******************************************************************************** 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_A.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 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 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 ******************************************************************************** ******************************************************************************** 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_A.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= 23 wnsites= 0.8 theta: prob= 1 spmap= uni spfuzz= 0.5 em: prior= dirichlet b= 0.01 maxiter= 50 distance= 0.001 data: n= 11523 N= 23 strands: + - sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.203 C 0.297 G 0.297 T 0.203 Background letter frequencies (from dataset with add-one prior applied): A 0.203 C 0.297 G 0.297 T 0.203 ******************************************************************************** ******************************************************************************** MOTIF 1 width = 10 sites = 22 llr = 238 E-value = 5.8e-017 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 224:::1:3: pos.-specific C :::::3::2: probability G :::1:::::: matrix T 8869a79a49 bits 2.3 * 2.1 * * 1.8 * ** * 1.6 ** ** ** * Information 1.4 ***** ** * content 1.2 ******** * (15.6 bits) 0.9 ******** * 0.7 ******** * 0.5 ********** 0.2 ********** 0.0 ---------- Multilevel TTTTTTTTTT consensus A A C A sequence C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- ---------- HsAhoxa11 - 275 1.17e-07 CCCTTTCCTT TTTTTTTTTT CCTCCTCTCC CfAhoxA11 - 291 1.17e-07 GCCTTTTTTT TTTTTTTTTT ATTCCCTTCC CfAhoxA2 + 399 1.17e-07 CTATGATAGA TTTTTTTTTT CCTCTGCTCT HsAhoxa2 - 363 6.39e-07 TGCTAGGGTG TTTTTTTTCT AATTCACTGA HsAhoxa3 + 289 8.10e-07 TGCTGACCAC TTTTTCTTTT ATGGCTTTCA CfAhoxA3 + 289 8.10e-07 TGCTGACCAC TTTTTCTTTT ATGGCTTTCA HsAhoxa1 + 417 2.80e-06 ATTCATATCA TTTTTCTTCT CCGGCCCCAT CfAhoxA1 + 417 2.80e-06 ATTCATATCA TTTTTCTTCT CCGGCCCCAT HsAhoxa9 - 272 3.26e-06 TTTGCAGTCA TAATTTTTAT AGCAAAAGCC HsAhoxa5 - 492 3.26e-06 . TTTGTTTTTT GATATGTGTG CfAhoxA9 - 269 3.26e-06 TTTGCAGTCA TAATTTTTAT AGCAAAAGCC HsAhoxa7 - 390 3.55e-06 ACCAAACCCC ATTTTCTTTT GGACGGAGCT CfAhoxA7 - 390 3.55e-06 ACCAAACCCC ATTTTCTTTT GGACGGAGCT HsAhoxa4 - 468 6.61e-06 GCAAAAATAC TAATTTTTCT CGCGTTGTCG CfAhoxA4 - 468 6.61e-06 GCAAAAATAC TAATTTTTCT CGCGTTGTCG CfAhoxA5 - 252 7.13e-06 GCAGCCCCTC TTATTTTTGT GTCGAGGTTG HsAhoxa10 + 350 1.25e-05 TACAGATTAC ATATTTATAT CAATCGCGGG HsA + 283 1.25e-05 TACAGATTAC ATATTTATAT CAATCGCGGG CfAhoxA10 + 283 1.25e-05 TACAGATTAC ATATTTATAT CAATCGTGGG CfAhoxA6 - 63 2.13e-05 ATTTTGCTGG TTTTTCTTTC CAAACAGGAA CfAhoxA13 - 82 3.90e-05 CCCCAGTGGC TTTGTTTTAA AAAGCCCCCA HsAhoxa6 - 86 4.76e-05 TCCTCCCCTT TTTGCTTTAT TGAATTTTGC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- HsAhoxa11 1.2e-07 274_[-1]_217 CfAhoxA11 1.2e-07 290_[-1]_201 CfAhoxA2 1.2e-07 398_[+1]_93 HsAhoxa2 6.4e-07 362_[-1]_129 HsAhoxa3 8.1e-07 288_[+1]_203 CfAhoxA3 8.1e-07 288_[+1]_203 HsAhoxa1 2.8e-06 416_[+1]_75 CfAhoxA1 2.8e-06 416_[+1]_75 HsAhoxa9 3.3e-06 271_[-1]_220 HsAhoxa5 3.3e-06 491_[-1] CfAhoxA9 3.3e-06 268_[-1]_223 HsAhoxa7 3.5e-06 389_[-1]_102 CfAhoxA7 3.5e-06 389_[-1]_102 HsAhoxa4 6.6e-06 467_[-1]_24 CfAhoxA4 6.6e-06 467_[-1]_24 CfAhoxA5 7.1e-06 251_[-1]_240 HsAhoxa10 1.2e-05 349_[+1]_142 HsA 1.2e-05 282_[+1]_209 CfAhoxA10 1.2e-05 282_[+1]_209 CfAhoxA6 2.1e-05 62_[-1]_429 CfAhoxA13 3.9e-05 81_[-1]_410 HsAhoxa6 4.8e-05 85_[-1]_406 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=10 seqs=22 HsAhoxa11 ( 275) TTTTTTTTTT 1 CfAhoxA11 ( 291) TTTTTTTTTT 1 CfAhoxA2 ( 399) TTTTTTTTTT 1 HsAhoxa2 ( 363) TTTTTTTTCT 1 HsAhoxa3 ( 289) TTTTTCTTTT 1 CfAhoxA3 ( 289) TTTTTCTTTT 1 HsAhoxa1 ( 417) TTTTTCTTCT 1 CfAhoxA1 ( 417) TTTTTCTTCT 1 HsAhoxa9 ( 272) TAATTTTTAT 1 HsAhoxa5 ( 492) TTTGTTTTTT 1 CfAhoxA9 ( 269) TAATTTTTAT 1 HsAhoxa7 ( 390) ATTTTCTTTT 1 CfAhoxA7 ( 390) ATTTTCTTTT 1 HsAhoxa4 ( 468) TAATTTTTCT 1 CfAhoxA4 ( 468) TAATTTTTCT 1 CfAhoxA5 ( 252) TTATTTTTGT 1 HsAhoxa10 ( 350) ATATTTATAT 1 HsA ( 283) ATATTTATAT 1 CfAhoxA10 ( 283) ATATTTATAT 1 CfAhoxA6 ( 63) TTTTTCTTTC 1 CfAhoxA13 ( 82) TTTGTTTTAA 1 HsAhoxa6 ( 86) TTTGCTTTAT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 10 n= 11316 bayes= 9.35955 E= 5.8e-017 17 -1110 -1110 193 -16 -1110 -1110 201 84 -1110 -1110 165 -1110 -1110 -112 209 -1110 -271 -1110 224 -1110 10 -1110 175 -57 -1110 -1110 209 -1110 -1110 -1110 230 65 -39 -271 101 -215 -271 -1110 216 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 10 nsites= 22 E= 5.8e-017 0.227273 0.000000 0.000000 0.772727 0.181818 0.000000 0.000000 0.818182 0.363636 0.000000 0.000000 0.636364 0.000000 0.000000 0.136364 0.863636 0.000000 0.045455 0.000000 0.954545 0.000000 0.318182 0.000000 0.681818 0.136364 0.000000 0.000000 0.863636 0.000000 0.000000 0.000000 1.000000 0.318182 0.227273 0.045455 0.409091 0.045455 0.045455 0.000000 0.909091 -------------------------------------------------------------------------------- Time 5.72 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 width = 10 sites = 23 llr = 206 E-value = 1.6e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A 3a8:1:::31 pos.-specific C :::1:11:73 probability G :::1:12a:2 matrix T 7:28987::4 bits 2.3 * 2.1 * 1.8 * 1.6 ** * * Information 1.4 ** * * content 1.2 ******** (12.9 bits) 0.9 ********* 0.7 ********* 0.5 ********* 0.2 ********** 0.0 ---------- Multilevel TAATTTTGCT consensus A AC sequence G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- ---------- HsAhoxa5 + 97 6.21e-07 GGAAATGCAA TAATTTTGCC ATAATGGGCT CfAhoxA5 + 412 6.21e-07 GGAAATGCAA TAATTTTGCC ATAATGGGCT HsAhoxa7 - 492 1.66e-06 . TAATTTTGAC CTGTGATTTG CfAhoxA7 - 492 1.66e-06 . TAATTTTGAC CTGTGATTTG HsAhoxa2 + 130 2.96e-06 AACATATATG TATTTTTGCT CTGAAAAAAG CfAhoxA2 + 128 4.86e-06 CACCTATATG TATTTTTGCC CTGAAAAAAG HsAhoxa6 + 294 5.40e-06 NGGCTGTTTG TAACTTTGCT GCCTCGGTCG CfAhoxA6 + 294 5.40e-06 GGGCTGTTTG TAACTTTGCT GCCTCGGTCG HsAhoxa9 + 103 1.01e-05 ATGGCGTGAT TAATTGTGAT ATAAAATAGT HsA - 481 1.01e-05 TGTTGTGGGA TAATTTGGCG AAGGGAGCAG CfAhoxA10 - 481 1.01e-05 TGTTGTGGGA TAATTTGGCG AAGGGAGCAG CfAhoxA9 + 93 1.01e-05 ATGGCGTGAT TAATTGTGAT ATAAAATAGT HsAhoxa4 + 479 1.26e-05 GAAAAATTAG TATTTTTGCA CTTCACAAAT CfAhoxA4 + 479 1.26e-05 GAAAAATTAG TATTTTTGCA CTTCACAAAT HsAhoxa3 + 273 1.92e-05 TCGTGCTGCT AAATATTGCT GACCACTTTT CfAhoxA3 + 273 1.92e-05 TCGTGCTGCT AAATATTGCT GACCACTTTT HsAhoxa13 - 46 2.42e-05 ACAGGTCAGG TAATTCTGCC GGCGGTCAGG CfAhoxA1 - 309 2.42e-05 GCCTCCTGCG AAAGTTTGCT GGCTCCCGCG HsAhoxa1 - 309 3.76e-05 GCCTCCTGCA AAAGTTTGCC GGCTTCCGCA HsAhoxa11 - 403 4.31e-05 CGTGAAGTAG AAATTTGGAG ACGTAAGCTG CfAhoxA11 - 406 4.31e-05 CGTGAAGTAG AAATTTGGAG ACGTAAGCTG HsAhoxa10 + 170 6.92e-04 CCCCACTTGT TAACTGCGCG GGGCCCAAGG CfAhoxA13 + 171 2.26e-02 GCCCACCGTC GAATNNNNNN NNNNNNNNNN -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- HsAhoxa5 6.2e-07 96_[+2]_395 CfAhoxA5 6.2e-07 411_[+2]_80 HsAhoxa7 1.7e-06 491_[-2] CfAhoxA7 1.7e-06 491_[-2] HsAhoxa2 3e-06 129_[+2]_362 CfAhoxA2 4.9e-06 127_[+2]_364 HsAhoxa6 5.4e-06 293_[+2]_198 CfAhoxA6 5.4e-06 293_[+2]_198 HsAhoxa9 1e-05 102_[+2]_389 HsA 1e-05 480_[-2]_11 CfAhoxA10 1e-05 480_[-2]_11 CfAhoxA9 1e-05 92_[+2]_399 HsAhoxa4 1.3e-05 478_[+2]_13 CfAhoxA4 1.3e-05 478_[+2]_13 HsAhoxa3 1.9e-05 272_[+2]_219 CfAhoxA3 1.9e-05 272_[+2]_219 HsAhoxa13 2.4e-05 45_[-2]_446 CfAhoxA1 2.4e-05 308_[-2]_183 HsAhoxa1 3.8e-05 308_[-2]_183 HsAhoxa11 4.3e-05 402_[-2]_89 CfAhoxA11 4.3e-05 405_[-2]_86 HsAhoxa10 0.00069 169_[+2]_322 CfAhoxA13 0.023 170_[+2]_321 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=10 seqs=23 HsAhoxa5 ( 97) TAATTTTGCC 1 CfAhoxA5 ( 412) TAATTTTGCC 1 HsAhoxa7 ( 492) TAATTTTGAC 1 CfAhoxA7 ( 492) TAATTTTGAC 1 HsAhoxa2 ( 130) TATTTTTGCT 1 CfAhoxA2 ( 128) TATTTTTGCC 1 HsAhoxa6 ( 294) TAACTTTGCT 1 CfAhoxA6 ( 294) TAACTTTGCT 1 HsAhoxa9 ( 103) TAATTGTGAT 1 HsA ( 481) TAATTTGGCG 1 CfAhoxA10 ( 481) TAATTTGGCG 1 CfAhoxA9 ( 93) TAATTGTGAT 1 HsAhoxa4 ( 479) TATTTTTGCA 1 CfAhoxA4 ( 479) TATTTTTGCA 1 HsAhoxa3 ( 273) AAATATTGCT 1 CfAhoxA3 ( 273) AAATATTGCT 1 HsAhoxa13 ( 46) TAATTCTGCC 1 CfAhoxA1 ( 309) AAAGTTTGCT 1 HsAhoxa1 ( 309) AAAGTTTGCC 1 HsAhoxa11 ( 403) AAATTTGGAG 1 CfAhoxA11 ( 406) AAATTTGGAG 1 HsAhoxa10 ( 170) TAACTGCGCG 1 CfAhoxA13 ( 171) GAATXXXXXX 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 10 n= 11316 bayes= 9.34284 E= 1.6e-001 36 -1117 -277 178 230 -1117 -1117 -1117 203 -1117 -1117 -22 -1117 -119 -177 195 -108 -451 -451 212 -451 -240 -105 196 -451 -240 -67 188 -451 -451 170 -451 41 125 -451 -451 -108 9 -37 82 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 10 nsites= 23 E= 1.6e-001 0.260870 0.000000 0.043478 0.695652 1.000000 0.000000 0.000000 0.000000 0.826087 0.000000 0.000000 0.173913 0.000000 0.130435 0.086957 0.782609 0.095768 0.012928 0.012928 0.878376 0.008811 0.056406 0.143363 0.791420 0.008811 0.056406 0.186841 0.747942 0.008811 0.012928 0.969450 0.008811 0.269681 0.708580 0.012928 0.008811 0.095768 0.317276 0.230319 0.356637 -------------------------------------------------------------------------------- Time 12.01 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 width = 10 sites = 21 llr = 199 E-value = 2.9e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A ::::::::41 pos.-specific C :::7:a:7:9 probability G 9aa2a:a26: matrix T :::::::1:: bits 2.3 2.1 1.8 ** *** 1.6 ** *** Information 1.4 ** *** content 1.2 *** *** * (13.6 bits) 0.9 *** *** ** 0.7 ********** 0.5 ********** 0.2 ********** 0.0 ---------- Multilevel GGGCGCGCGC consensus G A sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- ---------- HsAhoxa5 + 240 5.40e-06 CACGCGCCCG GGGCGCGCGC GCCACCCCCC HsAhoxa4 + 295 5.40e-06 GCACGGGGCG GGGCGCGCGC TGGGCTGGGG HsAhoxa1 + 129 5.40e-06 CAGCGGAGTC GGGCGCGCGC AGAACGCAGC CfAhoxA4 + 221 5.40e-06 TCCCGGGCGG GGGCGCGCGC GGGGCCGAGA HsAhoxa10 + 142 9.08e-06 AAGGCAGACT GGGCGCGCAC CATAAACACC HsAhoxa6 - 237 9.08e-06 XXAGATTAAT GGGCGCGCAC AGCTAGCCGG HsA + 75 9.08e-06 AAGGCAGACT GGGCGCGCAC CATAAACACC CfAhoxA6 - 237 9.08e-06 GCAGATTGAT GGGCGCGCAC AGCCAGCCGG HsAhoxa11 + 115 1.82e-05 CATGCTGCAT GGGGGCGCAC CCCAGCCTCT HsAhoxa9 + 373 2.36e-05 CGGCCAATGG GGGCGCGGGC GCCGGCAACT HsAhoxa7 + 237 2.36e-05 CAGGCCCGCC GGGCGCGGGC GGATTCTTTG CfAhoxA9 + 370 2.36e-05 CGGCCAATGG GGGCGCGGGC GCCGGCAACT CfAhoxA7 + 237 2.36e-05 CGGACCCGCG GGGCGCGGGC AGATTCGTTG HsAhoxa13 - 92 2.73e-05 GAGGGGAGGT GGGCGCGCGA TTGGGTTGCG CfAhoxA5 + 344 2.73e-05 CATCCTCGCC GGGCGCGCGA TCGGCAGCTG CfAhoxA10 + 74 5.49e-05 AGGCGGGCCA GGGTGCGCAC CATAAACACC CfAhoxA1 - 380 5.49e-05 GCGCAAGAGG GGGGGCGCGA GGGCGGAGGG HsAhoxa3 + 425 7.22e-05 ACGTGACCGC GGGGGCGTGC CAATGTGCGC CfAhoxA3 + 425 7.22e-05 ACGTGACCGC GGGGGCGTGC CAATGTGCGC CfAhoxA2 + 34 8.09e-05 ACACACTCCC AGGCGCGCAC ACCAGATCTG CfAhoxA11 + 54 1.15e-04 GCGAGCGGCA TGGGGCGCAC CCCAGCCTCG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- HsAhoxa5 5.4e-06 239_[+3]_252 HsAhoxa4 5.4e-06 294_[+3]_197 HsAhoxa1 5.4e-06 128_[+3]_363 CfAhoxA4 5.4e-06 220_[+3]_271 HsAhoxa10 9.1e-06 141_[+3]_350 HsAhoxa6 9.1e-06 236_[-3]_255 HsA 9.1e-06 74_[+3]_417 CfAhoxA6 9.1e-06 236_[-3]_255 HsAhoxa11 1.8e-05 114_[+3]_377 HsAhoxa9 2.4e-05 372_[+3]_119 HsAhoxa7 2.4e-05 236_[+3]_255 CfAhoxA9 2.4e-05 369_[+3]_122 CfAhoxA7 2.4e-05 236_[+3]_255 HsAhoxa13 2.7e-05 91_[-3]_400 CfAhoxA5 2.7e-05 343_[+3]_148 CfAhoxA10 5.5e-05 73_[+3]_418 CfAhoxA1 5.5e-05 379_[-3]_112 HsAhoxa3 7.2e-05 424_[+3]_67 CfAhoxA3 7.2e-05 424_[+3]_67 CfAhoxA2 8.1e-05 33_[+3]_458 CfAhoxA11 0.00011 53_[+3]_438 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=10 seqs=21 HsAhoxa5 ( 240) GGGCGCGCGC 1 HsAhoxa4 ( 295) GGGCGCGCGC 1 HsAhoxa1 ( 129) GGGCGCGCGC 1 CfAhoxA4 ( 221) GGGCGCGCGC 1 HsAhoxa10 ( 142) GGGCGCGCAC 1 HsAhoxa6 ( 237) GGGCGCGCAC 1 HsA ( 75) GGGCGCGCAC 1 CfAhoxA6 ( 237) GGGCGCGCAC 1 HsAhoxa11 ( 115) GGGGGCGCAC 1 HsAhoxa9 ( 373) GGGCGCGGGC 1 HsAhoxa7 ( 237) GGGCGCGGGC 1 CfAhoxA9 ( 370) GGGCGCGGGC 1 CfAhoxA7 ( 237) GGGCGCGGGC 1 HsAhoxa13 ( 92) GGGCGCGCGA 1 CfAhoxA5 ( 344) GGGCGCGCGA 1 CfAhoxA10 ( 74) GGGTGCGCAC 1 CfAhoxA1 ( 380) GGGGGCGCGA 1 HsAhoxa3 ( 425) GGGGGCGTGC 1 CfAhoxA3 ( 425) GGGGGCGTGC 1 CfAhoxA2 ( 34) AGGCGCGCAC 1 CfAhoxA11 ( 54) TGGGGCGCAC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 10 n= 11316 bayes= 9.37644 E= 2.9e-001 -209 -1104 160 -209 -1104 -1104 175 -1104 -1104 -1104 175 -1104 -1104 126 -32 -209 -1104 -1104 175 -1104 -1104 175 -1104 -1104 -1104 -1104 175 -1104 -1104 126 -64 -109 91 -1104 106 -1104 -50 153 -1104 -1104 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 10 nsites= 21 E= 2.9e-001 0.047619 0.000000 0.904762 0.047619 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.714286 0.238095 0.047619 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.714286 0.190476 0.095238 0.380952 0.000000 0.619048 0.000000 0.142857 0.857143 0.000000 0.000000 -------------------------------------------------------------------------------- Time 18.65 secs. ******************************************************************************** ******************************************************************************** MOTIF 4 width = 10 sites = 14 llr = 155 E-value = 6.4e-002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 4 Description -------------------------------------------------------------------------------- Simplified A ::a1:::6:1 pos.-specific C 1a:6:::4a9 probability G 1:::a:a::: matrix T 8::3:a:::: bits 2.3 * * 2.1 * * 1.8 ** *** * 1.6 ** *** * Information 1.4 ** *** * content 1.2 *** ****** (16.0 bits) 0.9 *** ****** 0.7 ********** 0.5 ********** 0.2 ********** 0.0 ---------- Multilevel TCACGTGACC consensus T C sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 4 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- ---------- HsAhoxa3 + 413 1.17e-06 CGGCGGAGTG TCACGTGACC GCGGGGGCGT CfAhoxA3 + 413 1.17e-06 CGGCGGAGCG TCACGTGACC GCGGGGGCGT HsAhoxa11 - 343 1.96e-06 GAGGTGCTGG TCATGTGACC CGATGTTGAA CfAhoxA11 - 346 1.96e-06 GAGGTGCTGG TCATGTGACC TGATGTTGAA HsAhoxa9 - 347 3.67e-06 GCCGTGCGCG TCACGTGCCC GTCCAGCAGA HsAhoxa1 + 349 3.67e-06 GCTGACACCG TCACGTGCCC CTCCTCCAGC CfAhoxA9 - 344 3.67e-06 GCCGCGCGCG TCACGTGCCC GCCCGGCAGA CfAhoxA1 + 349 3.67e-06 GCTGGCGGAG TCACGTGCCC CTCCCCCTGC HsAhoxa2 + 266 6.97e-06 GCAGAAGCAA TCATGTGACA GCCAATTCGG CfAhoxA2 + 264 6.97e-06 GCAGAAGCAA TCATGTGACA GCCAATTCGG HsAhoxa7 - 363 8.68e-06 GCTCGCCGCA GCACGTGACC GCCCACATGA CfAhoxA7 - 363 8.68e-06 GCTCGCCGCA GCACGTGACC GCCCACATGA CfAhoxA4 - 197 1.27e-05 CCGGGACCCA CCACGTGACC AGCCCCCGCC HsAhoxa4 - 363 1.47e-05 CCCCCCGCTG TCAAGTGCCC ACTCCTCCCC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 4 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- HsAhoxa3 1.2e-06 412_[+4]_79 CfAhoxA3 1.2e-06 412_[+4]_79 HsAhoxa11 2e-06 342_[-4]_149 CfAhoxA11 2e-06 345_[-4]_146 HsAhoxa9 3.7e-06 346_[-4]_145 HsAhoxa1 3.7e-06 348_[+4]_143 CfAhoxA9 3.7e-06 343_[-4]_148 CfAhoxA1 3.7e-06 348_[+4]_143 HsAhoxa2 7e-06 265_[+4]_226 CfAhoxA2 7e-06 263_[+4]_228 HsAhoxa7 8.7e-06 362_[-4]_129 CfAhoxA7 8.7e-06 362_[-4]_129 CfAhoxA4 1.3e-05 196_[-4]_295 HsAhoxa4 1.5e-05 362_[-4]_129 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 4 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 4 width=10 seqs=14 HsAhoxa3 ( 413) TCACGTGACC 1 CfAhoxA3 ( 413) TCACGTGACC 1 HsAhoxa11 ( 343) TCATGTGACC 1 CfAhoxA11 ( 346) TCATGTGACC 1 HsAhoxa9 ( 347) TCACGTGCCC 1 HsAhoxa1 ( 349) TCACGTGCCC 1 CfAhoxA9 ( 344) TCACGTGCCC 1 CfAhoxA1 ( 349) TCACGTGCCC 1 HsAhoxa2 ( 266) TCATGTGACA 1 CfAhoxA2 ( 264) TCATGTGACA 1 HsAhoxa7 ( 363) GCACGTGACC 1 CfAhoxA7 ( 363) GCACGTGACC 1 CfAhoxA4 ( 197) CCACGTGACC 1 HsAhoxa4 ( 363) TCAAGTGCCC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 4 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 10 n= 11316 bayes= 9.50061 E= 6.4e-002 -1045 -205 -106 195 -1045 175 -1045 -1045 230 -1045 -1045 -1045 -150 111 -1045 50 -1045 -1045 175 -1045 -1045 -1045 -1045 230 -1045 -1045 175 -1045 166 26 -1045 -1045 -1045 175 -1045 -1045 -50 153 -1045 -1045 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 4 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 10 nsites= 14 E= 6.4e-002 0.000000 0.071429 0.142857 0.785714 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.071429 0.642857 0.000000 0.285714 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.642857 0.357143 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.142857 0.857143 0.000000 0.000000 -------------------------------------------------------------------------------- Time 24.63 secs. ******************************************************************************** ******************************************************************************** MOTIF 5 width = 10 sites = 9 llr = 109 E-value = 3.7e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 5 Description -------------------------------------------------------------------------------- Simplified A :a7::64a8: pos.-specific C 9:::::6::a probability G :::::::::: matrix T 1:3aa4::2: bits 2.3 * ** * 2.1 * ** * 1.8 * ** * * 1.6 * ** *** Information 1.4 ****** *** content 1.2 ****** *** (17.5 bits) 0.9 ********** 0.7 ********** 0.5 ********** 0.2 ********** 0.0 ---------- Multilevel CAATTACAAC consensus T TA T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 5 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- ---------- HsAhoxa9 + 207 2.52e-07 TCGTTGGCCA CAATTAAAAC AAACCCCATC CfAhoxA9 + 204 2.52e-07 TCGTTGGCCA CAATTAAAAC AAACCCGATC HsAhoxa11 + 329 1.24e-06 AGCAGCTTGT CAATTTCAAC ATCGGGTCAC HsAhoxa2 + 288 1.24e-06 CAATTCGGTC CAATTTCAAC CTTGTCTCCA CfAhoxA11 + 332 1.24e-06 CGCAGCTTGT CAATTTCAAC ATCAGGTCAC CfAhoxA2 + 286 1.24e-06 CAATTCGGTC CAATTTCAAC CTTGTCTCCA HsAhoxa1 - 266 4.57e-06 GTTTTAGTGG CATTTAAATC CCCGGCGCTC CfAhoxA1 - 266 4.57e-06 GTTTCAGTGG CATTTAAATC CCCGGCGCTG CfAhoxA5 - 291 6.23e-06 ACTTGGATTT TATTTACAAC AACTTTATTT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 5 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- HsAhoxa9 2.5e-07 206_[+5]_285 CfAhoxA9 2.5e-07 203_[+5]_288 HsAhoxa11 1.2e-06 328_[+5]_163 HsAhoxa2 1.2e-06 287_[+5]_204 CfAhoxA11 1.2e-06 331_[+5]_160 CfAhoxA2 1.2e-06 285_[+5]_206 HsAhoxa1 4.6e-06 265_[-5]_226 CfAhoxA1 4.6e-06 265_[-5]_226 CfAhoxA5 6.2e-06 290_[-5]_201 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 5 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 5 width=10 seqs=9 HsAhoxa9 ( 207) CAATTAAAAC 1 CfAhoxA9 ( 204) CAATTAAAAC 1 HsAhoxa11 ( 329) CAATTTCAAC 1 HsAhoxa2 ( 288) CAATTTCAAC 1 CfAhoxA11 ( 332) CAATTTCAAC 1 CfAhoxA2 ( 286) CAATTTCAAC 1 HsAhoxa1 ( 266) CATTTAAATC 1 CfAhoxA1 ( 266) CATTTAAATC 1 CfAhoxA5 ( 291) TATTTACAAC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 5 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 10 n= 11316 bayes= 11.1435 E= 3.7e+001 -982 158 -982 -87 230 -982 -982 -982 172 -982 -982 72 -982 -982 -982 230 -982 -982 -982 230 145 -982 -982 113 113 90 -982 -982 230 -982 -982 -982 194 -982 -982 13 -982 175 -982 -982 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 5 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 10 nsites= 9 E= 3.7e+001 0.000000 0.888889 0.000000 0.111111 1.000000 0.000000 0.000000 0.000000 0.666667 0.000000 0.000000 0.333333 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.555556 0.000000 0.000000 0.444444 0.444444 0.555556 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.777778 0.000000 0.000000 0.222222 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- Time 31.19 secs. ******************************************************************************** ******************************************************************************** MOTIF 6 width = 10 sites = 11 llr = 133 E-value = 1.4e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 6 Description -------------------------------------------------------------------------------- Simplified A a:a6:aaa1: pos.-specific C :a::5::::7 probability G ::::5:::23 matrix T :::4::::7: bits 2.3 * * *** 2.1 * * *** 1.8 *** *** 1.6 *** *** Information 1.4 **** *** content 1.2 **** **** (17.4 bits) 0.9 **** ***** 0.7 ********** 0.5 ********** 0.2 ********** 0.0 ---------- Multilevel ACAAGAAATC consensus TC G sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 6 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- ---------- HsAhoxa7 + 478 7.38e-07 AAGCTGCCGG ACAACAAATC ACAGGTCAAA HsAhoxa6 + 467 7.38e-07 GTACTAATAC ACAACAAATC ACAGTCCTGC CfAhoxA7 + 478 7.38e-07 AAGCTGCCGG ACAACAAATC ACAGGTCAAA CfAhoxA6 + 467 7.38e-07 GTACTAATAC ACAACAAATC ACAGTCCTGC HsAhoxa9 + 435 1.11e-06 CCAAGTTGTT ACATGAAATC TGCAGTTTCA CfAhoxA9 + 436 1.11e-06 CCAAGTTGTT ACATGAAATC TGCAGTTTCA HsA + 443 1.85e-06 CATGTTTTGC ACAAGAAATG TCAGCCAGAA CfAhoxA10 + 443 1.85e-06 CATGTTTTGC ACAAGAAATG TCAGCCAGAA HsAhoxa3 - 302 5.31e-06 TAGCTAAGTG ACATGAAAGC CATAAAAGAA CfAhoxA3 - 302 5.31e-06 TAGCTAAGTG ACATGAAAGC CATAAAAGAA HsAhoxa5 + 332 8.42e-06 TTACGACTGG ACAACAAAAG CACGTGATTC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 6 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- HsAhoxa7 7.4e-07 477_[+6]_14 HsAhoxa6 7.4e-07 466_[+6]_25 CfAhoxA7 7.4e-07 477_[+6]_14 CfAhoxA6 7.4e-07 466_[+6]_25 HsAhoxa9 1.1e-06 434_[+6]_57 CfAhoxA9 1.1e-06 435_[+6]_56 HsA 1.8e-06 442_[+6]_49 CfAhoxA10 1.8e-06 442_[+6]_49 HsAhoxa3 5.3e-06 301_[-6]_190 CfAhoxA3 5.3e-06 301_[-6]_190 HsAhoxa5 8.4e-06 331_[+6]_160 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 6 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 6 width=10 seqs=11 HsAhoxa7 ( 478) ACAACAAATC 1 HsAhoxa6 ( 467) ACAACAAATC 1 CfAhoxA7 ( 478) ACAACAAATC 1 CfAhoxA6 ( 467) ACAACAAATC 1 HsAhoxa9 ( 435) ACATGAAATC 1 CfAhoxA9 ( 436) ACATGAAATC 1 HsA ( 443) ACAAGAAATG 1 CfAhoxA10 ( 443) ACAAGAAATG 1 HsAhoxa3 ( 302) ACATGAAAGC 1 CfAhoxA3 ( 302) ACATGAAAGC 1 HsAhoxa5 ( 332) ACAACAAAAG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 6 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 10 n= 11316 bayes= 11.0324 E= 1.4e-001 230 -1010 -1010 -1010 -1010 175 -1010 -1010 230 -1010 -1010 -1010 165 -1010 -1010 84 -1010 61 87 -1010 230 -1010 -1010 -1010 230 -1010 -1010 -1010 230 -1010 -1010 -1010 -115 -1010 -71 184 -1010 129 -12 -1010 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 6 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 10 nsites= 11 E= 1.4e-001 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.636364 0.000000 0.000000 0.363636 0.000000 0.454545 0.545455 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.090909 0.000000 0.181818 0.727273 0.000000 0.727273 0.272727 0.000000 -------------------------------------------------------------------------------- Time 37.64 secs. ******************************************************************************** ******************************************************************************** MOTIF 7 width = 10 sites = 5 llr = 67 E-value = 1.5e+004 ******************************************************************************** -------------------------------------------------------------------------------- Motif 7 Description -------------------------------------------------------------------------------- Simplified A :a6:4::a:: pos.-specific C :::::::::a probability G :::::a::a: matrix T a:4a6:a::: bits 2.3 ** * ** 2.1 ** * ** 1.8 ** * ***** 1.6 ** * ***** Information 1.4 ********** content 1.2 ********** (19.4 bits) 0.9 ********** 0.7 ********** 0.5 ********** 0.2 ********** 0.0 ---------- Multilevel TAATTGTAGC consensus T A sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 7 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- ---------- CfAhoxA5 + 115 3.69e-07 AACAGAGCCG TAATTGTAGC TGCTGCTGCG HsAhoxa3 + 198 1.11e-06 GTTAAGCAAA TATTTGTAGC TGCCAGTAAA HsAhoxa2 + 322 1.11e-06 TTCAATAGTT TAATAGTAGC GCGGTCCCCA CfAhoxA3 + 198 1.11e-06 GTTAAGCAAA TATTTGTAGC TGCCAGTAAA CfAhoxA2 + 320 1.11e-06 TTCAATAGTT TAATAGTAGC GCGGTCCCCA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 7 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- CfAhoxA5 3.7e-07 114_[+7]_377 HsAhoxa3 1.1e-06 197_[+7]_294 HsAhoxa2 1.1e-06 321_[+7]_170 CfAhoxA3 1.1e-06 197_[+7]_294 CfAhoxA2 1.1e-06 319_[+7]_172 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 7 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 7 width=10 seqs=5 CfAhoxA5 ( 115) TAATTGTAGC 1 HsAhoxa3 ( 198) TATTTGTAGC 1 HsAhoxa2 ( 322) TAATAGTAGC 1 CfAhoxA3 ( 198) TATTTGTAGC 1 CfAhoxA2 ( 320) TAATAGTAGC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 7 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 10 n= 11316 bayes= 10.5776 E= 1.5e+004 -897 -897 -897 230 230 -897 -897 -897 156 -897 -897 98 -897 -897 -897 230 98 -897 -897 156 -897 -897 175 -897 -897 -897 -897 230 230 -897 -897 -897 -897 -897 175 -897 -897 175 -897 -897 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 7 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 10 nsites= 5 E= 1.5e+004 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.600000 0.000000 0.000000 0.400000 0.000000 0.000000 0.000000 1.000000 0.400000 0.000000 0.000000 0.600000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- Time 44.75 secs. ******************************************************************************** ******************************************************************************** MOTIF 8 width = 10 sites = 15 llr = 157 E-value = 9.9e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif 8 Description -------------------------------------------------------------------------------- Simplified A 11a::::::: pos.-specific C 76:::::93: probability G 23:::aa:4a matrix T :::aa::13: bits 2.3 *** 2.1 *** 1.8 ***** * 1.6 ***** * Information 1.4 ****** * content 1.2 ****** * (15.1 bits) 0.9 ****** * 0.7 * ****** * 0.5 ********** 0.2 ********** 0.0 ---------- Multilevel CCATTGGCGG consensus GG T sequence C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 8 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- ---------- HsAhoxa1 + 333 1.17e-06 GGAGGCTCAG CCATTGGCTG ACACCGTCAC CfAhoxA1 + 333 1.17e-06 GGAGGCTCCG CCATTGGCTG GCGGAGTCAC HsAhoxa3 + 396 2.88e-06 CGCGGGGCGG CCATTGGCGG CGGAGTGTCA CfAhoxA4 + 182 2.88e-06 CGCGCCGTGC CCATTGGCGG GGGCTGGTCA HsAhoxa9 - 363 5.75e-06 GCCCGCGCCC CCATTGGCCG TGCGCGTCAC HsAhoxa6 + 350 5.75e-06 GCGTTCGCTC CCATTGGCCG CCGCCGCGTC CfAhoxA9 - 360 5.75e-06 GCCCGCGCCC CCATTGGCCG CGCGCGTCAC CfAhoxA6 + 350 5.75e-06 GCGCTCGCTC CCATTGGCCG CCGCCGCGTC HsAhoxa10 + 447 1.77e-05 CTCTGGCTCG GGATTGGCTG CGGGCGCCCG HsA + 380 1.77e-05 CTCTGGCTCG GGATTGGCTG CGGGCGCCCG CfAhoxA10 + 380 1.77e-05 CTCTGGCTCA GGATTGGCTG CGGGCACCCG CfAhoxA3 + 396 2.25e-05 CGCGGGGCGG CAATTGGCGG CGGAGCGTCA HsAhoxa7 + 337 2.37e-05 AGGACTGCTG AGATTGGCGG AGGCGGTCAT CfAhoxA7 + 337 2.37e-05 AGGGCTGCTG AGATTGGCGG AGGCGGTCAT HsAhoxa4 + 259 2.97e-05 CGCGGTGCGC CCATTGGTGG GGGCGCTGCA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 8 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- HsAhoxa1 1.2e-06 332_[+8]_159 CfAhoxA1 1.2e-06 332_[+8]_159 HsAhoxa3 2.9e-06 395_[+8]_96 CfAhoxA4 2.9e-06 181_[+8]_310 HsAhoxa9 5.8e-06 362_[-8]_129 HsAhoxa6 5.8e-06 349_[+8]_142 CfAhoxA9 5.8e-06 359_[-8]_132 CfAhoxA6 5.8e-06 349_[+8]_142 HsAhoxa10 1.8e-05 446_[+8]_45 HsA 1.8e-05 379_[+8]_112 CfAhoxA10 1.8e-05 379_[+8]_112 CfAhoxA3 2.3e-05 395_[+8]_96 HsAhoxa7 2.4e-05 336_[+8]_155 CfAhoxA7 2.4e-05 336_[+8]_155 HsAhoxa4 3e-05 258_[+8]_233 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 8 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 8 width=10 seqs=15 HsAhoxa1 ( 333) CCATTGGCTG 1 CfAhoxA1 ( 333) CCATTGGCTG 1 HsAhoxa3 ( 396) CCATTGGCGG 1 CfAhoxA4 ( 182) CCATTGGCGG 1 HsAhoxa9 ( 363) CCATTGGCCG 1 HsAhoxa6 ( 350) CCATTGGCCG 1 CfAhoxA9 ( 360) CCATTGGCCG 1 CfAhoxA6 ( 350) CCATTGGCCG 1 HsAhoxa10 ( 447) GGATTGGCTG 1 HsA ( 380) GGATTGGCTG 1 CfAhoxA10 ( 380) GGATTGGCTG 1 CfAhoxA3 ( 396) CAATTGGCGG 1 HsAhoxa7 ( 337) AGATTGGCGG 1 CfAhoxA7 ( 337) AGATTGGCGG 1 HsAhoxa4 ( 259) CCATTGGTGG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 8 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 10 n= 11316 bayes= 10.2322 E= 9.9e+000 -60 116 -57 -1055 -160 101 16 -1055 230 -1055 -1055 -1055 -1055 -1055 -1055 230 -1055 -1055 -1055 230 -1055 -1055 175 -1055 -1055 -1055 175 -1055 -1055 165 -1055 -160 -1055 -16 43 72 -1055 -1055 175 -1055 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 8 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 10 nsites= 15 E= 9.9e+000 0.133333 0.666667 0.200000 0.000000 0.066667 0.600000 0.333333 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.933333 0.000000 0.066667 0.000000 0.266667 0.400000 0.333333 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- Time 51.72 secs. ******************************************************************************** ******************************************************************************** MOTIF 9 width = 10 sites = 7 llr = 87 E-value = 3.6e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif 9 Description -------------------------------------------------------------------------------- Simplified A :a:6aa6a:9 pos.-specific C a::4::::a: probability G ::3::::::1 matrix T ::7:::4::: bits 2.3 * ** * 2.1 * ** * 1.8 ** ** ** 1.6 ** ** *** Information 1.4 *** ****** content 1.2 ********** (18.0 bits) 0.9 ********** 0.7 ********** 0.5 ********** 0.2 ********** 0.0 ---------- Multilevel CATAAAAACA consensus GC T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 9 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- ---------- HsAhoxa9 + 249 2.52e-07 GATCCCTTTA CATAAAAACA TATGGCTTTT CfAhoxA9 + 246 2.52e-07 GATCCCTTTG CATAAAAACA TATGGCTTTT HsAhoxa10 + 334 1.24e-06 TCTCCTGGCC CATCAATACA GATTACATAT HsA + 267 1.24e-06 TCTCCTGGCC CATCAATACA GATTACATAT CfAhoxA10 + 267 1.24e-06 TCTCCCGGCC CATCAATACA GATTACATAT CfAhoxA5 + 99 1.61e-06 CATGCACTCA CAGAAAAACA GAGCCGTAAT CfAhoxA4 + 450 5.42e-06 TCGGCGAGCC CAGAAAAACG ACAACGCGAG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 9 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- HsAhoxa9 2.5e-07 248_[+9]_243 CfAhoxA9 2.5e-07 245_[+9]_246 HsAhoxa10 1.2e-06 333_[+9]_158 HsA 1.2e-06 266_[+9]_225 CfAhoxA10 1.2e-06 266_[+9]_225 CfAhoxA5 1.6e-06 98_[+9]_393 CfAhoxA4 5.4e-06 449_[+9]_42 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 9 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 9 width=10 seqs=7 HsAhoxa9 ( 249) CATAAAAACA 1 CfAhoxA9 ( 246) CATAAAAACA 1 HsAhoxa10 ( 334) CATCAATACA 1 HsA ( 267) CATCAATACA 1 CfAhoxA10 ( 267) CATCAATACA 1 CfAhoxA5 ( 99) CAGAAAAACA 1 CfAhoxA4 ( 450) CAGAAAAACG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 9 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 10 n= 11316 bayes= 10.5016 E= 3.6e+003 -945 175 -945 -945 230 -945 -945 -945 -945 -945 -6 182 149 53 -945 -945 230 -945 -945 -945 230 -945 -945 -945 149 -945 -945 108 230 -945 -945 -945 -945 175 -945 -945 208 -945 -106 -945 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 9 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 10 nsites= 7 E= 3.6e+003 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.285714 0.714286 0.571429 0.428571 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.571429 0.000000 0.000000 0.428571 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.857143 0.000000 0.142857 0.000000 -------------------------------------------------------------------------------- Time 58.69 secs. ******************************************************************************** ******************************************************************************** MOTIF 10 width = 10 sites = 11 llr = 129 E-value = 6.7e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif 10 Description -------------------------------------------------------------------------------- Simplified A ::::44::2: pos.-specific C 9:1a65::8: probability G :::::::::: matrix T 1a9::2aa:a bits 2.3 * ** * 2.1 * ** * 1.8 *** ** * 1.6 *** ** * Information 1.4 **** ** * content 1.2 **** **** (16.9 bits) 0.9 ***** **** 0.7 ***** **** 0.5 ********** 0.2 ********** 0.0 ---------- Multilevel CTTCCCTTCT consensus AA sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 10 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- ---------- HsAhoxa7 + 280 5.41e-07 GCCTCTTGCC CTTCCATTCT AGGCGGCTGC CfAhoxA7 + 280 5.41e-07 GCCTCTTCCC CTTCCATTCT AGGCTGCCGC HsAhoxa1 + 12 1.71e-06 CGGGAGCCCT CTTCCCTTCT CACCTCTCGC CfAhoxA1 + 21 1.71e-06 ACGGAGCCCT CTTCCCTTCT CACCTCTCGC HsAhoxa13 + 439 2.25e-06 GCCGCGCGCT CTTCACTTCT TGGGGGCTTT CfAhoxA13 + 62 2.25e-06 GCCGCGCGCT CTTCACTTCT TGGGGGCTTT HsAhoxa11 - 243 2.79e-06 TCCCTCCCGG CTTCCTTTCT TTGTAGCCAC HsAhoxa9 + 21 4.32e-06 TTTTTTATGG CTTCAATTAT TGTCTAATTT CfAhoxA9 + 11 4.32e-06 TTTTTTATGG CTTCAATTAT TGTCTAATTT HsAhoxa3 + 74 7.21e-06 TCCCAGCCTT TTTCCTTTCT AGCCTATCAA CfAhoxA6 - 94 9.96e-06 CTCCTTCCTC CTCCCCTTCT TGCCTGGTCG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 10 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- HsAhoxa7 5.4e-07 279_[+10]_212 CfAhoxA7 5.4e-07 279_[+10]_212 HsAhoxa1 1.7e-06 11_[+10]_480 CfAhoxA1 1.7e-06 20_[+10]_471 HsAhoxa13 2.2e-06 438_[+10]_53 CfAhoxA13 2.2e-06 61_[+10]_430 HsAhoxa11 2.8e-06 242_[-10]_249 HsAhoxa9 4.3e-06 20_[+10]_471 CfAhoxA9 4.3e-06 10_[+10]_481 HsAhoxa3 7.2e-06 73_[+10]_418 CfAhoxA6 1e-05 93_[-10]_398 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 10 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 10 width=10 seqs=11 HsAhoxa7 ( 280) CTTCCATTCT 1 CfAhoxA7 ( 280) CTTCCATTCT 1 HsAhoxa1 ( 12) CTTCCCTTCT 1 CfAhoxA1 ( 21) CTTCCCTTCT 1 HsAhoxa13 ( 439) CTTCACTTCT 1 CfAhoxA13 ( 62) CTTCACTTCT 1 HsAhoxa11 ( 243) CTTCCTTTCT 1 HsAhoxa9 ( 21) CTTCAATTAT 1 CfAhoxA9 ( 11) CTTCAATTAT 1 HsAhoxa3 ( 74) TTTCCTTTCT 1 CfAhoxA6 ( 94) CTCCCCTTCT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 10 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 10 n= 11316 bayes= 10.3606 E= 6.7e+000 -1010 161 -1010 -115 -1010 -1010 -1010 230 -1010 -171 -1010 216 -1010 175 -1010 -1010 84 110 -1010 -1010 84 61 -1010 -16 -1010 -1010 -1010 230 -1010 -1010 -1010 230 -16 146 -1010 -1010 -1010 -1010 -1010 230 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 10 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 10 nsites= 11 E= 6.7e+000 0.000000 0.909091 0.000000 0.090909 0.000000 0.000000 0.000000 1.000000 0.000000 0.090909 0.000000 0.909091 0.000000 1.000000 0.000000 0.000000 0.363636 0.636364 0.000000 0.000000 0.363636 0.454545 0.000000 0.181818 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.181818 0.818182 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 -------------------------------------------------------------------------------- Time 64.39 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- CfAhoxA1 2.58e-08 20_[+10(1.71e-06)]_235_[-5(4.57e-06)]_33_[-2(2.42e-05)]_14_[+8(1.17e-06)]_6_[+4(3.67e-06)]_21_[-3(5.49e-05)]_27_[+1(2.80e-06)]_75 CfAhoxA2 6.87e-11 33_[+3(8.09e-05)]_84_[+2(4.86e-06)]_126_[+4(6.97e-06)]_12_[+5(1.24e-06)]_24_[+7(1.11e-06)]_31_[-1(6.39e-07)]_28_[+1(1.17e-07)]_93 CfAhoxA3 3.40e-09 197_[+7(1.11e-06)]_65_[+2(1.92e-05)]_6_[+1(8.10e-07)]_3_[-6(5.31e-06)]_84_[+8(2.25e-05)]_7_[+4(1.17e-06)]_2_[+3(7.22e-05)]_67 CfAhoxA4 4.07e-06 181_[+8(2.88e-06)]_5_[-4(1.27e-05)]_14_[+3(5.40e-06)]_219_[+9(5.42e-06)]_8_[-1(6.61e-06)]_1_[+2(1.26e-05)]_13 CfAhoxA5 7.62e-09 98_[+9(1.61e-06)]_6_[+7(3.69e-07)]_127_[-1(7.13e-06)]_29_[-5(6.23e-06)]_43_[+3(2.73e-05)]_58_[+2(6.21e-07)]_80 CfAhoxA6 3.43e-08 62_[-1(2.13e-05)]_21_[-10(9.96e-06)]_133_[-3(9.08e-06)]_47_[+2(5.40e-06)]_46_[+8(5.75e-06)]_74_[-7(3.81e-05)]_23_[+6(7.38e-07)]_14_[+3(3.71e-05)]_1 CfAhoxA7 1.10e-09 236_[+3(2.36e-05)]_33_[+10(5.41e-07)]_47_[+8(2.37e-05)]_16_[-4(8.68e-06)]_17_[-1(3.55e-06)]_78_[+6(7.38e-07)]_4_[-2(1.66e-06)] CfAhoxA9 1.96e-15 10_[+10(4.32e-06)]_5_[+1(8.77e-05)]_65_[-1(9.78e-06)]_65_[-6(3.61e-05)]_18_[+5(2.52e-07)]_32_[+9(2.52e-07)]_13_[-1(3.26e-06)]_3_[+9(8.41e-05)]_52_[-4(3.67e-06)]_6_[-8(5.75e-06)]_[+3(2.36e-05)]_56_[+6(1.11e-06)]_56 CfAhoxA10 3.23e-07 73_[+3(5.49e-05)]_183_[+9(1.24e-06)]_6_[+1(1.25e-05)]_87_[+8(1.77e-05)]_53_[+6(1.85e-06)]_28_[-2(1.01e-05)]_11 CfAhoxA11 2.79e-06 290_[-1(1.17e-07)]_31_[+5(1.24e-06)]_4_[-4(1.96e-06)]_50_[-2(4.31e-05)]_86 CfAhoxA13 8.51e-02 61_[+10(2.25e-06)]_10_[-1(3.90e-05)]_410 HsA 1.78e-07 74_[+3(9.08e-06)]_182_[+9(1.24e-06)]_6_[+1(1.25e-05)]_87_[+8(1.77e-05)]_53_[+6(1.85e-06)]_28_[-2(1.01e-05)]_11 HsAhoxa1 1.65e-09 11_[+10(1.71e-06)]_107_[+3(5.40e-06)]_127_[-5(4.57e-06)]_33_[-2(3.76e-05)]_14_[+8(1.17e-06)]_6_[+4(3.67e-06)]_58_[+1(2.80e-06)]_75 HsAhoxa2 1.10e-09 129_[+2(2.96e-06)]_126_[+4(6.97e-06)]_12_[+5(1.24e-06)]_24_[+7(1.11e-06)]_31_[-1(6.39e-07)]_28_[+1(1.91e-05)]_91 HsAhoxa3 4.05e-11 73_[+10(7.21e-06)]_114_[+7(1.11e-06)]_65_[+2(1.92e-05)]_6_[+1(8.10e-07)]_3_[-6(5.31e-06)]_84_[+8(2.88e-06)]_7_[+4(1.17e-06)]_2_[+3(7.22e-05)]_67 HsAhoxa4 3.06e-04 258_[+8(2.97e-05)]_26_[+3(5.40e-06)]_58_[-4(1.47e-05)]_95_[-1(6.61e-06)]_1_[+2(1.26e-05)]_13 HsAhoxa5 1.05e-05 28_[+3(2.73e-05)]_58_[+2(6.21e-07)]_122_[-3(3.71e-05)]_1_[+3(5.40e-06)]_82_[+6(8.42e-06)]_87_[+2(4.99e-05)]_53_[-1(3.26e-06)] HsAhoxa6 1.26e-06 74_[-2(4.12e-05)]_1_[-1(4.76e-05)]_141_[-3(9.08e-06)]_47_[+2(5.40e-06)]_46_[+8(5.75e-06)]_74_[-7(3.81e-05)]_23_[+6(7.38e-07)]_14_[+3(3.71e-05)]_1 HsAhoxa7 1.10e-09 236_[+3(2.36e-05)]_33_[+10(5.41e-07)]_47_[+8(2.37e-05)]_16_[-4(8.68e-06)]_17_[-1(3.55e-06)]_78_[+6(7.38e-07)]_4_[-2(1.66e-06)] HsAhoxa9 1.96e-15 9_[-9(7.38e-05)]_1_[+10(4.32e-06)]_5_[+1(8.77e-05)]_65_[-1(9.78e-06)]_58_[-6(3.61e-05)]_18_[+5(2.52e-07)]_32_[+9(2.52e-07)]_13_[-1(3.26e-06)]_3_[+9(8.41e-05)]_39_[-9(8.41e-05)]_3_[-4(3.67e-06)]_6_[-8(5.75e-06)]_[+3(2.36e-05)]_52_[+6(1.11e-06)]_57 HsAhoxa10 7.76e-05 141_[+3(9.08e-06)]_182_[+9(1.24e-06)]_6_[+1(1.25e-05)]_87_[+8(1.77e-05)]_45 HsAhoxa11 5.94e-09 114_[+3(1.82e-05)]_118_[-10(2.79e-06)]_22_[-1(1.17e-07)]_44_[+5(1.24e-06)]_4_[-4(1.96e-06)]_50_[-2(4.31e-05)]_89 HsAhoxa13 7.70e-03 45_[-2(2.42e-05)]_36_[-3(2.73e-05)]_44_[-10(5.06e-06)]_283_[+10(2.25e-06)]_53 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 10 reached. ******************************************************************************** CPU: hotchocolate.bioinf.uni-leipzig.de ********************************************************************************