AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i010_Nucleotide_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 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 HI1231 113 dihydrolipoamide dehydrogenase (lpdA) #9 HI1232 62 dihydrolipoamide acetyltransferase (aceF) #10 HI1233 299 pyruvate dehydrogenase, E1 component (aceE) #11 HI1741 260 guanosine-3',5'-bis(diphosphate) 3'- pyrophosphohydrolase (spoT) #12 HI1742 62 DNA-directed RNA polymerase, omega chain (rpoZ) #13 HI1743 249 guanylate kinase (gmk) Motif number 1 GAGAAGCTCAAAAGTGCGGCGAAAAAATTA 2 29 0 AAAGTGCGGC 0.99329 -70 ATAATGCTCAAAAGTGCGGTAAAAAAAGAA 7 126 0 AAAGTGCGGT 0.99859 -22 AAAGACCGTAAAAGTGCGGTCAATATTTTT 8 74 1 AAAGTGCGGT 0.99859 -40 TTGATGAAAACTGCGGTCAAAAAACAT 9 8 1 AAACTGCGGT 0.989237 -55 TGTTCCTTTTAAAGTGCGGTCATAAAACAC 9 39 0 AAAGTGCGGT 0.99859 -24 TAATTATTTGAAAGTGCGGTAATTTTTTTG 10 106 0 AAAGTGCGGT 0.99859 -194 TCTTTTAAAAGTGCGGTAAAAAATAAA 11 8 1 AAAGTGCGGT 0.99859 -253 TACTCTATTGAAAGGGCGTTATAATACTCA 12 19 0 AAAGGGCGTT 0.928204 -44 TTAGAATGAAAAAGTACCGTAAAAAATCAC 13 158 1 AAAGTACCGT 0.889172 -92 AAAATCATCAAAAGTGCGGTGATTTTTTAC 13 176 0 AAAGTGCGGT 0.99859 -74 ********** Masking position 3 Map Score: 36.8155 Number of sites scoring better than the average of aligned sites = 1115 Number in coding regions = 700 Number in noncoding regions = 415 Number of orfs with sites within 600 bp upstream = 285 Fraction of orfs with sites within 600 bp upstream = 0.0457758 Motif number 2 AAGCTCAAAAGTGCGGCGAAAAAATTATGTG 2 25 0 GTGCGGCAAA 0.980833 -74 ATGCTCAAAAGTGCGGTAAAAAAAGAAACGT 7 122 0 GTGCGGTAAA 0.996334 -26 GACCGTAAAAGTGCGGTCAATATTTTTAACG 8 77 1 GTGCGGTAAT 0.992955 -37 TTGATGAAAACTGCGGTCAAAAAACATTGTG 9 11 1 CTGCGGTAAA 0.992858 -52 TCCTTTTAAAGTGCGGTCATAAAACACAATG 9 35 0 GTGCGGTATA 0.989755 -28 TTATTTGAAAGTGCGGTAATTTTTTTGTGTT 10 102 0 GTGCGGTATT 0.980434 -198 TCTTTTAAAAGTGCGGTAAAAAATAAAGGTA 11 11 1 GTGCGGTAAA 0.996334 -250 GTATACCTACCCGCGGTAAAATACCTTTATT 11 32 0 CCGCGGTAAA 0.979667 -229 GTAGGTATACCCACGGTTAATTATGGTTATA 11 53 1 CCACGGTAAT 0.776389 -208 TCAATTTTATCTGCGGGCAAATACCCTTGAA 11 221 0 CTGCGGGAAA 0.963209 -40 GAATGAAAAAGTACCGTAAAAAATCACCGCA 13 161 1 GTACCGTAAA 0.800604 -89 ATCATCAAAAGTGCGGTGATTTTTTACGGTA 13 172 0 GTGCGGTATT 0.980434 -78 ******* *** Masking position 9 Map Score: 27.1939 Number of sites scoring better than the average of aligned sites = 1069 Number in coding regions = 678 Number in noncoding regions = 391 Number of orfs with sites within 600 bp upstream = 265 Fraction of orfs with sites within 600 bp upstream = 0.0425634 Motif number 3 CCTTTTTCTTTTTAAGTTCTTTTCTCAAGGTAGGATTT 3 32 1 TTTTTTCATA 0.770786 -28 TCGCTTTTATTTTGGGTGGATATTGTACCGAATAACCGAG 4 9 0 TTTGTTTAAA 0.978462 -69 TGATGCTATTTTTACCATAATCTTGAAAAATAAGCAGAAGGA 5 19 0 TTTTTTTATA 0.955187 -143 TATGGGTAAGTTTAGGGGTATTTTACCCAGTAAATTTACCTT 5 113 0 TTTGTTTCTA 0.927117 -49 AGGCTTAGATTTTCTAAGCCTTTTTATTTTAATCATTTGAAT 6 21 1 TTTGTTTTAA 0.839571 -76 ATTTGAATAATTTTCTTTTCTCTTTGAGAAAAAATAAATATA 6 55 1 TTTTTTTAAA 0.971577 -42 GAAGTTTTAATTCATCTTAAATTGTAAATTCAAACT 7 5 1 TTTTTTTATA 0.955197 -143 TTTTCCTCTCTTTCTATTTTTTTATGATAGAATGCCAATCTA 7 77 1 TTTTTTAAAA 0.903538 -71 CGGTCAATATTTTTAACGTTTTTACGAGGTAAAA 8 90 1 TTTGTTAAAA 0.929683 -24 GTTTTAAAGTTTTTTCAGATTTTTTTCAAAAAGGACTCAGCA 10 11 0 TTTGTTTCAA 0.954065 -289 GAATGCAATATTTTACTGGTTATTTTAGCGAACAAAAAAACA 10 64 1 TTTGTTTAAA 0.980063 -236 TCTTGTAAATTTTAGAAGATTTTTTGAGATAAAGATAGTGAA 10 176 0 TTTGTTTAAA 0.980067 -124 CGTATTCGTGTTTAGCCTTGTCTAAACTAATATTCACTCAAA 10 250 1 TTTTTTACTA 0.70793 -50 AGATTTTCACCTTTTATTTAAGTTAAACAAATCTGT 13 5 1 TTTTTTTAAA 0.972082 -245 GCGGTGATTTTTTACGGTACTTTTTCATTCTAATGATGATTT 13 149 0 TTTTTTTATA 0.955198 -101 TCACCGCACTTTTGATGATTTTTTATAGAGAAATCTGCATAA 13 184 1 TTTATTTAAA 0.845899 -66 *** * * ** * ** Masking position 11 Map Score: 19.8686 Number of sites scoring better than the average of aligned sites = 285 Number in coding regions = 186 Number in noncoding regions = 99 Number of orfs with sites within 600 bp upstream = 88 Fraction of orfs with sites within 600 bp upstream = 0.0141343 Motif number 4 TAAGCAGAAGGAGAATAATA 5 1 0 GAGAATAATA 0.703818 -161 TACCATAATCTTGAAAAATAAGCAGAAGGA 5 19 0 TTGAAAAATA 0.944594 -143 GAGTAATCGTTTGCATAATAAATTTTTATT 5 71 1 TTGCATAATA 0.853123 -91 TTTTAAAGCATTGAATAAAAATTTATTATG 5 84 0 TTGAATAAAA 0.922013 -78 TTTTAATCATTTGAATAATTTTCTTTTCTC 6 47 1 TTGAATAATT 0.922016 -50 TCTTTTCTCTTTGAGAAAAAATAAATATAG 6 68 1 TTGAGAAAAA 0.800763 -29 TGAGTCCTTTTTGAAAAAAATCTGAAAAAA 10 14 1 TTGAAAAAAA 0.845523 -286 TCTGTTTTGAGTGAATATTAGTTTAGACAA 10 267 0 GTGAATATTA 0.703818 -33 CTACTTATCGTTGAAAAATATCGCCTAGGG 11 153 0 TTGAAAAATA 0.944594 -108 GCAAATACCCTTGAATAATTCGATCTAAAT 11 206 0 TTGAATAATT 0.922016 -55 GGCGAAATTGAGTATTATAACGCCCTT 12 8 1 TTGAGTATTA 0.846699 -55 GCCCTTTCAATAGAGTAATTTTTGACAAAT 12 32 1 TAGAGTAATT 0.639404 -31 TCTGTTTGCTTTGAGTAATACTGCTCACTC 13 42 1 TTGAGTAATA 0.964339 -208 ********** Masking position 7 Map Score: 11.4302 Number of sites scoring better than the average of aligned sites = 376 Number in coding regions = 291 Number in noncoding regions = 85 Number of orfs with sites within 600 bp upstream = 80 Fraction of orfs with sites within 600 bp upstream = 0.0128493 Motif number 5 AGCCCACCGATTAATGAAATCTTTGGTGGGC 8 28 1 TTATGAAATC 0.916903 -86 TTGATGAAAACTGCGGTCAAA 9 1 1 TTATGAAAAC 0.608241 -62 GAAAAAACTTTAAAACAAAGCCCGATGGAAT 10 37 1 TAAACAAAGC 0.891469 -263 ATCAAATCATCATATCAAATCAGCTTTGCCA 10 140 0 CAATCAAATC 0.881195 -160 ATAGTGAATTTTCATCAAATCATCATATCAA 10 153 0 TTATCAAATC 0.976339 -147 CTATCTTTATCTCAAAAAATCTTCTAAAATT 10 180 1 CTAAAAAATC 0.712001 -120 TTCACAAACATTTAACAAATCTTGTAAATTT 10 206 0 TTAACAAATC 0.976339 -94 TAGAGTAATTTTTGACAAATCGGAGTAAATT 12 42 1 TTGACAAATC 0.885987 -21 TTTATTTAAGTTAAACAAATCTGTTTGCTTT 13 23 1 TTAACAAATC 0.976339 -227 GTGAGCAGTATTACTCAAAGCAAACAGATTT 13 39 0 TTCTCAAAGC 0.748899 -211 TTTTGTGATCTATATCAAATCATCATTAGAA 13 133 1 TAATCAAATC 0.955359 -117 CAGATTTCTCTATAAAAAATCATCAAAAGTG 13 190 0 TAAAAAAATC 0.787223 -60 ** ******** Masking position 7 Map Score: 8.5862 Number of sites scoring better than the average of aligned sites = 243 Number in coding regions = 211 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 6 AATCGCCCCTTTTTCTTTTTAAGTTCTTTT 3 25 1 TTTTCTTTTT 0.923759 -35 TTCCTGTCGCTTTTATTTTGGGTGGATATT 4 27 0 TTTTATTTTG 0.762866 -51 CCCAGTAAATTTACCTTTTTAAAGCATTGA 5 100 0 TTACCTTTTT 0.467794 -62 AATGATTTCCTTTTAAATATGGGTA 5 147 0 TTTCCTTTTA 0.924093 -15 TTCTAAGCCTTTTTATTTTAATCATTTGAA 6 32 1 TTTTATTTTA 0.89794 -65 ATTTGAATAATTTTCTTTTCTCTTTGAGAA 6 55 1 TTTTCTTTTC 0.95013 -42 AATTGGGGATTTTTATTTAAGTTTGAATTT 7 36 0 TTTTATTTAA 0.66344 -112 AATTGGGGATTTTTATTTTCCTCTCTTTCT 7 62 1 TTTTATTTTC 0.896091 -86 ATCTAAAAACGTTTCTTTTTTTACCGCACT 7 114 1 GTTTCTTTTT 0.807661 -34 TTTTTGTTCCTTTTAAAGTGCGGTC 9 48 0 GTTCCTTTTA 0.808399 -15 TACGGCAATATTTGCTTTTCACAAACATTT 10 224 0 TTTGCTTTTC 0.81656 -76 GATTTTCACCTTTTATTTAAGTTAAACAAA 13 12 1 TTTTATTTAA 0.66344 -238 ********** Masking position 6 Map Score: 5.73593 Number of sites scoring better than the average of aligned sites = 657 Number in coding regions = 454 Number in noncoding regions = 203 Number of orfs with sites within 600 bp upstream = 173 Fraction of orfs with sites within 600 bp upstream = 0.0277867 Motif number 7 CGAAAAAATTATGTGTATTTTATCGGATC 2 9 0 ATGTGATTTT 0.919573 -90 GGGTAAGTTTAGGGGTATTTTACCCAGTAAA 5 121 0 AGGGGATTTT 0.723637 -41 AAATCCCCAATTGGGGATTTTTATTTAAGTT 7 43 0 TTGGGATTTT 0.975796 -105 AAATCCCCAATTGGGGATTTTTATTTTCCTC 7 54 1 TTGGGATTTT 0.975796 -94 TACCGCACTTTTGAGCATTATTT 7 135 1 TTGAGATTAT 0.890136 -13 TCAAAAAACATTGTGTTTTATGACCGCACTT 9 27 1 TTGTGTTTAT 0.838114 -36 GGTAATTTTTTTGTGTTTTTTTGTTCGCTAA 10 88 0 TTGTGTTTTT 0.919573 -212 GAGATAAAGATAGTGAATTTTCATCAAATCA 10 162 0 TAGTGATTTT 0.866381 -138 TTAACAAATCTTGTAAATTTTAGAAGATTTT 10 195 0 TTGTAATTTT 0.782301 -105 GGCGAAATTGAGTATTATAACGCCCTTT 12 8 1 TTGAGATTAT 0.890136 -55 ***** ***** Masking position 8 Map Score: 7.24869 Number of sites scoring better than the average of aligned sites = 279 Number in coding regions = 231 Number in noncoding regions = 48 Number of orfs with sites within 600 bp upstream = 51 Fraction of orfs with sites within 600 bp upstream = 0.00819146 Motif number 8 ATAAAAATCCCCAATTGGGGATTTTTATTT 7 48 0 CCAATTGGGG 0.98383 -100 ATAGTTGTCCCCCTTTGGGGAACGTAATTT 11 81 1 CCCTTTGGGG 0.975546 -180 CTAAATGTTACCCTTTGGGGTAGAAATTAC 11 104 0 CCCTTTGGGG 0.975546 -157 ********** Masking position 5 Map Score: 2.12216 Number of sites scoring better than the average of aligned sites = 8 Number in coding regions = 4 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 9 ATTACTCAGTGATAGAATGATGCTATTTTT 5 48 0 GATAGAATGA 0.9764 -114 ATCATAAAAAAATAGAAAGAGAGGAAAATA 7 75 0 AATAGAAAGA 0.866507 -73 ATTTTTTTATGATAGAATGCCAATCTAAAA 7 92 1 GATAGAATGC 0.971671 -56 AACAAAGCCCGATGGAATGCAATATTTTAC 10 50 1 GATGGAATGC 0.926152 -250 TCAAATCATCATTAGAATGAAAAAGTACCG 13 147 1 ATTAGAATGA 0.866507 -103 AAATCTGCATAATAGACTGAAATTGTCAGA 13 214 1 AATAGACTGA 0.905843 -36 ********** Masking position 6 Map Score: 1.56215 Number of sites scoring better than the average of aligned sites = 27 Number in coding regions = 19 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 10 AAATCCTACCTTGAGAAAAG 3 50 0 AAATCCTACC 0.735648 -10 AGAATGATGCTATTTTTACCATAATCTTGA 5 35 0 TATTTTTACC 0.933897 -127 TTTTACCCAGTAAATTTACCTTTTTAAAGC 5 105 0 TAAATTTACC 0.879916 -57 AAAATACCCCTAAACTTACCCATATTTAAA 5 131 1 TAAACTTACC 0.872655 -31 AAAACGTTTCTTTTTTTACCGCACTTTTGA 7 119 1 TTTTTTTACC 0.778046 -29 GTGCGGTCAATATTTTTAACGTTTTTACGA 8 87 1 TATTTTTAAC 0.662498 -27 AAAAACACAAAAAAATTACCGCACTTTCAA 10 99 1 AAAAATTACC 0.488194 -201 AAATACCTTTATTTTTTACCGCACTTTTAA 11 15 0 ATTTTTTACC 0.71802 -246 TAACCGTGGGTATACCTACCCGCGGTAAAA 11 42 0 TATACCTACC 0.880759 -219 TGGGGAACGTAATTTCTACCCCAAAGGGTA 11 96 1 AATTTCTACC 0.851572 -165 TAAGCTAGGGTCTACTTACCCTAGGCGATA 11 135 1 TCTACTTACC 0.733719 -126 AGAATATTTAACCTTCTCTGAC 13 238 0 AATATTTAAC 0.58778 -12 ********** Masking position 8 Map Score: 3.88794 Number of sites scoring better than the average of aligned sites = 758 Number in coding regions = 598 Number in noncoding regions = 160 Number of orfs with sites within 600 bp upstream = 114 Fraction of orfs with sites within 600 bp upstream = 0.0183103 Motif number 11 ATTTGAAATATCCTAAAAATGAGAGATGG 1 10 1 ATCCTAAAAA 0.948455 -28 GATCCGATAAAATACACATAA 2 2 1 ATCCGATAAA 0.849588 -97 TTGAGAAAAGAACTTAAAAAGAAAAAGGGG 3 30 0 AACTTAAAAA 0.609893 -30 TTTTACCATAATCTTGAAAAATAAGCAGAA 5 22 0 ATCTTGAAAA 0.885903 -140 TTGGCATTCTATCATAAAAAAATAGAAAGA 7 85 0 ATCATAAAAA 0.833876 -63 AAATAATGCTCAAAAGTGCGGTAAA 7 133 0 ATGCTCAAAA 0.657894 -15 GCAGAAACCCATCCTATAAAGACCGTAAAA 8 57 1 ATCCTATAAA 0.884955 -57 TTTGAAAAAAATCTGAAAAAACTTTAAAAC 10 23 1 ATCTGAAAAA 0.921033 -277 CACTATCTTTATCTCAAAAAATCTTCTAAA 10 178 1 ATCTCAAAAA 0.768126 -122 ATCTCAAAAAATCTTCTAAAATTTACAAGA 10 188 1 ATCTTCTAAA 0.884955 -112 CATTTAACAAATCTTGTAAATTTTAGAAGA 10 199 0 ATCTTGTAAA 0.764477 -101 TTCGATCTAAATCCGCAAACAGTTCCAAAG 11 188 0 ATCCGCAAAC 0.695418 -73 TCTATAAAAAATCATCAAAAGTGCGGTGAT 13 183 0 ATCATCAAAA 0.853258 -67 TTATAGAGAAATCTGCATAATAGACTGAAA 13 206 1 ATCTGCATAA 0.570786 -44 ********** Masking position 9 Map Score: 8.81012 Number of sites scoring better than the average of aligned sites = 520 Number in coding regions = 426 Number in noncoding regions = 94 Number of orfs with sites within 600 bp upstream = 87 Fraction of orfs with sites within 600 bp upstream = 0.0139737 Motif number 12 TCTGTAGGTGGGCTTTAAGCCCAC 8 5 1 TAGGTGGGCT 0.983929 -109 ATTTCATTAATCGGTGGGCTTAAAGCCCAC 8 18 0 TCGGTGGGCT 0.994047 -96 AATGAAATCTTTGGTGGGCAGAAACCCATC 8 40 1 TTGGTGGGCA 0.983929 -74 TTCAATTTTATCTGCGGGCAAATACCCTTG 11 223 0 TCTGCGGGCA 0.961018 -38 ********** Masking position 1 Map Score: 0.949951 Number of sites scoring better than the average of aligned sites = 42 Number in coding regions = 27 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 13 ********** No masking Map Score: -9.35484e-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 14 ********** No masking Map Score: -9.35484e-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 15 ********** No masking Map Score: -9.35484e-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