AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00360_ctra_reg_100.orf -o00360_ctra_100.ace -a/home/amcguire/genomes/ORF_ctra.txt -z/home/amcguire/genomes/ctra.fna -g0.41 -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 = 0.41 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 gatC 200 Glu-tRNA Gln Amidotransferase (C subunit) #2 htrB 131 Acyltransferase #3 ubiA 111 4-hydroxybenzoate octaphenyltransferase #4 yaeT 300 Omp85 Analog #5 CT242 68 (OmpH-Like Outer Membrane Protein) #6 lpxD 27 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase #7 CT389 181 hypothetical protein #8 aspC 89 Aspartate Aminotransferase #9 lpxC 100 UDP-3-O-Acyl GlcNAc Deacetylase #10 cutE 63 Apolipoprotein N-Acetyltransferase #11 yciA 135 Acyl-CoA Thioester Hydrolase #12 tyrB 187 Aromatic AA Aminotransferase #13 hemA 300 Glutamyl tRNA Reductase Motif number 1 TTAACTCTGACTTTTAATCTTTTTTGCAATTTAAT 1 37 1 CTTTATCTTT 0.932991 -164 AAAGTCTTTTTTTGTTCTCTCTATTAAAGATGCGT 1 72 1 TTTTTTCTCT 0.863969 -129 GCTTTTCGGGCTTTTTTTCGTTGTTTTCAAAGTTC 4 64 1 CTTTTTCGTT 0.895187 -237 CAAAGTTCTCTCTGTTCTCTTTTCTTCCTATATTT 4 91 1 TCTTTTCTTT 0.731145 -210 GTCAAATTATCCTCGATTCTCTATTGTAATTGGAT 4 135 1 CCTGATCTCT 0.915298 -166 CCGTCCACCATTTTGACTCTCCCGTGTTTC 8 70 1 TTTGATCTCT 0.748443 -20 TAAGGGGATTCTTTTTCTCTCATCTTGAATGTAAG 10 19 1 CTTTTTCTCT 0.974466 -45 TACAGGCCCACCTCTACTCCCCAGTCATCTCTGTA 11 60 0 CCTTATCCCT 0.789626 -76 AACATGATAACCTAGTTTCTTCCCTCGGGGTATTA 12 83 0 CCTGTTCTTT 0.936959 -105 AAGATGACAGCTTGTTGTCCTAAATCGTGTAAACA 12 114 0 CTTTTTCCTT 0.895187 -74 CGCACTGCTGCTTACTGTCTTTTTTTCCAGTAAGA 12 145 0 CTTCTTCTTT 0.849349 -43 CGTAGTATTTCTTTTAGTCTTCTGTCTCACTAAGC 13 71 1 CTTTATCTTT 0.932991 -230 ACGGCTTAATCTTAGTATCTCAAGTCCTCACCGCT 13 112 0 CTTGTTCTCT 0.971998 -189 GGCTCATTCTCTTTGTTTCGTATTTTTATACCAAT 13 234 0 CTTGTTCGTT 0.885953 -67 AGATTGTATGCTTCTTCTCTCGGTTGGCTCATTCT 13 259 0 CTTTTTCTCT 0.974466 -42 *** ** **** * Masking position 8 Map Score: 16.2953 Number of sites scoring better than the average of aligned sites = 160 Number in coding regions = 160 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 2 TGACTTTTAATCTTTTTTGCAATTTAATAAAG 1 44 1 TCTTTTTGAA 0.861901 -157 CTTTTTTTGTTCTCTCTATTAAAGATGCGTTT 1 77 1 TCTCTTATAA 0.751017 -124 CCTTCGTACTTTTTTACACTAAAAACACTCTT 1 133 0 TTTTTCACAA 0.841699 -68 CGTAAAAGCTTCTTTATATAAAACGCTGTTTC 2 35 0 TCTTTTATAA 0.818635 -97 TTCAACGTACTTTTTTCAGCAAGAAAAGCTCC 3 33 1 TTTTTCAGAA 0.964354 -79 TATCCTCGATTCTCTATTGTAATTGGATAGGT 4 142 1 TCTCTTTGAA 0.805217 -159 AGAATGGTGCTCTTCCCAGAAAGAGTAAGAAT 4 233 1 TCTTCCAGAA 0.888002 -68 TATTACTTCCTTTATCTAGAAAAGTCTGCGCT 4 279 0 TTTATTAGAA 0.75121 -22 ATTGGTTATATTTTTATAGGAAAGAATT 5 51 1 TTTTTTAGAA 0.963492 -18 TATCCTTTTTTTTTTTTAGCAAGCAAGCGATA 9 49 0 TTTTTTAGAA 0.970497 -52 TTACTGTCTTTTTTTCCAGTAAGATGACAGCT 12 137 0 TTTTTCAGAA 0.964354 -51 TAGCTGATTGTTTTCTCAGAAATTAT 13 5 0 TTTTCCAGAA 0.879423 -296 ATAGTTATGCTCTCTTTAGAAAAATAATGTAA 13 37 1 TCTCTTAGAA 0.947248 -264 TTGTTTCGTATTTTTATACCAATATTTTTGAG 13 225 0 TTTTTTACAA 0.866153 -76 ATACAATCTTTTTCTTTAGAAAGGGA 13 285 1 TTTCTTAGAA 0.687699 -16 ***** *** ** Masking position 11 Map Score: 17.4766 Number of sites scoring better than the average of aligned sites = 144 Number in coding regions = 144 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 3 AGTTAAGTATACATCTACGTTGGAGAAACGTC 1 9 0 AATTACGTGA 0.966879 -192 TTTAGTGTAAAAAAGTACGAAGGATTTTATTCTG 1 142 1 AAATACGAGA 0.976316 -59 ATGATTGACCATGTTTAGGATGGAAG 1 185 1 AGTTAGGTGA 0.836187 -16 TTATCTGTACGTTGAAACGAACTTCA 3 3 1 ACTTACGTGA 0.858917 -109 TCTTGCTGAAAAAAGTACGTTGAAGTTCGTTTCA 3 23 0 AAATACGTGA 0.971981 -89 CTAGCCCTACAAATATAGGAAGAAAAGAGAACAG 4 102 0 AATTAGGAGA 0.966762 -199 AGACTTTTCTAGATAAAGGAAGTAATA 4 284 1 AATAAGGAGA 0.787039 -17 CAGCCGCGTTATAACTCGGAAGTAGAGAAAAAAC 7 139 0 AAATCGGAGA 0.866826 -43 GTGCTCTCTAAAAATTACGCTGGACAGATGAGAG 8 20 1 AAATACGTGA 0.971981 -70 CAAGTGTTTTAGAACTAGGTAGTAATTTTTTGAT 9 16 1 AAATAGGAGA 0.971881 -85 ATATTGGTATAAAAATACGAAACAAAGAGAATGA 13 232 1 AAATACGAAA 0.764601 -69 * ** **** ** * Masking position 1 Map Score: 9.06518 Number of sites scoring better than the average of aligned sites = 24 Number in coding regions = 24 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 4 GCAGAATAAAATCCTTCGTACTTTTTTACACTA 1 144 0 ATCCTTCGTT 0.950474 -57 GCAAGAAAAGCTCCTTCTGATTACAATACAAGA 3 51 1 CTCCTTCTTA 0.880817 -61 AAACCCTTCGAATATTATGGGATTA 3 97 0 ACCCTTCGAT 0.844128 -15 GTGACCAGCACCCCCTCTGAGTTCTCCCCCGAA 4 16 1 CCCCCTCTTT 0.958204 -285 CCGAAAAGCAACCCCTCTAGCAGGTTCGGGGGA 4 40 0 ACCCCTCTAG 0.654539 -261 TGGGAAGAGCACCATTCTTACTTGGTCAGAAGC 4 218 0 ACCATTCTTT 0.912715 -83 GAAGGATGCTCTCCTTCTCCTTTCGGATT 5 7 0 CTCCTTCTTT 0.981316 -62 GAAGGAGAGCATCCTTCTCCTTTCACCTATTGG 5 23 1 ATCCTTCTTT 0.97437 -46 AACAAGCATACTCATTCTGGATTTCATTGCCTC 7 44 1 CTCATTCTTT 0.912715 -138 CCCGTATATTATCCTTTTTTTTTTTTAGCAAGC 9 57 0 ATCCTTTTTT 0.73174 -44 GAAAAAGAATCCCCTTAGAAGTTAC 10 3 0 CCCCTTAGTT 0.724402 -61 ATCACCCTTCTATATGAGTCTAATAG 11 120 0 ACCCTTCTTG 0.967065 -16 TCTCGGTTGGCTCATTCTCTTTGTTTCGTATTT 13 244 0 CTCATTCTTG 0.853925 -57 ******** ** Masking position 6 Map Score: 8.32079 Number of sites scoring better than the average of aligned sites = 343 Number in coding regions = 342 Number in noncoding regions = 1 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 5 GAGAGAACAAAAAAAGACTTTATTAAATTG 1 63 0 AAAAAGACTT 0.620389 -138 TGCTGTCGCAAAAGACGCTTCAGTAAGAGT 1 109 1 AAAGACGCTT 0.919685 -92 TTTTTACACTAAAAACACTCTTACTGAAGC 1 125 0 AAAAACACTC 0.777509 -76 GTTTCAGTTGAAAAACGCTCATCATAGCA 2 10 0 AAAAACGCTC 0.940583 -122 CGTTTTATATAAAGAAGCTTTTACGTAGAG 2 42 1 AAAGAAGCTT 0.932808 -90 TTTGTGATCGAGACAGGCTCTACGTAAAAG 2 59 0 AGACAGGCTC 0.812514 -73 GTAGTTACAGAAAGAAGCTTTGTGATCGAG 2 77 0 AAAGAAGCTT 0.932808 -55 TTTTTCAGCAAGAAAAGCTCCTTCTGATTA 3 44 1 AGAAAAGCTC 0.898291 -68 AAAACAACGAAAAAAAGCCCGAAAAGCAAC 4 61 0 AAAAAAGCCC 0.927144 -240 GTCAAATCCGAAAGAAGCCGACACTCGAGC 7 89 1 AAAGAAGCCG 0.805704 -93 AAACCCTGACAAAGAGACCCCGTATATTAT 9 78 0 AAAGAGACCC 0.904644 -23 GATGAGAGAAAAAGAATCCCCTTAGAAGTT 10 13 0 AAAGAATCCC 0.83147 -51 TAAAGGGGCTCCCTTACTAGC 10 53 0 AAAGGGGCTC 0.904348 -11 CAGAGAACGAAGAGAGTCTCAAAAATATTG 13 208 1 AGAGAGTCTC 0.82127 -93 ********** Masking position 3 Map Score: 9.13981 Number of sites scoring better than the average of aligned sites = 646 Number in coding regions = 644 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 6 GATCTTATGCAGAATAAAATCCTTCGTACTT 1 154 0 AGAAAAAATC 0.95141 -47 TTACTTGGTCAGAAGCCAATCTCATAGGCGT 4 203 0 AGAACCAATC 0.930094 -98 ATCCGAAAGAAGCCGACACTCGAGCGCTCTT 7 94 1 AGCCACACTC 0.880736 -88 GTCTCGATATAGAAGAAAATCAAGAAATTCC 11 19 0 AGAAAAAATC 0.95141 -117 TTCTATATCGAGACTACTATCCATTACAGAG 11 36 1 AGACACTATC 0.897948 -100 ATAATTTCTGAGAAAACAATCAGCTAATAGT 13 11 1 AGAAACAATC 0.980428 -290 TGTAGTCTGGAGACGAAAATAGAAAAACCGT 13 163 0 AGACAAAATA 0.681853 -138 CGAGAGAAGAAGCATACAATCTTTTTCTTTA 13 272 1 AGCAACAATC 0.965947 -29 **** ****** Masking position 1 Map Score: 4.24025 Number of sites scoring better than the average of aligned sites = 84 Number in coding regions = 84 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 CATCTTTAATAGAGAGAACAAAAAAAGACT 1 74 0 AGAGAGAACA 0.884711 -127 AGCAGGTTCGGGGGAGAACTCAGAGGGGGT 4 25 0 GGGGAGAACT 0.847156 -276 AAAAGAGAACAGAGAGAACTTTGAAAACAA 4 84 0 AGAGAGAACT 0.909027 -217 CTCTTTCTGGGAAGAGCACCATTCTTACTT 4 228 0 GAAGAGCACC 0.962263 -73 GAAAGGAGAAGGAGAGCATCCTTCTCCTTT 5 16 1 GGAGAGCATC 0.938729 -53 ATTTTTAGGAGAAGAGCGCTCGAGTGTCGG 7 106 0 GAAGAGCGCT 0.902365 -76 CGTAATTTTTAGAGAGCACTGAGAAAAG 8 9 0 AGAGAGCACT 0.956653 -81 AAACCCTGACAAAGAGACCCCGTATATTAT 9 78 0 AAAGAGACCC 0.779036 -23 TAAGCTAGTAAGGGAGCCCCTTTA 10 50 1 AGGGAGCCCC 0.878144 -14 AGCTCAGTTGGTAGAGCGCAACAATGGCAT 12 54 0 GTAGAGCGCA 0.68329 -134 ATTTTTCTAAAGAGAGCATAACTATTAGCT 13 32 0 AGAGAGCATA 0.789141 -269 TGCAGAGAACGAAGAGAGTCTCAAAAATAT 13 206 1 GAAGAGAGTC 0.644698 -95 ********** Masking position 5 Map Score: 7.49899 Number of sites scoring better than the average of aligned sites = 325 Number in coding regions = 324 Number in noncoding regions = 1 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 8 TAGATGTATACTTAACTCTGACTTTTAATCTT 1 26 1 CAACTCTGAC 0.964248 -175 AAACTTCATCCCTAGCGCAGACTTTTCTAGAT 4 266 1 CAGCGCAGAC 0.971167 -35 GCGGCTGTCTCATAACCCACACTAAC 7 166 1 CAACCCACAC 0.953723 -16 GCAAAACCCTGACAAAGAGACCC 9 88 0 CAACCCTGAC 0.98659 -13 ATAGCGGGATCGAACCGCTGACCTCAACAATG 12 25 1 CACCGCTGAC 0.991426 -163 ATCTCAAGTCCTCACCGCTCACACTGCTTAGT 13 99 0 CACCGCTCAC 0.981949 -202 * ********* Masking position 4 Map Score: 2.64276 Number of sites scoring better than the average of aligned sites = 13 Number in coding regions = 13 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 AAGTACGAAGGATTTTATTCTGCATAAGAT 1 154 1 GATTTTATTC 0.942217 -47 GGTCAATCATGATCTTATGCAGAATAAAAT 1 165 0 GATCTTATGC 0.861485 -36 TACAATACAAGATCTTTTACACCTATAATC 3 72 1 GATCTTTTAC 0.695142 -40 TGCTTTTCGGGCTTTTTTTCGTTGTTTTCA 4 63 1 GCTTTTTTTC 0.812566 -238 ACGCCTATGAGATTGGCTTCTGACCAAGTA 4 203 1 GATTGGCTTC 0.821015 -98 GGAATTTCTTGATTTTCTTCTATATCGAGA 11 19 1 GATTTTCTTC 0.946291 -117 ACTATTAGCTGATTGTTTTCTCAGAAATTA 13 12 0 GATTGTTTTC 0.941169 -289 TAAAGAAAAAGATTGTATGCTTCTTCTCTC 13 273 0 GATTGTATGC 0.914993 -28 ********** Masking position 3 Map Score: 1.08321 Number of sites scoring better than the average of aligned sites = 169 Number in coding regions = 169 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: -6.4493e-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 11 ********** No masking Map Score: -6.4493e-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: -6.4493e-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