AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_mjan.txt -z/home/amcguire/genomes/mjan.fna -imodE_mjan_opreg_100.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 MJ0718 25 chromate resistance protein (chrA) #3 MJ0719 55 RNase L inhibitor #4 MJ0720 194 3-isopropylmalate dehydrogenase 1 (leuB1) #5 MJ0824 100 molybdenum cofactor biosynthesis protein (moaA) #6 MJ1135 217 molybdenum cofactor biosynthesis protein (moaC) #7 MJ1368 122 sulfate transport system permease protein (cysT) Motif number 1 ATTTTATTTTTAAAATTTTTAA 1 2 1 TTTTATTTTA 0.962881 -121 TTTTAAAATTTTTAATTTTTATTATTAATAT 1 18 1 TTTAATTTTA 0.968145 -105 AATTTTTATTATTAATATTTTACTTCCTTCC 1 31 1 ATTAATTTTT 0.865647 -92 CTTTTGTTATTTTAATTTATATTCATTAATT 1 76 1 TTTAATTATA 0.967474 -47 ATTTATATTCATTAATTTATATATTTATTTA 1 90 1 ATTAATTATA 0.948882 -33 TTTCCACCGTTTAAATAAATATATAAATTAA 1 101 0 TTAAATAATA 0.884166 -22 ATTAATCTATTTTTCTTTAGA 3 1 1 ATTAATTATT 0.865645 -55 AATTTTTAAAATAAAAGAATAGAAAAGCTTT 3 31 0 ATAAAAAATA 0.496238 -25 TTTAAATTTTTAAAATAAAAGA 3 44 0 TTAAATTTTA 0.913426 -12 CCCTTAAAAGTTTTATTTTTAATTTTAAAAT 4 26 0 TTTTATTTTA 0.962881 -169 CATTATAAGTATTTATATTTTGTGTTGTTTT 4 65 1 ATTTATTTTT 0.845558 -130 TGTTGAGTATTTTAATCATTTTTGATATGGT 4 97 1 TTTAATATTT 0.884174 -98 GTGAAAGTATTTTTATTAATATTGCTATAAT 4 154 1 TTTTATAATA 0.948937 -41 TATTGCTATAATTAATCTTTTTGGTGATAAG 4 173 1 ATTAATTTTT 0.865647 -22 TTTTAGATTAATTAAAGTATATAAAT 5 6 0 ATTAAATATA 0.798676 -95 TACGTAGCTTTTTTATAATTAATTTCCCAAT 5 41 1 TTTTATATTA 0.94955 -60 AAAATTAAGGTTTTAAAAATAGAATTGGGAA 5 64 0 TTTTAAAATA 0.799744 -37 TATATGTAAGTTTAAAGTTTA 6 1 0 TTTAAATTTA 0.867082 -217 TTAAACTTACATATATGAATATATTTATAAA 6 17 1 ATATATAATA 0.797755 -201 TATAAATCATTTTTATAAATATATTCATATA 6 28 0 TTTTATAATA 0.949545 -190 TATAAAAATGATTTATATATAGAACTTTCGC 6 42 1 ATTTATTATA 0.940779 -176 CTTTCGCAACTTATATTTTTAAAAAGGTATT 6 66 1 TTATATTTTA 0.899797 -152 TTTAATAAATTTTTAATGAAA 7 1 1 TTTAATAATT 0.88417 -122 AACACAAATTTTATATAATTAGGTAATTTAA 7 65 1 TTATATATTA 0.866427 -58 ****** **** Masking position 2 Map Score: 36.686 Number of sites scoring better than the average of aligned sites = 2095 Number in coding regions = 1410 Number in noncoding regions = 685 Number of orfs with sites within 600 bp upstream = 489 Fraction of orfs with sites within 600 bp upstream = 0.0785416 Motif number 2 ATTAAAAATTTTAAAAATAAAAT 1 4 0 TTAAAAATAA 0.975019 -119 AATATTAATAATAAAAATTAAAAATTTTAA 1 20 0 ATAAAAATTA 0.960317 -103 AAATTAATGAATATAAATTAAAATAACAAA 1 78 0 ATATAAATTA 0.886731 -45 TTAAATAAATATATAAATTAATGAATATAA 1 92 0 ATATAAATTA 0.886731 -31 TTCTTTTATTTTAAAAATTTAAA 3 43 1 TTAAAAATTT 0.934505 -13 GATTTTAAAATTAAAAATAAAACTTTTAAG 4 25 1 TTAAAAATAA 0.975019 -170 ACAACACAAAATATAAATACTTATAATGCA 4 63 0 ATATAAATAC 0.758834 -132 TTAAACCATATCAAAAATGATTAAAATACT 4 102 0 TCAAAAATGA 0.824249 -93 ATACTTTCACATAAAAATGTTTTGTTGGTG 4 134 0 ATAAAAATGT 0.916402 -61 AGCAATATTAATAAAAATACTTTCACATAA 4 150 0 ATAAAAATAC 0.906705 -45 CGTAGCTTTTTTATAATTAATTTCCCAATT 5 43 1 TTATAATTAA 0.500875 -58 AATTAAGGTTTTAAAAATAGAATTGGGAAA 5 63 0 TTAAAAATAG 0.881627 -38 TACTCACTACTAAAAAATTAAGGTTTTAAA 5 78 0 TAAAAAATTA 0.744967 -23 GAATATATTTATAAAAATGATTTATATATA 6 33 1 ATAAAAATGA 0.963254 -185 AAATACCTTTTTAAAAATATAAGTTGCGAA 6 68 0 TTAAAAATAT 0.942749 -150 AATATTTTCATTAAAAATTTATTAAA 7 7 0 TTAAAAATTT 0.934505 -116 TTTAATTACCTTAAAAATGATTAAGATTGA 7 91 1 TTAAAAATGA 0.973636 -32 ********** Masking position 5 Map Score: 24.7419 Number of sites scoring better than the average of aligned sites = 1549 Number in coding regions = 1068 Number in noncoding regions = 481 Number of orfs with sites within 600 bp upstream = 409 Fraction of orfs with sites within 600 bp upstream = 0.0656923 Motif number 3 TTAATCACCAAAATGATTTTAAA 4 2 1 TATCACCAAA 0.992678 -193 ATGATTAAAATACTCAACAAAAAACAACACAA 4 84 0 TATCAACAAA 0.98149 -111 GATATGGTTTAAGTCACCAACAAAACATTTTT 4 120 1 AATCACCAAA 0.955341 -75 ACTTATCACCAAAAAGATTAATTA 4 181 0 TTTCACCAAA 0.977205 -14 ACTTACTCACTACTAAAAAATTAAG 5 86 0 TATCACTACA 0.971211 -15 TAGGCATCAATATTCAATAAAACATTTTATTC 6 107 1 TATCAATAAA 0.964122 -111 ATACTACAATTATACAATAACATTATAATCAT 6 169 0 TAACAATAAA 0.809743 -49 TTAATCACCACTACTTTATTAAA 6 205 0 TATCACCACA 0.985126 -13 TAGTATAATATTTTCATTAAAAATTTATTAAA 7 11 0 TTTCATTAAA 0.767681 -112 ** ******* * Masking position 6 Map Score: 11.2716 Number of sites scoring better than the average of aligned sites = 181 Number in coding regions = 133 Number in noncoding regions = 48 Number of orfs with sites within 600 bp upstream = 51 Fraction of orfs with sites within 600 bp upstream = 0.00819146 Motif number 4 ATTTTATTTTTAAAATTTTTAATTTTTAT 1 8 1 TTTAAAATTT 0.740342 -115 AACAAAAGAATTCTAAAGTTTTGGAAGGAAGT 1 52 0 TTTAAAGTTT 0.970269 -71 CTATTTTTCTTTAGAAAGCTTTTCTATTCTTT 3 17 1 TTGAAAGCTT 0.929088 -39 ATATAAATACTTATAATGCATTACTTCCCTTA 4 51 0 TTTAATGCAT 0.670893 -144 AACATTTTTATGTGAAAGTATTTTTATTAATA 4 143 1 TGGAAAGTAT 0.967481 -52 AAAATAGAATTGGGAAATTAATTATAAAAAAG 5 48 0 TGGAAATTAT 0.820902 -53 AAATATAAGTTGCGAAAGTTCTATATATAAAT 6 52 0 TGGAAAGTTT 0.976166 -166 ATTTTATTCCTGCGAAAGTTCTATATAGTTTA 6 130 1 TGGAAAGTTT 0.976166 -88 TCGGCAATGATTATAATGTTATTGTATAATTG 6 163 1 TTTAATGTTT 0.890078 -55 GTATTTGGTTTAATAAAGTAGTGGTGATTAA 6 197 1 TATAAAGTAT 0.896678 -21 TTTAATAAATTTTTAATGAAAATA 7 3 1 TATAAATTTT 0.647959 -120 TCTTAATCATTTTTAAGGTAATTAAATTACCT 7 85 0 TTTAAGGTAT 0.831759 -38 ** ******* * Masking position 6 Map Score: 9.48219 Number of sites scoring better than the average of aligned sites = 679 Number in coding regions = 549 Number in noncoding regions = 130 Number of orfs with sites within 600 bp upstream = 125 Fraction of orfs with sites within 600 bp upstream = 0.0200771 Motif number 5 AAAATATTAATAATAAAAATTAAAAATTTT 1 22 0 TAATAAAAAT 0.758149 -101 ATATATAAATTAATGAATATAAATTAAAAT 1 84 0 TAATGAATAT 0.814407 -39 AAAAGCTTTCTAAAGAAAAATAGATTAAT 3 10 0 TAAAGAAAAA 0.894959 -46 TTTAAATTTTTAAAATAAAAGAATAGAAAA 3 36 0 TAAAATAAAA 0.724969 -20 ATTAAAATACTCAACAAAAAACAACACAAA 4 83 0 TCAACAAAAA 0.693213 -112 GTTGGTGACTTAAACCATATCAAAAATGAT 4 111 0 TAAACCATAT 0.877464 -84 ATAGCAATATTAATAAAAATACTTTCACAT 4 152 0 TAATAAAAAT 0.758149 -43 TTAGATTAATTAAAGTATATAAAT 5 5 0 TAAAGTATAT 0.844823 -96 ATACTTTAATTAATCTAAAATCATTACGTA 5 17 1 TAATCTAAAA 0.845696 -84 TAAACTTTAAACTTACATAT 6 1 1 TAAACTTTAA 0.397686 -217 CATTGCCGAATAAACTATATAGAACTTTCG 6 142 0 TAAACTATAT 0.914101 -76 ATACTACAATTATACAATAACATTATAATC 6 171 0 TATACAATAA 0.508188 -47 ACTACTTTATTAAACCAAATACTACAATTA 6 189 0 TAAACCAAAT 0.913535 -29 AATAAATTTTTAATGAAAATATTATACTAT 7 14 1 TAATGAAAAT 0.86621 -109 AAATTTGTGTTAAACAAAATTGATGACATT 7 46 0 TAAACAAAAT 0.960894 -77 ********** Masking position 9 Map Score: 11.7697 Number of sites scoring better than the average of aligned sites = 1130 Number in coding regions = 943 Number in noncoding regions = 187 Number of orfs with sites within 600 bp upstream = 194 Fraction of orfs with sites within 600 bp upstream = 0.0311597 Motif number 6 ********** No masking Map Score: -2.32047e-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 7 ********** No masking Map Score: -2.32047e-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 8 ********** No masking Map Score: -2.32047e-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