AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_rpxx.txt -z/home/amcguire/genomes/rpxx.fna -inarL_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 RP128 133 SUCCINATE DEHYDROGENASE FLAVOPROTEIN SUBUNIT (sdhA) #2 RP265 102 ISOCITRATE DEHYDROGENASE (icd) #3 RP266 90 unknown #4 RP267 83 unknown #5 RP397 187 THIOL:DISULFIDE INTERCHANGE PROTEIN TLPA (tlpA) #6 RP588 101 CYTOCHROME C-TYPE BIOGENESIS PROTEIN CCME (ccmE) #7 RP702 300 unknown #8 RP794 300 HEME EXPORTER PROTEIN A (ccmA) #9 RP830 144 HEME EXPORTER PROTEIN C (ccmC) Motif number 1 GCAGTTCTGGAATATTGAAAAACAATTAATAGCATTATT 1 26 1 ATAAAAATAA 0.918339 -108 GTTAACACTTAACTTAAGCACATTATTAAGTAATTCAAT 1 69 0 ATACATATAA 0.89625 -65 GATATACCGTATCAAAAGTAAAAAATTAATTGA 1 111 1 AAAAAAATAA 0.950897 -23 TTTTTTGCATAGTCTACTTATACAATCAACTTGGTAACA 2 23 0 ATATAAACAA 0.399973 -80 CTTTTCGTAAACCAATGTTAAATTACCATTGTTTATTTT 2 58 0 AAAAATACAT 0.77847 -45 GTAGTTTGAGATAACTGTTACATTAATAACATTATAAAA 3 59 1 ACACATATAA 0.668442 -32 GTTTTATATGATTCTCATGTCAAAACTATATGTTTCTTA 4 32 1 ATTCAAATAT 0.598309 -52 TTTATACCACAACTAAATATAAATACTAATATGAAAAAA 5 126 1 AATAATATAA 0.859405 -62 AAAAAATAATAAAATGCCTTCATTACTATAAATTATTAT 5 159 1 ATTCATATAT 0.619734 -29 AAAAAGGTAAATAAATATGATACTAATATACAA 6 5 0 AAATATATAT 0.745827 -97 TTTTTAAATTATAAAATATTAAAAAATAAACAAAACTTT 6 72 1 AATAAAATAA 0.848837 -30 ATCAAGTACAATCATTAGTACAGTATTATCAGATAAATG 7 39 1 ATACATATAT 0.848582 -262 GAGTATATTGACTCATCTAAAATTATCATTTATCTGATA 7 65 0 AAAAATACAT 0.778473 -236 TATTTTAAAAATCGTATAGAAAGAAGTATATTAACTGCT 7 112 0 ATAAAAATAT 0.879465 -189 AAACATTAGGAAAAATCTATAATTATTAATATAATTATT 7 245 1 AATAATATAA 0.859401 -56 TAGAATATAAATTAACTATAAATAATTATATTAATAATT 7 265 0 AAAAAAATAT 0.926465 -36 AAAAAAGAATACAAAAATACTAAAGTACAATAT 8 5 1 AAAAATATAA 0.954705 -296 TACAATATGTATTAAAGTTAAACAACTAATAATAGGAAA 8 36 1 AAAAAAATAA 0.950891 -265 TAATAATAAAATAGATAATACAAAATTAACTAGTGTTAC 8 141 1 AAACAAATAA 0.931817 -160 GTACACTCCAAGATATCTCATAAAATTATTAGCAGTTAC 8 262 0 AAATAAATAT 0.744516 -39 TTTATCACAGAATAACTTGAAAATACTAATATTAGTATT 9 15 1 AAAAATATAA 0.954705 -130 TGATCATGTGATACAGCTAAAAATACTAATATTAGTATT 9 36 0 AAAAATATAA 0.954703 -109 GCTTTGTAAAAATGTCTTCAAAGAAGTAATAAAAAT 9 119 1 ATAAAAATAA 0.918339 -26 * * *** ** *** Masking position 12 Map Score: 23.9244 Number of sites scoring better than the average of aligned sites = 1312 Number in coding regions = 832 Number in noncoding regions = 480 Number of orfs with sites within 600 bp upstream = 213 Fraction of orfs with sites within 600 bp upstream = 0.0342114 Motif number 2 ATAATGCTATTAATTGTTTTTCAATATTCCAGAA 1 30 0 TAATGTTTAA 0.70931 -104 ACGAAAAGATGAGAGTATTTTAAT 2 89 1 GAGATTTTAT 0.715017 -14 GTAGATTATTATCAAAGCGTGACTC 3 2 1 TAGATTTTAA 0.866167 -89 TTTTTTTATAATGTTATTAATGTAACAGTT 3 71 0 TATATTTTAA 0.943022 -20 TAAGATGTTTTATATGATTCTCATGTCAAAACTA 4 26 1 TATAGTTTAT 0.917496 -58 ATGTCAAAACTATATGTTTCTTATCGCAATGACG 4 48 1 TATAGTTTAT 0.917496 -36 CGCAGCAAGAGATAGTATTGTCATCATATGGAAT 5 75 0 GATATTTTAT 0.86516 -113 GAAGGCATTTTATTATTTTTTCATATTAGTATTT 5 146 0 TATTTTTTAT 0.943023 -42 TTGTATATTAGTATCATATTTATTTAC 6 4 1 TATATGTTAT 0.669054 -98 GTTTATTTTTTAATATTTTATAATTTAAAAAATT 6 69 0 TAATTTTTAT 0.842753 -33 GATGAGTCAATATACTCTTATTAAAAGCAGTTAA 7 87 1 TATATTTTAA 0.943022 -214 TACTTCTTTCTATACGATTTTTAAAATAACAAGA 7 123 1 TATAGTTTAA 0.901518 -178 TGGTCATTGTGAATTTCTTGTTATTTTAAAAATC 7 138 0 GAATTTTTAT 0.631032 -163 TTATTCAGTATATACTCTGGTCATTGTGAATTTC 7 155 0 TATATTGTAT 0.893928 -146 CAATACATATTAGTATATTTTAAAAAAACATTAG 7 220 1 TAGTTTTTAA 0.841961 -81 CATTTCCTATTATTAGTTGTTTAACTTTAATACA 8 43 0 TATTGTGTAA 0.759526 -258 GAGTGTCTATTAAAGTTTGATTATGCAGGACTTA 8 84 0 TAAATTGTAT 0.73183 -217 TTGTATTATCTATTTTATTATTAATACCAAATCC 8 130 0 TATTTTTTAA 0.931619 -171 CAATAGATATCATTGTATTGTAATACAACGGTAT 8 220 1 CATTTTTTAT 0.663327 -81 ATTTTCAAGTTATTCTGTGATAAAATGC 9 5 0 TATTTTGTAA 0.85098 -140 **** * ** * ** Masking position 11 Map Score: 17.7454 Number of sites scoring better than the average of aligned sites = 1096 Number in coding regions = 674 Number in noncoding regions = 422 Number of orfs with sites within 600 bp upstream = 197 Fraction of orfs with sites within 600 bp upstream = 0.0316415 Motif number 3 TAATAGCATTATTGTGTATTGAATTACTTAA 1 52 1 ATTGTTATTG 0.769444 -82 TATTTTTTGCATAGTCTACTTATACAATCAA 2 33 0 ATAGTTACTT 0.755298 -70 TTAAATTACCATTGTTTATTTTTTGCATAGT 2 49 0 ATTGTTATTT 0.954873 -54 TGTGTGTCCCATTGTCAATTCCATATGATGA 5 58 1 ATTGTAATTC 0.717045 -130 GATATTGTTAATAGTAAATTTTTTAAATTAT 6 53 1 ATAGTAATTT 0.941404 -49 TAAAGTTTTGTTTATTTTTTAATATTT 6 85 0 TTTGTTATTT 0.916488 -17 TTGTGAATTTCTTGTTATTTTAAAAATCGTA 7 135 0 CTTGTATTTT 0.669077 -166 TACTCTGGTCATTGTGAATTTCTTGTTATTT 7 146 0 ATTGTAATTT 0.941407 -155 GCAATACATATTAGTATATTTTAAAAAAACA 7 219 1 TTAGTTATTT 0.916488 -82 ATAATTATTTATAGTTAATTTATATTCTAAC 7 275 1 ATAGTAATTT 0.941404 -26 ATATTGTACTTTAGTATTTTTGTATTCTTTT 8 13 0 TTAGTTTTTT 0.762571 -288 TTAATTTTGTATTATCTATTTTATTATTAAT 8 139 0 ATTATTATTT 0.562941 -162 TAATGTAACACTAGTTAATTTTGTATTATCT 8 153 0 CTAGTAATTT 0.873553 -148 AATACTAATATTAGTATTTTTAGCTGTATCA 9 36 1 TTAGTTTTTT 0.762571 -109 ***** ***** Masking position 5 Map Score: 12.6036 Number of sites scoring better than the average of aligned sites = 464 Number in coding regions = 308 Number in noncoding regions = 156 Number of orfs with sites within 600 bp upstream = 91 Fraction of orfs with sites within 600 bp upstream = 0.0146161 Motif number 4 CAGAACTGCTGGATAACAATTGTG 1 3 0 GGATAAATTG 0.846515 -131 TACACAATAATGCTATTAATTGTTTTTCAATA 1 38 0 TGCTATATTG 0.968017 -96 ATGATGACAATACTATCTCTTGCTGCGGTGCT 5 82 1 TACTATCTTG 0.8177 -106 ATGCCTTCATTACTATAAATTATTAT 5 172 1 TACTATATTA 0.799738 -16 ACTTGATTTCTGCTAAGCATTGGTTTTGAAAG 7 14 0 TGCTAAATTG 0.962222 -287 GATAATACTGTACTAATGATTGTACTTGATTT 7 37 0 TACTAAATTG 0.956461 -264 TAAAATATACTAATATGTATTGCAATACGTAA 7 210 0 TAATATATTG 0.921358 -91 ATAATTATATTAATAATTATAGATTTTTCCTA 7 251 0 TAATAAATAG 0.612433 -50 TCTTTGTTAGAATATAAATTAACTATAAATA 7 280 0 GAATATATTA 0.461852 -21 TGTTTAACTTTAATACATATTGTACTTTAGTA 8 28 0 TAATACATTG 0.779901 -273 TACAATACAATGATATCTATTGGTTTTCACAA 8 210 0 TGATATATTG 0.949679 -91 TAAGAGTAACTGCTAATAATTTTATGAGATAT 8 257 1 TGCTAAATTT 0.689952 -44 ****** **** Masking position 5 Map Score: 6.38657 Number of sites scoring better than the average of aligned sites = 224 Number in coding regions = 158 Number in noncoding regions = 66 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 5 ATACCGTATCAAAAGTAAAAAATTAATTGA 1 114 1 AAATAAAAAA 0.88494 -20 AGACTATGCAAAAAATAAACAATGGTAATTTA 2 47 1 AAATAAACAA 0.727188 -56 TTACATTAATAACATTATAAAAAAA 3 76 1 AAATATAAAA 0.950761 -15 TTGACATGAGAATCATATAAAACATCTTAAGA 4 23 0 AACTATAAAA 0.906956 -61 CTAATATGAAAAAATAATAAAATGCCTTCATT 5 151 1 AAAAATAAAA 0.899386 -37 TAAATTATAAAATATTAAAAAATAAACAAAAC 6 76 1 AAATAAAAAA 0.88494 -26 TTATTTTAAAAATCGTATAGAAAGAAGTATAT 7 120 0 AACTATAGAA 0.647352 -181 TGCAATACGTAATCCTATAAAAGCTGTGGTAC 7 190 0 AACTATAAAA 0.906957 -111 ATTTTAAAAAAACATTAGGAAAAATCTATAAT 7 236 1 AAATAGGAAA 0.859087 -65 AAAAAAGAATACAAAAATACTAAA 8 3 1 AAAAATACAA 0.755979 -298 TTAAACAACTAATAATAGGAAATGTATTTGAT 8 53 1 AAATAGGAAA 0.859087 -248 ACATTAGATGAACATAATGAAAATTAAACTTA 8 178 1 AAAAATGAAA 0.867793 -123 GTTGTATTACAATACAATGATATCTATTGGTT 8 217 0 AAAAATGATA 0.41125 -84 ** * ******* Masking position 7 Map Score: 8.56051 Number of sites scoring better than the average of aligned sites = 698 Number in coding regions = 445 Number in noncoding regions = 253 Number of orfs with sites within 600 bp upstream = 152 Fraction of orfs with sites within 600 bp upstream = 0.0244137 Motif number 6 AAACAATCTTAAGATGTTTTATATGATTCT 4 17 1 AAGATGTTTT 0.841914 -67 TCTTATCGCAATGACGTTTTAAAATAAT 4 66 1 ATGACGTTTT 0.92065 -18 GGTGCTTCTAAAGGCTTTTTTATACCACAA 5 108 1 AAGGCTTTTT 0.941408 -80 TATAGTAATGAAGGCATTTTATTATTTTTT 5 159 0 AAGGCATTTT 0.965098 -29 TACTTCTTTGAAGACATTTTTACAAAGCTC 9 117 0 AAGACATTTT 0.947883 -28 ********** Masking position 7 Map Score: 0.643649 Number of sites scoring better than the average of aligned sites = 47 Number in coding regions = 31 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 7 GGTAATTTAACATTGGTTTACGAAAAGATG 2 70 1 CATTGGTTTA 0.926039 -33 TTCTGCTAAGCATTGGTTTTGAAAGTAC 7 9 0 CATTGGTTTT 0.958951 -292 CCACAGCTTTTATAGGATTACGTATTGCAA 7 193 1 TATAGGATTA 0.741006 -108 TATTAATAATTATAGATTTTTCCTAATGTT 7 246 0 TATAGATTTT 0.77 -55 CAATGATATCTATTGGTTTTCACAATAAGT 8 205 0 TATTGGTTTT 0.955831 -96 CGCATGTGTAGATAGGTTTTTCACTTGTAA 9 86 0 GATAGGTTTT 0.926975 -59 ********** Masking position 3 Map Score: 0.54416 Number of sites scoring better than the average of aligned sites = 96 Number in coding regions = 71 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 8 GTAGATTATTATCAAAGCGTGA 3 3 1 AGATTATTAT 0.641564 -88 CATATAAAACATCTTAAGATTGTTTCGTCA 4 12 0 ATCTTAAGAT 0.429966 -72 TGATCACGGTATCTAAGGATACATTCTGTA 5 25 1 ATCTAAGGAT 0.752651 -163 TTTATACCACAACTAAATATAAATACTAAT 5 126 1 AACTAAATAT 0.536884 -62 TTATTTTTTCATATTAGTATTTATATTTAG 5 138 0 ATATTAGTAT 0.860775 -50 TAATGAAGGCATTTTATTATTTTTTCATAT 5 154 0 ATTTTATTAT 0.679903 -34 TCATTACTATAAATTATTAT 5 178 1 AAATTATTAT 0.82934 -10 TTGTATATTAGTATCATATTTATT 6 5 1 ATATTAGTAT 0.860775 -97 TTAAAAAGGTAAATAAATATGATACTAATA 6 16 0 AAATAAATAT 0.611351 -86 AATCGTATAGAAAGAAGTATATTAACTGCT 7 112 0 AAAGAAGTAT 0.432044 -189 ATTGCAATACATATTAGTATATTTTAAAAA 7 216 1 ATATTAGTAT 0.860775 -85 ATAATTATTAATATAATTATTTATAGTTAA 7 263 1 ATATAATTAT 0.814579 -38 ACTCATGAGAAACTTAGGATTTGGTATTAA 8 114 1 AACTTAGGAT 0.771109 -187 TGTATTATCTATTTTATTATTAATACCAAA 8 133 0 ATTTTATTAT 0.679903 -168 GAAAATACTAATATTAGTATTTTTAGCTGT 9 33 1 ATATTAGTAT 0.860775 -112 ********** Masking position 6 Map Score: 10.7828 Number of sites scoring better than the average of aligned sites = 633 Number in coding regions = 369 Number in noncoding regions = 264 Number of orfs with sites within 600 bp upstream = 147 Fraction of orfs with sites within 600 bp upstream = 0.0236107 Motif number 9 ********** No masking Map Score: -1.93024e-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: -1.93024e-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: -1.93024e-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