AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_rpxx.txt -z/home/amcguire/genomes/rpxx.fna -inarP_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 RP265 102 ISOCITRATE DEHYDROGENASE (icd) #2 RP266 90 unknown #3 RP267 83 unknown #4 RP397 187 THIOL:DISULFIDE INTERCHANGE PROTEIN TLPA (tlpA) #5 RP588 101 CYTOCHROME C-TYPE BIOGENESIS PROTEIN CCME (ccmE) #6 RP702 300 unknown #7 RP794 300 HEME EXPORTER PROTEIN A (ccmA) #8 RP830 144 HEME EXPORTER PROTEIN C (ccmC) Motif number 1 GACTATGCAAAAAATAAACAATGGTAATTTAACATT 1 48 1 AAAAAAATTA 0.899936 -55 TTTTTTTATAATGTTATTAATGTAAC 2 75 0 TTTTAAATTA 0.819767 -16 TTGACGAAACAATCTTAAGATGTTTTA 3 2 1 TAAAAAATTA 0.892044 -82 CATATAGTTTTGACATGAGAATCATATAAAACATCT 3 28 0 TATGAAATTA 0.953216 -56 GTCAATTCCATATGATGACAATACTATCTCTTGCTG 4 71 1 TTTGAAATTA 0.901284 -117 ATAAATACTAATATGAAAAAATAATAAAATGCCTTC 4 144 1 AAAAAAATTA 0.899936 -44 AAAGGTAAATAAATATGATACTAATATACAA 5 6 0 AATGAACTTA 0.88703 -96 ACAATATCGCTAAGGTTAAAAAGGTAAATAAATATG 5 25 0 TATTAAAATA 0.854936 -77 TAAATTTTTTAAATTATAAAATATTAAAAAATAAAC 5 67 1 AAATAAATTA 0.919691 -35 GTATTATCAGATAAATGATAATTTTAGATGAGTCAA 6 61 1 AATGAAATTA 0.956831 -240 ATTTTAGATGAGTCAATATACTCTTATTAAAAGCAG 6 81 1 ATATAACTTA 0.645072 -220 AATTTCTTGTTATTTTAAAAATCGTATAGAAAGAAG 6 125 0 TTTAAAATTA 0.850559 -176 TAATGTTTTTTTAAAATATACTAATATGTATTGCAA 6 217 0 TAATAACTTA 0.788366 -84 TATAAATAATTATATTAATAATTATAGATTTTTCCT 6 252 0 TTTAAAATTA 0.822805 -49 AAAAAAGAATACAAAAATACTAAAGTACA 7 4 1 AAATAAAATA 0.806762 -297 CAATATGTATTAAAGTTAAACAACTAATAATAGGAA 7 38 1 TATTAACATA 0.676116 -263 TTTAATAGACACTCATGAGAAACTTAGGATTTGGTA 7 104 1 ATTGAAAATA 0.783757 -197 ATAATAAAATAGATAATACAAAATTAACTAGTGTTA 7 143 1 AAATAAAATA 0.806778 -158 TACCGTTGTATTACAATACAATGATATCTATTGGTT 7 217 0 TAATAAATTA 0.913204 -84 CATAAGAGTAACTGCTAATAATTTTATGAGATATCT 7 255 1 ATTAAAATTA 0.861027 -46 TATCACAGAATAACTTGAAAATACTAATATTAGTAT 8 17 1 TATGAAATTA 0.953213 -128 ATCATGTGATACAGCTAAAAATACTAATATTAGTAT 8 37 0 AATAAAATTA 0.93254 -108 TCGCGGGATTACAAGTGAAAAACCTATCTACACATG 8 78 1 AATGAAAATA 0.88995 -67 * * *** *** ** Masking position 15 Map Score: 26.2011 Number of sites scoring better than the average of aligned sites = 1338 Number in coding regions = 847 Number in noncoding regions = 491 Number of orfs with sites within 600 bp upstream = 223 Fraction of orfs with sites within 600 bp upstream = 0.0358175 Motif number 2 TTAATAACATTATAAAAAAA 2 81 1 TATAAAAAAA 0.922282 -10 ATGAGAATCATATAAAACATCTTAAGATTG 3 20 0 TATAAAACAT 0.871946 -64 GCAATGACGTTTTAAAATAAT 3 73 1 TTTAAAATAA 0.810697 -11 TTAGTTGTGGTATAAAAAAGCCTTTAGAAG 4 112 0 TATAAAAAAG 0.842432 -76 CACAACTAAATATAAATACTAATATGAAAA 4 133 1 TATAAATACT 0.73956 -55 CCTTCATTACTATAAATTATTAT 4 175 1 TATAAATTAT 0.943831 -13 TATTTTATAATTTAAAAAATTTACTATTAA 5 60 0 TTTAAAAAAT 0.914648 -42 TTTTTTAAATTATAAAATATTAAAAAATAA 5 71 1 TATAAAATAT 0.956765 -31 CTATACGATTTTTAAAATAACAAGAAATTC 6 132 1 TTTAAAATAA 0.810697 -169 CTAATGTTTTTTTAAAATATACTAATATGT 6 224 0 TTTAAAATAT 0.902449 -77 TAAATAATTATATTAATAATTATAGATTTT 6 256 0 TATTAATAAT 0.785081 -45 ATAAATTAACTATAAATAATTATATTAATA 6 268 0 TATAAATAAT 0.951139 -33 TTTGTTAGAATATAAATTAACTATAAATAA 6 279 0 TATAAATTAA 0.886092 -22 TAGGATTTGGTATTAATAATAAAATAGATA 7 128 1 TATTAATAAT 0.785081 -173 ********** Masking position 5 Map Score: 13.0202 Number of sites scoring better than the average of aligned sites = 918 Number in coding regions = 529 Number in noncoding regions = 389 Number of orfs with sites within 600 bp upstream = 193 Fraction of orfs with sites within 600 bp upstream = 0.030999 Motif number 3 GTTTACGAAAAGATGAGAGTATTTTAAT 1 85 1 AGAAGAGTAT 0.913949 -18 CATATAGTTTTGACATGAGAATCATATAAAAC 3 32 0 TGATGAGAAT 0.724919 -52 CTTGCATAATTGATCACGGTATCTAAGGATAC 4 15 1 TGAACGGTAT 0.946125 -173 TGGGACACACATATTACAGAATGTATCCTTAG 4 37 0 ATAACAGAAT 0.819859 -151 AGTACAATCATTAGTACAGTATTATCAGATAA 6 43 1 TTAACAGTAT 0.966317 -258 TAACTGCTTTTAATAAGAGTATATTGACTCAT 6 88 0 TAAAGAGTAT 0.804882 -213 AAATTCACAATGACCAGAGTATATACTGAATA 6 156 1 TGAAGAGTAT 0.96385 -145 GCTGTGGTACTTTATTCAGTATATACTCTGGT 6 168 0 TTTTCAGTAT 0.638523 -133 TTGTATTGTAATACAACGGTATCCATAAGAGT 7 232 1 ATAACGGTAT 0.814073 -69 TATCTTGGAGTGTACACAGTATTAC 7 286 1 TGTACAGTAT 0.919049 -15 GCATTTTATCACAGAATAACTTGAAAA 8 6 1 TTAACAGAAT 0.919541 -139 *** ******* Masking position 11 Map Score: 6.32654 Number of sites scoring better than the average of aligned sites = 153 Number in coding regions = 84 Number in noncoding regions = 69 Number of orfs with sites within 600 bp upstream = 45 Fraction of orfs with sites within 600 bp upstream = 0.00722775 Motif number 4 CTTTTCGTAAACCAATGTTAAATTACCATTGT 1 65 0 ACCAAGTAAA 0.807026 -38 TTATAATGTTATTAATGTAACAGTTATCTCAA 2 64 0 ATTAAGTACA 0.848467 -27 TTTATATGATTCTCATGTCAAAACTATATGTT 3 34 1 TCTCAGTAAA 0.851956 -50 GATCACGGTATCTAAGGATACATTCTGTAATA 4 26 1 TCTAAGAACA 0.698202 -162 TTATACCACAACTAAATATAAATACTAATATG 4 127 1 ACTAATAAAA 0.586924 -61 AAATATAAATACTAATATGAAAAAATAATAAA 4 140 1 ACTAAATAAA 0.897866 -48 TAAATATGATACTAATATACAA 5 1 0 ACTAAATCAA 0.807876 -101 TAACAATATCGCTAAGGTTAAAAAGGTAAATA 5 31 0 GCTAAGTAAA 0.844596 -71 GCTTAGCAGAAATCAAGTACAATCATTAGTAC 6 28 1 AATCAGTCAA 0.606726 -273 GAGTATATTGACTCATCTAAAATTATCATTTA 6 72 0 ACTCACTAAA 0.654486 -229 CTATACGATTTTTAAAATAACAAGAAATTCAC 6 132 1 TTTAAATACA 0.299587 -169 GTATATACTGAATAAAGTACCACAGCTTTTAT 6 174 1 AATAAGTCCA 0.672617 -127 ATACAAAAATACTAAAGTACAATATGTATTAA 7 19 1 ACTAAGTCAA 0.946844 -282 TACAATATGTATTAAAGTTAAACAACTAATAA 7 36 1 ATTAAGTAAA 0.892567 -265 TTTAATAGACACTCATGAGAAACTTAGGATTT 7 104 1 ACTCAGAAAA 0.842887 -197 AGGATTTGGTATTAATAATAAAATAGATAATA 7 129 1 ATTAAAAAAA 0.384856 -172 ATTATGTTCATCTAATGTAACACTAGTTAATT 7 164 0 TCTAAGTACA 0.884789 -137 TTTATCACAGAATAACTTGAAAATACTAATAT 8 15 1 AATAATTAAA 0.46075 -130 ***** ** *** Masking position 5 Map Score: 7.5089 Number of sites scoring better than the average of aligned sites = 514 Number in coding regions = 355 Number in noncoding regions = 159 Number of orfs with sites within 600 bp upstream = 88 Fraction of orfs with sites within 600 bp upstream = 0.0141343 Motif number 5 TTATTTTTTGCATAGTCTACTTATACAATCAACT 1 31 0 CATAGTTTTT 0.732125 -72 GTTAAATTACCATTGTTTATTTTTTGCATAGTCT 1 47 0 CATTGTTTTT 0.96524 -56 TTTTTTTATAATGTTATTAATGTAACA 2 74 0 TTTTATATTT 0.625329 -17 TCTTAAGATGTTTTATATGATTCTCATGTCAAAA 3 23 1 TTTTATTTTT 0.687305 -61 CAAGAGATAGTATTGTCATCATATGGAATTGACA 4 70 0 TATTGTAATT 0.806292 -118 GTAATGAAGGCATTTTATTATTTTTTCATATTAG 4 151 0 CATTTTTTTT 0.810537 -37 TAAAGTTTTGTTTATTTTTTAATATTTTA 5 83 0 TTTTGTTTTT 0.908733 -19 ATACTCTGGTCATTGTGAATTTCTTGTTATTTTA 6 144 0 CATTGTATTT 0.954722 -157 TCTTTGTTAGAATATAAATTAACTA 6 286 0 CTTTGTAATT 0.870015 -15 ACTTTAGTATTTTTGTATTCTTTTTT 7 3 0 TTTTGTTTTT 0.908733 -298 GTTTAATTTTCATTATGTTCATCTAATGTAACAC 7 173 0 CATTATTATT 0.719307 -128 CAATAGATATCATTGTATTGTAATACAACGGTAT 7 220 1 CATTGTTTAT 0.732125 -81 CTAATATTAGTATTTTCAAGTTATTCTGTGATAA 8 16 0 TATTTTATTT 0.60536 -129 CATGCGAGAGCTTTGTAAAAATGTCTTCAAAGAA 8 110 1 CTTTGTAATT 0.870015 -35 ****** * ** * Masking position 6 Map Score: 8.49951 Number of sites scoring better than the average of aligned sites = 344 Number in coding regions = 218 Number in noncoding regions = 126 Number of orfs with sites within 600 bp upstream = 72 Fraction of orfs with sites within 600 bp upstream = 0.0115644 Motif number 6 AATTTAAAAAATTTACTATTAACAATATCG 5 52 0 ATTTACTATT 0.732782 -50 CTTTTATAGGATTACGTATTGCAATACATA 6 199 1 ATTACGTATT 0.807674 -102 AAAATATACTAATATGTATTGCAATACGTA 6 211 0 AATATGTATT 0.757757 -90 TACTTTAGTATTTTTGTATTCTTTTTT 7 8 0 TTTTTGTATT 0.820522 -293 ACTAAAGTACAATATGTATTAAAGTTAAAC 7 29 1 AATATGTATT 0.757757 -272 TATCAAATACATTTCCTATTATTAGTTGTT 7 56 0 ATTTCCTATT 0.878922 -245 GAAACTTAGGATTTGGTATTAATAATAAAA 7 122 1 ATTTGGTATT 0.917778 -179 ACACTAGTTAATTTTGTATTATCTATTTTA 7 147 0 ATTTTGTATT 0.962083 -154 ********** Masking position 8 Map Score: 3.60225 Number of sites scoring better than the average of aligned sites = 216 Number in coding regions = 133 Number in noncoding regions = 83 Number of orfs with sites within 600 bp upstream = 57 Fraction of orfs with sites within 600 bp upstream = 0.00915516 Motif number 7 ********** No masking Map Score: 2.93697e-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 8 ********** No masking Map Score: 2.93697e-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: 2.93697e-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