AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/alignace/lib/ORF_hinf.txt -z/skink1/amcguire/genomes/hinf.fna -igalR_hinf_opreg_300.orf -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_HI0821 207 HI0820: galactose-1-phosphate uridylyltransferase (galT), HI0821: galactose operon repressor (galR) #5 HI0822 90 galactose ABC transporter, periplasmic-binding protein (mglB) #6 HI0823 65 galactoside ABC transporter, ATP-binding protein (mglA) Motif number 1 GATTGATTGATTGATTGATT 2 1 0 TTGATTGATT 0.998095 -300 GATTGATTGATTGATTGATTGATTGATTGA 2 17 0 TTGATTGATT 0.998095 -284 GATTGATTGATTGATTGATTGATTGATTGA 2 29 0 TTGATTGATT 0.998095 -272 GATTGATTGATTGATTGATTGATTGATTGA 2 41 0 TTGATTGATT 0.998095 -260 GATTGATTGATTGATTGATTGATTGATTGA 2 53 0 TTGATTGATT 0.998095 -248 GATTGATTGATTGATTGATTGATTGATTGA 2 73 0 TTGATTGATT 0.998095 -228 GATTGATTGATTGATTGATTGATTGATTGA 2 85 0 TTGATTGATT 0.998095 -216 GATTGATTGATTGATTGATTGATTGATTGA 2 97 0 TTGATTGATT 0.998095 -204 ATGACAGACTTTGATTGATTGATTGATTGA 2 109 0 TTGATTGATT 0.998095 -192 TAAACTATAGTCAATTGATTTTAAACTTGT 2 155 0 TCAATTGATT 0.896077 -146 AAATATAAGATTTATAGATTATAACAAGGA 4 18 0 TTTATAGATT 0.853323 -190 ********** Masking position 4 Map Score: 46.3744 Number of sites scoring better than the average of aligned sites = 88 Number in coding regions = 38 Number in noncoding regions = 50 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 2 ATTGATTGATTGATTGATTGATT 2 4 0 TGATTGATTG 0.998756 -297 ATTGATTGATTGATTGATTGATTGATTGAT 2 20 0 TGATTGATTG 0.998756 -281 ATTGATTGATTGATTGATTGATTGATTGAT 2 32 0 TGATTGATTG 0.998756 -269 ATTGATTGATTGATTGATTGATTGATTGAT 2 44 0 TGATTGATTG 0.998756 -257 ATTGATTGATTGATTGATTGATTGATTGAT 2 56 0 TGATTGATTG 0.998756 -245 ATTGATTGATTGATTGATTGATTGATTGAT 2 72 0 TGATTGATTG 0.998756 -229 ATTGATTGATTGATTGATTGATTGATTGAT 2 84 0 TGATTGATTG 0.998756 -217 ATTGATTGATTGATTGATTGATTGATTGAT 2 96 0 TGATTGATTG 0.998756 -205 TGACAGACTTTGATTGATTGATTGATTGAT 2 108 0 TGATTGATTG 0.998756 -193 CTTCAAAATAAAATTGATTGCAACGGAAAA 2 204 0 AAATTGATTG 0.908038 -97 ********** Masking position 5 Map Score: 50.4389 Number of sites scoring better than the average of aligned sites = 81 Number in coding regions = 28 Number in noncoding regions = 53 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 3 ACTCGCTACAACAATACTTTTTAGCAACAGG 1 66 1 ACAATACTTT 0.908212 -107 TTATTGAGACTAAAAAATTATATCACTATTT 1 135 0 TAAAAAATTT 0.921175 -38 TTTTTTAGTCTCAATAATTAACAAGGAAATC 1 149 1 TCAATAATTA 0.921044 -24 TGATCTTCAAAATAAAATTGATTGCAACGGA 2 207 0 AATAAAATTA 0.670343 -94 TCTTGCCAAGAAAATAATGATCTTCAAAATA 2 224 0 AAAATAATGT 0.727124 -77 GAACAATTAAAAAATACTTTTTTTATTTTCT 2 252 0 AAAATACTTT 0.879783 -49 ATAGTATTGCTCAAAAATTGTAGAACAATTA 2 274 0 TCAAAAATTT 0.93415 -27 TTTGAGCAATACTATACTTTT 2 290 1 ACTATACTTT 0.670511 -11 ATTTTGATCATAAATAATTTACGATAAATTG 4 44 1 TAAATAATTA 0.781522 -164 AACTAAATCATAAAAAATTTTGCTTATTTTC 4 99 1 TAAAAAATTT 0.915234 -109 CGGTTTATTTACAATAATTTAGTATAAATTA 4 150 1 ACAATAATTA 0.784646 -58 GTAAACGATTACATTAATTTATACTAAATTA 4 164 0 ACATTAATTA 0.761421 -44 AATGATTACATAAAAAATTATGAATTTGTGA 5 24 0 TAAAAAATTT 0.921175 -67 AAATAAATTATCGTAATTAAT 5 80 0 AAATAAATTT 0.750127 -11 TTAGATTACAACAAAAATTGATGGGAAA 6 8 0 ACAAAAATTA 0.93415 -58 ********* * Masking position 6 Map Score: 14.4184 Number of sites scoring better than the average of aligned sites = 658 Number in coding regions = 510 Number in noncoding regions = 148 Number of orfs with sites within 600 bp upstream = 150 Fraction of orfs with sites within 600 bp upstream = 0.0240925 Motif number 4 AGCAACAGGTTTTTTATTTTATTGAAAATCACC 1 88 1 TTTTATTATT 0.558657 -85 AATGATTTCCTTGTTAATTATTGAG 1 158 0 TGTTTTTGTT 0.904739 -15 GATTGATTGATTGATTGATTGATT 2 2 0 TTATTTTGAT 0.960637 -299 GATTGATTGATTGATTGATTGATTGATTGATTG 2 18 0 TTATTTTGAT 0.960637 -283 GATTGATTGATTGATTGATTGATTGATTGATTG 2 38 0 TTATTTTGAT 0.960637 -263 GATTGATTGATTGATTGATTGATTGATTGATTG 2 54 0 TTATTTTGAT 0.960637 -247 GATTGATTGATTGATTGATTGATTGATTGATTG 2 70 0 TTATTTTGAT 0.960637 -231 GATTGATTGATTGATTGATTGATTGATTGATTG 2 90 0 TTATTTTGAT 0.960637 -211 ATGACAGACTTTGATTGATTGATTGATTGATTG 2 106 0 TTATTTTGAT 0.960637 -195 AGTCAATTGATTTTAAACTTGTTCCATTACCTG 2 144 0 TTTAATTGTT 0.457615 -157 AAAAATACTTTTTTTATTTTCTTGCCAAGAAAA 2 241 0 TTTTATTCTT 0.7893 -60 AAAAAAAGTATTTTTTAATTGTTCTACAATTTT 2 259 1 TTTTTTTGTT 0.941348 -42 AACTTTTTCCTTGTTATAATCTATA 4 3 1 CTTTTTTGTT 0.904739 -205 ATCTATAAATCTTATATTTTGATCATAAATAAT 4 29 1 CTATATTGAT 0.913878 -179 AAATTGAAAGCGGTTACTTTCATAAGTATGAAC 4 69 1 CGTTATTCAT 0.688374 -139 AAATTTTTTATGATTTAGTTCATACTTATGAAA 4 86 0 TGTTTTTCAT 0.835543 -122 TAAAAAATTTTGCTTATTTTCTTATTTTGTGAC 4 109 1 TGTTATTCTT 0.689126 -99 TTAATGTAATCGTTTACATTGATAAAAAACAGG 4 178 1 CGTTATTGAT 0.874274 -30 TGCAAATTTGCTCATAGATTAATTACGATAATT 5 63 1 CTATATTAAT 0.532493 -28 ** *** ***** Masking position 9 Map Score: 30.2885 Number of sites scoring better than the average of aligned sites = 889 Number in coding regions = 675 Number in noncoding regions = 214 Number of orfs with sites within 600 bp upstream = 142 Fraction of orfs with sites within 600 bp upstream = 0.0228076 Motif number 5 AGATTATGATGTTTTCCGTTGCAATCAATTTTA 2 193 1 GTTTCTTGCA 0.953323 -108 ACTTATGAAAGTAACCGCTTTCAATTTATCGTA 4 63 0 GTACCTTTCA 0.985336 -145 TAAATAAACCGTGATCTTTGTCACAAAATAAGA 4 128 0 GTATCTGTCA 0.993479 -80 ATAAATTAATGTAATCGTTTACATTGATAAAAA 4 173 1 GTATCTTACA 0.982412 -35 TTATGAATTTGTGATCCATGTCACAAA 5 5 0 GTATCTGTCA 0.993479 -86 AATTTTTTATGTAATCATTTTCATTTTTGCAAA 5 36 1 GTATCTTTCA 0.994588 -55 ** *** ***** Masking position 9 Map Score: 6.64753 Number of sites scoring better than the average of aligned sites = 27 Number in coding regions = 21 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 6 GTAAGAATGGTGATTTTCAATAAAATAAAAA 1 98 0 TGATTTCAAT 0.960889 -75 ATATAATTTTTTAGTCTCAATAATTAACAAG 1 143 1 TTAGTTCAAT 0.906983 -30 TATAGTCAATTGATTTTAAACTTGTTCCATT 2 149 0 TGATTTAAAC 0.841228 -152 AAGAAAATAATGATCTTCAAAATAAAATTGA 2 217 0 TGATCTCAAA 0.807546 -84 TCTTATATTTTGATCATAAATAATTTACGAT 4 38 1 TGATCTAAAT 0.960889 -170 CGCTTTCAATTTATCGTAAATTATTTATGAT 4 50 0 TTATCTAAAT 0.957764 -158 TTATACTAAATTATTGTAAATAAACCGTGAT 4 146 0 TTATTTAAAT 0.954402 -62 TTACAATAATTTAGTATAAATTAATGTAATC 4 158 1 TTAGTTAAAT 0.9 -50 TGACTCCTGTTTTTTATCAATGTAAACGATT 4 185 0 TTTTTTCAAT 0.761379 -23 AAATAAATTATCGTAATTAATCTATGAG 5 73 0 TTATCTAATT 0.761385 -18 ***** ***** Masking position 7 Map Score: 7.63623 Number of sites scoring better than the average of aligned sites = 163 Number in coding regions = 117 Number in noncoding regions = 46 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 7 TATAGTCAGTCTCCCTCTTTAGCTTTAGCA 3 11 1 CTCCCTCTTT 0.985979 -27 GGAAGATCCACTTCCCCTTAGATTACAACA 6 26 0 CTTCCCCTTA 0.980849 -40 GGAAGTGGATCTTCCCCTTTTTAAAGAGGT 6 41 1 CTTCCCCTTT 0.992332 -25 ATCCAACCTCTTTAAAAAGGGGA 6 53 0 CAACCTCTTT 0.949437 -13 ********** Masking position 8 Map Score: 1.55452 Number of sites scoring better than the average of aligned sites = 17 Number in coding regions = 11 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 8 CAACAATACTTTTTAGCAACAGGTTTTTTA 1 74 1 TTTTAGCAAC 0.955583 -99 TTCTACAATTTTTGAGCAATACTATACTTT 2 280 1 TTTGAGCAAT 0.934442 -21 CCCTCTTTAGCTTTAGCAAAGAGGG 3 23 1 CTTTAGCAAA 0.936259 -15 GTAAATTATTTATGATCAAAATATAAGATT 4 36 0 TATGATCAAA 0.632481 -172 GACTCCTGTTTTTTATCAATGTAAACGATT 4 185 0 TTTTATCAAT 0.859708 -23 ATCATTTTCATTTTTGCAAATTTGCTCATA 5 49 1 TTTTTGCAAA 0.907768 -42 GTAATTAATCTATGAGCAAATTTGCAAAAA 5 59 0 TATGAGCAAA 0.932294 -32 ********** Masking position 8 Map Score: 4.29928 Number of sites scoring better than the average of aligned sites = 347 Number in coding regions = 301 Number in noncoding regions = 46 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467 Motif number 9 AATCAATCAATCAATCAATCAA 2 3 1 TCAATCAATC 0.997743 -298 AATCAATCAATCAATCAATCAATCAATCAA 2 19 1 TCAATCAATC 0.997743 -282 AATCAATCAATCAATCAATCAATCAATCAA 2 31 1 TCAATCAATC 0.997743 -270 AATCAATCAATCAATCAATCAATCAATCAA 2 43 1 TCAATCAATC 0.997743 -258 AATCAATCAATCAATCAATCAATCAATCAA 2 55 1 TCAATCAATC 0.997743 -246 AATCAATCAATCAATCAATCAATCAATCAA 2 67 1 TCAATCAATC 0.997743 -234 AATCAATCAATCAATCAATCAATCAATCAA 2 83 1 TCAATCAATC 0.997743 -218 AATCAATCAATCAATCAATCAATCAATCAA 2 95 1 TCAATCAATC 0.997743 -206 AATCAATCAATCAATCAATCAAAGTCTGTC 2 107 1 TCAATCAATC 0.997743 -194 GTTTTCCGTTGCAATCAATTTTATTTTGAA 2 203 1 GCAATCAATT 0.844854 -98 CTTGTTATAATCTATAAATCTTATATTTTG 4 20 1 TCTATAAATC 0.801379 -188 GTAACCGCTTTCAATTTATCGTAAATTATT 4 56 0 TCAATTTATC 0.801379 -152 ********** Masking position 4 Map Score: 51.0887 Number of sites scoring better than the average of aligned sites = 75 Number in coding regions = 26 Number in noncoding regions = 49 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 10 ATAACCTTATATCACACAACTAATGG 1 7 1 TTATATCACA 0.902873 -166 ATATGAGAGGTTATCTCACTCGCTACAACA 1 49 1 TTATCTCACT 0.860641 -124 ATCTCACTCGCTACAACAATACTTTTTAGC 1 61 1 CTACAACAAT 0.786762 -112 ATCACCATTCTTACCACACAAAATAGTGAT 1 115 1 TTACCACACA 0.892681 -58 GACTAAAAAATTATATCACTATTTTGTGTG 1 129 0 TTATATCACT 0.91699 -44 GATTTATAGATTATAACAAGGAAAAAGTT 4 10 0 TTATAACAAG 0.805137 -198 ACCGTGATCTTTGTCACAAAATAAGAAAAT 4 124 0 TTGTCACAAA 0.54331 -84 CACGGTTTATTTACAATAATTTAGTATAAA 4 148 1 TTACAATAAT 0.768041 -60 ATGTAAACGATTACATTAATTTATACTAAA 4 167 0 TTACATTAAT 0.768041 -41 GACTCCTGTTTTTTATCAATGTAAACGATT 4 185 0 TTTTATCAAT 0.630371 -23 ATGAAAATGATTACATAAAAAATTATGAAT 5 30 0 TTACATAAAA 0.611969 -61 TCCCCTTAGATTACAACAAAAATTGATGGG 6 14 0 TTACAACAAA 0.947605 -52 ********** Masking position 8 Map Score: 3.12338 Number of sites scoring better than the average of aligned sites = 754 Number in coding regions = 639 Number in noncoding regions = 115 Number of orfs with sites within 600 bp upstream = 111 Fraction of orfs with sites within 600 bp upstream = 0.0178285 Motif number 11 ********** No masking Map Score: -1.70998e-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 12 ********** No masking Map Score: -1.70998e-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 13 ********** No masking Map Score: -1.70998e-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