AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00640_rpxx_reg_300.orf -o00640_rpxx_300.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 RP109 300 PROBABLE PHOSPHATE ACETYLTRANSFERASE (ptb) #2 RP432 162 SUCCINYL-COA LIGASE (sucD) #3 RP433 154 SUCCINYL-COA SYNTHETASE BETA CHAIN (sucC) #4 RP434 275 unknown #5 RP436 169 unknown #6 RP618 92 PROPIONYL-COA CARBOXYLASE ALPHA CHAIN PRECURSOR (pccA) #7 RP619 300 PROPIONYL-COA CARBOXYLASE BETA CHAIN PRECURSOR (pccB) #8 RP738 300 POLY-BETA-HYDROXYBUTYRATE POLYMERASE (phbC1) Motif number 1 TTAACTTTAATATTAATAATGAATGATTTAGG 1 67 1 TATAATAATA 0.944683 -234 GTTATATAGCTTAGAAAAATCAATTTAGTATA 2 34 1 TTAAAAAATA 0.938856 -129 AGTAACATATAAAGTAAAATAAACAATAAAAA 2 131 1 AAATAAAATA 0.664066 -32 TAAAATAAACAATAAAAAATTATTTCAC 2 145 1 AATAAAAATA 0.954398 -18 GCTTTTATTATTTAAAAAATTATTTGAA 3 137 1 TTTAAAAATA 0.961906 -18 AAAATCAATCATTAAAAAATGATAATATCCGT 4 22 1 ATTAAAAATA 0.914262 -254 ATATCCGTTATATTAAAAATTTAAATTTTAGT 4 46 1 TATAAAAATT 0.735812 -230 GACTAATTAGTATAAATAATTAAAGGCTATAA 4 85 1 TATAATAATA 0.944685 -191 TATAATGCTGAATTAAAGATAATTTACAAAAT 4 119 1 AATAAAGATA 0.770219 -157 TTATTAAAGTTATATAAAATTACTATATCTTA 4 163 0 TATTAAAATA 0.885027 -113 TATATAACTTTAATAAAAATAAATTCTTATTT 4 179 1 TAAAAAAATA 0.967743 -97 TTAAAGTATTTAATAAAAATAAGAATTTATTT 4 195 0 TAAAAAAATA 0.967743 -81 ATATCTTAATATAAAAAAATAATCTTTTAAAG 4 221 0 ATAAAAAATA 0.866389 -55 TATATTAAGATATAAATGATAATCGTTTAATA 4 240 1 TATAATGATA 0.732291 -36 AAATAAAAAATATTAAAAATCAAAAATAATCA 5 17 0 TATAAAAATA 0.980221 -153 AAAAATACTAAATTAAAAATTAAATTTATTAT 5 60 1 AATAAAAATA 0.954398 -110 AAATATAAAGTAATAAAAATTACAATGTGCTT 5 100 0 TAAAAAAATA 0.967608 -70 TAATTTTTTCTTTGAATAATTATTTCTCTCAA 5 140 0 TTTAATAATA 0.896924 -30 TAAATATGCGTTTATAAAATAAGTAAATTCAT 7 11 0 TTTTAAAATA 0.796834 -290 TATTTATTGCTTATAAAAATTATTTTCTATTT 7 37 1 TTAAAAAATA 0.938588 -264 CTAGGTCTTATATCAAAAATGAGAAAATAGAA 7 61 0 TATAAAAATA 0.980221 -240 TACAGAAAGAAAAAAATAATAAAAAATATTGA 7 95 0 AAAAATAATA 0.814325 -206 TAATATAATATAATAATAATAAAGTAAAAAGA 7 244 0 TAAAATAATA 0.901998 -57 TTATTGGTATTTTGAAAAATAAAACTATTAAT 7 273 1 TTTAAAAATA 0.961906 -28 *** ****** * Masking position 10 Map Score: 41.1687 Number of sites scoring better than the average of aligned sites = 761 Number in coding regions = 472 Number in noncoding regions = 289 Number of orfs with sites within 600 bp upstream = 155 Fraction of orfs with sites within 600 bp upstream = 0.0248956 Motif number 2 GTTCATAAACATTTTATTATCCACTAT 1 8 0 ATTTTATTAT 0.796338 -293 AAATCATTCATTATTAATATTAAAGTTAAA 1 66 0 TTATTAATAT 0.806057 -235 TCTTAGTCCTTATTTACTTTTAGATACCGT 2 82 0 TATTTACTTT 0.78457 -81 TTTATTGTTTATTTTACTTTATATGTTACT 2 131 0 ATTTTACTTT 0.68389 -32 GTGAAATAATTTTTTATTGTTTATTTTACT 2 143 0 TTTTTATTGT 0.749887 -20 GCTTATAAATTAATTATTATACTGAGCTTT 3 112 1 TAATTATTAT 0.724397 -43 TTATACTGAGCTTTTATTATTTAAAAAATT 3 128 1 CTTTTATTAT 0.696484 -27 AAAATTTAAATTTTTAATATAACGGATATT 4 45 0 TTTTTAATAT 0.91562 -231 AAATAAGAATTTATTTTTATTAAAGTTATA 4 181 0 TTATTTTTAT 0.828389 -95 AAATAAATTCTTATTTTTATTAAATACTTT 4 195 1 TTATTTTTAT 0.828389 -81 AAAAGATTATTTTTTTATATTAAGATATAA 4 225 1 TTTTTTATAT 0.839112 -51 TTTCTATTTTTTTTTATTAAACGATTA 4 259 0 TTTTTTTTAT 0.923612 -17 TTATTTTTGATTTTTAATATTTTTTATTTC 5 20 1 TTTTTAATAT 0.91562 -150 TAATTTAGTATTTTTACTATATAATGAAAT 5 45 0 TTTTTACTAT 0.964713 -125 ATAAATTTAATTTTTAATTTAGTATTTTTA 5 59 0 TTTTTAATTT 0.846963 -111 TTAAAAATTAAATTTATTATAAAGATGGAA 5 72 1 AATTTATTAT 0.505609 -98 ATTGTAATTTTTATTACTTTATATTTCAAT 5 106 1 TTATTACTTT 0.847567 -64 AATGTAATAATTTTTTCTTTGAATAATTAT 5 149 0 TTTTTTCTTT 0.869914 -21 TTATAAAAATTATTTTCTATTTTCTCATTT 7 47 1 TATTTTCTAT 0.774342 -254 GTATCAATATTTTTTATTATTTTTTTCTTT 7 92 1 TTTTTATTAT 0.96181 -209 TTTTTATTATTTTTTTCTTTCTGTACTTTC 7 102 1 TTTTTTCTTT 0.869914 -199 AGTAAAAAGATAATTATTATGTCATCTACA 7 224 0 TAATTATTAT 0.724397 -77 AATAATTATCTTTTTACTTTATTATTATTA 7 236 1 TTTTTACTTT 0.933019 -65 TTTTACTTTATTATTATTATATTATATTAT 7 247 1 TTATTATTAT 0.909453 -54 AGTGCTTAACTTTTTTTTTTGTCCTTAGG 8 10 0 TTTTTTTTTT 0.860343 -291 ********** Masking position 5 Map Score: 30.8722 Number of sites scoring better than the average of aligned sites = 1322 Number in coding regions = 855 Number in noncoding regions = 467 Number of orfs with sites within 600 bp upstream = 233 Fraction of orfs with sites within 600 bp upstream = 0.0374237 Motif number 3 AATTTTTCCTTGATTAACTAACTTATATAT 1 246 1 TGATTAACTA 0.904877 -55 CTAATTGAGTTGATTAATTGATTCAGGTAT 1 279 1 TGATTAATTG 0.852468 -22 TACAGGGTTATACTAAATTGATTTTTCTAA 2 44 0 TACTAAATTG 0.480779 -119 TAGATACCGTTGCTAAACTACAGGGTTATA 2 62 0 TGCTAAACTA 0.908924 -101 TATATGTTACTGATTAACTTCATGATAAAA 2 112 0 TGATTAACTT 0.88309 -51 TCTTTACAGCTTATAAATTAATTATTATAC 3 104 1 TTATAAATTA 0.618373 -51 CATTTTTTAATGATTGATTTTATAGTACAT 4 13 0 TGATTGATTT 0.571156 -263 TAGTACAAAATGACTAATTAGTATAAATAA 4 74 1 TGACTAATTA 0.642448 -202 TAATTCAGCATTATAAATTATAGCCTTTAA 4 104 0 TTATAAATTA 0.618373 -172 TAATTTATAATGCTGAATTAAAGATAATTT 4 114 1 TGCTGAATTA 0.87087 -162 TGTCGTTGATTATTTTTGATTTTTAA 5 7 1 TGATTATTTT 0.473288 -163 ATAGTAAAAATACTAAATTAAAAATTAAAT 5 55 1 TACTAAATTA 0.706293 -115 TCCATCTTTATAATAAATTTAATTTTTAAT 5 71 0 TAATAAATTT 0.645739 -99 ATTTTTTCTTTGAATAATTATTTCTCTCAA 5 140 0 TGAATAATTA 0.546852 -30 TTAAGAGAGTTGATAAATTAGCAAATTTAG 7 154 1 TGATAAATTA 0.937318 -147 TCAAATCACTTGCTAAATTTGCTAATTTAT 7 166 0 TGCTAAATTT 0.924906 -135 AATCTTGAAGTGCTTAACTTTTTTTTTTGT 8 18 0 TGCTTAACTT 0.886826 -283 ATTCTGAAGGTGCTGAACTTAATACAATAT 8 99 1 TGCTGAACTT 0.771133 -202 ********** Masking position 9 Map Score: 8.11485 Number of sites scoring better than the average of aligned sites = 536 Number in coding regions = 371 Number in noncoding regions = 165 Number of orfs with sites within 600 bp upstream = 88 Fraction of orfs with sites within 600 bp upstream = 0.0141343 Motif number 4 AACTGAAAGAAGTTTTTAAAGAATTTAACTTTA 1 43 1 AGTTAAAGAA 0.641128 -258 CTAATAAGGGATAAGACACAGAATTATAGAAGA 1 132 0 ATACACAGAA 0.812559 -169 CTGAGCTTTTATTATTTAAAAAATTATTTGAA 3 133 1 ATATAAAAAA 0.913675 -22 TGAATTAAAGATAATTTACAAAATTATAATATC 4 127 1 ATATACAAAA 0.904321 -149 AATCTTTTAAAGTATTTAATAAAAATAAGAATT 4 200 0 AGATAATAAA 0.789213 -76 TTACTATATAATGAAATAAAAAATATTAAAAAT 5 29 0 ATATAAAAAA 0.913678 -141 AAATTGAAATATAAAGTAATAAAAATTACAATG 5 105 0 ATATAATAAA 0.599856 -65 GAGAGAAATAATTATTCAAAGAAAAAATTATTA 5 142 1 ATACAAAGAA 0.829194 -28 GCGTGGTATTAGGATACAAAAAATT 6 78 1 AGACAAAAAA 0.931404 -15 ATCAAAAATGAGAAAATAGAAAATAATTTTTAT 7 49 0 AGATAGAAAA 0.819437 -252 TACAGAAGAAAGAAAGTACAGAAAGAAAAAAAT 7 110 0 AGATACAGAA 0.95471 -191 ATACAAAAGAAGTACTCAAAAAAGTCAAATCAC 7 187 0 AGACAAAAAA 0.931404 -114 TGTCATCTACAGAAGATACAAAAGAAGTACTCA 7 202 0 AGATACAAAA 0.95936 -99 CCTAAGGACAAAAAAAAAAGTTAAGCA 8 5 1 AGAAAAAAAA 0.722367 -296 TATTAAGTTCAGCACCTTCAGAATGTAATAACA 8 90 0 AGATTCAGAA 0.749094 -211 GTACTCAGATAGGATTTTAAAAAGTTGTTTATT 8 155 1 AGATTAAAAA 0.789214 -146 TGAAGAACAGAGCATATACATAATATTTGAGCG 8 206 0 AGATACATAA 0.732209 -95 GTATATCCTAATTAAATAAAGAATAGCATAATG 8 273 0 ATATAAAGAA 0.904322 -28 ** * ******* Masking position 12 Map Score: 18.7083 Number of sites scoring better than the average of aligned sites = 652 Number in coding regions = 480 Number in noncoding regions = 172 Number of orfs with sites within 600 bp upstream = 83 Fraction of orfs with sites within 600 bp upstream = 0.0133312 Motif number 5 TTGTATGCTAATAAGGGATAAGACACAGAAT 1 141 0 ATAAGGATAA 0.863981 -160 ACTCAATTAGATAATATATAAGTTAGTTAAT 1 258 0 ATAATAATAA 0.72445 -43 CTAAAAGTAAATAAGGACTAAGATTTTATCA 2 89 1 ATAAGGCTAA 0.933474 -74 AAGAGAGTTTAAAATAACTAGTTATTCCACC 3 74 0 AAAATACTAG 0.687172 -81 TAATTAATTTATAAGCTGTAAAGAAGAGAGT 3 97 0 ATAAGCGTAA 0.810403 -58 ATTTTAGTACAAAATGACTAATTAGTATAAA 4 70 1 AAAATGCTAA 0.674785 -206 ATAATATCCAATAAGATATAGTAATTTTATA 4 152 1 ATAAGAATAG 0.870546 -124 TTTTTTTATATTAAGATATAAATGATAATCG 4 234 1 TTAAGAATAA 0.499542 -42 GATCGTCTGTAAAAGATCTAGTGGTTAGATA 6 45 1 AAAAGACTAG 0.894443 -48 ATGCGTTTATAAAATAAGTAAATTCAT 7 7 0 AAAATAGTAA 0.502252 -294 AATAATTTTTATAAGCAATAAATATGCGTTT 7 30 0 ATAAGCATAA 0.863959 -271 CATTTTTGATATAAGACCTAGTATCAATATT 7 72 1 ATAAGACTAG 0.936935 -229 ATAACAGTATATATGCTCTAAAGTTTTAGGG 8 65 0 ATATGCCTAA 0.580034 -236 ATAAACGTTAAAAAGAGCTAAGAGCTTAATA 8 239 0 AAAAGACTAA 0.927427 -62 ****** **** Masking position 3 Map Score: 7.03118 Number of sites scoring better than the average of aligned sites = 336 Number in coding regions = 235 Number in noncoding regions = 101 Number of orfs with sites within 600 bp upstream = 58 Fraction of orfs with sites within 600 bp upstream = 0.00931577 Motif number 6 TATATTATCTAATTGAGTTGATTAATTGATT 1 271 1 AATTGATTGA 0.924537 -30 GATCTAGTTTAATAGATTTGAAATACTGTAG 3 26 0 AATAGATTGA 0.947192 -129 AGCTGTAAAGAAGAGAGTTTAAAATAACTAG 3 84 0 AAGAGATTTA 0.951415 -71 ATTATTTAAAAAATTATTTGAA 3 143 1 AAATTATTGA 0.661662 -12 TGCTGAATTAAAGATAATTTACAAAATTATA 4 124 1 AAGATATTTA 0.817484 -152 CTAAATTAAAAATTAAATTTATTATAAAGAT 5 67 1 AATTAATTTA 0.544597 -103 TATTTCTCTCAAGAAAATTGAAATATAAAGT 5 121 0 AAGAAATTGA 0.913009 -49 ACTCTCTTAAAAAAGAATTTATACAGAAGAA 7 133 0 AAAAGATTTA 0.842293 -168 ATTCTTTTTTAAGAGAGTTGATAAATTAGCA 7 146 1 AAGAGATTGA 0.978672 -155 CAAATTTAGCAAGTGATTTGACTTTTTTGAG 7 175 1 AAGTGATTGA 0.969081 -126 ****** **** Masking position 6 Map Score: 7.26195 Number of sites scoring better than the average of aligned sites = 112 Number in coding regions = 80 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 7 GACACAGAATTATAGAAGATCACTTTACTT 1 121 0 TATAGAAGAT 0.918905 -180 TTATAAGCTGTAAAGAAGAGAGTTTAAAAT 3 90 0 TAAAGAAGAG 0.959573 -65 CTAGATCTTTTACAGACGATCTTCTTATGT 6 36 0 TACAGACGAT 0.932672 -57 AAAGAATTTATACAGAAGAAAGAAAGTACA 7 123 0 TACAGAAGAA 0.931896 -178 TTATGTCATCTACAGAAGATACAAAAGAAG 7 208 0 TACAGAAGAT 0.97827 -93 AAGAATAGCATAATGAAGATAAACGTTAAA 8 258 0 TAATGAAGAT 0.85599 -43 CCTAATTAAATAAAGAATAGCATAATGAAG 8 270 0 TAAAGAATAG 0.75483 -31 ********** Masking position 6 Map Score: 3.51835 Number of sites scoring better than the average of aligned sites = 80 Number in coding regions = 65 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 8 TTTTCTTTAGTTTGACTACAGTATTTCAAA 3 11 1 TTTGACTACA 0.943003 -144 ATGATTGATTTTATAGTACATAT 4 4 0 TTATAGTACA 0.857454 -272 AAAATTTAAATTTTAGTACAAAATGACTAA 4 61 1 TTTTAGTACA 0.960602 -215 ATTTGACTTTTTTGAGTACTTCTTTTGTAT 7 190 1 TTTGAGTACT 0.946814 -111 TAAAATCCTATCTGAGTACACTAAATTCTT 8 144 0 TCTGAGTACA 0.963482 -157 CGTCACAGTACTTGAGTACAAATAAACAAC 8 178 0 CTTGAGTACA 0.963483 -123 ********** Masking position 5 Map Score: 2.42221 Number of sites scoring better than the average of aligned sites = 37 Number in coding regions = 25 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 9 ATAATAAAATGTTTATGAACACTTAAACTG 1 18 1 GTTTATGAAC 0.764418 -283 ACAAATTGTTATTAAAGAACTGCTTCAATT 1 220 1 ATTAAAGAAC 0.753813 -81 ATATAAGTTAGTTAATCAAGGAAAAATTGA 1 244 0 GTTAATCAAG 0.77684 -57 ACCTGAATCAATTAATCAACTCAATTAGAT 1 277 0 ATTAATCAAC 0.947986 -24 TTTCTAAGCTATATAACAACATTCGCTTGC 2 21 0 ATATAACAAC 0.617052 -142 TAACCCTGTAGTTTAGCAACGGTATCTAAA 2 64 1 GTTTAGCAAC 0.897499 -99 AAAAATCAAAAATAATCAACGACA 5 5 0 AATAATCAAC 0.836234 -165 AAATTTGCTAATTTATCAACTCTCTTAAAA 7 152 0 ATTTATCAAC 0.947986 -149 AAATTAGCAAATTTAGCAAGTGATTTGACT 7 168 1 ATTTAGCAAG 0.767741 -133 CTTGAGTACAAATAAACAACTTTTTAAAAT 8 168 0 AATAAACAAC 0.760951 -133 ********** Masking position 5 Map Score: 2.83175 Number of sites scoring better than the average of aligned sites = 150 Number in coding regions = 113 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 10 AAACTGAAAGAAGTTTTTAAAGAATTTAAC 1 42 1 AAGTTTTTAA 0.847393 -259 AATAAGGACTAAGATTTTATCATGAAGTTA 2 98 1 AAGATTTTAT 0.904962 -65 CTGTAAAGAAGAGAGTTTAAAATAACTAGT 3 83 0 GAGAGTTTAA 0.76021 -72 TAATAAAAATAAGAATTTATTTTTATTAAA 4 187 0 AAGAATTTAT 0.904959 -89 TAATCTTTTAAAGTATTTAATAAAAATAAG 4 204 0 AAGTATTTAA 0.847393 -72 TCTCTTAAAAAAGAATTTATACAGAAGAAA 7 132 0 AAGAATTTAT 0.904959 -169 TAAAATCTTGAAGTGCTTAACTTTTTTTTT 8 21 0 AAGTGCTTAA 0.720168 -280 TAAGCACTTCAAGATTTTATGAAAAGATAT 8 32 1 AAGATTTTAT 0.904962 -269 GCTTTTTGTCAAGAATTTAGTGTACTCAGA 8 134 1 AAGAATTTAG 0.810947 -167 GTACTCAGATAGGATTTTAAAAAGTTGTTT 8 155 1 AGGATTTTAA 0.724162 -146 AAAAAGAGCTAAGAGCTTAATATGAAGAAC 8 231 0 AAGAGCTTAA 0.865972 -70 ********** Masking position 9 Map Score: 7.54478 Number of sites scoring better than the average of aligned sites = 215 Number in coding regions = 146 Number in noncoding regions = 69 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 11 ********** No masking Map Score: 5.89994e-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 12 ********** No masking Map Score: 5.89994e-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: 5.89994e-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