AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00310_rpxx_reg_100.orf -o00310_rpxx_100.ace -a/home/amcguire/genomes/ORF_rpxx.txt -z/home/amcguire/genomes/rpxx.fna -g0.29 -x5 -e 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 = 1 Input sequences: #1 RP009 300 UDP-3-O-[3-HYDROXYMYRISTOYL] GLUCOSAMINE N-ACYLTRANSFERASE (lpxD) #2 RP179 24 DIHYDROLIPOAMIDE ACETYLTRANSFERASE COMPONENT (sucB) #3 RP180 300 2-OXOGLUTARATE DEHYDROGENASE E1 COMPONENT (sucA) #4 RP219 138 MITOCHONDRIAL PROTEASE (mpp) #5 RP366 75 APOLIPOPROTEIN N-ACYLTRANSFERASE (lnt) #6 RP525 138 PROTEASE IV (sppA) #7 RP719 300 unknown #8 RP738 300 POLY-BETA-HYDROXYBUTYRATE POLYMERASE (phbC1) #9 RP743 79 SERINE HYDROXYMETHYLTRANSFERASE (glyA) #10 RP744 102 unknown #11 RP876 300 PROBABLE LIPOATE-PROTEIN LIGASE B (lipB) Motif number 1 CTAAGGTTTTTGTGTAGTTCTTTTATTTAGAGATTA 1 33 0 TTTATTTTTT 0.850176 -268 ATGTGAGAAATTTAAATTAATAATATTGATTTATTT 1 88 0 TTAATTAATT 0.854441 -213 TAAATTTGAGATTCAAGTTATTAATTGAAGTAGAAC 1 129 0 ATAATTTAAT 0.737468 -172 GTTTAAAATTACTATATTAGTATTTTTATAGTCAAG 1 165 1 ATTATTATTT 0.571773 -136 TTATATAATATCGCTAGTGATTAAGTCAGTTAAAGT 1 271 1 TGTATTTAAT 0.881118 -30 TAGATAATGATTTAAATTACTAAAATCACCCCTTAA 3 40 0 TTAATTAAAT 0.834579 -261 AACCGAAATTTCTCAAATTATTATTTAGATAATGAT 3 65 0 TTAATTTATT 0.890962 -236 ATTGTTGTTTGTATTGTTTATTTTTTTGTGCAA 3 278 0 TTTATTTATT 0.930734 -23 TTGGAAAATTCTTATTTACAGAATTTT 4 2 1 TGAATTTATT 0.818415 -137 TTCATTTTTCTGTAAAATGATTATTTAGAAAATAAA 4 105 1 TTAATTTATT 0.890959 -34 AATTTATTTTTATTTTCTAAATAATC 4 123 0 ATTATTATTT 0.584457 -16 TTATTTACTCATTATATTTAAACTTGC 5 2 1 TTTATTTATT 0.930729 -74 TGTTTTTCCTTGTATACTGATAAATTAACCTCACTT 7 176 0 TTTATTAAAT 0.90617 -125 TTTATTATCTAATATAATCGTAAAATGCAAATGTTC 7 227 0 ATTATTAAAT 0.756115 -74 AAGTCAAACATATTTATTGCTTTATTATCTAATATA 7 247 0 TTTATTTTAT 0.849896 -54 TATCTTCATTATGCTATTCTTTATTTAATTAGGATA 8 267 1 AGTATTTATT 0.718645 -34 TCACGGTATCTAGTCGTTTATTTTTCTTTGTA 9 7 1 TTTATTTTAT 0.850171 -73 TCCTCATATGTTTTTAGTATTTATCTGTATATGTGT 9 51 0 TTTATTTATT 0.930327 -29 TTGTTTGCTATTGCTATTCATTTAATATACTCAACT 10 38 1 TGTATTTTAT 0.757867 -65 AATATACTCAACTTTAATATTAAAGTAATAAACATA 10 61 1 ATTATTAAAT 0.47341 -42 CTTATCTCATTTAAAGTAATAAATTAATATTGTAG 11 10 1 TTAATTAAAT 0.834579 -291 AGGGTTTTGGTTTATACTCGTTAAATCTATTACTAC 11 42 0 TTTATTTAAT 0.930605 -259 TACATGATAATGGAAATTGATATAATCAATATTGCA 11 102 1 TGAATTATAT 0.578286 -199 TGCATTAATATTGGAAATGTTAATCTGAATTAAT 11 277 1 TGAATTAATT 0.764552 -24 * * ** * **** * Masking position 8 Map Score: 24.4584 Number of sites scoring better than the average of aligned sites = 902 Number in coding regions = 508 Number in noncoding regions = 394 Number of orfs with sites within 600 bp upstream = 190 Fraction of orfs with sites within 600 bp upstream = 0.0305172 Motif number 2 GAAGTAGAACATGTAATGTGAGAAATTTAAATTAATAATA 1 99 0 ATTAAAATTA 0.585991 -202 TTATGCTTTTATTATGCAATAAAATTGTAAGTTTTATATG 1 230 0 ATATGAAGTA 0.622227 -71 ATCGCTAGTGATTAAGTCAGTTAAAGTTTAT 1 280 1 ATAAGAATTA 0.784949 -21 TTCTCAAATTATTATTTAGATAATGATTTAAATTACTAAA 3 52 0 ATATTATTTA 0.664745 -249 TATGTAAGGTATCTAGAAGAGAAATATTTATAGGTTATAT 3 166 1 ATTAGAATTA 0.90147 -135 ATATTCTGAGATCTTTTATGTCATTGTTGACACTCGGTAG 3 202 1 ATTTTATTTA 0.832498 -99 TGTATTGTTTATTTTTTTGTGCAAATGTAATAGCTCACTT 3 262 0 ATTTTAAGTA 0.85718 -39 TACGCATTTCATTTTTCTGTAAAATGATTATTTAGAAAAT 4 98 1 ATTTTAAATA 0.601693 -41 TTAAATGAGCATATTTCGTAACAAATTTTAATCCCAATAC 7 104 0 ATTTTAATTA 0.942862 -197 AGCAATAAATATGTTTGACTTTATTTTTAATTGCTGTAAA 7 262 1 ATTTTATTTA 0.832498 -39 TTATGAAAAGATATTTCCCCTAAAACTTTAGAGCATATAT 8 48 1 ATTTTAATTA 0.942862 -253 AAAGAATAGCATAATGAAGATAAACGTTAAAAAGAGCTAA 8 249 0 ATATGAATTA 0.81912 -52 TGTTTTTAGTATTTATCTGTATATGTGTTACTACAGTACA 9 39 0 ATTATATGTA 0.593002 -41 TATTTCATATGTTTATTACTTTAATATTAAAGTTGAGTAT 10 64 0 GTTATAATTA 0.598692 -39 TACTCGTTAAATCTATTACTACAATATTAATTTATTACTT 11 24 0 ATTATAATTA 0.930072 -277 CCCTACACCAATGTTTCCTTGTAAATTTTACATGATAATG 11 74 1 ATTTTAATTA 0.942862 -227 AATGTATTACATATAGAGCTGTAAGCTTTAAACTACAGGA 11 149 1 ATTAGAATTA 0.90147 -152 TTTTAGATGCATTAATATTGGAAATGTTAATCTGAATTAA 11 270 1 ATAATAATTA 0.841426 -31 ** *** ** ** * Masking position 18 Map Score: 12.8695 Number of sites scoring better than the average of aligned sites = 675 Number in coding regions = 439 Number in noncoding regions = 236 Number of orfs with sites within 600 bp upstream = 124 Fraction of orfs with sites within 600 bp upstream = 0.0199165 Motif number 3 GATGAATCTCAAATAAATCAATATTATTAAT 1 78 1 AAATAAATAA 0.722228 -223 CGTTTTTAGGAGTAAAATAAATT 2 12 1 AGTAAAATAA 0.880743 -13 AGAAACACAAAAATATAAAAGATGATATA 3 9 1 AAAAATATAA 0.722228 -292 ACATTTGCACAAAAAAATAAACAATACAAAC 3 274 1 AAAAAAATAA 0.945153 -27 ATCATTTTACAGAAAAATGAAATGCGTAGAT 4 95 0 AGAAAAATAA 0.912405 -44 TATTTAGAAAATAAAAATAAATT 4 126 1 ATAAAAATAA 0.778743 -13 CATCGGTAAGGAAAAAGTTAAATTTTTGACG 6 20 1 GAAAAAGTAA 0.858926 -119 TTTTGACGAAGTAAAAATCAAAAATCTGATT 6 43 1 GTAAAAATAA 0.643845 -96 CACTATTAAAAATATAATAAATC 6 126 1 AATATAATAA 0.648321 -13 TAATGCAGGAAATAAAATTAAGTGAGGTTAA 7 157 1 AATAAAATAA 0.924347 -144 AGCAATTAAAAATAAAGTCAAACATATTTAT 7 266 0 AATAAAGTAA 0.893671 -35 AAGGACAAAAAAAAAAGTTAAGCACTTCAAG 8 14 1 AAAAAAGTAA 0.922203 -287 AGTATATCCTAATTAAATAAAGAATAGCATA 8 276 0 AATTAAATAA 0.648321 -25 TACAGTACAAAGAAAAATAAACGACTAGATA 9 17 0 AGAAAAATAA 0.912405 -63 AAACATATGAAATAAAGTAAACC 10 90 1 AATAAAGTAA 0.893671 -13 AATGGAAATTGATATAATCAATATTGCAGTA 11 110 1 GATATAATAA 0.486354 -191 CATTAATATTGGAAATGTTAATCTGAATTAA 11 279 1 GGAAATGTAA 0.357026 -22 ******** ** Masking position 8 Map Score: 13.688 Number of sites scoring better than the average of aligned sites = 693 Number in coding regions = 486 Number in noncoding regions = 207 Number of orfs with sites within 600 bp upstream = 128 Fraction of orfs with sites within 600 bp upstream = 0.0205589 Motif number 4 TTGTATTGTTTATTTTTTTGTGCAAATGTAAT 3 271 0 TTTTTTTGTG 0.917589 -30 ATTGTTGTTTGTATTGTTTATTT 3 288 0 TGTTTTTGTA 0.909538 -13 AATTTATTTTTATTTTCTAAATAATCATT 4 120 0 TTTATTTCTA 0.712929 -19 TAGCATGATGTATTATTTTGTAAACAAATAAT 5 46 1 TTTATTTGTA 0.955088 -30 TACACTGCTTTTTTAGCTTGTAATCAATACCT 7 11 0 TTTACTTGTA 0.930164 -290 TCATTACCTGTTTTTCCTTGTATACTGATAAA 7 188 0 TTTTCTTGTA 0.970963 -113 GTGCTTAACTTTTTTTTTTGTCCTTAGG 8 7 0 TTTTTTTGTC 0.917589 -294 TTTAAAAAGTTGTTTATTTGTACTCAAGTACT 8 170 1 TTTTTTTGTA 0.981614 -131 TAGTCGTTTATTTTTCTTTGTACTGTAGTAAC 9 21 1 TTTTTTTGTA 0.981614 -59 ATGTTTTTAGTATTTATCTGTATATGTGTTAC 9 48 0 TTTTTCTGTA 0.909538 -32 CCTACACCAATGTTTCCTTGTAAATTTTACAT 11 75 1 TTTTCTTGTA 0.970963 -226 * *** ****** Masking position 4 Map Score: 12.7389 Number of sites scoring better than the average of aligned sites = 68 Number in coding regions = 45 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 5 CTAATATAGTAATTTTAAACTAAATTTGAGATT 1 152 0 AATTTAACAA 0.929716 -149 AATCGGCTGAATTTTTTAACGAACCGAAATTTC 3 89 0 ATTTTTACAA 0.929716 -212 TTATTTACAGAATTTTTTACTAAGTTGCTTCGT 4 22 1 AATTTTACAA 0.979418 -117 ATTACTAGATAATTGTTCTCGCAATGTTGAGAA 4 58 1 AATTTTTCCA 0.826614 -81 TTTATCGATTATTTGTTTACAAAATAATACATC 5 52 0 ATTTTTACAA 0.929716 -24 GAAAAAGTTAAATTTTTGACGAAGTAAAAATCA 6 30 1 AATTTTACAA 0.979418 -109 CAATTCCCATAATTATTAACTCTTACATCTTTT 7 72 0 AATTTTACCT 0.904016 -229 TTGGGATTAAAATTTGTTACGAAATATGCTCAT 7 107 1 AATTGTACAA 0.908459 -194 GAGTACACTAAATTCTTGACAAAAAGCTGAATA 8 128 0 AATTTTACAA 0.979418 -173 AAACTACAGGAATTTTAAACTCTAAAATGAAAG 11 178 1 AATTTAACCT 0.723612 -123 **** ** ** ** Masking position 4 Map Score: 7.64814 Number of sites scoring better than the average of aligned sites = 44 Number in coding regions = 25 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 6 GTAGTTCTTTTATTTAGAGATTACTTAGTATT 1 24 0 TATTTAGATT 0.950186 -277 TTAAGGGGTGATTTTAGTAATTTAAATCATTA 3 40 1 ATTTTAGATT 0.650247 -261 CTCAAATTATTATTTAGATAATGATTTAAATT 3 58 0 TATTTAGAAT 0.957747 -243 TCACTAGCACTTTTTAGTAAATCGGCTGAATT 3 109 0 TTTTTAGAAT 0.950186 -192 GGAAAATTCTTATTTACAGAATTTTTTACTAA 4 13 1 TATTTACAAT 0.920615 -126 TTTACAGAATTTTTTACTAAGTTGCTTCGTCG 4 25 1 TTTTTACAGT 0.750184 -114 GTAAAATGATTATTTAGAAAATAAAAATAAAT 4 116 1 TATTTAGAAT 0.95763 -23 TTATTTACTCATTATATTTAAAC 5 2 1 TATTTACATT 0.907058 -74 ATCGATTATTTGTTTACAAAATAATACATCAT 5 50 0 TGTTTACAAT 0.781103 -26 TCCTCATATGTTTTTAGTATTTATCTGTATAT 9 55 0 TTTTTAGTTT 0.650272 -25 AATATTGCAGTATTTAGCAAAATGTATTACAT 11 129 1 TATTTAGAAA 0.724167 -172 ATTAGTAATGTTTTTAGTGATTTAGATGTTGA 11 227 1 TTTTTAGATT 0.941359 -74 ******* *** Masking position 6 Map Score: 7.23333 Number of sites scoring better than the average of aligned sites = 251 Number in coding regions = 174 Number in noncoding regions = 77 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 7 ACTGAACACGTTTTTGCCATATAAAACTTA 1 213 1 TTTTTGCCAT 0.661393 -88 AACTTACAATTTTATTGCATAATAAAAGCA 1 237 1 TTTATTGCAT 0.779852 -64 TCTGAGATCTTTTATGTCATTGTTGACACT 3 206 1 TTTATGTCAT 0.946212 -95 ATAGCTCACTTTTATATCCTGTCTGCTATT 3 243 0 TTTATATCCT 0.796121 -58 AATTTATTTTTATTTTCTAAATAATCAT 4 121 0 TTTATTTTCT 0.631936 -18 CTCACTTAATTTTATTTCCTGCATTAACTA 7 153 0 TTTATTTCCT 0.956121 -148 TATCATTACCTGTTTTTCCTTGTATACTGA 7 192 0 TGTTTTTCCT 0.688039 -109 TTAACTTTTTTTTTTGTCCTTAGG 8 5 0 TTTTTGTCCT 0.923166 -296 TATATTCAGCTTTTTGTCAAGAATTTAGTG 8 126 1 TTTTTGTCAA 0.545736 -175 TATGCTATTCTTTATTTAATTAGGATATAC 8 276 1 TTTATTTAAT 0.597111 -25 GGTTTACTTTATTTCATATGTTTATTA 10 86 0 TTTATTTCAT 0.949521 -17 GAAAATCCATTTTCTTTCATTTTAGAGTTT 11 194 0 TTTCTTTCAT 0.833228 -107 ********** Masking position 5 Map Score: 3.22749 Number of sites scoring better than the average of aligned sites = 325 Number in coding regions = 222 Number in noncoding regions = 103 Number of orfs with sites within 600 bp upstream = 66 Fraction of orfs with sites within 600 bp upstream = 0.0106007 Motif number 8 TAATATTGATTTATTTGAGATTCATCTTTGAA 1 72 0 TTATTAGATT 0.911201 -229 ATCAATATTATTAATTTAAATTTCTCACATTA 1 94 1 TTAATAAATT 0.689599 -207 ACTAGCGATATTATATAAGTTATGCTTTTATT 1 257 0 TTATTAGTTA 0.764297 -44 TCGCTAGTGATTAAGTCAGTTAAAGTTTAT 1 281 1 TTAATAGTTA 0.87747 -20 ATTTCCTGCATTAACTAATATTTCGTTTAAAT 7 138 0 TTAATATATT 0.689599 -163 GGAAATAAAATTAAGTGAGGTTAATTTATCAG 7 164 1 TTAATAGGTT 0.857532 -137 CATTTTACGATTATATTAGATAATAAAGCAAT 7 236 1 TTATTAGATA 0.911201 -65 TATTCTTTATTTAATTAGGATATACTCGAG 8 281 1 TTAATGGATA 0.825359 -20 ATTTATTACTTTAAATGAGATAAG 11 3 0 TTAATAGATA 0.957738 -298 ATTAATTCAGATTAACATTTCCA 11 288 0 TTAATAGATT 0.957738 -13 **** * ***** Masking position 6 Map Score: 3.90368 Number of sites scoring better than the average of aligned sites = 190 Number in coding regions = 127 Number in noncoding regions = 63 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 9 GTTTACAAAATAATACATCATGCTATCATTT 5 40 0 TAATACACAT 0.772779 -36 TTTTTTGAATTACTACATTCCTTGTAGTTGT 6 75 1 TACTACATCC 0.911564 -64 TATATACTGTTATTACATTCTGAAGGTGCTG 8 83 1 TATTACATCT 0.765383 -218 GTGCTGAACTTAATACAATATATTCAGCTTT 8 108 1 TAATACATAT 0.935718 -193 GTATATGTGTTACTACAGTACAAAGAAAAAT 9 30 0 TACTACATAC 0.947924 -50 TAAGTGCTACAGTATAGGCTCTTTG 10 5 1 TGCTACATAT 0.896915 -98 TTAAATCTATTACTACAATATTAATTTATTA 11 27 0 TACTACATAT 0.973849 -274 TTTTGCTAAATACTGCAATATTGATTATATC 11 120 0 TACTGCATAT 0.896915 -181 GCTCTATATGTAATACATTTTGCTAAATACT 11 137 0 TAATACATTT 0.751368 -164 ******* *** Masking position 7 Map Score: 3.16293 Number of sites scoring better than the average of aligned sites = 118 Number in coding regions = 76 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 10 TTAAATATAATGAGTAAATAA 5 2 0 TGAGTAAATA 0.736035 -74 TTCGTTTAAATGAGCATATTTCGTAACAAA 7 119 0 TGAGCATATT 0.947167 -182 CTAAAACTTTAGAGCATATATACTGTTATT 8 67 1 AGAGCATATA 0.970972 -234 TATGAAGAACAGAGCATATACATAATATTT 8 211 0 AGAGCATATA 0.970972 -90 AACAAAACAAAGAGCCTATACTGTAGCACT 10 13 0 AGAGCCTATA 0.924417 -90 ATATTAAAGTTGAGTATATTAAATGAATAG 10 51 0 TGAGTATATT 0.858311 -52 ********** Masking position 3 Map Score: 2.06802 Number of sites scoring better than the average of aligned sites = 39 Number in coding regions = 28 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 11 TTTAAATTTCTCACATTACATGTTCTACTTCAA 1 108 1 TCCATACTGT 0.984452 -193 AGTTGCTTCGTCGCATTACTAGATAATTGTTCT 4 44 1 TCCATACAGA 0.960943 -95 TTGTAGTTGTTCTCAATAACTGTGTGAGTGCAC 6 96 1 TCCATAATGT 0.961168 -43 TAGATATATGTCCCAGTTAGTGAAATTCTTGAA 7 41 1 TCCATTATGA 0.849583 -260 CAAATTTTAATCCCAATACAATTCCCATAATTA 7 90 0 TCCATACATT 0.815083 -211 TGTTCTTCCGTATCATTACCTGTTTTTCCTTGT 7 199 0 TACATACTGT 0.876102 -102 TATTTGAGCGTCACAGTACTTGAGTACAAATAA 8 183 0 TCCATACTGA 0.975289 -118 CTTATCTCATTTAAAGTAATAAATTAA 11 5 1 TCCATTAAGT 0.849587 -296 ** ** *** *** Masking position 5 Map Score: 2.83793 Number of sites scoring better than the average of aligned sites = 25 Number in coding regions = 17 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 12 ********** No masking Map Score: 6.99417e-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: 6.99417e-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: 6.99417e-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