AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_mthe.txt -z/home/amcguire/genomes/mthe.fna -intrC_mthe_opreg_100.orf -g0.495 -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 = 0.495 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 MTH133 167 cobalt transport ATP-binding protein O #2 MTH151 75 methyl coenzyme M reductase system, component A2 homolog #3 MTH478 49 sulfate transport system permease protein #4 MTH479 136 conserved protein #5 MTH604 116 adhesion protein #6 MTH695 248 conserved protein #7 MTH1370 137 ABC transporter (ATP-binding protein) #8 MTH1570 74 glutamine synthetase #9 MTH1571 300 molybdopterin biosynthesis protein MoeB homolog #10 MTH1705 33 cobalt transport membrane protein #11 MTH1707 300 cobalamin biosynthesis protein M Motif number 1 AGCCCACCATCTGGAGGTATCAGAAATCAA 1 47 0 CTGGAGGTAT 0.863828 -121 TTAGATTCTAATGAAGGACCTGAGAGTCAT 6 47 0 ATGAAGGACC 0.90999 -202 GAAAGGGAAGCTGAAGGACTGGAAAAGGAG 6 82 0 CTGAAGGACT 0.90999 -167 TGATTATATGATGGAGGTTCCTATTATAAC 6 226 0 ATGGAGGTTC 0.863828 -23 GGTCCTTTATATATAGGTCCATATAAGAGA 7 33 0 ATATAGGTCC 0.659139 -105 AATTAATTATATGGGGGTCCTTTATATATA 7 48 0 ATGGGGGTCC 0.978265 -90 CAGTCAGCCACTGGAGGTCCCGCTGTAGCG 7 109 0 CTGGAGGTCC 0.99601 -29 CAGTGGCTGACTGGGGGACTCA 7 126 1 CTGGGGGACT 0.970322 -12 CAGAATGGCTCCAGAGGACCGCCCCAGACA 9 124 1 CCAGAGGACC 0.897236 -177 GAGCCTATCACTGGAGATCCTGTGGGAAAG 9 179 0 CTGGAGATCC 0.947118 -122 GGGGGTCATCCTGTAGGACCACAGCCTTAT 9 224 0 CTGTAGGACC 0.969083 -77 ATGACCATTGCCGGGGGTCTCAGGGTGTAT 11 148 0 CCGGGGGTCT 0.939755 -153 ********** Masking position 6 Map Score: 15.2939 Number of sites scoring better than the average of aligned sites = 1409 Number in coding regions = 1345 Number in noncoding regions = 64 Number of orfs with sites within 600 bp upstream = 51 Fraction of orfs with sites within 600 bp upstream = 0.00819146 Motif number 2 AAGTCGGGGTCTTAAAAATAAAGTAGTATGTT 3 19 0 CTTAAAATAA 0.904192 -31 TAAATTTTAACATAAAATATATAAACATTTAT 5 27 0 CATAAAAAAT 0.923094 -90 TAATATAAACGATAAAATTTAATAAATTTTAA 5 49 0 GATAAAATAA 0.930569 -68 TCATCTGGAGCTTAAAAATAATTTAATGAAAA 6 19 0 CTTAAAATAT 0.857763 -230 GTTAAAGATCCATAAAAGTCAACCGCTACCAT 6 169 1 CATAAAATAA 0.967101 -80 AAAGGACCCCCATATAATTAATTCAGGAATTG 7 55 1 CATATAATAT 0.857764 -83 ACAAAAAATATATAAACCAGTAG 8 2 1 CAAAAAAAAT 0.793962 -73 CTTTTTTATCCTTAAAACAGAAAAGATGAATT 9 12 1 CTTAAAAAAA 0.857764 -289 GAATTCTTCTGAAAAAACAAAAATCACGTTTC 9 39 1 GAAAAAAAAA 0.733299 -262 TGTGTGTGTTGATATAAATCATGAGGGGGTCA 9 246 0 GATATAATAT 0.733299 -55 GACTTCACCAGAAAAAAATTAATTGGGAGGA 10 10 0 GAAAAAATAA 0.811425 -24 ATATAGATTCCATAAAATTAAAAACATCATTA 11 22 0 CATAAAATAA 0.967101 -279 ATCAAACATTCATATAATATAAAGGTTGAAGT 11 238 0 CATATAAAAA 0.857764 -63 ******* * ** Masking position 6 Map Score: 10.2441 Number of sites scoring better than the average of aligned sites = 112 Number in coding regions = 64 Number in noncoding regions = 48 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 3 TCATGAATGGATAAATTCATAGCCCACCAT 1 67 0 ATAAATTCAT 0.822838 -101 TGCTTCTAGTATATATTCATGGAGCCGGTG 2 52 1 ATATATTCAT 0.941121 -24 CGACATGGACATATATACATATCGGTTCTG 4 82 0 ATATATACAT 0.932192 -55 CAGAACACCTATATCGACATGGACATATAT 4 96 0 ATATCGACAT 0.80852 -41 AACATAAAATATATAAACATTTATTAAGAT 5 21 0 ATATAAACAT 0.928701 -96 CAACGCAACCATATAATAATTGTTAATATA 5 74 0 ATATAATAAT 0.594048 -43 AACCTCCATCATATAATCATCC 6 237 1 ATATAATCAT 0.929003 -12 CACAAAGTTTATATATAGATTCCATAAAAT 11 36 0 ATATATAGAT 0.827635 -265 CGCTGAACACATAAAGACATGGACCTTTTT 11 72 1 ATAAAGACAT 0.849011 -229 TGAATGTTTGATATAGTGATTGGAATTAAA 11 258 1 ATATAGTGAT 0.861926 -43 ********** Masking position 3 Map Score: 7.18668 Number of sites scoring better than the average of aligned sites = 65 Number in coding regions = 49 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 4 CATGATCTGTTTCATCGATCCGATAGGATTAA 1 92 1 TTCATGACCG 0.993382 -76 CTAGTATATATTCATGGAGCCGGTGGCGA 2 57 1 TTCATGACCG 0.993383 -19 TTCTCATTCCTTCACAGAACCGATATGTATAT 4 68 1 TTCACGACCG 0.997052 -69 ATAAAACCCCTTCCCTGAACCGAACTGTTTTT 9 86 1 TTCCCGACCG 0.99348 -215 ACATCTGCTTTTCACTGATCTGAAGAATCTTT 9 151 1 TTCACGACTG 0.984806 -150 ***** ** *** Masking position 8 Map Score: 7.13472 Number of sites scoring better than the average of aligned sites = 16 Number in coding regions = 14 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 5 AACATAAAATATATAAACATTTATTAAGAT 5 21 0 ATATAAACAT 0.705047 -96 ATAATTGTTAATATAAACGATAAAATTTAA 5 59 0 ATATAAACGA 0.957667 -58 ATATAGGTCCATATAAGAGAGTAGTTAAGC 7 23 0 ATATAAGAGA 0.755294 -115 ATGGACCTATATATAAAGGACCCCCATATA 7 41 1 ATATAAAGGA 0.957667 -97 ACAAAAAATATATAAACCAGTAGAAGGAA 8 10 1 ATATAAACCA 0.932907 -65 CTGCAAGCAGATATAAGGCTGTGGTCCTAC 9 212 1 ATATAAGGCT 0.871172 -89 GTGTGTGTTGATATAAATCATGAGGGGGTC 9 247 0 ATATAAATCA 0.72711 -54 TGGAATCTATATATAAACTTTGTGCATTGT 11 42 1 ATATAAACTT 0.705056 -259 TATTACCACAATATAAGGGAAACCGAAGAT 11 197 1 ATATAAGGGA 0.941545 -104 CATTCATATAATATAAAGGTTGAAGTGATT 11 234 0 ATATAAAGGT 0.939217 -67 ********** Masking position 5 Map Score: 6.78219 Number of sites scoring better than the average of aligned sites = 67 Number in coding regions = 53 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 6 GGTGAAGTTAAGCTCATGCCATGGAGGCAT 8 50 1 AGCTCATGCC 0.959391 -25 GGGTTATGCCTCCATGGCAT 8 65 0 GGGTTATGCC 0.793821 -10 TCCAGTGATAGGCTCATGCTGCAAGCAGAT 9 194 1 GGCTCATGCT 0.976592 -107 AATCATGAGGGGGTCATCCTGTAGGACCAC 9 232 0 GGGTCATCCT 0.976592 -69 CCGCCTATCTGGCACATCCCCACCATTTAT 11 103 0 GGCACATCCC 0.806835 -198 CCCCCGGCAATGGTCATCCCTCCGCTCAGG 11 161 1 TGGTCATCCC 0.962931 -140 ********** Masking position 6 Map Score: 4.04077 Number of sites scoring better than the average of aligned sites = 196 Number in coding regions = 186 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 7 TATCGGATCGATGAAACAGATCATGAATGG 1 87 0 ATGAAACAGA 0.862896 -81 ATCCGATAGGATTAAGCAGACTTAAATATA 1 109 1 ATTAAGCAGA 0.828576 -59 GTCCTGAAAGATAAAGAAGGACTACTCTGA 4 29 0 ATAAAGAAGG 0.885683 -108 AAATAATTTAATGAAAAAGGGAGTT 6 6 0 ATGAAAAAGG 0.96225 -243 GGATGATTATATGATGGAGGTTCCTATTAT 6 229 0 ATGATGGAGG 0.91931 -20 ATGCAAGAACATGAAAGAGGGTTTGA 9 285 1 ATGAAAGAGG 0.975658 -16 CCCACCATTTATTAAAAAGGTCCATGTCTT 11 85 0 ATTAAAAAGG 0.925047 -216 TTAAAAAAAGATTAAGGAGGCGAATAGC 11 283 1 ATTAAGGAGG 0.968535 -18 ********** Masking position 4 Map Score: 5.35348 Number of sites scoring better than the average of aligned sites = 218 Number in coding regions = 203 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 8 TCCTCTGAGATCTGCTGATATCCTCACA 1 7 1 GAGTTGCTGA 0.982776 -161 ATAGTTCTAATAGTTTTACTGACATAATAACT 2 18 0 TAGTTACTGA 0.928616 -58 TTAAGACCCCGACTTTTTCTGAAG 3 36 1 GACTTTCTGA 0.972954 -14 CATGTCGATATAGGTGTTCTGAGTTAATGGAG 4 105 1 TAGTTTCTGA 0.977168 -32 CAGAAAAGATGAATTCTTCTGAAAAAACAAAA 9 29 1 GAATTTCTGA 0.96043 -272 CGGTCCTCTGGAGCCATTCTGAAATCGAAAAA 9 113 0 GAGCTTCTGA 0.978865 -188 *** * ****** Masking position 7 Map Score: 1.4095 Number of sites scoring better than the average of aligned sites = 42 Number in coding regions = 37 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 9 GGGAATAACTCCCTCAGAGTAGTCCTTCTT 4 16 1 CCCTCAGAGT 0.937985 -121 CCTTCTTTATCTTTCAGGACGATCCCATGT 4 39 1 CTTTCAGGAC 0.860636 -98 CTCCAGATGACTCTCAGGTCCTTCATTAGA 6 41 1 CTCTCAGGTC 0.905052 -208 AGATGTGATTTCCACAGGGCTTAAGTTATA 6 202 1 TCCACAGGGC 0.881716 -47 AAGAATCTTTCCCACAGGATCTCCAGTGAT 9 173 1 CCCACAGGAT 0.980778 -128 AGGCTGTGGTCCTACAGGATGACCCCCTCA 9 227 1 CCTACAGGAT 0.909479 -74 CAGGATGACCCCCTCATGATTTATATCAAC 9 241 1 CCCTCATGAT 0.905084 -60 ATTGCCGGGGGTCTCAGGGTGTATAATGGT 11 142 0 GTCTCAGGGT 0.908935 -159 GTCATCCCTCCGCTCAGGGTGCGATATTAC 11 173 1 CGCTCAGGGT 0.972509 -128 ********** Masking position 6 Map Score: 4.21202 Number of sites scoring better than the average of aligned sites = 1531 Number in coding regions = 1462 Number in noncoding regions = 69 Number of orfs with sites within 600 bp upstream = 60 Fraction of orfs with sites within 600 bp upstream = 0.00963701 Motif number 10 AAAAACCGATGTGAGGATATCAGCAGATCTC 1 17 0 GTGAGATATC 0.922952 -151 GTTCTGGGAATAACTCCCTCAGAG 4 4 1 CTGGAATAAC 0.856821 -133 GCTGGTTAAAATGACAATCTCTGCTCTTTAT 6 128 1 ATGAAATCTC 0.715617 -121 CTTAAGCCCTGTGGAAATCACATCTGATGGT 6 196 0 GTGGAATCAC 0.977683 -53 TAGTTAAGCGGTGATGATCAC 7 1 0 GTGAGATCAC 0.59341 -137 AGGTCCCGCTGTAGCGATAACATTTTTATCG 7 94 0 GTAGGATAAC 0.874664 -44 CCCTTATATTGTGGTAATATCGCACCCTGAG 11 185 0 GTGGAATATC 0.950917 -116 CCGAAGATTAGTAATAATCACTTCAACCTTT 11 219 1 GTAAAATCAC 0.815422 -82 **** ****** Masking position 7 Map Score: 2.37989 Number of sites scoring better than the average of aligned sites = 146 Number in coding regions = 128 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 11 GGTCTTTAACCTCCATTAACTCAGA 4 122 0 TTAACCTCCA 0.97178 -15 TAAATTATTTTTAAGCTCCAGATGACTCTC 6 26 1 TTAAGCTCCA 0.980104 -223 TCTCTGCTCTTTATGCTCCATTCCGTTAAA 6 145 1 TTATGCTCCA 0.972221 -104 TCCATTCCGTTAAAGATCCATAAAAGTCAA 6 161 1 TAAAGATCCA 0.87031 -88 ATAATGGTAATAATCCTCCGCCTATCTGGC 11 120 0 TAATCCTCCG 0.883174 -181 ********** Masking position 7 Map Score: 0.657018 Number of sites scoring better than the average of aligned sites = 64 Number in coding regions = 52 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 12 TGAAGGACTGGAAAAGGAGAACACTTAGAT 6 71 0 GAAAAGGAGA 0.941769 -178 CACTTAGAAAGGGAAGCTGAAGGACTGGAA 6 88 0 GGGAAGCTGA 0.926507 -161 AAGTGGCTATGAAAAGCTGGTTAAAATGAC 6 113 1 GAAAAGCTGG 0.9655 -136 CCTTAAAACAGAAAAGATGAATTCTTCTGA 9 21 1 GAAAAGATGA 0.939889 -280 TCAGATCAGTGAAAAGCAGATGTCTGGGGC 9 144 0 GAAAAGCAGA 0.977454 -157 ********** Masking position 5 Map Score: 0.210566 Number of sites scoring better than the average of aligned sites = 43 Number in coding regions = 37 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 13 ********** No masking Map Score: -3.62134e-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: -3.62134e-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 ********** No masking Map Score: -3.62134e-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