AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00770_hinf_reg_100.orf -o00770_hinf_100.ace -a/home/amcguire/genomes/ORF_hinf.txt -z/home/amcguire/genomes/hinf.fna -g0.38 -x5 -e 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 = 1 Input sequences: #1 HI0631 300 pantothenate kinase (coaA) #2 HI0682 300 ketol-acid reductoisomerase (ilvC) #3 HI0737 247 acetohydroxy acid synthase II, putative #4 HI0738 71 dihydroxyacid dehydratase (ilvD) #5 HI1139 137 UDP-N-acetylmuramate--alanine ligase (murC) #6 HI1140 71 D-alanine--D-alanine ligase (ddlB) #7 HI1143 83 cell division protein (ftsZ) #8 HI1144 38 UDP-3-0-(3-hydroxymyristoyl) N-acetylglucosamine deacetylase (lpxC) #9 HI1193 300 branched-chain-amino-acid transaminase (ilvE) #10 HI1585 266 acetolactate synthase III large subunit (ilvI) Motif number 1 TTTATAAAAAAGTTTATTTTTTTGATTATTCGT 1 153 1 ATTTATTTTT 0.799269 -148 AAAAAATCACTTTTTTGATTGTGATTTAAACGA 1 182 0 TTTTTTTGTG 0.943184 -119 ATGAATGCTAAATTTTTATTTATAGCGTATATT 1 243 1 ATTTTTTTAT 0.86969 -58 TATAGCGTATATTTTTCTCTGTTTATTTAGCCA 1 263 1 ATTTTCTGTT 0.876902 -38 AATAATTTTATTTGATGGCTAAATAA 1 285 0 ATTTTTTGAT 0.852532 -16 AAATCGCTGTTCTTTGCTTTGTTTCAATTTTCT 2 42 0 TTTTGTTGTT 0.74474 -259 TTGTGCAATTATTTTTTTTTGTGAATTGGCATC 2 150 0 ATTTTTTGTG 0.920074 -151 TGATTATAGGATTTTTTGTTGTTGCGTAAAGTG 2 209 0 ATTTTTTGTT 0.960458 -92 TGTTTGCATATTTTTTTGTTGTGGTTTGATTAT 2 235 0 TTTTTTTGTG 0.943184 -66 ATATTGAAACTCTTTTCATTTTTTTACATAGGA 3 17 0 TTTTTTTTTT 0.975867 -231 TTTTTACCGCTCTTTTGGCTTATTTATTGACTG 3 66 0 TTTTTCTTAT 0.738402 -182 TCACCGCACTTTTTTTCGTTTTTTTCTCTCCAA 3 150 1 TTTTTTTTTT 0.975867 -98 TGTTTCCTGTTGTTTTTATTTTGGGGATAAGTT 3 219 0 TTTTTTTTTG 0.950408 -29 TTTTAACCGCACTTTTAGTTGAGTTTTGTCATT 5 96 1 ATTTTTTGAG 0.732611 -42 TTATTTTTCCTTTTCTCCCAATGA 5 124 0 TTTTTCTTTT 0.922236 -14 TTTCTATCCTGTTTTTCTTCTTACTGATGATA 6 50 0 TTTTTTTCTT 0.819353 -22 TTATTTTAATTTTTCATCTACAAT 7 2 1 TTTTTTTTTT 0.975867 -82 CCAAAATTTCATTATTCCTTTTTAGTTGGCTAA 9 182 1 ATATTTTTTT 0.844167 -119 TTACTTCCTTAATATTATTTTTTGAATGAAATT 9 277 0 ATATTTTTTT 0.844167 -24 AAATAGTAAAAATATTATTTTTTATTCAAATTT 10 29 0 ATATTTTTTT 0.844167 -238 TTTTGTCGCATTTTTTTATTTTTATTGATGGAA 10 76 1 TTTTTTTTTT 0.975867 -191 AATTTAGTTTTTTATAAATTTTTCCATCAATAA 10 97 0 TTATATTTTT 0.525908 -170 TAAAAAACTAAATTTTCATTTATATTTGGTTTT 10 116 1 ATTTTTTTAT 0.86969 -151 TATATTTGGTTTTTTATATTTTTTTAATTGATT 10 136 1 TTTTATTTTT 0.851678 -131 TTTTAATTGATTTTTTTGTTGTTTTAGTGGCTA 10 157 1 TTTTTTTGTT 0.972243 -110 CTAGACAAATTTTTTTTACTTTGTATTATGTGA 10 187 1 TTTTTCTTTG 0.848955 -80 ATTGACATAATCTGTTCGTTTTTTTAAAAGTGC 10 223 1 TTGTTTTTTT 0.77872 -44 * **** ***** Masking position 5 Map Score: 37.4268 Number of sites scoring better than the average of aligned sites = 1004 Number in coding regions = 711 Number in noncoding regions = 293 Number of orfs with sites within 600 bp upstream = 200 Fraction of orfs with sites within 600 bp upstream = 0.0321234 Motif number 2 AAGTGAGGCGTATTATATGGAAAAAACTTTAA 1 108 1 TATTATTGAA 0.770561 -193 AACTGACAAGTATTTTTTATAAAAAAGTTTAT 1 138 1 TATTTTTTAA 0.863569 -163 TAAAAAAGTTTATTTTTTTGATTATTCGTTTA 1 157 1 TATTTTTGAT 0.951859 -144 GCAATTATTTTTTTTTGTGAATTGGCATCGTA 2 147 0 TTTTTTTAAT 0.865524 -154 CGTAAAGTGATATTATGGGAATGTAATGTTGC 2 186 0 TATTATGAAT 0.741175 -115 TGTGTTTGCATATTTTTTTGTTGTGGTTTGAT 2 238 0 TATTTTTGTT 0.560503 -63 AAAATTGGCTTATTTTGAATATTCCTGTTCTT 3 119 0 TATTTTATAT 0.523536 -129 CTGTTGTTTTTATTTTGGGGATAAGTTCAGCA 3 214 0 TATTTTGGAT 0.794178 -34 GAATATTTTATCAATTAACGAAGAA 4 4 1 TATTTTTAAT 0.972679 -68 CAGTCATAAGTATTTTTTATATCCAAAAGTGC 5 37 1 TATTTTTTAT 0.938868 -101 AGGGAATTTATATTTTATATATTTAGTCAGCT 7 37 1 TATTTTTTAT 0.938867 -47 ATTTACTAGGTATTTTCTGAAACTTA 8 5 0 TATTTTTAAA 0.936199 -34 TTACTTCCTGTATATTATTAAACCGATTTGGT 9 73 1 TATATTTAAA 0.486095 -228 TTCGAGAATTTATTATTTAAATCACTTCAGGA 9 227 1 TATTATTAAT 0.936186 -74 TCCTTAATATTATTTTTTGAATGAAATTTCGC 9 273 0 TATTTTTAAT 0.97268 -28 ATATTTTTACTATTTTATAAAATGCGGCATTT 10 47 1 TATTTTTAAA 0.931526 -220 TGTCGCATTTTTTTATTTTTATTGATGGAAAA 10 79 1 TTTTATTTAT 0.53364 -188 GAAAATTTAGTTTTTTATAAATTTTTCCATCA 10 101 0 TTTTTTTAAT 0.864494 -166 TGGTTTTTTATATTTTTTTAATTGATTTTTTT 10 142 1 TATTTTTAAT 0.97268 -125 TTTTACTTTGTATTATGTGAAACATTGACATA 10 200 1 TATTATTAAA 0.8581 -67 AAAACGAACAGATTATGTCAATGTTTCACATA 10 213 0 GATTATTAAT 0.583819 -54 ****** * *** Masking position 6 Map Score: 24.5273 Number of sites scoring better than the average of aligned sites = 351 Number in coding regions = 213 Number in noncoding regions = 138 Number of orfs with sites within 600 bp upstream = 118 Fraction of orfs with sites within 600 bp upstream = 0.0189528 Motif number 3 TTTTCCATATAATACGCCTCACTTGCTTACGAC 1 99 0 AAACGCCCAT 0.991623 -202 CAATTTGCTGAACTCGCTACGCTCA 2 3 0 AATCGCTCGT 0.946349 -298 AGGCAAAGAAAACACGCCCCAGTTAAATCGCTG 2 66 0 AAACGCCCAT 0.991629 -235 ATAATTGCACAAATCGCAACATTACATTCCCAT 2 171 1 AATCGCACAT 0.985042 -130 ATGACTCGAAATTTCGCTACAATGCTGAACTTA 3 192 1 ATTCGCTCAT 0.853791 -56 GGCTATTTATAAAACGCCACAACCC 5 3 0 AAACGCCCAC 0.957102 -135 GGCGTTTTATAAATAGCCTCAGTCATAAGTATT 5 18 1 AATAGCCCAT 0.951688 -120 GTGCGGTTAAAATTCGCAACGTTTTTATTTCTA 5 75 0 AATCGCACGT 0.961934 -63 AGTTGGCTAAAAATTGCATCATTTCGAGAATTT 9 205 1 AATTGCACAT 0.919254 -96 AAAATGCGACAAAATGCCGCATTTTATAAAATA 10 57 0 AAATGCCCAT 0.953369 -210 TCACTCCTTAAATTCACCGCACTTTTAAAAAAA 10 241 0 AATCACCCAT 0.940576 -26 ** ***** ** * Masking position 1 Map Score: 14.173 Number of sites scoring better than the average of aligned sites = 166 Number in coding regions = 140 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 4 TGTCGTAAGCAAGTGAGGCGTATTATATGGA 1 98 1 AAGTGAGGCT 0.929632 -203 AATAAGCCAAAAGAGCGGTAAAAATTCACTA 3 75 1 AAGAGCGGTA 0.953116 -173 AAACGAAAAAAAGTGCGGTGAAAATTGGCTT 3 140 0 AAGTGCGGTA 0.992305 -108 TTTTGGGGATAAGTTCAGCATTGTAGCGAAA 3 203 0 AAGTTCAGCT 0.722327 -45 ACTCAACTAAAAGTGCGGTTAAAATTCGCAA 5 89 0 AAGTGCGGTA 0.992305 -49 ATTGTTACTCAAGTTCGGTTTCCCGAACTAT 9 31 0 AAGTTCGGTT 0.953722 -270 CTATTTTATAAAATGCGGCATTTTGTCGCAT 10 56 1 AAATGCGGCT 0.963683 -211 AAAAATAAAAAAATGCGACAAAATGCCGCAT 10 68 0 AAATGCGACA 0.762188 -199 GTTTTTTTAAAAGTGCGGTGAATTTAAGGAG 10 240 1 AAGTGCGGTA 0.992305 -27 ********* * Masking position 2 Map Score: 9.86912 Number of sites scoring better than the average of aligned sites = 1764 Number in coding regions = 1226 Number in noncoding regions = 538 Number of orfs with sites within 600 bp upstream = 343 Fraction of orfs with sites within 600 bp upstream = 0.0550916 Motif number 5 TGAGGCGTATTATATGGAAAAAACTTTAAC 1 111 1 TATATGGAAA 0.880545 -190 GATTTAAACGAATAATCAAAAAAATAAACT 1 163 0 AATAATCAAA 0.796177 -138 AAAGTGATTTTTTAATCAAATTAGCGTACA 1 202 1 TTTAATCAAA 0.894474 -99 TTAGCGTACATTTAATGAAAAATGAATGCT 1 222 1 TTTAATGAAA 0.869688 -79 CAAAAAATCCTATAATCAAACCACAACAAA 2 224 1 TATAATCAAA 0.917681 -77 ACAACAAAAAAATATGCAAACACAACATCA 2 246 1 AATATGCAAA 0.767376 -55 TAGATTTCATTATATTGAAACTCTTTTCAT 3 31 0 TATATTGAAA 0.917469 -217 GAAGAACAGGAATATTCAAAATAAGCCAAT 3 118 1 AATATTCAAA 0.832635 -130 AAGTATTTTTTATATCCAAAAGTGCTAATA 5 44 1 TATATCCAAA 0.83121 -94 GCCAGATGGATTGATTGAAAATCTTAGTAT 6 12 1 TTGATTGAAA 0.77341 -60 TTTCCCGAACTATATGCAAACACAACATCA 9 14 0 TATATGCAAA 0.904047 -287 GAGAGCAGCGTTTAACCAAATCGGTTTAAT 9 89 0 TTTAACCAAA 0.75212 -212 ACTAAAAAGGAATAATGAAATTTTGGAAAC 9 178 0 AATAATGAAA 0.753459 -123 ATATTATTTTTTGAATGAAATTTCGCTTAA 9 269 0 TTGAATGAAA 0.728216 -32 AATATTATTTTTTATTCAAATTTTTGAATG 10 22 0 TTTATTCAAA 0.917646 -245 TTTATTTTTATTGATGGAAAAATTTATAAA 10 90 1 TTGATGGAAA 0.693559 -177 ********** Masking position 4 Map Score: 16.6679 Number of sites scoring better than the average of aligned sites = 390 Number in coding regions = 287 Number in noncoding regions = 103 Number of orfs with sites within 600 bp upstream = 91 Fraction of orfs with sites within 600 bp upstream = 0.0146161 Motif number 6 TAATTGCACAAATCGCAACATTACATTCCC 2 172 1 AATCGCAACA 0.945827 -129 CCTATAATCAAACCACAACAAAAAAATATG 2 232 1 AACCACAACA 0.955414 -69 AAAAATATGCAAACACAACATCATACAATT 2 253 1 AAACACAACA 0.985844 -48 TCCCCAAAATAAAAACAACAGGAAACAAAC 3 225 1 AAAAACAACA 0.886064 -23 GCTATTTATAAAACGCCACAACCC 5 5 0 AAACGCCACA 0.979433 -133 CCCAATGACAAAACTCAACTAAAAGTGCGG 5 102 0 AAACTCAACT 0.885701 -36 AACTATATGCAAACACAACATCATAC 9 7 0 AAACACAACA 0.985844 -294 GGGATGAAAAAAACGCCACTCAATGAGAGC 9 113 0 AAACGCCACT 0.945752 -188 ********** Masking position 8 Map Score: 9.53525 Number of sites scoring better than the average of aligned sites = 111 Number in coding regions = 89 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 7 AAGTATTTTTTATAAAAAAGTTTATTTTTT 1 145 1 TATAAAAAAG 0.935736 -156 TTTACTCGTGTAAAAGAAAGTAGGCAAAGA 2 90 0 TAAAAGAAAG 0.883581 -211 TTTACACGAGTAAAAGAAAGTAGGTCGTTC 2 106 1 TAAAAGAAAG 0.883581 -195 GCCAATTCACAAAAAAAAATAATTGCACAA 2 153 1 AAAAAAAAAT 0.534796 -148 TTATCCTATGTAAAAAAATGAAAAGAGTTT 3 14 1 TAAAAAAATG 0.918441 -234 GGCTTGGAGAGAAAAAAACGAAAAAAAGTG 3 156 0 GAAAAAAACG 0.880209 -92 CACTTTTGGATATAAAAAATACTTATGACT 5 38 0 TATAAAAAAT 0.743517 -100 TAATATTAGAAATAAAAACGTTGCGAATTT 5 69 1 AATAAAAACG 0.709856 -69 AAATCGGGATGAAAAAAACGCCACTCAATG 9 118 0 GAAAAAAACG 0.880209 -183 TGCCGCATTTTATAAAATAGTAAAAATATT 10 46 0 TATAAAATAG 0.57136 -221 TCAATAAAAATAAAAAAATGCGACAAAATG 10 74 0 TAAAAAAATG 0.918441 -193 TGGAAAAATTTATAAAAAACTAAATTTTCA 10 104 1 TATAAAAAAC 0.629689 -163 AAAAATCAATTAAAAAAATATAAAAAACCA 10 142 0 TAAAAAAATA 0.47014 -125 TAATACAAAGTAAAAAAAATTTGTCTAGCC 10 185 0 TAAAAAAAAT 0.849137 -82 ACCGCACTTTTAAAAAAACGAACAGATTAT 10 229 0 TAAAAAAACG 0.958776 -38 ********** Masking position 5 Map Score: 11.7159 Number of sites scoring better than the average of aligned sites = 304 Number in coding regions = 194 Number in noncoding regions = 110 Number of orfs with sites within 600 bp upstream = 98 Fraction of orfs with sites within 600 bp upstream = 0.0157404 Motif number 8 TAAGCCAAAAGAGCGGTAAAAATTCACTAA 3 77 1 GAGCGGTAAA 0.970225 -171 ACGAAAAAAAGTGCGGTGAAAATTGGCTTA 3 139 0 GTGCGGTGAA 0.994006 -109 TCAACTAAAAGTGCGGTTAAAATTCGCAAC 5 88 0 GTGCGGTTAA 0.983818 -50 TTTGCATATAGTTCGGGAAACCGAACTTGA 9 24 1 GTTCGGGAAA 0.902458 -277 TTTTTTAAAAGTGCGGTGAATTTAAGGAGT 10 242 1 GTGCGGTGAA 0.994006 -25 ********** Masking position 9 Map Score: 5.21461 Number of sites scoring better than the average of aligned sites = 432 Number in coding regions = 237 Number in noncoding regions = 195 Number of orfs with sites within 600 bp upstream = 133 Fraction of orfs with sites within 600 bp upstream = 0.021362 Motif number 9 CGACTTAGCTCAGTAGGTAGAGCAACTGACT 1 64 0 CAGTAGGAGA 0.79694 -237 GTGTAAAAGAAAGTAGGCAAAGAAAACACGC 2 82 0 AAGTAGGAAA 0.83556 -219 TTACACAATTAAGGACAAAAA 2 290 1 AAGGACAAAA 0.80469 -11 ATAAAAACAACAGGAAACAAACACC 3 233 1 CAGGAAAAAA 0.960572 -15 ATTGGGAGAAAAGGAAAAATAA 5 126 1 AAGGAAAATA 0.712747 -12 AAAGTATCATCAGTAAGAAGAAAAACAGGAT 6 46 1 CAGTAAGAGA 0.862376 -26 AGAAGAAAAACAGGATAGAAA 6 61 1 CAGGATAAAA 0.793415 -11 CTAGTAAATGAAGGTAGTAGA 8 28 1 AAGGTAGAGA 0.626743 -11 TAATAATATACAGGAAGTAAATGAGTAACAA 9 62 0 CAGGAAGAAA 0.974996 -239 GGAAACAGGGCAGGAAATAACGATATAGTTA 9 153 0 CAGGAAAAAC 0.7935 -148 AAATAATATTAAGGAAGTAAA 9 290 1 AAGGAAGAAA 0.965782 -11 ACATAATACAAAGTAAAAAAAATTTGTCTAG 10 187 0 AAGTAAAAAA 0.835222 -80 CGGTGAATTTAAGGAGTGAAAA 10 255 1 AAGGAGTAAA 0.696318 -12 ******* *** Masking position 9 Map Score: 6.80215 Number of sites scoring better than the average of aligned sites = 237 Number in coding regions = 178 Number in noncoding regions = 59 Number of orfs with sites within 600 bp upstream = 62 Fraction of orfs with sites within 600 bp upstream = 0.00995824 Motif number 10 TAATCAGTAGGTCATCAGTTCGATTCCGAT 1 32 0 GTCATCAGTT 0.965571 -269 CAACTGACTTGTAATCAGTAGGTCATCAGT 1 43 0 GTAATCAGTA 0.931413 -258 ATGAAATCTAATCATCAGTCAATAAATAAG 3 51 1 ATCATCAGTC 0.948582 -197 AATAGCCTCAGTCATAAGTATTTTTTATAT 5 29 1 GTCATAAGTA 0.931408 -109 TTAGAAAAGTATCATCAGTAAGAAGAAAAA 6 41 1 ATCATCAGTA 0.969186 -31 ********** Masking position 5 Map Score: 1.34258 Number of sites scoring better than the average of aligned sites = 16 Number in coding regions = 13 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 11 TCACAATCAAAAAAGTGATTTTTTAATCAAAT 1 191 1 AAAGGATTTT 0.8348 -110 TCAATTTTCTTAACGGCAATTTGCTGAACTCG 2 20 0 TACGCAATTT 0.759819 -281 TGTTGTTGCGTAAAGTGATATTATGGGAATGT 2 194 0 TAAGGATATT 0.89038 -107 CCCTAAAAAATTTAGTGAATTTTTACCGCTCT 3 86 0 TTAGGAATTT 0.932329 -162 AATATTCAAAATAAGCCAATTTTCACCGCACT 3 128 1 AAAGCAATTT 0.671607 -120 AGTTCAGCATTGTAGCGAAATTTCGAGTCATT 3 191 0 TTAGGAAATT 0.845864 -57 TCATCTACAATAAAGGGAATTTATATTTTATA 7 24 1 TAAGGAATTT 0.971891 -60 AATTGCATCATTTCGAGAATTTATTATTTAAA 9 216 1 TTCGGAATTT 0.840961 -85 ACACCATTCCTGAAGTGATTTAAATAATAAAT 9 234 0 TAAGGATTTA 0.721546 -67 ATGGTGTAGATTAAGCGAAATTTCATTCAAAA 9 259 1 TAAGGAAATT 0.932329 -42 TTATATTTTTTTAATTGATTTTTTTGTTGTTT 10 149 1 TAATGATTTT 0.616386 -118 * *** ****** Masking position 8 Map Score: 4.2138 Number of sites scoring better than the average of aligned sites = 336 Number in coding regions = 268 Number in noncoding regions = 68 Number of orfs with sites within 600 bp upstream = 56 Fraction of orfs with sites within 600 bp upstream = 0.00899454 Motif number 12 ********** No masking Map Score: 4.21595e-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: 4.21595e-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 14 ********** No masking Map Score: 4.21595e-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