AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_rpxx.txt -z/home/amcguire/genomes/rpxx.fna -ipdhR_rpxx_opreg_300.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 RP459 300 unknown #2 RP460 146 DIHYDROLIPOAMIDE DEHYDROGENASE PRECURSOR (pdhD) #3 RP530 125 DIHYDROLIPOAMIDE ACETYLTRANSFERASE COMPONENT (pdhC) #4 RP531 49 TRANSLATION INITIATION FACTOR IF-3 (infC) #5 RP532 300 unknown #6 RP805 249 DIHYDROLIPOAMIDE DEHYDROGENASE (pdhD) #7 RP806 300 unknown Motif number 1 AGAAACTGCATTTTATTTTTATTCAAAAAG 1 14 0 TTTTATTTTT 0.861941 -287 TTATTTTAGTTATAATATATCTCTTTTTTT 1 142 0 TATAATATAT 0.775905 -159 TAATTAAATCTTTTATTTTAGTTATAATAT 1 154 0 TTTTATTTTA 0.861587 -147 CTCTCACTTGTTTTAATTAAATCTTTTATT 1 167 0 TTTTAATTAA 0.905261 -134 AATTTTAGCCTATTAAATATATAACTCTCT 1 193 0 TATTAAATAT 0.841255 -108 AATAATCTTTTTTAAAATATCGTAGTCACA 2 45 0 TTTAAAATAT 0.750635 -102 TAGTTATAATATAATCACGTGTGT 3 5 1 TATAATATAA 0.775331 -121 AGATTTATGTTATTATTTTTTTTGCATAAG 3 97 0 TATTATTTTT 0.877773 -29 TTTAAAGATATTATTTACTTGTAATTTT 4 9 1 TATTATTTAC 0.746882 -41 ATTTAACTTATTTTATTTAAAATTACAAGT 4 27 0 TTTTATTTAA 0.904938 -23 TATAGCATTATTTAATTTATTGCAATAGAC 5 65 0 TTTAATTTAT 0.861938 -236 TAAATAATGCTATAAATTTTAGTAACAAAT 5 81 1 TATAAATTTT 0.824325 -220 AACAAGACTTTATAAATTTAGTATAATCAA 5 122 1 TATAAATTTA 0.82432 -179 TTTCAACTATTTTAAAATAATCAATTAATT 5 242 0 TTTAAAATAA 0.750626 -59 TCGAAATGTATATAATATATTACTTTCAAC 5 265 0 TATAATATAT 0.775905 -36 ATTCCTTTTTAATTTTTCGAAATGTA 5 285 0 TTTTAATTTT 0.861945 -16 TGTATCGTTGTTTTATATTTTTTAGTTTTT 6 22 1 TTTTATATTT 0.75063 -228 GAGCTAAATGTTTTATATTTCTTAACTGCA 6 68 0 TTTTATATTT 0.75063 -182 TATTTTAAGGTATAAATTATTCCAAAAAAG 6 208 0 TATAAATTAT 0.877775 -42 TTTATTTTTATTTTATTGGTTCTAT 6 235 0 TTTTATTTTA 0.861587 -15 ATTTCCGTCATATTATTTTATATATGGTAA 7 35 1 TATTATTTTA 0.877537 -266 ATTTGAAGCATATTAATTTAGCTATAATTA 7 115 1 TATTAATTTA 0.877773 -186 ATAATTATATTATTAATTAATAGTTAATTT 7 138 1 TATTAATTAA 0.916606 -163 CAAAATGATATATAAATTAACTATTAATTA 7 151 0 TATAAATTAA 0.877771 -150 AATTAAAAATTTTTAAATACAAAGGAATAG 7 181 0 TTTTAAATAC 0.552935 -120 ATTTAAAAATTTTTAATTAAATAATTAATA 7 193 1 TTTTAATTAA 0.905261 -108 TTCTATTATATATTAATTATTTAATTAAAA 7 203 0 TATTAATTAT 0.916608 -98 TAGAAAATTATATAATTTAATATCGCTTGA 7 228 1 TATAATTTAA 0.877346 -73 ********** Masking position 5 Map Score: 35.6027 Number of sites scoring better than the average of aligned sites = 1980 Number in coding regions = 1161 Number in noncoding regions = 819 Number of orfs with sites within 600 bp upstream = 308 Fraction of orfs with sites within 600 bp upstream = 0.04947 Motif number 2 AGTTATAATATATCTCTTTTTTTGATAATCTGATACT 1 128 0 TTTCTTTTTA 0.923046 -173 TTACGGTGATCTTGTAATTTTAGCCTATTAAATATAT 1 201 0 CTTATTTTTA 0.719613 -100 TGTTTATAATATTGTAGTATTGTAATGCC 2 3 1 TTTATATTTA 0.94197 -144 GTGTTGACACTGTGTTCTAGTATTATAAGGTTTATAT 3 31 1 TTTTTAGTTA 0.799569 -95 GATTTATGTTATTATTTTTTTTGCATAAGCCTTCACG 3 89 0 ATTTTTTTTA 0.440735 -37 GCATTTAACTTATTTTATTTAAAATTACAAGTAAATA 4 22 0 TTTTTTTATA 0.421247 -28 ATATCATATCTTATTCTTCTAACAATGATTA 5 5 1 CTTCTATTTA 0.621511 -296 TATAGCATTATTTAATTTATTGCAATAGACATCCTGT 5 58 0 TTATTATTTA 0.553861 -243 ACAACAAGACTTTATAAATTTAGTATAATCAATGAAA 5 120 1 TTTAATTTTA 0.652714 -181 TTTAGCTCTATATATACTAGTTTTATAAAACTACGTT 5 155 0 TTTATAGTTA 0.826417 -146 TGTCTTTTTTTTTTTTGCTGTTGTTTAAAACTTTTCA 5 206 0 TTTTCTGTTA 0.57911 -95 ATGTATATAATATATTACTTTCAACTATTTTAAAATA 5 253 0 TTTTCTTTTA 0.824168 -48 ATTCCTTTTTAATTTTTCGAAATGTATATAAT 5 279 0 TTTATTTTAA 0.703893 -22 TTGAAAAATTTGTATCGTTGTTTTATATTTTTTAGTT 6 12 1 TTTCTTGTTA 0.77889 -238 TGTTTTATATTTTTTAGTTTTTAAGTACTAGTATGTA 6 30 1 TTTATTTTTA 0.945827 -220 AAGAGCTAAATGTTTTATATTTCTTAACTGCAATACA 6 63 0 TTTTTATTAA 0.649376 -187 TACTAAATTCTATATATTTTTTCAGTAAAGGTTAAAA 6 112 1 TTTATTTTTA 0.94583 -138 ATGCTGAGGTTATCTCATTTTACCATAGATTTCACCT 6 173 1 TTTCTTTTTA 0.922922 -77 ACTTCTATTCTTTTTTAGTACTTAATTTCC 7 4 1 TTTTTTTTTA 0.935997 -297 GTACTTAATTTCCGTCATATTATTTTATATATGGTAA 7 28 1 TCTCTATTTA 0.611983 -273 AACATTTGATTGTCTTGAATTACCATATATAAAATAA 7 47 0 TTTTAATTTA 0.595874 -254 GACAATCAAATGTTTTGTATTAGATAATTTTCTTAGT 7 70 1 TTTTTATTAA 0.649376 -231 TTAGATAATTTTCTTAGTATTATCCTATTTGAAGCAT 7 89 1 TCTATATTTA 0.69631 -212 ATAGTTAATTTATATATCATTTTGCTATTCCTTTGTA 7 157 1 TTTACATTTA 0.838947 -144 TTCTATTATATATTAATTATTTAATTAAAAATTTTTA 7 196 0 TTAATATTTA 0.597136 -105 GATATTAAATTATATAATTTTCTATTATATATTAATT 7 215 0 TTTATTTTTA 0.945832 -86 ACTTTTTGAGTTTATAACATTTCTTTAGATACTTCAA 7 254 0 TTTACATTTA 0.838964 -47 * * ** **** ** Masking position 17 Map Score: 28.6303 Number of sites scoring better than the average of aligned sites = 790 Number in coding regions = 498 Number in noncoding regions = 292 Number of orfs with sites within 600 bp upstream = 154 Fraction of orfs with sites within 600 bp upstream = 0.024735 Motif number 3 ATTATCAAAAAAAGAGATATATTATAACTA 1 136 1 AAAGAGATAT 0.775361 -165 AACTAAAATAAAAGATTTAATTAAAACAAG 1 161 1 AAAGATTTAA 0.667173 -140 ATGCTTTATAAATAAGCTATTACTTATTCC 1 251 0 AATAAGCTAT 0.584342 -50 GCATGCAGCTAATGATATAATAAGTCGGTT 1 277 1 AATGATATAA 0.940785 -24 ACAATACTACAATATTATAAACA 2 4 0 AATATTATAA 0.83026 -143 CAAAAAAAATAATAACATAAATCTCAATAA 3 103 1 AATAACATAA 0.803675 -23 TTTTAAATAAAATAAGTTAAATGCA 4 35 1 AATAAGTTAA 0.780293 -15 TTGTTAGAAGAATAAGATATGATAT 5 6 0 AATAAGATAT 0.865175 -295 TAAATTAAATAATGCTATAAATTTTAGTAA 5 76 1 AATGCTATAA 0.668306 -225 AGAGCTAAAGAATATCATAAATATGAAAAG 5 183 1 AATATCATAA 0.586742 -118 ATAAATATGAAAAGTTTTAAACAACAGCAA 5 199 1 AAAGTTTTAA 0.410117 -102 TTAAAAACTAAAAAATATAAAACAACGATA 6 24 0 AAAAATATAA 0.870696 -226 ATGATCTTTAAAAGAGCTAAATGTTTTATA 6 81 0 AAAGAGCTAA 0.61296 -169 CCTTTACTGAAAAAATATATAGAATTTAGT 6 113 0 AAAAATATAT 0.762756 -137 TCTATGGTAAAATGAGATAACCTCAGCATT 6 172 0 AATGAGATAA 0.938044 -78 CCTTTTTTGGAATAATTTATACCTTAAAAT 6 207 1 AATAATTTAT 0.640211 -43 AAATAGAACCAATAAAATAAAAATAAA 6 233 1 AATAAAATAA 0.600129 -17 ATATGCTTCAAATAGGATAATACTAAGAAA 7 98 0 AATAGGATAA 0.630232 -203 ACTATTAATTAATAATATAATTATAGCTAA 7 132 0 AATAATATAA 0.933788 -169 GGAATAGCAAAATGATATATAAATTAACTA 7 158 0 AATGATATAT 0.883528 -143 TATATAATAGAAAATTATATAATTTAATAT 7 221 1 AAAATTATAT 0.52721 -80 TATCTAAAGAAATGTTATAAACTCAAAAAG 7 260 1 AATGTTATAA 0.846398 -41 ********** Masking position 8 Map Score: 18.9604 Number of sites scoring better than the average of aligned sites = 1033 Number in coding regions = 650 Number in noncoding regions = 383 Number of orfs with sites within 600 bp upstream = 192 Fraction of orfs with sites within 600 bp upstream = 0.0308384 Motif number 4 TTATAATATATCTCTTTTTTTGATAATCTGA 1 132 0 TCTCTTTTTT 0.937259 -169 TTTAATTAAATCTTTTATTTTAGTTATAATA 1 155 0 TCTTTATTTT 0.793567 -146 TATAACTCTCTCACTTGTTTTAATTAAATCT 1 173 0 TCACTGTTTT 0.941912 -128 ATCTTTATAATAATCTTTTTTAAAATATCGT 2 52 0 TAATTTTTTT 0.881441 -95 TATAATATAATCACGTGTGTTGACACTGTGT 3 15 1 TCACTGTGTT 0.702855 -111 AGATTTATGTTATTATTTTTTTTGCATAAGC 3 96 0 TATTTTTTTT 0.792922 -30 TGCATTTAACTTATTTTATTTAAAATT 4 33 0 TAACTATTTT 0.785035 -17 CAATTAATTGTCTTTTTTTTTTTTGCTGTTG 5 220 0 TCTTTTTTTT 0.915344 -81 TATATTACTTTCAACTATTTTAAAATAATCA 5 249 0 TCAATATTTT 0.702261 -52 TATCGTTGTTTTATATTTTTTAGTTTTTAAG 6 24 1 TTATTTTTTT 0.647162 -226 ACCATAGATTTCACCTTTTTTGGAATAATTT 6 194 1 TCACTTTTTT 0.966672 -56 ACTTCTATTCTTTTTTAGTACTTAAT 7 6 1 TATTTTTTTT 0.792922 -295 TTAATTTCCGTCATATTATTTTATATATGGT 7 32 1 TCATTTATTT 0.657752 -269 TTCAAGACAATCAAATGTTTTGTATTAGATA 7 65 1 TCAATGTTTT 0.787632 -236 TTTGAGTTTATAACATTTCTTTAGATACTTC 7 256 0 TAACTTTCTT 0.599739 -45 **** ****** Masking position 6 Map Score: 10.728 Number of sites scoring better than the average of aligned sites = 488 Number in coding regions = 374 Number in noncoding regions = 114 Number of orfs with sites within 600 bp upstream = 76 Fraction of orfs with sites within 600 bp upstream = 0.0122069 Motif number 5 ATAGGCTAAAATTACAAGATCACCGTAATA 1 210 1 ATTACAAGAT 0.923783 -91 GCATTACAATACTACAATATTATAAACA 2 9 0 ACTACAATAT 0.951493 -138 CTGTTGTGTGACTACGATATTTTAAAAAAG 2 39 1 ACTACGATAT 0.95948 -108 CCGTATATTGACTACGGTATCTAATCTTTA 2 76 0 ACTACGGTAT 0.958705 -71 TAATTGCGTGACTTCAGGATATAAACCTTA 3 56 0 ACTTCAGGAT 0.771545 -70 AGTAAAAATTATTACAGGATGTCTATTGCA 5 45 1 ATTACAGGAT 0.922366 -256 TTGTTGTGGTATTACGATTTGTTACTAAAA 5 97 0 ATTACGATTT 0.727968 -204 ATTGTCTTGAATTACCATATATAAAATAAT 7 46 0 ATTACCATAT 0.84781 -255 ********** Masking position 1 Map Score: 3.40481 Number of sites scoring better than the average of aligned sites = 152 Number in coding regions = 86 Number in noncoding regions = 66 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714 Motif number 6 GCGTATTGATAATTAAGTATCAGATTATCA 1 113 1 AATTAAGTAT 0.672937 -188 TCACCGTAATAATTCAGTAGCAGGAATAAG 1 229 1 AATTCAGTAG 0.954365 -72 TGTTTATAATATTGTAGTATTGTAATG 2 8 1 AATATTGTAG 0.84035 -139 TCTTTTTTAAAATATCGTAGTCACACAACA 2 40 0 AATATCGTAG 0.954365 -107 ATAAAGATTAGATACCGTAGTCAATATACG 2 75 1 GATACCGTAG 0.87026 -72 TATGATGTGTAATACCGTATATTGACTACG 2 90 0 AATACCGTAT 0.908018 -57 AGACTTTATAAATTTAGTATAATCAATGAA 5 126 1 AATTTAGTAT 0.87129 -175 AAATATATAGAATTTAGTAGATGATCTTTA 6 101 0 AATTTAGTAG 0.945409 -149 ********** Masking position 2 Map Score: 3.56475 Number of sites scoring better than the average of aligned sites = 99 Number in coding regions = 71 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 7 GAGCTTTTTGAATAAAAATAAAAT 1 3 1 GCTTTTAATA 0.826166 -298 GTTTGCTGACACTTTAAAAATATTCTCAGTAT 1 49 0 ACTTAAAATA 0.867139 -252 GAATGGGTTTGCTATATTAATATGATGACGTT 1 78 0 GCTTATAATA 0.971238 -223 TATTTAATAGGCTAAAATTACAAGATCACCGT 1 204 1 GCTAAATACA 0.670392 -97 TTAGCTGCATGCTTTATAAATAAGCTATTACT 1 257 0 GCTTATAATA 0.971224 -44 CATTGATTATACTAAATTTATAAAGTCTTGTT 5 122 0 ACTAATTATA 0.81678 -179 ATATTCTTTAGCTCTATATATACTAGTTTTAT 5 166 0 GCTTATTATA 0.938627 -135 TTTAACCTTTACTGAAAAAATATATAGAATTT 6 116 0 ACTAAAAATA 0.816785 -134 CATTTAAAGAACTTTATCAACACTTGATTTTA 6 144 0 ACTTATAACA 0.861069 -106 TATAATTATAGCTAAATTAATATGCTTCAAAT 7 115 0 GCTAATAATA 0.958449 -186 *** *** **** Masking position 3 Map Score: 7.38255 Number of sites scoring better than the average of aligned sites = 235 Number in coding regions = 180 Number in noncoding regions = 55 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 8 TAAATATGCCAAGAATTTGATTTA 2 133 1 AAGAATTTGA 0.95614 -14 ATGCAAAAAAAATAATAACATAAATCTCAA 3 100 1 AATAATAACA 0.793818 -26 TCATTGTTAGAAGAATAAGATATGATAT 5 9 0 AAGAATAAGA 0.95614 -292 TATAGAGCTAAAGAATATCATAAATATGAA 5 180 1 AAGAATATCA 0.955075 -121 CCATATATAAAATAATATGACGGAAATTAA 7 32 0 AATAATATGA 0.932175 -269 AAAAGTTCATAAGAATTTGAGGATAT 7 285 1 AAGAATTTGA 0.95614 -16 ********** Masking position 5 Map Score: 3.32725 Number of sites scoring better than the average of aligned sites = 79 Number in coding regions = 62 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 9 ********** No masking Map Score: 1.87173e-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 10 ********** No masking Map Score: 1.87173e-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 11 ********** No masking Map Score: 1.87173e-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