AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i010_Nucleotide_Metabolism_hinf_reg_100.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 HI0329 37 conserved hypothetical protein #2 HI0330 98 opacity associated protein (oapA) #3 HI0331 59 opacity associated protein (oapB) #4 HI0334 77 GTP pyrophosphokinase (relA) #5 HI0668 161 conserved hypothetical protein #6 HI0669 96 mioC protein (mioC) #7 HI1230 147 adenine phosphoribosyltransferase (apt) #8 HI1741 260 guanosine-3',5'-bis(diphosphate) 3'- pyrophosphohydrolase (spoT) Motif number 1 TCAAACCATCTCTCATTTTTAGGATATTTC 1 15 0 TCTCATTTTT 0.845546 -23 CTTTTGAGCTTCTCAATTTTGTGGCTAATT 2 45 1 TCTCAATTTT 0.85981 -54 ATCGCCCCTTTTTCTTTTTAAGTTCTTTTC 3 26 1 TTTCTTTTTA 0.918693 -34 TTCTTTTTAAGTTCTTTTCTCAAGGTAGGA 3 37 1 GTTCTTTTCT 0.875128 -23 CTTCCTGTCGCTTTTATTTTGGGTGGATAT 4 28 0 CTTTTATTTT 0.757256 -50 TTCTCCTTCTGCTTATTTTTCAAGATTATG 5 16 1 GCTTATTTTT 0.539399 -146 GCATAATAAATTTTTATTCAATGCTTTAAA 5 83 1 TTTTTATTCA 0.780548 -79 TTTCTAAGCCTTTTTATTTTAATCATTTGA 6 31 1 TTTTTATTTT 0.955328 -66 TTTGAATAATTTTCTTTTCTCTTTGAGAAA 6 56 1 TTTCTTTTCT 0.947152 -41 TTATCCTATATTTATTTTTTCTCAAAGAGA 6 73 0 TTTATTTTTT 0.857793 -24 GAAGTTTTAATTCATCTTAAATTG 7 5 1 TTTTAATTCA 0.605406 -143 CAATTGGGGATTTTTATTTAAGTTTGAATT 7 37 0 TTTTTATTTA 0.873816 -111 CAATTGGGGATTTTTATTTTCCTCTCTTTC 7 61 1 TTTTTATTTT 0.955328 -87 TTTTCCTCTCTTTCTATTTTTTTATGATAG 7 77 1 TTTCTATTTT 0.975058 -71 TCTAAAAACGTTTCTTTTTTTACCGCACTT 7 115 1 TTTCTTTTTT 0.97214 -33 GTAAAATACCTTTATTTTTTACCGCACTTT 8 18 0 TTTATTTTTT 0.857793 -243 CGCTTGATGAGTTCAATTTTATCTGCGGGC 8 234 0 GTTCAATTTT 0.868317 -27 ********** Masking position 7 Map Score: 19.0304 Number of sites scoring better than the average of aligned sites = 1232 Number in coding regions = 843 Number in noncoding regions = 389 Number of orfs with sites within 600 bp upstream = 277 Fraction of orfs with sites within 600 bp upstream = 0.0444908 Motif number 2 AATTTTTTCGCCGCACTTTTGAGCTTCTCAAT 2 30 1 CCGCCTTTGA 0.970493 -69 TACAATATCCACCCAAAATAAAAGCGACAGGA 4 24 1 ACCCAATAAA 0.662488 -54 AATACCCCCTTGTTGATGAAGAGCAA 4 62 0 CCCCTTTTGA 0.948712 -16 CCCTAAACTTACCCATATTTAAAAGGAAATCA 5 138 1 ACCCTATTAA 0.918933 -24 TCTTTTTTTACCGCACTTTTGAGCATTATTT 7 127 1 CCGCCTTTGA 0.970493 -21 TTATTTTTTACCGCACTTTTAAAAGA 8 5 0 CCGCCTTTAA 0.972353 -256 GGGTATACCTACCCGCGGTAAAATACCTTTAT 8 33 0 ACCCCGTAAA 0.969191 -228 GGGTAGGTATACCCACGGTTAATTATGGTTAT 8 51 1 ACCCCGTTAA 0.992175 -210 GGGTAAGTAGACCCTAGCTTAACTAAATGTTA 8 124 0 ACCCAGTTAA 0.966666 -137 GCGGGCAAATACCCTTGAATAATTCGATCTAA 8 208 0 ACCCTGATAA 0.84076 -53 AAACGCACGCTTGATGAGTTCAAT 8 247 0 ACGCCGTTGA 0.985734 -14 **** ** **** Masking position 12 Map Score: 12.5056 Number of sites scoring better than the average of aligned sites = 232 Number in coding regions = 166 Number in noncoding regions = 66 Number of orfs with sites within 600 bp upstream = 53 Fraction of orfs with sites within 600 bp upstream = 0.00851269 Motif number 3 GAGAAGCTCAAAAGTGCGGCGAAAAAATTATG 2 27 0 AAAGGCGGGA 0.996179 -72 ACTTAAAAAGAAAAAGGGGCGATTACTCGCCC 3 17 0 AAAAGGGGGA 0.977271 -43 TCGTAGTAAAAGGCTTAGATTTTCTAAGC 6 8 1 AAAAGCTTGA 0.864092 -89 GATTAAAATAAAAAGGCTTAGAAAATCTAAGC 6 23 0 AAAAGCTTGA 0.864092 -74 AAAAAAATAGAAAGAGAGGAAAATAAAAATCC 7 68 0 AAAGGAGGAA 0.962157 -80 ATAATGCTCAAAAGTGCGGTAAAAAAAGAAAC 7 124 0 AAAGGCGGAA 0.993952 -24 TCTTTTAAAAGTGCGGTAAAAAATAAAGG 8 8 1 AAAGGCGGAA 0.993952 -253 TACGTTCCCCAAAGGGGGACAACTATAACCAT 8 75 0 AAAGGGGAAA 0.914738 -186 **** **** ** Masking position 3 Map Score: 9.23543 Number of sites scoring better than the average of aligned sites = 1164 Number in coding regions = 742 Number in noncoding regions = 422 Number of orfs with sites within 600 bp upstream = 280 Fraction of orfs with sites within 600 bp upstream = 0.0449727 Motif number 4 TCTTTTCTCAAGGTAGGATTT 3 49 1 AGGTAGGATT 0.828032 -11 CTTTTATTTTGGGTGGATATTGTACCGAAT 4 18 0 GGGTGGATAT 0.776307 -60 TTCAAGATTATGGTAAAAATAGCATCATTC 5 34 1 TGGTAAAAAT 0.839657 -128 TGCTTTAAAAAGGTAAATTTACTGGGTAAA 5 104 1 AGGTAAATTT 0.835885 -58 TAAATTTACTGGGTAAAATACCCCTAAACT 5 117 1 GGGTAAAATA 0.954534 -45 TTTTAAATATGGGTAAGTTTAGGGGTATTT 5 132 0 GGGTAAGTTT 0.955114 -30 CTCAAAAGTGCGGTAAAAAAAGAAACGTTT 7 120 0 CGGTAAAAAA 0.915189 -28 TTTAAAAGTGCGGTAAAAAATAAAGGTATT 8 14 1 CGGTAAAAAA 0.915189 -247 TACCTACCCGCGGTAAAATACCTTTATTTT 8 30 0 CGGTAAAATA 0.903051 -231 ATTTTACCGCGGGTAGGTATACCCACGGTT 8 41 1 GGGTAGGTAT 0.947647 -220 TTACCCTTTGGGGTAGAAATTACGTTCCCC 8 97 0 GGGTAGAAAT 0.971779 -164 CTACCCCAAAGGGTAACATTTAGTTAAGCT 8 111 1 GGGTAACATT 0.904377 -150 ATATCGCCTAGGGTAAGTAGACCCTAGCTT 8 136 0 GGGTAAGTAG 0.852061 -125 ********** Masking position 4 Map Score: 12.6098 Number of sites scoring better than the average of aligned sites = 499 Number in coding regions = 390 Number in noncoding regions = 109 Number of orfs with sites within 600 bp upstream = 90 Fraction of orfs with sites within 600 bp upstream = 0.0144555 Motif number 5 ATTTGAAATATCCTAAAAATGAGAGAT 1 6 1 AAATACCAAA 0.948361 -32 GATCCGATAAAATACACATAATTTTTTCGCC 2 10 1 AAATAACTAA 0.855565 -89 TATTTATATTAATTAGCCACAAAATTGAGAAG 2 53 0 AATTACCCAA 0.93792 -46 TTACTGGGTAAAATACCCCTAAACTTACCCAT 5 122 1 AAATACCTAA 0.983719 -40 AAACTTAAATAAAAATCCCCAATTGGGGATTT 7 42 1 AAAAACCCAA 0.980497 -106 AGAGGAAAATAAAAATCCCCAATTGGGGATTT 7 54 0 AAAAACCCAA 0.980497 -94 AGGGGGACAACTATAACCATAATTAACCGTGG 8 63 0 CTATACCTAA 0.903224 -198 ATAATTCGATCTAAATCCGCAAACAGTTCCAA 8 190 0 CTAAACCCAA 0.885918 -71 ATCTGCGGGCAAATACCCTTGAATAATTCGAT 8 212 0 AAATACCTGA 0.933851 -49 ***** ** *** Masking position 5 Map Score: 8.12983 Number of sites scoring better than the average of aligned sites = 246 Number in coding regions = 203 Number in noncoding regions = 43 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 6 TTTTCAAACCATCTCTCATTTT 1 26 0 TTTTCAACAT 0.974961 -12 AGAATGATGCTATTTTTACCATAATCTTGAAA 5 33 0 TATTTTACAT 0.848531 -129 AAAAATTTATTATGCAAACGATTACTCAGTGA 5 66 0 TATGCAAGAT 0.865715 -96 TAAATTTACCTTTTTAAAGCATTGAATAAAAA 5 93 0 TTTTTAACAT 0.960858 -69 AAGGCTTAGATTTTCTAAGCCTTTTTATTTTA 6 20 1 TTTTCAACCT 0.911834 -77 AAAAGAAAATTATTCAAATGATTAAAATAAAA 6 42 0 TATTCAAGAT 0.960431 -55 TCTCTTTCTATTTTTTTATGATAGAATGCCAA 7 83 1 TTTTTTAGAT 0.899867 -65 CTAGGCGATATTTTTCAACGATAAGTAGGTCT 8 155 1 TTTTTAAGAT 0.960858 -106 ***** ** *** Masking position 8 Map Score: 3.80868 Number of sites scoring better than the average of aligned sites = 127 Number in coding regions = 103 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 7 ********** No masking Map Score: -2.46258e-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 8 ********** No masking Map Score: -2.46258e-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 9 ********** No masking Map Score: -2.46258e-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