AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_mjan.txt -z/home/amcguire/genomes/mjan.fna -icarP_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 MJ1019 132 carbamoyl-phosphate synthase, small (or glutamine) subunit (carA) #2 MJ1378 184 carbamoyl-phosphate synthase, medium subunit (carB1) #3 MJ1379 196 conserved hypothetical protein #4 MJ1381 124 carbamoyl-phosphate synthase, large subunit (carB2) Motif number 1 AATTTATGGTTGTTAATAATTGATGAAATGGTGAATAGA 1 12 0 TATATTTGAT 0.899338 -121 CTATCACATATATATATGATTGGGATAATCATCTATCTA 1 80 0 TATATTGAAT 0.955743 -53 ATATTTCACCAAAATACCTATAAACTATCACATA 1 109 0 TAAATATAAA 0.950691 -24 TACTTAAAGTTAAGTAACATAAATATAGTTATGCAATTT 2 70 1 TAAATATAAT 0.978778 -115 TAAAAGCTCATCCTCAATATTAAGATAATCTGAATAATA 2 109 1 TAAATTGAAT 0.986635 -76 ACAATAATATTTTACAATATTTATATATTTAACTATTAT 2 145 0 TAAATTTAAT 0.976061 -40 AATATAAGATTCATCAAAATTAATATATTTATTTTGGTT 3 31 0 TAAATTTAAT 0.983638 -166 CCAACTAAAGTTACCAATATTCTTCCAGTTATTAAAGCC 3 88 0 TAAATTTCAT 0.919084 -109 GTAACTTTAGTTGGAATTATATGTGTAATTAATGGATTA 3 113 1 TATATATGAT 0.872062 -84 TAAAGAGGGTTAAAGAAGAATAAGAAATATAGTATATAG 3 159 1 TAAAATGAAA 0.751874 -38 TTCATAAATATTTTGGGATTGATTATATCC 4 2 1 TAAATTGGAT 0.973874 -123 TATATCCTTCTTTGGAAGATAGTTAAAGAAGACGTTCCT 4 34 1 TAAATATAAA 0.94121 -91 AAAGAAGACGTTCCTAAAATAAAGAAAGAAGTTGAGATA 4 58 1 TAAATAGAAA 0.959076 -67 TTGAGATAGTTTTAAAAGATATTGAAAATAAAAAATAGG 4 89 1 TAAATAGAAT 0.982477 -36 * ** *** ** * * Masking position 9 Map Score: 19.6702 Number of sites scoring better than the average of aligned sites = 593 Number in coding regions = 449 Number in noncoding regions = 144 Number of orfs with sites within 600 bp upstream = 142 Fraction of orfs with sites within 600 bp upstream = 0.0228076 Motif number 2 GTTTTTAAAGTTAATGGTAGGTAAATGGTGATA 2 13 0 TTAATGTATA 0.963831 -172 AAAAGGATACTTAAAGTTAAGTAACATAAATAT 2 63 1 TTAAAGTATA 0.969403 -122 GTTAAGTAACATAAATATAGTTATGCAATTTTA 2 78 1 ATAAATTATA 0.8224 -107 ATAATAATAGTTAAATATATAAATATTGTAAAA 2 142 1 TTAAATTAAA 0.965642 -43 AGAAACCAAAATAAATATATTAATTTTGATGAA 3 28 1 ATAAATTAAA 0.88702 -169 GCCAATAATGTTAATGCTACAAATATAAGATTC 3 58 0 TTAATGTAAA 0.975421 -139 CTTCCAGTTATTAAAGCCAATAATGTTAATGCT 3 73 0 TTAAAGCAAA 0.951337 -124 ATAATTCCAACTAAAGTTACCAATATTCTTCCA 3 100 0 CTAAAGTAAA 0.926228 -97 CAATAATCCATTAATTACACATATAATTCCAAC 3 122 0 TTAATTCATA 0.897606 -75 TTAACCCTCTTTAATGCCAATAATCCATTAATT 3 139 0 TTAATGCAAA 0.675266 -58 AACTTCTTTCTTTATTTTAGGAACGTCTTCTTT 4 58 0 TTTATTTAAA 0.751272 -67 ****** ** ** Masking position 9 Map Score: 11.299 Number of sites scoring better than the average of aligned sites = 732 Number in coding regions = 573 Number in noncoding regions = 159 Number of orfs with sites within 600 bp upstream = 159 Fraction of orfs with sites within 600 bp upstream = 0.0255381 Motif number 3 GACATTATGCATTTTATAATTTATGGTTGT 1 38 0 ATTTTATAAT 0.678882 -95 CTACCATTAACTTTAAAAACCTTAACTGAT 2 26 1 CTTTAAAAAC 0.879194 -159 TGAGGATGAGCTTTTAAAATTGCATAACTA 2 95 0 CTTTTAAAAT 0.85694 -90 ATTTTGGTTTCTTTTTTCATAATTTCCCA 3 10 0 CTTTTTTCAT 0.832642 -187 ACATTATTGGCTTTAATAACTGGAAGAATA 3 80 1 CTTTAATAAC 0.941311 -117 CTTCTTTAACCCTCTTTAATGCCAATAATC 3 147 0 CCTCTTTAAT 0.804109 -50 ATTTCTTATTCTTCTTTAACCCTCTTTAAT 3 157 0 CTTCTTTAAC 0.971813 -40 TTAGGAACGTCTTCTTTAACTATCTTCCAA 4 45 0 CTTCTTTAAC 0.971813 -80 TTTTCAATATCTTTTAAAACTATCTCAACT 4 87 0 CTTTTAAAAC 0.943183 -38 ********** Masking position 3 Map Score: 7.49002 Number of sites scoring better than the average of aligned sites = 1138 Number in coding regions = 1025 Number in noncoding regions = 113 Number of orfs with sites within 600 bp upstream = 110 Fraction of orfs with sites within 600 bp upstream = 0.0176678 Motif number 4 TTCATCAATTATTAACAACCATAAATTATAA 1 24 1 ATTAACACCA 0.850721 -109 TATGATTGGGATAATCATCTATCTACTGCTT 1 74 0 ATAATCACTA 0.96175 -59 CAAAATACCTATAAACTATCACATATATATA 1 103 0 ATAAACTTCA 0.861615 -30 CCTTTTCCTAATAATCAGTTAAGGTTTTTAA 2 38 0 ATAATCATTA 0.940004 -147 ATATTTAACTATTATTATTCAGATTATCTTA 2 129 0 ATTATTATCA 0.705393 -56 ATCCACCACAATAATATTTTACAATATTTAT 2 160 0 ATAATATTTA 0.529232 -25 CAATATCCACCACAATAATATT 2 173 0 AATATCCCCA 0.778389 -12 TTCTTTTTTCATAATTTCCCA 3 1 0 ATAATTTCCA 0.87075 -196 AAAGTTACCAATATTCTTCCAGTTATTAAAG 3 90 0 ATATTCTCCA 0.839759 -107 TTTAATGCCAATAATCCATTAATTACACATA 3 132 0 ATAATCCTTA 0.898705 -65 AAAGAAGGATATAATCAATCCCAAAATATTT 4 16 0 ATAATCATCC 0.828768 -109 GTCTTCTTTAACTATCTTCCAAAGAAGGATA 4 36 0 ACTATCTCCA 0.839059 -89 TTTTATTTTCAATATCTTTTAAAACTATCTC 4 91 0 AATATCTTTA 0.646038 -34 ATAATCACCTATTTTTTATTT 4 114 0 ATAATCACTA 0.96175 -11 ******* *** Masking position 1 Map Score: 8.69211 Number of sites scoring better than the average of aligned sites = 1210 Number in coding regions = 1076 Number in noncoding regions = 134 Number of orfs with sites within 600 bp upstream = 121 Fraction of orfs with sites within 600 bp upstream = 0.0194346 Motif number 5 TAATTGATGAAATGGTGAATAGAC 1 5 0 AATGGTGAAT 0.922 -128 AAAGCAGTAGATAGATGATTATCCCAATCA 1 73 1 ATAGATGATT 0.942588 -60 TATCACATATATATATGATTGGGATAATCA 1 88 0 ATATATGATT 0.822669 -45 AATCATATATATATGTGATAGTTTATAGGT 1 98 1 ATATGTGATA 0.880997 -35 TTATAGGTATTTTGGTGAAATAT 1 120 1 TTTGGTGAAA 0.879359 -13 ATGGTAGGTAAATGGTGATAAT 2 3 0 AATGGTGATA 0.945587 -182 TGGGAAATTATGAAAAAAGAAACCA 3 6 1 AATTATGAAA 0.67518 -191 ATATATTAATTTTGATGAATCTTATATTTG 3 42 1 TTTGATGAAT 0.813351 -155 ATATTTTGGGATTGATTATATCCTTCTTTG 4 18 1 ATTGATTATA 0.677122 -107 AAAATAAAAAATAGGTGATTAT 4 113 1 ATAGGTGATT 0.963283 -12 ********** Masking position 6 Map Score: 6.52495 Number of sites scoring better than the average of aligned sites = 1290 Number in coding regions = 1054 Number in noncoding regions = 236 Number of orfs with sites within 600 bp upstream = 262 Fraction of orfs with sites within 600 bp upstream = 0.0420816 Motif number 6 ACTATTATTATTCAGATTATCTTAATATTG 2 123 0 TTCAGATTAT 0.887863 -62 ACAATAATATTTTACAATATTTATATATTT 2 154 0 TTTACAATAT 0.910884 -31 ATTTGTAGCATTAACATTATTGGCTTTAAT 3 67 1 TTAACATTAT 0.96259 -130 CCAACTAAAGTTACCAATATTCTTCCAGTT 3 97 0 TTACCAATAT 0.904245 -100 GGTTTCACACTATATACTATATT 3 184 0 TTCACACTAT 0.977337 -13 TCAATATCTTTTAAAACTATCTCAACTTCT 4 84 0 TTAAAACTAT 0.884456 -41 ********** Masking position 6 Map Score: 2.04449 Number of sites scoring better than the average of aligned sites = 179 Number in coding regions = 139 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 42 Fraction of orfs with sites within 600 bp upstream = 0.0067459 Motif number 7 ********** No masking Map Score: 1.5372e-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: 1.5372e-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 ********** No masking Map Score: 1.5372e-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