AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i02020_hinf_reg_100.orf -o02020_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 HI0220 114 arcB; aerobic respiration control sensor protein arcB homolog #2 HI0266 82 conserved hypothetical protein #3 HI0267 41 nitrate/nitrite sensor protein (narQ) #4 HI0726 205 nitrate/nitrite response regulator protein (narP) #5 HI0837 53 response regulator (cpxR) #6 HI0839 116 conserved hypothetical protein #7 HI0884 191 aerobic respiration control protein ARCA (arcA) #8 HI1379 94 phosphate regulon transcriptional regulatory protein (phoB) #9 HI1382 90 phosphate ABC transporter, permease protein (pstC) #10 HI1383 300 phosphate ABC transporter, periplasmic-binding protein (pstS) #11 HI1708 62 transcriptional regulatory protein (ygiX) #12 HI1709 114 conserved hypothetical protein Motif number 1 GAAATTTAGAAAAGTGCGGTAAAATTT 3 8 0 AAAGTGCGGT 0.999013 -34 TTATCTTAAAAAAGAGCGGTAAAAAATTAT 4 17 1 AAAGAGCGGT 0.993032 -189 AAAAATAGAAAAAGTGCGGTAGAAAAATAG 4 47 0 AAAGTGCGGT 0.999013 -159 TCTTGCTGAAAAAGTGCGGTTATAATTTGC 6 81 1 AAAGTGCGGT 0.999013 -36 TAACAATAAAAAAGTGCGGTGATTTTTTAC 7 105 0 AAAGTGCGGT 0.999013 -87 TTAAAAAGTAAAAGTTTGGTGAGAATGTAT 8 29 1 AAAGTTTGGT 0.896648 -66 TTATGGCATAAAAGTGAAGTGAGAAATAAT 8 57 0 AAAGTGAAGT 0.896648 -38 GGTTTTGTATAAAGTGCGGTATAAAATAAA 9 17 0 AAAGTGCGGT 0.999013 -74 TAACATTAATAAAGTGCGGTTATCTTAAAT 9 54 1 AAAGTGCGGT 0.999013 -37 TTTTGTTTATAAAGTGCGGTCAATTTTTT 11 44 1 AAAGTGCGGT 0.999013 -19 ********** Masking position 3 Map Score: 42.0316 Number of sites scoring better than the average of aligned sites = 1115 Number in coding regions = 700 Number in noncoding regions = 415 Number of orfs with sites within 600 bp upstream = 285 Fraction of orfs with sites within 600 bp upstream = 0.0457758 Motif number 2 AAATTTTACCGCACTTTTCTAAAT 3 3 1 ATTACCGCAC 0.996351 -39 AATAGATAATTTTTTACCGCTCTTTTTTAAGA 4 20 0 TTTACCGCTC 0.978565 -186 ATTATCTATTTTTCTACCGCACTTTTTCTATT 4 42 1 TTCACCGCAC 0.992883 -164 TCTTTTTATTTTCACCACACTACAATAAGA 5 9 1 TTTACCACAC 0.962356 -45 TTGCCGCAAATTATAACCGCACTTTTTCAGCA 6 84 0 TATACCGCAC 0.992322 -33 CTTTGAAAAATTTGCCGCAAATTATAACCG 6 97 0 ATTGCCGCAA 0.891971 -20 ATCAGGTAAAAAATCACCGCACTTTTTTATTG 7 100 1 AATACCGCAC 0.990889 -92 ATCTCTTTATTTTATACCGCACTTTATACAAA 9 12 1 TTAACCGCAC 0.980824 -79 AAATTATTTAAGATAACCGCACTTTATTAATG 9 57 0 AATACCGCAC 0.990889 -34 AATTTGCTGTTGTCCGCCGCCCGAACCGATGG 10 240 0 TTCGCCGCCC 0.917806 -61 AAAAAATTGACCGCACTTTATAAACA 11 47 0 ATTACCGCAC 0.996351 -16 * ** ******* Masking position 7 Map Score: 22.8102 Number of sites scoring better than the average of aligned sites = 1281 Number in coding regions = 844 Number in noncoding regions = 437 Number of orfs with sites within 600 bp upstream = 278 Fraction of orfs with sites within 600 bp upstream = 0.0446515 Motif number 3 GTTTTTCATTTCTTACGCATA 1 2 1 TTTTTCATTT 0.804361 -113 AACAATCTCGTTTACTTTATGGATATAATA 1 41 1 TTTACTTTAT 0.84323 -74 GCATATAGGCTTTATTATATCCATAAAGTA 1 53 0 TTTATTATAT 0.803247 -62 TATGCACAGGTTTTTTTTATAACGATAATA 1 78 1 TTTTTTTTAT 0.898152 -37 TATTTCTTATCTTAAAAAAGAG 4 3 1 TTTCTTATCT 0.72193 -203 CTACCGCACTTTTTCTATTTTTATCCATCA 4 55 1 TTTTCTATTT 0.842202 -151 TAAATCAAATTTTTTTCTATTCTAGATTGG 4 117 1 TTTTTTCTAT 0.771927 -89 AATTTCTCCTTTAGTGGTTAGA 4 194 0 TTTCTCCTTT 0.812326 -12 ATAAGCCAAATTTTTTTTATTTTTAACATT 6 11 0 TTTTTTTTAT 0.898152 -106 ACCTAAATAATTTCTTTTTTCTTGCTGAAA 6 62 1 TTTCTTTTTT 0.942512 -55 TTTACCTGATTTTCCTTTTTGTGATCTAAA 7 80 0 TTTCCTTTTT 0.936062 -112 TCACCAAACTTTTACTTTTTAATAAGAGAA 8 21 0 TTTACTTTTT 0.84323 -74 AATCTCTTTATTTTATACCGCACTTT 9 7 1 TTTATTTTAT 0.85762 -84 AATAAGATTTTTTTTCATTTTATGCATAAA 10 72 0 TTTTTCATTT 0.804361 -229 CTGGAGCGTCTTTCCCTTATCCAATTTATG 10 156 1 TTTCCCTTAT 0.909672 -145 TCCCAGTTTCTTTCTCATATAAAGATGCCC 10 192 0 TTTCTCATAT 0.884309 -109 AACGTTTCCTTTTTAAGTTAGTTA 12 101 0 TTTCCTTTTT 0.936062 -14 ********** Masking position 3 Map Score: 18.3232 Number of sites scoring better than the average of aligned sites = 629 Number in coding regions = 405 Number in noncoding regions = 224 Number of orfs with sites within 600 bp upstream = 198 Fraction of orfs with sites within 600 bp upstream = 0.0318021 Motif number 4 TCTCGTTTACTTTATGGATATAATAAAGCCTAT 1 46 1 TTTTGGTAAA 0.978072 -69 CTAAAACATTATTATCGTTATAAAAAAAACCTG 1 84 0 ATTTCGTAAA 0.797623 -31 TATGCTATCAATTTTGGGTAGAATAACGAACAG 2 39 1 ATTTGGTAAA 0.959697 -44 GGTAGGTTTATTGATGGATAAAAATAGAAAAAG 4 63 0 TTGTGGTAAA 0.895327 -143 ATAGAATTGAATTCTTTATAAAATGTTATGCTT 4 148 1 ATTTTTTAAA 0.632816 -58 AATTTCTCCTTTAGTGGTTAGAAGTCCACTTTA 4 183 0 TTATGGTAAA 0.950808 -23 TACAATAAGAATAATTGGTAAAAGGAATCTCCA 5 31 1 ATATTGTAAA 0.861165 -23 TGATACCCGATTATTTGGTAGAACCTAAATAAT 6 40 1 TTATTGTAAA 0.923265 -77 TAATTTCTTTTTTCTTGCTGAAAAAGTGCGGTT 6 69 1 TTTTTGTGAA 0.817593 -48 ACCGCACTTTTTTATTGTTACAATAATGTTGCA 7 115 1 TTTTTGTAAA 0.966441 -77 CTTCATTTGATTTATGGCATAAAAGTGAAGTGA 8 65 0 TTTTGGATAA 0.537451 -30 ATTTGTTATGTTTATGCATAAAATGAAAAAAAA 10 62 1 TTTTGCTAAA 0.803708 -239 ACAACAGCAAATTATTGCAAAAACGGTTGATTT 10 259 1 ATTTTGAAAA 0.718177 -42 TAGCTCGCTGTTTTTGTTTATAAAGTGCGGTCA 11 33 1 TTTTGTTAAA 0.842993 -30 TTATTAAGATTTATTTGTTTTAATACACACATC 12 48 1 TTATTGTTAA 0.693144 -67 *** *** ** ** Masking position 12 Map Score: 12.623 Number of sites scoring better than the average of aligned sites = 394 Number in coding regions = 290 Number in noncoding regions = 104 Number of orfs with sites within 600 bp upstream = 109 Fraction of orfs with sites within 600 bp upstream = 0.0175072 Motif number 5 TATTTCTTATCTTAAAAAAGAGCGGTAA 4 9 1 ATCTTAAAAA 0.970425 -197 CAATAAACCTACCTCAAATAGTAAGTTTTT 4 83 1 ACCTCAAATA 0.827421 -123 AATTTGATTTATCTCAAAAACTTACTATTT 4 98 0 ATCTCAAAAA 0.96446 -108 TTAGAAGTCCACTTTAAAAAGCATAACATT 4 169 0 ACTTTAAAAA 0.671728 -37 AATGTTAAAAATAAAAAAAAT 6 2 1 ATGTTAAAAA 0.809837 -115 ATTTGGTAGAACCTAAATAATTTCTTTTTT 6 52 1 ACCTAAATAA 0.77355 -65 TATGATTTAGATCACAAAAAGGAAAATCAG 7 75 1 ATCACAAAAA 0.775196 -117 AAGTGCGGTTATCTTAAATAATTTTGGAAA 9 65 1 ATCTTAAATA 0.890861 -26 TCGCTACGCAATCTAAATAACACTCAAGGA 10 30 1 ATCTAAATAA 0.827518 -271 AAACAAATAAATCTTAATAAAAGATTAAGA 12 38 0 ATCTTAATAA 0.929088 -77 GAAATTAACTAACTTAAAAAGGAAACGTT 12 96 1 AACTTAAAAA 0.854977 -19 ********** Masking position 6 Map Score: 7.75345 Number of sites scoring better than the average of aligned sites = 224 Number in coding regions = 163 Number in noncoding regions = 61 Number of orfs with sites within 600 bp upstream = 52 Fraction of orfs with sites within 600 bp upstream = 0.00835207 Motif number 6 TATTATCGTTATAAAAAAAACCTGTGCATA 1 78 0 ATAAAAAAAA 0.76999 -37 AATTGATAGCATACGCCTACAATAATTTTA 2 22 0 ATACGCCTAC 0.596836 -61 TTATCCATCAATAAACCTACCTCAAATAGT 4 75 1 ATAAACCTAC 0.760655 -131 AGTTTTTGAGATAAATCAAATTTTTTTCTA 4 106 1 ATAAATCAAA 0.841211 -100 GTCCACTTTAAAAAGCATAACATTTTATAA 4 163 0 AAAAGCATAA 0.730676 -43 CCACACTACAATAAGAATAATTGGTAAAAG 5 25 1 ATAAGAATAA 0.803123 -29 AATGTTAAAAATAAAAAAAATTTGGCTTAT 6 11 1 ATAAAAAAAA 0.76999 -106 ATCGGGTATCATAAGCCAAATTTTTTTTAT 6 21 0 ATAAGCCAAA 0.958575 -96 CTTTGATAGCATACGCCAAAATAAGTATAA 7 163 1 ATACGCCAAA 0.870412 -29 ATACGCCAAAATAAGTATAAGGATGGAAA 7 173 1 ATAAGTATAA 0.841561 -19 TCTCTTATTAAAAAGTAAAAGTTTGGTGAG 8 22 1 AAAAGTAAAA 0.567603 -73 CTTTTATGCCATAAATCAAATGAAGGAGTA 8 73 1 ATAAATCAAA 0.841211 -22 CATTTTATGCATAAACATAACAAATTCTCC 10 57 0 ATAAACATAA 0.900087 -244 ACCGCACTTTATAAACAAAAACAGCGAGCT 11 34 0 ATAAACAAAA 0.922266 -29 ********** Masking position 3 Map Score: 10.6367 Number of sites scoring better than the average of aligned sites = 587 Number in coding regions = 469 Number in noncoding regions = 118 Number of orfs with sites within 600 bp upstream = 105 Fraction of orfs with sites within 600 bp upstream = 0.0168648 Motif number 7 TATAACGATAATAATGTTTTAGGAGATTTG 1 95 1 ATAATGTTTA 0.868121 -20 TACGCCTACAATAATTTTAGAGGAAACCTT 2 10 0 ATAATTTTGA 0.928826 -73 AGAAAAATAGATAATTTTTTACCGCTCTTTT 4 26 0 ATAATTTTTA 0.954204 -180 GATAAATCAAATTTTTTTCTATTCTAGATTG 4 115 1 ATTTTTTTTA 0.755907 -91 ATGATACCCGATTATTTGGTAGAACCTAAAT 6 39 1 ATTATTTGTA 0.876283 -78 AAGTGCGGTTATAATTTGCGGCAAATTTTTC 6 92 1 ATAATTTGGG 0.751703 -25 TCGAGCATCTATATTTTTATACTCAATTCT 7 10 0 ATATTTTTTA 0.86995 -182 TATTGTTACAATAATGTTGCACAGATAGAAT 7 127 1 ATAATGTTCA 0.738934 -65 GTTATCTTAAATAATTTTGGAAAATACTT 9 72 1 ATAATTTTGA 0.928826 -19 CACAATTATTTTCTACACTTCGCTA 10 5 1 ATTATTTTTA 0.906067 -296 ACACTCAAGGAGAATTTGTTATGTTTATGCA 10 49 1 AGAATTTGTA 0.707016 -252 ACGTAATAAGATTTTTTTTCATTTTATGCAT 10 75 0 ATTTTTTTCA 0.571104 -226 CGTTTTTGCAATAATTTGCTGTTGTCCGCCG 10 253 0 ATAATTTGTG 0.828581 -48 ******** ** Masking position 1 Map Score: 8.2207 Number of sites scoring better than the average of aligned sites = 367 Number in coding regions = 287 Number in noncoding regions = 80 Number of orfs with sites within 600 bp upstream = 73 Fraction of orfs with sites within 600 bp upstream = 0.011725 Motif number 8 TTGTAGGCGTATGCTATCAATTTTGGGTAG 2 30 1 ATGCTATCAA 0.974778 -53 GATGCTCGAAATTCTATCACAAAGAAATTT 7 32 1 ATTCTATCAC 0.936708 -160 CAAAGCTATCATTCTATCTGTGCAACATTA 7 138 0 ATTCTATCTG 0.892267 -54 ATTTTGGCGTATGCTATCAAAGCTATCATT 7 155 0 ATGCTATCAA 0.974778 -37 AGCACCAGTGATGCTATTAGCTTGAGCAAA 10 128 0 ATGCTATTAG 0.921624 -173 ********** Masking position 5 Map Score: 1.0984 Number of sites scoring better than the average of aligned sites = 20 Number in coding regions = 18 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 9 ********** No masking Map Score: -4.59421e-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 10 ********** No masking Map Score: -4.59421e-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: -4.59421e-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