AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00010_rpxx_reg_100.orf -o00010_rpxx_100.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 RP258 126 unknown #2 RP259 56 PENICILLIN-BINDING PROTEIN 4* (pbpE) #3 RP261 92 PYRUVATE DEHYDROGENASE E1 COMPONENT, ALPHA SUBUNIT PRECURSOR (pdhA) #4 RP262 161 PYRUVATE DEHYDROGENASE E1 COMPONENT, BETA SUBUNIT PRECURSOR (pdhB) #5 RP460 146 DIHYDROLIPOAMIDE DEHYDROGENASE PRECURSOR (pdhD) #6 RP530 125 DIHYDROLIPOAMIDE ACETYLTRANSFERASE COMPONENT (pdhC) #7 RP805 249 DIHYDROLIPOAMIDE DEHYDROGENASE (pdhD) Motif number 1 TGTGGTGAAGTTTGTATTGTTTACATAGTTCG 1 18 1 TTTTATTGTT 0.991114 -109 AATTTGGTATTATTTATTGCTTGATCGCATGT 1 57 1 TATTATTGTT 0.987042 -70 TATTTTATTGTATGTATTGATTCTGCCACTTT 1 91 0 TATTATTGTT 0.987033 -36 TTAGAACTTTTTATTATTTTATTGTATGT 1 108 0 TTTTATTATT 0.945219 -19 AATATATTAGTATATATTGGTTTGACTGAATA 4 62 0 TATTATTGTT 0.987039 -100 GAGATTTATGTTATTATTTTTTTTGCATAAGC 6 96 0 TTATATTTTT 0.888738 -30 GTATCGTTGTTTTATATTTTTTAGTTTTTAAG 7 23 1 TTTTATTTTT 0.982689 -227 AGCTAAATGTTTTATATTTCTTAACTGCAATA 7 65 0 TTTTATTTTT 0.982689 -185 TACTAAATTCTATATATTTTTTCAGTAAAGGT 7 112 1 TATTATTTTT 0.974838 -138 TTTATTTTTATTTTATTGGTTCTATTTTAAG 7 229 0 ATTTATTGTT 0.940096 -21 *** ***** ** Masking position 6 Map Score: 18.8743 Number of sites scoring better than the average of aligned sites = 227 Number in coding regions = 135 Number in noncoding regions = 92 Number of orfs with sites within 600 bp upstream = 64 Fraction of orfs with sites within 600 bp upstream = 0.0102795 Motif number 2 AACTTTTTATTATTTTATTGTATGTATTGAT 1 102 0 TATTTTATGT 0.802865 -25 TGTTATATTGTTCGAGCGGGA 3 1 1 TGTTATATGT 0.93607 -92 TAAGAATTATTGTAATCAAGTTATAAAGTTA 3 61 0 TGTAATCAGT 0.954803 -32 ACAGCTTATTTATTATACTGTATCACCCCAT 4 18 1 TATTATACGT 0.942959 -144 TTACTTATAATGTAATCACGTAAATTAACAA 4 109 0 TGTAATCAGT 0.954803 -53 TGTTTATAATATTGTAGTATTGTAA 5 5 1 TATAATATGT 0.958507 -142 TAATCTTTTTTAAAATATCGTAGTCACACAA 5 42 0 TAAAATATGT 0.825117 -105 TAAAAAAGATTATTATAAAGATTAGATACCG 5 61 1 TATTATAAGA 0.782561 -86 CCTTATGATGTGTAATACCGTATATTGACTA 5 92 0 TGTAATACGT 0.93361 -55 TAGTTATAATATAATCACGTGTGTTGACAC 6 10 1 TATAATCAGT 0.966408 -116 TGTGTTCTAGTATTATAAGGTTTATATCCTG 6 41 1 TATTATAAGT 0.971281 -85 CAGTAAAGGTTAAAATCAAGTGTTGATAAAG 7 134 1 TAAAATCAGT 0.854566 -116 TTATTGGTTCTATTTTAAGGTATAAATTATT 7 217 0 TATTTTAAGT 0.873537 -33 ******** ** Masking position 6 Map Score: 16.0852 Number of sites scoring better than the average of aligned sites = 264 Number in coding regions = 141 Number in noncoding regions = 123 Number of orfs with sites within 600 bp upstream = 60 Fraction of orfs with sites within 600 bp upstream = 0.00963701 Motif number 3 GTTTACATAGTTCGAGAAATGAATTTGGTATTATT 1 36 1 TTAAAATGTT 0.629245 -91 ACATGCGATCAAGCAATAAATAATACCAAATTCAT 1 54 0 AAATAAATTA 0.640079 -73 AATCAATACATACAATAAAATAATAAAAAGTTCTA 1 101 1 TAAAAAATTA 0.816551 -26 CTTGTCTCTTAAAATAAATTGTATATAGCTCCG 2 9 1 TTATAAATTA 0.965828 -48 TATAACTTGATTACAATAATTCTTAAGGAGTAATT 3 67 1 TTATAATTTA 0.945526 -26 CCCTTTTTATTTAAATTAAATATTTTCATTTACTT 4 134 0 TTATAAATTT 0.885015 -28 GACTACGATATTTTAAAAAAGATTATTATAAAGAT 5 48 1 TTAAAAAGTA 0.920641 -99 TTTGAAAAATTTGTATCGTTGTTTT 7 1 1 TTAAAATTTA 0.91603 -249 TTTAAAGATCATCTACTAAATTCTATATATTTTTT 7 99 1 ATATAAATTA 0.886244 -151 CTATATATTTTTTCAGTAAAGGTTAAAATCAAGTG 7 121 1 TTATAAAGTA 0.95163 -129 TTCACCTTTTTTGGAATAATTTATACCTTAAAATA 7 203 1 TTATAATTTA 0.945526 -47 ** * ***** ** Masking position 8 Map Score: 6.99849 Number of sites scoring better than the average of aligned sites = 443 Number in coding regions = 259 Number in noncoding regions = 184 Number of orfs with sites within 600 bp upstream = 102 Fraction of orfs with sites within 600 bp upstream = 0.0163829 Motif number 4 ATGCCGTAACTTTATAACTTGATTACAATA 3 55 1 TTTATAACTT 0.732676 -38 TAATTACTCCTTAAGAATTATT 3 81 0 ATTACTCCTT 0.826029 -12 TTCTTGGCATATTTAACCTTATGATCCTTA 5 118 0 ATTTAACCTT 0.96085 -29 GACTTCAGGATATAAACCTTATAATACTAG 6 47 0 TATAAACCTT 0.81476 -79 CAACACTTGATTTTAACCTTTACTGAAAAA 7 129 0 TTTTAACCTT 0.960851 -121 AGGTTATCTCATTTTACCATAGATTTCACC 7 179 1 ATTTTACCAT 0.814735 -71 TTTACCATAGATTTCACCTTTTTTGGAATA 7 191 1 ATTTCACCTT 0.96363 -59 TTTGGAATAATTTATACCTTAAAATAGAAC 7 212 1 TTTATACCTT 0.960851 -38 ********** Masking position 3 Map Score: 4.43045 Number of sites scoring better than the average of aligned sites = 161 Number in coding regions = 131 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 5 ATACAATAAAATAATAAAAAGTTCTAA 1 110 1 ATAATAAAAA 0.889964 -17 CAATGCAATCTAGCTAAAAATATATTAGTA 4 82 0 TAGCTAAAAA 0.851894 -80 ACATTATAAGTAAATGAAAATATTTAATTT 4 127 1 TAAATGAAAA 0.925987 -35 ATATTTAATTTAAATAAAAAGGGAAA 4 146 1 TAAATAAAAA 0.956694 -16 TTATGCAAAAAAAATAATAACATAAATCTC 6 98 1 AAAATAATAA 0.798359 -28 TAGTACTTAAAAACTAAAAAATATAAAACA 7 30 0 AAACTAAAAA 0.955861 -220 ATTTTAACCTTTACTGAAAAAATATATAGA 7 120 0 TTACTGAAAA 0.817825 -130 TAGAACCAATAAAATAAAAATAAA 7 236 1 AAAATAAAAA 0.956699 -14 ********** Masking position 7 Map Score: 5.66953 Number of sites scoring better than the average of aligned sites = 376 Number in coding regions = 248 Number in noncoding regions = 128 Number of orfs with sites within 600 bp upstream = 75 Fraction of orfs with sites within 600 bp upstream = 0.0120463 Motif number 6 GTTCGAGAAATGAATTTGGTATTATTTATT 1 45 1 TGAATTTGGT 0.764854 -82 CTTTATAACTTGATTACAATAATTCTTAAG 3 64 1 TGATTACAAT 0.827009 -29 TTGGTTTGACTGAATACAGTGTACAAGAGA 4 48 0 TGAATACAGT 0.961462 -114 GCCTGTTGTGTGACTACGATATTTTAAAAA 5 37 1 TGACTACGAT 0.967603 -110 TACCGTATATTGACTACGGTATCTAATCTT 5 78 0 TGACTACGGT 0.988813 -69 CTTAATTGCGTGACTTCAGGATATAAACCT 6 58 0 TGACTTCAGG 0.916777 -68 ********** Masking position 5 Map Score: 1.60715 Number of sites scoring better than the average of aligned sites = 52 Number in coding regions = 31 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 7 AGCTAAAAATATATTAGTATATATTGGTTT 4 71 0 ATATTAGTAT 0.600163 -91 AGGCATTACAATACTACAATATTATAAACA 5 11 0 ATACTACAAT 0.85327 -136 ACACGTGATTATATTATAACTA 6 3 0 ATATTATAAC 0.858896 -123 AAACCTTATAATACTAGAACACAGTGTCAA 6 34 0 ATACTAGAAC 0.931326 -92 ACTGCAATACATACTAGTACTTAAAAACTA 7 44 0 ATACTAGTAC 0.653849 -206 ********** Masking position 5 Map Score: 0.155093 Number of sites scoring better than the average of aligned sites = 79 Number in coding regions = 58 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 8 ********** No masking Map Score: 3.03645e-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 9 ********** No masking Map Score: 3.03645e-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: 3.03645e-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