AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/alignace/lib/ORF_hinf.txt -z/skink1/amcguire/genomes/hinf.fna -inagC_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 HI0140 272 N-acetylglucosamine-6-phosphate deacetylase (nagA) #2 HI0141 285 glucosamine-6-phosphate isomerase (nagB) #3 HI0144 45 glucose kinase, putative #4 HI0145 300 conserved hypothetical protein #5 HI0429 111 glucosamine--fructose-6-phosphate aminotransferase (glmS) #6 HI0431 35 conserved hypothetical protein #7 HI0432 66 conserved hypothetical protein #8 HI0433 75 orfG protein #9 HI0439 98 competence protein A (comA) #10 HI0638 128 conserved hypothetical protein #11 HI0639 22 adenylosuccinate lyase (purB) #12 HI0640 271 ribosomal protein L10 (rpL10) #13 HI0641 54 ribosomal protein L7/L12 (rpL7/L12) #14 HI0642 159 UDP-N-acetylglucosamine pyrophosphorylase (glmU) Motif number 1 GCGAATGTAATTCGCCCCTACATAAAGATGAAG 1 20 0 TTGCCCCTAT 0.970229 -253 GCGAATTACATTCGCCCTATAATCTCAACAAGA 1 38 1 TTGCCCTAAT 0.961752 -235 GCGAATGTAATTCGCCCCTACATAAAGATGAAG 1 156 0 TTGCCCCTAT 0.970229 -117 GCGAATTACATTCGCCCTATAATCACAAACAAT 1 174 1 TTGCCCTAAT 0.961752 -99 GTAAGGACAATTTGCCCTATGATTGTTTGTGAT 1 195 0 TTGCCCTAAT 0.961752 -78 GGGAGGTAAGTTTTTTCTAATTTAAATAT 2 7 0 TTTTTCTATT 0.566931 -279 AAGAAATTCTTTTGCTCCAATAATTTACGACAG 2 146 0 TTGCTCCAAA 0.900011 -140 TTTACGAGTTTTATTTCCAAAATGAGAAGTTGA 4 108 1 TTTTTCCAAT 0.90686 -193 TTTTGAAGTGTTTTTTCATAAATGTGATCAACT 4 135 0 TTTTTCATAT 0.57567 -166 CTTATTTCCTTAATTCGTAAGAGT 6 22 0 TTTTTCCTAT 0.886979 -14 TTTTTCTCCATAAAAATAACCGCA 7 53 0 TTTCTCCAAA 0.84823 -14 TCCCGATACTTTCTCTCAAGTATTTAGGACATA 8 50 1 TTTCTCAAAT 0.87215 -26 AAATGTTTGCTCCAGAATTGTA 11 5 0 TTGCTCCAAT 0.984509 -18 GAATTTGGCTCTTTTTTCAACAATATT 12 5 1 TTGCTCTTTT 0.873213 -267 AGAACATAGCTTTTCTCTATAATCCTGCGCCTG 12 45 1 TTTCTCTAAT 0.960846 -227 TGGCTTTTAGCTCCTGAATACACTCCGAT 12 253 0 TTGCTCCTAT 0.980852 -19 AAACCATCGGTTTTTTCTTATATAAAAGTTTGT 14 51 1 TTTTTCTTAT 0.829946 -109 AAATTTTCTCTTTATTCATCAATAAC 14 144 0 TTTCTCTTTT 0.810475 -16 ** ****** ** Masking position 2 Map Score: 22.777 Number of sites scoring better than the average of aligned sites = 273 Number in coding regions = 211 Number in noncoding regions = 62 Number of orfs with sites within 600 bp upstream = 54 Fraction of orfs with sites within 600 bp upstream = 0.00867331 Motif number 2 GTGAAATATTTTACTGAATTAGAAGGCGCGGTTGC 1 87 1 TTCTGATTAG 0.863195 -186 AGCAATATAGTTGCTATGTTAAACTGATGTTGATA 1 235 1 TTCTATTTAT 0.817948 -38 ATTCTGTTCCTAATATCAACATCAGTTTAAC 1 252 0 TTCTAAATAA 0.863138 -21 AGGTAAGTTTTTTCTAATTTAAATAT 2 2 0 TTCTAATTAA 0.909455 -284 AGGAAAGTGCTTGCTGACTTGCTGTTCTGTTTGTA 2 55 0 TTCTGATTTT 0.944122 -231 GTGCGGCAATTTTCTATCTTGTTTTTAAAAAGAAA 2 173 0 TTCTATTTTT 0.817948 -113 ATTAGCCTTCCTTTATTATTGACCGTGATGAT 2 264 0 TTCTTTTTTA 0.650528 -22 ATTTATTCTATTACTAAGTTTGTTTTTACATTTGC 5 76 0 TTCTAATTTT 0.947486 -36 AAGTTTTCCTTATTTATTCTATTACTAAGT 5 92 0 TTCTTATTTT 0.929198 -20 CTTATTTCCTTAATTCGTAAGAGTTGGAAT 6 16 0 TTCTTATTTA 0.882026 -20 AAGCCTAGAGTTTCTGATATGATGTGTGAACAGTT 10 32 0 TTCTGAATTT 0.911824 -97 CGGAAACGTTTTCCTGATATTTACTA 10 113 1 TTCTGAATAT 0.911824 -16 TTATTAAGCGTTTCTTACTTCATCTAACTTTATTT 13 11 1 TTCTTATTTT 0.929198 -44 AACAATCAATTCCTAAAATAAATAAAGTTAGATG 13 31 0 TTCTAAATAA 0.86312 -24 CCATCGGTTTTTTCTTATATAAAAGTTTGTTATAG 14 54 1 TTCTTAATAG 0.755057 -106 ATTTGCTATCTTTCTAAGATAGAATATTACCCGTT 14 109 1 TTCTAAATAT 0.876524 -51 ** **** ** * * Masking position 10 Map Score: 11.6957 Number of sites scoring better than the average of aligned sites = 375 Number in coding regions = 268 Number in noncoding regions = 107 Number of orfs with sites within 600 bp upstream = 101 Fraction of orfs with sites within 600 bp upstream = 0.0162223 Motif number 3 AGATCTATTCTTCATCTTTATGTA 1 5 1 CTATTCTTCA 0.971856 -268 AAATAGAGATCTATTCTTCATCTTTATGTA 1 141 1 CTATTCTTCA 0.971856 -132 CACTTCAAAAATATTCTTTAAAATGGCATT 4 158 1 ATATTCTTTA 0.947447 -143 ATATGCTTATATTTTCATCATTTAACCTTA 4 202 0 ATTTTCATCA 0.761586 -99 CTTGACAAGAATATTCATTAACGAAGCGAG 9 20 0 ATATTCATTA 0.918287 -79 ATTCTTTCCTATTCTTTAAAGGCTGAAT 9 81 0 CTATTCTTTA 0.956084 -18 TTTTTCAACAATATTCTTTACAAGAACATA 12 23 1 ATATTCTTTA 0.947447 -249 AATTTTCTCTTTATTCATCAATAACAACGG 14 139 0 TTATTCATCA 0.844178 -21 ********** Masking position 10 Map Score: 8.50568 Number of sites scoring better than the average of aligned sites = 114 Number in coding regions = 100 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 4 AGATCTATTCTTCATCTTTATG 1 1 1 AACTATTCTT 0.947516 -272 GGATAAATAGAGATCTATTCTTCATCTTTATG 1 137 1 AACTATTCTT 0.947516 -136 TTGTTTTTAAAAAGAAATTCTTTTGCTCCAAT 2 158 0 AAAAATTCTT 0.920789 -128 AAAACACTTCAAAAATATTCTTTAAAATGGCA 4 154 1 AAATATTCTT 0.818664 -147 TGCGGTCATTATAAATCTTCTTTTATAACTCA 7 11 0 AAATCTTCTT 0.907205 -56 CGCTTCGTTAATGAATATTCTTGTCAAGAGAC 9 22 1 AGATATTCTT 0.724822 -77 CTCTTTTTTCAACAATATTCTTTACAAGAACA 12 19 1 ACATATTCTT 0.802964 -253 TATAGAGAAAAGCTATGTTCTTGTAAAGAATA 12 34 0 ACATGTTCTT 0.847458 -238 CCCAGAAGCAAGAAAAATTCTTATTCTGTTCA 12 174 0 AAAAATTCTT 0.920789 -98 * * ******** Masking position 8 Map Score: 7.94508 Number of sites scoring better than the average of aligned sites = 48 Number in coding regions = 37 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 5 ACGGAATAAAACAGGGGGAGGTAAGTTTTTT 2 24 0 ACAGGGGAGG 0.997741 -262 TCCCCCGTAAACAGGGGAAGGAAAGTGCTTG 2 77 0 ACAGGGGAGG 0.997741 -209 TCCCCTGTTTACGGGGGAAGGTGCCCGAAGG 2 90 1 ACGGGGGAGG 0.997907 -196 AGGTGCCCGAAGGGCGGAAGGGGGCAACTTC 2 108 1 AGGGCGGAGG 0.974662 -178 ATTGACTAACACAGGCGCAGGATTATAGAGA 12 58 0 ACAGGCGAGG 0.99204 -214 ******* *** Masking position 9 Map Score: 7.42405 Number of sites scoring better than the average of aligned sites = 6 Number in coding regions = 1 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 6 CCGTGAAATATTTTACTGAATTAGAAGGCG 1 85 1 TTTTACTGAA 0.785681 -188 AGATCTCTATTTATCCTGATAATCCGTACC 1 123 0 TTATCCTGAT 0.933221 -150 AGTTGCTATGTTAAACTGATGTTGATATTA 1 243 1 TTAAACTGAT 0.646066 -30 AACTTATCCTTATAGTGTAAAGT 3 33 0 TTATCCTTAT 0.937274 -13 TTTTCATCATTTAACCTTATTATATGAAAA 4 191 0 TTAACCTTAT 0.84148 -110 AAGTTTTCCTTATTTATTCTATT 5 99 0 TTTTCCTTAT 0.953642 -13 CTTATTTCCTTAATTCGTAAGAG 6 23 0 ATTTCCTTAA 0.552728 -13 GCTGAATCTTTTATACTTAACAGCCAAATC 9 58 0 TTATACTTAA 0.740067 -41 AACGGAAACGTTTTCCTGATATTTACTA 10 111 1 TTTTCCTGAT 0.950589 -18 TCGGAATTAATTTACCTAATCCTAAGACTA 12 220 0 TTTACCTAAT 0.567209 -52 AACCATCGGTTTTTTCTTATATAAAAGTTT 14 52 1 TTTTTCTTAT 0.696712 -108 TTGTTATAGTTTTTACTTAAAAACTTACCA 14 80 1 TTTTACTTAA 0.796742 -80 ********** Masking position 9 Map Score: 8.93441 Number of sites scoring better than the average of aligned sites = 323 Number in coding regions = 230 Number in noncoding regions = 93 Number of orfs with sites within 600 bp upstream = 111 Fraction of orfs with sites within 600 bp upstream = 0.0178285 Motif number 7 GAATGTAATTCGCCCCTACATAAAGATGAA 1 21 0 CGCCCCTACA 0.99073 -252 TACCAGCAACCGCGCCTTCTAATTCAGTAA 1 97 0 CGCGCCTTCT 0.885906 -176 GAATGTAATTCGCCCCTACATAAAGATGAA 1 157 0 CGCCCCTACA 0.99073 -116 TTGCCCCCTTCCGCCCTTCGGGCACCTTCC 2 105 0 CCGCCCTTCG 0.954052 -181 GGACTTTAGCCCACCCTACACCAAAGGATC 2 215 0 CCACCCTACA 0.973056 -71 GGGCTAAAGTCCAGCCTACGATATGAATAG 2 233 1 CCAGCCTACG 0.959939 -53 ATTAAGATTACTCCCCTACGGTCTTGGATG 12 128 0 CTCCCCTACG 0.976905 -144 ********** Masking position 7 Map Score: 6.37889 Number of sites scoring better than the average of aligned sites = 33 Number in coding regions = 12 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 8 TCTTGTTGAGATTATAGGGCGAATGTAATT 1 41 0 ATTATAGGGC 0.989245 -232 ATTTTACTGAATTAGAAGGCGCGGTTGCTG 1 94 1 ATTAGAAGGC 0.888146 -179 ATTGTTTGTGATTATAGGGCGAATGTAATT 1 177 0 ATTATAGGGC 0.989245 -96 ATCACAAACAATCATAGGGCAAATTGTCCT 1 195 1 ATCATAGGGC 0.990028 -78 TAACAGCCAAATCATAGGTCTCTTGACAAG 9 41 0 ATCATAGGTC 0.950067 -58 ********** Masking position 6 Map Score: 4.81242 Number of sites scoring better than the average of aligned sites = 7 Number in coding regions = 4 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 1 Fraction of orfs with sites within 600 bp upstream = 0.000160617 Motif number 9 TATGAAAAAACACTTCAAAAATATTCTTTA 4 148 1 CACTTCAAAA 0.950237 -153 CTGAATAAATCACTTTAAAATTAATTTAAT 4 261 0 CACTTTAAAA 0.981211 -40 CACGCGTTTACACAATAAAAAACCCCTGCG 5 46 0 CACAATAAAA 0.873501 -66 AAAATAACCGCACTTTCAAAAGTGCGGTCA 7 35 0 CACTTTCAAA 0.950237 -32 TTTGAACTCGAACATTAAAAAAGCCTAGAG 10 57 0 AACATTAAAA 0.812386 -72 CTATTTTAACCACTTTAAAATTCAAAAAAC 14 14 1 CACTTTAAAA 0.981211 -146 ********** Masking position 8 Map Score: 3.58142 Number of sites scoring better than the average of aligned sites = 79 Number in coding regions = 52 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 10 AACAAGAGCTAAAAGTGAAAACCGTGAAATATTTT 1 64 1 AAAGTGAACT 0.876494 -209 GGATCATTATAAGTGCGGCAATTTTCTATCTTGTT 2 185 0 AAGGCGGATT 0.987165 -101 GTTTTTTCATAAATGTGATCAACTTCTCATTTTGG 4 124 0 AAAGTGAACT 0.876503 -177 TATTGTGTAAACGCGTGGCAAATGTAAAAACAAAC 5 59 1 ACGGTGGATT 0.939087 -53 GCACTTTCAAAAGTGCGGTCATTATAAATCTTCTT 7 21 0 AAGGCGGATT 0.987601 -46 GCACTTTTGAAAGTGCGGTTATTTTTATGGAGAAA 7 40 1 AAGGCGGATT 0.9876 -27 CTGGAAAAAAAAGCGCGATAAGCGTATTATTCCCG 8 20 1 AAGGCGAACT 0.980074 -56 TTCTGATATGATGTGTGAACAGTTTTAAGGTATTA 10 21 0 ATGGTGAATT 0.867944 -108 *** **** * * * Masking position 11 Map Score: 2.93397 Number of sites scoring better than the average of aligned sites = 823 Number in coding regions = 508 Number in noncoding regions = 315 Number of orfs with sites within 600 bp upstream = 223 Fraction of orfs with sites within 600 bp upstream = 0.0358175 Motif number 11 AGATCTATTCTTCATCTTTATGT 1 2 1 GATTATTCTC 0.649408 -271 GAAGAATAGATCTCTATTTATCCTGATAATCC 1 128 0 TCTTATTTAC 0.912003 -145 GACTTGCTGTTCTGTTTGTAACGGAATAAAAC 2 43 0 TCTTTTGTAC 0.759872 -243 GCCAAAAATGTATGTTTTCTCCCCCAAAATAG 4 31 1 TATTTTTCTC 0.792049 -270 GTAATATGCTTATATTTTCATCATTTAACCTT 4 203 0 TATTTTTCAC 0.893748 -98 CGCTTATCGCGCTTTTTTTTCCAGTGCTTTAT 8 12 0 GCTTTTTTTC 0.830278 -64 GGTTAAAAATGCTATATTTAACGGAAACGTTT 10 92 1 GCTTATTTAC 0.880488 -37 GAATTTGGCTCTTTTTTCAACAATATTCTTT 12 10 1 TCTTTTTCAC 0.967545 -262 TTTCTATTTTAACCACTTTAAAAT 14 3 1 TCTTTTTAAC 0.821809 -157 AAATTTTCTCTTTATTCATCAATAACAACG 14 140 0 TCTTATTCAC 0.953178 -20 *** ****** * Masking position 7 Map Score: 3.64056 Number of sites scoring better than the average of aligned sites = 204 Number in coding regions = 156 Number in noncoding regions = 48 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 12 GCAAGTCAGCAAGCACTTTCCTTCCCCTGT 2 68 1 AAGCACTTTC 0.797456 -218 TAATATGAGAATCAATTTAGGCCAAAAAT 4 10 1 AATCAATTTA 0.94057 -291 AGAGTAAAAAAACAAATTTAAAATAGTTTT 4 81 1 AACAAATTTA 0.808863 -220 ATCACTTTAAAATTAATTTAATCCACACAA 4 253 0 AATTAATTTA 0.811939 -48 AATCTGAATAAATCACTTTAAAATTAATTT 4 264 0 AATCACTTTA 0.928848 -37 TAGTCAATCTAACAAATTTCTGGTTGGTGC 12 81 1 AACAAATTTC 0.777312 -191 GATTACTCGGAATTAATTTACCTAATCCTA 12 226 0 AATTAATTTA 0.811939 -46 AACAATCAATTCCTAAAATAAAT 13 42 0 AATCAATTCC 0.753092 -13 TTTCTATTTTAACCACTTTAAAATTCAAAA 14 11 1 AACCACTTTA 0.927513 -149 ********** Masking position 5 Map Score: 2.32413 Number of sites scoring better than the average of aligned sites = 249 Number in coding regions = 215 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 13 ACTGAATTAGAAGGCGCGGTTGCTGGTACG 1 99 1 AAGGCGCGGT 0.971094 -174 CGCACTTTCAAAAGTGCGGTCATTATAAAT 7 27 0 AAAGTGCGGT 0.981548 -40 CGCACTTTTGAAAGTGCGGTTATTTTTATG 7 39 1 AAAGTGCGGT 0.981548 -28 ACTGGAAAAAAAAGCGCGATAAGCGTATTA 8 19 1 AAAGCGCGAT 0.966743 -57 TTCGAGTTCAAAAGCTAGGTTAAAAATGCT 10 75 1 AAAGCTAGGT 0.96272 -54 ATTATAGAGAAAAGCTATGTTCTTGTAAAG 12 38 0 AAAGCTATGT 0.770083 -234 TAAAATAAATAAAGTTAGATGAAGTAAGAA 13 22 0 AAAGTTAGAT 0.773296 -33 ********** Masking position 2 Map Score: 5.36028 Number of sites scoring better than the average of aligned sites = 1294 Number in coding regions = 836 Number in noncoding regions = 458 Number of orfs with sites within 600 bp upstream = 311 Fraction of orfs with sites within 600 bp upstream = 0.0499518 Motif number 14 ATTAGCCTTCCTTTATTATTGACCGTGA 2 268 0 TCCTTTATTA 0.850204 -18 CACAAAACAATCTTTTATAAGTTGTAATAT 4 228 0 TCTTTTATAA 0.901396 -73 CTTATTTCCTTAATTCGTAAGAGTTG 6 20 0 TCCTTAATTC 0.900512 -16 TTATAAATCTTCTTTTATAACTCA 7 5 0 TCTTTTATAA 0.901396 -62 AATTATGTCCTAAATACTTGAGAGAAA 8 59 0 TCCTAAATAC 0.912936 -17 AAAGGCTGAATCTTTTATACTTAACAGCCA 9 62 0 TCTTTTATAC 0.947261 -37 AATCAATCCTTAATACCTTAAAACTG 10 7 1 TCCTTAATAC 0.966265 -122 GGCTTTTAGCTCCTGAATACACTCCGATTA 12 251 0 TCCTGAATAC 0.8981 -21 ATCGGTTTTTTCTTATATAAAAGTTTGTTA 14 56 1 TCTTATATAA 0.769939 -104 ********** Masking position 4 Map Score: 6.31055 Number of sites scoring better than the average of aligned sites = 71 Number in coding regions = 51 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 15 AACCGCGCCTTCTAATTCAGTAAAATATTT 1 90 0 TCTAATTCAG 0.760289 -183 ACCGTGATGATCCTATTCATATCGTAGGCT 2 245 0 TCCTATTCAT 0.933444 -41 TGCTCTCGAATCCTATTTTGGGGGAGAAAA 4 45 0 TCCTATTTTG 0.87156 -256 TAAATATTCCAACTCTTACGAATTAAG 6 8 1 TCCAACTCTT 0.880213 -28 ATTCTTTCCTATTCTTTAAAGGCTGA 9 83 0 TCCTATTCTT 0.974561 -16 TACAATTCTGGAGCAAACAT 11 1 1 TACAATTCTG 0.808787 -22 CAAGAAAAATTCTTATTCTGTTCACCATCT 12 168 0 TCTTATTCTG 0.93288 -104 GCCGAAGTCATCCTAGTCTTAGGATTAGGT 12 207 1 TCCTAGTCTT 0.921802 -65 ********** Masking position 5 Map Score: 1.49171 Number of sites scoring better than the average of aligned sites = 137 Number in coding regions = 119 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987