AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_mjan.txt -z/home/amcguire/genomes/mjan.fna -iphoB_mjan_opreg_100.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 MJ0301 48 conserved hypothetical protein #2 MJ0302 117 phosphoribosyl-AMP cyclohydrolase/phosphoribosyl-ATP pyrophosphohydrolase (hisIE) #3 MJ1009 51 phosphate transport system regulatory protein (phoU) #4 MJ1010 300 M. jannaschii predicted coding region MJ1010 #5 MJ1012 30 phosphate specific transport complex component (pstB) #6 MJ1014 164 phosphate transport system permease protein C (pstC) #7 MJ1015 230 periplasmic phosphate-binding protein (pstS) #8 MJ1027 125 formate hydrogenlyase, subunit 5 #9 MJ1028 60 DNA topoisomerase VI, subunit B (top6B) #10 MJ1266 189 high-affinity branched-chain amino acid transport protein (braC) #11 MJ1267 96 high-affinity branched-chain amino acid transport ATP-binding protein (braF) #12 MJ1368 122 sulfate transport system permease protein (cysT) Motif number 1 TTCAGTTTTAAAAATAAAAAAAGATTGTA 1 10 0 AAAATAAAAA 0.827691 -39 TGTCTTCTAAAATTATAAAAAATTTTTA 2 9 1 AAAATTATAA 0.949979 -109 AAAATTATAAAAAATTTTTATGAAATTGAA 2 19 1 AAAATTTTTA 0.883486 -99 TAGTTATTACAAAATGTTTTGAAAGACACT 2 81 1 AAAATGTTTT 0.554637 -37 TTGGCAATATAAAAGTAAAATAAAGTATAG 3 11 0 AAAAGTAAAA 0.800897 -41 ATATTGCCAAAAAATTATATGGAGGGAAAT 3 31 1 AAAATTATAT 0.921003 -21 AACTTTTGCAAAAACTATAAACACATCTTC 4 51 0 AAAACTATAA 0.859402 -250 TAGTTTTTGCAAAAGTTATTAAAATTAAAA 4 64 1 AAAAGTTATT 0.496909 -237 AAAAGTTATTAAAATTAAAAATAAAAATTT 4 74 1 AAAATTAAAA 0.912885 -227 ATTAAAAATAAAAATTTGAACGCCCCCACT 4 87 1 AAAATTTGAA 0.83867 -214 TATATATTTCAAAATGTTTTGCAAAAACTA 4 138 1 AAAATGTTTT 0.554637 -163 ATGTTTTGCAAAAACTATAATGTTGCTATT 4 151 1 AAAACTATAA 0.859402 -150 CCAATATAGGAAAATATTTAGAAAGATGCG 4 194 1 AAAATATTTA 0.763631 -107 CCAGTAATTAAAAAGTATATCTCTTTTCTA 4 243 0 AAAAGTATAT 0.817367 -58 TACTGGCAAAAAAATGATATGAAATATATA 4 267 1 AAAATGATAT 0.884629 -34 AATTTTATAAAATATAAAAAAGGGATAG 5 9 1 AAAATATAAA 0.849307 -22 AAAATATTAAAAAATTAGAT 6 1 0 AAAATTAGAT 0.731178 -164 TTGGATTTAAAAAATATTAAAAAATTAGAT 6 11 0 AAAATATTAA 0.910695 -154 TTGCTTAATAAAAATATTATTCCCAAATAT 6 61 0 AAAATATTAT 0.847708 -104 ACTCAATATAAAAAGTAAAACACTTCTTTG 7 18 0 AAAAGTAAAA 0.800897 -213 GAATGTTCATAAAATATGAACTTTAATTCA 7 65 1 AAAATATGAA 0.704399 -166 TTCAAAATAGAAAACTTTATATACCTTTAT 7 91 1 AAAACTTTAT 0.814666 -140 GAAGGCGTTCAAAATTTTCATTAGTAGATT 7 168 0 AAAATTTTCA 0.613031 -63 TTATTAAAACAAAACTATATAAAAGGTTAA 8 21 1 AAAACTATAT 0.78958 -105 AAAACTATATAAAAGGTTAAGCTAATTATC 8 31 1 AAAAGGTTAA 0.849118 -95 AAATATCAGTAAAATAAATAATGTAACAAA 9 40 0 AAAATAAATA 0.620856 -21 TCTATCTCGAAAAATTTAAATATTGCTCAT 10 116 1 AAAATTTAAA 0.924785 -74 TCATATATAAAAAATGAAATTGCCATAACA 10 142 1 AAAATGAAAT 0.808888 -48 GTATCACCTCAAAATGTTATGGCAATTTCA 10 156 0 AAAATGTTAT 0.894919 -34 TGATACCATTAAAAGAATAA 10 180 1 AAAAGAATAA 0.769681 -10 AAAATTCCTAAAACTTTAAATAACTCTTT 11 10 1 AAAACTTTAA 0.877626 -87 GCATATCTTAAAAATTTAAAAAAGAGTTAT 11 30 0 AAAATTTAAA 0.924785 -67 TTTAAAGAATAAAATTTATAATCTTAGAAC 11 62 0 AAAATTTATA 0.807373 -35 AAAAATGATAAAAAGTTTAAA 11 86 0 AAAATGATAA 0.925899 -11 ATTTTCATTAAAAATTTATTAAA 12 4 0 AAAATTTATT 0.719982 -119 ATTTTTAATGAAAATATTATACTATCAAAT 12 19 1 AAAATATTAT 0.847708 -104 AATTACCTTAAAAATGATTAAGATTGATTA 12 94 1 AAAATGATTA 0.809834 -29 ********** Masking position 4 Map Score: 48.0981 Number of sites scoring better than the average of aligned sites = 2871 Number in coding regions = 1933 Number in noncoding regions = 938 Number of orfs with sites within 600 bp upstream = 605 Fraction of orfs with sites within 600 bp upstream = 0.0971731 Motif number 2 CCTTTCTTTGGAAGGCATTCAATTTCATAAA 2 35 0 GAGGCATTCA 0.990401 -83 CCTTCCAAAGAAAGGTGTTCATTAGTGCCTT 2 51 1 AAGGTGTTCA 0.906192 -67 CCTTATCCATAGTGTCTTTCAAAACATTTTG 2 90 0 AGGTCTTTCA 0.829209 -28 GCCCCCAAGTGGGGGCGTTCAAATTTTTATT 4 93 0 GGGGCGTTCA 0.998336 -208 GCCCCCACTTGGGGGCGTTCATATATATCCT 4 108 1 GGGGCGTTCA 0.998336 -193 TGTAAATTATGGTGTCATTCAAAAATAACAA 7 137 1 GGGTCATTCA 0.973979 -94 CCTTCTAAAAGAAGGCGTTCAAAATTTTCAT 7 177 0 GAGGCGTTCA 0.997363 -54 CCTTCTTTTAGAAGGCGTTCATCTATACCTT 7 193 1 GAGGCGTTCA 0.997363 -38 ** ******** Masking position 11 Map Score: 16.1316 Number of sites scoring better than the average of aligned sites = 49 Number in coding regions = 11 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 3 TACAATCTTTTTTTATTTTTAAAACT 1 7 1 CTTTTTTTAT 0.889929 -42 ATTGATGATTCAGTTTTAAAAATAAAAAAA 1 18 0 CAGTTTTAAA 0.544273 -31 CCTCCTGCTATATTGATGATTCAGTTT 1 32 0 CTATATTGAT 0.718661 -17 CTATACTTTATTTTACTTTTATATT 3 6 1 CTTTATTTTA 0.348257 -46 TATAATGTTGCTATTGTGAATGAGCTAACC 4 166 1 CTATTGTGAA 0.555948 -135 AAGTATATCTCTTTTCTAAAGTCATTTGCA 4 231 0 CTTTTCTAAA 0.614746 -70 TTCTATCCCTTTTTTATATTTTATAAAA 5 13 0 CTTTTTTATA 0.787614 -18 ATCTAATTTTTTAATATTTTTTAAA 6 6 1 ATTTTTTAAT 0.528174 -159 ATTTTTTAATATTTTTTAAATCCAAATTTA 6 16 1 ATTTTTTAAA 0.528175 -149 TTTATAAGTTCTATTTTAATAAGACTTTCG 6 119 0 CTATTTTAAT 0.929628 -46 CCTTTTTTAATCCTTATCTTA 6 154 0 CTTTTTTAAT 0.948282 -11 TATGAACATTCAATTTTAATAGTTAAAAAC 7 46 0 CAATTTTAAT 0.863795 -185 ATAAAGTTTTCTATTTTGAATTAAAGTTCA 7 81 0 CTATTTTGAA 0.886585 -150 ATCTTACAATCTATTGTAAATTATGGTGTC 7 123 1 CTATTGTAAA 0.67905 -108 AACTTTTTTAATGATTTAAGGT 7 219 0 CTTTTTTAAT 0.948282 -12 CTCGATAACTTTATTAAAACAAAACTAT 8 9 1 CTTTATTAAA 0.856969 -117 AGCTAATTATCATTATTAATTATGATAAAT 8 50 1 CATTATTAAT 0.742025 -76 ATTAACTAAACTATTTTTAAACT 9 4 0 CTATTTTTAA 0.853482 -57 TAGTTAATTTCTATTTTGTTACATTATTTA 9 26 1 CTATTTTGTT 0.612559 -35 TATTTTGTTACATTATTTATTTTACTGATA 9 37 1 CATTATTTAT 0.559147 -24 TATATATGAGCAATATTTAAATTTTTCGAG 10 121 0 CAATATTTAA 0.47748 -69 ATGGCAATTTCATTTTTTATATATGAGCAA 10 138 0 CATTTTTTAT 0.79514 -52 TTAAATAACTCTTTTTTAAATTTTTAAGAT 11 26 1 CTTTTTTAAA 0.948282 -71 CAAATGTCATCAATTTTGTTTAACACAAAT 12 44 1 CAATTTTGTT 0.431497 -79 CAATCTTAATCATTTTTAAGGTAATTAAAT 12 90 0 CATTTTTAAG 0.581298 -33 ********** Masking position 4 Map Score: 20.7247 Number of sites scoring better than the average of aligned sites = 2471 Number in coding regions = 2039 Number in noncoding regions = 432 Number of orfs with sites within 600 bp upstream = 349 Fraction of orfs with sites within 600 bp upstream = 0.0560553 Motif number 4 CCTTTCTTTGGAAGGCATTCAATTTCATAA 2 36 0 GAAGGCATTC 0.753072 -82 CCTTCCAAAGAAAGGTGTTCATTAGTGCCT 2 51 1 AAAGGTGTTC 0.904247 -67 GCCCCCAAGTGGGGGCGTTCAAATTTTTAT 4 94 0 GGGGGCGTTC 0.995274 -207 GCCCCCACTTGGGGGCGTTCATATATATCC 4 108 1 GGGGGCGTTC 0.995274 -193 CCTTCTAAAAGAAGGCGTTCAAAATTTTCA 7 178 0 GAAGGCGTTC 0.762669 -53 CCTTCTTTTAGAAGGCGTTCATCTATACCT 7 193 1 GAAGGCGTTC 0.762669 -38 ********** Masking position 8 Map Score: 12.4821 Number of sites scoring better than the average of aligned sites = 41 Number in coding regions = 8 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 5 ATTTCATAAAAATTTTTTATAATTTTAGAAG 2 14 0 AATTTTTATA 0.654412 -104 GAAGGCATTCAATTTCATAAAAATTTTTTAT 2 25 0 AATTTATAAA 0.892243 -93 CTCCTCAAATTTACTATATATTTCATAT 4 283 0 AATTTCTATA 0.854462 -18 AATTTTATAAAATATAAAAAA 5 1 1 AATTTATAAA 0.892243 -30 ATCTAATTTTTTAATATTTTTTAAA 6 5 1 AATTTTTAAT 0.811118 -160 AAAGATAAGAAATTTTATATTTGGGAATAAT 6 45 1 AATTTATATT 0.784298 -120 ACAATGTTACAATTATTTAATCCTGCGAAAG 6 94 1 AATTATTAAT 0.743524 -71 AAAATAACAAAATCTACTAATGAAAATTTTG 7 158 1 AATCTCTAAT 0.572422 -73 TAATAATGATAATTAGCTTAACCTTTTATAT 8 37 0 AATTACTTAA 0.632179 -89 AATTATGATAAATTATCTATTCATTACCTTA 8 67 1 AATTACTATT 0.798514 -59 ACAAAATAGAAATTAACTAAACTATTTTTAA 9 14 0 AATTACTAAA 0.899882 -47 AATATCAGTAAAATAAATAATGTAACAAAAT 9 38 0 AAATAATAAT 0.516636 -23 TAATAATAGTAATTATATAATATCAAAAGCG 10 19 0 AATTAATAAT 0.84824 -171 ATGTTATGGCAATTTCATTTTTTATATATGA 10 142 0 AATTTATTTT 0.411059 -48 AAAATTCCTAAAACTTTAAATA 11 2 1 AAATTCTAAA 0.717993 -95 TTAAAGAATAAAATTTATAATCTTAGAACTT 11 60 0 AAATTATAAT 0.6129 -37 TTTCATTAAAAATTTATTAAA 12 1 0 AATTTTTAAA 0.811125 -122 GTTTAACACAAATTTTATATAATTAGGTAAT 12 61 1 AATTTATATA 0.784988 -62 AAGGTAATTAAATTACCTAATTATATAAAAT 12 72 0 AATTACTAAT 0.899882 -51 TAGGTAATTTAATTACCTTAAAAATGATTAA 12 84 1 AATTACTTAA 0.632179 -39 ***** ***** Masking position 8 Map Score: 20.2231 Number of sites scoring better than the average of aligned sites = 987 Number in coding regions = 735 Number in noncoding regions = 252 Number of orfs with sites within 600 bp upstream = 228 Fraction of orfs with sites within 600 bp upstream = 0.0366206 Motif number 6 CACTATGGATAAGGGATATCT 2 107 1 AAGGGATATC 0.955277 -11 GACTTTAGAAAAGAGATATACTTTTTAATT 4 238 1 AAGAGATATA 0.86014 -63 AAATATAAAAAAGGGATAGAA 5 20 1 AAGGGATAGA 0.982835 -11 AAGATACATAAAGGTATATAAAGTTTTCTA 7 98 0 AAGGTATATA 0.958255 -133 TTAATGATTTAAGGTATAGATGAACGCCTT 7 204 0 AAGGTATAGA 0.965185 -27 AACATGATAATAGGTATATGACTCACTAAG 8 94 0 TAGGTATATG 0.892231 -32 TAAGATTGATTAGGGATAGGC 12 112 1 TAGGGATAGG 0.953812 -11 ********** Masking position 6 Map Score: 4.90985 Number of sites scoring better than the average of aligned sites = 99 Number in coding regions = 80 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 7 AATCTTTTTTTATTTTTAAAACTGAATCAT 1 14 1 TATTTTTAAA 0.775883 -35 AGGCATTCAATTTCATAAAAATTTTTTATA 2 24 0 TTTCATAAAA 0.432997 -94 TTATCCATAGTGTCTTTCAAAACATTTTGT 2 89 0 TGTCTTTCAA 0.450811 -29 TCTTGCTAAGTATCTTTGAAACTCTTCATA 4 12 0 TATCTTTGAA 0.904108 -289 TAAAATTTCTTATCTTTAAATTTGGATTTA 6 32 0 TATCTTTAAA 0.962856 -133 TACCTTTATGTATCTTACAATCTATTGTAA 7 112 1 TATCTTACAA 0.706043 -119 TAGATTTTGTTATTTTTGAATGACACCATA 7 144 0 TATTTTTGAA 0.557367 -87 CTATACCTTAAATCATTAAAAAAGTT 7 215 1 AATCATTAAA 0.82015 -16 TTAACTAAACTATTTTTAAACT 9 3 0 TATTTTTAAA 0.775883 -58 TAAATATCAGTAAAATAAATAATG 9 47 0 TATCAGTAAA 0.50495 -14 CCGTATCAAAAAGCTTTAAAGTATTAGTAA 10 50 0 AAGCTTTAAA 0.609148 -140 ATATATGAGCAATATTTAAATTTTTCGAGA 10 120 0 AATATTTAAA 0.393787 -70 TTTGAGGTGATACCATTAAAAGAATAA 10 173 1 TACCATTAAA 0.691822 -17 AAAATTCCTAAAACTTTAAATAACTCTTTT 11 11 1 AAACTTTAAA 0.512562 -86 AGAACTTGCATATCTTAAAAATTTAAAAAA 11 37 0 TATCTTAAAA 0.905829 -60 TAAAATTTATAATCTTAGAACTTGCATATC 11 53 0 AATCTTAGAA 0.623864 -44 TATAAATTTTATTCTTTAAACTTTTTATCA 11 72 1 ATTCTTTAAA 0.726548 -25 AGTATAATATTTTCATTAAAAATTTATTAA 12 12 0 TTTCATTAAA 0.673688 -111 GTAATTTAATTACCTTAAAAATGATTAAGA 12 87 1 TACCTTAAAA 0.691831 -36 ********** Masking position 9 Map Score: 11.5824 Number of sites scoring better than the average of aligned sites = 1545 Number in coding regions = 1352 Number in noncoding regions = 193 Number of orfs with sites within 600 bp upstream = 178 Fraction of orfs with sites within 600 bp upstream = 0.0285898 Motif number 8 ATATAATTTTTTGGCAATATAAAAGTAAAAT 3 20 0 TTGCAATATA 0.91715 -32 TTGAAATATATAGGATATATATGAACGCCCC 4 119 0 TAGATATATA 0.920484 -182 TGCAAAACATTTTGAAATATATAGGATATAT 4 130 0 TTGAAATATA 0.930639 -171 GTGAATGAGCTAACCAATATAGGAAAATATT 4 181 1 TACCAATATA 0.914516 -120 AAAAAAATGATATGAAATATATAGTAAATTT 4 274 1 TAGAAATATA 0.972889 -27 AATTTTATAAAATATAAAAAAGGGAT 5 6 1 TAAAAATATA 0.824225 -25 AAAATATTATTCCCAAATATAAAATTTCTTA 6 50 0 TCCAAATATA 0.799638 -115 ATATTTTTATTAAGCAATATACAATGTTACA 6 74 1 TAGCAATATA 0.96797 -91 CAATAGATTGTAAGATACATAAAGGTATATA 7 108 0 TAGATACATA 0.729882 -123 ** ******** Masking position 7 Map Score: 4.73681 Number of sites scoring better than the average of aligned sites = 138 Number in coding regions = 109 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 9 TTGATGATTCAGTTTTAAAAATAAAAAAAG 1 17 0 AGTTTTAAAA 0.726016 -32 TGTCTTCTAAAATTATAAAAAATTTTTATG 2 11 1 AATTATAAAA 0.666306 -107 TTAGTGCCTTAGTTATTACAAAATGTTTTG 2 72 1 AGTTATTACA 0.900419 -46 TTTTTGCAAAAGTTATTAAAATTAAAAATA 4 67 1 AGTTATTAAA 0.977687 -234 TTTTTTTGCCAGTAATTAAAAAGTATATCT 4 251 0 AGTAATTAAA 0.957845 -50 TTAAAATAGAACTTATAAAAGCCATAAGAT 6 130 1 ACTTATAAAA 0.747598 -35 TAATAATAATAGTAATTATATAATATCAAA 10 23 0 AGTAATTATA 0.849978 -167 TTAAAGTATTAGTAATAATAATAGTAATTA 10 35 0 AGTAATAATA 0.746047 -155 TTGATACGGAAGTTATTAAAAATAATGATA 10 71 1 AGTTATTAAA 0.977687 -119 TTTAAAAAAGAGTTATTTAAAGTTTTAGGA 11 16 0 AGTTATTTAA 0.83631 -81 TTCATTAAAAATTTATTAAA 12 1 0 ATTTATTAAA 0.793411 -122 TCATTTTTAAGGTAATTAAATTACCTAATT 12 81 0 GGTAATTAAA 0.796828 -42 ********** Masking position 10 Map Score: 9.42505 Number of sites scoring better than the average of aligned sites = 541 Number in coding regions = 446 Number in noncoding regions = 95 Number of orfs with sites within 600 bp upstream = 100 Fraction of orfs with sites within 600 bp upstream = 0.0160617 Motif number 10 TGTCTTCTAAAATTATAAAAA 2 2 1 GTCTTCTAAA 0.965001 -116 GAAATTGAATGCCTTCCAAAGAAAGGTGTT 2 40 1 GCCTTCCAAA 0.988775 -78 TATCCATAGTGTCTTTCAAAACATTTTGTA 2 88 0 GTCTTTCAAA 0.821577 -30 AATTTTCGCATCTTTCTAAATATTTTCCTA 4 200 0 TCTTTCTAAA 0.707514 -101 CTAAAAGAAGGCGTTCAAAATTTTCATTAG 7 174 0 GCGTTCAAAA 0.901691 -57 ATAGATGAACGCCTTCTAAAAGAAGGCGTT 7 189 0 GCCTTCTAAA 0.987893 -42 ********** Masking position 5 Map Score: 1.27847 Number of sites scoring better than the average of aligned sites = 85 Number in coding regions = 65 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 11 ********** No masking Map Score: -8.28903e-13 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: -8.28903e-13 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 ********** No masking Map Score: -8.28903e-13 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