AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00272_hinf_reg_100.orf -o00272_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 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 HI0604 300 adenylate cyclase (cyaA) #7 HI0605 73 glycerol-3-phosphate dehydrogenase (NAD+) (gpsA) #8 HI1102 152 cysteine synthetase, putative (cysZ) #9 HI1103 98 cysteine synthetase (cysK) #10 HI1617 138 aspartate aminotransferase (aspC) Motif number 1 CCGCACTTTTATAGCACTTTTACCTCGATT 1 52 0 ATAGCACTTT 0.911358 -51 ATAAAAACAAACCGCACTTTTATAGCACTT 1 63 0 ACCGCACTTT 0.998105 -40 AGAAAAATTGACCGCACTTTAGCTAAAGAT 3 11 1 ACCGCACTTT 0.998105 -264 GCTGAAAATTACCGCACTTTTTATAAAAAA 5 64 1 ACCGCACTTT 0.998105 -159 TTTTAACTTGATCACAATTTTAGAATTTGC 5 95 1 ATCACAATTT 0.880849 -128 TGTGACATAAATCACAATTTTTCGAAAAAT 6 211 0 ATCACAATTT 0.880849 -90 CCTTTAAAATTCCACACTTTGAAGTATTTT 8 86 0 TCCACACTTT 0.96096 -67 CTTAAAACAGACCGCACTTTTCCTTTAAAA 8 107 0 ACCGCACTTT 0.998105 -46 TATTTATAGTACCGCACTTTTGATTAAAAA 9 42 0 ACCGCACTTT 0.998105 -57 GTAAAAAATGACCGCACTTTTTGATGAATA 10 12 1 ACCGCACTTT 0.998105 -127 ATAAAAATTAACCACGCTTTGATATTTTTA 10 44 0 ACCACGCTTT 0.973318 -95 ********** Masking position 8 Map Score: 32.4922 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 ACGGTTAGACAATTTTTTTAAATCTGTAATT 2 147 0 AATTTTTTAA 0.842196 -154 AACAAAATGAACTTTTTTTAAACGGTTAGAC 2 168 0 ACTTTTTTAA 0.796704 -133 AAATTTTATGTAATTTTCTAATTTCTACTTT 2 230 1 TATTTTCTAA 0.765926 -71 TTCTAATTTCTACTTTTATCACTTTTTCCTT 2 245 1 TATTTTATCA 0.9295 -56 AAAATGCTAAACGTTTTTTAACACGTAAA 2 282 1 ACTTTTTTAA 0.796704 -19 CTTAGGTGGCTTTTTTTATCATCAGAGATAA 3 54 0 TTTTTTATCA 0.899355 -221 ACCTAAGGTCGCTTTTTATAAATAATTGATA 3 78 1 GCTTTTATAA 0.885217 -197 TAACGAGCTTTAATTTTATCAATTATTTATA 3 94 0 TATTTTATCA 0.9295 -181 TGTTTTCTCTTTATTTTTTCCATTGCCTAAT 3 168 1 TTTTTTTTCC 0.809959 -107 TTTCATTTATTTTTATACGCAATCGGTG 5 8 1 TATTTTATAC 0.911363 -215 CAAGTTAAAATTTTTTTATAAAAAGTGCGGT 5 74 0 TTTTTTATAA 0.921731 -149 ATTGAGTAAGGTATTTTATAATACTTTGCGT 6 28 1 GTTTTTATAA 0.876797 -273 CAATCAAAATGACTTTTTTACCTAAGAGTGG 6 159 0 GATTTTTTAC 0.833591 -142 ACACTTTGAAGTATTTTTTCACCTACTGAAA 8 72 0 GTTTTTTTCA 0.813207 -81 ATCAAATAACTATTTTTTTAATCAAAAGTGC 9 28 1 TATTTTTTAA 0.933355 -71 AAAAGTGCGGTCATTTTTTACA 10 2 0 TCTTTTTTAC 0.858865 -137 AAGCGTGGTTAATTTTTATAAAATCTTTCTT 10 55 1 AATTTTATAA 0.868791 -84 TTCAGTCATTTTATTTTATCAAGAAAGATTT 10 75 0 TTTTTTATCA 0.899353 -64 GTGTGATGAATAGTTTTATACTTCAGTCATT 10 96 0 TATTTTATAC 0.911363 -43 ** ******** Masking position 6 Map Score: 18.8144 Number of sites scoring better than the average of aligned sites = 535 Number in coding regions = 356 Number in noncoding regions = 179 Number of orfs with sites within 600 bp upstream = 154 Fraction of orfs with sites within 600 bp upstream = 0.024735 Motif number 3 TGCTATAAAAGTGCGGTTTGTTTTTATTTCA 1 66 1 GTGCGGTTGT 0.990426 -37 GCTGTTATTGGTGCGCATTTTACGGAAATTC 2 105 1 GTGCGCATTT 0.909127 -196 TTTAGCTAAAGTGCGGTCAATTTTTCT 3 7 0 GTGCGGTAAT 0.946766 -268 TTTACTTCATCTGCGGTATTAGGCAATGGAA 3 185 0 CTGCGGTTTA 0.825074 -90 GTAAAATCAGGTGCGGATAGGAATTGAAACC 3 211 1 GTGCGGAAGG 0.906839 -64 TTTATAAAAAGTGCGGTAATTTTCAGCGACA 5 60 0 GTGCGGTATT 0.990024 -163 AATTTAGTTGGAGCGGATTTTGCTCTACAAA 5 165 1 GAGCGGATTT 0.91586 -58 ATACTTCAAAGTGTGGAATTTTAAAGGAAAA 8 89 1 GTGTGGATTT 0.870968 -64 TAAAGGAAAAGTGCGGTCTGTTTTAAGCATA 8 110 1 GTGCGGTTGT 0.990426 -43 TTAATCAAAAGTGCGGTACTATAAATAAACC 9 45 1 GTGCGGTCTA 0.925527 -54 TCATCAAAAAGTGCGGTCATTTTTTACA 10 8 0 GTGCGGTATT 0.990024 -131 ******* *** Masking position 5 Map Score: 14.0199 Number of sites scoring better than the average of aligned sites = 866 Number in coding regions = 588 Number in noncoding regions = 278 Number of orfs with sites within 600 bp upstream = 216 Fraction of orfs with sites within 600 bp upstream = 0.0346932 Motif number 4 TTTGTTTTCCCTCTAAAAAATTAAGGGT 1 7 1 TTCCCTTAAA 0.531095 -96 TGCGGTTTGTTTTTATTTCATTTTACGAGCTT 1 77 1 TTTTATTATT 0.795142 -26 TATTCCCGCATTCGCTGTTATTGGTGCGCATT 2 92 1 TTCGCTTATT 0.811484 -209 TTTTCCATCATTTTCTGTGATTTATTTGAACA 2 195 0 TTTTCTTATT 0.930293 -106 AAAAATGAAATTTTATGTAATTTTCTAATTTC 2 223 1 TTTTATTATT 0.795142 -78 TTATTTGTTGTTTTCTCTTTATTTTTTCCATT 3 160 1 TTTTCTTTAT 0.826321 -115 TTTCATTTATTTTTATACGCAA 5 1 1 TTTCATTTTT 0.845665 -222 CTCTTTGAGATTCTCTATTTATTGGCATAACA 5 124 1 TTCTCTTTAT 0.650407 -99 AAAATCTATATTTTCTATTATTAGTGGATAGC 6 77 0 TTTTCTTATT 0.930293 -224 TATTTTCCTGTGGTTGATAGGTTAC 7 4 1 TTTCCTTGTT 0.914299 -70 TCTATACTTATTTCCTCTTTTACTAGATAAAT 7 45 1 TTTCCTTTTA 0.824105 -29 AGACCGCACTTTTCCTTTAAAATTCCACACTT 8 97 0 TTTCCTTAAA 0.743263 -56 TTTTCTTTCCTTTCAATAAAAATATGC 8 136 0 TTTCCTTAAT 0.920939 -17 AAAATAGTTATTTGATCTATTTATAACTGTAG 9 12 0 TTTGATTTTT 0.708545 -87 AATATTTTCCTTTCGTTGGACTTCGTT 9 82 0 TTTCCTTGTT 0.914299 -17 TTAACCACGCTTTGATATTTTTAAATATTCAT 10 35 0 TTTGATTTTT 0.708545 -104 ****** * *** Masking position 6 Map Score: 10.9146 Number of sites scoring better than the average of aligned sites = 717 Number in coding regions = 503 Number in noncoding regions = 214 Number of orfs with sites within 600 bp upstream = 201 Fraction of orfs with sites within 600 bp upstream = 0.032284 Motif number 5 GTGGAATAATACAACCCTTAATTTTTTAGAGGGAA 1 17 0 AAACCTAATT 0.76099 -86 ACGGAAATTCAGATAACTGTCAATTACAGATTTAA 2 126 1 AATACTTCTT 0.746737 -175 AGAAATTAGAAAATTACATAAAATTTCATTTTTCC 2 221 0 AATTCAAATT 0.682116 -80 CCTTTGTGCCAAAATGCTAAACGTTTTTTAACACG 2 272 1 AAATCTAATT 0.938524 -29 AAAACAACAAATAATTCTGACGTCTACACAGAATC 3 139 0 AAATCTACCT 0.473086 -136 TATAGGGCAAAAATAACTATGGTTTCAATTCCTAT 3 227 0 AATACTTGTT 0.746675 -48 AAATTTCTCAAAATTCGTTAAAAAT 4 20 0 AATTCTAATT 0.938125 -15 ACTTTTTATAAAAAAATTTTAACTTGATCACAATT 5 79 1 AAAATTTATT 0.48992 -144 TTGGCATAACATAATACTCAAATTTAGTTGGAGCG 5 145 1 AAATCTAATT 0.938163 -78 TCCAAAGCATAAATTACTTAAATTTGTCAATTTGT 5 191 0 AATTCTAATT 0.920109 -32 AAGGTATTTTATAATACTTTGCGTTGATAAGAAAA 6 35 1 AAATCTTGTT 0.767634 -266 CTGCCGATATAAAAATCTATATTTTCTATTATTAG 6 85 0 AAAACTTATT 0.900136 -216 TTTATTGCGTAAATAGCTTAATTCTGCCGATATAA 6 108 0 AATACTAACT 0.749033 -193 AATTTTTCGAAAAATACTATAAATTTTACCTATCA 6 191 0 AAATCTTATT 0.922471 -110 AAAATGTGACATAAATCACAATTTTTCGAAAAATA 6 210 0 AAAACAAATT 0.658491 -91 GGTTACCGAAAGATATCTATACTTATTTCCTCTTT 7 30 1 AATACTTATA 0.453925 -44 TAAATAGATCAAATAACTATTTTTTTAATCAAAAG 9 21 1 AATACTTTTT 0.512784 -78 CCACGCTTTGATATTTTTAAATATTCATCAAAAAG 10 28 0 AATTTTAATT 0.571723 -111 * *** ** ** ** Masking position 3 Map Score: 7.69622 Number of sites scoring better than the average of aligned sites = 558 Number in coding regions = 429 Number in noncoding regions = 129 Number of orfs with sites within 600 bp upstream = 106 Fraction of orfs with sites within 600 bp upstream = 0.0170254 Motif number 6 TGTTTTTATTTCATTTTACGAGCTTAAAA 1 84 1 TATTCGGTAA 0.92694 -19 AACACGCCACGAATTGGAGCGGGAAACGAGGCTCGA 2 10 1 CATTAGGAAA 0.981402 -291 CAGATAACTGTCAATTACAGATTTAAAAAAATTGTCT 2 135 1 TATTAGTAAA 0.663011 -166 TTATTTAAATTAACTTATAGGGCAAAAATAACTATGG 3 240 0 TATTAGGAAA 0.957482 -35 AAAAGTGCGGTAATTTTCAGCGACAAAAAAATCGGTG 5 48 0 TATTAGGAAA 0.957482 -175 TTAAATTTGTCAATTTGTAGAGCAAAATCCGCTCCAA 5 172 0 CATTAGGAAA 0.981402 -51 AGGATAGTACCTAGTTTTATTGCGTAAATAGCTTAAT 6 121 0 CATTATGTAA 0.861704 -180 GAACAATTTACCACTTAGGGAGTATAAATGCAAAAAA 6 242 0 CATTGGGTAA 0.917291 -59 ATCTACAATTTATCTAGTAAAAGAGGAAATAA 7 52 0 CATTCTGAAA 0.882689 -22 GCACTCTCGCCGAACTATCGCGCGTAAGGAATAAAA 8 10 0 CACTCGGTAA 0.861114 -143 * * ** ** * *** Masking position 6 Map Score: 4.54818 Number of sites scoring better than the average of aligned sites = 164 Number in coding regions = 132 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 7 CGAGGTAAAAGTGCTATAAAAGTGCGGTTT 1 55 1 GTGCTATAAA 0.983936 -48 TTTACGTGTTAAAAAACGTTTAGCA 2 286 0 GTGTTAAAAA 0.811214 -15 TCAACGCAAAGTATTATAAAATACCTTACT 6 32 0 GTATTATAAA 0.909267 -269 TTTTCGAAAAATACTATAAATTTTACCTAT 6 193 0 ATACTATAAA 0.793691 -108 GCAAAAAAATGTGACATAAATCACAATTTT 6 220 0 GTGACATAAA 0.783167 -81 TTCGGCGAGAGTGCTATAAATGGTGCTAAT 8 33 1 GTGCTATAAA 0.983936 -120 CAAAAGTGCGGTACTATAAATAAACCAACA 9 50 1 GTACTATAAA 0.967382 -49 ********** Masking position 6 Map Score: 4.87747 Number of sites scoring better than the average of aligned sites = 58 Number in coding regions = 49 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 8 TAAACGGTTAGACAATTTTTTTAAATCTGT 2 151 0 GACAATTTTT 0.828126 -150 TTCTACTTTTATCACTTTTTCCTTTGTGCC 2 252 1 ATCACTTTTT 0.94258 -49 CTAAAGTGCGGTCAATTTTTCT 3 3 0 GTCAATTTTT 0.974309 -272 GCCACCTAAGGTCGCTTTTTATAAATAATT 3 75 1 GTCGCTTTTT 0.8973 -200 CTTTAATTTTATCAATTATTTATAAAAAGC 3 88 0 ATCAATTATT 0.732599 -187 ACTTAAATTTGTCAATTTGTAGAGCAAAAT 5 181 0 GTCAATTTGT 0.866854 -42 CTTACTCAATATCACTTATTAAGGAAT 6 8 0 ATCACTTATT 0.786232 -293 AACAATCAAAATGACTTTTTTACCTAAGAG 6 162 0 ATGACTTTTT 0.657188 -139 TGTGATTTATGTCACATTTTTTTGCATTTA 6 225 1 GTCACATTTT 0.854968 -76 TAAATTGTTCGCCAATTTTTGTTGTTCTGG 6 269 1 GCCAATTTTT 0.877178 -32 AAAAAGTGCGGTCATTTTTTACA 10 4 0 GTCATTTTTT 0.887306 -135 TCAAAGCGTGGTTAATTTTTATAAAATCTT 10 52 1 GTTAATTTTT 0.749261 -87 ********** Masking position 7 Map Score: 9.53094 Number of sites scoring better than the average of aligned sites = 489 Number in coding regions = 390 Number in noncoding regions = 99 Number of orfs with sites within 600 bp upstream = 95 Fraction of orfs with sites within 600 bp upstream = 0.0152586 Motif number 9 AAAATCAGGTGCGGATAGGAATTGAAACCA 3 213 1 GCGGATAGGA 0.962038 -62 AATACTTTGCGTTGATAAGAAAAATATCAA 6 47 1 GTTGATAAGA 0.908975 -254 TCTATTATTAGTGGATAGCTTGATATTTTT 6 66 0 GTGGATAGCT 0.958149 -235 CATTTTGATTGTTGATAGGTAAAATTTATA 6 179 1 GTTGATAGGT 0.986785 -122 TTTTCCTGTGGTTGATAGGTTACCGAAAGA 7 13 1 GTTGATAGGT 0.986785 -61 ********** Masking position 5 Map Score: 1.82191 Number of sites scoring better than the average of aligned sites = 15 Number in coding regions = 12 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 10 ********** 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 11 ********** 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 12 ********** 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