AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00460_rpxx_reg_300.orf -o00460_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 RP008 190 (3R)-HYDROXYMYRISTOYL-[ACYL CARRIER PROTEIN] DEHYDRATASE (fabZ) #2 RP009 300 UDP-3-O-[3-HYDROXYMYRISTOYL] GLUCOSAMINE N-ACYLTRANSFERASE (lpxD) #3 RP153 300 GLUTAMYL-tRNA AMIDOTRANSFERASE SUBUNIT C (gatC) #4 RP743 79 SERINE HYDROXYMETHYLTRANSFERASE (glyA) #5 RP744 102 unknown #6 RP745 52 GLUTAREDOXIN-LIKE PROTEIN GRLA (grxC2) Motif number 1 ATTGATTCATACAACAATAAAGTTATAGTAAA 1 6 0 AAAAAATATA 0.742687 -185 TTTAACCATTAGATCCAGAAAAATATATTTAATTGGG 1 62 1 AAAAAATATA 0.742687 -129 CTAAGTAATCTCTAAATAAAAGAACTACACAAAAACC 2 28 1 TTTAAAACTA 0.968103 -273 CAAAGATGAATCTCAAATAAATCAATATTATTAATTT 2 74 1 TTAAAAAATA 0.949888 -227 ATGTAATGTGAGAAATTTAAATTAATAATATTGATTT 2 92 0 AATAAAAATA 0.949908 -209 AATCTCAAATTTAGTTTAAAATTACTATATTAGTATT 2 152 1 TATAAAACTA 0.968104 -149 TACAGTGACTTGACTATAAAAATACTAATATAGTAAT 2 172 0 TATAAAACTA 0.968104 -129 ATTGATTCAAATACTTTTAAATGTCTACAACTTCTGT 3 48 0 AATAAATCTA 0.822054 -253 TTTTTTATGTTTTAATTAAAAATAATATCTTGTAGTT 3 105 0 TTTAAAAATA 0.968684 -196 ATTAAGATAGTTTTAGAAAAATAACTAATTAGCTTTT 3 165 1 TTAAAAACTA 0.948918 -136 AATTAGCTTTTATGACTTAATGAAATAAAATAGGATA 3 191 1 TTTAATAATA 0.720144 -110 CAAGCAAATTTTTACGTAAAAATAATAAAACT 3 279 1 TTTAAAAATA 0.968684 -22 TACAGTACAAAGAAAAATAAACGACTAGATACCGTGA 4 11 0 AAAAAAACTA 0.919155 -69 ATTAAAGTTGAGTATATTAAATGAATAGCAATAGCAA 5 42 0 ATTAAAAATA 0.949859 -61 ATACTCAACTTTAATATTAAAGTAATAAACATATGAA 5 64 1 TATAAAAATA 0.968654 -39 ATAGAAAGTGTATTTTAGAAAATAATATTTATATCAG 6 19 1 TTAAAAAATA 0.949001 -34 * * * *** **** Masking position 9 Map Score: 21.4269 Number of sites scoring better than the average of aligned sites = 869 Number in coding regions = 560 Number in noncoding regions = 309 Number of orfs with sites within 600 bp upstream = 150 Fraction of orfs with sites within 600 bp upstream = 0.0240925 Motif number 2 TTGCATAGAGCAATTTTATCTCTGTTATTC 1 117 0 CAATTTTATC 0.957303 -74 GTAATAAAGGCAAATTTATATTAAACAAGA 1 160 1 CAAATTTATA 0.695582 -31 TCAAATAAATCAATATTATTAATTTAAATT 2 86 1 CAATATTATT 0.954063 -215 ACTTGAATCTCAAATTTAGTTTAAAATTAC 2 147 1 CAAATTTAGT 0.900777 -154 TTTAAAATTACTATATTAGTATTTTTATAG 2 166 1 CTATATTAGT 0.870063 -135 ATAAAACTTACAATTTTATTGCATAATAAA 2 233 1 CAATTTTATT 0.978664 -68 ATTTTTTTACCTATTTTAGT 3 1 0 CTATTTTAGT 0.93666 -300 ATTCTATATCCTATTTTATTTCATTAAGTC 3 204 0 CTATTTTATT 0.954064 -97 ATCCAAGTTCTAATTTTATCAGAATTACAC 3 250 1 TAATTTTATC 0.687305 -51 AACCTGATATAAATATTATTTTCTAAAATA 6 29 0 AAATATTATT 0.670622 -24 ********** Masking position 6 Map Score: 8.5014 Number of sites scoring better than the average of aligned sites = 455 Number in coding regions = 330 Number in noncoding regions = 125 Number of orfs with sites within 600 bp upstream = 65 Fraction of orfs with sites within 600 bp upstream = 0.0104401 Motif number 3 AAAGAACTACACAAAAACCTTAGCTATTCAAA 2 46 1 AAAAAACTTA 0.953606 -255 AGCTATTCAAAGATGAATCTCAAATAAATCAA 2 67 1 AATGAACTCA 0.898411 -234 TCAATTAATAACTTGAATCTCAAATTTAGTTT 2 137 1 ATTGAACTCA 0.865302 -164 CGTTTTTGCCATATAAAACTTACAATTTTATT 2 221 1 AATAAACTTA 0.965866 -80 TTTATTGCATAATAAAAGCATAACTTATATAA 2 247 1 ATAAAACATA 0.885635 -54 TGATTAAGTCAGTTAAAGTTTAT 2 288 1 ATTAAATTTA 0.835836 -13 TAAAATAGGTAAAAAAATCTTAAGATCATTAT 3 13 1 AAAAAACTTA 0.953606 -288 GTATCAATGAATATAAACTACAAGATATTATT 3 90 1 AATAAATACA 0.670219 -211 TATTATTTTTAATTAAAACATAAAAAAGAAAT 3 115 1 ATTAAACATA 0.914241 -186 TAAAACATAAAAAAGAAATTTAACGACTGTTT 3 128 1 AAAGAATTTA 0.740015 -173 ACAGATAAATACTAAAAACATATGAGGATGC 4 59 1 ATAAAACATA 0.885635 -21 TCAAAACCTGATATAAATATTATTTTCTAAAA 6 31 0 AATAAAATTA 0.73503 -22 * ***** **** Masking position 6 Map Score: 8.48568 Number of sites scoring better than the average of aligned sites = 414 Number in coding regions = 261 Number in noncoding regions = 153 Number of orfs with sites within 600 bp upstream = 75 Fraction of orfs with sites within 600 bp upstream = 0.0120463 Motif number 4 TTATCTCTGTTATTCAATTATTTATTCACGG 1 101 0 TATTCATTAT 0.79118 -90 GATTACTTAGTATTCATAGATACGATA 2 7 0 TATTCAAGAT 0.97137 -294 GTAGTTCTTTTATTTAGAGATTACTTAGTAT 2 25 0 TATTTAAGAT 0.929885 -276 AAACCTTAGCTATTCAAAGATGAATCTCAAA 2 60 1 TATTCAAGAT 0.97137 -241 TGTTCAGTGTCATACAGTGACTTGACTATAA 2 190 0 CATACATGAC 0.846298 -111 CAACTTCTGTCATATAATGATCTTAAGATTT 3 27 0 CATATATGAT 0.890149 -274 TTGTAGTTTATATTCATTGATACTGCAGATT 3 82 0 TATTCATGAT 0.97137 -219 TGTAGTAACACATATACAGATAAATACTAAA 4 44 1 CATATAAGAT 0.890149 -36 ****** **** Masking position 6 Map Score: 5.21976 Number of sites scoring better than the average of aligned sites = 48 Number in coding regions = 25 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 5 AGGCAAATTTATATTAAACAAGAGACCTAGAT 1 167 1 ATATTAAAAG 0.968356 -24 TGTAAGTTTTATATGGCAAAAACGTGTTCAGT 2 213 0 ATATGGAAAA 0.903989 -88 ATCACTAGCGATATTATATAAGTTATGCTTTT 2 260 0 ATATTAAAAG 0.968324 -41 TAAGATCATTATATGACAGAAGTTGTAGACAT 3 33 1 ATATGAAAAG 0.973653 -268 AAAGTTGAGTATATTAAATGAATAGCAATAGC 5 44 0 ATATTAAGAA 0.902592 -59 CTCAACTTTAATATTAAAGTAATAAACATATG 5 67 1 ATATTAATAA 0.862073 -36 AGTAATAAACATATGAAATAAAGTAAACC 5 84 1 ATATGAAAAA 0.968357 -19 ****** * *** Masking position 8 Map Score: 3.77317 Number of sites scoring better than the average of aligned sites = 171 Number in coding regions = 118 Number in noncoding regions = 53 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 6 ********** No masking Map Score: -2.59815e-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: -2.59815e-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 8 ********** No masking Map Score: -2.59815e-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