AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_aquae.txt -z/home/amcguire/genomes/aquae.fna -irpoH_aquae_opreg_100.orf -g0.435 -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 = 0.435 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 aq_194 53 putative protein #2 lon 32 Lon protease #3 ribD2 139 riboflavin specific deaminase #4 dnaJ2 70 chaperone DnaJ #5 truB 30 tRNA pseudouridine 55 synthase #6 rpsU 285 ribosomal protein S21 #7 ftsH 49 cell division protein FtsH #8 trpS 48 tryptophanyl-tRNA synthetase #9 pncA 37 pyrazinamidase/nicotinamidase #10 dnaK 68 Hsp70 chaperone DnaK #11 gap 40 glyceraldehyde-3-phosphate dehydrogenase #12 hspC 60 small heat shock protein (class I) #13 gspD 300 general secretion pathway protein D #14 alaS 68 alanyl-tRNA synthetase #15 clpC 96 ATP-dependent Clp protease #16 tig 23 trigger factor #17 aq_1343 300 putative protein #18 rpoD 38 RNA polymerase sigma factor RpoD #19 dnaG 66 DNA primase #20 aq_1668 36 putative protein #21 clpB 104 ATPase subunit of ATP-dependent protease #22 aq_1731 195 hypothetical protein #23 dnaJ1 80 chaperone DnaJ #24 mopB 204 GroES Motif number 1 TTTAAAAACAAGGAGGAGAAAAG 2 20 1 AGGAGGAGAA 0.982819 -13 TGGTGTTTTAAGGAGGTTGAT 3 2 0 AGGAGGTTGA 0.887888 -138 CTGCTTCCCAAGCAGGAGGTCGCCGGTTCG 3 80 1 AGCAGGAGGT 0.932845 -60 AATCCGATAAAGGAGGTGATGCAAGC 6 270 1 AGGAGGTGAT 0.991305 -16 AGTAATCTTCAGGAGGAGGTC 7 39 1 AGGAGGAGGT 0.995041 -11 AGTTTTATCAAGGAGGTGGGAAT 9 25 1 AGGAGGTGGG 0.994065 -13 CAGGAAAGATAGGAGGTGATAAA 10 56 1 AGGAGGTGAT 0.991305 -13 AAATTGTTAAAGGAGGTGGGAACC 12 47 1 AGGAGGTGGG 0.994065 -14 CTACATAGCCATGAGGCGGTACTTCTGGAG 13 143 1 ATGAGGCGGT 0.847323 -158 ATTGACTGCGAGGAGGAAGTCCTCATAATA 17 140 0 AGGAGGAAGT 0.97572 -161 ATCGTGGAAGACGAGGAGAGGGGAATAAAA 17 179 0 ACGAGGAGAG 0.860649 -122 GAGATTCCGGAAGAGGAAGTCATAATCGTG 17 203 0 AAGAGGAAGT 0.800385 -98 TTAGAAATCAAGGAGGAGATTCCGGAAGAG 17 218 0 AGGAGGAGAT 0.990128 -83 TTTTAGAGTTAGGAGGTAAGAGA 18 26 1 AGGAGGTAAG 0.943716 -13 CTGCTTTTACAGGAGGGGAAGGCAAGAGTG 22 164 0 AGGAGGGGAA 0.938247 -32 CTGTAAAAGCAGGAGGCGGAAGAA 22 182 1 AGGAGGCGGA 0.982438 -14 GGATTTTGTCAAGAGGTAATTTAAGTTTTT 24 124 0 AAGAGGTAAT 0.694963 -81 TAAACCACGGAGGAGGTGGACGGA 24 191 1 AGGAGGTGGA 0.992372 -14 ********** Masking position 4 Map Score: 37.8573 Number of sites scoring better than the average of aligned sites = 371 Number in coding regions = 291 Number in noncoding regions = 80 Number of orfs with sites within 600 bp upstream = 87 Fraction of orfs with sites within 600 bp upstream = 0.0139737 Motif number 2 CTTATTAATAATATTTCTACAAGCTTAC 1 36 0 TTAAATTTCT 0.967571 -18 AACTTAAAAGTTGAGTTTATTTTTGTCAAGTTTC 4 20 0 TTATATTTTT 0.876698 -51 AACTCAACTTTTAAGTTATTTACTCTGGTAAACG 4 37 1 TTATTTTACT 0.691528 -34 TCTTGCGTACTTCAGGAGTTTTCTGTAATTAATC 6 45 1 TTAATTTTCT 0.943331 -241 GTACATAATCTTAATAACATTTTTAATGGTTTTC 6 195 0 TTAAATTTTT 0.888466 -91 CTTTTTGCAGTTTAACTATTTTTTAAAAGTAATC 7 12 1 TTATTTTTTT 0.798666 -38 TCCCACCTCCTTGATAAAACTTCTATTAAATAAA 9 12 0 TTAAACTTCT 0.915626 -26 TTAAAAAAAATTGACATAATTTCACTAAGGTTGT 10 11 1 TTATATTTCA 0.800727 -58 CCCACCTCCTTTAACAATTTTTCTTACATTAAAC 12 33 0 TTAATTTTCT 0.94333 -28 TTAACTTTAATAAATTTTTAGAGTTAGGA 18 6 1 TTAAATTTTT 0.888454 -33 CTCAAAAGAATTTATTTTATTTCTGATCTGTGTC 19 41 0 TTATATTTCT 0.96381 -26 CTCCCTCCACTATAATTAATTTCT 21 1 0 TAATATTTCT 0.681393 -104 TAATTTTCCTTTAATAATATTTCTTGAGTATAAT 21 65 0 TTAAATTTCT 0.967571 -40 CTCCTATACTTTAATATACTTTTGTTAAATTTT 24 10 1 TTAAACTTTT 0.7434 -195 TTTTTTGCACTTAAATAATCTTCAAGTACTTGAT 24 95 0 TTAATCTTCA 0.476833 -110 TCCGAGGATGTTAATATAATTTCTGGTGTAAGTA 24 151 1 TTATATTTCT 0.96381 -54 TCCTCCGTGGTTTACCTGTTTACTTACACCAGAA 24 171 0 TTATTTTACT 0.691533 -34 ** * * ****** Masking position 4 Map Score: 17.5298 Number of sites scoring better than the average of aligned sites = 250 Number in coding regions = 215 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 3 TTTAAAGGCTATTATAAAAGTGT 1 1 0 ATTTAAAGGT 0.874324 -53 AAAAAGTAAGCTTGTAGAAATATTATTAATAAG 1 31 1 CTTTAAAAAT 0.756285 -23 TGGTATAATTTTAAAAACAAGGAGGAGAAA 2 8 1 ATTTAAAAAA 0.797925 -25 TTATTATTAAATTTTATAATGGTGTTTTAAGGA 3 18 0 ATTTAAATGT 0.818063 -122 AAGCAAAATTGTACAAAAATTTGGAGCGGG 3 120 0 ATTTAAAAAT 0.956443 -20 ATTAAAATCTATTTTAGAGATGTTCAAGTACAT 6 223 0 ATTTAAGAGT 0.947218 -63 CAGTTTAACTATTTTTTAAAAGTAATCTTCAGG 7 19 1 ATTTTAAAGT 0.647895 -31 AGAAAGGCAAATTGTAAAATAATTTCCC 8 31 1 ATTTAAATAT 0.817498 -18 ATTTATTTAATAGAAGTTTTATCAAGG 9 5 1 ATTAAAGAGT 0.743392 -33 CATTTTATAAAGATAGACTTAAGT 12 2 1 ATTTAAAAAT 0.957489 -59 AAAGACATTATAAAGATATATAACACTGT 15 7 1 ATTTAAGAAT 0.948229 -90 GGTTTTTTTTATTTTATAAAAAACTGAGAGAGG 15 66 1 ATTTAAAAAA 0.795109 -31 AATAGATATTTTAAAGATATGGCTACATAC 17 281 0 ATTTAAGAAT 0.948172 -20 AATTTGATTTTACAGGTATTTCTTCAGCT 19 7 1 ATTTAAGGAT 0.841655 -60 TGTTAAGAAAATTTAACAAAAGTATATTAAAGT 24 18 0 ATTAAAAAGT 0.79456 -187 TACACCAGAAATTATATTAACATCCTCGGATTT 24 148 0 ATTTATAAAT 0.671804 -57 *** ** *** ** Masking position 3 Map Score: 12.3173 Number of sites scoring better than the average of aligned sites = 54 Number in coding regions = 30 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 4 TTCCCAAGCAGGAGGTCGCCGGTTCGAGTCCCGTCGCCCGCT 3 84 1 GGAGGCCACC 0.996813 -56 GCGTACTTCAGGAGTTTTCTGTAATTAATCCTCTCGTGAACT 6 49 1 GGAGTTCACT 0.794532 -237 GGGTGTGGAAGGAGTACACTGAAAGTTTCTACTTCTACTCAC 6 125 0 GGAGTCCTAC 0.95803 -161 AAGCCCAAGGGGAGTACTGGGGCTACATAGCCATGAGGCGGT 13 121 1 GGAGTCGACC 0.977294 -180 GCGTATCCGAGAAGGACACTCTGTATATGTCCTGCAAACACG 13 218 0 GAAGGCCACC 0.991581 -83 CAGCACCTTAGGAGTGCTCCTCTTTCTCCCACGGGAAGGAGA 13 263 1 GGAGTCCTAC 0.958207 -38 CGAAAGCTCCGAAGGGCAGGTCCTGTTCCTCTCCAAAAACCA 17 59 1 GAAGGCGTCT 0.645928 -242 CTGCGAGGAGGAAGTCCTCATAATAGAACAACCGATAGGAAA 17 123 0 GAAGTCCAAC 0.942008 -178 CACCCACGGTGTAGGCCCCATTGACAACCCCCGCACCACGAA 22 22 0 GTAGGCCACC 0.972646 -174 GAATCCTTCCGGAGTTCCCGAAGTCGACTTCCCTTACACCCA 22 58 0 GGAGTCCACC 0.916913 -138 GGGAACTCCGGAAGGATTCCCGAGGGACTTCCCACCTTAAAG 22 81 1 GAAGGTCACC 0.89694 -115 ACTGCGGCAGGGCGGACACTCTTGCCTTCCCCTCCTGTAAAA 22 148 1 GGCGGCCTCC 0.963648 -48 ***** * * * ** Masking position 4 Map Score: 12.7076 Number of sites scoring better than the average of aligned sites = 189 Number in coding regions = 164 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 5 TACTCTGGTAAACGGAGGAAAGTT 4 57 1 AACGAGGAAA 0.974845 -14 ACTCCTGAAGTACGCAAGAAAGCACGGCTTT 6 33 0 TACGAAGAAA 0.882293 -253 TATATGATAAAGCTCAAGAAAGGCAAATTGT 8 15 1 AGCTAAGAAA 0.873524 -34 TGTATAATAAAAGGCAGGAAAGATAGGAGGT 10 42 1 AAGGAGGAAA 0.970143 -27 ACTTAAGTTTAATGTAAGAAAAATTGTTAAA 12 27 1 AATGAAGAAA 0.812713 -34 CCGCCGTGTAAACGTAGTAAACGAGCTTCTC 13 24 0 AACGAGTAAA 0.843371 -277 AAAAGGCGATAAGGTAGGAAATAGCTCCGCT 13 63 0 AAGGAGGAAA 0.970143 -238 TTGGGCTTTTACGGGAAGAAAGAACTTTCTT 13 98 0 ACGGAAGAAA 0.881661 -203 AGACGAGGAGAGGGGAATAAAAAACATGGTA 17 170 0 AGGGAATAAA 0.784704 -131 ATCTGTGTCAAGCTGAAGAAATACCTGTAAA 19 19 0 AGCTAAGAAA 0.873524 -48 GACACAATTATACTCAAGAAATATTATTAAA 21 59 1 TACTAAGAAA 0.623308 -46 ATAAAACGACAGGGAAGGAAA 23 1 0 AGGGAGGAAA 0.96814 -80 **** ****** Masking position 6 Map Score: 9.94765 Number of sites scoring better than the average of aligned sites = 406 Number in coding regions = 382 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 6 TACTCCTTCCACACCCTCAGGGAGTAGATT 6 151 1 ACACCCTCAG 0.834702 -135 TATATAAAATAGTTCCACGAGTATAATTAA 11 16 1 AGTTCCACGA 0.807384 -25 TGCTCCTCTTTCTCCCACGGGAAGGAGACG 13 277 1 TCTCCCACGG 0.947367 -24 TATTATGAGGACTTCCTCCTCGCAGTCAAT 17 140 1 ACTTCCTCCT 0.691886 -161 CCTCTCCTCGTCTTCCACGATTATGACTTC 17 188 1 TCTTCCACGA 0.727533 -113 TTTCGTGCACACTCCCTCCACTATAATTAA 21 16 0 ACTCCCTCCA 0.915193 -89 GACTTCCCTTACACCCACGGTGTAGGCCCC 22 45 0 ACACCCACGG 0.974394 -151 TAAGGTGGGAAGTCCCTCGGGAATCCTTCC 22 90 0 AGTCCCTCGG 0.971079 -106 TAAAGCTCTGAGGCCCACGGCACTTCCTGC 22 118 1 AGGCCCACGG 0.896845 -78 AATTATATTAACATCCTCGGATTTTGTCAA 24 142 0 ACATCCTCGG 0.959637 -63 TCCGTCCACCTCCTCCGTGGTTTACCT 24 188 0 ACCTCCTCCG 0.860869 -17 ********** Masking position 5 Map Score: 6.43144 Number of sites scoring better than the average of aligned sites = 472 Number in coding regions = 452 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 7 AATAAAAAGCGGGCGTAGCTCAGAGGTAGAGCACCT 3 46 1 GGGGTGAAGG 0.994848 -94 TACAAAAATTTGGAGCGGGCGACGGGACTCGAACCG 3 103 0 TGGGCGAGGG 0.859517 -37 TGCTTATGAAGGAAGTTCACGAGAGGATTAATTACA 6 68 0 GGAGTCAAGG 0.975336 -218 CTATGAAGTAGGGAGTCGTTAAAAGGAAATAACTCC 13 169 0 GGGGTGAAGG 0.994848 -132 CTTTCGCTTTGGACTCAGAAGACGGGATAATTCTCT 17 29 0 GGATCGAGGG 0.910014 -272 TCATAATCGTGGAAGACGAGGAGAGGGGAATAAAAA 17 178 0 GGAGAGAAGG 0.941193 -123 AATCAAGGAGGAGATTCCGGAAGAGGAAGTCATAAT 17 207 0 GAGTTCAAGG 0.741617 -94 ATAGTGGAGGGAGTGTGCACGAAAGGTATAAAAGGT 21 22 1 GAGGTCAAGG 0.920555 -83 TTCGTGGTGCGGGGGTTGTCAATGGGGCCTACACCG 22 22 1 GGGGTGAGGG 0.994493 -174 TGGGTGTAAGGGAAGTCGACTTCGGGAACTCCGGAA 22 58 1 GGAGTGTGGG 0.923455 -138 TAACATCCTCGGATTTTGTCAAGAGGTAATTTAAGT 24 128 0 GGATTGAAGG 0.961757 -77 *** ** * * *** Masking position 15 Map Score: 11.5638 Number of sites scoring better than the average of aligned sites = 218 Number in coding regions = 199 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 8 TACAAGCTTACTTTTTAAAGGCTATTATAA 1 17 0 CTTTTTAAAG 0.681194 -37 TTGAGTTTATTTTTGTCAAGTTTCAAAATC 4 14 0 TTTTGTCAAG 0.965154 -57 TTAATAGAAGTTTTATCAAGGAGGTGGGAA 9 17 1 TTTTATCAAG 0.840708 -21 AAAACCTAAGCTTTTTCAAGGCTATGACAA 15 42 0 CTTTTTCAAG 0.953901 -55 TATTTCTGATCTGTGTCAAGCTGAAGAAAT 19 28 0 CTGTGTCAAG 0.961353 -39 CTTAGCTTATCTTTTTCAAT 20 27 1 CTTTTTCAAT 0.73416 -10 TTGAGTATAATTGTGTCAACCTTTTATACC 21 46 0 TTGTGTCAAC 0.751164 -59 CATCCTCGGATTTTGTCAAGAGGTAATTTA 24 131 0 TTTTGTCAAG 0.965154 -74 ********** Masking position 8 Map Score: 4.09449 Number of sites scoring better than the average of aligned sites = 138 Number in coding regions = 126 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 9 TTTTAAAAACAAGGAGGAGAAAAG 2 19 1 AAGGAGGAGA 0.902829 -14 CCTCCTGCTTGGGAAGCAGGTGCTCTACCT 3 69 0 GGGAAGCAGG 0.939446 -71 CCTGCTTCCCAAGCAGGAGGTCGCCGGTTC 3 79 1 AAGCAGGAGG 0.891166 -61 AAGTAATCTTCAGGAGGAGGTC 7 38 1 CAGGAGGAGG 0.923724 -12 GCCCGTTGTAGAGAAGCTCGTTTACTACGT 13 14 1 GAGAAGCTCG 0.450179 -287 GGGCTTTTACGGGAAGAAAGAACTTTCTTA 13 97 0 GGGAAGAAAG 0.330997 -204 TGGCGTATCCGAGAAGGACACTCTGTATAT 13 232 0 GAGAAGGACA 0.845115 -69 CTTCCCGTGGGAGAAAGAGGAGCACTCCTA 13 271 0 GAGAAAGAGG 0.926273 -30 TTTCTCCCACGGGAAGGAGACGTGGT 13 285 1 GGGAAGGAGA 0.939757 -16 TGATATATTAGAGAAACAGGTACTCAGCTC 14 28 0 GAGAAACAGG 0.811974 -41 GGTTTTTGGAGAGGAACAGGACCTGCCCTT 17 70 0 GAGGAACAGG 0.85908 -231 AATTGACTGCGAGGAGGAAGTCCTCATAAT 17 141 0 GAGGAGGAAG 0.953801 -160 AATCGTGGAAGACGAGGAGAGGGGAATAAA 17 180 0 GACGAGGAGA 0.759117 -121 TTTAGAAATCAAGGAGGAGATTCCGGAAGA 17 219 0 AAGGAGGAGA 0.902829 -82 CCTCCTGTAAAAGCAGGAGGCGGAAGAA 22 178 1 AAGCAGGAGG 0.891166 -18 TAAAACGACAGGGAAGGAAA 23 1 0 GGGAAGGAAA 0.721924 -80 GTAAACCACGGAGGAGGTGGACGGA 24 190 1 GAGGAGGTGG 0.949284 -15 ********** Masking position 5 Map Score: 17.472 Number of sites scoring better than the average of aligned sites = 1281 Number in coding regions = 1177 Number in noncoding regions = 104 Number of orfs with sites within 600 bp upstream = 85 Fraction of orfs with sites within 600 bp upstream = 0.0136524 Motif number 10 TTTCTACAAGCTTACTTTTTAAAGGCTATTA 1 20 0 CTTATTTTTA 0.914273 -34 TTTTCTCCTCCTTGTTTTTAAAATTATACCA 2 11 0 CTTGTTTTAA 0.905503 -22 AAGCCTTATTTTAAATTGATAATTT 5 5 1 CTTATTTAAA 0.764028 -26 AGTCAATTACCATGTTTTTTATTCCCCTCTC 17 163 1 CATGTTTTTA 0.820561 -138 GAATCTCCTCCTTGATTTCTAAACCGAGGTC 17 226 1 CTTGTTTCTA 0.959642 -75 CAGAGATCTTAATTTCTATCACGGGAAT 23 63 0 CTTATTTCTA 0.920081 -18 TCTTCAAGTACTTGATTTATAAGGCTTCGAA 24 80 0 CTTGTTTATA 0.93892 -125 **** ****** Masking position 11 Map Score: 0.78302 Number of sites scoring better than the average of aligned sites = 50 Number in coding regions = 41 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 11 ********** No masking Map Score: 3.08538e-14 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 12 ********** No masking Map Score: 3.08538e-14 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 13 AATAGCCTTTAAAAAGTAAGCTTGTAGAAATA 1 21 1 AAAAATAACT 0.821403 -33 TGAAACTTGACAAAAATAAACTCAACTTTTAA 4 19 1 CAAAATAACT 0.794479 -52 ATTATCAATTTAAAATAAGGCTT 5 2 0 TAAAAAAGCT 0.862222 -29 TCACACCTCGTAAAGGAAAACATGTTGCTTAT 6 97 0 TAAAGAAACA 0.689318 -189 AACTATTTTTTAAAAGTAATCTTCAGGAGGAG 7 25 1 TAAAATAACT 0.935709 -25 CATTTTATAAAGATAGACTTAAGTTTAAT 12 8 1 TAAAGTAGCT 0.871466 -53 TTTTATAAAATAAAAAAAACCTAAGCTTTTTC 15 55 0 TAAAAAAACT 0.935709 -42 AAGCTAAGCCTAAAATAAATCTCT 20 3 0 TAAAAAAACT 0.935709 -34 ATTGAAAAAGATAAGCTAAGCCTAAAA 20 20 0 AAAAGTAACT 0.832855 -17 GAAATATTATTAAAGGAAAATTAAACGGGAGG 21 76 1 TAAAGAAATT 0.579411 -29 ***** *** ** Masking position 8 Map Score: 2.35724 Number of sites scoring better than the average of aligned sites = 117 Number in coding regions = 100 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 14 ********** No masking Map Score: 3.08538e-14 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: 3.08538e-14 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