AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_hpyl.txt -z/home/amcguire/genomes/hpyl.fna -iphoB_hpyl_opreg_100.orf -g0.389 -x5 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 = 0.389 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 HP0166 235 response regulator (ompR) #2 HP0473 225 molybdenum ABC transporter, periplasmic molybdate-binding protein (modA) #3 HP0474 21 molybdenum ABC transporter, permease protein (modB) #4 HP1466 134 conserved hypothetical integral membrane protein Motif number 1 TAAAGTCTTATTTTTTAATGTTTTTAAACAATTC 1 24 0 TTTTTAATTT 0.984582 -212 CATTAATAACTATGATAATGTTTTGAATTTTTAT 1 95 1 TATATAATTT 0.949391 -141 TTGAATTTTTATTTTTAAGATATTTTCAAGGTAT 1 117 1 ATTTTAAATT 0.869205 -119 TCAAGGTATCTTTAATAATAAAATGCTAGAATTA 1 142 1 TTTATAAAAT 0.877842 -94 AACGATTAACTTTGTTAATGTTTTAGGGGACTAA 1 173 0 TTTTTAATTT 0.984582 -63 GATCGGTTATTTTTCTAAAAGTTTTAATTTTTTA 2 48 1 TTTCTAATTT 0.930158 -178 AATCTTCATCTTTGATAAAAAATTAAAACTTTTA 2 63 0 TTTATAAATT 0.976413 -163 TAAAAATTTGTATTTTAAAAGTTTGAGGCGGTTT 2 149 0 TATTTAATTT 0.970492 -77 TACCTATTTGTATCTTAAAAATTTGTATTTTAAA 2 164 0 TATTTAATTT 0.970492 -62 TACAAATAGGTATAATCACCAATTCCAATCATTT 2 186 1 TATATCAATT 0.743157 -40 AGAACTCCCTTTGATTAAATGATTGGAATTGGTG 2 202 0 TTGTTAAATT 0.951193 -24 CAATACTCTGTTTAATAAAGGATTAATTATTTTT 4 14 0 TTTATAAATT 0.976417 -121 AAACAGAGTATTGTTTAACCTTTTGTTTTATCAT 4 35 1 TTGTTAATTT 0.944885 -100 TTAAAACGACTATTTTAACACAATGATAAAACAA 4 57 0 TATTTAAAAT 0.866472 -78 CAAACAAAATTTTGTTAATAGATTTTACCTAATC 4 91 1 TTTTTAAATT 0.986412 -44 *** **** *** Masking position 8 Map Score: 25.3223 Number of sites scoring better than the average of aligned sites = 727 Number in coding regions = 546 Number in noncoding regions = 181 Number of orfs with sites within 600 bp upstream = 135 Fraction of orfs with sites within 600 bp upstream = 0.0216833 Motif number 2 AAATAAAGTCTTATTTTTTAATGTTTTTAA 1 31 0 TTATTTTTTA 0.92112 -205 AAATAAGACTTTATTTTTCAATATTCCATG 1 45 1 TTATTTTTCA 0.879723 -191 AATTTAAGGCTTTGTTTTCATGGAATATTG 1 63 0 TTTGTTTTCA 0.921498 -173 ATGTTTTGAATTTTTATTTTTAAGATATTT 1 112 1 TTTTTATTTT 0.910946 -124 TTCTAGCATTTTATTATTAAAGATACCTTG 1 143 0 TTATTATTAA 0.757403 -93 CTAAGATCGGTTATTTTTCTAAAAGTTTTA 2 44 1 TTATTTTTCT 0.892649 -182 TTTCTAAAAGTTTTAATTTTTTATCAAAGA 2 59 1 TTTTAATTTT 0.639681 -167 ATCCCACTTATTAGTATTTAACCAACATTT 2 106 0 TTAGTATTTA 0.917814 -120 TTTGAGGCGGTTTGTTTTGTGGGTGTATCC 2 132 0 TTTGTTTTGT 0.832719 -94 ATCTTAAAAATTTGTATTTTAAAAGTTTGA 2 157 0 TTTGTATTTT 0.935235 -69 ATTATACCTATTTGTATCTTAAAAATTTGT 2 172 0 TTTGTATCTT 0.678091 -54 AAAGGATTAATTATTTTTAAA 4 2 0 TTATTTTTAA 0.822726 -133 TGTTTAACCTTTTGTTTTATCATTGTGTTA 4 46 1 TTTGTTTTAT 0.894586 -89 TTAACAAAATTTTGTTTGTTAAAACGACTA 4 79 0 TTTGTTTGTT 0.75657 -56 TGAGAGAGAATTATATTTTA 4 125 1 TTATATTTTA 0.669619 -10 ********** Masking position 7 Map Score: 13.5155 Number of sites scoring better than the average of aligned sites = 1595 Number in coding regions = 1177 Number in noncoding regions = 418 Number of orfs with sites within 600 bp upstream = 241 Fraction of orfs with sites within 600 bp upstream = 0.0387086 Motif number 3 AAAACGATCAAAGGAATTGTTTAAAAACATT 1 7 1 ATCAAAGATT 0.980366 -229 AATATTGAAAAATAAAGTCTTATTTTTTAATGTTT 1 35 0 AATAAAGTAT 0.688717 -201 ATTCCATGAAAACAAAGCCTTAAATTTCCATTAAT 1 67 1 AACAAAGTAT 0.705831 -169 TCAAAACATTATCATAGTTATTAATGGAAATTTAA 1 86 0 ATCATAGATT 0.933339 -150 CTAAAACATTAACAAAGTTAATCGTTTTTAAAGTT 1 181 1 AACAAAGATT 0.971961 -55 TGCAGAAATCATTGAAGGAGTTAATTGAAGT 1 215 1 ATTGAAGGTT 0.690606 -21 TTCTTGTTGAATTAAAGTTACACCCTAAGATCGGT 2 20 1 ATTAAAGAAC 0.72928 -206 TTAATTTTTTATCAAAGATGAAGATTTTAGAGTGA 2 71 1 ATCAAAGGAT 0.937077 -155 GGAATTGGTGATTATACCTATTTGTATCTTAAAAA 2 177 0 ATTATACATT 0.701758 -49 CAATCATTTAATCAAAGGGAGTTCT 2 211 1 ATCAAAGATT 0.985255 -15 TTAATCCTTTATTAAACAGAGTATTGTTTAACCTT 4 22 1 ATTAAACATT 0.912016 -113 TAGTCGTTTTAACAAACAAAATTTTGTTAATAGAT 4 79 1 AACAAACATT 0.923248 -56 ******* * * * Masking position 6 Map Score: 8.54889 Number of sites scoring better than the average of aligned sites = 645 Number in coding regions = 560 Number in noncoding regions = 85 Number of orfs with sites within 600 bp upstream = 69 Fraction of orfs with sites within 600 bp upstream = 0.0110826 Motif number 4 AAAACGATCAAAGGAATTGT 1 1 1 AAAACGATCA 0.97195 -235 TGCAACTTTAAAAACGATTAACTTTGTTAA 1 189 0 AAAACGATTA 0.921672 -47 ATAAAAAATTAAAACTTTTAGAAAAATAAC 2 53 0 AAAACTTTTA 0.891349 -173 CTCTGTTTAATAAAGGATTAATTATTTTTA 4 13 0 TAAAGGATTA 0.806219 -122 TTTGTTTGTTAAAACGACTATTTTAACACA 4 69 0 AAAACGACTA 0.97195 -66 AGATTAGGTAAAATCTATTAACAAAATTTT 4 96 0 AAATCTATTA 0.891349 -39 ********** Masking position 3 Map Score: 3.82231 Number of sites scoring better than the average of aligned sites = 276 Number in coding regions = 235 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 5 ATAACCGATCTTAGGGTGTAACTTTAATTC 2 28 0 TTAGGGTGTA 0.981714 -198 GATGAAGATTTTAGAGTGAAAATGTTGGTT 2 87 1 TTAGAGTGAA 0.971993 -139 CGGTTTGTTTTGTGGGTGTATCCCACTTAT 2 125 0 TGTGGGTGTA 0.970474 -101 TTACCTAATCTGAGAGAGAATTATATTTTA 4 115 1 TGAGAGAGAA 0.955053 -20 ********** Masking position 1 Map Score: 0.566221 Number of sites scoring better than the average of aligned sites = 40 Number in coding regions = 38 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 6 ********** No masking Map Score: 1.45904e-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 7 ********** No masking Map Score: 1.45904e-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 8 ********** No masking Map Score: 1.45904e-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