AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_mjan.txt -z/home/amcguire/genomes/mjan.fna -imodE_mjan_opreg_300.orf -g0.314 -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 = 0.314 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 MJ0167 122 molybdenum cofactor biosynthesis protein (moaB) #2 MJ0168 230 archaeal histone A1 #3 MJ0718 25 chromate resistance protein (chrA) #4 MJ0719 55 RNase L inhibitor #5 MJ0720 194 3-isopropylmalate dehydrogenase 1 (leuB1) #6 MJ0824 100 molybdenum cofactor biosynthesis protein (moaA) #7 MJ0825 173 peptidyl-prolyl cis-trans isomerase, FKBP-type rotamase (slyD) #8 MJ1135 217 molybdenum cofactor biosynthesis protein (moaC) #9 MJ1368 122 sulfate transport system permease protein (cysT) Motif number 1 AATTAAAAATTTTAAAAATAAAAT 1 5 0 TTTAAAAATA 0.970597 -118 AAATATTAATAATAAAAATTAAAAATTTTA 1 21 0 AATAAAAATT 0.803258 -102 ATGAATATAAATTAAAATAACAAAAGAATT 1 72 0 ATTAAAATAA 0.847427 -51 TTTAAATAAATATATAAATTAATGAATATA 1 93 0 TATATAAATT 0.775 -30 ATGTCACAAATTTAAAATATAATTTTATGA 2 45 0 TTTAAAATAT 0.734065 -186 TGTGACATACATTATAAATAGTGTTTTTTA 2 67 1 ATTATAAATA 0.952684 -164 TGACACTAAAATTATAAAAAACACTATTTA 2 81 0 ATTATAAAAA 0.867624 -150 ATTCTTTTATTTTAAAAATTTAAA 4 42 1 TTTAAAAATT 0.933073 -14 TATTTTTAATTTTAAAATCATTTTGGTGAT 5 14 0 TTTAAAATCA 0.86499 -181 TGATTTTAAAATTAAAAATAAAACTTTTAA 5 24 1 ATTAAAAATA 0.96558 -171 AACAACACAAAATATAAATACTTATAATGC 5 64 0 AATATAAATA 0.873971 -131 TAGCAATATTAATAAAAATACTTTCACATA 5 151 0 AATAAAAATA 0.906258 -44 ACGTAGCTTTTTTATAATTAATTTCCCAAT 6 42 1 TTTATAATTA 0.935333 -59 AAATTAAGGTTTTAAAAATAGAATTGGGAA 6 64 0 TTTAAAAATA 0.970597 -37 AATTTTAAATATTATAATAAATCATAATTA 7 46 0 ATTATAATAA 0.800062 -128 TATTATAATATTTAAAATTTTTCGTTTTTG 7 57 1 TTTAAAATTT 0.894498 -117 ATATAAACCCTATATAAACATAACTGAACA 7 85 0 TATATAAACA 0.7234 -89 TAGGGTTTATATTAAAATTATGAAAGATTT 7 103 1 ATTAAAATTA 0.94463 -71 GATTAATGAGTTTAAAAAATCTTTCATAAT 7 119 0 TTTAAAAAAT 0.81946 -55 ATAAATCATTTTTATAAATATATTCATATA 8 28 0 TTTATAAATA 0.959241 -190 CAAATACCTTTTTAAAAATATAAGTTGCGA 8 69 0 TTTAAAAATA 0.970597 -149 ATACAATAACATTATAATCATTGCCGAATA 8 160 0 ATTATAATCA 0.796845 -58 TAATATTTTCATTAAAAATTTATTAAA 9 8 0 ATTAAAAATT 0.922163 -115 ACACAAATTTTATATAATTAGGTAATTTAA 9 66 1 TATATAATTA 0.8329 -57 ********** Masking position 3 Map Score: 35.6691 Number of sites scoring better than the average of aligned sites = 2096 Number in coding regions = 1452 Number in noncoding regions = 644 Number of orfs with sites within 600 bp upstream = 481 Fraction of orfs with sites within 600 bp upstream = 0.0772567 Motif number 2 ATAATAAAAATTAAAAATTTTAAAAATAAA 1 13 0 TTAAAAATTT 0.864611 -110 ATTTTTATTATTAATATTTTACTTCCTTCC 1 32 1 TTAATATTTT 0.945373 -91 TTAATTTATATTCATTAATTTATATATTTA 1 87 1 TTCATTAATT 0.525693 -36 TTAAACTCTATTAATTTATGTTTATCTATC 2 13 1 TTAATTTATG 0.449897 -218 AATAGTGTTTTTTATAATTTTAGTGTCACA 2 83 1 TTTATAATTT 0.690699 -148 TTCGGTCATTTTCATTTTTTGTGAAAGTCT 2 152 0 TTCATTTTTT 0.712311 -79 AATCCTTTATTTAAACTTTTCGGTCATTTT 2 170 0 TTAAACTTTT 0.90092 -61 ATTAATCTATTTTTCTTTAGA 4 2 1 TTAATCTATT 0.91703 -54 TTCTTTTATTTTAAAAATTTAAA 4 43 1 TTAAAAATTT 0.864611 -13 TTTTAATTTTAAAATCATTTTGGTGATTAA 5 11 0 AAAATCATTT 0.626892 -184 AAATTAAAAATAAAACTTTTAAGGGAAGTA 5 32 1 TAAAACTTTT 0.683906 -163 ATTATAAGTATTTATATTTTGTGTTGTTTT 5 66 1 TTTATATTTT 0.642259 -129 GTTGAGTATTTTAATCATTTTTGATATGGT 5 98 1 TTAATCATTT 0.974485 -97 ATTGCTATAATTAATCTTTTTGGTGATAAG 5 174 1 TTAATCTTTT 0.968461 -21 TAGCTTTTTTATAATTAATTTCCCAATTCT 6 45 1 ATAATTAATT 0.46764 -56 TTTTAAAACCTTAATTTTTTAGTAGTGAGT 6 77 1 TTAATTTTTT 0.913862 -24 TCCCAGTTGCTTAATTAATTATGATTTATT 7 31 1 TTAATTAATT 0.826113 -143 ATTATAATATTTAAAATTTTTCGTTTTTGT 7 58 1 TTAAAATTTT 0.836939 -116 TAAAAAATCTTTCATAATTTTAATATAAAC 7 107 0 TTCATAATTT 0.834203 -67 TTTAAACTCATTAATCATTGAACTTTGGCT 7 133 1 TTAATCATTG 0.891031 -41 ATCATTTTTATAAATATATTCATATATGTA 8 24 0 TAAATATATT 0.59707 -194 GTTCTATATATAAATCATTTTTATAAATAT 8 37 0 TAAATCATTT 0.900892 -181 CAATATTCAATAAAACATTTTATTCCTGCG 8 114 1 TAAAACATTT 0.729116 -104 CAATAACATTATAATCATTGCCGAATAAAC 8 157 0 ATAATCATTG 0.601895 -61 TTTAATAAATTTTTAATGAAA 9 2 1 TTAATAAATT 0.885877 -121 ATTTGATAGTATAATATTTTCATTAAAAAT 9 19 0 ATAATATTTT 0.755791 -104 CTAATCAATCTTAATCATTTTTAAGGTAAT 9 95 0 TTAATCATTT 0.974485 -28 ********** Masking position 4 Map Score: 31.1523 Number of sites scoring better than the average of aligned sites = 2248 Number in coding regions = 1706 Number in noncoding regions = 542 Number of orfs with sites within 600 bp upstream = 401 Fraction of orfs with sites within 600 bp upstream = 0.0644073 Motif number 3 CCAAAGACTTTCACAAAAAATGAAAATGAC 2 148 1 TCACAAAAAA 0.966337 -83 AAAATGAAAATGACCGAAAAGTTTAAATAA 2 164 1 TGACCGAAAA 0.931801 -67 TTAATCACCAAAATGATTTTAAAA 5 5 1 TCACCAAAAT 0.957432 -190 ATTAAAATACTCAACAAAAAACAACACAAA 5 83 0 TCAACAAAAA 0.966337 -112 ATGGTTTAAGTCACCAACAAAACATTTTTA 5 123 1 TCACCAACAA 0.970876 -72 AAAAATACTTTCACATAAAAATGTTTTGTT 5 138 0 TCACATAAAA 0.856315 -57 ACTTATCACCAAAAAGATTAATTAT 5 180 0 TCACCAAAAA 0.992095 -15 TAAACATAACTGAACAAAAACGAAAAATTT 7 71 0 TGAACAAAAA 0.910364 -103 ********** Masking position 7 Map Score: 9.85881 Number of sites scoring better than the average of aligned sites = 399 Number in coding regions = 278 Number in noncoding regions = 121 Number of orfs with sites within 600 bp upstream = 138 Fraction of orfs with sites within 600 bp upstream = 0.0221651 Motif number 4 ATAAAAATTAAAAATTTTAAAAATAAAAT 1 8 0 AAATTTTAAA 0.885995 -115 ACTTCCTTCCAAAACTTTAGAATTCTTTTGTT 1 52 1 AAACTTTAAA 0.936634 -71 AAGTCTTTGGAAAATTTTCCCACACATAAAGA 2 126 0 AAATTTTCCA 0.960689 -105 AAATTTTCCAAAGACTTTCACAAAAAATGAAA 2 141 1 AAACTTTCCA 0.978939 -90 GTTTAAATAAAGGATTTTATAACAGTATTTAT 2 184 1 AGATTTTAAA 0.829569 -47 AAAGAATAGAAAAGCTTTCTAAAGAAAAATAG 4 17 0 AAGCTTTCAA 0.930037 -39 TATTAATAAAAATACTTTCACATAAAAATGTT 5 143 0 AAACTTTCCA 0.978939 -52 CTAAAAAATTAAGGTTTTAAAAATAGAATTGG 6 67 0 AAGTTTTAAA 0.748914 -34 AAAATTATGAAAGATTTTTTAAACTCATTAAT 7 116 1 AAATTTTTAA 0.702568 -58 ATTTATATATAGAACTTTCGCAACTTATATTT 8 52 1 AGACTTTCCA 0.966791 -166 TAAACTATATAGAACTTTCGCAGGAATAAAAT 8 130 0 AGACTTTCCA 0.966791 -88 ** ****** ** Masking position 1 Map Score: 13.3681 Number of sites scoring better than the average of aligned sites = 284 Number in coding regions = 195 Number in noncoding regions = 89 Number of orfs with sites within 600 bp upstream = 76 Fraction of orfs with sites within 600 bp upstream = 0.0122069 Motif number 5 ATTTTATTTTTAAAATTTTTAATTTTTATTATTA 1 7 1 TTTTATAATT 0.43456 -116 TAAATATATAAATTAATGAATATAAATTAAAATAACAA 1 79 0 AATTTAAATT 0.521458 -44 GATAAACATAAATTAATAGAGTTTAATT 2 1 0 AATTTTAATT 0.437574 -230 TAATACCTTCTTTATGTGTGGGAAAATTTTCCAAAGAC 2 118 1 TTTATAAATT 0.781119 -113 TTCGGTCATTTTCATTTTTTGTGAAAGTCTTTGGAAAA 2 144 0 TTCATAAAGT 0.55032 -87 ATTAATCTATTTTTCTTTAGAAAGCTTTTCTATTC 4 8 1 TATTTAAAGC 0.849254 -48 TTAAAAGTTTTATTTTTAATTTTAAAATCATTTTGGTG 5 16 0 TATTTAAAAT 0.629418 -179 CTTATAATGCATTACTTCCCTTAAAAGTTTTATTTTTA 5 36 0 ATTATAAAGT 0.80848 -159 TTTTAATCATTTTTGATATGGTTTAAGTCACCAACAAA 5 106 1 TTTTTTAAGT 0.924076 -89 TACGTAATGATTTTAGATTAATTAAAGTATATAAAT 6 9 0 TTTTAAAAGT 0.883523 -92 AGAATTGGGAAATTAATTATAAAAAAGCTACGTAATGA 6 37 0 AATTTAAAGC 0.660309 -64 AACCTTAATTTTTTAGTAGTGAGTAAGT 6 83 1 TTTTTTAAGT 0.923968 -18 TATTTAAAATTTTTCGTTTTTGTTCAGTTATGTTTATA 7 65 1 TTTTTTCAGT 0.55032 -109 CTTCCACCTCTATTAATTTAGCCAAAGTTCAATGATTA 7 144 0 TATTTAAAGT 0.966411 -30 AATATATTCATATATGTAAGTTTAAAGTTTA 8 4 0 TATATAAAGT 0.909243 -214 CCTTTTTAAAAATATAAGTTGCGAAAGTTCTATATATA 8 55 0 AATAAAAAGT 0.42883 -163 CAATAAAACATTTTATTCCTGCGAAAGTTCTATATAGT 8 121 1 TTTTTAAAGT 0.972267 -97 ATAATTGTAGTATTTGGTTTAATAAAGTAGTGGTGATT 8 188 1 TATTGAAAGT 0.869396 -30 ATGTCATCAATTTTGTTTAACACAAATTTTATATAATT 9 47 1 TTTTTAAATT 0.911232 -76 TCTTAATCATTTTTAAGGTAATTAAATTACCTAATTAT 9 79 0 TTTTGAAATT 0.705462 -44 **** * ***** Masking position 16 Map Score: 10.0943 Number of sites scoring better than the average of aligned sites = 1332 Number in coding regions = 1022 Number in noncoding regions = 310 Number of orfs with sites within 600 bp upstream = 266 Fraction of orfs with sites within 600 bp upstream = 0.0427241 Motif number 6 ACATAAATTAATAGAGTTTAATT 2 4 0 ATAGAGTTTA 0.957448 -227 TACATTATAAATAGTGTTTTTTATAATTTT 2 74 1 ATAGTGTTTT 0.823674 -157 ATCATTTTTGATATGGTTTAAGTCACCAAC 5 111 1 ATATGGTTTA 0.976734 -84 TTATGTTTATATAGGGTTTATATTAAAATT 7 92 1 ATAGGGTTTA 0.980657 -82 CGAAAGTTCTATATAGTTTATTCGGCAATG 8 142 1 ATATAGTTTA 0.949065 -76 TAATTGTAGTATTTGGTTTAATAAAGTAGT 8 189 1 ATTTGGTTTA 0.948088 -29 AATGTCATCAATTTTGTTTAACACAAATTT 9 46 1 ATTTTGTTTA 0.89018 -77 ********** Masking position 1 Map Score: 7.42664 Number of sites scoring better than the average of aligned sites = 74 Number in coding regions = 63 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 7 TAAAAATTTTAAAAATAAAAT 1 2 0 AAAAATAAAA 0.960186 -121 GTAAAATATTAATAATAAAAATTAAAAATT 1 24 0 AATAATAAAA 0.839074 -99 TATAAATTAAAATAACAAAAGAATTCTAAA 1 67 0 AATAACAAAA 0.810525 -56 CCGTTTAAATAAATATATAAATTAATGAAT 1 96 0 AAATATATAA 0.564076 -27 TGAAAGATAGATAAACATAAATTAATAGAG 2 18 0 ATAAACATAA 0.808624 -213 GTCACAAATTTAAAATATAATTTTATGAAA 2 43 0 TAAAATATAA 0.798168 -188 GTGTGACACTAAAATTATAAAAAACACTAT 2 84 0 AAAATTATAA 0.564092 -147 GACTTTCACAAAAAATGAAAATGACCGAAA 2 153 1 AAAAATGAAA 0.840853 -78 TTTAAATTTTTAAAATAAAAGAATAGAAAA 4 36 0 TAAAATAAAA 0.847982 -20 TTTTAAAATTAAAAATAAAACTTTTAAGGG 5 27 1 AAAAATAAAA 0.960186 -168 AAAAACAACACAAAATATAAATACTTATAA 5 67 0 CAAAATATAA 0.698799 -128 ATACTCAACAAAAAACAACACAAAATATAA 5 77 0 AAAAACAACA 0.689376 -118 TTATAGCAATATTAATAAAAATACTTTCAC 5 154 0 ATTAATAAAA 0.610951 -41 TTAAGGTTTTAAAAATAGAATTGGGAAATT 6 61 0 AAAAATAGAA 0.81955 -40 ATAACTGAACAAAAACGAAAAATTTTAAAT 7 66 0 AAAAACGAAA 0.812549 -108 TAAACCCTATATAAACATAACTGAACAAAA 7 82 0 ATAAACATAA 0.808624 -92 ATACCTTTTTAAAAATATAAGTTGCGAAAG 8 66 0 AAAAATATAA 0.944749 -152 AAAATTTGTGTTAAACAAAATTGATGACAT 9 47 0 TTAAACAAAA 0.579553 -76 ********** Masking position 10 Map Score: 19.7463 Number of sites scoring better than the average of aligned sites = 1820 Number in coding regions = 1233 Number in noncoding regions = 587 Number of orfs with sites within 600 bp upstream = 405 Fraction of orfs with sites within 600 bp upstream = 0.0650498 Motif number 8 TGTCACACTTTTTAATACCTTCTTTATGTG 2 106 1 TTTAATACCT 0.882679 -125 TTAATCACCAAAATGATTTT 5 1 1 TTAATCACCA 0.966658 -194 ACTTATCACCAAAAAGATTAA 5 184 0 CTTATCACCA 0.920736 -11 CAATTCTATTTTTAAAACCTTAATTTTTTA 6 68 1 TTTAAAACCT 0.810125 -33 TTAATCACCACTACTTTATT 8 208 0 TTAATCACCA 0.966658 -10 ATCAATTTTGTTTAACACAAATTTTATATA 9 52 1 TTTAACACAA 0.789942 -71 ATTAGGTAATTTAATTACCTTAAAAATGAT 9 82 1 TTAATTACCT 0.882679 -41 ********** Masking position 4 Map Score: 1.51322 Number of sites scoring better than the average of aligned sites = 178 Number in coding regions = 125 Number in noncoding regions = 53 Number of orfs with sites within 600 bp upstream = 62 Fraction of orfs with sites within 600 bp upstream = 0.00995824 Motif number 9 ********** No masking Map Score: 1.97064e-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 10 ********** No masking Map Score: 1.97064e-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: 1.97064e-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