AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i008_Uracil_Utilization_hinf_reg_300.orf -a/home/amcguire/alignace/lib/ORF_hinf.txt -z/skink1/amcguire/genomes/hinf.fna -g0.38 -x5 Parameter values: expect = 5 ncols = 10 npass = 1000 maxnpass = 100 nruns = 1000 maxnruns = 100 repeat = 15 maxreps = 3 nread = 500 ncycles = 1 fragment = 1 psfact = 0.1 gcback = 0.38 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 HI1227 104 uracil permease (uraA) #2 HI1228 123 uracil phosphoribosyltransferase (upp) #3 HI1230 147 adenine phosphoribosyltransferase (apt) #4 HI1231 113 dihydrolipoamide dehydrogenase (lpdA) #5 HI1232 62 dihydrolipoamide acetyltransferase (aceF) #6 HI1233 299 pyruvate dehydrogenase, E1 component (aceE) Motif number 1 AAAGACGGCTTAAATGCCGTCTTGTTTTGG 1 14 0 TAAATGCCGT 0.89098 -91 AATTAACTTAAAAGTGCGGTCAGTTTTTCT 1 64 0 AAAGTGCGGT 0.998464 -41 ATTGTATTGAAAACTCCCGTTTCAAGTCAG 2 18 1 AAACTCCCGT 0.953588 -106 ATAATGCTCAAAAGTGCGGTAAAAAAAGAA 3 126 0 AAAGTGCGGT 0.998464 -22 AAAGACCGTAAAAGTGCGGTCAATATTTTT 4 74 1 AAAGTGCGGT 0.998464 -40 TTGATGAAAACTGCGGTCAAAAAACAT 5 8 1 AAACTGCGGT 0.996369 -55 TGTTCCTTTTAAAGTGCGGTCATAAAACAC 5 39 0 AAAGTGCGGT 0.998464 -24 TAATTATTTGAAAGTGCGGTAATTTTTTTG 6 106 0 AAAGTGCGGT 0.998464 -194 TGAAAAGCAAATATTGCCGTATTCGTGTTT 6 233 1 ATATTGCCGT 0.89098 -67 ********** Masking position 5 Map Score: 27.9257 Number of sites scoring better than the average of aligned sites = 1261 Number in coding regions = 810 Number in noncoding regions = 451 Number of orfs with sites within 600 bp upstream = 308 Fraction of orfs with sites within 600 bp upstream = 0.04947 Motif number 2 ACCTCTACCATTTTGTATTTTTTTAATCTAGAAT 2 61 1 TTTTTTTTTT 0.974042 -63 TTTTACTCTCCTTTTGACTCTTAAA 2 109 0 TTTTCCTTTT 0.937847 -15 AAATCCCCAATTGGGGATTTTTATTTAAGTTTGA 3 40 0 TTGTTTTTAT 0.983622 -108 AAATCCCCAATTGGGGATTTTTATTTTCCTCTCT 3 54 1 TTGTTTTTAT 0.983622 -94 TTTCCTCTCTTTCTATTTTTTTATGATAGAATGC 3 78 1 TTTTTTTTAT 0.969304 -70 TGACCGCACTTTTACGGTCTTTATAGGATGGGTT 4 62 0 TTGTCTTTAT 0.982506 -52 TTTTTGTTCCTTTTAAAGTGCGGT 5 49 0 TTGTCCTTTT 0.966329 -14 TTTAAAGTTTTTTCAGATTTTTTTCAAAAAGGAC 6 17 0 TTGTTTTTTT 0.986182 -283 ATGCAATATTTTACTGGTTATTTTAGCGAACAAA 6 66 1 TTGTTATTTT 0.918373 -234 GCGGTAATTTTTTTGTGTTTTTTTGTTCGCTAAA 6 87 0 TTTTTTTTTT 0.974042 -213 TTGATGAAAATTCACTATCTTTATCTCAAAAAAT 6 166 1 TTTTCTTTAT 0.967245 -134 ** * ******* Masking position 8 Map Score: 18.2888 Number of sites scoring better than the average of aligned sites = 139 Number in coding regions = 99 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 3 TTTCAACGCACGGAAAAAAGACGGCTTAAAT 1 29 0 CGAAAAAAGA 0.745985 -76 GACAAATTCTAGATTAAAAAAATACAAAATG 2 69 0 AGTTAAAAAA 0.745735 -55 CTCCTTTTGACTCTTAAAAAACAAATTGACA 2 96 0 CTTTAAAAAA 0.92575 -28 TAAATTCAAACTTAAATAAAAATCCCCAATT 3 35 1 CTAAATAAAA 0.747103 -113 GATTGGCATTCTATCATAAAAAAATAGAAAG 3 86 0 CTTCATAAAA 0.945949 -62 CTCAAAAGTGCGGTAAAAAAAGAAACGTTTT 3 119 0 CGTAAAAAAA 0.981579 -29 CTCGTAAAAACGTTAAAAATATTGACCGCAC 4 87 0 CGTAAAAATA 0.860566 -27 ATGAAAACTGCGGTCAAAAAACATTGTGTTT 5 14 1 CGTCAAAAAA 0.990229 -49 TTTTAAAGTGCGGTCATAAAACACAATGTTT 5 32 0 CGTCATAAAA 0.970182 -31 TCTGAAAAAACTTTAAAACAAAGCCCGATGG 6 34 1 CTTAAAACAA 0.831059 -266 GTTATTTTAGCGAACAAAAAAACACAAAAAA 6 82 1 CGACAAAAAA 0.970182 -218 AATTACCGCACTTTCAAATAATTATTTATGG 6 112 1 CTTCAAATAA 0.863275 -188 CACTATCTTTATCTCAAAAAATCTTCTAAAA 6 178 1 ATTCAAAAAA 0.873374 -122 ** ******** Masking position 6 Map Score: 15.2348 Number of sites scoring better than the average of aligned sites = 519 Number in coding regions = 410 Number in noncoding regions = 109 Number of orfs with sites within 600 bp upstream = 98 Fraction of orfs with sites within 600 bp upstream = 0.0157404 Motif number 4 AGACAATATTGTATTGAAAACTCCCGTTTC 2 11 1 GTATTGAAAA 0.826891 -113 ATGGTAGAGGTTTATAAAAATATTCTGACT 2 42 0 TTTATAAAAA 0.769213 -82 AGCCCACCGATTAATGAAATCTTTGGTGGG 4 28 1 TTAATGAAAT 0.88115 -86 TTGATGAAAACTGCGGTCAA 5 1 1 TTGATGAAAA 0.977984 -62 TGCTGAGTCCTTTTTGAAAAAAATCTGAAA 6 11 1 TTTTTGAAAA 0.878655 -289 ATATGATGATTTGATGAAAATTCACTATCT 6 156 1 TTGATGAAAA 0.977984 -144 TTGTTAAATGTTTGTGAAAAGCAAATATTG 6 219 1 TTTGTGAAAA 0.935032 -81 TCAAAACAGATTAAGGAAAACCT 6 287 1 TTAAGGAAAA 0.916563 -13 ********** Masking position 7 Map Score: 6.30225 Number of sites scoring better than the average of aligned sites = 387 Number in coding regions = 304 Number in noncoding regions = 83 Number of orfs with sites within 600 bp upstream = 82 Fraction of orfs with sites within 600 bp upstream = 0.0131706 Motif number 5 TTTTTCTTGTGTTTCAACGCACGGAAAAAAG 1 40 0 GTTTAACGCA 0.969206 -65 TCAACTCTCTGTTTGAATTAACTTAAAAGTG 1 78 0 GTTTAATTAA 0.956486 -27 TTAGTTTCAACTCTCTGTTTGAAT 1 91 0 GTTTAACTCT 0.955028 -14 GAAAACTCCCGTTTCAAGTCAGAATATTTTT 2 26 1 GTTTAAGTCA 0.974462 -98 GAAGTTTTAATTCATCTTAAATTG 3 4 1 GTTTAATTCA 0.98486 -144 TTTTATTTAAGTTTGAATTTACAATTTAAGA 3 25 0 GTTTAATTTA 0.925736 -123 GTTTAGCCTTGTCTAAACTAATATTCACTCA 6 259 1 GTCTAACTAA 0.914054 -41 **** ****** Masking position 6 Map Score: 5.34085 Number of sites scoring better than the average of aligned sites = 93 Number in coding regions = 76 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 6 TAGAATTTGTCAATTTGTTTTTTAAGAGTC 2 89 1 CAATTTGTTT 0.870021 -35 TCCTCTCTTTCTATTTTTTTATGATAGAAT 3 80 1 CTATTTTTTT 0.710499 -68 GTAAAAAAAGAAACGTTTTTAGATTGGCAT 3 108 0 AAACGTTTTT 0.90335 -40 TCAATATTTTTAACGTTTTTACGAGGTAAA 4 93 1 TAACGTTTTT 0.925221 -21 TCATAAAACACAATGTTTTTTGACCGCAGT 5 20 0 CAATGTTTTT 0.968338 -43 AAGTTTTTTCAGATTTTTTTCAAAAAGGAC 6 17 0 AGATTTTTTT 0.69818 -283 GGCTTTGTTTTAAAGTTTTTTCAGATTTTT 6 29 0 TAAAGTTTTT 0.819372 -271 GAAAGTGCGGTAATTTTTTTGTGTTTTTTT 6 97 0 TAATTTTTTT 0.928012 -203 AAGATTTGTTAAATGTTTGTGAAAAGCAAA 6 214 1 AAATGTTTGT 0.802239 -86 AGGTTTTCCTTAATCTGTTTTGAGTGAATA 6 280 0 TAATCTGTTT 0.714047 -20 ********** Masking position 6 Map Score: 3.97446 Number of sites scoring better than the average of aligned sites = 488 Number in coding regions = 371 Number in noncoding regions = 117 Number of orfs with sites within 600 bp upstream = 117 Fraction of orfs with sites within 600 bp upstream = 0.0187922 Motif number 7 TATGATAGAATGCCAATCTAAAAACGTTTC 3 99 1 TGCCAATCTA 0.93615 -49 GTGGGCTTAAAGCCCACCTACAGA 4 5 0 AGCCCACCTA 0.995698 -109 GTGGGCTTTAAGCCCACCGATTAATGAAAT 4 18 1 AGCCCACCGA 0.994886 -96 GATGGGTTTCTGCCCACCAAAGATTTCATT 4 40 0 TGCCCACCAA 0.992438 -74 ********** Masking position 6 Map Score: 2.93584 Number of sites scoring better than the average of aligned sites = 41 Number in coding regions = 27 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 8 GAGTTTTCAATACAATATTGTCT 2 4 0 TACAATATTG 0.897144 -120 CGTTTCAAGTCAGAATATTTTTATAAACCT 2 35 1 CAGAATATTT 0.905946 -89 TAAAAGTGCGGTCAATATTTTTAACGTTTT 4 82 1 GTCAATATTT 0.87041 -32 GGTCATAAAACACAATGTTTTTTGACCGCA 5 22 0 CACAATGTTT 0.878511 -41 CCCGATGGAATGCAATATTTTACTGGTTAT 6 57 1 TGCAATATTT 0.956707 -243 TTGTAAATTTTAGAAGATTTTTTGAGATAA 6 186 0 TAGAAGATTT 0.868061 -114 TTCTAAAATTTACAAGATTTGTTAAATGTT 6 201 1 TACAAGATTT 0.94897 -99 ACACGAATACGGCAATATTTGCTTTTCACA 6 231 0 GGCAATATTT 0.948241 -69 ********** Masking position 5 Map Score: 4.62129 Number of sites scoring better than the average of aligned sites = 290 Number in coding regions = 245 Number in noncoding regions = 45 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 9 AAAAAATACAAAATGGTAGAGGTTTATAAA 2 54 0 AAATGGTAGA 0.956257 -70 ACAAATTGACAAATTCTAGATTAAAAAAAT 2 77 0 AAATTCTAGA 0.934762 -47 AATTCATCTTAAATTGTAAATTCAAACTTA 3 19 1 AAATTGTAAA 0.943724 -129 TACCTCGTAAAAACGTTAAAAATATTGACC 4 91 0 AAACGTTAAA 0.914362 -23 AAATCTGAAAAAACTTTAAAACAAAGCCCG 6 31 1 AAACTTTAAA 0.927948 -269 CAAATCTTGTAAATTTTAGAAGATTTTTTG 6 192 0 AAATTTTAGA 0.960672 -108 ********** Masking position 7 Map Score: 3.10884 Number of sites scoring better than the average of aligned sites = 106 Number in coding regions = 89 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 10 ********** No masking Map Score: 6.20604e-13 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 11 ********** No masking Map Score: 6.20604e-13 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 12 ********** No masking Map Score: 6.20604e-13 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0