AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/alignace/lib/ORF_hinf.txt -z/skink1/amcguire/genomes/hinf.fna -ifnr_hinf_opreg_100.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 HI0179 130 pyruvate formate-lyase activating enzyme (act) #3 HI0180 27 formate acetyltransferase (pfl) #4 HI0181 300 formate transporter #5 HI0745 225 L-asparaginase II (ansB) #6 HI0747 203 NADH dehydrogenase (ndh) #7 HI0936 108 cytochrome C-type biogenesis #8 HI1068 43 nitrite reductase, cytochrome C-type protein (nrfB) #9 HI1069 161 nitrite reductase, cytochrome C552 (nrfA) #10 HI1076 300 cytochrome D ubiquinol oxidase, subunit I (cydA) Motif number 1 AAAGGCATCCAAAAAGGCGATATGGTAAAAA 1 31 1 AAAAAGCGAT 0.925471 -270 TCGTGGCTATATTAAAGCGGTCGCCGTGGTT 1 72 1 ATTAAGCGGT 0.951725 -229 ATGTTCCCGCCAAAGTGCGGTCAAAAATAAA 2 18 0 CAAAGGCGGT 0.993633 -113 GAAAGATAACCCAAGTGCGGTTATACTTGAG 5 46 0 CCAAGGCGGT 0.985316 -180 GATTCGATAACAAAGAACGGTGCTGAAATAG 6 16 1 CAAAGACGGT 0.947713 -188 TATTAGAACAACAAAAACGGTGCTATTTCAG 6 38 0 ACAAAACGGT 0.842255 -166 ACTTATATATCAAAGTGCGGTTATTTTTTTG 6 85 0 CAAAGGCGGT 0.993633 -119 ACTTTGATATATAAGTGCGGTTATTTTTATG 6 100 1 ATAAGGCGGT 0.988887 -104 ATAACAACGAAACAGGGCGGAAAACTTTCAT 6 128 0 AACAGGCGGA 0.866331 -76 GTTTGCACTAAAAAGTGCGGTGCATTTTTCA 8 12 0 AAAAGGCGGT 0.994205 -32 AATACTCAAAATTAAGGCGGTTTTATACCGC 9 18 1 ATTAAGCGGT 0.951725 -144 TTTTAAATAAATTAAGGCGGTATAAAACCGC 9 34 0 ATTAAGCGGT 0.951725 -128 TTAAAATACTCAAAAAGAGGTATATTGTTGT 9 64 0 CAAAAGAGGT 0.85548 -98 AACAATGATTAACAAGGCGATGCCTTAAATA 10 247 0 AACAAGCGAT 0.826565 -54 ***** ***** Masking position 4 Map Score: 20.7681 Number of sites scoring better than the average of aligned sites = 1844 Number in coding regions = 1305 Number in noncoding regions = 539 Number of orfs with sites within 600 bp upstream = 341 Fraction of orfs with sites within 600 bp upstream = 0.0547703 Motif number 2 GCGAAAAATTAGCGGCAGAAAAAGGC 1 6 1 AAATTAGCGC 0.910752 -295 CGACCGCTTTAATATAGCCACGACGAGAAGT 1 64 0 AATATAGCAC 0.841462 -237 GGAGGAGAGTAAAATAGCACCAATTATAGAA 4 204 1 AAAATAGCCC 0.993086 -97 ATAGGGCTCAAGTATAACCGCACTTGGGTTA 5 40 1 AGTATAACGC 0.743762 -186 GAACGGTGCTGAAATAGCACCGTTTTTGTTG 6 30 1 GAAATAGCCC 0.954448 -174 ATATCAACTTAAAATAACTCAAAAAAATAAC 6 66 1 AAAATAACCA 0.805024 -138 ATAACTCAAAAAAATAACCGCACTTTGATAT 6 79 1 AAAATAACGC 0.979984 -125 AACTTTCATAAAAATAACCGCACTTATATAT 6 106 0 AAAATAACGC 0.979984 -98 TTTTATAAGCACAATAGCACCTATCAAGGTG 7 12 1 ACAATAGCCC 0.961026 -97 AATAAAATTAAAAATAGCACCTTGATAGGTG 7 29 0 AAAATAGCCC 0.993086 -80 CGCATCAACGAAAAAAACGACGACATT 7 92 1 AAAAAAACAC 0.796287 -17 ATGAAAAATGCACCGCACTTTTTA 8 4 1 AAAAATGCCC 0.80535 -40 GTTTAGTAGTAGAATAGCCGCCAATTTGGAT 10 120 1 AGAATAGCGC 0.970376 -181 TTTAAAGGTTAAAAAAACACCAGTTATTATA 10 157 0 AAAAAAACCC 0.95204 -144 ******** ** Masking position 8 Map Score: 16.8671 Number of sites scoring better than the average of aligned sites = 319 Number in coding regions = 224 Number in noncoding regions = 95 Number of orfs with sites within 600 bp upstream = 74 Fraction of orfs with sites within 600 bp upstream = 0.0118856 Motif number 3 AGATATAGCTAAATTTTACCAAAGATTTAGTCTATA 2 86 0 AATTACAAAT 0.850823 -45 TAGCTATATCTAATTTTAGGAAATTTATGT 2 111 1 TATTAGAATT 0.968386 -20 TGAATGTATGAAATTGAGCGAATATTAATATGGGAA 4 90 1 AATTGGAATT 0.776664 -211 ATTTTGTCTTTAATTAAACAAACCTTGCAAAATATC 4 125 1 TATTAAAATT 0.943202 -176 AAGCAAAAATTATTTCAACAAACTTTGATATTTTGC 4 151 0 TATTAAAATT 0.943202 -150 GAAAATTTAATACTTTTAACAAGTTTACGACTACAA 4 239 0 TATTACAATT 0.980569 -62 AAAAGTATTAAATTTTCATCAACTTTTTCAATGTCA 4 258 1 AATTACAATT 0.784035 -43 TTAAATTCCGTACTTGCATAAAGGTTATACAATCAA 5 90 1 TATTAAAATT 0.943073 -136 TTAGTTAGACTACTTTGGAGAAATTTTTATTCATCT 5 188 1 TATTGGAATT 0.906207 -38 TAAGTGCGGTTATTTTTATGAAAGTTTTCCGCCCTG 6 111 1 TATTAGAATT 0.875296 -93 CGCCTTAATTTATTTAAAACAACAATATACCTCTTT 9 46 1 TATTACAAAT 0.959113 -116 CCTATTTTTGTATTTATATCAAAAATGTGATCTATA 10 55 1 TATTACAAAT 0.959049 -246 TAAACAACATTAGTTCCAACAATGATTAACAAGGCG 10 259 0 TATTACAAAT 0.959113 -42 ** ** * *** ** Masking position 11 Map Score: 16.4139 Number of sites scoring better than the average of aligned sites = 148 Number in coding regions = 104 Number in noncoding regions = 44 Number of orfs with sites within 600 bp upstream = 54 Fraction of orfs with sites within 600 bp upstream = 0.00867331 Motif number 4 CCTGATTTAAATCAGGCTCATACATATTATGTTCCC 2 41 0 ATGGCTACTA 0.936116 -90 CCTGATTTAAATCAGGCTCATTTTTTATAGACTAAA 2 61 1 ATGGCTATTT 0.982197 -70 CTAAAATTAGATATAGCTAAATTTTACCAAAGATTT 2 94 0 ATAGCTATTA 0.959256 -37 GTACGTCAAAATAGGGCTCAAGTATAACCGCACTTG 5 30 1 ATGGCTATTA 0.982197 -196 AAATTATGTGATCGAGATCATAAATTTGTTTTTCCA 5 132 1 ATAGATAATT 0.760481 -94 TTTGAGCTTGATCAAGCTTATCTTTTAAAATACTCA 9 83 0 ATAGCTATTT 0.959256 -79 AAATACAAAAATAGGGCTTATTTGTTATATTTTATT 10 34 0 ATGGCTATTT 0.982197 -267 AAAAAATGCTATATAGATCACATTTTTGATATAAAT 10 66 0 ATAGATATTT 0.909481 -235 ACTACTAAACATAAGGATAAAAAATAGTAAAAAATG 10 94 0 ATGGATAATA 0.881516 -207 ATAGCCGCCAATTTGGATTATCTCTATAATAACTGG 10 133 1 ATGGATATTA 0.959256 -168 ** **** * * ** Masking position 8 Map Score: 9.09605 Number of sites scoring better than the average of aligned sites = 114 Number in coding regions = 90 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 5 CCTCCCCAACTTTTTCAATATTTACCAAGAATGT 1 271 0 TTTTTTATTA 0.910623 -30 GTTGAAATAATTTTTGCTTTTCTTTGCAATGAAA 4 168 1 TTTTTTTTTT 0.939098 -133 TAAGCATAATTTTTTTGAAAGATAACCCAAGTGC 5 59 0 TTTTTAAGTA 0.71664 -167 ATCACATAATTTTTTTTGTTGATTGTATAACCTT 5 110 0 TTTTTTTGTT 0.949343 -116 CATAAATTTGTTTTTCCATTGTTTATAAATAACT 5 150 1 TTTTTTTGTT 0.949343 -76 AATAGCACCGTTTTTGTTGTTCTAATATCAACTT 6 42 1 TTTTTGTTTA 0.754097 -162 TTTTTGAGTTATTTTAAGTTGATATTAGAACAAC 6 57 0 ATTTTTTGTA 0.681203 -147 TAATGTAACATTTTTAACAATTTAAACTTTTAGG 6 172 1 TTTTTAATTA 0.675426 -32 CAAGGTGCTATTTTTAATTTTATTAATGAAACAT 7 36 1 TTTTTTTTTT 0.939098 -73 ATGTCGTCGTTTTTTTCGTTGATGCGCAGATAAA 7 84 0 TTTTTTTGTG 0.852211 -25 AATATACCTCTTTTTGAGTATTTTAAAAGATAAG 9 69 1 TTTTTTATTT 0.897905 -93 TAGAAAAACTTTTTTCTTTTGGTATCTTACGCTT 9 136 1 TTTTTTTGTA 0.955967 -26 ATAAGCCCTATTTTTGTATTTATATCAAAAATGT 10 49 1 TTTTTTTTTA 0.946988 -252 CTATATAGCATTTTTTACTATTTTTTATCCTTAT 10 86 1 TTTTTTATTT 0.897905 -215 ***** *** ** Masking position 5 Map Score: 12.5584 Number of sites scoring better than the average of aligned sites = 530 Number in coding regions = 376 Number in noncoding regions = 154 Number of orfs with sites within 600 bp upstream = 124 Fraction of orfs with sites within 600 bp upstream = 0.0199165 Motif number 6 CAAAGTGCGGTCAAAAATAAACATGTTT 2 9 0 TCAAAAATAA 0.74054 -122 CTTTGTTAATTAATAAATAAATCT 3 5 0 TAATAAATAA 0.832929 -23 TTTCCATTGTTTATAAATAACTTAATTTAG 5 162 1 TTATAAATAA 0.883217 -64 CTAATATCAACTTAAAATAACTCAAAAAAA 6 63 1 CTTAAAATAA 0.515739 -141 AAAATAACTCAAAAAAATAACCGCACTTTG 6 76 1 AAAAAAATAA 0.783252 -128 GAAAACTTTCATAAAAATAACCGCACTTAT 6 110 0 ATAAAAATAA 0.849741 -94 ATTAATAAAATTAAAAATAGCACCTTGATA 7 33 0 TTAAAAATAG 0.808917 -76 TATATTGTTGTTTTAAATAAATTAAGGCGG 9 45 0 TTTTAAATAA 0.765372 -117 AAGCTTATCTTTTAAAATACTCAAAAAGAG 9 76 0 TTTAAAATAC 0.638971 -86 GATCTAAGTCAATTAAATAAAATATAACAA 10 19 1 AATTAAATAA 0.49117 -282 AAATAAAATATAACAAATAAGCCCTATTTT 10 33 1 TAACAAATAA 0.645864 -268 CACATTTTTGATATAAATACAAAAATAGGG 10 54 0 ATATAAATAC 0.556026 -247 AACATAAGGATAAAAAATAGTAAAAAATGC 10 93 0 TAAAAAATAG 0.730115 -208 TTTTTAACCTTTAAAAATAATTATGTAGAT 10 173 1 TTAAAAATAA 0.92426 -128 ********** Masking position 5 Map Score: 4.82443 Number of sites scoring better than the average of aligned sites = 683 Number in coding regions = 426 Number in noncoding regions = 257 Number of orfs with sites within 600 bp upstream = 229 Fraction of orfs with sites within 600 bp upstream = 0.0367812 Motif number 7 TAGCCACGACGAGAAGTAATTTTTACCATATCGC 1 47 0 GAGAATTTTT 0.688456 -254 TCCCCCAGATAATCATCCACTTTTC 4 2 0 AATAACTTTT 0.890437 -299 GTATTACGCGAATAAAACAAGTTTCAAATTAAGT 4 43 1 AATAAAGTTT 0.583984 -258 ACAAGTTTCAAATTAAGTACTTTACTTACTCTGA 4 59 1 AATAACTTTA 0.864543 -242 AGCGAATATTAATATGGGAATTTTGTCTTTAATT 4 106 1 AATTAATTTT 0.733448 -195 ATCAAAGTTTGTTGAAATAATTTTTGCTTTTCTT 4 158 1 GTTAAATTTT 0.481289 -143 AACTTGTTAAAAGTATTAAATTTTCATCAACTTT 4 250 1 AAGAAATTTT 0.900882 -51 ACCTTTATGCAAGTACGGAATTTAAGCATAATTT 5 81 0 AAGAAATTTA 0.877133 -145 TTATGATCTCGATCACATAATTTTTTTTGTTGAT 5 121 0 GATAAATTTT 0.915568 -105 ATAAACAATGGAAAAACAAATTTATGATCTCGAT 5 142 0 GAAAAATTTA 0.519656 -84 ATTGTTTATAAATAACTTAATTTAGTTAGACTAC 5 167 1 AATAAATTTA 0.89682 -59 TCATTACATTAATGTAACATTTTTAACAATTTAA 6 163 1 AATTATTTTT 0.405838 -41 AAACATACTTGATTAGCGACTTTATCTGCGCATC 7 64 1 GATAACTTTA 0.862108 -45 AAGCTTGATCAAGCTCAAACTTTAGCATTCTGCG 9 100 1 AAGTACTTTA 0.5659 -62 AAGATACCAAAAGAAAAAAGTTTTTCTACTCGCA 9 130 0 AAGAAGTTTT 0.654709 -32 TAATTATGTAGATAAGTCAATTTAAACTTAGCTG 10 190 1 GATAAATTTA 0.894896 -111 *** * ****** Masking position 9 Map Score: 3.50735 Number of sites scoring better than the average of aligned sites = 520 Number in coding regions = 388 Number in noncoding regions = 132 Number of orfs with sites within 600 bp upstream = 122 Fraction of orfs with sites within 600 bp upstream = 0.0195952 Motif number 8 ********** No masking Map Score: 5.31729e-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 9 CGGTCGCCGTGGTTACAAAACGTCTTAAAG 1 89 1 GGTTACAAAA 0.920755 -212 CAAAGATTTAGTCTATAAAAAATGAGCCTG 2 73 0 GTCTATAAAA 0.825032 -58 CTTGCATAAAGGTTATACAATCAACAAAAA 5 102 1 GGTTATACAA 0.947339 -124 TTTTTCCATTGTTTATAAATAACTTAATTT 5 160 1 GTTTATAAAT 0.72317 -66 GTGCTATTGTGCTTATAAAAA 7 2 0 GCTTATAAAA 0.899765 -107 CTAAACATAAGGATAAAAAATAGTAAAAAA 10 96 0 GGATAAAAAA 0.741647 -205 TATTTTTAAAGGTTAAAAAAACACCAGTTA 10 162 0 GGTTAAAAAA 0.932538 -139 AACTAATGTTGTTTATACAAAGGAGTTGAG 10 280 1 GTTTATACAA 0.896398 -21 ********** Masking position 5 Map Score: 1.38783 Number of sites scoring better than the average of aligned sites = 127 Number in coding regions = 92 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 10 ********** No masking Map Score: 5.31729e-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 11 ********** No masking Map Score: 5.31729e-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: 5.31729e-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