AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00290_rpxx_reg_100.orf -o00290_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 RP258 126 unknown #2 RP259 56 PENICILLIN-BINDING PROTEIN 4* (pbpE) #3 RP261 92 PYRUVATE DEHYDROGENASE E1 COMPONENT, ALPHA SUBUNIT PRECURSOR (pdhA) #4 RP262 161 PYRUVATE DEHYDROGENASE E1 COMPONENT, BETA SUBUNIT PRECURSOR (pdhB) #5 RP420 300 unknown #6 RP421 64 LEUCYL-TRNA SYNTHETASE (leuS) #7 RP428 121 BRANCHED-CHAIN AMINO ACID AMINOTRANSFERASE (ilvE) #8 RP617 300 PROBABLE ISOLEUCYL-TRNA SYNTHETASE (ileS) #9 RP687 300 VALYL-TRNA SYNTHETASE (valS) Motif number 1 TTTTGTGGTGAAGTTTGTATTGTTTACATAGTTCGA 1 15 1 AATTTATTTA 0.968705 -112 TCGAGAAATGAATTTGGTATTATTTATTGCTTGATC 1 47 1 AATTTATTTA 0.968647 -80 TTAGAACTTTTTATTATTTTATTGTATGTA 1 107 0 AATTTATTTT 0.879136 -20 AGCTATATACAATTTATTTTAAGAGACAAG 2 5 0 AATTTTTGGA 0.897835 -52 TTGCACAGCTTATTTATTATACTGTATCACCCCATC 4 14 1 TATTTATTTA 0.899768 -148 AATATATACTAATATATTTTTAGCTAGATTGCATTG 4 76 1 AAATTTTGTA 0.72904 -86 CTAGATTGCATTGTTAATTTACGTGATTACATTATA 4 99 1 TTTTTTTGGA 0.424993 -63 TTATTTAAATTAAATATTTTCATTTACTTATAATGT 4 127 0 TAATTTTTTA 0.47168 -35 ACTCAAAATTATCTTATTATACTTTATAAGCTATTA 5 27 0 ATTTTATTTA 0.899771 -274 AAATAAACAAAACTTTGTTTTTTCTATATATGTATG 5 193 1 AATTTTTTTA 0.966033 -108 ATTAATATCATAGTTGTTTTTGGCTTTCGTGGTCAA 7 56 1 TATTTTTGTT 0.628879 -66 TAAGTTATATTTATATTAGATTAGAAACTCAT 7 100 0 ATTTTATGTT 0.648405 -22 GTTAAATTAAAAGTTAATATTTGTTATTTTTGCTTG 8 13 0 AATTTATGTA 0.964301 -288 TGAACACATGAATTTGTAATAAGTTAAATTAAAAGT 8 35 0 AATTAATGTA 0.613363 -266 CAGTAATACGAAATTGATATTTTTGAAGATAATTTT 8 94 0 AATTTATTGA 0.916381 -207 TGAAAAAGAAAAATTGTTATTTTCTTTTAAATATAC 8 128 1 AATTTATTTT 0.87932 -173 AAGTTGTAATATTTTTGTATAAGGTATATTTAAAAG 8 151 0 ATTTTATGTA 0.886818 -150 CTCTTGAAATTTATTAGTTTAGTATAAATTATGTAT 8 219 1 TTTTTTTTTA 0.705184 -82 AAATTATTATAATTTGGTTTAATATAATAGATAATG 8 267 0 AATTTTTTTA 0.96603 -34 CTTGAGAACAAATTTGTTTTGCTATATTACCACTTT 9 69 0 AATTTTTTTA 0.966033 -232 CAAGGACTAAAAATTTCTATGATTGATTAGGTTAAA 9 113 1 AATTTATTGA 0.916381 -188 GAATGCATAAAAGTTTCTTTAATATCTTTAACCTAA 9 139 0 AATTTTTTTC 0.750985 -162 TATCGTCGTTAAATTACTTTTTTATAATTGAATGCA 9 168 0 AATTTTTTTA 0.966033 -133 ** ** *** * ** Masking position 10 Map Score: 26.4835 Number of sites scoring better than the average of aligned sites = 792 Number in coding regions = 460 Number in noncoding regions = 332 Number of orfs with sites within 600 bp upstream = 164 Fraction of orfs with sites within 600 bp upstream = 0.0263412 Motif number 2 CTTTTTATTATTTTATTGTATGTATTGATTCTG 1 98 0 TTTATGTATT 0.727978 -29 TATAACTTGATTACAATAATTCTTAAGGAGTAA 3 67 1 TTAATAATTT 0.829908 -26 GCTAAAAATATATTAGTATATATTGGTTTGACT 4 67 0 TATATATATT 0.837618 -95 ATTTACGTGATTACATTATAAGTAAATGAAAAT 4 115 1 TTAATATAAT 0.804149 -47 CCCTTTTTATTTAAATTAAATATTTTCATTTAC 4 136 0 TTAATAAATT 0.904924 -26 AAAAAAATTTTTTCATTAAATATCTAAACTGGT 5 73 0 TTTATAAATT 0.959774 -228 GGAGTCCTGATTTAAAAAAATTTTTTCATTAAA 5 86 0 TTTAAAAATT 0.643576 -215 ATATGGAAGATTTAATTATTTCTTAGCATAAAT 5 128 0 TTTATATTTT 0.924414 -173 AAAACTTTGTTTTTTCTATATATGTATGACATA 5 201 1 TTTTTATATT 0.64357 -100 ATACAATTAGTTTAAATAATTTTTGACTAATAG 5 231 1 TTTATAATTT 0.924415 -70 ATAAAGGAGCTTTGACTATTAGTCAAAAATTAT 5 246 0 TTTATATTAT 0.840651 -55 CATCAAGCACTTTAATTAAATTTGTT 5 285 1 TTTATAAATT 0.959773 -16 ACAACTATGATATTAATAATTTTGAACCCGTGG 7 40 0 TATATAATTT 0.725586 -82 TCTAATCTAATATAAATATAACTTA 7 107 1 TATATATAAT 0.689932 -15 TTGTAATAAGTTAAATTAAAAGTTAATATTTGT 8 25 0 TTAATAAAAT 0.804149 -276 GTGTTCAATATTTGAATATATTTTTCTACAAAA 8 64 1 TTTATATATT 0.959774 -237 GTTATTTTCTTTTAAATATACCTTATACAAAAA 8 143 1 TTTATATACT 0.790057 -158 TACATAATCTTTATAATAATATTCTTAACACGA 9 269 1 TTAATAATAT 0.677904 -32 *** * ***** * Masking position 1 Map Score: 14.4458 Number of sites scoring better than the average of aligned sites = 851 Number in coding regions = 536 Number in noncoding regions = 315 Number of orfs with sites within 600 bp upstream = 168 Fraction of orfs with sites within 600 bp upstream = 0.0269836 Motif number 3 CTTGATTACAATAATTCTTAAGGAGTAATT 3 72 1 ATAATTCTTA 0.879387 -21 TAAGTAAATGAAAATATTTAATTTAAATAA 4 133 1 AAAATATTTA 0.610086 -29 GTATAATAAGATAATTTTGAGTTTGTGATA 5 41 1 ATAATTTTGA 0.870854 -260 ATTTAATGAAAAAATTTTTTTAAATCAGGA 5 85 1 AAAATTTTTT 0.664075 -216 CTCCAGATTTAAAATTTATGCTAAGAAATA 5 115 1 AAAATTTATG 0.661692 -186 TTTCGCTTTTAAAATTCTGACTTTTGCTAA 5 166 0 AAAATTCTGA 0.740331 -135 ATTAGTTTAAATAATTTTTGACTAATAGTC 5 236 1 ATAATTTTTG 0.912458 -65 TATGATATTAATAATTTTGAACCCGTGGTC 7 38 0 ATAATTTTGA 0.870854 -84 ATTTTTGAAGATAATTTTTGTAGAAAAATA 8 82 0 ATAATTTTTG 0.912458 -219 CTGAAAAAGAAAAATTGTTATTTTCTTTTA 8 127 1 AAAATTGTTA 0.731169 -174 CTAAAGTTGTAATATTTTTGTATAAGGTAT 8 160 0 AATATTTTTG 0.627217 -141 AGATAAATACATAATTTATACTAAACTAAT 8 231 0 ATAATTTATA 0.763924 -70 CCAAATTATAATAATTTCTAGAATA 8 286 1 ATAATTTCTA 0.833483 -15 TCAAGGACTAAAAATTTCTATGATTGATTA 9 112 1 AAAATTTCTA 0.833482 -189 ATAATCATACATAATCTTTATAATAATATT 9 262 1 ATAATCTTTA 0.700571 -39 TCTTTATAATAATATTCTTAACACGAATAA 9 276 1 AATATTCTTA 0.540641 -25 ********** Masking position 5 Map Score: 10.0868 Number of sites scoring better than the average of aligned sites = 1156 Number in coding regions = 737 Number in noncoding regions = 419 Number of orfs with sites within 600 bp upstream = 196 Fraction of orfs with sites within 600 bp upstream = 0.0314809 Motif number 4 TTTACATAGTTCGAGAAATGAATTTGGTATTA 1 37 1 TCAGAATGAA 0.962791 -90 GAACATGCGATCAAGCAATAAATAATACCAAA 1 59 0 TCAGAATAAA 0.972406 -68 CTTGTCTCTTAAAATAAATTGTATATAG 2 7 1 TCTAAATAAA 0.673624 -50 GGAGTAGGAATCCAGAAACAAATGTCATGCCG 3 29 1 TCAGAACAAA 0.880225 -64 ATTATTGTAATCAAGTTATAAAGTTACGGCAT 3 55 0 TCAGTATAAA 0.96817 -38 AACAATGCAATCTAGCTAAAAATATATTAGTA 4 82 0 TCAGTAAAAA 0.915359 -80 AAATCTGGAGTCCTGATTTAAAAAAATTTTTT 5 93 0 TCTGTTTAAA 0.833458 -208 AAATCAGGACTCCAGATTTAAAATTTATGCTA 5 106 1 TCAGTTTAAA 0.915179 -195 AAAAATATATTCAAATATTGAACACATGAATT 8 57 0 TCAAATTGAA 0.537882 -244 CTGGAAGGAGTCATGGTATAAAATAAGAACAC 9 21 1 TCTGTATAAA 0.933696 -280 AAATTTGTTCTCAAGTAAAGAATCAAGGACTA 9 90 1 TCAGAAAGAA 0.901958 -211 AAGTAAAGAATCAAGGACTAAAAATTTCTATG 9 102 1 TCAGACTAAA 0.880223 -199 ATTCTTTATTCGTGTTAAGAATATTATTATA 9 280 0 TCTGTAAGAA 0.786158 -21 ** ** ****** Masking position 11 Map Score: 12.5978 Number of sites scoring better than the average of aligned sites = 242 Number in coding regions = 165 Number in noncoding regions = 77 Number of orfs with sites within 600 bp upstream = 48 Fraction of orfs with sites within 600 bp upstream = 0.0077096 Motif number 5 CACTGTATTCAGTCAAACCAATATATACTA 4 57 1 AGTCAAACCA 0.988225 -105 TTTGACTAATAGTCAAAGCTCCTTTATGAT 5 252 1 AGTCAAAGCT 0.925323 -49 TTGAACCCGTGGTCAAACCACGAGATGTAA 7 22 0 GGTCAAACCA 0.992356 -100 TGGCTTTCGTGGTCAAACCACGGGATGAGT 7 76 1 GGTCAAACCA 0.992356 -46 ********** Masking position 5 Map Score: 3.19606 Number of sites scoring better than the average of aligned sites = 6 Number in coding regions = 2 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 6 CCGTGGTCAAACCACGAGATGTAAAATGAG 7 16 0 ACCACGAGAT 0.986624 -106 TCGTGGTTTGACCACGGGTTCAAAATTATT 7 29 1 ACCACGGGTT 0.981102 -93 CCGTGGTTTGACCACGAAAGCCAAAAACAA 7 69 0 ACCACGAAAG 0.942742 -53 TCGTGGTCAAACCACGGGATGAGTTTCTAA 7 82 1 ACCACGGGAT 0.989733 -40 ********** Masking position 4 Map Score: 2.11023 Number of sites scoring better than the average of aligned sites = 8 Number in coding regions = 1 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 7 TTTGTATTGTTTACATAGTTCGAGAAATGA 1 28 1 TTACATAGTT 0.844244 -99 TTAGAACTTTTTATTATTTT 1 117 0 TTAGAACTTT 0.904527 -10 TGTAATCAAGTTATAAAGTTACGGCATGAC 3 52 0 TTATAAAGTT 0.666956 -41 TTTATTTAAATTAAATATTTTCATTTACTT 4 134 0 TTAAATATTT 0.690051 -28 GAACATATTAAATAGTTAATAGCTTAT 5 8 1 TTAAATAGTT 0.646833 -293 TAAGACCAGTTTAGATATTTAATGAAAAAA 5 69 1 TTAGATATTT 0.906835 -232 TTATATTAGATTAGAAACTCATCCCGTGGT 7 92 0 TTAGAAACTC 0.580766 -30 ATTTAACTTATTACAAATTCATGTGTTCAA 8 42 1 TTACAAATTC 0.800535 -259 TACAAAAATATTACAACTTTAGCATTAGAA 8 168 1 TTACAACTTT 0.865103 -133 AACTTTAGCATTAGAAAGTTCTTGATTGTG 8 182 1 TTAGAAAGTT 0.939169 -119 TTTTGCTATATTACCACTTTGTTATGTGCG 9 59 0 TTACCACTTT 0.502856 -242 CTAATCAATCATAGAAATTTTTAGTCCTTG 9 113 0 ATAGAAATTT 0.666351 -188 TCGCTTTGGTTTAGAGATTTAGCATTTGTA 9 216 0 TTAGAGATTT 0.814294 -85 ********** Masking position 3 Map Score: 3.98292 Number of sites scoring better than the average of aligned sites = 508 Number in coding regions = 326 Number in noncoding regions = 182 Number of orfs with sites within 600 bp upstream = 98 Fraction of orfs with sites within 600 bp upstream = 0.0157404 Motif number 8 GAATTTGGTATTATTTATTGCTTGATCGCA 1 56 1 TTATTTATTG 0.845875 -71 CTTGTCTCTTAAAATAAATTG 2 2 1 TTGTCTCTTA 0.931368 -55 TTTGCACAGCTTATTTATTATACTGTATCA 4 13 1 TTATTTATTA 0.937385 -149 GAAGATTTAATTATTTCTTAGCATAAATTT 5 126 0 TTATTTCTTA 0.959347 -175 AATTATGTATTTATCTCTTAGTCATTATCT 8 245 1 TTATCTCTTA 0.973755 -56 CTCTTAGTCATTATCTATTATATTAAACCA 8 259 1 TTATCTATTA 0.959195 -42 ********** Masking position 6 Map Score: 3.5509 Number of sites scoring better than the average of aligned sites = 66 Number in coding regions = 42 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 9 AATTTAAATAAAAAGGGAAA 4 152 1 AAAAGGGAAA 0.941248 -10 TCAGAATTTTAAAAGCGAAATAAACAAAAC 5 176 1 AAAAGCGAAA 0.977245 -125 CACAAGCAAAAATAACAAATA 8 2 1 ACAAGCAAAA 0.90898 -299 GTATTACTGAAAAAGAAAAATTGTTATTTT 8 121 1 AAAAGAAAAA 0.923791 -180 AGGTATATTTAAAAGAAAATAACAATTTTT 8 136 0 AAAAGAAAAT 0.749406 -165 ATCTCTAAACCAAAGCGAAACAACACATCT 9 228 1 CAAAGCGAAA 0.940131 -73 ********** Masking position 4 Map Score: 0.911997 Number of sites scoring better than the average of aligned sites = 95 Number in coding regions = 70 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 10 ********** No masking Map Score: -1.89472e-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 11 ********** No masking Map Score: -1.89472e-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: -1.89472e-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