AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00550_rpxx_reg_100.orf -o00550_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 RP247 182 UDP-N-ACETYLMURAMATE--ALANINE LIGASE (murC) #2 RP249 115 D-ALANINE--D-ALANINE LIGASE (ddlB) #3 RP410 149 UDP-N-ACETYLMURAMOYLALANINE--D-GLUTAMATE LIGASE (murD) #4 RP411 74 CELL DIVISION PROTEIN FTSW (ftsW) #5 RP595 166 PHOSPHO-N-ACETYLMURAMOYL-PENTAPEPTIDE- TRANSFERASE (mraY1) #6 RP596 106 UDP-N-ACETYLMURAMOYLALANYL-D-GLUTAMYL- 2,6-DIAMINOPIMELATE--D-ALANYL-D-ALANYL LIGASE (murF) #7 RP597 120 UDP-N-ACETYLMURAMOYLALANYL-D-GLUTAMATE-- 2,6-DIAMINOPIMELATE LIGASE (murE) #8 RP825 300 UNDECAPRENYL-PHOSPHATE ALPHA-N-ACETYLGLUCOSAMINYLTRANSFERASE (mraY2) Motif number 1 AAACGTTATAATTATAACAAGATCAATTTTGAAACTCT 1 10 1 AATAAAATTT 0.819124 -173 ATCAATTATTATACTTTATAACATAGGTAATGATCTTTA 1 122 1 ATATTAATTA 0.659268 -61 TTTATGACGAATTCAATTTTAAATTATTAAACTTAA 1 157 1 ATTATAATTA 0.938286 -26 AAGGCTTTTCAAACATACTGATATTACTTTATCGCAACT 2 53 1 AAAAAAATTT 0.883465 -63 TTCTTATAGAATTAATTAGCAAATTTTTAAAGTGCATCA 3 17 0 ATTATAATTA 0.94138 -133 AACTGGAGGTATTAAGTCACAGTTTTTTATCTTCACTGT 3 54 1 ATTATATTTA 0.681841 -96 ATGACTTCAAAAAGAATATGAAATTAATACAGTGAAGAT 3 82 0 AAAATAATTA 0.853377 -68 TATCTAAGACAAATAGATAGAGATGACTTCAAAAAGAAT 3 104 0 AAAAAAATTT 0.884076 -46 CAATCTAATCAAATATTCTGAGATTCCTTAGTAAATAA 4 10 0 AAAATAATTT 0.922995 -65 ATACATTAGGATATTCTTAATAATCATGT 5 1 1 ATAATAATTA 0.964341 -166 CGGGAATGACATTGAGAGACACATGATTATTAAGAATAT 5 21 0 ATTAAAATTA 0.905091 -146 TGATTGCGTAATAAAATTAAAGATTACTAGATTCACACT 5 64 0 ATAATAATTA 0.96434 -103 CTAGCTATATAAAAATACTTAAATACTTTTAATTTAAAT 5 132 1 AAAAAAATTT 0.882344 -35 AGTGTTGTTTATATAATATTAGATAAATTACATTATGAC 6 35 1 ATAATAATTT 0.943892 -72 TAAGCAAATGACAAAGTGCCATATGTTTTTTCTCTGCAT 7 19 0 ACAATAATTT 0.7733 -102 ATCCAAAATAATACAAATAGAGTTTTTTATTTTTATTAC 7 59 0 ATAAAATTTA 0.681839 -62 AAATAATATGACATCCTTAACGTGCAATA 7 102 0 AAAATAATTA 0.942607 -19 TTGCTCTAATATTGATATTCATATGACTAATAAAATATT 8 189 1 ATTAAAATTA 0.905091 -112 AGTAACATAATTAAATTTAATATTTATTATTACTGATC 8 273 0 ATTATAATTT 0.831955 -28 *** * * * ** ** Masking position 14 Map Score: 25.8613 Number of sites scoring better than the average of aligned sites = 782 Number in coding regions = 465 Number in noncoding regions = 317 Number of orfs with sites within 600 bp upstream = 153 Fraction of orfs with sites within 600 bp upstream = 0.0245744 Motif number 2 TTAAGTTTAATAATTTAAAATTGAATTC 1 165 0 TTTATATTAA 0.61453 -18 ATTCTACTTTTTTATTAGTATGACTAAAATATT 2 93 0 TTTATATTGA 0.871774 -23 ACTTAATACCTCCAGTTCTTATAGAATTAATTA 3 38 0 TCCATTTATA 0.682353 -112 GTCATCTCTATCTATTTGTCTTAGATACTAAAC 3 116 1 TCTATTTTTA 0.954541 -34 ACCAATCTAATCAAATATTCTGAGATTCCTTAG 4 18 0 TCAATATTGA 0.746228 -57 TCTAGTAATCTTTAATTTTATTACGCAATCAAG 5 72 1 TTTATTTTTA 0.948595 -95 ATAAAAATACTTAAATACTTTTAATTTAAATCT 5 140 1 TTAATATTTA 0.91178 -27 TACGTGTTGTTCTATTGCTTTTAAAAAGCATCT 6 77 0 TCTATGTTTA 0.922423 -30 AATAGAGTTTTTTATTTTTATTACTTAAGCAAA 7 50 0 TTTATTTTTA 0.948598 -71 AATAAAAAACTCTATTTGTATTATTTTGGATCA 7 67 1 TCTATTTTTA 0.954541 -54 ATGAACTACTTCAAGTATTGTTATTATCGTCTA 8 58 1 TCAATATTTA 0.921913 -243 AGTTTACGTCTTTATTAGTGATAGACGATAATA 8 79 0 TTTATATATA 0.898135 -222 TATTACAGATTTAATTAATCTTAATAAGAGAAG 8 128 1 TTAATATTTA 0.912091 -173 ATTAATATATTTCATTGGTGTTAAATTCTTCTC 8 155 0 TTCATGTTTA 0.767523 -146 TTAATTTTGCTCTAATATTGATATTCATATGAC 8 183 1 TCTATATATA 0.909343 -118 TCATTAATATTTTATTAGTCATATGAATATCAA 8 200 0 TTTATATATA 0.898135 -101 AAATATTAAATTTAATTATGTTACT 8 286 1 TTTATTTTTA 0.948441 -15 **** ** * *** Masking position 6 Map Score: 22.6379 Number of sites scoring better than the average of aligned sites = 604 Number in coding regions = 392 Number in noncoding regions = 212 Number of orfs with sites within 600 bp upstream = 116 Fraction of orfs with sites within 600 bp upstream = 0.0186315 Motif number 3 AAATACTATGTAATACTATAATTTTGCTTA 1 85 0 TAATACTATA 0.568683 -98 GATGCACTACAAATACTATGTAATACTATA 1 95 0 AAATACTATG 0.914708 -88 GTAGTGCATCAATTATTATACTTTATAACA 1 115 1 AATTATTATA 0.855534 -68 TTCAATTTTAAATTATTAAACTTAA 1 168 1 AATTATTAAA 0.655347 -15 AGTATGACTAAAATATTAAGTTGCGATAAA 2 80 0 AAATATTAAG 0.875682 -36 AAGAATATGAAATTAATACAGTGAAGATAA 3 80 0 AATTAATACA 0.63923 -70 ATGACTTCAAAAAGAATATGAAATTAATAC 3 91 0 AAAGAATATG 0.719858 -59 CAATCTAATCAAATATTCTGAGATTCCTTA 4 19 0 AAATATTCTG 0.748545 -56 CTATTGCTTGAAATAATATGTAAT 4 61 1 AAATAATATG 0.949847 -14 CAAAAATATTATGTATCATCACG 6 4 1 AAATATTATG 0.956408 -103 GTAATTTATCTAATATTATATAAACAACAC 6 36 0 TAATATTATA 0.72953 -71 ATGTGATCCAAAATAATACAAATAGAGTTT 7 73 0 AAATAATACA 0.822995 -48 AAATAATATGACATCCTTAA 7 111 0 AAATAATATG 0.949847 -10 ATTAGAGCAAAATTAATATATTTCATTGGT 8 169 0 AATTAATATA 0.8364 -132 CAGTAATAATAAATATTAAATTTAATTATG 8 276 1 AAATATTAAA 0.833047 -25 ********** Masking position 5 Map Score: 15.2593 Number of sites scoring better than the average of aligned sites = 441 Number in coding regions = 288 Number in noncoding regions = 153 Number of orfs with sites within 600 bp upstream = 108 Fraction of orfs with sites within 600 bp upstream = 0.0173466 Motif number 4 TCAAAATTGATCTTGTTATAATTATAACGTTT 1 6 0 TTTGTATTAA 0.954961 -177 AATACTATAATTTTGCTTACTTATTAAGTATATGCCT 1 67 0 TTTGTCTTAA 0.951993 -116 AAAGTATAATAATTGATGCACTACAAATACTATGTAA 1 102 0 ATTGTATAAA 0.929621 -81 AATAATTTAAAATTGAATTCGTCATAAAGATCATTAC 1 148 0 ATTGACTTAA 0.925106 -35 TATATTTGATGCACTTTAAAAATTTGCTAA 3 4 1 ATTGTATAAA 0.929619 -146 TAATACCTCCAGTTCTTATAGAATTAATTAGCAAATT 3 31 0 ATTCTAATAA 0.72487 -119 ATTACATATTATTTCAAGCAATAGTAAACTGAGTACC 4 48 0 ATTCAATTAA 0.83726 -27 TCATACCGTGACTTGATTGCGTAATAAAATTAAAGAT 5 79 0 ATTGTCTTAA 0.980309 -88 GCACTTTGTCATTTGCTTAAGTAATAAAAATAAAAAA 7 39 1 ATTGTATTAA 0.981562 -82 ATTGGTGTTAAATTCTTCTCTTATTAAGATTAATTAA 8 138 0 ATTCTCTTAA 0.95096 -163 AATATATTAATTTTGCTCTAATATTGATATTCATATG 8 177 1 TTTGTATTGA 0.79973 -124 * *** * * * *** Masking position 17 Map Score: 6.46436 Number of sites scoring better than the average of aligned sites = 249 Number in coding regions = 161 Number in noncoding regions = 88 Number of orfs with sites within 600 bp upstream = 52 Fraction of orfs with sites within 600 bp upstream = 0.00835207 Motif number 5 GTAATACTATAATTTTGCTTACTTATTAAG 1 76 0 AATTTTGCTT 0.90264 -107 TGCACTTTAAAAATTTGCTAATTAATTCTA 3 20 1 AAATTTGCTA 0.845353 -130 AGATCGAGTTAATTTTTCTAGCTATATAAA 5 115 1 AATTTTTCTA 0.968867 -52 GTCATAATGTAATTTATCTAATATTATATA 6 44 0 AATTTATCTA 0.847952 -63 ATGATCAGAAAATTTTTCCCATTATGAACT 8 35 1 AATTTTTCCC 0.908938 -266 CTAACTTGTTAATTTTTATATTACAGATTT 8 110 1 AATTTTTATA 0.776543 -191 ATTGGTGTTAAATTCTTCTCTTATTAAGAT 8 145 0 AATTCTTCTC 0.908938 -156 GAAATATATTAATTTTGCTCTAATATTGAT 8 175 1 AATTTTGCTC 0.97357 -126 ********** Masking position 2 Map Score: 4.42198 Number of sites scoring better than the average of aligned sites = 279 Number in coding regions = 213 Number in noncoding regions = 66 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 6 CATTACCTATGTTATAAAGTATAATAATTGA 1 123 0 GTATAAAGTA 0.970403 -60 ATATTAAGTTGCGATAAAGTAATATCAGTAT 2 67 0 GCATAAAGTA 0.909817 -49 AGTCATACTAATAAAAAAGTAGAAT 2 101 1 ATAAAAAGTA 0.849322 -15 TTTGTCTTAGATACTAAACTACAATGACTA 3 130 1 ATCTAAACTA 0.778385 -20 TATTAAGAATATCCTAATGTAT 5 2 0 ATCTAATGTA 0.93347 -165 AGCATCTAGTGTCATAATGTAATTTATCTAA 6 53 0 GTATAATGTA 0.961797 -54 ATTAAGGTACATGATAATGTAATGATCAGTA 8 250 1 ATATAATGTA 0.954235 -51 ** ******** Masking position 6 Map Score: 1.38568 Number of sites scoring better than the average of aligned sites = 160 Number in coding regions = 103 Number in noncoding regions = 57 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 7 TACATAGTATTTGTAGTGCATCAATTATTATAC 1 103 1 TTGGTCATCA 0.912444 -80 TGAATTCGTCATAAAGATCATTACCTATGTTAT 1 139 0 ATAGACATTA 0.835439 -44 TAGCAAATTTTTAAAGTGCATCAAATATA 3 7 0 TTAGTCATCA 0.982247 -143 CAAAAATATTATGTATCATCACGTAGTGTTG 6 9 1 TTATACATCA 0.921656 -98 GTAGTGTTGTTTATATAATATTAGATAAATTAC 6 33 1 TTATATATTA 0.563155 -74 ATAATATTAGATAAATTACATTATGACACTAGA 6 47 1 ATATTCATTA 0.759817 -60 TCTATTTGTATTATTTTGGATCACATATTGCAC 7 77 1 TTATTGATCA 0.747094 -44 TATGACATCCTTAACGTGCAATATGTGATCCAA 7 92 0 TTAGTCAATA 0.815136 -29 AGTATTGTTATTATCGTCTATCACTAATAAAGA 8 71 1 TTAGTTATCA 0.9011 -230 ACTTTAAACATTAAGGTACATGATAATGTAATG 8 241 1 TTAGTCATGA 0.926643 -60 ATATTTATTATTACTGATCATTACATTATCATG 8 259 0 TTAGACATTA 0.953403 -42 *** ** ***** Masking position 10 Map Score: 4.02227 Number of sites scoring better than the average of aligned sites = 177 Number in coding regions = 118 Number in noncoding regions = 59 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 8 ********** No masking Map Score: -8.50219e-13 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: -8.50219e-13 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: -8.50219e-13 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