AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_mthe.txt -z/home/amcguire/genomes/mthe.fna -iargR_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 MTH174 169 sensory transduction histidine kinase #2 MTH175 128 conserved protein #3 MTH176 168 tRNA-guanine transglycosylase #4 MTH179 117 unknown #5 MTH181 49 unknown #6 MTH182 36 glutamate N-acetyltransferase #7 MTH243 231 conserved protein #8 MTH248 195 conserved protein #9 MTH249 64 conserved protein #10 MTH250 23 tRNA intron endonuclease #11 MTH251 54 tryptophanyl-tRNA synthetase #12 MTH252 22 conserved protein #13 MTH253 75 threonine synthase #14 MTH254 206 histone HMtB #15 MTH255 269 ribosomal protein L7a #16 MTH256 49 ribosomal protein S28 #17 MTH261 24 translation initiation factor eIF-2, gamma subunit #18 MTH262 24 conserved protein #19 MTH846 170 N-acetyl-gamma-glutamyl-phosphate reductase #20 MTH997 31 carbamoyl-phosphate synthase, large subunit #21 MTH1254 135 argininosuccinate synthase #22 MTH1337 81 N-acetylornithine aminotransferase #23 MTH1445 64 glycinamide ribonucleotide synthetase Motif number 1 CCGACTCTGATTCAGGGGTAATGGCAAAATT 2 80 1 TTCAGGGGAA 0.973271 -49 TGATGAGGATTCCATGAGAATAGTTCTCAAT 4 78 1 TCCATGAGAT 0.753602 -40 TGTAACCGGAATCATGGGCCATCCCCTGGGC 7 28 0 ATCATGGGCA 0.792407 -204 TATTGTAAGTACCATGAGAAAAAAAATCAGA 7 146 0 ACCATGAGAA 0.753602 -86 TTTATTTACCATCAGCGATAAATATTGTTGC 7 177 1 ATCAGCGAAA 0.431458 -55 TTACCTATAATCCAGGGGAGAGTGTGAC 7 214 1 TCCAGGGGGA 0.940096 -18 GAGTGTTGAGTTCCTGAGGAATATTATACCT 8 23 1 TTCCTGAGAA 0.561546 -173 GCCTTCCGTGTTCCTGGGGAATATTCCGCTG 8 86 1 TTCCTGGGAA 0.939302 -110 CCAGCACCCCTCCAGCGGAATATTCCCCAGG 8 98 0 TCCAGCGGAT 0.776534 -98 CAGATAGAGTTCCCTGGAAAACCAGCACCCC 8 119 0 TCCCTGGAAA 0.905824 -77 ACCCTGACCCTCCAGGGGAAATCCTTCAGGG 8 161 0 TCCAGGGGAA 0.980071 -35 AAAGGGGTCTTCCATGGATGACTGCAGCGA 9 10 0 TCCATGGAGA 0.832129 -55 ACCTGAATTAACCAGGGAAATTAAACGGGGT 13 11 0 ACCAGGGAAT 0.577158 -65 TTTTCTATTTTTCATCGGACAACTTGAAGTT 14 50 1 TTCATCGGCA 0.741354 -157 CATCGGTTGGTTCATGGGGCACCTTCAACCC 14 118 0 TTCATGGGCA 0.925607 -89 AATCCTTGTTTTCCTGGGCGTCTTACTGGAT 15 89 1 TTCCTGGGGT 0.702646 -181 TTACTGGATGATCCGGGATAATTCAGAATAC 15 111 1 ATCCGGGAAA 0.671057 -159 GATACAGATTTTCATGAGAAATCGTATTCTG 15 134 0 TTCATGAGAA 0.880605 -136 TTTTCTACCATCCATCGGTAATTACACCAAT 15 244 0 TCCATCGGAA 0.923842 -26 CCTTTAACTGTCCATGGGGATATCTTCCCC 19 10 0 TCCATGGGAT 0.941683 -161 TTATAAGTATTTCATGGACAACCTTTAACTG 19 31 0 TTCATGGAAA 0.920008 -140 GCTGGCCCACTTCCGGAAAAATCCGTATACC 21 18 1 TTCCGGAAAA 0.557332 -118 ******** ** Masking position 3 Map Score: 26.5144 Number of sites scoring better than the average of aligned sites = 1203 Number in coding regions = 1119 Number in noncoding regions = 84 Number of orfs with sites within 600 bp upstream = 65 Fraction of orfs with sites within 600 bp upstream = 0.0104401 Motif number 2 CCTGACGCAGCATGTCTGCCCCACTATGTTATTA 1 89 0 CGCTGCCCAC 0.937483 -81 CCCCCGATTTACATCATGCCCCTCTGTGGAGGAA 1 123 0 ATATGCCCTC 0.982311 -47 TCAAGTTATGATTTTCAGACCCTCCAAGACCCAC 2 36 0 ATCAGCCCTC 0.934254 -93 CCCTGGGCACAGCCTCTCGCCCATA 7 2 0 ACCTCCCCAT 0.743077 -230 GGCTGTGCCCAGGGGATGGCCCATGATTCCGGTT 7 22 1 AGATGCCCAT 0.845717 -210 AAATTATCTCAAACCCTGACCCTCCAGGGGAAAT 8 170 0 ACCTGCCCTC 0.983598 -26 ACTTGAAGTTAATTTCTCACCCTCCAAGCACTCG 14 71 1 ATCTCCCCTC 0.977057 -136 GAACATATAAAGGTACTCACCCACTTCATGTTAA 15 185 1 ATCTCCCCAC 0.977057 -85 CCTCCCACCCATATAATGTCCATCACTGACCCGG 19 78 0 ATATGCCATC 0.885265 -93 ATACCCACCTATATAATGTCCATCACTGACCTGG 19 145 0 ATATGCCATC 0.885265 -26 CTGAATTGCTGGCCCACTTCCGGAAAA 21 4 1 ATCTGCCCAC 0.991915 -132 ATAAGTTATAAGTGTATGTCCCACCTGCCGCAGG 21 47 0 AGATGCCCAC 0.975333 -89 * * *** ***** Masking position 10 Map Score: 13.1857 Number of sites scoring better than the average of aligned sites = 333 Number in coding regions = 311 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 3 ATTCTGTTCAATCAGTTTCCATCCAGAATTTCAT 1 19 1 ATCAGTTCTC 0.988837 -151 TTACCCCTGAATCAGAGTCGGTGCCTGCTCATCA 2 67 0 ATCAGATCTC 0.969223 -62 TTACATATTAATCAGTATCATCGTGGATATACAC 3 80 1 ATCAGTTCCT 0.82528 -89 ACATGCTCAGATCAGTGTATATCCACGATGATAC 3 94 0 ATCAGTTATC 0.985076 -75 GTACCTGTTAATCAGTATCATTCTGC 3 153 1 ATCAGTTCTT 0.92485 -16 TTTTCCAGTTATCAGTTTATCACCCCGGCATTAC 7 64 1 ATCAGTTAAC 0.902795 -168 GAGAAAAAAAATCAGATTCTATACTGACCGGTGC 7 128 0 ATCAGATCTC 0.969223 -104 CCTTCAACCCAGCAGTATATCCACGAGTGCTTGG 14 94 0 AGCAGTTACC 0.813044 -113 TTCCGGAAAAATCCGTATACCTGCGGCAGGTGGG 21 28 1 ATCCGTTATC 0.918904 -108 GGGATAAGTTATAAGTGTATGTCCCACCTGCCGC 21 50 0 ATAAGTTATC 0.825663 -86 ACATGAGCGTATCAGAATGATTCCATTTATAAG 21 113 1 ATCAGATGTC 0.878357 -23 AATATTTATTATCAGTTTAGGTTCAACATTAATA 22 28 1 ATCAGTTATC 0.985076 -54 ****** ** * * Masking position 1 Map Score: 13.101 Number of sites scoring better than the average of aligned sites = 71 Number in coding regions = 57 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 4 TGAGGCATGGATTATGTGGGAGGATTTTTA 3 41 1 ATTATGTGGG 0.893323 -128 TGTAATATGTATTATATGAGTTAATATCTT 4 47 0 ATTATATGAG 0.793518 -71 CAGCGAACTTTTTTTACGGGAGA 6 24 1 TTTTTACGGG 0.859355 -13 AACCAGGGAAATTAAACGGGGT 13 3 0 ATTAAACGGG 0.759538 -73 TAGCGATATATTTATATAGGATTATATGAA 14 169 1 TTTATATAGG 0.940218 -38 GCAGCAAAACTTTATATGTGATGAAGCTTT 15 49 1 TTTATATGTG 0.79354 -221 AGTGATGGACATTATATGGGTGGGAGGCCC 19 85 1 ATTATATGGG 0.979911 -86 AGTGATGGACATTATATAGGTGGGTATAG 19 152 1 ATTATATAGG 0.940218 -19 ACTATAGATATTAATATGGGATAAGTTATA 21 71 0 TTAATATGGG 0.916174 -65 AGGTTCAACATTAATACAGGTCCCCATATA 22 46 1 TTAATACAGG 0.663386 -36 TCACCAAAAATTTATATGGGGACCTGTATT 22 58 0 TTTATATGGG 0.979911 -24 GAAAGTATATATTTTATAGGAAATATGTCA 23 39 0 ATTTTATAGG 0.779015 -26 ********** Masking position 2 Map Score: 10.8127 Number of sites scoring better than the average of aligned sites = 186 Number in coding regions = 151 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714 Motif number 5 GGGGGTGATGTAGGTGGGGGTTTTCCC 1 153 1 TGTGGGTTCC 0.947187 -17 TGATCTGTGATTTGAGGGTATTCCTGTGGGTCTT 2 9 1 GTTGGGTTCC 0.987691 -120 AACACTGGAAGCAGGGCTGGATCACATA 3 3 0 GGGGGGCACA 0.835105 -166 AAAAAAGTTCGCTGGGGTCGTCTCCCA 6 2 0 GGGGCGTCCC 0.948183 -35 GTCCCGTGATGCCCGGGAGGCCTTCCGTGTTCCTGG 8 67 1 GCGGGGTTCC 0.989456 -129 TTCCGCTGGAGGGGTGCTGGTTTTCCAGGGAACTCT 8 109 1 GGTGGGTTCC 0.995088 -87 GGGTGTCAGCGCCCTGAAGGATTTCCCCTGGAGGGT 8 150 1 GCTGGGTTCC 0.988587 -46 ATATACTGCTGGGTTGAAGGTGCCCCATGAACCAAC 14 108 1 GTTGGGCCCC 0.970009 -99 GGATTAACATGAAGTGGGTGAGTACCTTTATATGTT 15 186 0 GGTGTGTACC 0.880486 -84 GTCTGCGAGGGTATGGTGGGGCCTCCCACCCATATA 19 97 0 GTGGGGCTCC 0.984092 -74 * *** ** **** Masking position 15 Map Score: 7.81222 Number of sites scoring better than the average of aligned sites = 362 Number in coding regions = 343 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 6 AACTTGATGAGCAGGCACCGACTCTGATTCAGGG 2 63 1 GGGCACGCTC 0.988753 -66 CATGTAGTATCTGGTGGTAGCCACTGCAGAGTAC 3 123 1 CGTGGTGCAC 0.93807 -46 CTGCCGGGACGGTCTCATCCCTCAAA 4 3 1 GGGGACGCTC 0.986106 -115 AAAAAAGTTCGCTGGGGTCGTCTCCCA 6 4 0 GGGGGTGCTC 0.978951 -33 GGGCCATCCCCTGGGCACAGCCTCTCGCCCATA 7 10 0 CGGCACGCTC 0.986069 -222 GGAAATCCTTCAGGGCGCTGACACCCCAGATAGA 8 142 0 CGGCGCGCAC 0.991195 -54 GGTGGTCATAGACACCAATTTTTT 18 2 1 GGTCATGCAC 0.94753 -23 CATCACTGACCCGGTCGTGGCCACCAAAATTTAT 19 58 0 CGTCGTGCAC 0.949356 -113 ACCTGCGGCAGGTGGGACATACACTTATAACTTA 21 46 1 GGGGACTCAC 0.895537 -90 * ***** * *** Masking position 12 Map Score: 7.72041 Number of sites scoring better than the average of aligned sites = 173 Number in coding regions = 161 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 7 ACCCCCACCTACATCACCCCCCGATTTACA 1 144 0 ACATCACCCC 0.970325 -26 TTAAATTTTGCCATTACCCCTGAATCAGAG 2 84 0 CCATTACCCC 0.967442 -45 TAATATGTAATCAGCACCCTAAAAATCCTC 3 60 0 TCAGCACCCT 0.960188 -109 TGAGTTAATATCTTTACCCCTCAGTTTGAG 4 31 0 TCTTTACCCC 0.90008 -87 AGTTATCAGTTTATCACCCCGGCATTACAG 7 70 1 TTATCACCCC 0.923156 -162 CCCTGGAAAACCAGCACCCCTCCAGCGGAA 8 109 0 CCAGCACCCC 0.992208 -87 ATCTGGGGTGTCAGCGCCCTGAAGGATTTC 8 145 1 TCAGCGCCCT 0.864974 -51 TCATGGGGCACCTTCAACCCAGCAGTATAT 14 108 0 CCTTCAACCC 0.841544 -99 ********** Masking position 8 Map Score: 4.74847 Number of sites scoring better than the average of aligned sites = 487 Number in coding regions = 458 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 8 TCATACATCAGATATAAATTGATGGAATTGATGA 1 49 0 GATAATTGAG 0.794247 -121 GGGTCTGAAAATCATAACTTGATGAGCAGGCACC 2 48 1 ATTACTTGAG 0.983575 -81 CATATAATACATATTACATTGATGAGGATTCCAT 4 59 1 ATTAATTGAG 0.942315 -59 ATTCCCCTTAATATTATCTTGAAGTATCCTTAAA 5 22 0 ATTACTTGAG 0.983575 -28 CCTGAGGAATATTATACCTTGAGGGGCCCCGGGT 8 35 1 ATTACTTGAG 0.983575 -161 AAAAAAGAGAAAGGTATCTTCAAGAATTCAGGGG 14 12 0 AATACTTCAG 0.950993 -195 GGAGGGTGAGAAATTAACTTCAAGTTGTCCGATG 14 62 0 AATACTTCAG 0.950993 -145 ** ** ***** * Masking position 6 Map Score: 2.85606 Number of sites scoring better than the average of aligned sites = 36 Number in coding regions = 30 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 9 TTCTGTTCAATCAGTTTCCATCCAGAATTT 1 20 1 TCAGTTTCCA 0.886945 -150 ACATGCTGCGTCAGGTTCCTCCACAGAGGG 1 108 1 TCAGGTTCCT 0.866738 -62 AGTTGTAATTACTGTATCATTTAACC 2 113 1 ACTGTATCAT 0.665774 -16 TAATATGTAATCAGCACCCTAAAAATCCTC 3 60 0 TCAGCACCCT 0.827849 -109 TACATATTAATCAGTATCATCGTGGATATA 3 81 1 TCAGTATCAT 0.939643 -88 TACCTGTTAATCAGTATCATTCTGC 3 154 1 TCAGTATCAT 0.939643 -15 CTCTCATCTGCATCCATTATTCCTTC 15 7 1 TCTGCATCCA 0.931318 -263 CTCATGAAAATCTGTATCCAGCAAGTTTTA 15 147 1 TCTGTATCCA 0.952721 -123 ATTACACCAATCTGGATCAATAATCCAAGT 15 225 0 TCTGGATCAA 0.873445 -45 ********** Masking position 8 Map Score: 2.88989 Number of sites scoring better than the average of aligned sites = 376 Number in coding regions = 348 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 10 ATCAGTATCATCGTGGATATACACTGATCT 3 90 1 TCGTGGATAT 0.948725 -79 TGACTTAATAACGGTGATATGA 11 43 1 ACGGTGATAT 0.934252 -12 CTCCAAGCACTCGTGGATATACTGCTGGGT 14 92 1 TCGTGGATAT 0.948725 -115 TACTGGATGATCCGGGATAATTCAGAATAC 15 112 1 TCCGGGATAA 0.85013 -158 TTAACTGTCCATGGGGATATCTTCCCC 19 8 0 ATGGGGATAT 0.961861 -163 GATGAGAGGAATGGGGATAAA 20 21 1 ATGGGGATAA 0.916469 -11 ATATAAATTTTTGGTGATATC 22 71 1 TTGGTGATAT 0.899584 -11 ********** Masking position 7 Map Score: 2.40677 Number of sites scoring better than the average of aligned sites = 161 Number in coding regions = 145 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 11 TCGGGGGGTGATGTAGGTGGGGGTTTTCCC 1 150 1 ATGTAGGTGG 0.982608 -20 GGCATGGATTATGTGGGAGGATTTTTAGGG 3 44 1 ATGTGGGAGG 0.963717 -125 ATACTTATAAATTTTGGTGGCCACGACCGG 19 52 1 ATTTTGGTGG 0.921545 -119 GATGGACATTATATGGGTGGGAGGCCCCAC 19 88 1 ATATGGGTGG 0.982608 -83 GATGGACATTATATAGGTGGGTATAG 19 155 1 ATATAGGTGG 0.97335 -16 ********** Masking position 4 Map Score: 2.84792 Number of sites scoring better than the average of aligned sites = 24 Number in coding regions = 19 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 12 GTGGAGGAACCTGACGCAGCATGTCTGCCC 1 102 0 CTGACGCAGC 0.96752 -68 GGCACCGACTCTGATTCAGGGGTAATGGCA 2 76 1 CTGATTCAGG 0.882935 -53 AGTTCTCAATCAGGTGCAGGGAGAGAGCA 4 99 1 CAGGTGCAGG 0.977641 -19 TCTATACTGACCGGTGCAGCATCTAAACCC 7 115 0 CCGGTGCAGC 0.980944 -117 GGGGAATATTCCGCTGGAGGGGTGCTGGTT 8 101 1 CCGCTGGAGG 0.928427 -95 ACCCCTTTAACAGATGCAGCCATACACAAG 9 33 1 CAGATGCAGC 0.968647 -32 TATGTCCCACCTGCCGCAGGTATACGGATT 21 37 0 CTGCCGCAGG 0.976619 -99 ********** Masking position 8 Map Score: 3.79989 Number of sites scoring better than the average of aligned sites = 303 Number in coding regions = 280 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 13 ATGATATAATTAATAACATAGTGGGGCAGACA 1 79 1 TATACATAGT 0.924517 -91 TTTAGGGTGCTGATTACATATTAATCAGTATC 3 67 1 TATACATATT 0.971012 -102 AATTAAAGCTTCATCACATATAAAGTTTTGCT 15 51 0 TATACATATA 0.892054 -219 CACTTATAACTTATCCCATATTAATATCTATA 21 67 1 TATCCATATT 0.924517 -69 TCATTAATAATAATGACAGATTCCGTTCAAG 23 10 0 TATACAGATT 0.924517 -55 TCATTATTATTAATGACATATTTCCTATAAAA 23 26 1 TATACATATT 0.971012 -39 * ** ******* Masking position 8 Map Score: 1.02871 Number of sites scoring better than the average of aligned sites = 4 Number in coding regions = 0 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 14 TGATTGAACAGAATACTGGAAA 1 3 0 GAATACTGGA 0.963782 -167 GGAATTGATGAAATTCTGGATGGAAACTGA 1 30 0 AAATTCTGGA 0.907099 -140 CATGCCTCAGAAACACTGGAAGCAGGGCTG 3 20 0 AAACACTGGA 0.856442 -149 TGATTAACAGGTACTCTGCAGTGGCTACCA 3 137 0 GTACTCTGCA 0.833731 -32 CCCCCTGAATTCTTGAAGATACCTTT 14 7 1 GAATTCTTGA 0.826602 -200 AAAAGGGAAGGAATAATGGATGCAGATGAG 15 13 0 GAATAATGGA 0.748211 -257 ATGAGAAATCGTATTCTGAATTATCCCGGA 15 122 0 GTATTCTGAA 0.775364 -148 ACTGACCTGGGTACTCTGGATAGTCTGCGA 19 125 0 GTACTCTGGA 0.963076 -46 ********** Masking position 3 Map Score: 1.1305 Number of sites scoring better than the average of aligned sites = 349 Number in coding regions = 318 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 15 ACCCCTGAATCAGAGTCGGTGCCTGCTCAT 2 69 0 CAGAGTCGGT 0.85631 -60 CTGCCGGGACGGTCTCATCCCTC 4 4 1 CCGGGACGGT 0.983836 -114 TAGATGCTGCACCGGTCAGTATAGAATCTG 7 120 1 ACCGGTCAGT 0.879566 -112 AAGATATCCCCATGGACAGTTAAAGGTTGT 19 15 1 CATGGACAGT 0.862398 -156 GTGGCCACGACCGGGTCAGTGATGGACATT 19 68 1 CCGGGTCAGT 0.992739 -103 TCCAGAGTACCCAGGTCAGTGATGGACATT 19 135 1 CCAGGTCAGT 0.971878 -36 ********** Masking position 10 Map Score: 0.865445 Number of sites scoring better than the average of aligned sites = 138 Number in coding regions = 130 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432