AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i038_Galactose_Metabolism__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 HI0351 172 UDP-glucose 4-epimerase (galE) #2 HI0352 300 conserved hypothetical protein #3 HI0819 37 galactokinase (galK) #4 HI0820 207 galactose-1-phosphate uridylyltransferase (galT) Motif number 1 TTGATTGATTGATTGATTGATT 2 1 0 GTTGATGATT 0.999059 -300 TTGATTGATTGATTGATTGATTGATTGATTGA 2 17 0 GTTGATGATT 0.999059 -284 TTGATTGATTGATTGATTGATTGATTGATTGA 2 29 0 GTTGATGATT 0.999059 -272 TTGATTGATTGATTGATTGATTGATTGATTGA 2 41 0 GTTGATGATT 0.999059 -260 TTGATTGATTGATTGATTGATTGATTGATTGA 2 53 0 GTTGATGATT 0.999059 -248 TTGATTGATTGATTGATTGATTGATTGATTGA 2 69 0 GTTGATGATT 0.999059 -232 TTGATTGATTGATTGATTGATTGATTGATTGA 2 81 0 GTTGATGATT 0.999059 -220 TTGATTGATTGATTGATTGATTGATTGATTGA 2 93 0 GTTGATGATT 0.999059 -208 GACAGACTTTGATTGATTGATTGATTGATTGA 2 105 0 GTTGATGATT 0.999059 -196 CAAAATATAAGATTTATAGATTATAACAAGGA 4 18 0 GTTTATGATT 0.989385 -190 * ***** **** Masking position 6 Map Score: 52.0127 Number of sites scoring better than the average of aligned sites = 71 Number in coding regions = 26 Number in noncoding regions = 45 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 2 TGGTGATTTTCAATAAAATAAAAAACCTGTT 1 91 0 CAATAAATAA 0.972979 -82 AATCAATCAATCAATCAATCAATC 2 4 1 CAATCAACAA 0.998648 -297 ATCAATCAATCAATCAATCAATCAATCAATC 2 16 1 CAATCAACAA 0.998648 -285 ATCAATCAATCAATCAATCAATCAATCAATC 2 28 1 CAATCAACAA 0.998648 -273 ATCAATCAATCAATCAATCAATCAATCAATC 2 40 1 CAATCAACAA 0.998648 -261 ATCAATCAATCAATCAATCAATCAATCAATC 2 52 1 CAATCAACAA 0.998648 -249 ATCAATCAATCAATCAATCAATCAATCAATC 2 72 1 CAATCAACAA 0.998648 -229 ATCAATCAATCAATCAATCAATCAATCAATC 2 84 1 CAATCAACAA 0.998648 -217 ATCAATCAATCAATCAATCAATCAATCAATC 2 96 1 CAATCAACAA 0.998648 -205 ATCAATCAATCAATCAATCAAAGTCTGTCAT 2 108 1 CAATCAACAA 0.998648 -193 ATTTTCTTGCCAAGAAAATAATGATCTTCAA 2 228 0 CAAGAAATAA 0.925813 -73 ATTTTCTTGGCAAGAAAATAAAAAAAGTATT 2 240 1 CAAGAAATAA 0.925813 -61 ******* *** Masking position 6 Map Score: 51.8772 Number of sites scoring better than the average of aligned sites = 125 Number in coding regions = 51 Number in noncoding regions = 74 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 3 CCTGTTGCTAAAAAGTATTGTTGTAGCGAG 1 67 0 AAAAGTATTG 0.964254 -106 TTGAGACTAAAAAATTATATCACTATTTTG 1 133 0 AAAATTATAT 0.909999 -40 GATTTCCTTGTTAATTATTGAGACTAAAAA 1 150 0 TTAATTATTG 0.783735 -23 CTTTAGGTAATAAACTATAGTCAATTGATT 2 165 0 TAAACTATAG 0.791295 -136 TCTTCAAAATAAAATTGATTGCAACGGAAA 2 205 0 AAAATTGATT 0.626381 -96 AGAAAATAAAAAAAGTATTTTTTAATTGTT 2 252 1 AAAAGTATTT 0.924246 -49 GTATTGCTCAAAAATTGTAGAACAATTAAA 2 272 0 AAAATTGTAG 0.895549 -29 AAAAGTATAGTATTGCTCAA 2 291 0 AAAAGTATAG 0.933296 -10 CAATTTATCGTAAATTATTTATGATCAAAA 4 45 0 TAAATTATTT 0.934043 -163 GAAAATAAGCAAAATTTTTTATGATTTAGT 4 100 0 AAAATTTTTT 0.73098 -108 TAATTTATACTAAATTATTGTAAATAAACC 4 151 0 TAAATTATTG 0.969028 -57 TAATTTAGTATAAATTAATGTAATCGTTTA 4 164 1 TAAATTAATG 0.875159 -44 ********** Masking position 4 Map Score: 11.3203 Number of sites scoring better than the average of aligned sites = 684 Number in coding regions = 589 Number in noncoding regions = 95 Number of orfs with sites within 600 bp upstream = 84 Fraction of orfs with sites within 600 bp upstream = 0.0134918 Motif number 4 ACAACAATACTTTTTAGCAACAGGTTTTTTAT 1 73 1 TTTTTCAACA 0.829977 -100 GTAAGAATGGTGATTTTCAATAAAATAAAAAA 1 97 0 TGATTCAATA 0.930819 -76 ATATAATTTTTTAGTCTCAATAATTAACAAGG 1 143 1 TTAGTCAATA 0.943582 -30 ACTTGTTCCATTACCTGCAATAATGACAGACT 2 129 0 TTACCCAATA 0.877932 -172 TGACTATAGTTTATTACCTAAAGATTATGATG 2 172 1 TTATTCTAAA 0.79093 -129 AAGAAAATAATGATCTTCAAAATAAAATTGAT 2 216 0 TGATCCAAAA 0.825937 -85 GTTCTACAATTTTTGAGCAATACTATACTTTT 2 279 1 TTTTGCAATA 0.762231 -22 CGTAAATTATTTATGATCAAAATATAAGATTT 4 35 0 TTATGCAAAA 0.646703 -173 TTGAAAGCGGTTACTTTCATAAGTATGAACTA 4 72 1 TTACTCATAA 0.619412 -136 AACCGTGATCTTTGTCACAAAATAAGAAAATA 4 123 0 TTTGTCAAAA 0.876808 -85 AGATCACGGTTTATTTACAATAATTTAGTATA 4 144 1 TTATTCAATA 0.974554 -64 TGACTCCTGTTTTTTATCAATGTAAACGATTA 4 184 0 TTTTTCAATG 0.775913 -24 ***** ***** Masking position 1 Map Score: 6.66403 Number of sites scoring better than the average of aligned sites = 681 Number in coding regions = 551 Number in noncoding regions = 130 Number of orfs with sites within 600 bp upstream = 116 Fraction of orfs with sites within 600 bp upstream = 0.0186315 Motif number 5 CTCAATAATTAACAAGGAAATCATT 1 158 1 AACAAGGAAA 0.877798 -15 AATCAATCAATCAATCAATCA 2 2 1 ATCAATCAAT 0.987489 -299 CAATCAATCAATCAATCAATCAATCAATCA 2 14 1 ATCAATCAAT 0.987489 -287 CAATCAATCAATCAATCAATCAATCAATCA 2 34 1 ATCAATCAAT 0.987489 -267 CAATCAATCAATCAATCAATCAATCAATCA 2 50 1 ATCAATCAAT 0.987489 -251 CAATCAATCAATCAATCAATCAATCAATCA 2 62 1 ATCAATCAAT 0.987489 -239 CAATCAATCAATCAATCAATCAATCAATCA 2 82 1 ATCAATCAAT 0.987489 -219 CAATCAATCAATCAATCAATCAATCAATCA 2 98 1 ATCAATCAAT 0.987489 -203 CAATCAATCAATCAATCAAAGTCTGTCATT 2 110 1 ATCAATCAAA 0.987927 -191 AAAATTGTAGAACAATTAAAAAATACTTTT 2 262 0 AACAATTAAA 0.749434 -39 TATAGATTATAACAAGGAAAAAGTT 4 6 0 AACAAGGAAA 0.877798 -202 AAAATAAGAAAATAAGCAAAATTTTTTATG 4 107 0 AATAAGCAAA 0.646625 -101 TTTAGTATAAATTAATGTAATCGTTTACAT 4 167 1 ATTAATGTAA 0.448646 -41 CCTGTTTTTTATCAATGTAAACGATTACAT 4 181 0 ATCAATGTAA 0.875104 -27 ********** Masking position 5 Map Score: 35.393 Number of sites scoring better than the average of aligned sites = 354 Number in coding regions = 273 Number in noncoding regions = 81 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467 Motif number 6 GTGATTTTCAATAAAATAAAAAACCTGTTG 1 90 0 ATAAAATAAA 0.499843 -83 CATTCTTACCACACAAAATAGTGATATAAT 1 120 1 ACACAAAATA 0.848599 -53 ATAATGATCTTCAAAATAAAATTGATTGCA 2 212 0 TCAAAATAAA 0.932553 -89 TGTAGAACAATTAAAAAATACTTTTTTTAT 2 257 0 TTAAAAAATA 0.830319 -44 TTATTTATGATCAAAATATAAGATTTATAG 4 31 0 TCAAAATATA 0.918186 -177 TATATTTTGATCATAAATAATTTACGATAA 4 41 1 TCATAAATAA 0.761364 -167 ATGAACTAAATCATAAAAAATTTTGCTTAT 4 96 1 TCATAAAAAA 0.952924 -112 GTGATCTTTGTCACAAAATAAGAAAATAAG 4 121 0 TCACAAAATA 0.94663 -87 TCGTTTACATTGATAAAAAACAGGAGTCAA 4 187 1 TGATAAAAAA 0.795567 -21 ********** Masking position 5 Map Score: 4.2341 Number of sites scoring better than the average of aligned sites = 529 Number in coding regions = 379 Number in noncoding regions = 150 Number of orfs with sites within 600 bp upstream = 151 Fraction of orfs with sites within 600 bp upstream = 0.0242531 Motif number 7 CCATTAGTTGTGTGATATAAGGTTAT 1 7 0 TGTGATATAA 0.967427 -166 TGTTGTAGCGAGTGAGATAACCTCTCATAT 1 49 0 AGTGAGATAA 0.97782 -124 CACACAAAATAGTGATATAATTTTTTAGTC 1 129 1 AGTGATATAA 0.986866 -44 AATCGTTTACATTGATAAAAAACAGGAGTC 4 185 1 ATTGATAAAA 0.881558 -23 ********** Masking position 5 Map Score: 1.46214 Number of sites scoring better than the average of aligned sites = 32 Number in coding regions = 22 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 8 ********** No masking Map Score: 1.17483e-12 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 9 ********** No masking Map Score: 1.17483e-12 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 10 ********** No masking Map Score: 1.17483e-12 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