AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_rpxx.txt -z/home/amcguire/genomes/rpxx.fna -ifis_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 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 TATGTTGAATAAAAGTTATATTTGTATTATATAGTAAA 1 35 0 AAATTTGATT 0.726118 -37 TAATAAGTTTAATATATTCTGTAATATACCGTAATA 2 9 0 AAATTAAATA 0.974988 -292 ATGGTAGTACAACACGTTTAATTAAATTGTTTACTGCT 2 55 1 AAATTTAATT 0.856376 -246 ATTTATTACTAATAATTCAACTAATATATATACTATAA 2 181 0 AAATTAAATA 0.973136 -120 AATTATTAGTAATAAATAAACTAAAATCTTATATTAAA 2 202 1 AAATTAAATC 0.950212 -99 TTATGATTATAATACGAATATTAAGATATTTAATATAA 2 230 0 AAAATAAATA 0.947279 -71 TAATTGCTAAAAAATGATTATTATGATTATAATACGAA 2 250 0 AAAATATATT 0.710045 -51 TTTAGCAATTAATACTTAAAGTAATATTTAAACA 2 277 1 AAATTAAATT 0.5947 -24 GTTAAACTCAAAAATTTGGTGTAAGATTACATGCAAAA 3 70 1 AAATTAAATT 0.979359 -95 ATTACATGCAAAAAATTATTCTATAATTTCTCTAGCTC 3 95 1 AAATTATATT 0.881682 -70 AATTTTTTAAAAAAACTGTTTAAGTATCGCATTATTGT 4 31 0 AAATAAGATC 0.693067 -270 TGTCAAGTCAAAAATCTAAAAAAAAATAAAATATTTAT 4 161 1 AAATAAAATA 0.935858 -140 ACACGAGAATAATAATTTATTCAATATAAATATTTTAT 4 186 0 AAATCAAATA 0.867479 -115 TATACTCTTCAAGATATTATTTAGCATATAAATATTTA 5 65 0 AAATTAGATA 0.961021 -236 TATCTTATGCAAGAAGTCTAATAAAATAAAAATAGCTA 5 133 0 AAATTAAATA 0.982212 -168 GTATAAAGAAAAAGTAGAAGAAAAATTCCATATTAGT 6 10 1 AAAAAAAATT 0.809536 -291 AATATATATAAAGTGTTGCTGAAAAATAGTAATCGCTC 6 133 0 AATTAAAATA 0.635769 -168 GCAACAGCACAATATCTTAGATAATATATAAATATTAT 6 181 1 AAATTAAATA 0.98123 -120 TAATAGGAATAAAAGTATTGATAATATTTATATATTAT 6 201 0 AAAATAAATT 0.937513 -100 CTAATATTTTAATATAACAATTAAGATTAAAGATCCTA 6 237 0 AAAATAAATT 0.91438 -64 ATATTTTTAAAAGTAATATCTTAGCATACTAATATTTT 6 265 0 AATTTAGATA 0.746806 -36 ** * * *** *** Masking position 17 Map Score: 26.0386 Number of sites scoring better than the average of aligned sites = 694 Number in coding regions = 430 Number in noncoding regions = 264 Number of orfs with sites within 600 bp upstream = 117 Fraction of orfs with sites within 600 bp upstream = 0.0187922 Motif number 2 TATTATAATTATGTTGAATAAAAGTTATAT 1 52 0 ATAATTTAAA 0.731004 -20 TAATAAGTTTAATATATTCTGTAATATACCGTAATA 2 11 0 AATATATAAA 0.840271 -290 ATTTATTACTAATAATTCAACTAATATATATACTAT 2 183 0 AATAATAAAA 0.922495 -118 AATTATTAGTAATAAATAAACTAAAATCTTATATTA 2 202 1 AATAAAAAAA 0.876053 -99 TAATACGAATATTAAGATATTTAATATAAGATTTTA 2 223 0 ATTAAGTAAA 0.789277 -78 TACTTTAAGTATTAATTGCTAAAAAATGATTATTAT 2 264 0 ATTAATTAAA 0.898568 -37 GTTAAACTCAAAAATTTGGTGTAAGATTACATGCAA 3 70 1 AAAATTTAAA 0.898568 -95 ATTACATGCAAAAAATTATTCTATAATTTCTCTAGC 3 95 1 AAAAATTATA 0.639676 -70 AGCTCACGATAAAAAACCTTTAAACAATGTAATATT 3 128 1 AAAAAATAAA 0.944901 -37 TTATTGTTGAAAAAAATAATACAAAAG 4 2 0 AAAAAATAAA 0.944901 -299 ACGAGATATCAAAATTTTTTAAAAAAACTGTTTAAG 4 45 0 AAAATTTAAA 0.898568 -256 TCAAAAATCTAAAAAAAAATAAAATATTTATATTGA 4 168 1 AAAAAATAAA 0.944901 -133 ACACGAGAATAATAATTTATTCAATATAAATATTTT 4 188 0 AATAATTAAA 0.966532 -113 CATTTTTGCAAAAAAGCATTATAATAACGACTATAA 4 259 1 AAAAAGTAAA 0.924301 -42 AATGAAAGTGAATAATGTCACTAATAAT 5 3 0 AATAATAAAA 0.922495 -298 TTTATATCTAATTAAACATTTAAATATTTATATGCT 5 45 1 ATTAAATAAA 0.840271 -256 TTATATGCTAAATAATATCTTGAAGAGTATAATATT 5 72 1 AATAATTAAA 0.966532 -229 GTATAAAGAAAAAGTAGAAGAAAAATTCCATATT 6 9 1 AAAAAGAAAA 0.834228 -292 CAAAATTTTAAAAAATTCTCGCAATACTCTTTGTGA 6 60 1 AAAAATCAAA 0.785516 -241 TAGATAATATATAAATATTATCAATACTTTTATTCC 6 198 1 ATAAATAAAA 0.785 -103 CTAATATTTTAATATAACAATTAAGATTAAAGATCC 6 239 0 AATATAAAAA 0.684359 -62 CAGTAATAATATTTTTAAAAGTAATATCTT 6 281 0 AATAATTAAA 0.966531 -20 ****** * ** * Masking position 4 Map Score: 27.2833 Number of sites scoring better than the average of aligned sites = 946 Number in coding regions = 617 Number in noncoding regions = 329 Number of orfs with sites within 600 bp upstream = 175 Fraction of orfs with sites within 600 bp upstream = 0.0281079 Motif number 3 AAAAAAACGTTTAACCTTTTTGAA 1 4 1 AAAACTTTAA 0.628061 -68 CTACCATTACAATAGTAATAAGTTTAATATA 2 31 0 AATAGAATAA 0.831016 -270 GGATCATTTGATTAGATATAATAGGATATTA 2 136 0 ATTAGTATAA 0.957114 -165 CATCTTCCATATTAGTTATAGTATATATATT 2 166 1 ATTAGTATAG 0.929609 -135 TAGTTGAATTATTAGTAATAAATAAACTAAA 2 196 1 ATTAGAATAA 0.892258 -105 CTCACGATAAAAAACCTTTAAACAATGTAAT 3 130 1 AAAACTTTAA 0.628061 -35 ACAATGTAATATTAGTAATAAATT 3 151 1 ATTAGAATAA 0.892258 -14 TTGGTATTTTATTAGATCTAGATACGAGATA 4 73 0 ATTAGTCTAG 0.733629 -228 CTTGACAAAAATAAGATTTAGTTACTATACA 4 137 0 ATAAGTTTAG 0.810478 -164 ATAGATACTAATTGGTTATAGTCGTTATTAT 4 279 0 ATTGGTATAG 0.583402 -22 TAAATGTTTAATTAGATATAAAGTGAATAAT 5 36 0 ATTAGTATAA 0.957114 -265 ATAGCTACCTAATAGCTTTAATGCAAGGGTA 5 109 0 AATAGTTTAA 0.929838 -192 TGACATACAAATGACCTTTAGAAAGAGGCTA 5 244 1 ATGACTTTAG 0.582467 -57 AAATTTTGTAAATAGCTTTAACTAATATGGA 6 37 0 AATAGTTTAA 0.929838 -264 AAAAATGTATATGAGTTTTAACGAGCGATTA 6 111 1 ATGAGTTTAA 0.856966 -190 AACTAATTTAAATATATATAAAGTGTTGCTG 6 150 0 AATATTATAA 0.446513 -151 TAAAGATCCTAATAGGAATAAAAGTATTGAT 6 217 0 AATAGAATAA 0.831016 -84 ATATTTTAATATAACAATTAAGATTAAAGAT 6 241 0 ATAACATTAA 0.513422 -60 ATGCTAAGATATTACTTTTAAAAATATTATT 6 276 1 ATTACTTTAA 0.897767 -25 ***** ***** Masking position 9 Map Score: 16.7553 Number of sites scoring better than the average of aligned sites = 930 Number in coding regions = 680 Number in noncoding regions = 250 Number of orfs with sites within 600 bp upstream = 121 Fraction of orfs with sites within 600 bp upstream = 0.0194346 Motif number 4 TATAATTATGTTGAATAAAAGTTATATTTG 1 49 0 TTGAATAAAA 0.906855 -23 TAGTAATAAGTTTAATATATTCTGTAATAT 2 20 0 TTTAATATAT 0.671514 -281 GTACAACACGTTTAATTAAATTGTTTACTG 2 61 1 TTTAATTAAA 0.484819 -240 TCCTATTATATCTAATCAAATGATCCATCT 2 141 1 TCTAATCAAA 0.833161 -160 TATTAAGATATTTAATATAAGATTTTAGTT 2 220 0 TTTAATATAA 0.86173 -81 ATAAAAAACCTTTAAACAATGTAATATTAG 3 136 1 TTTAAACAAT 0.569693 -29 CGCATTATTGTTGAAAAAAATAATACAAAA 4 12 0 TTGAAAAAAA 0.847085 -289 ATCAAAATTTTTTAAAAAAACTGTTTAAGT 4 44 0 TTTAAAAAAA 0.936979 -257 CGTATCTAGATCTAATAAAATACCAATCTT 4 78 1 TCTAATAAAA 0.947925 -223 AAGTCAAAAATCTAAAAAAAAATAAAATAT 4 165 1 TCTAAAAAAA 0.91286 -136 AATATTTATATTGAATAAATTATTATTCTC 4 190 1 TTGAATAAAT 0.762691 -111 TCACTTTATATCTAATTAAACATTTAAATA 5 41 1 TCTAATTAAA 0.70818 -260 ATGCAAGAAGTCTAATAAAATAAAAATAGC 5 135 0 TCTAATAAAA 0.947925 -166 TTTACAAAATTTTAAAAAATTCTCGCAATA 6 56 1 TTTAAAAAAT 0.83135 -245 ACAGGAGCTGATTAATAAAAATGTATATGA 6 95 1 ATTAATAAAA 0.669145 -206 ATACTAATATTTTAATATAACAATTAAGAT 6 248 0 TTTAATATAA 0.86173 -53 AGATATTACTTTTAAAAATATTATTACTG 6 282 1 TTTAAAAATA 0.550252 -19 ********** Masking position 5 Map Score: 18.6504 Number of sites scoring better than the average of aligned sites = 799 Number in coding regions = 515 Number in noncoding regions = 284 Number of orfs with sites within 600 bp upstream = 132 Fraction of orfs with sites within 600 bp upstream = 0.0212014 Motif number 5 ATTGAAAATACAAGATATGACTTTTCAAGT 2 107 0 CAAGATATGA 0.757532 -194 TTAGATATAATAGGATATTATTGAAAATAC 2 126 0 TAGGATATTA 0.85865 -175 ATATTTAATATAAGATTTTAGTTTATTTAT 2 213 0 TAAGATTTTA 0.628004 -88 ATACGAATATTAAGATATTTAATATAAGAT 2 227 0 TAAGATATTT 0.864246 -74 TATTAATTGCTAAAAAATGATTATTATGAT 2 261 0 TAAAAAATGA 0.585628 -40 TGTTTAAATATTACTTTAAGTAT 2 288 0 TTAAATATTA 0.617462 -13 AGATTACATGCAAAAAATTATTCTATAATT 3 93 1 CAAAAAATTA 0.767501 -72 ACAGTTTTTTTAAAAAATTTTGATATCTCG 4 50 1 TAAAAAATTT 0.598411 -251 TAAAAAAAAATAAAATATTTATATTGAATA 4 177 1 TAAAATATTT 0.824769 -124 TTATATTGAATAAATTATTATTCTCGTGTC 4 195 1 TAAATTATTA 0.602672 -106 TTATACTCTTCAAGATATTATTTAGCATAT 5 74 0 CAAGATATTA 0.932934 -227 AATGCAAGGGTAAAATATTATACTCTTCAA 5 91 0 TAAAATATTA 0.881953 -210 TCGCAATAATTAGGAAATTACAT 5 288 1 TAGGAAATTA 0.646919 -13 AAGCTATTTACAAAATTTTAAAAAATTCTC 6 50 1 CAAAATTTTA 0.489019 -251 ATATATTATCTAAGATATTGTGCTGTTGCA 6 180 0 TAAGATATTG 0.785354 -121 ATTGTTATATTAAAATATTAGTATGCTAAG 6 254 1 TAAAATATTA 0.881953 -47 ATTAGTATGCTAAGATATTACTTTTAAAAA 6 270 1 TAAGATATTA 0.953709 -31 TATTACTTTTAAAAATATTATTACTG 6 285 1 AAAAATATTA 0.664719 -16 ********** Masking position 8 Map Score: 19.8933 Number of sites scoring better than the average of aligned sites = 762 Number in coding regions = 495 Number in noncoding regions = 267 Number of orfs with sites within 600 bp upstream = 120 Fraction of orfs with sites within 600 bp upstream = 0.019274 Motif number 6 TGAATAAAAGTTATATTTGTATTATATAGT 1 38 0 TTATATTTGT 0.857732 -34 GATCCATCTTCCATATTAGTTATAGTATAT 2 162 1 CCATATTAGT 0.957586 -139 GTTATAGTATATATATTAGTTGAATTATTA 2 180 1 ATATATTAGT 0.892469 -121 TTAAATATCTTAATATTCGTATTATAATCA 2 235 1 TAATATTCGT 0.795579 -66 TTAAACAATGTAATATTAGTAATAAATT 3 147 1 TAATATTAGT 0.936114 -18 TAACTAAATCTTATTTTTGTCAAGTCAAAA 4 144 1 TTATTTTTGT 0.626309 -157 AAAAATGACACCATTTTAGTGTATAGAACT 4 236 0 CCATTTTAGT 0.862596 -65 AAGAAAAATTCCATATTAGTTAAAGCTATT 6 28 1 CCATATTAGT 0.957586 -273 TTATATATATTTAAATTAGTTGCAACAGCA 6 160 1 TTAAATTAGT 0.728601 -141 TGTTATATTAAAATATTAGTATGCTAAGAT 6 256 1 AAATATTAGT 0.864389 -45 ********** Masking position 6 Map Score: 6.55884 Number of sites scoring better than the average of aligned sites = 211 Number in coding regions = 141 Number in noncoding regions = 70 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 7 CGTTTAACCTTTTTGAATTTACTATATAATA 1 18 1 TTTTGAATTA 0.890324 -54 ATTATAATTATGTTGAATAAAAGTTATATTT 1 50 0 TGTTGAATAA 0.764654 -22 AATAGGATATTATTGAAAATACAAGATATGA 2 117 0 TATTGAAATA 0.778941 -184 ATAATCATTTTTTAGCAATTAATACTTAAAG 2 267 1 TTTAGCAATA 0.831524 -34 GGTATATGATTTATGTAACTATATAT 3 6 0 TTATGTAATA 0.530269 -159 TAGAATAATTTTTTGCATGTAATCTTACACC 3 87 0 TTTTGCATTA 0.939179 -78 ATCGCATTATTGTTGAAAAAAATAATACAAA 4 13 0 TGTTGAAAAA 0.835603 -288 AAAATATTTATATTGAATAAATTATTATTCT 4 188 1 TATTGAATAA 0.590294 -113 TATAATGCTTTTTTGCAAAAATGACACCATT 4 251 0 TTTTGCAAAA 0.93903 -50 CAAGATATTATTTAGCATATAAATATTTAAA 5 63 0 TTTAGCATTA 0.759257 -238 ATTAGCTATCTTATGCAAGAAGTCTAATAAA 5 146 0 TTATGCAAAA 0.759258 -155 TTTTTTAAAATTTTGTAAATAGCTTTAACTA 6 44 0 TTTTGTAATA 0.846158 -257 GATATTGTGCTGTTGCAACTAATTTAAATAT 6 166 0 TGTTGCAATA 0.938025 -135 ******** ** Masking position 7 Map Score: 9.13732 Number of sites scoring better than the average of aligned sites = 487 Number in coding regions = 359 Number in noncoding regions = 128 Number of orfs with sites within 600 bp upstream = 77 Fraction of orfs with sites within 600 bp upstream = 0.0123675 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