AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_mthe.txt -z/home/amcguire/genomes/mthe.fna -iphoB_mthe_opreg_300.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 MTH478 49 sulfate transport system permease protein #2 MTH479 136 conserved protein #3 MTH480 91 unknown #4 MTH604 116 adhesion protein #5 MTH676 151 unknown #6 MTH777 48 conserved protein #7 MTH778 68 unknown #8 MTH779 300 conserved protein #9 MTH870 103 conserved protein #10 MTH874 113 porphobilinogen deaminase #11 MTH877 275 unknown #12 MTH922 67 unknown #13 MTH923 21 unknown #14 MTH925 32 conserved protein #15 MTH927 139 ferredoxin #16 MTH928 300 cobalamin biosynthesis protein N #17 MTH1727 117 phosphate-binding protein PstS #18 MTH1728 83 phosphate-binding protein PstS homolog #19 MTH1734 21 phosphate transport system regulator Motif number 1 GATCCTATCTTAATAAATGTTTATATATTTTATGTTA 4 15 1 TAAAATTATA 0.97391 -102 CGATAAAATTTAATAAATTTTAACATAAAATATATAA 4 35 0 TAAAATTATA 0.974016 -82 CGCAACCATATAATAATTGTTAATATAAACGATAAAA 4 64 0 TAAAATTATA 0.974018 -53 ACAGCACACTTTATAAGACTTGAGCACATATGTCATA 5 45 1 TTAAATTAAC 0.793123 -107 TGCAGGACAATAAAAACAGTTTAAAAAACAGTTTTGA 8 130 1 TAAAATTAAA 0.966031 -171 ACTTTAAATATTAAAAGGCTTAATGTATACTTTGTTG 8 242 0 TTAAATTATA 0.916468 -59 ACTGAATTCCTATAAAGCTTTTATATAATGTCCACTG 9 68 0 TATAATTATA 0.916466 -36 TGGGGAGTATTAATAACCTTTCATTACCCCATAGTTA 11 244 1 TAAAATTAAC 0.929077 -32 TGAGGTCCATTAAGAAAGATTTATATATGGACCTGTG 15 102 1 TAAAATTATA 0.97391 -38 GTTAAAGCCCTTTAAACGTTTCAGAAAAATTCTGAAT 16 44 0 TTTAATTAAA 0.709145 -257 GTTATATTTATAAAAATTTTTAATTTCTTGAGTTACA 16 87 1 TAAAATTATC 0.945211 -214 GTGATGAATGTATTAAATTTTCATATAATTATTACTT 16 178 1 TATAATTATA 0.916466 -123 ATTCTTGCTCTAATAAAAATTAAGTAATAATTATATG 16 199 0 TAAAATTAAA 0.965955 -102 AAAAAATTAATAAAAAGTCTTAAATAATCTTCATACC 16 244 1 TAAAATTAAA 0.966063 -57 *** ** ** * ** Masking position 6 Map Score: 19.7692 Number of sites scoring better than the average of aligned sites = 24 Number in coding regions = 9 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 2 ACGATAAAATTTAATAAATTTTAACATAAAATATATAA 4 35 0 TATAATTACA 0.849717 -82 AGTGTGCTGTTCAATAACATTACCATGACCTAAGGAGA 5 17 0 TATAATTCAA 0.934731 -135 CTTCATTTAATCAGTAAAAATAAATGCAGGACAATAAA 8 106 1 TATAAATATA 0.84589 -195 CGTCGAAGATTTAATAAGGTTAACTTTAAATATTAAAA 8 263 0 TATAATTATA 0.929245 -38 AAACTCCAGTTTATTAAAAATCACATAATTATGGCTAC 10 20 0 TATAAATAAA 0.922082 -94 TGTATCCTATTATATAACTTTTCAAAAACTCCAGTTTA 10 45 0 TTTAATTCAA 0.584962 -69 ATTTCTCAAATGATTAACGTTTACTGGAGATGATTCA 10 87 1 TATAATTATA 0.929245 -27 GTCAGATCCATGATTAATTTTCAGATAATGCCCTGCAG 11 179 0 TATAATTAAA 0.965949 -97 AAAGGTGTGCTGAATTACTTTCAGATTACCTTGAA 12 43 1 TATTATTAAA 0.736292 -25 GATAAAATATTCATTAATTATGCAATAACGCGTGATGA 16 147 1 TATAAATCAA 0.856861 -154 TAATAAAAATTAAGTAATAATTATATGAAAATTTAATA 16 188 0 TATAAATAAA 0.922204 -113 TTAAGACTTTTTATTAATTTTTTTATTACATATTCTTG 16 229 0 TATAATTTAA 0.782273 -72 TAAAAAGTCTTAAATAATCTTCATACCATATCCACAAT 16 254 1 TATAATTAAA 0.96595 -47 CACCTATTGGTTAATAAAGTTCACTTGAAGGTGACGGA 18 40 0 TATAATTATA 0.929243 -44 * * *** ** * * * Masking position 7 Map Score: 12.46 Number of sites scoring better than the average of aligned sites = 35 Number in coding regions = 12 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 3 GTGTTCTGAGTTAATGGAGGTTAAAGACC 2 118 1 TAATGGATAA 0.978217 -19 TGTATTACTTTATCTGGATTTAACACAGAATAATTAT 5 96 1 TTCTGGATAA 0.89864 -56 TCACTCATTCTAACAGGAGGTAAGATTA 9 2 0 TACAGGATAT 0.60612 -102 ATGTGGGACTTCAATGTATATCTATTAATTCAGTGGA 9 38 1 TAATGTATTA 0.728718 -66 ATCTATTAATTCAGTGGACATTATATAAAAGCTTTAT 9 57 1 TAGTGGATAA 0.903524 -47 TATAAAAGCTTTATAGGAATTCAGTAAGCTGATT 9 80 1 TATAGGATAA 0.626174 -24 GATTTTTAATAAACTGGAGTTTTTGAAAAGTTATATA 10 36 1 AACTGGATTA 0.608571 -78 TGATTAACGTTTACTGGAGATGATTCA 10 97 1 TACTGGATAA 0.970564 -17 TTCTGTTTTATTAAAGGAAATTACAAAAAAGGAGTTT 11 51 0 TAAAGGATAA 0.923518 -225 TTTTGATGGATAAATGGATCTCTATCAGGGACATCTG 11 129 0 TAATGGATTA 0.958546 -147 CCTGCAGTTCTGAATGGATGTTTTGATGGATAAATGG 11 149 0 TAATGGATTT 0.800563 -127 TAAATCTTTCTTAATGGACCTCATGAAAACAGTACTG 15 88 0 TAATGGATAA 0.97821 -52 GAAAGATTTATATATGGACCTGTGGAATATACGAT 15 115 1 TTATGGATTA 0.861478 -25 GTATTACCGATGTATGTAACTCAAGAAATTAAAAATT 16 101 0 TTATGTATAA 0.583759 -200 CGGTAATACATAAATGCAGATAAAATATTCATTAATT 16 129 1 TAATGCATAA 0.814262 -172 * ****** * * * Masking position 8 Map Score: 9.21196 Number of sites scoring better than the average of aligned sites = 152 Number in coding regions = 122 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 4 TAAGACCCCGACTTTTTCTGAAG 1 37 1 ATTTTTCTGA 0.9002 -13 AGTCCTTCTTTATCTTTCAGGACGATCCCAT 2 36 1 TTCTTTCAGG 0.800844 -101 CTTCCGGATATCTTTATCAGTTTGTCCATGA 3 11 1 TTTTATCAGT 0.805414 -81 ATCATGTATTACTTTATCTGGATTTAACACA 5 92 1 ATTTATCTGG 0.936489 -60 AGTAAGTAATAATTATTCTGTGTTAAATCCA 5 110 0 ATTATTCTGT 0.79039 -42 GATTAAATGAAGTTTTTCAGGTTTCCTTATT 8 87 0 ATTTTTCAGG 0.952197 -214 GAAAAACTTCATTTAATCAGTAAAAATAAAT 8 100 1 ATTAATCAGT 0.675298 -201 TCTTTGACTTATTTATTCTGTTTTATTAAAG 11 72 0 ATTATTCTGT 0.79039 -204 GATAAATGGATCTCTATCAGGGACATCTGAA 11 127 0 TTCTATCAGG 0.719848 -149 AAGATGAACATTTTTTTCTGAGCTGGGGAGT 11 221 1 TTTTTTCTGA 0.852153 -55 TCAATTTTTTTATTTTTCAGGAAATACGTGA 15 13 1 TTTTTTCAGG 0.927157 -127 ATCGATTCAGAATTTTTCTGAAACGTTTAAA 16 40 1 ATTTTTCTGA 0.900201 -261 ATTAATGAATATTTTATCTGCATTTATGTAT 16 134 0 ATTTATCTGC 0.771736 -167 * ********* Masking position 7 Map Score: 6.8976 Number of sites scoring better than the average of aligned sites = 262 Number in coding regions = 175 Number in noncoding regions = 87 Number of orfs with sites within 600 bp upstream = 73 Fraction of orfs with sites within 600 bp upstream = 0.011725 Motif number 5 TCCATCACCAGTAAGTAATAATTATTCTGTG 5 119 0 GTAAGAATAA 0.682539 -33 GACTCCCTTTAAACTTAAAAATCATTGGGCA 8 23 1 AAACTAAAAA 0.681031 -278 TTTCCTTATTAAAATAAAAAAATCATTCCAG 8 66 0 AAAATAAAAA 0.911016 -235 TTTATTAAAGGAAATTACAAAAAAGGAGTTT 11 51 0 GAAATACAAA 0.833419 -225 AAACCAGAGAATAAGGAAAAATTAGTTCTTT 11 98 0 ATAAGAAAAA 0.767479 -178 TATTTCCTGAAAAATAAAAAAATTGAAA 15 8 0 AAAATAAAAA 0.911016 -132 TGTAACTCAAGAAATTAAAAATTTTTATAAA 16 93 0 GAAATAAAAA 0.959984 -208 GCAAGAATATGTAATAAAAAAATTAATAAAA 16 228 1 GTAATAAAAA 0.915703 -73 GAAGGTGACGGAAAGAAAAAATGTTGTGGTT 18 21 0 GAAAGAAAAA 0.944694 -63 ACCAATAGGTGAAATCAATAACTGAAG 18 67 1 GAAATAATAA 0.869601 -17 ***** ***** Masking position 7 Map Score: 5.12462 Number of sites scoring better than the average of aligned sites = 90 Number in coding regions = 43 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 6 TTAATAAATGTTTATATATTTTATGTTAAA 4 24 1 TTTATATATT 0.916865 -93 CATGATTGTCTTCATATATGACATATGTGC 5 68 0 TTCATATATG 0.854027 -84 TATGAAGACAATCATGTATTACTTTATCTG 5 82 1 ATCATGTATT 0.774596 -70 TTGCAACTAGATCATATATTGAGGG 7 6 0 ATCATATATT 0.898086 -63 TAAGGTTAACTTTAAATATTAAAAGGCTTA 8 257 0 TTTAAATATT 0.641622 -44 CTATAAAGCTTTTATATAATGTCCACTGAA 9 66 0 TTTATATAAT 0.758232 -38 TTTATTAAAAATCACATAATTATGGCTACC 10 19 0 ATCACATAAT 0.59037 -95 TTAAGAAAGATTTATATATGGACCTGTGGA 15 111 1 TTTATATATG 0.813284 -29 TTTATCTGCATTTATGTATTACCGATGTAT 16 123 0 TTTATGTATT 0.812577 -178 GTATTAAATTTTCATATAATTATTACTTAA 16 187 1 TTCATATAAT 0.85652 -114 TAATTTTTTTATTACATATTCTTGCTCTAA 16 223 0 ATTACATATT 0.722718 -78 ********** Masking position 4 Map Score: 2.87169 Number of sites scoring better than the average of aligned sites = 97 Number in coding regions = 58 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 50 Fraction of orfs with sites within 600 bp upstream = 0.00803084 Motif number 7 TCAGTTTGTCCATGAATCTGATGTTCAGTGA 3 27 1 CAGAATCTGA 0.933782 -65 AGTGGACTGGCCGGGATTTGAACCCGGGGCC 8 166 1 CCGGATTTGA 0.986602 -135 GAAAATTAATCATGGATCTGACCGGTAAGAT 11 195 1 CAGGATCTGA 0.9866 -81 TTTAAACCAGGATCTGATACC 13 7 1 CCGGATCTGA 0.993779 -15 TAAAAGTCCTCCTGGATTTTA 19 1 0 CCGGATTTTA 0.933823 -21 ** ******** Masking position 6 Map Score: 2.31154 Number of sites scoring better than the average of aligned sites = 33 Number in coding regions = 20 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 8 CTCCATTAACTCAGAACACCTATATCGACA 2 107 0 TCAGAACACC 0.911324 -30 TAATCTTACCTCCTGTTAGA 9 1 1 TAATCTTACC 0.820732 -103 AATCAGCTTACTGAATTCCTAT 9 92 0 TCAGCTTACT 0.904358 -12 AAAAAAATGTTCATCTTACCGGTCAGATCC 11 208 0 TCATCTTACC 0.972449 -68 TGAAAGTAATTCAGCACACCTTTCAGGAGC 12 36 0 TCAGCACACC 0.974142 -32 TGAATTACTTTCAGATTACCTTGAA 12 53 1 TCAGATTACC 0.952122 -15 TCTTAAATAATCTTCATACCATATCCACAA 16 261 1 TCTTCATACC 0.849114 -40 ********** Masking position 8 Map Score: 2.0449 Number of sites scoring better than the average of aligned sites = 191 Number in coding regions = 169 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 9 GAGGGAGTTATTCCCAGAAC 2 1 0 TTCCCAGAAC 0.96517 -136 TTCTCATTCCTTCACAGAACCGATATGTAT 2 68 1 TTCACAGAAC 0.958242 -69 AATGTATTTTTTCACTGAACATCAGATTCA 3 39 0 TTCACTGAAC 0.967617 -53 GTAATGTTATTGAACAGCACACTTTATAAG 5 32 1 TGAACAGCAC 0.812757 -120 TCCGGATTTTTGCCCTGAAAC 7 58 1 TGCCCTGAAA 0.870818 -11 TTTCAGATAATGCCCTGCAGTTCTGAATGG 11 169 0 TGCCCTGCAG 0.923461 -107 TAGGACAGTTCACTGCACTGGAAACGCT 12 9 1 TTCACTGCAC 0.973034 -59 ********** Masking position 9 Map Score: 2.25367 Number of sites scoring better than the average of aligned sites = 195 Number in coding regions = 179 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 10 TTTATCTGGATTTAACACAGAATAATTATT 5 104 1 TTTAACACAG 0.856452 -48 AATCCGGACCCTGAAACCAGAGATATGGGG 7 36 0 CTGAAACCAG 0.966148 -33 ATGCAGGACAATAAAAACAGTTTAAAAAAC 8 129 1 ATAAAAACAG 0.690873 -172 TGGCCGGGATTTGAACCCGGGGCCTCCGCC 8 173 1 TTGAACCCGG 0.838485 -128 TCAGGGACATCTGAAACCAGAGAATAAGGA 11 112 0 CTGAAACCAG 0.966148 -164 TTTAAACCAGGATCTGATAC 13 1 1 TTTAAACCAG 0.943541 -21 TCAGCTGCCATGTAAAACAGTACTGTTTTC 15 71 1 TGTAAAACAG 0.736736 -69 AATGGACCTCATGAAAACAGTACTGTTTTA 15 83 0 ATGAAAACAG 0.921028 -57 ********** Masking position 5 Map Score: 0.703756 Number of sites scoring better than the average of aligned sites = 130 Number in coding regions = 112 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 11 AACCTCCATTAACTCAGAACACCTATATCG 2 110 0 AACTCAGAAC 0.907002 -27 CCAGCGATAACATCCATCACCAGTAAGTAA 5 132 0 CATCCATCAC 0.898828 -20 CCGGCCAGTCCACTCAAAACTGTTTTTTAA 8 150 0 CACTCAAAAC 0.879003 -151 TCAAAACATCCATTCAGAACTGCAGGGCAT 11 160 1 CATTCAGAAC 0.972079 -116 ATCTGAAAGTAATTCAGCACACCTTTCAGG 12 39 0 AATTCAGCAC 0.948713 -29 AAATTTAATACATTCATCACGCGTTATTGC 16 168 0 CATTCATCAC 0.96047 -133 ********** Masking position 6 Map Score: 0.255634 Number of sites scoring better than the average of aligned sites = 76 Number in coding regions = 66 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 12 GTTCTTGATCATTCACCAGCTGGGACCGC 6 10 0 ATTCACCAGC 0.888057 -39 GTTTAAAGGGAGTCACCGGGATGTCC 8 7 0 AGTCACCGGG 0.96593 -294 AAATCATTCCAGGCCACAGGGAAGTGCCCA 8 48 0 AGGCCACAGG 0.96593 -253 GGCATGGCGGAGGCCCCGGGTTCAAATCCC 8 178 0 AGGCCCCGGG 0.985828 -123 GGTTATTAATACTCCCCAGCTCAGAAAAAA 11 232 0 ACTCCCCAGC 0.951768 -44 ATCGTATATTCCACAGGTCCATATATA 15 123 0 ATTCCACAGG 0.938187 -17 ********** Masking position 1 Map Score: 0.124905 Number of sites scoring better than the average of aligned sites = 238 Number in coding regions = 229 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 13 ********** No masking Map Score: -6.86852e-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: -6.86852e-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: -6.86852e-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