******************************************************************************** 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_X.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ HsA 1.0000 501 HsAhoxa1 1.0000 501 HsAhoxa2 1.0000 501 HsAhoxa3 1.0000 501 HsAhoxa4 1.0000 501 HsAhoxa5 1.0000 501 HsAhoxa6 1.0000 501 HsAhoxa7 1.0000 501 HsAhoxa9 1.0000 501 HsAhoxa10 1.0000 501 HsAhoxa11 1.0000 501 HsAhoxa13 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 HsChoxC4 1.0000 501 HsChoxC5 1.0000 501 HsDhoxD1 1.0000 501 HsDhoxD3 1.0000 501 HsDhoxD4 1.0000 501 HsDhoxD8 1.0000 501 HsDhoxD9 1.0000 501 HsDhoxD10 1.0000 501 HsDhoxD11 1.0000 501 CfAhoxA1 1.0000 501 CfAhoxA2 1.0000 501 CfAhoxA3 1.0000 501 CfAhoxA4 1.0000 501 CfAhoxA5 1.0000 501 CfAhoxA6 1.0000 501 CfAhoxA7 1.0000 501 CfAhoxA9 1.0000 501 CfAhoxA10 1.0000 501 CfAhoxA11 1.0000 501 CfAhoxA13 1.0000 501 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 CfChoxC4 1.0000 501 CfChoxC5 1.0000 501 CfChoxC6 1.0000 501 CfChoxC8 1.0000 501 CfChoxC10 1.0000 501 CfChoxC11 1.0000 501 CfChoxC12 1.0000 501 CfChoxC13 1.0000 501 CfDhoxD1 1.0000 501 CfDhoxD3 1.0000 501 CfDhoxD4 1.0000 501 CfDhoxD8 1.0000 501 CfDhoxD9 1.0000 501 CfDhoxD10 1.0000 501 CfDhoxD11 1.0000 501 CfDhoxD12 1.0000 501 CfDhoxD13 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_X.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= 68 wnsites= 0.8 theta: prob= 1 spmap= uni spfuzz= 0.5 em: prior= dirichlet b= 0.01 maxiter= 50 distance= 0.001 data: n= 34068 N= 68 strands: + - sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.210 C 0.290 G 0.290 T 0.210 Background letter frequencies (from dataset with add-one prior applied): A 0.210 C 0.290 G 0.290 T 0.210 ******************************************************************************** ******************************************************************************** MOTIF 1 width = 10 sites = 61 llr = 581 E-value = 9.5e-037 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A a498899695 pos.-specific C :1::::1::1 probability G :2::21:::: matrix T :312:::414 bits 2.3 2.0 1.8 * * * 1.6 * * ** * Information 1.4 * ******* content 1.1 * ******* (13.7 bits) 0.9 * ******** 0.7 * ******** 0.5 * ******** 0.2 ********** 0.0 ---------- Multilevel AAAAAAAAAA consensus T TG T T sequence G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- ---------- CfChoxC10 + 438 1.65e-07 CGGATGGGGG AAAAAAAAAA GATGTCAGCT CfChoxC5 - 477 1.65e-07 GGGAGGGCCC AAAAAAAAAA TTTTCTGCAC CfBhoxB2 + 321 1.65e-07 CCCAAAATTT AAAAAAAAAA AAANNNNNNN CfAhoxA11 + 291 1.65e-07 GGAAGGGAAT AAAAAAAAAA AAAAAAAGGC CfAhoxA2 - 399 1.65e-07 AGAGCAGAGG AAAAAAAAAA TCTATCATAG HsDhoxD9 - 308 1.65e-07 TGCTGTGATT AAAAAAAAAA TCATCAACAT HsChoxC5 - 174 1.65e-07 XXXXXXXXAA AAAAAAAAAA GGTTCTTGGA HsAhoxa11 + 275 1.65e-07 GGAGAGGAGG AAAAAAAAAA AAGGAAAGGG CfChoxC11 + 102 3.31e-07 CAGCTAGGGG AAAAAAAAAT ACAATTACCC HsBhoxB3 - 159 6.62e-07 ACTAAAAAAT AAAAAAATAA ATAAAGACTA HsDhoxD8 - 5 1.39e-06 TGGAGGGAAA AGAAAAAAAA CACC HsAhoxa2 + 363 1.39e-06 TCAGTGAATT AGAAAAAAAA CACCCTAGCA CfAhoxA3 - 289 2.57e-06 TGAAAGCCAT AAAAGAAAAA GTGGTCAGCA HsAhoxa3 - 289 2.57e-06 TGAAAGCCAT AAAAGAAAAA GTGGTCAGCA CfBhoxB7 - 134 3.36e-06 GTAGGAGGGA AAATAAATAA CCTCTGAGCC CfAhoxA7 + 390 3.36e-06 AGCTCCGTCC AAAAGAAAAT GGGGTTTGGT HsBhoxB7 - 134 3.36e-06 GTGGAAGGGA AAATAAATAA CCTCGGGGCG HsAhoxa7 + 390 3.36e-06 AGCTCCGTCC AAAAGAAAAT GGGGTTTGGT CfChoxC6 + 454 4.08e-06 CTGGAGACAG AAATAAATAT TAAAGAAATC CfBhoxB6 - 64 4.08e-06 CCCAGTGATT AAATAAATAT ATCCCTCCCC HsBhoxB6 - 78 4.08e-06 CCGGGTGATT AAATAAATAT GTCTCTCCCC CfDhoxD13 - 88 4.71e-06 CGCAGACTTT AAAAAAAATT CAAGGTTTTT CfChoxC4 + 315 4.71e-06 NNNNNNACAC AAAAAAAATT GGATACATTT CfBhoxB13 - 47 7.20e-06 AGGCCGAGGG AAAAAAAAAC AGGGGGCCAT CfAhoxA10 - 283 7.20e-06 CCCACGATTG ATATAAATAT GTAATCTGTA HsChoxC4 + 314 7.20e-06 CACCACACAC ACAAAAAAAT TGGATACATT HsAhoxa10 - 350 7.20e-06 CCCGCGATTG ATATAAATAT GTAATCTGTA HsA - 283 7.20e-06 CCCGCGATTG ATATAAATAT GTAATCTGTA CfAhoxA1 - 417 8.14e-06 ATGGGGCCGG AGAAGAAAAA TGATATGAAT HsAhoxa1 - 417 8.14e-06 ATGGGGCCGG AGAAGAAAAA TGATATGAAT CfAhoxA5 + 252 9.76e-06 CAACCTCGAC ACAAAAATAA GAGGGGCTGC CfAhoxA9 + 269 1.11e-05 GGCTTTTGCT ATAAAAATTA TGACTGCAAA HsAhoxa9 + 272 1.11e-05 GGCTTTTGCT ATAAAAATTA TGACTGCAAA HsAhoxa5 + 492 1.11e-05 CACACATATC AAAAAACAAA CfBhoxB8 - 178 1.19e-05 CACCCCCCAA ACAAAAATAT ACCGCCACTT HsBhoxB8 - 179 1.19e-05 CACCCCCCAA ACAAAAATAT ACCACCACTT CfDhoxD3 + 163 1.36e-05 ACAATCTTGA AGAAAGAAAA TAGTGTCTGC CfDhoxD4 + 468 1.71e-05 AGACAACACG AGAAAAATTA GTATTTTCTA CfAhoxA4 + 468 1.71e-05 CGACAACGCG AGAAAAATTA GTATTTTTGC HsDhoxD4 + 468 1.71e-05 AGACAACACG AGAAAAATTA GTATTTTCTA HsAhoxa4 + 468 1.71e-05 CGACAACGCG AGAAAAATTA GTATTTTTGC CfBhoxB9 + 169 1.82e-05 TTGCATCAGC ATAAAACAAT CCATCCTCGA HsBhoxB9 + 169 1.82e-05 TTGCATCAGC ATAAAACAAT CCATCCTCGA CfBhoxB3 + 138 2.11e-05 TTTGAAGTGG AAATAAAAAC TGGTGGGCTT CfBhoxB4 - 334 3.60e-05 CGATTCCCGG ATAAGGAAAT CTGCTCACCC HsBhoxB4 - 334 3.60e-05 CGATTCCCGG ATAAGGAAAT CTGCTCACCC HsBhoxB2 + 362 3.94e-05 GCCCAAAATT AAAAAAAAGA GAGACCGAAA CfDhoxD11 + 302 4.30e-05 GCGAGAGCTG ATATAGATAT AAGGACATTT HsDhoxD11 + 302 4.30e-05 GCGAGCGTTG ATATAGATAT AAGGACATTT HsAhoxa6 + 86 7.90e-05 GCAAAATTCA ATAAAGCAAA AAGGGGAGGA CfBhoxB5 - 38 8.43e-05 CCGCCGGGAG AGAAAGAAAC CCGGGCTGGG HsBhoxB5 - 28 8.43e-05 TCGCCGGGAG AGAAAGAAAC CCGGCCAAGG CfChoxC13 - 307 9.67e-05 GACACTCCTC ATTAAGAAAT CCGCCGCCTC CfAhoxA6 + 63 1.03e-04 TTCCTGTTTG GAAAGAAAAA CCAGCAAAAT CfDhoxD10 - 373 1.58e-04 AGCCAATGAG ATTTGAAAAT GGCCTTGAGC HsDhoxD10 - 373 1.58e-04 AGCCAATGAG ATTTGAAAAT GGCCTTGAGC HsDhoxD3 - 402 1.58e-04 GTGACCTGTC AGAAGAAAAG CAAGAGGCCC CfBhoxB1 - 121 2.65e-04 GGTAAAAGTT AGAGGAATAT TCAAGACTTT CfAhoxA13 + 82 2.65e-04 TGGGGGCTTT TTAAAACAAA GCCACTGGGG HsBhoxB1 - 122 2.97e-04 GGAAAAAGTT AGGAGAATAT TCAAGACTTT CfChoxC12 - 248 2.57e-03 XXXXXXXXXX XXXXAAATAT CATATAAAAC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- CfChoxC10 1.7e-07 437_[+1]_54 CfChoxC5 1.7e-07 476_[-1]_15 CfBhoxB2 1.7e-07 320_[+1]_171 CfAhoxA11 1.7e-07 290_[+1]_201 CfAhoxA2 1.7e-07 398_[-1]_93 HsDhoxD9 1.7e-07 307_[-1]_184 HsChoxC5 1.7e-07 173_[-1]_318 HsAhoxa11 1.7e-07 274_[+1]_217 CfChoxC11 3.3e-07 101_[+1]_390 HsBhoxB3 6.6e-07 158_[-1]_333 HsDhoxD8 1.4e-06 4_[-1]_487 HsAhoxa2 1.4e-06 362_[+1]_129 CfAhoxA3 2.6e-06 288_[-1]_203 HsAhoxa3 2.6e-06 288_[-1]_203 CfBhoxB7 3.4e-06 133_[-1]_358 CfAhoxA7 3.4e-06 389_[+1]_102 HsBhoxB7 3.4e-06 133_[-1]_358 HsAhoxa7 3.4e-06 389_[+1]_102 CfChoxC6 4.1e-06 453_[+1]_38 CfBhoxB6 4.1e-06 63_[-1]_428 HsBhoxB6 4.1e-06 77_[-1]_414 CfDhoxD13 4.7e-06 87_[-1]_404 CfChoxC4 4.7e-06 314_[+1]_177 CfBhoxB13 7.2e-06 46_[-1]_445 CfAhoxA10 7.2e-06 282_[-1]_209 HsChoxC4 7.2e-06 313_[+1]_178 HsAhoxa10 7.2e-06 349_[-1]_142 HsA 7.2e-06 282_[-1]_209 CfAhoxA1 8.1e-06 416_[-1]_75 HsAhoxa1 8.1e-06 416_[-1]_75 CfAhoxA5 9.8e-06 251_[+1]_240 CfAhoxA9 1.1e-05 268_[+1]_223 HsAhoxa9 1.1e-05 271_[+1]_220 HsAhoxa5 1.1e-05 491_[+1] CfBhoxB8 1.2e-05 177_[-1]_314 HsBhoxB8 1.2e-05 178_[-1]_313 CfDhoxD3 1.4e-05 162_[+1]_329 CfDhoxD4 1.7e-05 467_[+1]_24 CfAhoxA4 1.7e-05 467_[+1]_24 HsDhoxD4 1.7e-05 467_[+1]_24 HsAhoxa4 1.7e-05 467_[+1]_24 CfBhoxB9 1.8e-05 168_[+1]_323 HsBhoxB9 1.8e-05 168_[+1]_323 CfBhoxB3 2.1e-05 137_[+1]_354 CfBhoxB4 3.6e-05 333_[-1]_158 HsBhoxB4 3.6e-05 333_[-1]_158 HsBhoxB2 3.9e-05 361_[+1]_130 CfDhoxD11 4.3e-05 301_[+1]_190 HsDhoxD11 4.3e-05 301_[+1]_190 HsAhoxa6 7.9e-05 85_[+1]_406 CfBhoxB5 8.4e-05 37_[-1]_454 HsBhoxB5 8.4e-05 27_[-1]_464 CfChoxC13 9.7e-05 306_[-1]_185 CfAhoxA6 0.0001 62_[+1]_429 CfDhoxD10 0.00016 372_[-1]_119 HsDhoxD10 0.00016 372_[-1]_119 HsDhoxD3 0.00016 401_[-1]_90 CfBhoxB1 0.00026 120_[-1]_371 CfAhoxA13 0.00026 81_[+1]_410 HsBhoxB1 0.0003 121_[-1]_370 CfChoxC12 0.0026 247_[-1]_244 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=10 seqs=61 CfChoxC10 ( 438) AAAAAAAAAA 1 CfChoxC5 ( 477) AAAAAAAAAA 1 CfBhoxB2 ( 321) AAAAAAAAAA 1 CfAhoxA11 ( 291) AAAAAAAAAA 1 CfAhoxA2 ( 399) AAAAAAAAAA 1 HsDhoxD9 ( 308) AAAAAAAAAA 1 HsChoxC5 ( 174) AAAAAAAAAA 1 HsAhoxa11 ( 275) AAAAAAAAAA 1 CfChoxC11 ( 102) AAAAAAAAAT 1 HsBhoxB3 ( 159) AAAAAAATAA 1 HsDhoxD8 ( 5) AGAAAAAAAA 1 HsAhoxa2 ( 363) AGAAAAAAAA 1 CfAhoxA3 ( 289) AAAAGAAAAA 1 HsAhoxa3 ( 289) AAAAGAAAAA 1 CfBhoxB7 ( 134) AAATAAATAA 1 CfAhoxA7 ( 390) AAAAGAAAAT 1 HsBhoxB7 ( 134) AAATAAATAA 1 HsAhoxa7 ( 390) AAAAGAAAAT 1 CfChoxC6 ( 454) AAATAAATAT 1 CfBhoxB6 ( 64) AAATAAATAT 1 HsBhoxB6 ( 78) AAATAAATAT 1 CfDhoxD13 ( 88) AAAAAAAATT 1 CfChoxC4 ( 315) AAAAAAAATT 1 CfBhoxB13 ( 47) AAAAAAAAAC 1 CfAhoxA10 ( 283) ATATAAATAT 1 HsChoxC4 ( 314) ACAAAAAAAT 1 HsAhoxa10 ( 350) ATATAAATAT 1 HsA ( 283) ATATAAATAT 1 CfAhoxA1 ( 417) AGAAGAAAAA 1 HsAhoxa1 ( 417) AGAAGAAAAA 1 CfAhoxA5 ( 252) ACAAAAATAA 1 CfAhoxA9 ( 269) ATAAAAATTA 1 HsAhoxa9 ( 272) ATAAAAATTA 1 HsAhoxa5 ( 492) AAAAAACAAA 1 CfBhoxB8 ( 178) ACAAAAATAT 1 HsBhoxB8 ( 179) ACAAAAATAT 1 CfDhoxD3 ( 163) AGAAAGAAAA 1 CfDhoxD4 ( 468) AGAAAAATTA 1 CfAhoxA4 ( 468) AGAAAAATTA 1 HsDhoxD4 ( 468) AGAAAAATTA 1 HsAhoxa4 ( 468) AGAAAAATTA 1 CfBhoxB9 ( 169) ATAAAACAAT 1 HsBhoxB9 ( 169) ATAAAACAAT 1 CfBhoxB3 ( 138) AAATAAAAAC 1 CfBhoxB4 ( 334) ATAAGGAAAT 1 HsBhoxB4 ( 334) ATAAGGAAAT 1 HsBhoxB2 ( 362) AAAAAAAAGA 1 CfDhoxD11 ( 302) ATATAGATAT 1 HsDhoxD11 ( 302) ATATAGATAT 1 HsAhoxa6 ( 86) ATAAAGCAAA 1 CfBhoxB5 ( 38) AGAAAGAAAC 1 HsBhoxB5 ( 28) AGAAAGAAAC 1 CfChoxC13 ( 307) ATTAAGAAAT 1 CfAhoxA6 ( 63) GAAAGAAAAA 1 CfDhoxD10 ( 373) ATTTGAAAAT 1 HsDhoxD10 ( 373) ATTTGAAAAT 1 HsDhoxD3 ( 402) AGAAGAAAAG 1 CfBhoxB1 ( 121) AGAGGAATAT 1 CfAhoxA13 ( 82) TTAAAACAAA 1 HsBhoxB1 ( 122) AGGAGAATAT 1 CfChoxC12 ( 248) XXXXAAATAT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 10 n= 33456 bayes= 9.78803 E= 9.5e-037 218 -592 -378 -340 103 -204 -31 34 213 -592 -378 -199 185 -592 -378 5 188 -1257 -34 -1257 202 -1257 -98 -1257 213 -182 -1257 -1257 157 -1257 -1257 85 202 -1257 -414 -68 123 -214 -414 102 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 10 nsites= 61 E= 9.5e-037 0.954259 0.004757 0.021150 0.019833 0.429669 0.070331 0.234265 0.265735 0.921473 0.004757 0.021150 0.052620 0.757538 0.004757 0.021150 0.216555 0.770492 0.000000 0.229508 0.000000 0.852459 0.000000 0.147541 0.000000 0.918033 0.081967 0.000000 0.000000 0.622951 0.000000 0.000000 0.377049 0.852459 0.000000 0.016393 0.131148 0.491803 0.065574 0.016393 0.426230 -------------------------------------------------------------------------------- Time 55.84 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 width = 10 sites = 64 llr = 545 E-value = 2.4e-014 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A :11:4:111: pos.-specific C ::1:3::::: probability G a98a19989a matrix T ::::21:::: bits 2.3 2.0 1.8 * 1.6 ** * * Information 1.4 ** * * ** content 1.1 ** * ** ** (12.3 bits) 0.9 ** * ***** 0.7 **** ***** 0.5 **** ***** 0.2 ********** 0.0 ---------- Multilevel GGGGAGGGGG consensus C sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- ---------- CfChoxC12 + 120 3.06e-06 TAATACATCT GGGGAGGGGG GTGCATGGTG CfBhoxB2 - 477 3.06e-06 TTCAATGGTG GGGGAGGGGG CCTGCTGGGG CfAhoxA1 + 64 3.06e-06 TGTGCTCGGT GGGGAGGGGG CGGAGACGGG HsBhoxB4 + 270 3.06e-06 GTGGGTGGGT GGGGAGGGGG AAGGGAAGAA HsBhoxB2 - 477 3.06e-06 TTCAATGGTG GGGGAGGGGG CTGCTGGGGG HsAhoxa1 + 55 3.06e-06 ATTGAACGGT GGGGAGGGGG CGGGAGCGGG CfDhoxD10 + 176 7.29e-06 CCCGGAGGCC GGGGCGGGGG GCGCGAGCGG CfChoxC13 + 277 7.29e-06 CGGGAGGGGC GGGGCGGGGG GGCCGCGCGG CfBhoxB13 - 463 7.29e-06 ATGGGGCGCT GGGGCGGGGG GATCCGGGGG HsDhoxD4 + 134 7.29e-06 TTGGTGTCGG GGGGCGGGGG TTGCATTCAG CfChoxC6 + 48 1.04e-05 AATTTTAGAA GGGGTGGGGG AGATAGAAAA CfBhoxB8 + 192 1.04e-05 TTTTGTTTGG GGGGTGGGGG GTGGGGGGAG CfBhoxB3 + 239 1.04e-05 TGAAGATGTT GGGGTGGGGG AGAAGAAGAA HsBhoxB8 + 193 1.04e-05 TTTTGTTTGG GGGGTGGGGG GTGGGGGGAG HsBhoxB6 + 62 1.04e-05 AATCCTGCGT GGGGTGGGGG AGAGACATAT HsBhoxB5 - 344 1.04e-05 GGTTGGAAGG GGGGTGGGGG GGCGTTAGGG HsAhoxa7 + 110 1.04e-05 GCGGGGGGGC GGGGTGGGGG GTGCTGCGTG CfDhoxD3 + 185 1.26e-05 GTGTCTGCGT GGGGAGGGAG CCCCTTCTCT CfBhoxB4 + 268 1.26e-05 GTGGGTGGGT GGGGAGGGAG AAAGAGAAGA HsAhoxa4 - 174 1.26e-05 CCCTGGGCTG GGGGAGGGAG CAGGAGCTTT CfChoxC10 - 419 1.90e-05 TCCCCCATCC GGGGGGGGGG CGGCTGGAGG CfBhoxB5 - 361 1.90e-05 CCAAATATGG GGGGGGGGGG TTGGAAGGGG CfAhoxA9 - 408 1.90e-05 GGTGGCACCA GGGGGGGGGG AAGTACAGTC CfAhoxA6 + 98 1.90e-05 CAGGCAAGAA GGGGAGGAGG AAGGAGCGGG HsBhoxB3 + 391 1.90e-05 GAGGGGAGGT GGGGGGGGGG GGGTCCGGCG HsAhoxa6 + 98 1.90e-05 AAAGCAAAAA GGGGAGGAGG AAGGAGGGGA CfChoxC11 - 444 2.43e-05 GACCCGATCT GGCGAGGGGG GAAAAATTTG CfBhoxB9 - 228 2.43e-05 AAATCAATCG GGCGAGGGGG CTGCGCTCTC CfBhoxB6 + 82 2.43e-05 TTAATCACTG GGGGATGGGG TGGTCTCAAT HsBhoxB9 - 228 2.43e-05 AAATCAATCG GGCGAGGGGG CTGCGCTCTC HsAhoxa5 - 255 2.43e-05 GTTGGGTGGA GGCGAGGGGG GTGGCGCGCG CfBhoxB1 - 139 2.65e-05 GGGACCAGAG GGAGAGGGGG TAAAAGTTAG HsBhoxB1 - 140 2.65e-05 GGGACCAGAG GGAGAGGGGG AAAAAGTTAG CfAhoxA7 + 69 2.96e-05 AGACAGGACG GGGGCGGGAG GGCCCGCAGG CfBhoxB7 - 226 4.88e-05 CCTGCGGATT GGGGCTGGGG GCTCAAGGGC HsBhoxB7 - 226 4.88e-05 CCTGTGGATT GGGGCTGGGG GCTCAAGGGC CfAhoxA13 - 141 5.40e-05 TCGATCCGCG GGGGTGGAGG AGCACGGCGG HsAhoxa13 + 342 5.40e-05 CGCCGTGGGC GGAGCGGGGG GGCCGGGCCA CfAhoxA4 + 71 5.93e-05 TCAAACTTGG GGGGTTGGGG GGGACCGAGA HsChoxC4 - 281 7.45e-05 GTGGTGCTGG GAGGCGGGGG TGGGTGGTGA HsAhoxa9 + 144 7.45e-05 GTGTGTGTAT GGGGGGGGAG ACGGGAGAGT HsAhoxa2 - 80 7.45e-05 GGAGTACGTG GGGGCGAGGG TGCCTGCGTG CfAhoxA10 + 404 7.98e-05 CACCCGCCGC GGTGCGGGGG GATTGCTAAT HsAhoxa10 + 471 7.98e-05 CGCCCGCCGC GGTGCGGGGG GATTGCTAAT HsA + 404 7.98e-05 CGCCCGCCGC GGTGCGGGGG GATTGCTAAT CfDhoxD11 + 223 9.27e-05 AGCGCCGGCT GGAGAGGGAG ACCGGTCCGC HsDhoxD1 - 45 9.27e-05 GGTATTGGGC GAGGTGGGGG GAGAAAGGCA HsAhoxa11 + 265 1.11e-04 GGGAGGGAGG GGAGAGGAGG AAAAAAAAAA CfAhoxA5 - 172 1.25e-04 TATCACCTTC GGGGAAGGGG GGAGGCCATT CfAhoxA3 - 152 1.25e-04 GGGGTTTTCC GGGGAGAGAG GAGGAGAGTC CfDhoxD9 - 469 1.49e-04 CGTGGACGTG GAGGAGGAGG TGGAGGTGGC HsDhoxD11 + 89 1.49e-04 TACTTAAAGC GGCGCGGGAG GGCGGACGCG HsAhoxa3 - 152 1.49e-04 GGGATTTTCC GGGGAGAAGG AGAATGAGTG HsDhoxD9 - 172 1.96e-04 ATCCAGAGGA GGCGCTGGGG ACTATTTGTT CfDhoxD12 + 358 2.21e-04 GGGGGGAAAC GGGTCGGGGG ATGTAGGCGG HsDhoxD10 - 94 2.21e-04 ACGCACGGAC GGGGAGGGAA GCCAGAGTGC CfDhoxD13 + 456 2.56e-04 TTTTATACCA GGGGATGTGG CTCTAAATCA CfDhoxD8 - 298 2.56e-04 CGAGCTCATC GGGGCGGCGG CGGCTTTGGC CfDhoxD4 - 107 2.56e-04 CACAGTTCAA GGGGGGGGGA TGAAACTCCA CfDhoxD1 + 307 2.84e-04 GGCCGCGGGC GGGGCGCGGG GCGCGGGCCT CfAhoxA11 - 63 2.84e-04 GGAGCGCGGC GAGGCTGGGG TGCGCCCCAT CfChoxC5 - 491 3.17e-04 T GGCGGGGAGG GCCCAAAAAA HsChoxC5 - 491 3.17e-04 T GGCGGGGAGG GCCCAAAAAA HsDhoxD3 - 304 3.49e-04 ACTTCACGGC GGGGAGATGG GCAAGGTGCT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- CfChoxC12 3.1e-06 119_[+2]_372 CfBhoxB2 3.1e-06 476_[-2]_15 CfAhoxA1 3.1e-06 63_[+2]_428 HsBhoxB4 3.1e-06 269_[+2]_222 HsBhoxB2 3.1e-06 476_[-2]_15 HsAhoxa1 3.1e-06 54_[+2]_437 CfDhoxD10 7.3e-06 175_[+2]_316 CfChoxC13 7.3e-06 276_[+2]_215 CfBhoxB13 7.3e-06 462_[-2]_29 HsDhoxD4 7.3e-06 133_[+2]_358 CfChoxC6 1e-05 47_[+2]_444 CfBhoxB8 1e-05 191_[+2]_300 CfBhoxB3 1e-05 238_[+2]_253 HsBhoxB8 1e-05 192_[+2]_299 HsBhoxB6 1e-05 61_[+2]_430 HsBhoxB5 1e-05 343_[-2]_148 HsAhoxa7 1e-05 109_[+2]_382 CfDhoxD3 1.3e-05 184_[+2]_307 CfBhoxB4 1.3e-05 267_[+2]_224 HsAhoxa4 1.3e-05 173_[-2]_318 CfChoxC10 1.9e-05 418_[-2]_73 CfBhoxB5 1.9e-05 360_[-2]_131 CfAhoxA9 1.9e-05 407_[-2]_84 CfAhoxA6 1.9e-05 97_[+2]_394 HsBhoxB3 1.9e-05 390_[+2]_101 HsAhoxa6 1.9e-05 97_[+2]_394 CfChoxC11 2.4e-05 443_[-2]_48 CfBhoxB9 2.4e-05 227_[-2]_264 CfBhoxB6 2.4e-05 81_[+2]_410 HsBhoxB9 2.4e-05 227_[-2]_264 HsAhoxa5 2.4e-05 254_[-2]_237 CfBhoxB1 2.6e-05 138_[-2]_353 HsBhoxB1 2.6e-05 139_[-2]_352 CfAhoxA7 3e-05 68_[+2]_423 CfBhoxB7 4.9e-05 225_[-2]_266 HsBhoxB7 4.9e-05 225_[-2]_266 CfAhoxA13 5.4e-05 140_[-2]_351 HsAhoxa13 5.4e-05 341_[+2]_150 CfAhoxA4 5.9e-05 70_[+2]_421 HsChoxC4 7.5e-05 280_[-2]_211 HsAhoxa9 7.5e-05 143_[+2]_348 HsAhoxa2 7.5e-05 79_[-2]_412 CfAhoxA10 8e-05 403_[+2]_88 HsAhoxa10 8e-05 470_[+2]_21 HsA 8e-05 403_[+2]_88 CfDhoxD11 9.3e-05 222_[+2]_269 HsDhoxD1 9.3e-05 44_[-2]_447 HsAhoxa11 0.00011 264_[+2]_227 CfAhoxA5 0.00013 171_[-2]_320 CfAhoxA3 0.00013 151_[-2]_340 CfDhoxD9 0.00015 468_[-2]_23 HsDhoxD11 0.00015 88_[+2]_403 HsAhoxa3 0.00015 151_[-2]_340 HsDhoxD9 0.0002 171_[-2]_320 CfDhoxD12 0.00022 357_[+2]_134 HsDhoxD10 0.00022 93_[-2]_398 CfDhoxD13 0.00026 455_[+2]_36 CfDhoxD8 0.00026 297_[-2]_194 CfDhoxD4 0.00026 106_[-2]_385 CfDhoxD1 0.00028 306_[+2]_185 CfAhoxA11 0.00028 62_[-2]_429 CfChoxC5 0.00032 490_[-2]_1 HsChoxC5 0.00032 490_[-2]_1 HsDhoxD3 0.00035 303_[-2]_188 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=10 seqs=64 CfChoxC12 ( 120) GGGGAGGGGG 1 CfBhoxB2 ( 477) GGGGAGGGGG 1 CfAhoxA1 ( 64) GGGGAGGGGG 1 HsBhoxB4 ( 270) GGGGAGGGGG 1 HsBhoxB2 ( 477) GGGGAGGGGG 1 HsAhoxa1 ( 55) GGGGAGGGGG 1 CfDhoxD10 ( 176) GGGGCGGGGG 1 CfChoxC13 ( 277) GGGGCGGGGG 1 CfBhoxB13 ( 463) GGGGCGGGGG 1 HsDhoxD4 ( 134) GGGGCGGGGG 1 CfChoxC6 ( 48) GGGGTGGGGG 1 CfBhoxB8 ( 192) GGGGTGGGGG 1 CfBhoxB3 ( 239) GGGGTGGGGG 1 HsBhoxB8 ( 193) GGGGTGGGGG 1 HsBhoxB6 ( 62) GGGGTGGGGG 1 HsBhoxB5 ( 344) GGGGTGGGGG 1 HsAhoxa7 ( 110) GGGGTGGGGG 1 CfDhoxD3 ( 185) GGGGAGGGAG 1 CfBhoxB4 ( 268) GGGGAGGGAG 1 HsAhoxa4 ( 174) GGGGAGGGAG 1 CfChoxC10 ( 419) GGGGGGGGGG 1 CfBhoxB5 ( 361) GGGGGGGGGG 1 CfAhoxA9 ( 408) GGGGGGGGGG 1 CfAhoxA6 ( 98) GGGGAGGAGG 1 HsBhoxB3 ( 391) GGGGGGGGGG 1 HsAhoxa6 ( 98) GGGGAGGAGG 1 CfChoxC11 ( 444) GGCGAGGGGG 1 CfBhoxB9 ( 228) GGCGAGGGGG 1 CfBhoxB6 ( 82) GGGGATGGGG 1 HsBhoxB9 ( 228) GGCGAGGGGG 1 HsAhoxa5 ( 255) GGCGAGGGGG 1 CfBhoxB1 ( 139) GGAGAGGGGG 1 HsBhoxB1 ( 140) GGAGAGGGGG 1 CfAhoxA7 ( 69) GGGGCGGGAG 1 CfBhoxB7 ( 226) GGGGCTGGGG 1 HsBhoxB7 ( 226) GGGGCTGGGG 1 CfAhoxA13 ( 141) GGGGTGGAGG 1 HsAhoxa13 ( 342) GGAGCGGGGG 1 CfAhoxA4 ( 71) GGGGTTGGGG 1 HsChoxC4 ( 281) GAGGCGGGGG 1 HsAhoxa9 ( 144) GGGGGGGGAG 1 HsAhoxa2 ( 80) GGGGCGAGGG 1 CfAhoxA10 ( 404) GGTGCGGGGG 1 HsAhoxa10 ( 471) GGTGCGGGGG 1 HsA ( 404) GGTGCGGGGG 1 CfDhoxD11 ( 223) GGAGAGGGAG 1 HsDhoxD1 ( 45) GAGGTGGGGG 1 HsAhoxa11 ( 265) GGAGAGGAGG 1 CfAhoxA5 ( 172) GGGGAAGGGG 1 CfAhoxA3 ( 152) GGGGAGAGAG 1 CfDhoxD9 ( 469) GAGGAGGAGG 1 HsDhoxD11 ( 89) GGCGCGGGAG 1 HsAhoxa3 ( 152) GGGGAGAAGG 1 HsDhoxD9 ( 172) GGCGCTGGGG 1 CfDhoxD12 ( 358) GGGTCGGGGG 1 HsDhoxD10 ( 94) GGGGAGGGAA 1 CfDhoxD13 ( 456) GGGGATGTGG 1 CfDhoxD8 ( 298) GGGGCGGCGG 1 CfDhoxD4 ( 107) GGGGGGGGGA 1 CfDhoxD1 ( 307) GGGGCGCGGG 1 CfAhoxA11 ( 63) GAGGCTGGGG 1 CfChoxC5 ( 491) GGCGGGGAGG 1 HsChoxC5 ( 491) GGCGGGGAGG 1 HsDhoxD3 ( 304) GGGGAGATGG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 10 n= 33456 bayes= 9.02721 E= 2.4e-014 -1264 -1264 178 -1264 -175 -1264 169 -1264 -142 -121 137 -216 -1264 -1264 176 -374 101 3 -121 -43 -374 -1264 159 -94 -175 -421 167 -1264 -75 -421 151 -275 -58 -1264 157 -1264 -275 -1264 174 -1264 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 10 nsites= 64 E= 2.4e-014 0.000000 0.000000 1.000000 0.000000 0.062500 0.000000 0.937500 0.000000 0.078125 0.125000 0.750000 0.046875 0.000000 0.000000 0.984375 0.015625 0.421875 0.296875 0.125000 0.156250 0.015625 0.000000 0.875000 0.109375 0.062500 0.015625 0.921875 0.000000 0.125000 0.015625 0.828125 0.031250 0.140625 0.000000 0.859375 0.000000 0.031250 0.000000 0.968750 0.000000 -------------------------------------------------------------------------------- Time 115.30 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 width = 10 sites = 43 llr = 418 E-value = 5.0e-012 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A 2::a:2::4: pos.-specific C ::a:a:::36 probability G 81:::7:a31 matrix T :9::::a::3 bits 2.3 * 2.0 * * 1.8 ** ** 1.6 **** ** Information 1.4 **** ** content 1.1 ***** ** (14.0 bits) 0.9 ******** 0.7 ******** 0.5 ********** 0.2 ********** 0.0 ---------- Multilevel GTCACGTGAC consensus A A GT sequence C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- ---------- CfDhoxD11 + 333 1.16e-06 TCTCCATGGC GTCACGTGAC ATAATTACCA CfChoxC5 + 322 1.16e-06 GGCCGCTCGA GTCACGTGAC TCTATTTAAG CfAhoxA3 + 412 1.16e-06 GCGGCGGAGC GTCACGTGAC CGCGGGGGCG HsDhoxD11 + 333 1.16e-06 TCTTCATGGC GTCACGTGAC ATAATTACCA HsChoxC5 + 326 1.16e-06 GGCCGCTCGA GTCACGTGAC TCTATTTAAG HsBhoxB3 + 412 1.16e-06 GGTCCGGCGT GTCACGTGAC CCCCAGGGTT HsAhoxa3 + 412 1.16e-06 GCGGCGGAGT GTCACGTGAC CGCGGGGGCG CfAhoxA9 - 345 5.19e-06 GGCCGCGCGC GTCACGTGCC CGCCCGGCAG CfAhoxA1 + 348 5.19e-06 GGCTGGCGGA GTCACGTGCC CCTCCCCCTG HsAhoxa9 - 348 5.19e-06 GGCCGTGCGC GTCACGTGCC CGTCCAGCAG HsAhoxa1 + 348 5.19e-06 GGCTGACACC GTCACGTGCC CCTCCTCCAG CfBhoxB7 + 371 8.02e-06 CGTGGGCGGG GTCACGTGGT CCGGAGAGGA CfAhoxA11 + 347 8.02e-06 TCAACATCAG GTCACATGAC CAGCACCTCC CfAhoxA4 + 198 8.02e-06 GCGGGGGCTG GTCACGTGGT GGGTCCCGGG HsBhoxB7 + 371 8.02e-06 CGTGGGCGGG GTCACGTGGT CCGGAGAGGA HsAhoxa11 + 344 8.02e-06 TCAACATCGG GTCACATGAC CAGCACCTCC CfDhoxD10 + 337 9.18e-06 CGGGCTCCGG AGCACGTGAC CTGCGAGGAG CfAhoxA7 + 364 9.18e-06 CATGTGGGCG GTCACGTGCT GCGGCGAGCT HsDhoxD10 + 337 9.18e-06 CAGGCTCTGG AGCACGTGAC CCGAGAGGAG HsAhoxa7 + 364 9.18e-06 CATGTGGGCG GTCACGTGCT GCGGCGAGCT CfAhoxA2 - 263 1.04e-05 CGAATTGGCT GTCACATGAT TGCTTCTGCC HsAhoxa2 - 265 1.04e-05 CGAATTGGCT GTCACATGAT TGCTTCTGCC CfBhoxB3 - 412 1.15e-05 ACCCGCGGGG GTCACGTGAG GCGCCGGAXX CfDhoxD4 + 393 1.39e-05 GGCTGGCCTG GTCACATGGC CGCCAACTTT CfChoxC10 + 331 1.39e-05 TGGTCTAGCC GTCACATGGC GAGGCCCGAA HsDhoxD4 + 392 1.39e-05 GGCTGGCCTG GTCACATGGC TGCCCAACTT CfChoxC4 + 397 1.85e-05 GGCCGGCGGA GTCACATGGT GAAAGTAACT HsChoxC4 + 397 1.85e-05 GGCCGGAGGA GTCACATGGT GAAAGTAACT CfChoxC11 + 381 2.01e-05 TCTACTTTGG ATCACGTGCT CGGGGAGAGA CfBhoxB5 - 322 2.01e-05 GCGTTAGGGA ATCACGTGCT TTTGTTGACC HsBhoxB5 - 323 2.01e-05 GCGTTAGGGA ATCACGTGCT TTTGTTGACC HsAhoxa5 - 340 2.01e-05 ACGACTTCGA ATCACGTGCT TTTGTTGTCC CfChoxC13 + 237 2.38e-05 CGGCCCCGGA GTCACGTGCG GGGGCCGCGT CfBhoxB4 + 381 3.31e-05 GGCTCCGAGG ATCACGTGGG TCCCTAACTT HsDhoxD9 + 374 3.31e-05 GGTAAATATG ATCACGTGGG CCGCGCGACC HsBhoxB4 + 381 3.31e-05 GGCTCGGAGG ATCACGTGGG CGCCTAACTT CfBhoxB9 + 123 3.98e-05 TCGGGCTGAG GTTACGTGGC CGCCGGAGCC HsBhoxB9 + 123 3.98e-05 TGGGGCTGAG GTTACGTGGC CGCCGGAGCC CfBhoxB2 + 210 4.25e-05 GCCGAGGCCA GTCCCGTGAC CATGAATTCC HsBhoxB2 + 252 4.25e-05 GCGGAGGCCG GTCCCGTGAC CACGAATTCC CfBhoxB1 + 328 6.20e-05 CCTGGGAGAG ATCACATGCG CCCCTCCACC HsDhoxD1 + 258 9.88e-05 GCCGGCCAGC GCCACGTGGC CGCCCCCGCC HsAhoxa4 + 364 1.96e-04 GGGAGGAGTG GGCACTTGAC AGCGGGGGGA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- CfDhoxD11 1.2e-06 332_[+3]_159 CfChoxC5 1.2e-06 321_[+3]_170 CfAhoxA3 1.2e-06 411_[+3]_80 HsDhoxD11 1.2e-06 332_[+3]_159 HsChoxC5 1.2e-06 325_[+3]_166 HsBhoxB3 1.2e-06 411_[+3]_80 HsAhoxa3 1.2e-06 411_[+3]_80 CfAhoxA9 5.2e-06 344_[-3]_147 CfAhoxA1 5.2e-06 347_[+3]_144 HsAhoxa9 5.2e-06 347_[-3]_144 HsAhoxa1 5.2e-06 347_[+3]_144 CfBhoxB7 8e-06 370_[+3]_121 CfAhoxA11 8e-06 346_[+3]_145 CfAhoxA4 8e-06 197_[+3]_294 HsBhoxB7 8e-06 370_[+3]_121 HsAhoxa11 8e-06 343_[+3]_148 CfDhoxD10 9.2e-06 336_[+3]_155 CfAhoxA7 9.2e-06 363_[+3]_128 HsDhoxD10 9.2e-06 336_[+3]_155 HsAhoxa7 9.2e-06 363_[+3]_128 CfAhoxA2 1e-05 262_[-3]_229 HsAhoxa2 1e-05 264_[-3]_227 CfBhoxB3 1.2e-05 411_[-3]_80 CfDhoxD4 1.4e-05 392_[+3]_99 CfChoxC10 1.4e-05 330_[+3]_161 HsDhoxD4 1.4e-05 391_[+3]_100 CfChoxC4 1.8e-05 396_[+3]_95 HsChoxC4 1.8e-05 396_[+3]_95 CfChoxC11 2e-05 380_[+3]_111 CfBhoxB5 2e-05 321_[-3]_170 HsBhoxB5 2e-05 322_[-3]_169 HsAhoxa5 2e-05 339_[-3]_152 CfChoxC13 2.4e-05 236_[+3]_255 CfBhoxB4 3.3e-05 380_[+3]_111 HsDhoxD9 3.3e-05 373_[+3]_118 HsBhoxB4 3.3e-05 380_[+3]_111 CfBhoxB9 4e-05 122_[+3]_369 HsBhoxB9 4e-05 122_[+3]_369 CfBhoxB2 4.3e-05 209_[+3]_282 HsBhoxB2 4.3e-05 251_[+3]_240 CfBhoxB1 6.2e-05 327_[+3]_164 HsDhoxD1 9.9e-05 257_[+3]_234 HsAhoxa4 0.0002 363_[+3]_128 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=10 seqs=43 CfDhoxD11 ( 333) GTCACGTGAC 1 CfChoxC5 ( 322) GTCACGTGAC 1 CfAhoxA3 ( 412) GTCACGTGAC 1 HsDhoxD11 ( 333) GTCACGTGAC 1 HsChoxC5 ( 326) GTCACGTGAC 1 HsBhoxB3 ( 412) GTCACGTGAC 1 HsAhoxa3 ( 412) GTCACGTGAC 1 CfAhoxA9 ( 345) GTCACGTGCC 1 CfAhoxA1 ( 348) GTCACGTGCC 1 HsAhoxa9 ( 348) GTCACGTGCC 1 HsAhoxa1 ( 348) GTCACGTGCC 1 CfBhoxB7 ( 371) GTCACGTGGT 1 CfAhoxA11 ( 347) GTCACATGAC 1 CfAhoxA4 ( 198) GTCACGTGGT 1 HsBhoxB7 ( 371) GTCACGTGGT 1 HsAhoxa11 ( 344) GTCACATGAC 1 CfDhoxD10 ( 337) AGCACGTGAC 1 CfAhoxA7 ( 364) GTCACGTGCT 1 HsDhoxD10 ( 337) AGCACGTGAC 1 HsAhoxa7 ( 364) GTCACGTGCT 1 CfAhoxA2 ( 263) GTCACATGAT 1 HsAhoxa2 ( 265) GTCACATGAT 1 CfBhoxB3 ( 412) GTCACGTGAG 1 CfDhoxD4 ( 393) GTCACATGGC 1 CfChoxC10 ( 331) GTCACATGGC 1 HsDhoxD4 ( 392) GTCACATGGC 1 CfChoxC4 ( 397) GTCACATGGT 1 HsChoxC4 ( 397) GTCACATGGT 1 CfChoxC11 ( 381) ATCACGTGCT 1 CfBhoxB5 ( 322) ATCACGTGCT 1 HsBhoxB5 ( 323) ATCACGTGCT 1 HsAhoxa5 ( 340) ATCACGTGCT 1 CfChoxC13 ( 237) GTCACGTGCG 1 CfBhoxB4 ( 381) ATCACGTGGG 1 HsDhoxD9 ( 374) ATCACGTGGG 1 HsBhoxB4 ( 381) ATCACGTGGG 1 CfBhoxB9 ( 123) GTTACGTGGC 1 HsBhoxB9 ( 123) GTTACGTGGC 1 CfBhoxB2 ( 210) GTCCCGTGAC 1 HsBhoxB2 ( 252) GTCCCGTGAC 1 CfBhoxB1 ( 328) ATCACATGCG 1 HsDhoxD1 ( 258) GCCACGTGGC 1 HsAhoxa4 ( 364) GGCACTTGAC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 10 n= 33456 bayes= 10.6095 E= 5.0e-012 15 -1207 140 -1207 -1207 -364 -206 211 -1207 172 -1207 -217 218 -264 -1207 -1207 -1207 178 -1207 -1207 15 -1207 136 -317 -1207 -1207 -1207 225 -1207 -1207 178 -1207 91 -6 17 -1207 -1207 94 -106 53 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 10 nsites= 43 E= 5.0e-012 0.232558 0.000000 0.767442 0.000000 0.000000 0.023256 0.069767 0.906977 0.000000 0.953488 0.000000 0.046512 0.953488 0.046512 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.232558 0.000000 0.744186 0.023256 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.395349 0.279070 0.325581 0.000000 0.000000 0.558140 0.139535 0.302326 -------------------------------------------------------------------------------- Time 171.98 secs. ******************************************************************************** ******************************************************************************** MOTIF 4 width = 10 sites = 2 llr = 31 E-value = 1.5e+006 ******************************************************************************** -------------------------------------------------------------------------------- Motif 4 Description -------------------------------------------------------------------------------- Simplified A ::aa::aaa: pos.-specific C ::::a::::: probability G :::::::::: matrix T aa:::a:::a bits 2.3 **** ***** 2.0 **** ***** 1.8 ********** 1.6 ********** Information 1.4 ********** content 1.1 ********** (22.1 bits) 0.9 ********** 0.7 ********** 0.5 ********** 0.2 ********** 0.0 ---------- Multilevel TTAACTAAAT consensus sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 4 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- ---------- CfDhoxD4 - 315 2.29e-07 TTTCACAAAT TTAACTAAAT AACATACGTG HsDhoxD4 - 314 2.29e-07 TTTCACAAAT TTAACTAAAT AACATACGTG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 4 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- CfDhoxD4 2.3e-07 314_[-4]_177 HsDhoxD4 2.3e-07 313_[-4]_178 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 4 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 4 width=10 seqs=2 CfDhoxD4 ( 315) TTAACTAAAT 1 HsDhoxD4 ( 314) TTAACTAAAT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 4 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 10 n= 33456 bayes= 12.2641 E= 1.5e+006 -765 -765 -765 225 -765 -765 -765 225 225 -765 -765 -765 225 -765 -765 -765 -765 178 -765 -765 -765 -765 -765 225 225 -765 -765 -765 225 -765 -765 -765 225 -765 -765 -765 -765 -765 -765 225 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 4 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 10 nsites= 2 E= 1.5e+006 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 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 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 -------------------------------------------------------------------------------- Time 229.42 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- HsA 1.97e-02 282_[-1(7.20e-06)]_111_[+2(7.98e-05)]_88 HsAhoxa1 9.81e-05 54_[+2(3.06e-06)]_2_[+2(5.40e-05)]_11_[-2(9.27e-05)]_250_[+3(5.19e-06)]_21_[-2(2.96e-05)]_28_[-1(8.14e-06)]_75 HsAhoxa2 2.30e-04 79_[-2(7.45e-05)]_175_[-3(1.04e-05)]_88_[+1(1.39e-06)]_26_[-1(3.60e-05)]_93 HsAhoxa3 1.28e-05 71_[-1(8.97e-05)]_107_[+4(2.75e-05)]_90_[-1(2.57e-06)]_113_[+3(1.16e-06)]_80 HsAhoxa4 7.11e-03 150_[+2(4.88e-05)]_13_[-2(1.26e-05)]_195_[+2(7.98e-05)]_79_[+1(1.71e-05)]_24 HsAhoxa5 8.51e-04 254_[-2(2.43e-05)]_75_[-3(2.01e-05)]_142_[+1(1.11e-05)] HsAhoxa6 5.33e-02 85_[+1(7.90e-05)]_2_[+2(1.90e-05)]_394 HsAhoxa7 2.05e-04 109_[+2(1.04e-05)]_244_[+3(9.18e-06)]_16_[+1(3.36e-06)]_102 HsAhoxa9 6.97e-04 35_[-1(8.97e-05)]_65_[+1(1.97e-05)]_23_[+2(7.45e-05)]_118_[+1(1.11e-05)]_66_[-3(5.19e-06)]_144 HsAhoxa10 1.97e-02 349_[-1(7.20e-06)]_111_[+2(7.98e-05)]_21 HsAhoxa11 8.49e-05 180_[+3(9.88e-05)]_84_[+1(1.65e-07)]_59_[+3(8.02e-06)]_148 HsAhoxa13 5.74e-01 99_[-2(6.37e-05)]_232_[+2(5.40e-05)]_150 HsBhoxB1 1.81e-01 139_[-2(2.65e-05)]_189_[-2(4.15e-05)]_153 HsBhoxB2 5.13e-05 251_[+3(4.25e-05)]_97_[+1(1.71e-05)]_37_[+4(2.75e-05)]_61_[-2(3.06e-06)]_15 HsBhoxB3 6.53e-06 158_[-1(6.62e-07)]_[-1(7.90e-05)]_2_[+1(7.36e-05)]_8_[-1(1.39e-06)]_31_[+1(2.57e-06)]_116_[+2(3.70e-05)]_15_[+2(1.90e-05)]_11_[+3(1.16e-06)]_80 HsBhoxB4 6.18e-04 269_[+2(3.06e-06)]_54_[-1(3.60e-05)]_37_[+3(3.31e-05)]_111 HsBhoxB5 2.09e-03 27_[-1(8.43e-05)]_285_[-3(2.01e-05)]_11_[-2(1.04e-05)]_8_[-2(1.90e-05)]_130 HsBhoxB6 2.36e-05 61_[+2(1.04e-05)]_8_[-4(7.88e-07)]_258_[-1(5.44e-05)]_144 HsBhoxB7 2.73e-04 133_[-1(3.36e-06)]_17_[-2(7.45e-05)]_55_[-2(4.88e-05)]_121_[+3(2.17e-05)]_4_[+3(8.02e-06)]_121 HsBhoxB8 9.56e-03 178_[-1(1.19e-05)]_4_[+2(1.04e-05)]_299 HsBhoxB9 2.11e-03 36_[-2(3.70e-05)]_76_[+3(3.98e-05)]_36_[+1(1.82e-05)]_49_[-2(2.43e-05)]_264 HsChoxC4 1.35e-03 280_[-2(7.45e-05)]_23_[+1(7.20e-06)]_73_[+3(1.85e-05)]_65_[+1(1.71e-05)]_20 HsChoxC5 1.94e-05 173_[-1(1.65e-07)]_142_[+3(1.16e-06)]_141_[-1(8.53e-06)]_15 HsDhoxD1 2.21e-01 44_[-2(9.27e-05)]_203_[+3(9.88e-05)]_234 HsDhoxD3 3.97e-01 501 HsDhoxD4 7.16e-07 133_[+2(7.29e-06)]_170_[-4(2.29e-07)]_45_[-2(8.67e-05)]_13_[+3(1.39e-05)]_48_[+1(5.44e-05)]_8_[+1(1.71e-05)]_24 HsDhoxD8 6.98e-02 4_[-1(1.39e-06)]_62_[-1(2.32e-05)]_415 HsDhoxD9 2.17e-04 307_[-1(1.65e-07)]_56_[+3(3.31e-05)]_118 HsDhoxD10 3.44e-02 336_[-3(9.18e-06)]_155 HsDhoxD11 1.92e-03 301_[+1(4.30e-05)]_21_[+3(1.16e-06)]_159 CfAhoxA1 9.81e-05 63_[+2(3.06e-06)]_22_[-2(9.27e-05)]_5_[+2(7.45e-05)]_227_[+3(5.19e-06)]_59_[-1(8.14e-06)]_75 CfAhoxA2 2.93e-04 262_[-3(1.04e-05)]_88_[+1(1.39e-06)]_28_[-1(1.65e-07)]_93 CfAhoxA3 1.11e-05 70_[-1(8.43e-05)]_108_[+4(2.75e-05)]_90_[-1(2.57e-06)]_113_[+3(1.16e-06)]_80 CfAhoxA4 2.15e-03 70_[+2(5.93e-05)]_117_[+3(8.02e-06)]_260_[+1(1.71e-05)]_24 CfAhoxA5 2.39e-02 251_[+1(9.76e-06)]_34_[+1(8.97e-05)]_196 CfAhoxA6 1.22e-01 97_[+2(1.90e-05)]_394 CfAhoxA7 3.88e-04 68_[+2(2.96e-05)]_285_[+3(9.18e-06)]_16_[+1(3.36e-06)]_102 CfAhoxA9 3.24e-04 25_[-1(8.97e-05)]_65_[+1(1.97e-05)]_39_[+2(1.26e-05)]_109_[+1(1.11e-05)]_66_[-3(5.19e-06)]_53_[-2(1.90e-05)]_84 CfAhoxA10 1.97e-02 282_[-1(7.20e-06)]_111_[+2(7.98e-05)]_88 CfAhoxA11 1.72e-04 290_[+1(1.65e-07)]_46_[+3(8.02e-06)]_145 CfAhoxA13 3.50e-01 140_[-2(5.40e-05)]_351 CfBhoxB1 3.62e-02 138_[-2(2.65e-05)]_179_[+3(6.20e-05)]_2_[-2(5.40e-05)]_152 CfBhoxB2 9.01e-06 80_[+2(3.70e-05)]_119_[+3(4.25e-05)]_101_[+1(1.65e-07)]_146_[-2(3.06e-06)]_15 CfBhoxB3 4.65e-04 18_[+2(1.90e-05)]_109_[+1(2.11e-05)]_8_[-1(8.97e-05)]_2_[+1(2.51e-05)]_61_[+2(1.04e-05)]_163_[-3(1.15e-05)]_80 CfBhoxB4 1.87e-03 267_[+2(1.26e-05)]_56_[-1(3.60e-05)]_37_[+3(3.31e-05)]_111 CfBhoxB5 3.33e-03 37_[-1(8.43e-05)]_274_[-3(2.01e-05)]_12_[-2(2.43e-05)]_7_[-2(1.90e-05)]_131 CfBhoxB6 4.78e-05 48_[+2(7.98e-05)]_7_[-4(7.88e-07)]_6_[+2(2.43e-05)]_256_[-1(5.44e-05)]_144 CfBhoxB7 2.73e-04 85_[+2(6.37e-05)]_38_[-1(3.36e-06)]_82_[-2(4.88e-05)]_121_[+3(2.17e-05)]_4_[+3(8.02e-06)]_121 CfBhoxB8 9.56e-03 177_[-1(1.19e-05)]_4_[+2(1.04e-05)]_139_[-2(3.70e-05)]_50_[-1(1.71e-05)]_91 CfBhoxB9 2.11e-03 35_[-2(3.70e-05)]_77_[+3(3.98e-05)]_36_[+1(1.82e-05)]_49_[-2(2.43e-05)]_264 CfBhoxB13 2.58e-03 46_[-1(7.20e-06)]_22_[-2(1.90e-05)]_374_[-2(7.29e-06)]_29 CfChoxC4 4.77e-03 314_[+1(4.71e-06)]_72_[+3(1.85e-05)]_65_[+1(1.71e-05)]_20 CfChoxC5 1.94e-05 321_[+3(1.16e-06)]_145_[-1(1.65e-07)]_15 CfChoxC6 5.87e-04 47_[+2(1.04e-05)]_[+1(3.60e-05)]_174_[-1(5.02e-05)]_[+1(6.18e-06)]_62_[-1(7.90e-05)]_48_[-1(9.67e-05)]_62_[+1(4.08e-06)]_38 CfChoxC8 9.97e-01 501 CfChoxC10 3.95e-05 48_[-2(2.65e-05)]_272_[+3(1.39e-05)]_37_[-2(5.40e-05)]_1_[-2(2.96e-05)]_20_[-2(1.90e-05)]_9_[+1(1.65e-07)]_54 CfChoxC11 4.92e-05 58_[+2(9.27e-05)]_33_[+1(3.31e-07)]_269_[+3(2.01e-05)]_53_[-2(2.43e-05)]_48 CfChoxC12 1.50e-03 43_[-4(8.54e-06)]_66_[+2(3.06e-06)]_177_[-2(1.04e-05)]_36_[+2(1.04e-05)]_139 CfChoxC13 4.17e-03 236_[+3(2.38e-05)]_8_[+3(2.17e-05)]_12_[+2(7.29e-06)]_20_[-1(9.67e-05)]_185 CfDhoxD1 8.39e-01 501 CfDhoxD3 1.21e-02 162_[+1(1.36e-05)]_12_[+2(1.26e-05)]_307 CfDhoxD4 8.20e-06 292_[+3(4.53e-05)]_12_[-4(2.29e-07)]_68_[+3(1.39e-05)]_47_[+1(5.44e-05)]_8_[+1(1.71e-05)]_24 CfDhoxD8 9.34e-01 501 CfDhoxD9 8.55e-01 501 CfDhoxD10 3.09e-03 175_[+2(7.29e-06)]_151_[-3(9.18e-06)]_155 CfDhoxD11 1.36e-03 222_[+2(9.27e-05)]_69_[+1(4.30e-05)]_21_[+3(1.16e-06)]_159 CfDhoxD12 3.76e-02 455_[+4(8.54e-06)]_36 CfDhoxD13 3.34e-02 87_[-1(4.71e-06)]_191_[-1(8.43e-05)]_57_[-1(8.14e-06)]_61_[-1(7.20e-06)]_65 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because motif E-value > 1.00e+07. ******************************************************************************** CPU: hotchocolate.bioinf.uni-leipzig.de ********************************************************************************