AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/alignace/lib/ORF_hinf.txt -z/skink1/amcguire/genomes/hinf.fna -inarP_hinf_opreg_300.orf -g0.38 -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 = 0.38 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 HI0007 300 formate dehydrogenase, beta subunit (fdxH) #2 HI0340 82 conserved hypothetical protein #3 HI0341 84 conserved hypothetical protein #4 HI0342 205 ferredoxin-type protein (napF) #5 HI0343 180 napD protein (napD) #6 HI0345 300 ferredoxin-type protein (napG) #7 HI0936 108 cytochrome C-type biogenesis #8 HI0937 200 extragenic suppressor (suhB) #9 HI1068 43 nitrite reductase, cytochrome C-type protein (nrfB) #10 HI1069 161 nitrite reductase, cytochrome C552 (nrfA) #11 HI1074 264 conserved hypothetical protein #12 HI1076 300 cytochrome D ubiquinol oxidase, subunit I (cydA) #13 HI1089 248 heme exporter ATP-binding protein A (ccmA) #14 HI1091 57 heme exporter protein C (ccmC) #15 HI1092 41 heme exporter protein D (ccmD) #16 HI1095 138 thiol:disulfide interchange protein (dsbE) Motif number 1 TTCCACTTTTACCGCACATTTTTTGAAGTC 6 215 0 ACCGCACATT 0.992896 -86 GTAAAAATCAACCGCACTTTATTTTCTCCC 6 264 1 ACCGCACTTT 0.998516 -37 CCAATTTTCCACCGCACTTTAACCATAAAT 8 19 1 ACCGCACTTT 0.998516 -182 TGAAAAATGCACCGCACTTTTTAGTGCAAA 9 12 1 ACCGCACTTT 0.998516 -32 CATTTTTTTAACCGCACTTT 11 255 1 ACCGCACTTT 0.998516 -10 GAGAAAAACCACCGCACTTTTATACGATGA 14 17 0 ACCGCACTTT 0.998516 -41 TTTTTACCGCACTTTTTCATTAACT 16 124 0 ACCGCACTTT 0.998516 -15 ********** Masking position 6 Map Score: 28.3035 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 CCTCCCCAACTTTTTCAATATTTACCAAGAATGTTTTGTATTCTGGT 1 258 0 TTTTTTTATT 0.944865 -43 ATTATACCAATTTTTCTCGTATAATAGGGCAAATTTTTTCCAAGGTT 2 15 0 TTTTTATATT 0.683748 -68 ATTGCTATGCTGTTTTGTTTTAATCCCTTGCAAAATTCATTAAACCT 4 37 1 TGTTTTATTT 0.595839 -169 TTTGTTTTAGATCATTCATTGTTATTGCATTCACGGGGCAG 5 150 0 TTTTATTATT 0.883132 -31 TGCGGTTGATTTTTACATGGTTTTTACGCAGCCTTTTCCACTTTTAC 6 233 0 TTTTATTTTT 0.944865 -68 AAGGTGCTATTTTTAATTTTATTAATGAAACATACTTGATTAGCGAC 7 37 1 TTTTAATATT 0.488059 -72 AAAACAGTGGTTTTTATAGGTTTTCAGAAAAACTTTGCGATACAGAT 8 85 0 TTTTTTTTTG 0.883508 -116 TAAAAACCACTGTTTTATGATTTTCAACTAGTTATTTTGGCAAATCT 8 116 1 TGTTTTTTTT 0.92117 -85 AATATACCTCTTTTTGAGTATTTTAAAAGATAAGCTTGATCAAGCTC 10 69 1 TTTTTTTTTT 0.974915 -93 CAAATTTACCTTTTTTTTCTTTATTGATGGTGCATTTCGCGCTAGCC 11 65 0 TTTTTTTTTT 0.974915 -200 TAATGAACCCTTTTTAACTTTTCTCATTTATCTTTTTCTCAACAACA 11 158 1 TTTTTTTTTT 0.974915 -107 TGGAAAATAATTTTACGAATTTCTATGCTAGAATATTTACCAAAATT 11 206 1 TTTTATTTTT 0.944865 -59 ATTTGTTATATTTTATTTAATTGACTTAGATCAAATTGAC 12 4 0 TTTTATTATT 0.883132 -297 CTATATAGCATTTTTTACTATTTTTTATCCTTATGTTTAGTAGTAGA 12 86 1 TTTTTTTTTT 0.974915 -215 TACATAATTATTTTTAAAGGTTAAAAAAACACCAGTTATTATAGAGA 12 153 0 TTTTTTTATT 0.944865 -148 AGGCATCGCCTTGTTAATCATTGTTGGAACTAATGTTGTTTATACAA 12 253 1 TTGTTTTTTT 0.796239 -48 CTAAATCAATTTTTTTGCTATTATTTGCTCAATTTTGGTTATAGACC 13 55 0 TTTTTTTTTG 0.883508 -194 GATCATTAAATGTTTTTCCTTTTTTAAAAAGTGAATTTATTAAATTT 13 101 1 TGTTTTTTTT 0.92117 -148 AGTGCGGTGGTTTTTCTCTTTAATTTTTAAGGATTTTTT 14 29 1 TTTTTTATTT 0.830598 -29 TGCGGTTAGTTTTTAGCGATTTTTTATAAGGAATATTTT 15 13 1 TTTTATTTTT 0.944865 -29 ***** ** * ** Masking position 4 Map Score: 22.7629 Number of sites scoring better than the average of aligned sites = 447 Number in coding regions = 309 Number in noncoding regions = 138 Number of orfs with sites within 600 bp upstream = 130 Fraction of orfs with sites within 600 bp upstream = 0.0208802 Motif number 3 GCCTTTTTCTGCCGCTAATTTTTCGC 1 6 0 GCCCTAATTT 0.958551 -295 GTACGACACGCCCATCAATTTCGAGATCTTT 1 115 0 CCCTCAATTT 0.97542 -186 TGGTATAATCGCCGCCAATTTTTTCACGAAC 2 53 1 GCCCCAATTT 0.973694 -30 GTTGTGCTACGCCACCCATTTGTAATTTGAA 5 70 0 GCCCCCATTT 0.958648 -111 AAAACGCTCCAATTTTCCACCGCAC 8 5 1 CGCCCAATTT 0.961149 -196 GATTTTTCTACCCATTCATTTATGGTTAAAG 8 35 0 CCCTTCATTT 0.9395 -166 GGTATAAAACCGCCTTAATTTTGAGTATTAT 10 16 0 CGCTTAATTT 0.906166 -146 GGTTTTATACCGCCTTAATTTATTTAAAACA 10 36 1 CGCTTAATTT 0.906166 -126 TCATTATGAACCCTTTTATTTAGTTGGTAAA 11 133 0 CCCTTTATTT 0.796273 -132 TAGTAGAATAGCCGCCAATTTGGATTATCTC 12 126 1 GCCCCAATTT 0.973694 -175 GGTGGTTTTTCTCTTTAATTTTTAAGGATTT 14 34 1 CTCTTAATTT 0.70851 -24 TTAACTTTGCTCCACCCATTTATGGGGGGAG 16 99 0 TCCCCCATTT 0.816256 -40 *** ******* Masking position 8 Map Score: 11.9616 Number of sites scoring better than the average of aligned sites = 167 Number in coding regions = 138 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 4 AACTTTTTCAATATTTACCAAGAATGTTTTGTAT 1 264 0 ATTTACAAAA 0.896462 -37 ATTCTATATTAAATTCATCAATTAGGCATCGAGT 3 26 0 AATTACAATA 0.898166 -59 AGATTTTTTGATCTATAACAAATAAAGTTCAAAT 4 85 1 ATTAACAATA 0.869662 -121 GCCTTAATTTATTTAAAACAACAATATACCTCTT 10 47 1 ATTAACAAAA 0.854428 -115 AAAAAAGGTAAATTTGAGGAATAAATGATTTAAG 11 96 1 AATTAGAAAA 0.719274 -169 ATGATTTAAGAATTTTACCAACTAAATAAAAGGG 11 120 1 AATTACAATA 0.91795 -145 AATGGAAAATAATTTTACGAATTTCTATGCTAGA 11 204 1 AATTAGAATT 0.526717 -61 CTATGCTAGAATATTTACCAAAATTTCCATTTTT 11 228 1 ATTTACAAAT 0.766653 -37 CAATTAAATAAAATATAACAAATAAGCCCTATTT 12 28 1 AATAACAATA 0.88352 -273 CTATTTTTGTATTTATATCAAAAATGTGATCTAT 12 56 1 ATTAACAAAA 0.85441 -245 TCTATAACCAAAATTGAGCAAATAATAGCAAAAA 13 57 1 AATTACAATA 0.916376 -192 ACATTTAATGATCTAAATCAATTTTTTTGCTATT 13 80 0 ATTAACAATT 0.716883 -169 AGGTTTATTGATTTAAAACAAAATTTAATAAATT 13 134 0 ATTAACAAAT 0.691032 -115 GAGTTGCGAAAATTTCATCAAATATTAGAATACT 13 198 1 AATTACAATA 0.898166 -51 GGGTGGAGCAAAGTTAATGAAAAAGTGCGGTAAA 16 113 1 AATTAGAAAA 0.719528 -26 ** ** * *** ** Masking position 7 Map Score: 13.3338 Number of sites scoring better than the average of aligned sites = 334 Number in coding regions = 247 Number in noncoding regions = 87 Number of orfs with sites within 600 bp upstream = 91 Fraction of orfs with sites within 600 bp upstream = 0.0146161 Motif number 5 CGAAAAATTAGCGGCAGAAAAAGGCATCCA 1 12 1 GCGGCAGAAA 0.952729 -289 CAAAAAATGTGCGGTAAAAGTGGAAAAGGC 6 220 1 GCGGTAAAAG 0.96318 -81 TGGTTAAAGTGCGGTGGAAAATTGGAGCGT 8 14 0 GCGGTGGAAA 0.985199 -187 ATAAATTAAGGCGGTATAAAACCGCCTTAA 10 29 0 GCGGTATAAA 0.913513 -133 AAAGTGCGGTTAAAAAAATGGAAAT 11 250 0 GCGGTTAAAA 0.890252 -15 TCCCCCGCAAGCAGGGGAAGGCAAGAATAA 16 13 0 GCAGGGGAAG 0.830586 -126 TCCCCTGCTTGCGGGGGAAGGTGCCCGAAG 16 25 1 GCGGGGGAAG 0.97773 -114 ATGAAAAAGTGCGGTAAAAA 16 129 1 GCGGTAAAAA 0.963884 -10 ********** Masking position 8 Map Score: 5.90148 Number of sites scoring better than the average of aligned sites = 425 Number in coding regions = 316 Number in noncoding regions = 109 Number of orfs with sites within 600 bp upstream = 78 Fraction of orfs with sites within 600 bp upstream = 0.0125281 Motif number 6 CCACGACGAGAAGTAATTTTTACCATATCGC 1 47 0 AAGTATTTTT 0.769769 -254 CTCGTATAATAGGGCAAATTTTTTCCAAGGT 2 16 0 AGGGAAATTT 0.857374 -67 GTTATATTTGAAGGCATATTCTATATTAAAT 3 46 0 AAGGATATTC 0.774375 -39 TCTCCTATTAAGGTTATATTTGAAGGCATAT 3 58 0 AGGTATATTT 0.896408 -27 GCACCTATCAAGGTGCTATTTTTAATTTTAT 7 28 1 AGGTCTATTT 0.669081 -81 AAATCAGATCAAGTGATTTTTCTACCCATTC 8 49 0 AAGTATTTTT 0.769823 -152 CTATAATGGCACGGAATTTTTCTGTTCTTTA 8 165 1 ACGGATTTTT 0.761371 -36 AAAGAAAAAAAAGGTAAATTTGAGGAATAAA 11 90 1 AAGGAAATTT 0.817493 -175 ATACAAAAATAGGGCTTATTTGTTATATTTT 12 37 0 AGGGTTATTT 0.914433 -264 TTGAGTAATTAGGGATTATTTAAGGCATCGC 12 231 1 AGGGTTATTT 0.914431 -70 TTTAATTTTTAAGGATTTTTT 14 47 1 AAGGTTTTTT 0.805072 -11 GATTTTTTATAAGGAATATTTT 15 30 1 AAGGATATTT 0.952329 -12 **** ****** Masking position 1 Map Score: 5.76846 Number of sites scoring better than the average of aligned sites = 178 Number in coding regions = 133 Number in noncoding regions = 45 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467 Motif number 7 TAAAGCGGTCGCCGTGGTTACAAAACGTCT 1 84 1 GCCGTGGTTA 0.846137 -217 GGCAAAGGTAACCGTGGATTCTCTACGAAT 1 190 1 ACCGTGGATT 0.906001 -111 AATTTTTTCCAAGGTTGATT 2 1 0 AAGGTTGATT 0.717809 -82 ACTAAGCCACGAGGTGGTTTATTACGTCCG 6 106 0 GAGGTGGTTT 0.967084 -195 AAAATAAAGTGCGGTTGATTTTTACATGGT 6 259 0 GCGGTTGATT 0.925457 -42 TGGTTAAAGTGCGGTGGAAAATTGGAGCGT 8 14 0 GCGGTGGAAA 0.78631 -187 AAATCATAAAACAGTGGTTTTTATAGGTTT 8 109 0 ACAGTGGTTT 0.719642 -92 ACTAAAAAGTGCGGTGCATTTTTCAT 9 7 0 GCGGTGCATT 0.904785 -37 ACTCAAAATTAAGGCGGTTTTATACCGCCT 10 21 1 AAGGCGGTTT 0.734973 -141 GTATAAAAGTGCGGTGGTTTTTCTCTTTAA 14 22 1 GCGGTGGTTT 0.984827 -36 CGAAGGGCGGAAGGGGGATTACGTATCCCC 16 50 1 AAGGGGGATT 0.875413 -89 CGAAGTGACTGAGGGGGATACGTAATCCCC 16 63 0 GAGGGGGATA 0.846602 -76 ********** Masking position 4 Map Score: 4.98232 Number of sites scoring better than the average of aligned sites = 465 Number in coding regions = 388 Number in noncoding regions = 77 Number of orfs with sites within 600 bp upstream = 56 Fraction of orfs with sites within 600 bp upstream = 0.00899454 Motif number 8 CCATATCGCCTTTTTGGATGCCTTTTTCTG 1 26 0 TTTTTGGATG 0.699015 -275 AAACCTTAGATTTTTTGATCTATAACAAAT 4 78 1 TTTTTTGATC 0.882809 -128 GTTGTTTTCATTCATTCATCGTAAACACAT 4 142 1 TTCATTCATC 0.717638 -64 ATTTACCACTTTCTTTGATGCAGGTCAGCT 6 136 1 TTCTTTGATG 0.915342 -165 TTACCGCACATTTTTTGAAGTCGGTTTCTT 6 207 0 TTTTTTGAAG 0.610434 -94 CTTCCTCTTTTATTGATGGGAGAAAATA 6 283 0 TTTATTGATG 0.965975 -18 TATTTTTAATTTTATTAATGAAACATACTT 7 44 1 TTTATTAATG 0.712674 -65 CGTCGTTTTTTTCGTTGATGCGCAGATAAA 7 84 0 TTCGTTGATG 0.829664 -25 TTTCTACCCATTCATTTATGGTTAAAGTGC 8 32 0 TTCATTTATG 0.645557 -169 CTTTTTTTTCTTTATTGATGGTGCATTTCG 11 73 0 TTTATTGATG 0.965975 -192 AGGAAAAACATTTAATGATCTAAATCAATT 13 91 0 TTTAATGATC 0.607173 -158 GATCGATAGGTTTATTGATTTAAAACAAAA 13 145 0 TTTATTGATT 0.735675 -104 TTTTATTCATCGTATAAAAGT 14 2 1 TTTATTCATC 0.775845 -56 ********** Masking position 8 Map Score: 4.9296 Number of sites scoring better than the average of aligned sites = 339 Number in coding regions = 290 Number in noncoding regions = 49 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 9 CACGGTTACCTTTGCCATTTAATGCCTTCA 1 176 0 TTTGCCATTT 0.788136 -125 GACTATGCTGTTTTCAATTTAGA 4 4 0 TTTTCAATTT 0.808861 -202 ACGCCACCCATTTGTAATTTGAAACGAATC 5 63 0 TTTGTAATTT 0.805691 -118 GGCGAAATGATTTCTTATTTAGATACTCGC 6 77 1 TTTCTTATTT 0.725378 -224 TACGCAGCCTTTTCCACTTTTACCGCACAT 6 226 0 TTTCCACTTT 0.819416 -75 CAAGGTGCTATTTTTAATTTTATTAATGAA 7 36 1 TTTTTAATTT 0.725045 -73 CGCACTTTCTAGTTTGCACTAAAAA 9 29 0 TTTCTAGTTT 0.738734 -15 TAGAAAAACTTTTTTCTTTTGGTATCTTAC 10 136 1 TTTTTCTTTT 0.517107 -26 GGGTGTATTGTTTGCAATTTGGCTAGCGCG 11 45 1 TTTGCAATTT 0.869352 -220 CTTTTTAACTTTTCTCATTTATCTTTTTCT 11 167 1 TTTCTCATTT 0.856143 -98 GTAAAATTATTTTCCATTGTTGTTGAGAAA 11 192 0 TTTCCATTGT 0.644161 -73 TTTACCAAAATTTCCATTTTTTTAACCGCA 11 241 1 TTTCCATTTT 0.925428 -24 ATTAAATGTTTTTCCTTTTTTAAAAAGTGA 13 105 1 TTTCCTTTTT 0.754849 -144 ATACTGTCACTTTCTATTTTCCCTCTGTAA 13 227 1 TTTCTATTTT 0.885491 -22 ********** Masking position 3 Map Score: 6.69015 Number of sites scoring better than the average of aligned sites = 531 Number in coding regions = 408 Number in noncoding regions = 123 Number of orfs with sites within 600 bp upstream = 96 Fraction of orfs with sites within 600 bp upstream = 0.0154192 Motif number 10 ACCAAGAATGTTTTGTATTCTGGTGTTTGCGTGATTG 1 245 0 TTTTCTTGTT 0.963444 -56 TTTCAAATATTTCTGAATGCTTCTGTAGGCAACGGAT 4 173 0 TTTTCTTGTA 0.825269 -33 GAAATTGGGTCTGTCGCATCTAGTGTTAAGCTATTTG 6 168 0 CTTACTTGTT 0.969537 -133 TTCTGAAAACCTATAAAAACCACTGTTTTATGATTTT 8 103 1 CTTACCTGTT 0.894218 -98 TTTTTTACTATTTTTTATCCTTATGTTTAGTAGTAGA 12 96 1 TTTTCTTGTT 0.963444 -205 TGGATTATCTCTATAATAACTGGTGTTTTTTTAACCT 12 146 1 CTTACTTGTT 0.969537 -155 TTGTTAATCATTGTTGGAACTAATGTTGTTTATACAA 12 263 1 TTTACTTGTT 0.963444 -38 AATGTATTCCTTCTATTGTTAAAAACAGAT 13 4 1 GTTTCTTGTT 0.922316 -245 ** * * ** **** Masking position 4 Map Score: 1.49629 Number of sites scoring better than the average of aligned sites = 61 Number in coding regions = 50 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 11 ********** No masking Map Score: 1.55852e-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 CATCCAAAAAGGCGATATGGTAAAAATTACTTCTCG 1 36 1 GGCGATAAAA 0.977256 -265 TTGTAACCACGGCGACCGCTTTAATATAGCCACGAC 1 71 0 GGCGATTAAA 0.984352 -230 GCCCATCAATTTCGAGATCTTTAAGACGTTTTGTAA 1 101 0 TTCGATTAAA 0.827289 -200 GTGGATTCTCTACGAATACCTTAACACCATCTTGGG 1 203 1 TACGATTAAA 0.827181 -98 GTCCAGCTAATGCGATTCGTTTCAAATTACAAATGG 5 50 1 TGCGATTCAA 0.910616 -131 TTTACGTCATGGCGATAAAATTAAGATTTCATCTCG 6 37 1 GGCGATTAAA 0.984352 -264 TTATTACGTCCGCGAGTATCTAAATAAGAAATCATT 6 82 0 CGCGATAAAA 0.92426 -219 CAGGTCAGCTTGCAAATAGCTTAACACTAGATGCGA 6 156 1 TGCAATTAAA 0.810187 -145 AAAAGATAAATGAGAAAAGTTAAAAAGGGTTCATTA 11 158 0 TGAGATAAAA 0.744623 -107 TGATTAACAAGGCGATGCCTTAAATAATCCCTAATT 12 237 0 GGCGATAAAA 0.977256 -64 ***** **** * Masking position 11 Map Score: 4.11544 Number of sites scoring better than the average of aligned sites = 100 Number in coding regions = 86 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 13 ********** No masking Map Score: 1.55852e-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: 1.55852e-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 CATCAATTAGGCATCGAGTTTGCCTAAAAC 3 15 0 GCATCGAGTT 0.873159 -70 AAACAAAACAGCATAGCAATTTTGACTATG 4 27 0 GCATAGCAAT 0.867909 -179 GCTTCTGTAGGCAACGGATTATGTGTTTAC 4 162 0 GCAACGGATT 0.759396 -44 CATTGCACCGTATTGAATGCCGAA 5 5 1 GCACCGTATT 0.853125 -176 AATTTGAAACGAATCGCATTAGCTGGACAA 5 48 0 GAATCGCATT 0.839941 -133 GCCATTACAAGCATCGAAATTAACTAAAGG 5 100 0 GCATCGAAAT 0.941711 -81 ATGAAAAATGCACCGCACTTTTTAGTGCA 9 10 1 GCACCGCACT 0.917242 -34 AAATATTCTAGCATAGAAATTCGTAAAATT 11 214 0 GCATAGAAAT 0.76084 -51 ATTATTTAAGGCATCGCCTTGTTAATCATT 12 245 1 GCATCGCCTT 0.934287 -56 ********** Masking position 3 Map Score: 0.108108 Number of sites scoring better than the average of aligned sites = 208 Number in coding regions = 184 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049