AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_rpxx.txt -z/home/amcguire/genomes/rpxx.fna -ifis_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 RP114 71 PROTEIN-EXPORT MEMBRANE PROTEIN SECF (secF) #2 RP213 300 S-ADENOSYLMETHIONINE:tRNA RIBOSYLTRANSFERASE-ISOMERASE (queA) #3 RP512 164 RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE BETA CHAIN (nrdB) #4 RP513 300 RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE ALPHA CHAIN (nrdA) #5 RP585 300 unknown #6 RP721 300 QUEUINE TRNA-RIBOSYLTRANSFERASE (tgt) Motif number 1 TGAATTTACTATATAATACAAATATAACTTTTAT 1 31 1 ATAAATAATA 0.925733 -41 CAAATATAACTTTTATTCAACATAATTATAATA 1 49 1 TTTATTCATA 0.739583 -23 TGTACTACCATTACAATAGTAATAAGTTTAATAT 2 32 0 TTAAATAATA 0.963106 -269 CAGTAAACAATTTAATTAAACGTGTTGTACTACC 2 57 0 TTTATTAGTG 0.621149 -244 AGATGGATCATTTGATTAGATATAATAGGATATT 2 137 0 TTTATTAATA 0.968913 -164 TCCATATTAGTTATAGTATATATATTAGTTGAAT 2 171 1 TTAAGTAATA 0.900474 -130 ATTTTAGTTTATTTATTACTAATAATTCAACTAA 2 195 0 ATTATTAATA 0.937006 -106 AACTAAAATCTTATATTAAATATCTTAATATTCG 2 220 1 TTAATTAATC 0.835921 -81 ATTATTATGATTATAATACGAATATTAAGATATT 2 238 0 TTAAATAATA 0.963108 -63 ATATATAGTTACATAAATCATATACCAAATCG 3 9 1 TTAATAAATA 0.817351 -156 AATTTATTACTAATATTACATTGTT 3 150 0 ATTATTAATA 0.937006 -15 TCTAGATCTAATAAAATACCAATCTTTATGGAGA 4 82 1 ATAAATAATC 0.708668 -219 AAATGCAGCTTTTAATTACCAATGTATAGTAACT 4 115 1 TTTATTAATG 0.858815 -186 ATAATAATTTATTCAATATAAATATTTTATTTTT 4 182 0 ATTAATAATA 0.937038 -119 TATTTAAATGTTTAATTAGATATAAAGTGAATAA 5 37 0 TTTATTAATA 0.968913 -264 TAATTAAACATTTAAATATTTATATGCTAAATAA 5 53 1 TTTAATAATA 0.963155 -248 AAGAAGTCTAATAAAATAAAAATAGCTACCTAAT 5 127 0 ATAAATAATA 0.925733 -174 TTGTATGTCAATTCAGTACTCGTATTCTCACGTT 5 220 0 ATTAGTAGTA 0.581637 -81 TTGCAACTAATTTAAATATATATAAAGTGTTGCT 6 151 0 TTTAATAATA 0.968835 -150 GCACAATATCTTAGATAATATATAAATATTATCA 6 187 1 TTAATAAATA 0.817352 -114 AATTGTTATATTAAAATATTAGTATGCTAAGATA 6 253 1 TTAAATAGTA 0.875568 -48 GTAATAATATTTTTAAAAGTAATATCTTAGCATA 6 275 0 TTTAAAAATA 0.842346 -26 *** **** *** Masking position 2 Map Score: 26.3782 Number of sites scoring better than the average of aligned sites = 726 Number in coding regions = 440 Number in noncoding regions = 286 Number of orfs with sites within 600 bp upstream = 149 Fraction of orfs with sites within 600 bp upstream = 0.0239319 Motif number 2 AATAAAAGTTATATTTGTATTATATAGTAAA 1 35 0 ATATTTTATT 0.915241 -37 TATATTAAACTTATTACTATTGTAATGGTAG 2 31 1 TTATTATATT 0.894663 -270 AAAATACAAGATATGACTTTTCAAGTGGCAA 2 102 0 ATATGATTTT 0.864111 -199 AATTCAACTAATATATATACTATAACTAATA 2 175 0 ATATATTACT 0.553028 -126 TATGATTATAATACGAATATTAAGATATTTA 2 236 0 ATACGATATT 0.928264 -65 AATTGCTAAAAAATGATTATTATGATTATAA 2 256 0 AAATGATATT 0.698169 -45 AATTTATTACTAATATTACATTGTTTA 3 148 0 TTACTATATT 0.857027 -17 TATAAATATTTTATTTTTTTTTAGATTTTTG 4 169 0 TTATTTTTTT 0.565017 -132 AAAAAATAAAATATTTATATTGAATAAATTA 4 181 1 ATATTTTATT 0.915241 -120 TATATTGAATAAATTATTATTCTCGTGTCTA 4 196 1 AAATTATATT 0.755469 -105 ATTATTTAGCATATAAATATTTAAATGTTTA 5 57 0 ATATAATATT 0.903214 -244 TAACGTGAGAATACGAGTACTGAATTGACAT 5 219 1 ATACGATACT 0.795533 -82 ATAAAAATGTATATGAGTTTTAACGAGCGAT 6 109 1 ATATGATTTT 0.864113 -192 TAACGAGCGATTACTATTTTTCAGCAACACT 6 129 1 TTACTATTTT 0.675222 -172 CAGCAACACTTTATATATATTTAAATTAGTT 6 150 1 TTATATTATT 0.588003 -151 CTTAGATAATATATAAATATTATCAATACTT 6 196 1 ATATAATATT 0.903214 -105 AATATTATCAATACTTTTATTCCTATTAGGA 6 211 1 ATACTTTATT 0.884004 -90 ATATCTTAGCATACTAATATTTTAATATAAC 6 257 0 ATACTATATT 0.945304 -44 GTATGCTAAGATATTACTTTTAAAAATATTA 6 274 1 ATATTATTTT 0.894662 -27 ACTTTTAAAAATATTATTACTG 6 289 1 ATATTATACT 0.880428 -12 ****** **** Masking position 8 Map Score: 22.0056 Number of sites scoring better than the average of aligned sites = 1116 Number in coding regions = 703 Number in noncoding regions = 413 Number of orfs with sites within 600 bp upstream = 168 Fraction of orfs with sites within 600 bp upstream = 0.0269836 Motif number 3 ATAAGTTTAATATATTCTGTAATATACCGTAATA 2 10 0 TATCTAATAT 0.972321 -291 TCATATCTTGTATTTTCAATAATATCCTATTATAT 2 117 1 TATCTAATAT 0.972321 -184 AATAATATCCTATTATATCTAATCAAATGATCCAT 2 134 1 TATATAATCA 0.762727 -167 CTAATATATATACTATAACTAATATGGAAGATGGA 2 164 0 TATATAATAT 0.97521 -137 TTATTACTAATAATTCAACTAATATATATACTATA 2 182 0 TACATAATAT 0.833025 -119 TATAAGATTTTAGTTTATTTATTACTAATAATTCA 2 200 0 TATATATTAC 0.667685 -101 ATACGAATATTAAGATATTTAATATAAGATTTTAG 2 222 0 TATATAATAT 0.97521 -79 GTTTAAATATTACTTTAAGTATTAATTGCTAAAAA 2 275 0 TATATATTAA 0.816852 -26 AAAAAACCTTTAAACAATGTAATATTAGTAATAAA 3 138 1 TAAATAATAT 0.77096 -27 ACGAGAATAATAATTTATTCAATATAAATATTTTA 4 187 0 TATACAATAT 0.833024 -114 ACTAATTGGTTATAGTCGTTATTATAATGCTTTTT 4 269 0 TATCTATTAT 0.919193 -32 TGAAAGTGAATAATGTCACTAATAAT 5 2 0 TATCTAATAA 0.924808 -299 TAAATATTTATATGCTAAATAATATCTTGAAGAGT 5 65 1 TATATAATAT 0.97521 -236 ACTTCTTGCATAAGATAGCTAATAATGGTAAATTT 5 154 1 TATATAATAA 0.932311 -147 ATGTAATTTCCTAATTATTGCGATAGCC 5 283 0 TATCAATTAT 0.493237 -18 AACAGCACAATATCTTAGATAATATATAAATATTA 6 183 1 TATATAATAT 0.97521 -118 TTATTCCTATTAGGATCTTTAATCTTAATTGTTAT 6 227 1 TATCTAATCT 0.891287 -74 ** ** ****** Masking position 11 Map Score: 23.7129 Number of sites scoring better than the average of aligned sites = 366 Number in coding regions = 243 Number in noncoding regions = 123 Number of orfs with sites within 600 bp upstream = 81 Fraction of orfs with sites within 600 bp upstream = 0.01301 Motif number 4 AAAAAAACGTTTAACCTTTTTGAA 1 1 1 AAAAAACTTA 0.97726 -71 GATTACATGCAAAAAATTATTCTATAATTTCTCT 3 94 1 AAAAAATTTA 0.981217 -71 AGCTCACGATAAAAAACCTTTAAACAATGTAATA 3 128 1 AAAAAACTTA 0.97732 -37 ATTATTGTTGAAAAAAATAATACAAAAG 4 5 0 AAAAAATATA 0.942893 -296 AAATTTTTTAAAAAAACTGTTTAAGTATCGCATT 4 36 0 AAAAAATTTA 0.981217 -265 CAGTTTTTTTAAAAAATTTTGATATCTCGTATCT 4 51 1 AAAAAATTGA 0.941439 -250 AAAAATCTAAAAAAAAATAAAATATTTATATTGA 4 170 1 AAAAAATAAA 0.774154 -131 TCATTTTTGCAAAAAAGCATTATAATAACGACTA 4 258 1 AAAAAACTTA 0.977271 -43 ACAAAATTTTAAAAAATTCTCGCAATACTCTTTG 6 59 1 AAAAAATTCA 0.941442 -242 ****** * ** * Masking position 6 Map Score: 8.35423 Number of sites scoring better than the average of aligned sites = 168 Number in coding regions = 108 Number in noncoding regions = 60 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 5 ACGTTTAACCTTTTTGAATTTACTATATAATA 1 17 1 TTTTGAATTA 0.915773 -55 TCCATATTAGTTATAGTATATATATTAGTTGA 2 171 1 TTATGTATTA 0.832492 -130 AATAATCATTTTTTAGCAATTAATACTTAAAG 2 266 1 TTTTGCAATA 0.833356 -35 ACAAATTACGATTTGGTATATGATTTATGTAA 3 19 0 ATTTGTATTG 0.797655 -146 TTACACCAAATTTTTGAGTTTAACATGCAGTA 3 62 0 TTTTGAGTTA 0.845889 -103 ATAGAATAATTTTTTGCATGTAATCTTACACC 3 87 0 TTTTGCATTA 0.960597 -78 AAATTTTGATATCTCGTATCTAGATCTAATAA 4 64 1 ATCTGTATTA 0.896502 -237 TAAATTATTATTCTCGTGTCTACTTAATTGAA 4 205 1 TTCTGTGTTA 0.872502 -96 AATGACACCATTTTAGTGTATAGAACTTCAAT 4 231 0 TTTTGTGTTA 0.951797 -70 GACTATAACCAATTAGTATCTATA 4 287 1 AATTGTATTA 0.836193 -14 TCAAGATATTATTTAGCATATAAATATTTAAA 5 63 0 ATTTGCATTA 0.939954 -238 ATTCTCACGTTATTCGTATCTACTATGTGCTG 5 199 0 TATTGTATTA 0.888746 -102 ATTTTTTAAAATTTTGTAAATAGCTTTAACTA 6 44 0 ATTTGTAATA 0.836186 -257 **** **** ** Masking position 4 Map Score: 9.02182 Number of sites scoring better than the average of aligned sites = 294 Number in coding regions = 185 Number in noncoding regions = 109 Number of orfs with sites within 600 bp upstream = 62 Fraction of orfs with sites within 600 bp upstream = 0.00995824 Motif number 6 TTAGATATAATAGGATATTATTGAAAATAC 2 126 0 TAGGATATTA 0.753628 -175 GATCATTTGATTAGATATAATAGGATATTA 2 136 0 TTAGATATAA 0.787687 -165 ATATTTAATATAAGATTTTAGTTTATTTAT 2 213 0 TAAGATTTTA 0.656093 -88 ATACGAATATTAAGATATTTAATATAAGAT 2 227 0 TAAGATATTT 0.91854 -74 TGTTTAAATATTACTTTAAGTAT 2 288 0 TTAAATATTA 0.849847 -13 TTATTTTTTTTTAGATTTTTGACTTGACAA 4 160 0 TTAGATTTTT 0.516721 -141 TAAAAAAAAATAAAATATTTATATTGAATA 4 177 1 TAAAATATTT 0.845095 -124 TTATATTGAATAAATTATTATTCTCGTGTC 4 195 1 TAAATTATTA 0.531308 -106 AAATGTTTAATTAGATATAAAGTGAATAAT 5 36 0 TTAGATATAA 0.787687 -265 AATTAAACATTTAAATATTTATATGCTAAA 5 54 1 TTAAATATTT 0.803994 -247 TTATACTCTTCAAGATATTATTTAGCATAT 5 74 0 CAAGATATTA 0.759678 -227 AATGCAAGGGTAAAATATTATACTCTTCAA 5 91 0 TAAAATATTA 0.751251 -210 TGCAACTAATTTAAATATATATAAAGTGTT 6 154 0 TTAAATATAT 0.475705 -147 ATATATTATCTAAGATATTGTGCTGTTGCA 6 180 0 TAAGATATTG 0.807508 -121 TTGATAATATTTATATATTATCTAAGATAT 6 192 0 TTATATATTA 0.474572 -109 ATTGTTATATTAAAATATTAGTATGCTAAG 6 254 1 TAAAATATTA 0.751251 -47 ATTAGTATGCTAAGATATTACTTTTAAAAA 6 270 1 TAAGATATTA 0.924621 -31 TATTACTTTTAAAAATATTATTACTG 6 285 1 AAAAATATTA 0.492307 -16 ********** Masking position 6 Map Score: 20.2305 Number of sites scoring better than the average of aligned sites = 692 Number in coding regions = 432 Number in noncoding regions = 260 Number of orfs with sites within 600 bp upstream = 116 Fraction of orfs with sites within 600 bp upstream = 0.0186315 Motif number 7 TTTTCAACAATAATGCGATACTTAAACAGT 4 25 1 TAATGCGATA 0.92033 -276 TATAATGCTTTTTTGCAAAAATGACACCAT 4 252 0 TTTTGCAAAA 0.471748 -49 CTAATAGCTTTAATGCAAGGGTAAAATATT 5 102 0 TAATGCAAGG 0.895188 -199 ATTAGCTATCTTATGCAAGAAGTCTAATAA 5 147 0 TTATGCAAGA 0.908447 -154 ATTTCCTAATTATTGCGATAGCCTTCCTCT 5 276 0 TATTGCGATA 0.706743 -25 TCACAAAGAGTATTGCGAGAATTTTTTAAA 6 66 0 TATTGCGAGA 0.940185 -235 ********** Masking position 4 Map Score: 0.629149 Number of sites scoring better than the average of aligned sites = 62 Number in coding regions = 45 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 8 ********** No masking Map Score: -1.58208e-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 9 ********** No masking Map Score: -1.58208e-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 10 ********** No masking Map Score: -1.58208e-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