AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00272_hinf_reg_300.orf -o00272_hinf_300.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 HI0078 102 cysteinyl-tRNA synthetase (cysS) #2 HI0086 300 cystathionine gamma-synthase (metB) #3 HI0122 274 cystathionine beta-lyase (metC) #4 HI0288 34 L-serine deaminase (sdaA) #5 HI0289 222 serine transporter (sdaC) #6 HI0291 74 H. influenzae predicted coding region HI0291 #7 HI0292 76 mercuric ion scavenger protein (merP) #8 HI0604 300 adenylate cyclase (cyaA) #9 HI0605 73 glycerol-3-phosphate dehydrogenase (NAD+) (gpsA) #10 HI1102 152 cysteine synthetase, putative (cysZ) #11 HI1103 98 cysteine synthetase (cysK) #12 HI1615 160 phosphoribosylaminoimidazole carboxylase, catalytic subunit (purE) #13 HI1616 69 phosphoribosylaminoimidazole carboxylase, ATPase subunit (purK) #14 HI1617 138 aspartate aminotransferase (aspC) Motif number 1 AATCGAGGTAAAAGTGCTATAAAAGTGCGG 1 52 1 AAAGTGCTAT 0.861424 -51 AAGTGCTATAAAAGTGCGGTTTGTTTTTAT 1 63 1 AAAGTGCGGT 0.998054 -40 ATCTTTAGCTAAAGTGCGGTCAATTTTTCT 3 11 0 AAAGTGCGGT 0.998054 -264 TTTTTTATAAAAAGTGCGGTAATTTTCAGC 5 64 0 AAAGTGCGGT 0.998054 -159 GCAAATTCTAAAATTGTGATCAAGTTAAAA 5 95 0 AAATTGTGAT 0.867684 -128 ATTTTTCGAAAAATTGTGATTTATGTCACA 8 211 1 AAATTGTGAT 0.867684 -90 AAAATACTTCAAAGTGTGGAATTTTAAAGG 10 86 1 AAAGTGTGGA 0.947039 -67 TTTTAAAGGAAAAGTGCGGTCTGTTTTAAG 10 107 1 AAAGTGCGGT 0.998054 -46 TTTTTAATCAAAAGTGCGGTACTATAAATA 11 42 1 AAAGTGCGGT 0.998054 -57 ATTCTTATAAAAATTGTGCTTAGGATAAAA 12 21 1 AAATTGTGCT 0.79367 -140 CCGCACTTTAAAAGTGCGGTCAGATCTAAA 13 18 0 AAAGTGCGGT 0.998054 -52 CCGCACTTTTAAAGTGCGGTTGTTTTTTTC 13 29 1 AAAGTGCGGT 0.998054 -41 TATTCATCAAAAAGTGCGGTCATTTTTTAC 14 12 0 AAAGTGCGGT 0.998054 -127 TAAAAATATCAAAGCGTGGTTAATTTTTAT 14 44 1 AAAGCGTGGT 0.963639 -95 ********** Masking position 3 Map Score: 44.6975 Number of sites scoring better than the average of aligned sites = 1371 Number in coding regions = 884 Number in noncoding regions = 487 Number of orfs with sites within 600 bp upstream = 318 Fraction of orfs with sites within 600 bp upstream = 0.0510761 Motif number 2 ATGAAATAAAAACAAACCGCACTTTTATAGCA 1 66 0 AACACCGCAC 0.996361 -37 AGAAAAATTGACCGCACTTTAGCTAAA 3 6 1 AATACCGCAC 0.986787 -269 TTGTCGCTGAAAATTACCGCACTTTTTATAAA 5 59 1 AAAACCGCAC 0.994209 -164 ACTAGGTACTATCCTACCACTCTTAGGTAAAA 8 143 1 ATCACCACTC 0.853353 -158 CTTTTCCTTTAAAATTCCACACTTTGAAGTAT 10 89 0 AAATCCACAC 0.865111 -64 ATATGCTTAAAACAGACCGCACTTTTCCTTTA 10 110 0 AACACCGCAC 0.996361 -43 TGGTTTATTTATAGTACCGCACTTTTGATTAA 11 45 0 ATAACCGCAC 0.988894 -54 ACATCTTTAGATCTGACCGCACTTTTAAAGTG 13 13 1 ATCACCGCAC 0.993007 -57 TTTACGAAAAAAACAACCGCACTTTAAAAGTG 13 32 0 AAAACCGCAC 0.994209 -38 TGTAAAAAATGACCGCACTTTTTGATGA 14 7 1 AAAACCGCAC 0.994209 -132 ATTTTATAAAAATTAACCACGCTTTGATATTT 14 47 0 AATACCACGC 0.819373 -92 AAAACTATTCATCACACAACACATACATAAGG 14 110 1 ATCACAACAC 0.766686 -29 *** ******* Masking position 1 Map Score: 26.2077 Number of sites scoring better than the average of aligned sites = 901 Number in coding regions = 589 Number in noncoding regions = 312 Number of orfs with sites within 600 bp upstream = 228 Fraction of orfs with sites within 600 bp upstream = 0.0366206 Motif number 3 TGCTATAAAAGTGCGGTTTGTTTTTATTTCA 1 66 1 GTGCGGTTGT 0.987201 -37 GCTGTTATTGGTGCGCATTTTACGGAAATTC 2 105 1 GTGCGCATTT 0.809053 -196 TTTAGCTAAAGTGCGGTCAATTTTTCT 3 7 0 GTGCGGTCAT 0.95007 -268 TTTACTTCATCTGCGGTATTAGGCAATGGAA 3 185 0 CTGCGGTATA 0.725363 -90 GTAAAATCAGGTGCGGATAGGAATTGAAACC 3 211 1 GTGCGGATGG 0.881606 -64 TTTATAAAAAGTGCGGTAATTTTCAGCGACA 5 60 0 GTGCGGTATT 0.98703 -163 AATTTAGTTGGAGCGGATTTTGCTCTACAAA 5 165 1 GAGCGGATTT 0.822027 -58 ATACTTCAAAGTGTGGAATTTTAAAGGAAAA 10 89 1 GTGTGGAATT 0.698831 -64 TAAAGGAAAAGTGCGGTCTGTTTTAAGCATA 10 110 1 GTGCGGTCGT 0.99003 -43 TTAATCAAAAGTGCGGTACTATAAATAAACC 11 45 1 GTGCGGTATA 0.964356 -54 CACTTTAAAAGTGCGGTCAGATCTAAAGATG 13 14 0 GTGCGGTCGA 0.972455 -56 CACTTTTAAAGTGCGGTTGTTTTTTTCGTAA 13 32 1 GTGCGGTTTT 0.989446 -38 TCATCAAAAAGTGCGGTCATTTTTTACA 14 8 0 GTGCGGTCTT 0.991783 -131 ******** ** Masking position 5 Map Score: 20.666 Number of sites scoring better than the average of aligned sites = 956 Number in coding regions = 665 Number in noncoding regions = 291 Number of orfs with sites within 600 bp upstream = 220 Fraction of orfs with sites within 600 bp upstream = 0.0353357 Motif number 4 CAATTACAGATTTAAAAAAATTGTCTAACC 2 146 1 TTTAAAAAAA 0.889008 -155 TGTCTAACCGTTTAAAAAAAGTTCATTTTG 2 167 1 TTTAAAAAAA 0.889008 -134 AAAAGTAGAAATTAGAAAATTACATAAAAT 2 232 0 ATTAGAAAAT 0.67379 -69 ATTATCTCTGATGATAAAAAAAGCCACCTA 3 53 1 ATGATAAAAA 0.895521 -222 TTATCAATTATTTATAAAAAGCGACCTTAG 3 80 0 TTTATAAAAA 0.947653 -195 TTATAAATAATTGATAAAATTAAAGCTCGT 3 93 1 TTGATAAAAT 0.921227 -182 TACCGCACTTTTTATAAAAAAATTTTAACT 5 73 1 TTTATAAAAA 0.947653 -150 AACGCAAAGTATTATAAAATACCTTACTCA 8 30 0 ATTATAAAAT 0.841207 -271 ATACTTTGCGTTGATAAGAAAAATATCAAG 8 48 1 TTGATAAGAA 0.856317 -253 CGCACTTTTGATTAAAAAAATAGTTATTTG 11 30 0 ATTAAAAAAA 0.770294 -69 AAGCACAATTTTTATAAGAATAGGTCAAAT 12 12 0 TTTATAAGAA 0.867293 -149 AATTAGAAAATTGAGAAAATAGC 12 148 1 TTGAGAAAAT 0.818007 -13 CAAGAAAGATTTTATAAAAATTAACCACGC 14 57 0 TTTATAAAAA 0.947653 -82 AAAATCTTTCTTGATAAAATAAAATGACTG 14 74 1 TTGATAAAAT 0.921227 -65 ********** Masking position 6 Map Score: 16.0342 Number of sites scoring better than the average of aligned sites = 409 Number in coding regions = 245 Number in noncoding regions = 164 Number of orfs with sites within 600 bp upstream = 128 Fraction of orfs with sites within 600 bp upstream = 0.0205589 Motif number 5 ACTTTTATCACTTTTTCCTTTGTGCCAAAA 2 256 1 CTTTTTCCTT 0.868615 -45 TTATTTGTTGTTTTCTCTTTATTTTTTCCA 3 160 1 TTTTCTCTTT 0.685336 -115 TTTCTCTTTATTTTTTCCATTGCCTAATAC 3 171 1 TTTTTTCCAT 0.816872 -104 TTTTACTCCTTGTTAGTTGTT 6 64 0 TTTACTCCTT 0.905845 -11 TTTTACTCCTTGTTAGTTGTT 7 66 0 TTTACTCCTT 0.905845 -11 CAAAATGACTTTTTTACCTAAGAGTGGTAG 8 156 0 TTTTTACCTA 0.828276 -145 TATTTTCCTGTGGTTGATAG 9 1 1 TATTTTCCTG 0.732075 -73 TTTTATTCCTTACGCGCGATA 10 2 1 TTTATTCCTT 0.929088 -151 TTGAAGTATTTTTTCACCTACTGAAATATG 10 68 0 TTTTCACCTA 0.77982 -85 TTTTCTTTCCTTTCAATAAAAA 10 141 0 TTCTTTCCTT 0.868615 -12 AATATTTTCCTTTCGTTGGACT 11 87 0 TATTTTCCTT 0.929088 -12 AAGGATAAAATTTTATCCTAAGCACAATTT 12 31 0 TTTTATCCTA 0.873348 -130 TAGGATAAAATTTTATCCTTAAAGTTGCAA 12 41 1 TTTTATCCTT 0.923606 -120 GTTGCAATGGTATTTTCCTATAAAAGCCAT 12 64 1 TATTTTCCTA 0.881975 -97 GTGCGGTTGTTTTTTTCGTAAATTTAACGA 13 42 1 TTTTTTCGTA 0.714884 -28 ********** Masking position 7 Map Score: 10.9205 Number of sites scoring better than the average of aligned sites = 427 Number in coding regions = 276 Number in noncoding regions = 151 Number of orfs with sites within 600 bp upstream = 166 Fraction of orfs with sites within 600 bp upstream = 0.0266624 Motif number 6 AACCGTTTAAAAAAAGTTCATTTTGTTCAAA 2 172 1 AAAAAGTCAT 0.751084 -129 AAATTTCTCAAAATTCGTTAA 4 24 0 AAATTTTCAA 0.866005 -11 CTTTTTATAAAAAAATTTTAACTTGATCACA 5 80 1 AAAAATTTAA 0.77153 -143 TAAATTACTTAAATTTGTCAATTTGTAGAGC 5 186 0 AAATTTTCAA 0.866005 -37 AAAAATTTCAATTCAGATTGG 6 1 1 AAAAATTCAA 0.956369 -74 CGTTGATAAGAAAAATATCAAGCTATCCACT 8 56 1 AAAAATTCAA 0.956369 -245 TTTATTGCGTAAATAGCTTAATTCTGCCGAT 8 112 0 AAATAGTTAA 0.813001 -189 GTAGGTGAAAAAATACTTCAAAGTGTGGAAT 10 77 1 AAATACTCAA 0.889072 -76 CTACAGTTATAAATAGATCAAATAACTATTT 11 12 1 AAATAGTCAA 0.965777 -87 ATTTTTATAAGAATAGGTCAAATT 12 4 0 GAATAGTCAA 0.841633 -157 ATGAATATTTAAAAATATCAAAGCGTGGTTA 14 35 1 AAAAATTCAA 0.956369 -104 ****** **** Masking position 3 Map Score: 8.8426 Number of sites scoring better than the average of aligned sites = 157 Number in coding regions = 117 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 45 Fraction of orfs with sites within 600 bp upstream = 0.00722775 Motif number 7 AAAATTAAGGGTTGTATTATTCCACAATCG 1 27 1 GTTGTATTAT 0.93706 -76 TTTAGCTAAAGATGGTTTATTCTAAATTAT 3 28 1 GATGGTTTAT 0.909242 -247 AGAATTATTTGTTGTTTTCTCTTTATTTTT 3 156 1 GTTGTTTTCT 0.963264 -119 CTCCTTGTTAGTTGTTTTATTGATGAATGC 6 50 0 GTTGTTTTAT 0.986247 -25 CTCCTTGTTAGTTGTTTTATTGATGGTTAA 7 52 0 GTTGTTTTAT 0.986247 -25 CTTCGTTAATGTTGGTTTATTTATAGTACC 11 59 0 GTTGGTTTAT 0.979698 -40 TTAAAGTGCGGTTGTTTTTTTCGTAAATTT 13 37 1 GTTGTTTTTT 0.946501 -33 ********** Masking position 7 Map Score: 9.32116 Number of sites scoring better than the average of aligned sites = 40 Number in coding regions = 30 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 8 GACGTCAGAATTATTTGTTGTTTTCTCTTTAT 3 150 1 TTTTTGTTGT 0.975681 -125 TCGCACCGATTTTTTTGTCGCTGAAAATTACC 5 45 1 TTTTTGTCGT 0.95784 -178 TTTTACTCCTTGTTAGTTGTTTTATTGATGA 6 54 0 TTTTAGTTGT 0.95464 -21 TTTTACTCCTTGTTAGTTGTTTTATTGATGG 7 56 0 TTTTAGTTGT 0.95464 -21 ATATTTTCTATTATTAGTGGATAGCTTGATAT 8 70 0 TTTTAGTGGT 0.866235 -231 AAAAGTCATTTTGATTGTTGATAGGTAAAATT 8 173 1 TTATTGTTGT 0.863476 -128 TTGTTCGCCAATTTTTGTTGTTCTGGTAGGGA 8 273 1 ATTTTGTTGT 0.95464 -28 AATATTTCTCGTTAAATTTACGA 13 57 0 ATTTTCTCGT 0.784017 -13 TTTTTATAAAATCTTTCTTGATAAAATAAAAT 14 67 1 ATTTTCTTGT 0.865054 -72 ** ******* * Masking position 5 Map Score: 6.02689 Number of sites scoring better than the average of aligned sites = 107 Number in coding regions = 79 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 9 TAAGCTCGTAAAATGAAATAAAAACAAACCG 1 79 0 AAATAAATAA 0.91329 -24 TTGTTCAAATAAATCACAGAAAATGATGGAA 2 194 1 AAATACAGAA 0.94791 -107 AGAAATTAGAAAATTACATAAAATTTCATTT 2 225 0 AAATACATAA 0.943809 -76 CCTATAAGTTAATTTAAATAAGGAAATAT 3 256 1 AATTAAATAA 0.597106 -19 TTGCGTATAAAAATAAATGAAA 5 2 0 AAATAATGAA 0.886291 -221 TCCAAAGCATAAATTACTTAAATTTGTCAAT 5 195 0 AAATACTTAA 0.919825 -28 TTTATTGCGTAAATAGCTTAATTCTGCCGAT 8 112 0 AAATGCTTAA 0.705243 -189 ATTTTTATTGAAAGGAAAGAAAA 10 140 1 AAAGAAAGAA 0.704123 -13 AGTTATAAATAGATCAAATAACTATTTTTTT 11 16 1 AGATAAATAA 0.687165 -83 TGATAAAATAAAATGACTGAAGTATAAAACT 14 85 1 AAATACTGAA 0.925538 -54 **** ****** Masking position 10 Map Score: 2.60313 Number of sites scoring better than the average of aligned sites = 318 Number in coding regions = 244 Number in noncoding regions = 74 Number of orfs with sites within 600 bp upstream = 70 Fraction of orfs with sites within 600 bp upstream = 0.0112432 Motif number 10 TTATAAATAATTGATAAAATTAAAGCTCGT 3 93 1 TTGATAAAAT 0.703956 -182 AATTAACTTATAGGGCAAAAATAACTATGG 3 240 0 TAGGGCAAAA 0.891293 -35 GAGAATCTCAAAGAGCAAATTCTAAAATTG 5 109 0 AAGAGCAAAT 0.775868 -114 TGTCAATTTGTAGAGCAAAATCCGCTCCAA 5 172 0 TAGAGCAAAA 0.870906 -51 ACATAAGGTTAAGGTCAAGAAGTTTTTT 7 9 0 AAGGTCAAGA 0.293836 -68 CTACCACTCTTAGGTAAAAAAGTCATTTTG 8 156 1 TAGGTAAAAA 0.849217 -145 TGATTGTTGATAGGTAAAATTTATAGTATT 8 184 1 TAGGTAAAAT 0.908043 -117 TATCTAGTAAAAGAGGAAATAAGTATAGAT 9 44 0 AAGAGGAAAT 0.550506 -30 CCTCTTTTACTAGATAAATTGTAGAT 9 58 1 TAGATAAATT 0.463705 -16 CATATTTCAGTAGGTGAAAAAATACTTCAA 10 68 1 TAGGTGAAAA 0.761294 -85 CAGTTATAAATAGATCAAATAACTATTTTT 11 15 1 TAGATCAAAT 0.928594 -84 TTTATAAGAATAGGTCAAATT 12 2 0 TAGGTCAAAT 0.940493 -159 AATTAGAAAATTGAGAAAATAGC 12 148 1 TTGAGAAAAT 0.683824 -13 AAAATCTTTCTTGATAAAATAAAATGACTG 14 74 1 TTGATAAAAT 0.703956 -65 ********** Masking position 7 Map Score: 6.62588 Number of sites scoring better than the average of aligned sites = 381 Number in coding regions = 280 Number in noncoding regions = 101 Number of orfs with sites within 600 bp upstream = 101 Fraction of orfs with sites within 600 bp upstream = 0.0162223 Motif number 11 TTCCCTCTAAAAAATTAAGGGTTGTATTAT 1 17 1 AAAATTAAGG 0.713477 -86 TTAAGCTCGTAAAATGAAATAAAAACAAAC 1 81 0 AAAATGAAAT 0.856706 -22 TTATTTGAACAAAATGAACTTTTTTTAAAC 2 176 0 AAAATGAACT 0.88502 -125 AAATGATGGAAAAATGAAATTTTATGTAAT 2 214 1 AAAATGAAAT 0.856706 -87 TAGAAATTAGAAAATTACATAAAATTTCAT 2 227 0 AAAATTACAT 0.788981 -74 AGAAAAATTGACCGCACTTTAGCT 3 5 1 AAATTGACCG 0.740118 -270 AATAATTGATAAAATTAAAGCTCGTTAGCA 3 98 1 AAAATTAAAG 0.871962 -177 AAATTCGTTAAAAATTAAAGGCGA 4 5 0 AAAATTAAAG 0.871962 -30 ATTGCGTATAAAAATAAATGAAA 5 4 0 AAAATAAATG 0.511551 -219 TTTGTCGCTGAAAATTACCGCACTTTTTAT 5 58 1 AAAATTACCG 0.923743 -165 ATCAACAATCAAAATGACTTTTTTACCTAA 8 165 0 AAAATGACTT 0.837371 -136 TGTAAAAAATGACCGCACTTTTTGA 14 6 1 AAAATGACCG 0.963979 -133 TTGATAAAATAAAATGACTGAAGTATAAAA 14 84 1 AAAATGACTG 0.928353 -55 ********** Masking position 7 Map Score: 12.1458 Number of sites scoring better than the average of aligned sites = 395 Number in coding regions = 305 Number in noncoding regions = 90 Number of orfs with sites within 600 bp upstream = 80 Fraction of orfs with sites within 600 bp upstream = 0.0128493 Motif number 12 CGTAAAATGAAATAAAAACAAACCGCACTT 1 74 0 AATAAAAACA 0.716735 -29 ACCGATTGCGTATAAAAATAAATGAAA 5 8 0 TATAAAAATA 0.946505 -215 CCGCACTTTTTATAAAAAAATTTTAACTTG 5 75 1 TATAAAAAAA 0.850317 -148 CGCATTCATCAATAAAACAACTAACAAGGA 6 49 1 AATAAAACAA 0.740949 -26 TTTAACCATCAATAAAACAACTAACAAGGA 7 51 1 AATAAAACAA 0.740949 -26 TTGCGTTGATAAGAAAAATATCAAGCTATC 8 53 1 AAGAAAAATA 0.679402 -248 ATTCTGCCGATATAAAAATCTATATTTTCT 8 93 0 TATAAAAATC 0.752329 -208 CTATTTACGCAATAAAACTAGGTACTATCC 8 127 1 AATAAAACTA 0.899082 -174 CTTTCCTTTCAATAAAAATATGCTTAAAAC 10 129 0 AATAAAAATA 0.930728 -24 CACTTTTGATTAAAAAAATAGTTATTTGAT 11 28 0 TAAAAAAATA 0.653141 -71 GACCTATTCTTATAAAAATTGTGCTTAGGA 12 16 1 TATAAAAATT 0.783267 -145 TTGATGAATATTTAAAAATATCAAAGCGTG 14 32 1 TTTAAAAATA 0.635241 -107 AGAAAGATTTTATAAAAATTAACCACGCTT 14 55 0 TATAAAAATT 0.783267 -84 ATGACTGAAGTATAAAACTATTCATCACAC 14 97 1 TATAAAACTA 0.921463 -42 ********** Masking position 5 Map Score: 10.9961 Number of sites scoring better than the average of aligned sites = 301 Number in coding regions = 182 Number in noncoding regions = 119 Number of orfs with sites within 600 bp upstream = 107 Fraction of orfs with sites within 600 bp upstream = 0.017186 Motif number 13 ********** No masking Map Score: 3.19987e-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: 3.19987e-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 15 ********** No masking Map Score: 3.19987e-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