ATGATCATGA CfBhoxB3 + 295 2.03e-06 AGCTCCTAAG ATGGATTCGA GCCCCAGTCC CfBhoxB1 + 404 2.03e-06 GGGCCAGGCC ATGGATGCAA GCTTCAGCGC HsBhoxB2 - 183 2.50e-06 ATTTGGTTTA ATTGATTCAA AAACACCAGA CfBhoxB2 - 141 2.50e-06 ATTTGCTTTA ATTGATTCAA AAACTCTAGA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 7 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- HsBhoxB8 2e-06 42_[+7]_449 HsBhoxB3 2e-06 285_[+7]_206 HsBhoxB1 2e-06 403_[+7]_88 CfBhoxB8 2e-06 41_[+7]_450 CfBhoxB3 2e-06 294_[+7]_197 CfBhoxB1 2e-06 403_[+7]_88 HsBhoxB2 2.5e-06 182_[-7]_309 CfBhoxB2 2.5e-06 140_[-7]_351 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 7 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 7 width=10 seqs=8 HsBhoxB8 ( 43) ATGGATGCAA 1 HsBhoxB3 ( 286) ATGGATTCGA 1 HsBhoxB1 ( 404) ATGGATTCGA 1 CfBhoxB8 ( 42) ATGGATGCAA 1 CfBhoxB3 ( 295) ATGGATTCGA 1 CfBhoxB1 ( 404) ATGGATGCAA 1 HsBhoxB2 ( 183) ATTGATTCAA 1 CfBhoxB2 ( 141) ATTGATTCAA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 7 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 10 n= 9348 bayes= 10.1892 E= 8.9e+001 216 -965 -965 -965 -965 -965 -965 216 -965 -965 144 16 -965 -965 185 -965 216 -965 -965 -965 -965 -965 -965 216 -965 -965 44 149 -965 185 -965 -965 149 -965 44 -965 216 -965 -965 -965 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 7 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 10 nsites= 8 E= 8.9e+001 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.750000 0.250000 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 0.375000 0.625000 0.000000 1.000000 0.000000 0.000000 0.625000 0.000000 0.375000 0.000000 1.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- Time 30.83 secs. ******************************************************************************** ******************************************************************************** MOTIF 8 width = 10 sites = 6 llr = 77 E-value = 4.9e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif 8 Description -------------------------------------------------------------------------------- Simplified A aa:::a7:aa pos.-specific C :::37::::: probability G :::::::::: matrix T ::a73:3a:: bits 2.2 *** * *** 1.9 *** * *** 1.7 *** * *** 1.5 *** * *** Information 1.3 *** ***** content 1.1 ********** (18.6 bits) 0.9 ********** 0.6 ********** 0.4 ********** 0.2 ********** 0.0 ---------- Multilevel AATTCAATAA consensus CT T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 8 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- ---------- HsBhoxB8 + 490 3.78e-07 GCCGCCTCAA AATTCAATAA AA CfBhoxB8 + 490 3.78e-07 NNNNNNTCAA AATTCAATAA AA HsBhoxB5 + 419 1.06e-06 GCATCGCTAT AATTCATTAA TACATCATAA CfBhoxB5 + 419 1.06e-06 GCATCGCTAT AATTCATTAA TACATCATAA HsBhoxB1 + 61 2.21e-06 AATTTGTCCA AATCTAATAA CCCAGGAGCC CfBhoxB1 + 60 2.21e-06 AATTTGTCCA AATCTAATAA CCCGGGAGCC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 8 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- HsBhoxB8 3.8e-07 489_[+8]_2 CfBhoxB8 3.8e-07 489_[+8]_2 HsBhoxB5 1.1e-06 418_[+8]_73 CfBhoxB5 1.1e-06 418_[+8]_73 HsBhoxB1 2.2e-06 60_[+8]_431 CfBhoxB1 2.2e-06 59_[+8]_432 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 8 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 8 width=10 seqs=6 HsBhoxB8 ( 490) AATTCAATAA 1 CfBhoxB8 ( 490) AATTCAATAA 1 HsBhoxB5 ( 419) AATTCATTAA 1 CfBhoxB5 ( 419) AATTCATTAA 1 HsBhoxB1 ( 61) AATCTAATAA 1 CfBhoxB1 ( 60) AATCTAATAA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 8 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 10 n= 9348 bayes= 11.0523 E= 4.9e+003 216 -923 -923 -923 216 -923 -923 -923 -923 -923 -923 216 -923 27 -923 158 -923 127 -923 58 216 -923 -923 -923 158 -923 -923 58 -923 -923 -923 216 216 -923 -923 -923 216 -923 -923 -923 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 8 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 10 nsites= 6 E= 4.9e+003 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 0.333333 0.000000 0.666667 0.000000 0.666667 0.000000 0.333333 1.000000 0.000000 0.000000 0.000000 0.666667 0.000000 0.000000 0.333333 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- Time 35.13 secs. ******************************************************************************** ******************************************************************************** MOTIF 9 width = 10 sites = 12 llr = 134 E-value = 2.4e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif 9 Description -------------------------------------------------------------------------------- Simplified A :::68aa3:: pos.-specific C :aa12:::49 probability G :::3:::8:: matrix T a:::::::61 bits 2.2 * ** 1.9 *** ** 1.7 *** ** 1.5 *** *** * Information 1.3 *** *** * content 1.1 *** ****** (16.1 bits) 0.9 *** ****** 0.6 ********** 0.4 ********** 0.2 ********** 0.0 ---------- Multilevel TCCAAAAGTC consensus G AC sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 9 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- ---------- HsBhoxB8 - 245 7.24e-07 CAGAGAAGCC TCCAAAAGTC TAAGCTTGCA HsBhoxB1 + 165 7.24e-07 GTCCCTTCTT TCCAAAAGTC TTTGAAGAAA CfBhoxB8 - 244 7.24e-07 CAGCGAAGCC TCCAAAAGTC TAAGCTTGCA CfBhoxB1 + 164 7.24e-07 GTCCCTTCTT TCCAAAAGTC TTTGAAGAAA HsBhoxB9 + 399 4.22e-06 GGGGGTCGCG TCCGAAAGCC CTCACACCGG HsBhoxB4 - 425 4.22e-06 TTTTCCTGTT TCCGAAAGCC CTCCTACTTA CfBhoxB9 + 399 4.22e-06 GGGGGTCGCG TCCGAAAGCC CTCACACCGG CfBhoxB4 - 425 4.22e-06 TTTTCCTGTT TCCGAAAGCC CTCCTACTTA HsBhoxB5 + 470 1.19e-05 ACGACCACGA TCCACAAATC AAGCCCTCCA CfBhoxB5 + 470 1.19e-05 ACGACCACGA TCCACAAATC AAGCCCTCCA CfBhoxB2 - 5 1.38e-05 GATGGGAGGT TCCAAAAGCT GGGA HsBhoxB2 + 390 1.57e-05 AATCTCCCCC TCCCAAAATC GCTCCATTAC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 9 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- HsBhoxB8 7.2e-07 244_[-9]_247 HsBhoxB1 7.2e-07 164_[+9]_327 CfBhoxB8 7.2e-07 243_[-9]_248 CfBhoxB1 7.2e-07 163_[+9]_328 HsBhoxB9 4.2e-06 398_[+9]_93 HsBhoxB4 4.2e-06 424_[-9]_67 CfBhoxB9 4.2e-06 398_[+9]_93 CfBhoxB4 4.2e-06 424_[-9]_67 HsBhoxB5 1.2e-05 469_[+9]_22 CfBhoxB5 1.2e-05 469_[+9]_22 CfBhoxB2 1.4e-05 4_[-9]_487 HsBhoxB2 1.6e-05 389_[+9]_102 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 9 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 9 width=10 seqs=12 HsBhoxB8 ( 245) TCCAAAAGTC 1 HsBhoxB1 ( 165) TCCAAAAGTC 1 CfBhoxB8 ( 244) TCCAAAAGTC 1 CfBhoxB1 ( 164) TCCAAAAGTC 1 HsBhoxB9 ( 399) TCCGAAAGCC 1 HsBhoxB4 ( 425) TCCGAAAGCC 1 CfBhoxB9 ( 399) TCCGAAAGCC 1 CfBhoxB4 ( 425) TCCGAAAGCC 1 HsBhoxB5 ( 470) TCCACAAATC 1 CfBhoxB5 ( 470) TCCACAAATC 1 CfBhoxB2 ( 5) TCCAAAAGCT 1 HsBhoxB2 ( 390) TCCCAAAATC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 9 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 10 n= 9348 bayes= 10.7042 E= 2.4e+000 -1023 -1023 -1023 216 -1023 185 -1023 -1023 -1023 185 -1023 -1023 139 -173 27 -1023 190 -73 -1023 -1023 216 -1023 -1023 -1023 216 -1023 -1023 -1023 16 -1023 144 -1023 -1023 59 -1023 139 -1023 173 -1023 -142 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 9 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 10 nsites= 12 E= 2.4e+000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.583333 0.083333 0.333333 0.000000 0.833333 0.166667 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.250000 0.000000 0.750000 0.000000 0.000000 0.416667 0.000000 0.583333 0.000000 0.916667 0.000000 0.083333 -------------------------------------------------------------------------------- Time 39.46 secs. ******************************************************************************** ******************************************************************************** MOTIF 10 width = 10 sites = 17 llr = 163 E-value = 4.0e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 10 Description -------------------------------------------------------------------------------- Simplified A :1:82:6::: pos.-specific C :13::::::4 probability G a8718a:aa6 matrix T :1:1::4::: bits 2.2 1.9 * * ** 1.7 * * ** 1.5 * * ** Information 1.3 * ****** content 1.1 * ******* (13.8 bits) 0.9 ********** 0.6 ********** 0.4 ********** 0.2 ********** 0.0 ---------- Multilevel GGGAGGAGGG consensus C T C sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 10 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- ---------- HsBhoxB6 - 125 1.72e-06 GTGCCTTTGA GGGAGGAGGG AACGTTTAGA CfBhoxB8 - 343 1.72e-06 GAGAGGGAAA GGGAGGAGGG GGAAXXXXXX CfBhoxB6 - 111 1.72e-06 GTGTCTTGGA GGGAGGAGGG AGCATTTGGA CfBhoxB13 - 292 3.45e-06 CGCGGCCTGC GGGAGGAGGC TAATAAAATC CfBhoxB7 + 87 5.17e-06 CAACCGGCTG GGGAGGTGGG TGGTGGTGGT CfBhoxB2 + 424 6.90e-06 ACCTGGGGGG GGCAGGAGGG GGGGTCCCTT HsBhoxB5 + 131 8.62e-06 GTCGGTCGCC GGGAGGTGGC GCGCTCTGCT CfBhoxB5 + 130 8.62e-06 GCCGACCACC GGGAGGTGGC GCGCTCTGCT HsBhoxB7 + 104 1.97e-05 TGAAGAGGAT GGGTGGAGGG TGACACGGAT HsBhoxB1 + 450 2.70e-05 AAGGTTGTAG GGCAAGAGGG TGTCTCCCCC CfBhoxB1 + 450 2.70e-05 AAGGTTGTAG GGCAAGAGGG TGTCTCCCCC CfBhoxB3 + 205 2.97e-05 TTTCAGGTCA GGGAAGTGGC CTCAGCATCT HsBhoxB9 - 426 3.73e-05 CCCAAGCAGG GAGAGGTGGC ACCCGGACCG CfBhoxB9 - 426 3.73e-05 CCCAAGCAGG GAGAGGTGGC ACCCAGACCG HsBhoxB2 - 453 6.11e-05 TGGGGGGGGC GTCAGGAGGG AGGATCGGAA HsBhoxB4 - 5 8.39e-05 TCCTCCCCTC GGCGGGAGGG AGCG CfBhoxB4 + 209 1.46e-04 AGAGAGCTGG GCGTGGAGGC GGTCGCCCCG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 10 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- HsBhoxB6 1.7e-06 124_[-10]_367 CfBhoxB8 1.7e-06 342_[-10]_149 CfBhoxB6 1.7e-06 110_[-10]_381 CfBhoxB13 3.4e-06 291_[-10]_200 CfBhoxB7 5.2e-06 86_[+10]_405 CfBhoxB2 6.9e-06 423_[+10]_68 HsBhoxB5 8.6e-06 130_[+10]_361 CfBhoxB5 8.6e-06 129_[+10]_362 HsBhoxB7 2e-05 103_[+10]_388 HsBhoxB1 2.7e-05 449_[+10]_42 CfBhoxB1 2.7e-05 449_[+10]_42 CfBhoxB3 3e-05 204_[+10]_287 HsBhoxB9 3.7e-05 425_[-10]_66 CfBhoxB9 3.7e-05 425_[-10]_66 HsBhoxB2 6.1e-05 452_[-10]_39 HsBhoxB4 8.4e-05 4_[-10]_487 CfBhoxB4 0.00015 208_[+10]_283 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 10 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 10 width=10 seqs=17 HsBhoxB6 ( 125) GGGAGGAGGG 1 CfBhoxB8 ( 343) GGGAGGAGGG 1 CfBhoxB6 ( 111) GGGAGGAGGG 1 CfBhoxB13 ( 292) GGGAGGAGGC 1 CfBhoxB7 ( 87) GGGAGGTGGG 1 CfBhoxB2 ( 424) GGCAGGAGGG 1 HsBhoxB5 ( 131) GGGAGGTGGC 1 CfBhoxB5 ( 130) GGGAGGTGGC 1 HsBhoxB7 ( 104) GGGTGGAGGG 1 HsBhoxB1 ( 450) GGCAAGAGGG 1 CfBhoxB1 ( 450) GGCAAGAGGG 1 CfBhoxB3 ( 205) GGGAAGTGGC 1 HsBhoxB9 ( 426) GAGAGGTGGC 1 CfBhoxB9 ( 426) GAGAGGTGGC 1 HsBhoxB2 ( 453) GTCAGGAGGG 1 HsBhoxB4 ( 5) GGCGGGAGGG 1 CfBhoxB4 ( 209) GCGTGGAGGC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 10 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 10 n= 9348 bayes= 8.97034 E= 4.0e+001 -1073 -1073 185 -1073 -92 -223 146 -192 -1073 9 135 -1073 188 -1073 -223 -92 -34 -1073 157 -1073 -1073 -1073 185 -1073 154 -1073 -1073 66 -1073 -1073 185 -1073 -1073 -1073 185 -1073 -1073 57 109 -1073 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 10 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 10 nsites= 17 E= 4.0e+001 0.000000 0.000000 1.000000 0.000000 0.117647 0.058824 0.764706 0.058824 0.000000 0.294118 0.705882 0.000000 0.823529 0.000000 0.058824 0.117647 0.176471 0.000000 0.823529 0.000000 0.000000 0.000000 1.000000 0.000000 0.647059 0.000000 0.000000 0.352941 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.411765 0.588235 0.000000 -------------------------------------------------------------------------------- Time 43.48 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- CfBhoxB1 4.93e-11 59_[+8(2.21e-06)]_33_[+4(2.21e-05)]_18_[+3(8.96e-06)]_23_[+9(7.24e-07)]_12_[-2(5.20e-05)]_113_[+5(3.89e-06)]_27_[-1(8.67e-06)]_48_[+7(2.03e-06)]_36_[+10(2.70e-05)]_42 CfBhoxB2 9.12e-10 4_[-9(1.38e-05)]_65_[+4(1.82e-05)]_7_[+1(6.06e-05)]_34_[-7(2.50e-06)]_3_[+6(9.70e-06)]_28_[+5(2.53e-05)]_119_[+2(2.07e-05)]_59_[+9(1.57e-05)]_24_[+10(6.90e-06)]_18_[-10(6.11e-05)]_15_[-1(4.28e-06)]_15 CfBhoxB3 2.48e-06 [+1(4.87e-05)]_7_[+4(2.21e-05)]_96_[-2(3.93e-05)]_3_[+2(1.84e-05)]_58_[+10(2.97e-05)]_24_[+1(2.14e-06)]_46_[+7(2.03e-06)]_11_[-4(3.29e-05)]_106_[-5(9.48e-06)]_60 CfBhoxB4 3.37e-08 8_[+1(5.21e-05)]_36_[+1(1.68e-05)]_202_[+4(1.39e-06)]_16_[+2(1.84e-05)]_61_[+5(1.39e-06)]_51_[-9(4.22e-06)]_23_[-3(2.10e-06)]_34 CfBhoxB5 1.22e-09 129_[+10(8.62e-06)]_37_[-4(1.33e-05)]_4_[+3(2.04e-05)]_51_[-6(1.69e-06)]_82_[-1(2.81e-05)]_7_[-1(6.94e-06)]_48_[+8(1.06e-06)]_3_[+2(1.64e-05)]_28_[+9(1.19e-05)]_22 CfBhoxB6 2.76e-10 28_[+3(1.05e-06)]_9_[+4(1.07e-05)]_7_[-2(3.74e-06)]_7_[+1(2.81e-05)]_19_[-10(1.72e-06)]_195_[+5(1.36e-05)]_122_[+6(4.69e-07)]_34_[-4(7.54e-05)] CfBhoxB7 2.31e-13 86_[+10(5.17e-06)]_38_[-2(3.04e-07)]_17_[-4(2.51e-06)]_17_[-10(5.44e-05)]_26_[-1(1.08e-05)]_63_[+3(4.69e-07)]_30_[+5(1.39e-06)]_40_[-3(1.52e-05)]_82_[+6(1.32e-06)]_12 CfBhoxB8 1.41e-13 18_[-5(2.53e-05)]_13_[+7(2.03e-06)]_30_[+6(2.75e-06)]_26_[-2(4.58e-05)]_51_[-2(3.74e-06)]_3_[+1(2.14e-06)]_3_[+4(3.64e-05)]_29_[-9(7.24e-07)]_89_[-10(1.72e-06)]_137_[+8(3.78e-07)]_2 CfBhoxB9 7.88e-07 22_[-4(3.92e-05)]_1_[-4(7.94e-05)]_44_[+1(3.24e-05)]_75_[+6(1.14e-05)]_60_[-2(3.06e-06)]_25_[-3(1.63e-06)]_111_[+9(4.22e-06)]_17_[-10(3.73e-05)]_66 CfBhoxB13 6.16e-04 45_[-2(1.00e-05)]_23_[-1(6.94e-06)]_203_[-10(3.45e-06)]_130_[+4(5.35e-06)]_20_[-1(1.95e-05)]_30 HsBhoxB1 1.25e-11 60_[+8(2.21e-06)]_28_[+4(4.49e-05)]_23_[+3(1.05e-06)]_23_[+9(7.24e-07)]_12_[-2(5.20e-05)]_113_[+5(3.89e-06)]_27_[-1(8.67e-06)]_47_[+7(2.03e-06)]_36_[+10(2.70e-05)]_42 HsBhoxB2 1.59e-10 68_[-3(9.69e-06)]_30_[+4(5.35e-06)]_64_[-7(2.50e-06)]_3_[+6(9.70e-06)]_28_[+5(2.53e-05)]_116_[+2(6.09e-05)]_20_[+9(1.57e-05)]_7_[+2(1.47e-05)]_12_[+1(1.47e-05)]_14_[-10(6.11e-05)]_14_[-1(4.28e-06)]_15 HsBhoxB3 1.54e-08 32_[+4(1.33e-05)]_113_[-2(3.04e-07)]_64_[+4(1.07e-05)]_46_[+7(2.03e-06)]_11_[-4(3.29e-05)]_67_[+10(5.17e-06)]_38_[-5(9.48e-06)]_60 HsBhoxB4 3.80e-08 4_[-10(8.39e-05)]_1_[+4(4.95e-05)]_5_[-9(9.75e-05)]_229_[+1(4.28e-06)]_13_[+2(1.84e-05)]_61_[+5(1.39e-06)]_51_[-9(4.22e-06)]_23_[-3(2.10e-06)]_34 HsBhoxB5 2.96e-10 130_[+10(8.62e-06)]_37_[-4(1.33e-05)]_4_[+3(1.29e-05)]_51_[-6(1.69e-06)]_81_[-1(2.14e-06)]_8_[-1(6.94e-06)]_47_[+8(1.06e-06)]_3_[+2(1.64e-05)]_28_[+9(1.19e-05)]_22 HsBhoxB6 4.81e-11 41_[+3(1.05e-06)]_10_[+1(2.14e-06)]_7_[-2(3.74e-06)]_36_[-10(1.72e-06)]_61_[+4(5.35e-06)]_110_[+5(1.36e-05)]_122_[+6(4.69e-07)]_34_[-4(7.54e-05)] HsBhoxB7 6.94e-13 103_[+10(1.97e-05)]_21_[-2(3.04e-07)]_17_[-4(2.51e-06)]_17_[-10(5.44e-05)]_26_[-1(1.08e-05)]_63_[+3(4.69e-07)]_30_[+5(1.39e-06)]_40_[-3(1.52e-05)]_82_[+6(1.32e-06)]_12 HsBhoxB8 2.16e-12 19_[-5(2.53e-05)]_13_[+7(2.03e-06)]_30_[+6(2.75e-06)]_26_[-2(4.58e-05)]_51_[-2(3.74e-06)]_3_[+1(2.14e-06)]_3_[+4(3.64e-05)]_29_[-9(7.24e-07)]_235_[+8(3.78e-07)]_2 HsBhoxB9 9.24e-07 23_[-4(3.92e-05)]_1_[-4(7.94e-05)]_41_[+1(1.47e-05)]_77_[+6(1.14e-05)]_60_[-2(8.31e-06)]_25_[-3(1.63e-06)]_111_[+9(4.22e-06)]_17_[-10(3.73e-05)]_66 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 10 reached. ******************************************************************************** CPU: hotchocolate.bioinf.uni-leipzig.de ********************************************************************************