AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00251_hinf_reg_100.orf -o00251_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 Purged sequences: HI1739.2 29 glutamate racemase (murI) Input sequences: #1 HI0161 215 glutathione reductase (gor) #2 HI0189 300 glutamate dehydrogenase (gdhA) #3 HI0222 109 GMP synthase (guaA) #4 HI0274 300 glutamyl-tRNA synthetase (gltX) #5 HI0429 111 glucosamine--fructose-6-phosphate aminotransferase (glmS) #6 HI0596 300 ornithine carbamoyltransferase (arcB) #7 HI0865 230 glutamine synthetase (glnA) #8 HI1205 214 conserved hypothetical protein #9 HI1206 86 colicin V production protein (cvpA) #10 HI1354 300 glutaminyl-tRNA synthetase (glnS) #11 HI1617 138 aspartate aminotransferase (aspC) #12 HI1741 260 guanosine-3',5'-bis(diphosphate) 3'- pyrophosphohydrolase (spoT) Motif number 1 GCCTAGTATGTAGAATGAAATAGCGTGATAGA 1 54 0 TAATGAAATA 0.363477 -162 TTATAGCATTCTTTATAAAAATTAGGCAGAAT 1 160 1 CTATAAAAAT 0.900952 -56 CGAAAATATGTTTTATGAAAAAACAAAATTAG 2 12 0 TTATGAAAAA 0.90724 -289 TAATGATATTTTCAATAAAAATATAGAGCAGA 2 73 0 TTATAAAAAT 0.937402 -228 ATCGTATTTATTAGATAAAAAATAAAAAACGA 2 120 0 TTATAAAAAA 0.960976 -181 AGTAAAGAAATTATCTAAAAAATATCGTATTT 2 143 0 TTCTAAAAAA 0.882944 -158 TTTAAATTTCCTTTATAAAAATGGTTGCAAGA 2 186 1 CTATAAAAAT 0.900952 -115 ACGAGGCGAATACAATAAAAATACAATACACA 2 252 1 TAATAAAAAT 0.769714 -49 CGCCCACCACTTCTCTAAAAAGTTTTCTTAAT 4 42 0 TTCTAAAAAG 0.637811 -259 TAAAAAGGTATTGACTGAAAATGCATTCTCCC 4 165 0 TTCTGAAAAT 0.645817 -136 TTAAACAAAATTTAATAAAAAGGTATTGACTG 4 180 0 TTATAAAAAG 0.851769 -121 TGTTTGACTTCTAAATAAAAAAGCGGATTTTA 4 230 0 CTATAAAAAA 0.937345 -71 ATAACCTATCTTCAATAAAATATTAGTCGTTA 4 275 0 TTATAAAATA 0.865562 -26 CACGCGTTTACACAATAAAAAACCCCTGCGCA 5 44 0 CAATAAAAAA 0.769542 -68 ATTATTAGAATTTAATAAAATAATCTAACTCT 6 114 0 TTATAAAATA 0.865553 -187 CTAAAAATCTCGCAATAAAATTCTACATACTG 6 147 1 CGATAAAATT 0.390651 -154 TATGTAACAATGCAATAAAAATTGCATCTTAT 7 30 0 TGATAAAAAT 0.801441 -201 TATTGCATTGTTACATAAAAAATGGCGCAATG 7 45 1 TTATAAAAAA 0.960976 -186 GAAAAATAAATTTCATGAAAAAATAGCATGGC 7 157 1 TTATGAAAAA 0.907283 -74 TTAAACTATTTTTACTAAAAATAGACTTAAAA 8 154 1 TTCTAAAAAT 0.821067 -61 TAAAAAATCTCTCAATGAAAAACGGCCGTTTA 9 65 0 CTATGAAAAA 0.856008 -22 TGTAAAAACTTGCCATAAAAAACCGCCACGAA 10 170 0 TGATAAAAAA 0.869068 -131 AATACTAGATTTAAATAAAAGATTGTAAAAAC 10 193 0 TTATAAAAGA 0.701863 -108 TTTCTCTCGTTAAAATAAAAAAATATTCGGCT 10 279 0 TAATAAAAAA 0.846071 -22 TCAAGAAAGATTTTATAAAAATTAACCACGCT 11 56 0 TTATAAAAAT 0.937341 -83 TAAAATCTTTCTTGATAAAATAAAATGACTGA 11 73 1 CTATAAAATA 0.79639 -66 ** ******** Masking position 6 Map Score: 30.8561 Number of sites scoring better than the average of aligned sites = 566 Number in coding regions = 323 Number in noncoding regions = 243 Number of orfs with sites within 600 bp upstream = 196 Fraction of orfs with sites within 600 bp upstream = 0.0314809 Motif number 2 GTAATTGGTTTTATGAATATTTTTTACTCTTTTG 1 120 0 TTATATTTTT 0.796274 -96 CCTAATTTTGTTTTTTCATAAAACA 2 2 1 CTTTGTTTTT 0.833242 -299 ATTTGTAATCTGCTCTATATTTTTATTGAAAATA 2 65 1 TGTTATTTTT 0.968361 -236 GGTTTTCTGTCGTTTTTTATTTTTTATCTAATAA 2 111 1 CGTTATTTTT 0.948718 -190 TGATGTTGTGTGTATTGTATTTTTATTGTATTCG 2 258 0 TGTTATTTTT 0.968361 -43 AAAGCGGATTTTATGCTTATTTTTACGACAATTA 4 209 0 TTCTATTTTT 0.858072 -92 TATTCTATTACTAAGTTTGTTTTTACATTTGCCA 5 74 0 CTTTGTTTTT 0.833242 -38 GAAAATATGTTTTAGTTTATTTTTGATGAAGAGG 6 37 0 TTTTATTTTT 0.962832 -264 AGGAAAAATTATACATGTATTTTTCTTTTTCTGC 7 109 1 ATTTATTTTT 0.908017 -122 TATTTTTTCATGAAATTTATTTTTCTTATTCTAG 7 148 0 TGTTATTTTT 0.968342 -83 AAATACAAACTTTATCGTATTTTTTGAAAAATTA 8 123 1 TTCTATTTTT 0.858072 -92 TTTAGTAAAAATAGTTTAATTTTTCAAAAAATAC 8 139 0 ATTAATTTTT 0.735383 -76 ATACGCTATTTTAAGTCTATTTTTAGTAAAAATA 8 160 0 TTTTATTTTT 0.962832 -55 GTATGATAAGTGCGGTCAATTTTTGAGGTGTTTT 8 190 1 TGTAATTTTT 0.896008 -25 CGTTTTCTTTTTGGCTTTATTTTTGTAGAATAGC 9 21 1 TTTTATTTTT 0.962832 -66 ATGCACAAAGTGCGGTAAGTTTTTTGAATGTTTA 10 116 0 TGTAGTTTTT 0.733299 -185 TGTATAGAATAGCCGAATATTTTTTTATTTTAAC 10 269 1 AGATATTTTT 0.637653 -32 AATATCAAAGCGTGGTTAATTTTTATAAAATCTT 11 48 1 CGTAATTTTT 0.838917 -91 CCGCGGTAAAATACCTTTATTTTTTACCGCACTT 12 19 0 ATTTATTTTT 0.908018 -242 ** * ******* Masking position 10 Map Score: 21.9703 Number of sites scoring better than the average of aligned sites = 287 Number in coding regions = 186 Number in noncoding regions = 101 Number of orfs with sites within 600 bp upstream = 87 Fraction of orfs with sites within 600 bp upstream = 0.0139737 Motif number 3 TTTGCTGTTTAAAGTGCGGTTGGTTTTTGC 3 37 1 AAAGTGCGGT 0.992837 -73 CCCCTCCTTGTAAGGGAGGTGCTCTCCCAA 4 96 1 TAAGGGAGGT 0.937134 -205 CCCACAACATTAAGGGCGATTAGCTCAGTT 4 124 0 TAAGGGCGAT 0.881256 -177 AGTTGCATTATAAGAGAGGTAAAATGAAAT 6 206 0 TAAGAGAGGT 0.905989 -95 TAGCGTATGATAAGTGCGGTCAATTTTTGA 8 186 1 TAAGTGCGGT 0.991189 -29 ACATCACATTAAAAAGCGGTATCGCCGTGA 10 28 1 AAAAAGCGGT 0.855305 -273 ATAAATGCACAAAGTGCGGTAAGTTTTTTG 10 124 0 AAAGTGCGGT 0.992837 -177 TATTCATCAAAAAGTGCGGTCATTTTTTAC 11 12 0 AAAGTGCGGT 0.992837 -127 TCTTTTAAAAGTGCGGTAAAAAATAAA 12 8 1 AAAGTGCGGT 0.992837 -253 ********** Masking position 3 Map Score: 17.997 Number of sites scoring better than the average of aligned sites = 1575 Number in coding regions = 1074 Number in noncoding regions = 501 Number of orfs with sites within 600 bp upstream = 325 Fraction of orfs with sites within 600 bp upstream = 0.0522004 Motif number 4 CCTGATGGTTTTCTGTCGTTTTTTATTTTTTAT 2 105 1 TTGCGTTTTT 0.950064 -196 TATCTAATAAATACGATATTTTTTAGATAATTT 2 135 1 ATGTATTTTT 0.769858 -166 AATTTAATCTTGCAACCATTTTTATAAAGGAAA 2 192 0 TGACATTTTT 0.568227 -109 CTGTCGATTGCGCAGGGGTTTTTTATTGTGTAA 5 36 1 CGGGGTTTTT 0.846114 -76 TAGAATTTTATTGCGAGATTTTTAGTATTATTA 6 139 0 TTGGATTTTT 0.914453 -162 AAATGAAATTTGTTGTCGTTTTTCAACTGGTAA 6 182 0 TGGCGTTTTT 0.939793 -119 GTGCAATTCATTGCGCCATTTTTTATGTAACAA 7 52 0 TTGCATTTTT 0.948302 -179 TTTTGAAAAATTAAACTATTTTTACTAAAAATA 8 144 1 TTATATTTTT 0.499888 -71 CGCACTTATCATACGCTATTTTAAGTCTATTTT 8 171 0 ATGTATTTTA 0.41969 -44 CGGTCAATTTTTGAGGTGTTTTT 8 202 1 TTGTGTTTTT 0.922213 -13 TGTAGAATAGCTCGGTCGTTTTAAACGGCCGTT 9 44 1 CTGCGTTTTA 0.713164 -43 CCGTTTTTCATTGAGAGATTTTTTA 9 72 1 TTGGATTTTT 0.914453 -15 TGATAGGAAATTTTGCTGTTTTTGCCTGCATTC 10 56 0 TTGTGTTTTT 0.922213 -245 ACGATAATTTCGTGGCGGTTTTTTATGGCAAGT 10 162 1 CGGGGTTTTT 0.846114 -139 CATCAAAAAGTGCGGTCATTTTTTACA 11 5 0 TGGCATTTTT 0.937691 -134 ATTAACCACGCTTTGATATTTTTAAATATTCAT 11 35 0 CTGTATTTTT 0.87356 -104 AGTTTTATACTTCAGTCATTTTATTTTATCAAG 11 83 0 TTGCATTTTA 0.798619 -56 TACTTACCCTAGGCGATATTTTTCAACGATAAG 12 147 1 AGGTATTTTT 0.732938 -114 ** * ******* Masking position 9 Map Score: 16.063 Number of sites scoring better than the average of aligned sites = 676 Number in coding regions = 514 Number in noncoding regions = 162 Number of orfs with sites within 600 bp upstream = 147 Fraction of orfs with sites within 600 bp upstream = 0.0236107 Motif number 5 GATTGTTCAATCTTCCTCACTGTAGATATGTG 1 12 0 TCTTCCTACG 0.667558 -204 GATTGAACAATCTTCCTCTTTTTCTATCACGC 1 32 1 TCTTCCTTTT 0.918216 -184 TATGAATATTTTTTACTCTTTTGAACAGATGA 1 111 0 TTTTACTTTT 0.717976 -105 TTTCTTTACTTTTTCCTTTTCTTTAAATTTCC 2 165 1 TTTTCCTTTT 0.976648 -136 AATGAATTTCCCTCTTTGTTGATGTTGT 2 283 0 TTTCCCTTTG 0.83363 -18 CTCTAAAAAGTTTTCTTAATTTTACTAAGTTT 4 30 0 TTTTCTTATT 0.835658 -271 AAGTTTTCCTTATTTATTCTATTAC 5 97 0 TTTTCCTATT 0.955634 -15 CAAATTTCATTTTACCTCTCTTATAATGCAAC 6 203 1 TTTACCTTCT 0.635084 -98 CATGTATAATTTTTCCTTTTCGACAAATGTAG 7 94 0 TTTTCCTTTG 0.971711 -137 ATACATGTATTTTTCTTTTTCTGCTATGACTA 7 119 1 TTTTCTTTTT 0.908028 -112 TGAAATTTATTTTTCTTATTCTAGTCATAGCA 7 140 0 TTTTCTTTTT 0.908028 -91 AGTTTGTATTTTTTCCTTACCGATGAATTTAT 8 102 0 TTTTCCTACG 0.882075 -113 TACGCAAACGTTTTCTTTTTGGCTTTATTTTT 9 13 1 TTTTCTTTTG 0.890217 -74 TGATAGGAAATTTTGCTGTTTTTGCCTGCATT 10 57 0 TTTTGCTTTT 0.790496 -244 AGCTTTTCCTTATGTATGTGTTGTG 11 124 0 TTTTCCTATT 0.955634 -15 ******* ** * Masking position 7 Map Score: 14.1966 Number of sites scoring better than the average of aligned sites = 330 Number in coding regions = 230 Number in noncoding regions = 100 Number of orfs with sites within 600 bp upstream = 116 Fraction of orfs with sites within 600 bp upstream = 0.0186315 Motif number 6 ATGTAATTGGTTTTATGAATATTTTTTACT 1 126 0 TTTTATGAAT 0.917659 -90 TCTGCCTAATTTTTATAAAGAATGCTATAA 1 160 0 TTTTATAAAG 0.762538 -56 CGAAAATATGTTTTATGAAAAAACAAAATT 2 14 0 TTTTATGAAA 0.716741 -287 TTGCAACCATTTTTATAAAGGAAATTTAAA 2 186 0 TTTTATAAAG 0.762538 -115 TTTTATTAAGTATAGATAGA 6 1 1 TTTTATTAAG 0.662562 -300 TTAGTTTATTTTTGATGAAGAGGAATGTGT 6 30 0 TTTGATGAAG 0.959151 -271 GAAAAATAAATTTCATGAAAAAATAGCATG 7 157 1 TTTCATGAAA 0.41087 -74 GAATACACCTTTTGATGAATAAAATAAATT 8 79 1 TTTGATGAAT 0.92825 -136 CGCTTTTTAATGTGATGTAGTGGAGGGAGG 10 16 0 TGTGATGTAG 0.467323 -285 GTGCGGTAAGTTTTTTGAATGTTTAGCTTA 10 111 0 TTTTTTGAAT 0.557534 -190 GACCGCACTTTTTGATGAATATTTAAAAAT 11 21 1 TTTGATGAAT 0.92825 -118 AGTCATTTTATTTTATCAAGAAAGATTTTA 11 73 0 TTTTATCAAG 0.729511 -66 GTATGTGTTGTGTGATGAATAGTTTTATAC 11 106 0 TGTGATGAAT 0.812462 -33 ********** Masking position 9 Map Score: 7.33027 Number of sites scoring better than the average of aligned sites = 344 Number in coding regions = 280 Number in noncoding regions = 64 Number of orfs with sites within 600 bp upstream = 59 Fraction of orfs with sites within 600 bp upstream = 0.00947639 Motif number 7 AAGAGTAAAAAATATTCATAAAACCAATTACAT 1 123 1 ATATCAAAAA 0.504879 -93 AAAATTAGGCAGAATACAAAAAAATTTTAGTTT 1 177 1 AAAACAAAAA 0.85259 -39 ATGTTTTATGAAAAAACAAAATTAGG 2 4 0 AAAACAAATT 0.615808 -297 TTTATTAGATAAAAAATAAAAAACGACAGAAAA 2 113 0 AAAATAAAAA 0.535206 -188 CAATAAAAATACAATACACACAACATCAACAAA 2 264 1 AAAACAACAA 0.952655 -37 TTTTTTATTTAGAAGTCAAACAAGTCGTAGTAG 4 240 1 AAATCAACAA 0.94556 -61 ATCTACTATTAGAAATCAAACAAATAACAATAA 6 81 1 AAATCAACAA 0.94556 -220 TACATTGGGGAATAAACATACATCATTCGAGAT 6 254 0 ATAACAACAT 0.780099 -47 GTCGAAAAGGAAAAATTATACATGTATTTTTCT 7 102 1 AAATTAACAT 0.749053 -129 AGATGGTTTGAAAAATCAGACATAGAATACACC 8 55 1 AAATCAACAT 0.937472 -160 CGGTAAGGAAAAAATACAAACTTTATCGTATTT 8 112 1 AAAACAACTT 0.847938 -103 GTATTTTTTGAAAAATTAAACTATTTTTACTAA 8 139 1 AAATTAACTA 0.526104 -76 TATTCATCACACAACACATACATAAGGAAAAGC 11 115 1 AAAACAACAT 0.94556 -24 * ** *** **** Masking position 8 Map Score: 6.50212 Number of sites scoring better than the average of aligned sites = 161 Number in coding regions = 123 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 8 AGGCTTCACATAAAATCATTTCAAACTAAT 1 82 1 TAAAATCATT 0.767886 -134 AAAAACGACAGAAAACCATCAGGTAATGAT 2 98 0 GAAAACCATC 0.929367 -203 AACAAAGAGGGAAATTCATT 2 291 1 GAAATTCATT 0.89382 -10 TATTTTCGTTTAAATTCATCTACTATTAGA 6 64 1 TAAATTCATC 0.931399 -237 AATGTAGGGTGCAATTCATTGCGCCATTTT 7 63 0 GCAATTCATT 0.826594 -168 GAGGTTAATAGAAATCCATCATCTAAGATG 8 30 1 GAAATCCATC 0.954768 -185 GTCTGATTTTTCAAACCATCTTAGATGATG 8 46 0 TCAAACCATC 0.824485 -169 ATGAATAAAATAAATTCATCGGTAAGGAAA 8 93 1 TAAATTCATC 0.931399 -122 ********** Masking position 4 Map Score: 3.62221 Number of sites scoring better than the average of aligned sites = 199 Number in coding regions = 176 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 9 GCTGTTTAAAGTGCGGTTGGTTTTTGCAAA 3 40 1 GTGCGGTTGG 0.960601 -70 TTGACCAAGCGGGCGATTAGC 4 2 0 GGGCGATTAG 0.934124 -299 ACAACATTAAGGGCGATTAGCTCAGTTGGG 4 121 0 GGGCGATTAG 0.934124 -180 ACGTTATAATGTGCGCTTATCTTAATAAGA 7 190 1 GTGCGCTTAT 0.876724 -41 CGTATGATAAGTGCGGTCAATTTTTGAGGT 8 189 1 GTGCGGTCAA 0.962567 -26 AATGCACAAAGTGCGGTAAGTTTTTTGAAT 10 121 0 GTGCGGTAAG 0.980079 -180 TCATCAAAAAGTGCGGTCATTTTTTACA 11 9 0 GTGCGGTCAT 0.962567 -130 TCTTTTAAAAGTGCGGTAAAAAATAAAGGT 12 11 1 GTGCGGTAAA 0.94326 -250 ********** Masking position 7 Map Score: 6.90827 Number of sites scoring better than the average of aligned sites = 931 Number in coding regions = 593 Number in noncoding regions = 338 Number of orfs with sites within 600 bp upstream = 244 Fraction of orfs with sites within 600 bp upstream = 0.0391905 Motif number 10 ATCACTACGAAAATATGTTTTATGAAAAAA 2 21 0 AAATATGTTT 0.84296 -280 GATTTACTAGAAATATGATTTGTAATCTGC 2 48 1 AAATATGATT 0.871637 -253 TTTTTATTGAAAATATCATTACCTGATGGT 2 84 1 AAATATCATT 0.871637 -217 TTTATCTAATAAATACGATATTTTTTAGAT 2 133 1 AAATACGATA 0.70906 -168 CCTTTTCTTTAAATTTCCTTTATAAAAATG 2 179 1 AAATTTCCTT 0.623038 -122 CATTTTCAGTCAATACCTTTTTATTAAATT 4 174 1 CAATACCTTT 0.602487 -127 AATAAGCATAAAATCCGCTTTTTTATTTAG 4 222 1 AAATCCGCTT 0.689778 -79 ATTTAAACGAAAATATGTTTTAGTTTATTT 6 49 0 AAATATGTTT 0.84296 -252 AAACGACAACAAATTTCATTTTACCTCTCT 6 194 1 AAATTTCATT 0.627729 -107 ATTTTTCAAAAAATACGATAAAGTTTGTAT 8 125 0 AAATACGATA 0.70906 -90 ACCCGCGGTAAAATACCTTTATTTTTTACC 12 25 0 AAATACCTTT 0.898132 -236 ATCTGCGGGCAAATACCCTTGAATAATTCG 12 214 0 AAATACCCTT 0.914247 -47 ********** Masking position 3 Map Score: 3.78435 Number of sites scoring better than the average of aligned sites = 239 Number in coding regions = 198 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467 Motif number 11 ********** No masking Map Score: 2.29749e-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 12 ********** No masking Map Score: 2.29749e-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: 2.29749e-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