AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00290_rpxx_reg_300.orf -o00290_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 RP257 300 CYTOCHROME C OXIDASE ASSEMBLY PROTEI (coxW) #2 RP258 126 unknown #3 RP259 56 PENICILLIN-BINDING PROTEIN 4* (pbpE) #4 RP261 92 PYRUVATE DEHYDROGENASE E1 COMPONENT, ALPHA SUBUNIT PRECURSOR (pdhA) #5 RP262 161 PYRUVATE DEHYDROGENASE E1 COMPONENT, BETA SUBUNIT PRECURSOR (pdhB) #6 RP420 300 unknown #7 RP421 64 LEUCYL-TRNA SYNTHETASE (leuS) #8 RP428 121 BRANCHED-CHAIN AMINO ACID AMINOTRANSFERASE (ilvE) #9 RP617 300 PROBABLE ISOLEUCYL-TRNA SYNTHETASE (ileS) #10 RP687 300 VALYL-TRNA SYNTHETASE (valS) Motif number 1 TGATTCAGTTATCTTGTTATTTTTTACCGTGAAATT 1 78 1 ATTTTATTTA 0.941007 -223 TTTTACCGTGAAATTATGATAATCTATATCTAAACT 1 99 1 AATTGATTTA 0.770594 -202 TTACGTTAAGTATTTTAAATTATTTAGCTTCTATCA 1 254 1 TATTAATTTA 0.654334 -47 TTGTCTTATATTTTTTATTATTGATAGAAGCTAA 1 277 0 TATTTATTGA 0.886403 -24 TTTTGTGGTGAAGTTTGTATTGTTTACATAGTTCGA 2 15 1 AATTTATTTA 0.970937 -112 TCGAGAAATGAATTTGGTATTATTTATTGCTTGATC 2 47 1 AATTTATTTA 0.970936 -80 TTAGAACTTTTTATTATTTTATTGTATGTATTGATT 2 101 0 TTTTTTTTTA 0.841954 -26 AGCTATATACAATTTATTTTAAGAGACAAG 3 5 0 AATTTTTGGA 0.848304 -52 TTGCACAGCTTATTTATTATACTGTATCACCCCATC 5 14 1 TATTTATTTA 0.941006 -148 CTAGATTGCATTGTTAATTTACGTGATTACATTATA 5 99 1 TTTTTTTGGA 0.560412 -63 ACTCAAAATTATCTTATTATACTTTATAAGCTATTA 6 27 0 ATTTTATTTA 0.941007 -274 AAATAAACAAAACTTTGTTTTTTCTATATATGTATG 6 193 1 AATTTTTTTA 0.958963 -108 GTTAAATTAAAAGTTAATATTTGTTATTTTTGCTTG 9 13 0 AATTTATGTA 0.942339 -288 TGAACACATGAATTTGTAATAAGTTAAATTAAAAGT 9 35 0 AATTAATGTA 0.661596 -266 CAGTAATACGAAATTGATATTTTTGAAGATAATTTT 9 94 0 AATTTATTGA 0.942339 -207 AAAAGAAAAATTGTTATTTTCTTTTAAATATACCTT 9 131 1 TTTTTTTTTA 0.841954 -170 AAGTTGTAATATTTTTGTATAAGGTATATTTAAAAG 9 151 0 ATTTTATGTA 0.886404 -150 CTCTTGAAATTTATTAGTTTAGTATAAATTATGTAT 9 219 1 TTTTTTTTTA 0.841954 -82 AAATTATTATAATTTGGTTTAATATAATAGATAATG 9 267 0 AATTTTTTTA 0.958962 -34 CTTGAGAACAAATTTGTTTTGCTATATTACCACTTT 10 69 0 AATTTTTTTA 0.958963 -232 CAAGGACTAAAAATTTCTATGATTGATTAGGTTAAA 10 113 1 AATTTATTGA 0.942339 -188 TATCGTCGTTAAATTACTTTTTTATAATTGAATGCA 10 168 0 AATTTTTTTA 0.958963 -133 ** ** *** * ** Masking position 10 Map Score: 29.4824 Number of sites scoring better than the average of aligned sites = 682 Number in coding regions = 396 Number in noncoding regions = 286 Number of orfs with sites within 600 bp upstream = 153 Fraction of orfs with sites within 600 bp upstream = 0.0245744 Motif number 2 TTAGATATAGATTATCATAATTTCACGGTAAAA 1 99 0 ATATATAATT 0.701042 -202 ATCTTCGGGAACAAAAAAAACTTATATAAGTTT 1 130 0 AAAAAAAATT 0.865463 -171 TTGTTCCCGAAGATATAATACTTATGAACATGC 1 149 1 AATAAATATT 0.778121 -152 AAGCTAAATAATTTAAAATACTTAACGTAAATT 1 251 0 ATTAAATATT 0.561102 -50 AACTATGTAAACAATACAAACTTCACCACAAAA 2 15 0 AAATCAAATT 0.468409 -112 ATACAATAAAATAATAAAAAGTTCTAA 2 110 1 AAATAAAATT 0.913613 -17 GTCATGCCGTAACTTTATAACTTGATTACAATA 4 52 1 ACTTATAATT 0.480719 -41 CTTTTTATTTAAATTAAATATTTTCATTTACTT 5 134 0 AATTAATATT 0.802285 -28 GAACATATTAAATAGTTAATAGCTTAT 6 5 1 AATTAATATT 0.85215 -296 TATAAAGTATAATAAGATAATTTTGAGTTTGTG 6 35 1 ATAAATAATT 0.587657 -266 TGGAGTCCTGATTTAAAAAAATTTTTTCATTAA 6 87 0 ATTAAAAATT 0.751536 -214 TCAGGACTCCAGATTTAAAATTTATGCTAAGAA 6 109 1 AATTAAAATT 0.929626 -192 ATGCTAAGAAATAATTAAATCTTCCATATGTTC 6 132 1 AAATAAATTT 0.621663 -169 TAAAAGCGAAATAAACAAAACTTTGTTTTTTCT 6 185 1 AAAAAAAATT 0.865465 -116 ACATACAATTAGTTTAAATAATTTTTGACTAAT 6 229 1 ATTTAATATT 0.677455 -72 AACAACTATGATATTAATAATTTTGAACCCGTG 8 41 0 AATTATAATT 0.891276 -81 CTAATCTAATATAAATATAACTTA 8 108 1 AAAAATAATT 0.79641 -14 AGTTAAATTAAAAGTTAATATTTGTTATTTTTG 9 17 0 AAGTAATATT 0.456177 -284 GTAGAAAAATATATTCAAATATTGAACACATGA 9 60 0 AATTAAATTT 0.679612 -241 CAGTAATACGAAATTGATATTTTTGAAGATAAT 9 97 0 AATTATATTT 0.561719 -204 CGTATTACTGAAAAAGAAAAATTGTTATTTTCT 9 120 1 AAAAAAAATT 0.865389 -181 TGCACTCTTGAAATTTATTAGTTTAGTATAAAT 9 215 1 AATTATTATT 0.768755 -86 ACTAAGAGATAAATACATAATTTATACTAAACT 9 234 0 AATAATAATT 0.833424 -67 TATTCTAGAAATTATTATAATTTGGTTTAATAT 9 278 0 ATATATAATT 0.700795 -23 * *** **** ** Masking position 12 Map Score: 20.9396 Number of sites scoring better than the average of aligned sites = 1362 Number in coding regions = 844 Number in noncoding regions = 518 Number of orfs with sites within 600 bp upstream = 225 Fraction of orfs with sites within 600 bp upstream = 0.0361388 Motif number 3 CACCTCAATACTTAAGTAAATATAAGCATTAAG 1 189 1 CTTATAAATT 0.347597 -112 GTTAAGTATTTTAAATTATTTAGCTTCTATCAA 1 258 1 TTAATATTTG 0.58358 -43 TTGTCTTATATTTTTTATTATTGATAGA 1 283 0 TTAATTTTTT 0.371831 -18 CTTGTCTCTTAAAATAAATTGTATATAGCTC 3 9 1 TTAATAAATG 0.702303 -48 TATAACTTGATTACAATAATTCTTAAGGAGTAA 4 67 1 TTAATAATTT 0.930811 -26 ATTTACGTGATTACATTATAAGTAAATGAAAAT 5 115 1 TTAATATAAT 0.552444 -47 CCCTTTTTATTTAAATTAAATATTTTCATTTAC 5 136 0 TTAATAAATT 0.897461 -26 AAAAAAATTTTTTCATTAAATATCTAAACTGGT 6 73 0 TTTATAAATT 0.859593 -228 GGAGTCCTGATTTAAAAAAATTTTTTCATTAAA 6 86 0 TTTAAAAATT 0.264425 -215 ATATGGAAGATTTAATTATTTCTTAGCATAAAT 6 128 0 TTTATATTTT 0.784509 -173 CAAAAATTATTTAAACTAATTGTATGTCATACA 6 223 0 TTAATAATTT 0.930811 -78 TTAAATAATTTTTGACTAATAGTCAAAGCTCCT 6 242 1 TTTATAATAT 0.774279 -59 CATCAAGCACTTTAATTAAATTTGTT 6 285 1 TTTATAAATT 0.859593 -16 TTATACTCATTTTACATCTCGTG 8 1 1 TTAATCATTT 0.56257 -121 ACAACTATGATATTAATAATTTTGAACCCGTGG 8 40 0 TATATAATTT 0.355895 -82 TAAGTTATATTTATATTAGATTAGAAA 8 105 0 TTAATTATAT 0.358058 -17 TTGTAATAAGTTAAATTAAAAGTTAATATTTGT 9 25 0 TTAATAAAAT 0.761368 -276 GTGTTCAATATTTGAATATATTTTTCTACAAAA 9 64 1 TTTATATATT 0.703135 -237 AATTTTTCTTTTTCAGTAATACGAAATTGATAT 9 110 0 TTTATAATAG 0.480405 -191 AATGCTAAAGTTGTAATATTTTTGTATAAGGTA 9 161 0 TTGATATTTT 0.43157 -140 TTAAACCAAATTATAATAATTTCTAGAATA 9 281 1 TTAATAATTC 0.574953 -20 CTTATCGTCGTTAAATTACTTTTTTATAATTGA 10 173 0 TTAATACTTT 0.615605 -128 TACATAATCTTTATAATAATATTCTTAACACGA 10 269 1 TTAATAATAT 0.830625 -32 *** * ***** * Masking position 5 Map Score: 10.917 Number of sites scoring better than the average of aligned sites = 1236 Number in coding regions = 749 Number in noncoding regions = 487 Number of orfs with sites within 600 bp upstream = 212 Fraction of orfs with sites within 600 bp upstream = 0.0340508 Motif number 4 TATCATAATTTCACGGTAAAAAATAACAAGAT 1 88 0 TCAGTAAAAA 0.95233 -213 TATTATATCTTCGGGAACAAAAAAAACTTATA 1 137 0 TCGGACAAAA 0.941246 -164 TTTACATAGTTCGAGAAATGAATTTGGTATTA 2 37 1 TCGGAATGAA 0.887746 -90 GAACATGCGATCAAGCAATAAATAATACCAAA 2 59 0 TCAGAATAAA 0.913355 -68 ATTATTGTAATCAAGTTATAAAGTTACGGCAT 4 55 0 TCAGTATAAA 0.935532 -38 AACAATGCAATCTAGCTAAAAATATATTAGTA 5 82 0 TCTGTAAAAA 0.805729 -80 TGGTTTGACCACGGGTTCAAAATTATTAATAT 8 32 1 ACGGTCAAAA 0.718671 -90 TTTTTGGCTTTCGTGGTCAAACCACGGGATGA 8 72 1 TCGGTCAAAC 0.791064 -50 CTGGAAGGAGTCATGGTATAAAATAAGAACAC 10 21 1 TCAGTATAAA 0.935532 -280 AAATTTGTTCTCAAGTAAAGAATCAAGGACTA 10 90 1 TCAGAAAGAA 0.890263 -211 AAGTAAAGAATCAAGGACTAAAAATTTCTATG 10 102 1 TCAGACTAAA 0.896607 -199 ATTCTTTATTCGTGTTAAGAATATTATTATA 10 280 0 TCGGTAAGAA 0.937452 -21 *** * ****** Masking position 11 Map Score: 9.32163 Number of sites scoring better than the average of aligned sites = 141 Number in coding regions = 98 Number in noncoding regions = 43 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 5 TATCGCTTCAATTACTGCTAAAGTATCTTTA 1 10 0 ATACTGCAAA 0.914459 -291 TTTATTATTGATAGAAGCTAAATAATTTAAAA 1 266 0 ATGAAGCAAA 0.779812 -35 AGTTTAGATATTTAATGAAAAAATTTTTTTAA 6 76 1 TTAATGAAAA 0.745915 -225 AGTCAGAATTTTAAAAGCGAAATAAACAAAAC 6 174 1 TTAAAGCAAA 0.920632 -127 TGGTTTGACCACGAAAGCCAAAAACAACTATG 8 64 0 ACAAAGCAAA 0.94845 -58 TCAATTTCGTATTACTGAAAAAGAAAAATTGT 9 113 1 ATACTGAAAA 0.648883 -188 TCAAGAACTTTCTAATGCTAAAGTTGTAATAT 9 175 0 TCAATGCAAA 0.948449 -126 TTTTTTATAATTGAATGCATAAAAGTTTCTTT 10 155 0 TTAATGCTAA 0.704974 -146 TACATGCTGTACAAATGCTAAATCTCTAAACC 10 207 1 ACAATGCAAA 0.964204 -94 AAATCTCTAAACCAAAGCGAAACAACACATCT 10 226 1 ACAAAGCAAA 0.94845 -75 ** ***** *** Masking position 11 Map Score: 4.64298 Number of sites scoring better than the average of aligned sites = 229 Number in coding regions = 173 Number in noncoding regions = 56 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 6 TGAACATGCGATCAAGCAATAAATAATACC 2 62 0 ATCAAGCAAT 0.955139 -65 TATGATTTCCATCAAGCACTTTAATTAAAT 6 276 1 ATCAAGCACT 0.988317 -25 GCAATGCACAATCAAGAACTTTCTAATGCT 9 188 0 ATCAAGAACT 0.968764 -113 CAAGTAAAGAATCAAGGACTAAAAATTTCT 10 101 1 ATCAAGGACT 0.978708 -200 ********** Masking position 5 Map Score: 2.1 Number of sites scoring better than the average of aligned sites = 13 Number in coding regions = 10 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 7 GAGGTGATATATCGCATGTTCATAAGTATTAT 1 163 0 ATCCTGTTCA 0.989683 -138 TTATTGCTTGATCGCATGTTCAAAGTGGCAGA 2 70 1 ATCCTGTTCA 0.989683 -57 GTATCACCCCATCTCTTGTACACTGTATTCAG 5 37 1 ATCCTGTACA 0.966841 -125 AATAATTTTGAACCCGTGGTCAAACCACGAGA 8 27 0 AACCTGGTCA 0.969208 -95 TTATGTATTTATCTCTTAGTCATTATCTATTA 9 247 1 ATCCTAGTCA 0.952025 -54 *** * ****** Masking position 7 Map Score: 1.71083 Number of sites scoring better than the average of aligned sites = 6 Number in coding regions = 3 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 8 TTTACTTAAGTATTGAGGTGATATATCGCAT 1 178 0 TATGAGGTGA 0.937312 -123 TTAAGGACACTTTAGTGGTGATTATGTAAAA 1 217 1 TTTGTGGTGA 0.989633 -84 AATGTTTTGTGGTGAAGTTTGTATT 2 5 1 TTTGTGGTGA 0.989633 -122 TGTTTTTGGCTTTCGTGGTCAAACCACGGGA 8 70 1 TTTGTGGTCA 0.972683 -52 *** ******* Masking position 3 Map Score: 0.455199 Number of sites scoring better than the average of aligned sites = 4 Number in coding regions = 2 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 9 ATGATAATCTATATCTAAACTTATATAAGT 1 114 1 ATATCTAAAC 0.929983 -187 TTAGTGGTGATTATGTAAAAATGAATTTAC 1 228 1 TTATGTAAAA 0.813741 -73 ATTTCTCGAACTATGTAAACAATACAAACT 2 26 0 CTATGTAAAC 0.803417 -101 TTTTCATTAAATATCTAAACTGGTCTTATC 6 67 0 ATATCTAAAC 0.929983 -234 TCTGGAGTCCTGATTTAAAAAAATTTTTTC 6 92 0 TGATTTAAAA 0.720359 -209 TCAGGACTCCAGATTTAAAATTTATGCTAA 6 109 1 AGATTTAAAA 0.830817 -192 TAGTCAAAAATTATTTAAACTAATTGTATG 6 230 0 TTATTTAAAC 0.852281 -71 TCAAACCACGAGATGTAAAATGAGTATAA 8 10 0 AGATGTAAAA 0.855704 -112 TGTATAAGGTATATTTAAAAGAAAATAACA 9 142 0 ATATTTAAAA 0.873371 -159 CAAATGCTAAATCTCTAAACCAAAGCGAAA 10 218 1 ATCTCTAAAC 0.734746 -83 ********** Masking position 6 Map Score: 4.16255 Number of sites scoring better than the average of aligned sites = 269 Number in coding regions = 168 Number in noncoding regions = 101 Number of orfs with sites within 600 bp upstream = 55 Fraction of orfs with sites within 600 bp upstream = 0.00883392 Motif number 10 TAAAGATACTTTAGCAGTAA 1 1 1 TAAAGATACT 0.939197 -300 TACAGTATAATAAATAAGCTGTGCAAATT 5 10 0 TAAATAAGCT 0.939197 -152 ATGGAAATCATAAAGGAGCTTTGACTATTA 6 258 0 TAAAGGAGCT 0.898796 -43 TATTTTCTTTTAAATATACCTTATACAAAA 9 145 1 TAAATATACC 0.782224 -156 TGTAAATATGCTGGAAGGAGTC 10 3 1 TAAATATGCT 0.939197 -298 TTAAAGATATTAAAGAAACTTTTATGCATT 10 144 1 TAAAGAAACT 0.939197 -157 ********** Masking position 4 Map Score: 0.258642 Number of sites scoring better than the average of aligned sites = 120 Number in coding regions = 95 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 11 ********** No masking Map Score: 2.60302e-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: 2.60302e-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: 2.60302e-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