AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00710_rpxx_reg_300.orf -o00710_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 RP091 174 ASPARTATE AMINOTRANSFERASE A (aatA) #2 RP299 223 GALACTOSE-6-PHOSPHATE ISOMERASE LACB SUBUNIT (lacA) #3 RP376 300 MALATE DEHYDROGENASE (mdh) #4 RP492 300 PYRUVATE,PHOSPHATE DIKINASE PRECURSOR (ppdK) Motif number 1 TATTATAGTGTAAATAATATGAATTTAGTA 1 19 0 TAAATAATAT 0.934701 -156 TATTATTTACACTATAATAAAGCATATCTT 1 30 1 ACTATAATAA 0.656767 -145 AAAGCATATCTTAATAAATTTTTAAATAAA 1 48 1 TTAATAAATT 0.882562 -127 AATAAATTTTTAAATAAAATAATTTTATTG 1 60 1 TAAATAAAAT 0.909044 -115 AATTTTAATCTCAATAAAATTATTTTATTT 1 71 0 TCAATAAAAT 0.864556 -104 TAGAATAACATTAATAATAAACGATAATAC 1 104 0 TTAATAATAA 0.889424 -71 TTCGGATTCTTATATACTTTAGAATAACAT 1 123 0 TATATACTTT 0.749621 -52 ATTATATCAAATAATAATTTTGTTGAATAT 2 11 0 ATAATAATTT 0.845946 -213 GTGCTCTGTAAAAATAAATAAAGAATAAAT 2 54 1 AAAATAAATA 0.814152 -170 AAATAAAGAATAAATACATTAAAAAAATGT 2 69 1 TAAATACATT 0.803299 -155 TGTTAATATGAAAATAATTAAAGATTTCTA 2 96 1 AAAATAATTA 0.862021 -128 TTTCTAAAAATTTATAATTATAGCAAAAAA 2 120 1 TTTATAATTA 0.815433 -104 AATTTTAAAGTTAATAATTTTTTTTGCTAT 2 139 0 TTAATAATTT 0.914982 -85 CGCTTAGCTGTAAATAAATTTTAAAGTTAA 2 155 0 TAAATAAATT 0.914698 -69 GCTTACATAGTATATAATTTTTATCATAAT 2 184 1 TATATAATTT 0.887149 -40 AGTCTATCTTTTAATAAAAAAATCACAGAA 3 39 1 TTAATAAAAA 0.848913 -262 GAAGTAATCATCAATAATATAAAACCATTT 3 77 0 TCAATAATAT 0.902 -224 ATTTAATTTGTATATAAAAATGAAGTAATC 3 98 0 TATATAAAAA 0.803611 -203 TACCACGATAAATATAAAAATACACTTTTT 3 140 0 AATATAAAAA 0.675523 -161 TTTTAAATTGTAAATACATAAATCACTTTG 3 212 0 TAAATACATA 0.766249 -89 TTTAATACGCATAATACTATATTACAAATG 3 260 0 ATAATACTAT 0.660855 -41 TTATGCGTATTAAATAATATATTATAGAGG 3 276 1 TAAATAATAT 0.934701 -25 CTTAAATTAGTCAATAATATGTTAAAAGAA 4 82 1 TCAATAATAT 0.902 -219 TATTGTGTGTACAATAATTACAATAAATTT 4 142 0 ACAATAATTA 0.801791 -159 TTGTACACACAATATAATTACAATTATAAT 4 158 1 AATATAATTA 0.762513 -143 TATAATTACAATTATAATAACAAATTCCAT 4 170 1 ATTATAATAA 0.677078 -131 TACTACATTATTTATACATTAGGAAAAAAA 4 247 0 TTTATACATT 0.592677 -54 ********** Masking position 5 Map Score: 30.2242 Number of sites scoring better than the average of aligned sites = 3132 Number in coding regions = 1964 Number in noncoding regions = 1168 Number of orfs with sites within 600 bp upstream = 365 Fraction of orfs with sites within 600 bp upstream = 0.0586251 Motif number 2 TTTACACTATAATAAAGCATATCTTAATAAATTTTTA 1 35 1 AATAGAATAA 0.923647 -140 GAGCTTTGAGAATCTTAAAATACTGAATTCGGATTCT 1 143 0 AATTAATTAA 0.901133 -32 TGCTCTGTAAAAATAAATAAAGAATAAATACATTAAA 2 55 1 AAAAAAAAAA 0.690597 -169 AGAATAAATACATTAAAAAAATGTTAATATGAAAATA 2 75 1 CATAAAATAA 0.74486 -149 ATATGAAAATAATTAAAGATTTCTAAAAATTTATAAT 2 101 1 AATAAATTAA 0.981315 -123 GCTGTAAATAAATTTTAAAGTTAATAATTTTTTTTGC 2 142 0 AATTAATAAA 0.727335 -82 TTATGATAAAAATTATATACTATGTAAGCGCTTAGCT 2 176 0 AATAAATGAA 0.900156 -48 TGTATATAAAAATGAAGTAATCATCAATAATATAAAA 3 83 0 AATAGATTAA 0.96946 -218 TTTATATACAAATTAAATATTCATGAATTTAAAAAGT 3 110 1 AATAAATTAA 0.981315 -191 CGATAAATATAAAAATACACTTTTTAAATTCATGAAT 3 128 0 AAAAAATTAA 0.952411 -173 TGGCTTTAAGAAAAAAGAATTTTTAAATTGTAAATAC 3 225 0 AAAAGATTAA 0.923647 -76 TATGCCCTCTATAATATATTATTTAATACGCATAAT 3 275 0 TATAAATTAA 0.837883 -26 TTACAATTATAATAACAAATTCCATAATGTCAATTCT 4 175 1 AATAAATAAA 0.938912 -126 TCAATTCTTTAAAGAAAGATATCTTAATTTAACATTG 4 204 1 AAAAAAATAA 0.88408 -97 CTAATGTATAAATAATGTAGTACTTAAAAACATATAC 4 255 1 AATAGATTAA 0.96946 -46 *** * * * * * ** Masking position 9 Map Score: 17.6245 Number of sites scoring better than the average of aligned sites = 471 Number in coding regions = 292 Number in noncoding regions = 179 Number of orfs with sites within 600 bp upstream = 102 Fraction of orfs with sites within 600 bp upstream = 0.0163829 Motif number 3 TCAATAAAATTATTTTATTTAAAAATTTATTAAG 1 57 0 TATTTTTTAA 0.935945 -118 ATAATACAGCAATTTTAATCTCAATAAAATTATT 1 77 0 AATTTTATAA 0.969304 -98 GTTTATTATTAATGTTATTCTAAAGTATATAAGA 1 112 1 AATGTTTTAA 0.935614 -63 ATCAAATAATAATTTTGTTGAATAT 2 2 0 AATTTTTTTA 0.92958 -222 ACATTAAAAAAATGTTAATATGAAAATAATTAAA 2 84 1 AATGTTATAA 0.935614 -140 TAAAGTTAATAATTTTTTTTGCTATAATTATAAA 2 130 0 AATTTTTTTA 0.92958 -94 GCTGTAAATAAATTTTAAAGTTAATAATTTTTTT 2 145 0 AATTTTAAAA 0.756566 -79 CATAGTATATAATTTTTATCATAATTTTCCATCA 2 189 1 AATTTTATAA 0.969304 -35 TATATTCTGTGATTTTTTTATTAAAAGATAGACT 3 39 0 GATTTTTTAA 0.868167 -262 ATGAATATTTAATTTGTATATAAAAATGAAGTAA 3 100 0 AATTTGATAA 0.821628 -201 TTAAAAAGTGTATTTTTATATTTATCGTGGTACT 3 138 1 TATTTTATTA 0.859367 -163 ATATAATTACAATTATAATAACAAATTCCATAAT 4 169 1 AATTATATAA 0.756566 -132 ACATTGCTACTATTTTTTTCCTAATGTATAAATA 4 235 1 TATTTTTTAA 0.935973 -66 TAATAGTGTATATGTTTTTAAGTACTACATTATT 4 265 0 TATGTTTTTA 0.737465 -36 ****** ** ** Masking position 2 Map Score: 15.2738 Number of sites scoring better than the average of aligned sites = 836 Number in coding regions = 524 Number in noncoding regions = 312 Number of orfs with sites within 600 bp upstream = 164 Fraction of orfs with sites within 600 bp upstream = 0.0263412 Motif number 4 TTATTTACACTATAATAAAGCATATCTTAAT 1 32 1 TATAATAAAC 0.415467 -143 TAATAAAGCATATCTTAATAAATTTTTAAAT 1 44 1 TATCTTAATA 0.66705 -131 GAGCTTTGAGAATCTTAAAATACTGAATTCG 1 149 0 AATCTTAAAT 0.602386 -26 ATATTAACATTTTTTTAATGTATTTATTCTT 2 74 0 TTTTTTAATT 0.501349 -150 TAATTAAAGATTTCTAAAAATTTATAATTAT 2 110 1 TTTCTAAAAT 0.660681 -114 ATATAATTTTTATCATAATTTTCCATCAAAA 2 195 1 TATCATAATT 0.914806 -29 ATTTAATTTGTATATAAAAATGAAGTAATCA 3 97 0 TATATAAAAT 0.426897 -204 TAGGCCTAGTTATATTAATCTCTTTGAATAA 3 178 1 TATATTAATT 0.829949 -123 AAAATTCTTTTTTCTTAAAGCCATTTGTAAT 3 239 1 TTTCTTAAAC 0.765154 -62 TAAGAAAAGCTACCATAATCTAAATGGTCGT 4 55 0 TACCATAATT 0.819497 -246 TATGGTAGCTTTTCTTAAATTAGTCAATAAT 4 69 1 TTTCTTAAAT 0.918157 -232 GTACAATAATTACAATAAATTTTCCCCTCAG 4 133 0 TACAATAAAT 0.508676 -168 TAATAACAAATTCCATAATGTCAATTCTTTA 4 184 1 TTCCATAATT 0.754728 -117 TAAAGAAAGATATCTTAATTTAACATTGCTA 4 213 1 TATCTTAATT 0.949562 -88 CTACTATTTTTTTCCTAATGTATAAATAATG 4 241 1 TTTCCTAATT 0.726858 -60 ********* * Masking position 7 Map Score: 5.40836 Number of sites scoring better than the average of aligned sites = 843 Number in coding regions = 530 Number in noncoding regions = 313 Number of orfs with sites within 600 bp upstream = 167 Fraction of orfs with sites within 600 bp upstream = 0.026823 Motif number 5 ********** No masking Map Score: -2.59896e-14 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: -2.59896e-14 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: -2.59896e-14 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