AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_rpxx.txt -z/home/amcguire/genomes/rpxx.fna -icpxR_rpxx_opreg_100.orf -g0.290 -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 = 0.29 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 RP025 90 unknown #2 RP071 196 TRANSCRIPTIONAL ACTIVATOR PROTEIN CZCR (czcR) #3 RP076 75 unknown #4 RP123 143 HFLC PROTEIN (hflC) #5 RP124 30 PROBABLE PERIPLASMIC SERINE PROTEASE DO-LIKE PRECURSOR (htrA) #6 RP303 89 RNA POLYMERASE SIGMA-32 FACTOR (rpoH) #7 RP317 138 PROTEIN KINASE C INHIBITOR 1 (pkcI) #8 RP427 121 PETR PROTEIN (ompR) #9 RP696 300 PROBABLE TRANSPORT ATP-BINDING PROTEIN MSBA (msbA2) #10 RP755 282 PROLINE/BETAINE TRANSPORTER (proP5) #11 RP785 112 unknown #12 RP822 300 unknown #13 RP852 211 PROLINE/BETAINE TRANSPORTER (proP6) #14 RP881 300 PROLINE/BETAINE TRANSPORTER (proP7) Motif number 1 ATAATTTGATTAAATATTCTTTACTTATATTATTAA 2 80 1 TAATTTTACT 0.930569 -117 ATTAACTAAATTATAATTTTTTATCTAGTGCTTTAT 2 123 0 TAATTTTATT 0.960089 -74 ATAATTTAGTTAATAATTATTAACTAAATTATTATC 2 145 1 TAATTTAACA 0.938659 -52 TCCATAAAATTCAATTTTGATAATAATTTAGTTAAT 2 163 0 TATTTTAATA 0.725808 -34 TTAATATTCCTTATTATTTTATAATA 4 128 0 TAATTTTATA 0.949672 -16 GACCACGGGTTCAAAATTATTAATATCATAGTTGTT 8 69 0 TAATTTAATT 0.975141 -53 ATAATCTAGATTAACATTGTTAATTTTATGGCGAGT 9 62 1 TAATTTAATT 0.975268 -239 TCACAATTACTAATAATTAGTAATCACATAACAACT 9 177 0 TAATTTAATA 0.767266 -124 TTTGTAGAAGTTAAAATTTTTTACGTGAATAAGTTA 11 25 0 TAATTTTACT 0.930569 -88 CTCGTTGTTTTTATAATTCATAATAAACTATCGTCA 11 70 0 TAATTTAATA 0.767266 -43 ATGATGATTTATTATTTGGTACTGTAT 12 2 1 TAATTTTATT 0.959891 -299 AATAGAGCTTGAAAATTTTCTATATCATCTTTGAA 13 10 1 TAATTCTATT 0.753733 -202 ATGTTTTATATTAAGATTCGTAACATCTTAAAAGTC 14 118 0 TAATTTAACT 0.95633 -183 ATAATGGTTTTAAGTATTTATAATCTAGTTTAGCAC 14 161 0 TAATTTAATT 0.975061 -140 CATTATCCTGTAATCATTCCTAATAAAACTTTCTTA 14 191 1 TAATTTAATA 0.968387 -110 TTGTCTATAATAATAATTAGTAATTAATTTATTTTA 14 269 1 TAATTTAATA 0.767266 -32 * * *** **** * Masking position 8 Map Score: 24.3865 Number of sites scoring better than the average of aligned sites = 301 Number in coding regions = 170 Number in noncoding regions = 131 Number of orfs with sites within 600 bp upstream = 73 Fraction of orfs with sites within 600 bp upstream = 0.011725 Motif number 2 AAATATATACTTTATAATAGAAGCAAAAT 1 3 0 TTATATGAAA 0.916944 -88 TATTATAAAGTATATATTTTTATTGAAATAAAATTGA 1 21 1 TTATTTTAAA 0.822455 -70 TAGTAAAAATTTTATAATTTGATTAAATATTCTTTAC 2 67 1 TTATATTAAA 0.973441 -130 TATACGTTCATTAATAATATAAGTAAAGAATATTTAA 2 89 0 TAATATTAAA 0.713294 -108 TATAATAATTTCTATAATTTCACTTAAATGTCTTGAC 3 38 0 TTATATTAAA 0.973488 -38 AGGCTTTTTTAGTATGATATTATAAAATAATAAGGAA 4 111 1 ATATATTAAA 0.906568 -33 ATAAACTTTTTCTATAATTTTTTTAAATAAAATCAAA 6 13 0 TTATATTTAA 0.973446 -77 TACTAACATATATATGATCTAAAATAAACTTTTTCTA 6 36 0 TTATATTAAA 0.973488 -54 TAAGTTATATTTATATTAGATTAGAAACTCATCCCG 8 10 1 TTATTTGTAA 0.58209 -112 TTATATAGAAAATATGAATTTATACAACA 9 3 0 ATATAATAAA 0.732014 -298 ACGATAGTTTATTATGAATTATAAAAACAACGAGCAT 11 72 1 ATATAATTAA 0.731983 -41 TTTGGTACTGTATATAACATGTATAAAGCTGAGGCAG 12 25 1 TTATACTTAA 0.822553 -276 TAAGGTACATTATATAAACTATATAAAGATAATATAC 12 78 0 TTATAATTAA 0.894369 -223 TATAGGATCTTTTATTATTTTTTGTAAAAAAGTTGCT 12 140 0 TTATATTTAA 0.973485 -161 GAAAATTTTCTATATCATCTTTGAAAATTATTGGATA 13 21 1 TTATATTTAA 0.973488 -191 CACTATTCCTTTTATTATCTTTTTAAATAAATAAAGT 13 179 1 TTATATTTAA 0.970753 -33 ACCATACTACTTTTTTATATAAACTAAGTTTTGATTT 14 26 0 TTTTATTAAA 0.71353 -275 ACATAAAATATTTATGATATATGGAAGACTACTCAGA 14 83 1 TTATATTTAG 0.786869 -218 ATAAAGTGTAAATATCATTTTAACTAAGAATAAGAAA 14 220 0 ATATATTAAA 0.906568 -81 ATATTTACACTTTATAAATGATGTAAATTGTCTATAA 14 242 1 TTATAAGTAA 0.749929 -59 * *** ** * * ** Masking position 5 Map Score: 20.2621 Number of sites scoring better than the average of aligned sites = 391 Number in coding regions = 230 Number in noncoding regions = 161 Number of orfs with sites within 600 bp upstream = 96 Fraction of orfs with sites within 600 bp upstream = 0.0154192 Motif number 3 AAGTATATATTTTTATTGAAATAAAATTGATACAC 1 28 1 TTATAAATAA 0.84429 -63 AAATTCTACCTTTAATTGAAAAACAACAATATTAT 2 30 0 TTATAAAAAA 0.929834 -167 TTAACTAAATTATTATCAAAATTGAATTTTATGGA 2 164 1 TTATAAATTA 0.599739 -33 ATGTCTTGACTTTTAACATAAAAGAATTCTATCTT 3 13 0 TTAATAAAAA 0.922739 -63 TGAGATAAAATCTTATCCTAAATGATGTGAACATC 4 39 0 TTATTAAATA 0.649998 -105 TATTTTATAATATCATACTAAAAAAGCCTTGTAAG 4 105 0 TTATTAAAAA 0.881634 -39 TGTTTGATTTTATTTAAAAAAATTATAGAAAA 6 8 1 TTATAAAAAA 0.921456 -82 CTAACATATATATGATCTAAAATAAACTTTTTCTA 6 36 0 TTATAAAATA 0.784276 -54 GAGTTTCTAATCTAATATAAATATAACTTA 8 6 0 TTATAAATAA 0.854649 -116 TCTCGTAACTTATTCACGTAAAAAATTTTAACTTC 11 20 1 TTCATAAAAA 0.699724 -93 GATAGTTTATTATGAATTATAAAAACAACGAGCAT 11 74 1 TTAAATAAAA 0.601326 -39 ATATAAACTATATAAAGATAATATACTTTTTGCAC 12 69 0 TTAATAATAA 0.831181 -232 AATAGCAACTTTTTTACAAAAAATAATAAAAGATC 12 137 1 TTTAAAAAAA 0.625007 -164 ATGAGTACATTATAAAGCAAAAAAAACTCTATAGT 12 184 0 TTAAAAAAAA 0.958985 -117 TTGATCAGGTTGTCCATAAAAAAGACTGGATACCG 12 255 0 TTCAAAAAAA 0.820161 -46 TAGTGTACTTTCTCAAGTAAAAACATAACCCAAAT 13 149 0 TTAAAAAAAA 0.958993 -63 TTTATTATCTTTTTAAATAAATAAAGTAACTGA 13 189 1 TTAAAAATAA 0.905529 -23 TAAGCATTGCTATAAACATAAAATATTTATGATAT 14 68 1 TTAATAAAAA 0.922751 -233 ATGTTACGAATCTTAATATAAAACATTTAACAAGT 14 128 1 TTAATAAAAA 0.921813 -173 GTAAATATCATTTTAACTAAGAATAAGAAAGTTTT 14 215 0 TTAAAAGAAA 0.690905 -86 TGAATTTAAAATAAATTAATTACTAATTA 14 282 0 TTAAAAATTA 0.705875 -19 * * ** ***** * Masking position 3 Map Score: 23.1596 Number of sites scoring better than the average of aligned sites = 579 Number in coding regions = 361 Number in noncoding regions = 218 Number of orfs with sites within 600 bp upstream = 121 Fraction of orfs with sites within 600 bp upstream = 0.0194346 Motif number 4 TTTAATTGAAAAACAACAATATTATTGGATAA 2 23 0 AAACACATAT 0.935427 -174 ATGAACGTATAAAGCACTAGATAAAAAATTAT 2 115 1 AAAGACTGAT 0.95881 -82 TTTTAACATAAAAGAATTCTATCTTTT 3 6 0 AAAGATTTAT 0.696616 -70 GAAATTATTATAAGTACTATATA 3 63 1 TAAGACTTAT 0.662661 -13 AATTACCATAAAACTACAGGATAAAAGAA 7 120 1 AAACACAGAT 0.940173 -19 TTTCGTGGTCAAACCACGGGATGAGTTTCTAA 8 31 0 AAACACGGAT 0.884813 -91 ACCCGTGGTCAAACCACGAGATGTAAAATGAG 8 95 1 AAACACGGAT 0.884813 -27 AGTAATTGTGAAAAGACATTATTGCATAGATT 9 202 1 AAAAACATAT 0.901314 -99 CATAGATTGGAAAACACACTATTTTTCATTCT 9 226 1 AAAAACATAT 0.901304 -75 AAAATCCTTCAAAGACCTTGATGTAAAGGTGG 10 122 0 AAAGCCTGAT 0.759519 -161 CACAGTGCAAAAAGTATATTATCTTTATATAG 12 65 1 AAAGATATAT 0.727104 -236 AGATACTCATAAGGTACATTATATAAACTATA 12 92 0 AAGGACATAT 0.771315 -209 TATAAAGCAAAAAAAACTCTATAGTCAAACTA 12 177 0 AAAAACTTAT 0.887417 -124 TTGTCCATAAAAAAGACTGGATACCGGTGGTC 12 249 0 AAAAACTGAT 0.895313 -52 TTTACTTGAGAAAGTACACTATTCCTTTTATT 13 163 1 AAAGACATAT 0.961306 -49 **** *** *** Masking position 2 Map Score: 12.3355 Number of sites scoring better than the average of aligned sites = 207 Number in coding regions = 118 Number in noncoding regions = 89 Number of orfs with sites within 600 bp upstream = 61 Fraction of orfs with sites within 600 bp upstream = 0.00979762 Motif number 5 TTAGAAACTCATCCCGTGGTTTGACCACGA 8 31 1 ATCCCGTGGT 0.990382 -91 AATAATTTTGAACCCGTGGTCAAACCACGA 8 84 1 AACCCGTGGT 0.994439 -38 CTCATTTTACATCTCGTGGTTTGACCACGG 8 97 0 ATCTCGTGGT 0.944987 -25 ACGGGATTCGAACCCGTGGCCCTCAGAACC 9 128 0 AACCCGTGGC 0.994239 -173 TTAGTACTAATACCCGTGGCTTGACCACCG 12 227 1 TACCCGTGGC 0.98941 -74 AAAGACTGGATACCGGTGGTCAAGCCACGG 12 240 0 TACCGGTGGT 0.962756 -61 ********** Masking position 7 Map Score: 8.57675 Number of sites scoring better than the average of aligned sites = 8 Number in coding regions = 2 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 6 TAAAAAATTATAATTTAGTTAATAATTATTAAC 2 136 1 TATTAGTAAT 0.892596 -61 ATTTTGATAATAATTTAGTTAATAATTATTAAC 2 153 0 TATTAGTAAT 0.892596 -44 ACTGTCGTCTTTATTTGGAGTAT 5 18 1 TATTGGGTAT 0.610774 -13 AGAAAAAGTTTATTTTAGATCATATATATGTTA 6 37 1 TTTTAGTCAT 0.65742 -53 CCTGAAAAACTATTTTCGTTTATACTAACATAT 6 62 0 TTTTCGTTAT 0.65742 -28 ACGAAAATAGTTTTTCAGGTTATT 6 76 1 TTTCAGTTAT 0.893271 -14 GTCAAGAATATTATATAGAAAATATGAATTTAT 9 17 0 TATTAGAAAT 0.54066 -284 TTAACAATGTTAATCTAGATTATCAGAAGGATT 9 52 0 TATTAGTTAT 0.965026 -249 TGTCTAATACTCATTCAGTTTAGATATATGAAG 10 88 1 TATCAGTTAG 0.77119 -195 GAGTAAGGCGTCTTGCAGCTTATAACAGAAGCG 10 199 1 TTTCAGTTAT 0.893271 -84 GAGTAAGGCGTCTTGCAGCTTATAATACTCACG 10 244 0 TTTCAGTTAT 0.893271 -39 TGCCTCAGCTTTATACATGTTATATACAGTACC 12 28 0 TATCATTTAT 0.447435 -273 TATATTATCTTTATATAGTTTATATAATGTACC 12 79 1 TATTAGTTAT 0.965026 -222 ATAGTTTATATAATGTACCTTATGAGTATCTCC 12 93 1 TATTACTTAT 0.788692 -208 CTATAGAGTTTTTTTTGCTTTATAATGTACTCA 12 185 1 TTTTGCTTAT 0.477534 -116 TTTTCAAAGATGATATAGAAAATTTTCAAGCTC 13 15 0 TATTAGAAAT 0.54066 -197 CTCTCTTATTTTATTTGGGTTATGTTTTTACTT 13 137 1 TATTGGTTAT 0.929487 -75 TATAAAAAAGTAGTATGGTTTATCTAAGCATTG 14 44 1 TGTTGGTTAT 0.675229 -257 TAAGTATTTATAATCTAGTTTAGCACTTGTTAA 14 154 0 TATTAGTTAG 0.850651 -147 * ** *** **** Masking position 4 Map Score: 11.0151 Number of sites scoring better than the average of aligned sites = 488 Number in coding regions = 368 Number in noncoding regions = 120 Number of orfs with sites within 600 bp upstream = 72 Fraction of orfs with sites within 600 bp upstream = 0.0115644 Motif number 7 TCAATAAAAATATATACTTTATAATAGAAGCAAAAT 1 6 0 TATCTTAAAC 0.657802 -85 ATTTATTCCTTTTGACTATTAACCATTCTACAA 1 68 0 TTTCTTAAAC 0.94317 -23 AATTATAAAATTTTTACTATTAAATTCTACCTTTAATTGAA 2 45 0 TTTCTTATAC 0.94317 -152 CATTGGATCTTTGCTCTTTTTGAAGTTGATCTTCTTACAAG 4 72 1 TTTTTTATAC 0.967413 -72 TTAATATTCCTTATTATTTTATAATATCATACTAAAAAAGC 4 113 0 TTTTTTAAAA 0.680518 -31 AACTTTTTCTATAATTTTTTTAAATAAAATCAAACA 6 6 0 ATTTTTAAAC 0.774694 -84 GCAAGACGCCTTACTCTTTTCCAAATCCAACGAGTATACAT 10 174 0 TTTTTTATAC 0.967412 -109 GCAAGACGCCTTACTCTTTTCCAAATCCAACT 10 261 1 TTTTTTATAC 0.967412 -22 ATGCTCGTTGTTTTTATAATTCATAATAAACTATCGTCATC 11 68 0 TTTTATAAAC 0.774699 -45 TAGAGATAGCTTGCTTTTTTAAAAGTTGATCCTCATCTATC 13 94 1 TTTTTTATAC 0.96741 -118 AAACTAAGTTTTGATTTTGTAAAGCTTTATCT 14 2 0 TTTTTTATAC 0.967413 -299 TAATTACTAATTATTATTATAGACAATTTACATCATTTATA 14 254 0 TTTTTTAATC 0.774699 -47 ** * ** * * * * * Masking position 13 Map Score: 7.84067 Number of sites scoring better than the average of aligned sites = 124 Number in coding regions = 78 Number in noncoding regions = 46 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 8 ACTTTATAATAGAAGCAAAAT 1 1 0 AGAGCAAAAT 0.876852 -90 ATATTTTTATTGAAATAAAATTGATACACTC 1 34 1 TGAATAAAAT 0.96152 -57 ATAAAGCACTAGATAAAAAATTATAATTTAG 2 123 1 AGAAAAAAAT 0.669709 -74 AAAGATCCAATGAGATAAAATCTTATCCTAA 4 53 0 TGAATAAAAT 0.96152 -91 TATAATTTTTTTAAATAAAATCAAACA 6 7 0 TTAATAAAAT 0.68584 -83 AACATATATATGATCTAAAATAAACTTTTTC 6 38 0 TGACTAAAAT 0.901348 -52 ATCATCATTGTGAGGTAAAATTTAGATGCTG 7 36 1 TGAGTAAAAT 0.969852 -103 TCAAACCACGAGATGTAAAATGAGTATAA 8 103 1 AGAGTAAAAT 0.935761 -19 ATCTACGTGGTGACACAAAATT 12 289 1 TGAACAAAAT 0.924323 -12 ACTTTATAAATGATGTAAATTGTCTATAATA 14 250 1 TGAGTAAATT 0.819057 -51 *** ******* Masking position 7 Map Score: 6.81897 Number of sites scoring better than the average of aligned sites = 135 Number in coding regions = 87 Number in noncoding regions = 48 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467 Motif number 9 ATCCAATAATATTGTTGTTTTTCAATTAAAG 2 25 1 ATTGTTTTTT 0.674932 -172 TCATTGGATCTTTGCTCTTTTTGAAGTTGAT 4 71 1 TTTGCTTTTT 0.875626 -73 TTAATATTCCTTATTATTTTATAATATCAT 4 124 0 CTTATTTTTT 0.932683 -20 GATTGGAAAACACACTATTTTTCATTCTGTG 9 230 1 CACACTTTTT 0.475536 -71 TGGCTCGTTTTTTGTTATTTTCTGGATACTG 9 263 0 TTTGTTTTTT 0.839902 -38 TGCAAGACGCCTTACTCTTTTCCAAATCCAA 10 185 0 CTTACTTTTT 0.948962 -98 TGCAAGACGCCTTACTCTTTTCCAAATCCAA 10 260 1 CTTACTTTTT 0.948962 -23 ATTCTTGATGCTCGTTGTTTTTATAATTCAT 11 85 0 CTCGTTTTTT 0.877089 -28 TATAGGATCTTTTATTATTTTTTGTAAAAAA 12 146 0 TTTATTTTTT 0.796304 -155 GTAGAGATAGCTTGCTTTTTTAAAAGTTGAT 13 93 1 CTTGCTTTTT 0.961467 -119 TATCTACTCTCTTATTTTATTTGGGTTATGT 13 131 1 CTTATTTATT 0.637738 -81 ****** **** Masking position 6 Map Score: 7.01566 Number of sites scoring better than the average of aligned sites = 189 Number in coding regions = 140 Number in noncoding regions = 49 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 10 AGTACTTTAGCATGATATATCTAATT 4 4 0 CTATTATCTA 0.963924 -140 GCACACATATCTTAAAATATTGATTAGATTGTG 7 66 1 CTAATATTGA 0.797401 -73 TAAAGGTGGACTTCATATATCTAAACTGAATGA 10 98 0 CTATTATCTA 0.963924 -185 TTATGGACAACCTGATCAATCTACGTGGTGACA 12 271 1 CTATAATCTA 0.827239 -30 CAGCGTATATCATTAAACATTTAGTATCCAATA 13 49 0 CTAACATTTA 0.817328 -163 AAAAGTTGATCCTCATCTATCTACTCTCTTATT 13 114 1 CTATTATCTA 0.963924 -98 TCAGTTACTTTATTTATTTAAAAAGATAAT 13 192 0 CTATTATTTA 0.954032 -20 TTGCTATAAACATAAAATATTTATGATATATGG 14 74 1 CTAATATTTA 0.943964 -227 AGGATAATGGTTTTAAGTATTTATAATCTAGTT 14 167 0 TTAATATTTA 0.622848 -134 * * ** ****** Masking position 5 Map Score: 3.09563 Number of sites scoring better than the average of aligned sites = 76 Number in coding regions = 50 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 11 AAACAACAATATTATTGGATAATTAGGTAAT 2 14 0 ATATTGGATA 0.962138 -183 TTACCATAAAACTACAGGATAAAAGAA 7 122 1 ATACAGGATA 0.955381 -17 GTGAAAAGACATTATTGCATAGATTGGAAAA 9 209 1 ATATTGCATA 0.853515 -92 GTCCATAAAAAAGACTGGATACCGGTGGTCA 12 248 0 AGACTGGATA 0.935937 -53 ATCTTTGAAAATTATTGGATACTAAATGTTT 13 37 1 ATATTGGATA 0.962138 -175 ATTAGGAATGATTACAGGATAATGGTTTTAA 14 184 0 ATACAGGATA 0.955381 -117 * ********* Masking position 4 Map Score: 2.15062 Number of sites scoring better than the average of aligned sites = 24 Number in coding regions = 16 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 12 ********** No masking Map Score: -5.39769e-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 13 ********** No masking Map Score: -5.39769e-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: -5.39769e-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