AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_rpxx.txt -z/home/amcguire/genomes/rpxx.fna -inarP_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 RP264 300 unknown #2 RP265 102 ISOCITRATE DEHYDROGENASE (icd) #3 RP266 90 unknown #4 RP267 83 unknown #5 RP396 140 unknown #6 RP397 187 THIOL:DISULFIDE INTERCHANGE PROTEIN TLPA (tlpA) #7 RP585 300 unknown #8 RP587 147 SCO2 PROTEIN PRECURSOR (sco2) #9 RP588 101 CYTOCHROME C-TYPE BIOGENESIS PROTEIN CCME (ccmE) #10 RP702 300 unknown #11 RP794 300 HEME EXPORTER PROTEIN A (ccmA) #12 RP830 144 HEME EXPORTER PROTEIN C (ccmC) #13 RP831 25 unknown #14 RP832 121 PROTEIN P34 (p34) Motif number 1 AAAAGCATTTTTAATTATTTTTTGGATTGCT 1 206 0 TTAATATTTT 0.779475 -95 TAATCAAATTATTTTTATTCTCATTTGATTA 5 64 0 ATTTTATTCT 0.783983 -77 TAAATCAATTATTTTTATTAATCAAATTATT 5 82 0 ATTTTATTAA 0.858777 -59 ATTTTTTCATATTAGTATTTATATTTAGTTG 6 135 0 ATTATATTTA 0.935628 -53 ATGAAGGCATTTTATTATTTTTTCATATTAG 6 151 0 TTTATATTTT 0.911331 -37 TATTTAGCATATAAATATTTAAATGTTTAAT 7 55 0 ATAATATTTA 0.833578 -246 TTAGGTAGCTATTTTTATTTTATTAGACTTC 7 128 1 ATTTTATTTT 0.935628 -173 GTCGATAATGATTTTTATTATATTATTGTGT 8 17 1 ATTTTATTAT 0.894066 -131 AATTCATTTCATTATTATTTTGTGGCTTGAG 8 120 0 ATTATATTTT 0.952764 -28 TATTAGTATCATATTTATTTACCTTTTTAAC 9 16 1 ATATTATTTA 0.783022 -86 ATTTAAAAAATTTACTATTAACAATATCGCT 9 50 0 TTTATATTAA 0.811335 -52 TTGTTTATTTTTTAATATTTTATAATTTAAA 9 74 0 TTTATATTTT 0.911337 -28 GGAAAAATCTATAATTATTAATATAATTATT 10 253 1 ATAATATTAA 0.725775 -48 AATTATTAATATAATTATTTATAGTTAATTT 10 265 1 ATAATATTTA 0.833303 -36 TTTATAGTTAATTTATATTCTAACAAAGA 10 282 1 ATTTTATTCT 0.783983 -19 CATATTGTACTTTAGTATTTTTGTATTCTTT 11 14 0 TTTATATTTT 0.911337 -287 CTAAAGTACAATATGTATTAAAGTTAAACAA 11 30 1 ATATTATTAA 0.676968 -271 TATTATCTATTTTATTATTAATACCAAATCC 11 130 0 TTTATATTAA 0.811142 -171 CACTAGTTAATTTTGTATTATCTATTTTATT 11 145 0 TTTTTATTAT 0.811337 -156 AAATACTAATATTAGTATTTTCAAGTTATTC 12 24 0 ATTATATTTT 0.952772 -121 AAATACTAATATTAGTATTTTTAGCTGTATC 12 35 1 ATTATATTTT 0.952772 -110 ATCCTCTCTAATTATTATTTAAATAAGTATA 14 14 1 ATTATATTTA 0.935624 -108 ACTCATTGAATTTTATATTTTCTTTGTTAAA 14 73 1 TTTTTATTTT 0.88103 -49 AATCTTCTAAATTTATATTATAAGTTTAACA 14 97 0 ATTTTATTAT 0.894073 -25 **** ****** Masking position 6 Map Score: 32.5872 Number of sites scoring better than the average of aligned sites = 883 Number in coding regions = 525 Number in noncoding regions = 358 Number of orfs with sites within 600 bp upstream = 183 Fraction of orfs with sites within 600 bp upstream = 0.0293929 Motif number 2 TAAGCAATCTTTTTAAAAAGCATTTTTAATTATTT 1 217 0 TTTTAAAATT 0.970891 -84 TTTTTTTATAATGTTATTAATGTAACA 3 74 0 TTTTTAAATT 0.970891 -17 TTTTTATAACTATCTTTATAGAGTT 5 126 0 TTTTTAAATT 0.970891 -15 TGTGCTGGGTTTTTTACAAATTTACCATTATTAGC 7 171 0 TTTTTAAATC 0.829508 -130 TCGATAATGATTTTTATTATATTATTGTGTACCGT 8 18 1 TTTTTATATT 0.862226 -130 TATTTTATAATTTAAAAAATTTACTATTAACAATA 9 55 0 TTTAAAAAAT 0.54012 -47 TTTTGTTTATTTTTTAATATTTTATAATTTAAAAA 9 72 0 TTTTTATATT 0.862236 -30 TATTAACTGCTTTTAATAAGAGTATATTGACTCAT 10 88 0 TTTTAAAATT 0.970891 -213 TTTCTTGTTATTTTAAAAATCGTATAGAAAGAAGT 10 124 0 TTTTAAAATT 0.970891 -177 TATTAGTATATTTTAAAAAAACATTAGGAAAAATC 10 227 1 TTTTAAAAAT 0.862237 -74 TTTGAAGACATTTTTACAAAGCTCTCGCATGTGTA 12 106 0 TTTTTAAATT 0.970891 -39 AAAAACTTATTTTAATAATTTTTTC 13 10 1 TTTTAAAATT 0.970891 -16 CTAATTATTATTTAAATAAGTATATGGTTTTTAGA 14 21 1 TTTAAAAATT 0.862236 -101 AAGTATATGGTTTTTAGAATTTTGTAAAGTATAAA 14 38 1 TTTTTAAATT 0.970891 -84 ****** ** * * Masking position 9 Map Score: 19.8992 Number of sites scoring better than the average of aligned sites = 275 Number in coding regions = 162 Number in noncoding regions = 113 Number of orfs with sites within 600 bp upstream = 74 Fraction of orfs with sites within 600 bp upstream = 0.0118856 Motif number 3 AAATTGAATGCTGTGCAAATAATTAACAATATATAATAA 1 11 0 CTTTATAACA 0.747782 -290 ACATTAAGTAATTTGTCTATAATTAAAAACTGCACCTTT 1 114 0 ATTTATAAAA 0.95458 -187 TTACAATGACATCTCTTATTAATCTAAGATAAATAACAT 1 149 0 ATTTATTAAA 0.967365 -152 AACAATGGTAATTTAACATTGGTTTACGAAAAGATGAGA 2 64 1 ATTTGTTACA 0.866961 -39 TAGTATTTATATTTAGTTGTGGTATAAAAAAGCCTTTAG 6 115 0 ATTTGTTAAA 0.915118 -73 TCATTATTCACTTTATATCTAATTAAACATTTAAATATT 7 34 1 CTTTATAAAA 0.830651 -267 AAACATTTAAATATTTATATGCTAAATAATATCTTGAAG 7 58 1 ATTTGTAATA 0.609564 -243 AGGTAAATAAATATGATACTAATATACAA 9 1 0 ATTTATTACA 0.947137 -101 AGTTTTGTTTATTTTTTAATATTTTATAATTTAAAAAAT 9 70 0 ATTTATTATA 0.858239 -32 ATTATCATTTATCTGATAATACTGTACTAATGATTGTAC 10 44 0 ATTTATTACA 0.947137 -257 AGATGAGTCAATATACTCTTATTAAAAGCAGTTAATATA 10 86 1 ATTTATAAAC 0.714437 -215 GTCATTGTGAATTTCTTGTTATTTTAAAAATCGTATAGA 10 131 0 ATTTATTAAA 0.967365 -170 ATTGCAATACATATTAGTATATTTTAAAAAAACATTAGG 10 216 1 ATTTATTAAA 0.967365 -85 ATTAGGAAAAATCTATAATTATTAATATAATTATTTATA 10 249 1 ATTTATATAA 0.76025 -52 GAAACTTAGGATTTGGTATTAATAATAAAATAGATAATA 11 122 1 ATTTATATAA 0.76025 -179 AATTTTCATTATGTTCATCTAATGTAACACTAGTTAATT 11 164 0 ATTTATTAAA 0.967364 -137 AAACCAATAGATATCATTGTATTGTAATACAACGGTATC 11 216 1 ATTTATTAAA 0.967365 -85 ** * ** * *** * Masking position 10 Map Score: 17.3169 Number of sites scoring better than the average of aligned sites = 189 Number in coding regions = 88 Number in noncoding regions = 101 Number of orfs with sites within 600 bp upstream = 59 Fraction of orfs with sites within 600 bp upstream = 0.00947639 Motif number 4 AAGTAATTTGTCTATAATTAAAAACTGCACCTTT 1 114 0 TTATATAAAA 0.84008 -187 CTCTTATTAATCTAAGATAAATAACATTAAGTAA 1 142 0 TTAAGTAAAA 0.957655 -159 ACATACACTGTTTAAGCTCTATAAGGATCAAAG 1 278 1 TTAAGTTAAA 0.912776 -23 TTTAATTAGATATAAAGTGAATAATGAAAGTGAA 7 27 0 TTAAATAAAA 0.942427 -274 TTTAAATATTTATATGCTAAATAATATCTTGAAG 7 63 1 TTATGTAAAA 0.878945 -238 TAACAATATCGCTAAGGTTAAAAAGGTAAATAAA 9 29 0 GTAAGTAAAA 0.877225 -73 TAGTAAATTTTTTAAATTATAAAATATTAAAAAA 9 64 1 TTAAATTAAA 0.883419 -38 TATAAAATATTAAAAAATAAACAAAACTTTA 9 81 1 TAAAATAAAA 0.840136 -21 ATGACCAGAGTATATACTGAATAAAGTACCACAG 10 165 1 TTATATAAAA 0.840136 -136 AAAAACATTAGGAAAAATCTATAATTATTAATAT 10 243 1 GAAAATTAAA 0.434589 -58 ACAATATGTATTAAAGTTAAACAACTAATAATAG 11 37 1 TAAAGTAAAA 0.878945 -264 TTTAGAATTTTGTAAAGTATAAAACTCATTGAAT 14 50 1 TTAAATTAAA 0.883423 -72 AAATTTATATTATAAGTTTAACAAAGAAAATATA 14 86 0 TTAAGTAAAA 0.957655 -36 * **** * ** ** Masking position 4 Map Score: 11.1072 Number of sites scoring better than the average of aligned sites = 175 Number in coding regions = 115 Number in noncoding regions = 60 Number of orfs with sites within 600 bp upstream = 52 Fraction of orfs with sites within 600 bp upstream = 0.00835207 Motif number 5 TCTTAGATTAATAAGAGATGTCATTGTAAGGAGGA 1 159 1 ATAAATTATT 0.932938 -142 TATGCAAAAAATAAACAATGGTAATTTAACATTGG 2 51 1 ATAAATGAAT 0.886754 -52 TGAGAATCATATAAAACATCTTAAGATTGTTTCGT 4 14 0 ATAAATTAAG 0.812664 -70 TCATTTGATTATTAATGAATTGATTGTTATAGTAA 5 40 0 ATTAAATATT 0.651159 -101 AAATGAGAATAAAAATAATTTGATTAATAAAAATA 5 69 1 AAAAATTATT 0.819135 -72 ATTAATAAAAATAATTGATTTAAATTTAGATTTAG 5 91 1 ATAAATTAAT 0.938503 -50 ATAATAATTTATAGTAATGAAGGCATTT 6 170 0 ATAAATGAAT 0.887925 -18 TATAAAGTGAATAATGAAAGTGAATAATGTCACTA 7 16 0 ATAAAATAAT 0.832452 -285 TTTATATCTAATTAAACATTTAAATATTTATATGC 7 45 1 ATTAATTAAT 0.862798 -256 ATTTACCATTATTAGCTATCTTATGCAAGAAGTCT 7 152 0 ATTAATTATG 0.619744 -149 ACACAATAATATAATAAAAATCATTATCGACAACT 8 13 0 ATAAAATATT 0.819139 -135 CACCTAACCTATAGCTCATTGAAATTACGATATTA 8 76 1 ATAGATGAAT 0.430989 -72 TACGATATTAATAAGTTATCTCAAGCCACAAAATA 8 101 1 ATAAATTAAG 0.812664 -47 AAGATATAATTCATTTCATTATTATTTTGT 8 128 0 ATAAATTATT 0.932938 -20 GCTAAGGTTAAAAAGGTAAATAAATATGATACTAA 9 18 0 AAAAAATAAT 0.617965 -84 CTTTTATAGGATTACGTATTGCAATACATATTAGT 10 199 1 ATTAATGAAT 0.764435 -102 AAAATCTATAATTATTAATATAATTATTTATAGTT 10 256 1 ATTAATTATT 0.851484 -45 TTAATTTTGTATTATCTATTTTATTATTAATACCA 11 135 0 ATTAATTATT 0.851335 -166 GAACATAATGAAAATTAAACTTATTGTGAAAACCA 11 187 1 AAAAAATATT 0.59588 -114 AAAAACTTATTTTAATAATTTTTTC 13 2 1 AAAAATTAAT 0.832281 -24 TGTAAAGTATAAAACTCATTGAATTTTATATTTTC 14 60 1 AAAAATGATT 0.701622 -62 **** ** * *** Masking position 8 Map Score: 20.0188 Number of sites scoring better than the average of aligned sites = 743 Number in coding regions = 477 Number in noncoding regions = 266 Number of orfs with sites within 600 bp upstream = 125 Fraction of orfs with sites within 600 bp upstream = 0.0200771 Motif number 6 TTATTATATATTGTTAATTATTTGC 1 6 1 ATATATTGTT 0.759061 -295 ACCTCATATAACATAGTGTTAATCTTCTAA 1 58 0 ACATAGTGTT 0.787004 -243 GAGAAATTGGAGCTATAGTTCGAGTCACGC 3 27 0 AGCTATAGTT 0.75344 -64 GCGATAAGAAACATATAGTTTTGACATGAG 4 45 0 ACATATAGTT 0.818362 -39 GTTATAATTCAGATATTATTCTTT 5 5 0 AGATATTATT 0.946499 -136 CCGCAGCAAGAGATAGTATTGTCATCATAT 6 80 0 AGATAGTATT 0.883815 -108 ATACTCTTCAAGATATTATTTAGCATATAA 7 72 0 AGATATTATT 0.946499 -229 AAGATATAATTCATTTCATTA 8 137 0 AGATATAATT 0.902713 -11 TTAACCTTAGCGATATTGTTAATAGTAAAT 9 42 1 CGATATTGTT 0.854727 -60 GAAAACCAATAGATATCATTGTATTGTAAT 11 214 1 AGATATCATT 0.844806 -87 ********** Masking position 5 Map Score: 3.44064 Number of sites scoring better than the average of aligned sites = 143 Number in coding regions = 93 Number in noncoding regions = 50 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 7 ATTGCTTGCAATAATGCAGGTAACATACAC 1 256 1 ATAATGCAGG 0.97034 -45 ACCGTGATCAATTATGCAAGTATA 6 5 0 ATTATGCAAG 0.975284 -183 TATAAAGTGAATAATGAAAGTGAATAATGT 7 21 0 ATAATGAAAG 0.859251 -280 CCTAATAGCTTTAATGCAAGGGTAAAATAT 7 103 0 TTAATGCAAG 0.923043 -198 TATTAGCTATCTTATGCAAGAAGTCTAATA 7 148 0 CTTATGCAAG 0.946698 -153 TTAAAGTTTGATTATGCAGGACTTATCAAA 11 79 0 ATTATGCAGG 0.97034 -222 ********** Masking position 5 Map Score: 3.57893 Number of sites scoring better than the average of aligned sites = 26 Number in coding regions = 17 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 8 CCATTACTGCACATGAGACATCAGCACCTC 1 83 0 ACATGAGACA 0.938827 -218 ATCTCAAACTACAAGAGAAATTGGAGCTAT 3 41 0 ACAAGAGAAA 0.955943 -50 TATAGTTTTGACATGAGAATCATATAAAAC 4 32 0 ACATGAGAAT 0.974558 -52 ATTAATAATCAAATGAGAATAAAAATAATT 5 59 1 AAATGAGAAT 0.832454 -82 GATACGAATAACGTGAGAATACGAGTACTG 7 211 1 ACGTGAGAAT 0.921792 -90 TAATAGACACTCATGAGAAACTTAGGATTT 11 106 1 TCATGAGAAA 0.911932 -195 TCGCGGGATTACAAGTGAAAAACCTATCTA 12 78 1 ACAAGTGAAA 0.818336 -67 ********** Masking position 8 Map Score: 2.00852 Number of sites scoring better than the average of aligned sites = 31 Number in coding regions = 22 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 9 CATAGTGTTAATCTTCTAACTTAACATAAA 1 47 0 ATCTTCTAAC 0.88972 -254 ACATCAGCACCTCATATAACATAGTGTTAA 1 66 0 CTCATATAAC 0.803679 -235 TGACATGAGAATCATATAAAACATCTTAAG 4 24 0 ATCATATAAA 0.934884 -60 GATATTATTTAGCATATAAATATTTAAATG 7 61 0 AGCATATAAA 0.711396 -240 AGAATGCTGCATCACCTAACCTATAGCTCA 8 64 1 ATCACCTAAC 0.840043 -84 GTACAGTATTATCAGATAAATGATAATTTT 10 56 1 ATCAGATAAA 0.749649 -245 AGTATATTGACTCATCTAAAATTATCATTT 10 73 0 CTCATCTAAA 0.85217 -228 GCAATACGTAATCCTATAAAAGCTGTGGTA 10 191 0 ATCCTATAAA 0.792263 -110 TAGTTAATTTATATTCTAACAAAGA 10 286 1 ATATTCTAAC 0.528513 -15 ACTCCAAGATATCTCATAAAATTATTAGCA 11 267 0 ATCTCATAAA 0.764663 -34 TGTTAAACTTATAATATAAATTTAGAAGAT 14 97 1 ATAATATAAA 0.666107 -25 AACAAATCTTCTAAATTTATATTAT 14 107 0 ATCTTCTAAA 0.907467 -15 ********** Masking position 8 Map Score: 3.10462 Number of sites scoring better than the average of aligned sites = 298 Number in coding regions = 219 Number in noncoding regions = 79 Number of orfs with sites within 600 bp upstream = 42 Fraction of orfs with sites within 600 bp upstream = 0.0067459 Motif number 10 TTGAATGCTGTGCAAATAATTAACAATATA 1 17 0 TGCAAATAAT 0.412115 -284 AGTCACGCTTTGATAATAATCTAC 3 5 0 TGATAATAAT 0.826894 -86 ACAATCAATTCATTAATAATCAAATGAGAA 5 48 1 CATTAATAAT 0.614434 -93 ATAATTTGATTAATAAAAATAATTGATTTA 5 83 1 TAATAAAAAT 0.639279 -58 TGAATAATGTCACTAATAAT 7 1 0 CACTAATAAT 0.878329 -300 AAGTCTAATAAAATAAAAATAGCTACCTAA 7 128 0 AAATAAAAAT 0.581854 -173 TGCATAAGATAGCTAATAATGGTAAATTTG 7 160 1 AGCTAATAAT 0.884969 -141 GAAGTTGTCGATAATGATTTTTATTATA 8 9 1 CGATAATGAT 0.355355 -139 TCAAGCCACAAAATAATAATGAAATGAATT 8 121 1 AAATAATAAT 0.831733 -27 GATAATACTGTACTAATGATTGTACTTGAT 10 39 0 TACTAATGAT 0.727186 -262 TAAATAATTATATTAATAATTATAGATTTT 10 256 0 TATTAATAAT 0.740296 -45 AAAGTTAAACAACTAATAATAGGAAATGTA 11 49 1 AACTAATAAT 0.910224 -252 TAGGATTTGGTATTAATAATAAAATAGATA 11 128 1 TATTAATAAT 0.740296 -173 TAAGAGTAACTGCTAATAATTTTATGAGAT 11 257 1 TGCTAATAAT 0.907391 -44 AACTTGAAAATACTAATATTAGTATTTTTA 12 28 1 TACTAATATT 0.480211 -117 CATGTGATACAGCTAAAAATACTAATATTA 12 41 0 AGCTAAAAAT 0.684122 -104 TTCAAAGAAGTAATAAAAAT 12 135 1 TAATAAAAAT 0.639279 -10 ATACTTATTTAAATAATAATTAGAGAGGAT 14 14 0 AAATAATAAT 0.831733 -108 TTCTTTGTTAAACTTATAATATAAATTTAG 14 92 1 AACTTATAAT 0.420421 -30 ********** Masking position 10 Map Score: 14.302 Number of sites scoring better than the average of aligned sites = 740 Number in coding regions = 482 Number in noncoding regions = 258 Number of orfs with sites within 600 bp upstream = 150 Fraction of orfs with sites within 600 bp upstream = 0.0240925 Motif number 11 ********** No masking Map Score: -2.42762e-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: -2.42762e-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 13 ********** No masking Map Score: -2.42762e-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