AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00660_rpxx_reg_300.orf -o00660_rpxx_300.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 RP432 162 SUCCINYL-COA LIGASE (sucD) #2 RP433 154 SUCCINYL-COA SYNTHETASE BETA CHAIN (sucC) #3 RP434 275 unknown #4 RP436 169 unknown Motif number 1 TTTTTATTGTTTATTTTACTTTATATGTTACT 1 131 0 TTATTTATTT 0.840347 -32 GTGAAATAATTTTTTATTGTTTATTTTA 1 145 0 TAATTTTATT 0.981881 -18 AAGCTCAGTATAATAATTAATTTATAAGCTGT 2 109 0 TAATATTATT 0.949457 -46 TTCAAATAATTTTTTAAATAATAAAAGC 2 137 0 TAATTTTAAA 0.935192 -18 TATCATTTTTTAATGATTGATTTTATAGTACA 3 14 0 TAATATTATT 0.960454 -262 ATAATATCCGTTATATTAAAAATTTAAATTTT 3 43 1 TTATTTAAAA 0.79124 -233 TTATAGCCTTTAATTATTTATACTAATTAGTC 3 85 0 TAATATTATA 0.953878 -191 ATTTTGTAAATTATCTTTAATTCAGCATTATA 3 119 0 TTATTTTATT 0.980311 -157 TAAGATATAGTAATTTTATATAACTTTAATAA 3 163 1 TAATTTAATA 0.935189 -113 AAATAAGAATTTATTTTTATTAAAGTTATATA 3 179 0 TTATTTTTTA 0.934999 -97 AAATAAATTCTTATTTTTATTAAATACTTTAA 3 195 1 TTATTTTTTA 0.934999 -81 TATAAAAAAATAATCTTTTAAAGTATTTAATA 3 212 0 TAATTTTAAA 0.935229 -64 TAAAAGATTATTTTTTTATATTAAGATATAAA 3 224 1 TTTTTTAATT 0.610174 -52 TATTAAACGATTATCATTTATATCTTAATATA 3 240 0 TTATATTATA 0.95344 -36 TTTCTATTTTTTTTTATTAAACGATTAT 3 258 0 TTTTTTTATT 0.843684 -18 TGTCGTTGATTATTTTTGATTTTTAATATTT 4 10 1 TTATTTTATT 0.980311 -160 TTTTGATTTTTAATATTTTTTATTTCATTATA 4 24 1 TAATTTTTTA 0.946422 -146 ATAATAAATTTAATTTTTAATTTAGTATTTTT 4 60 0 TAATTTTATT 0.981837 -110 GCTTCCATCTTTATAATAAATTTAATTTTTAA 4 72 0 TTATATAATT 0.863237 -98 AAGCACATTGTAATTTTTATTACTTTATATTT 4 100 1 TAATTTTTTA 0.919847 -70 TTTTATTACTTTATATTTCAATTTTCTTGAGA 4 114 1 TTATTTTAAT 0.935231 -56 TTGAGAGAAATAATTATTCAAAGAAAAAATTA 4 140 1 TAATATTAAA 0.863473 -30 AAATGTAATAATTTTTTCTTTGAATAA 4 153 0 TAATATTTTT 0.897229 -17 **** *** *** Masking position 7 Map Score: 42.6569 Number of sites scoring better than the average of aligned sites = 1451 Number in coding regions = 905 Number in noncoding regions = 546 Number of orfs with sites within 600 bp upstream = 243 Fraction of orfs with sites within 600 bp upstream = 0.0390299 Motif number 2 TATAGCTTAGAAAAATCAATTTAGTATAACCC 1 38 1 AAAATCAATT 0.736327 -125 AATAAACAATAAAAAATTATTTCAC 1 148 1 AAAAATTATT 0.746833 -15 AGAGAGTTTAAAATAACTAGTTATTCCACCCT 2 72 0 AAATACTAGT 0.732894 -83 ATAATTTTTTAAATAATAAAAGCTCAGTATAA 2 128 0 AAATATAAAG 0.823446 -27 TTTATTATTTAAAAAATTATTTGAA 2 140 1 AAAAATTATT 0.746833 -15 AATCATTAAAAAATGATAATATCCGTTATATT 3 28 1 AAATATAATT 0.954876 -248 ATTTTGTACTAAAATTTAAATTTTTAATATAA 3 53 0 AAAATTAAAT 0.653587 -223 TTTTAGTACAAAATGACTAATTAGTATAAATA 3 71 1 AAATACTAAT 0.901125 -205 TAATTAGTATAAATAATTAAAGGCTATAATTT 3 88 1 AAATATTAAG 0.793368 -188 AATGCTGAATTAAAGATAATTTACAAAATTAT 3 122 1 TAAAATAATT 0.566303 -154 ATAATTTACAAAATTATAATATCCAATAAGAT 3 137 1 AAATATAATT 0.743094 -139 AAGTTATATAAAATTACTATATCTTATTGGAT 3 157 0 AAATACTATT 0.939593 -119 TATTTAATAAAAATAAGAATTTATTTTTATTA 3 189 0 AAATAGAATT 0.631671 -87 TCTTAATATAAAAAAATAATCTTTTAAAGTAT 3 218 0 AAAAATAATT 0.945493 -58 ATTAAGATATAAATGATAATCGTTTAATAAAA 3 243 1 AAATATAATG 0.900851 -33 TTATATAGTAAAAATACTAAATTAAAAATTAA 4 51 1 AAAAACTAAT 0.860444 -119 ATACTAAATTAAAAATTAAATTTATTATAAAG 4 64 1 AAAATTAAAT 0.653605 -106 AAAGTAATAAAAATTACAATGTGCTTCCATCT 4 94 0 AAATACAATT 0.948506 -76 TTCTTGAGAGAAATAATTATTCAAAGAAAAAA 4 137 1 AAATATTATC 0.589524 -33 TTCAAAGAAAAAATTATTACATTT 4 156 1 AAATATTACT 0.782248 -14 **** ***** * Masking position 9 Map Score: 26.4021 Number of sites scoring better than the average of aligned sites = 1290 Number in coding regions = 848 Number in noncoding regions = 442 Number of orfs with sites within 600 bp upstream = 193 Fraction of orfs with sites within 600 bp upstream = 0.030999 Motif number 3 AGTTAATCAGTAACATATAAAGTAAAATAA 1 123 1 TAACATATAA 0.808611 -40 GTATAATAATTAATTTATAAGCTGTAAAGA 2 104 0 TAATTTATAA 0.960263 -51 TGAGCTTTTATTATTTAAAAAATTATTTGA 2 134 1 TTATTTAAAA 0.744405 -21 ATATGTACTATAAAATCAATCATTA 3 6 1 TACTATAAAA 0.903234 -270 TTAAAGGCTATAATTTATAATGCTGAATTA 3 104 1 TAATTTATAA 0.960263 -172 GAATTAAAGATAATTTACAAAATTATAATA 3 128 1 TAATTTACAA 0.865107 -148 TAATATCCAATAAGATATAGTAATTTTATA 3 153 1 TAAGATATAG 0.553679 -123 TTTATTAAAGTTATATAAAATTACTATATC 3 166 0 TTATATAAAA 0.656536 -110 TTTTATTAAATACTTTAAAAGATTATTTTT 3 209 1 TACTTTAAAA 0.913939 -67 TTTTTTATATTAAGATATAAATGATAATCG 3 235 1 TAAGATATAA 0.885252 -41 GATAATCGTTTAATAAAAAAAAATAGAAA 3 257 1 TAATAAAAAA 0.584187 -19 TTAGTATTTTTACTATATAATGAAATAAAA 4 41 0 TACTATATAA 0.939495 -129 ATAATAAATTTAATTTTTAATTTAGTATTT 4 62 0 TAATTTTTAA 0.842251 -108 AAGCACATTGTAATTTTTATTACTTTATAT 4 100 1 TAATTTTTAT 0.500823 -70 TAATTTTTATTACTTTATATTTCAATTTTC 4 110 1 TACTTTATAT 0.777491 -60 ********** Masking position 9 Map Score: 14.0186 Number of sites scoring better than the average of aligned sites = 976 Number in coding regions = 554 Number in noncoding regions = 422 Number of orfs with sites within 600 bp upstream = 200 Fraction of orfs with sites within 600 bp upstream = 0.0321234 Motif number 4 AACTACAGGGTTATACTAAATTGATTTTTC 1 47 0 TTATACTAAA 0.964638 -116 GATACCGTTGCTAAACTACAGGGTTATACT 1 60 0 CTAAACTACA 0.717361 -103 CAACGGTATCTAAAAGTAAATAAGGACTAA 1 80 1 TAAAAGTAAA 0.825615 -83 TCAGTAACATATAAAGTAAAATAAACAATA 1 129 1 ATAAAGTAAA 0.91937 -34 AATACTGTAGTCAAACTAAAGAAAA 2 6 0 TCAAACTAAA 0.799166 -149 TTCAAATCTATTAAACTAGATCCTGAGATT 2 35 1 TTAAACTAGA 0.799166 -120 ATGATTGATTTTATAGTACATAT 3 4 0 TTATAGTACA 0.879857 -272 ATAATATCCGTTATATTAAAAATTTAAATT 3 43 1 TTATATTAAA 0.86183 -233 ATTAGTCATTTTGTACTAAAATTTAAATTT 3 62 0 TTGTACTAAA 0.775761 -214 CTTTAATTATTTATACTAATTAGTCATTTT 3 80 0 TTATACTAAT 0.871532 -196 ATCCAATAAGATATAGTAATTTTATATAAC 3 157 1 ATATAGTAAT 0.739312 -119 ATAACTTTAATAAAAATAAATTCTTATTTT 3 182 1 TAAAAATAAA 0.519898 -94 TTATTTCATTATATAGTAAAAATACTAAAT 4 43 1 ATATAGTAAA 0.919381 -127 AGTAAAAATACTAAATTAAAAATTAAATTT 4 57 1 CTAAATTAAA 0.683751 -113 GCTTCCATCTTTATAATAAATTTAATTTTT 4 74 0 TTATAATAAA 0.861869 -96 AAATTGAAATATAAAGTAATAAAAATTACA 4 108 0 ATAAAGTAAT 0.739309 -62 ********** Masking position 5 Map Score: 14.0648 Number of sites scoring better than the average of aligned sites = 966 Number in coding regions = 557 Number in noncoding regions = 409 Number of orfs with sites within 600 bp upstream = 197 Fraction of orfs with sites within 600 bp upstream = 0.0316415 Motif number 5 ********** No masking Map Score: 1.41641e-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 6 ********** No masking Map Score: 1.41641e-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 7 ********** No masking Map Score: 1.41641e-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