AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00650_ctra_reg_100.orf -o00650_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 htrB 131 Acyltransferase #2 yaeT 300 Omp85 Analog #3 CT242 68 (OmpH-Like Outer Membrane Protein) #4 lpxD 27 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase #5 pdhA 221 Pyruvate Dehydrogenase Alpha #6 lpxC 100 UDP-3-O-Acyl GlcNAc Deacetylase #7 cutE 63 Apolipoprotein N-Acetyltransferase #8 yciA 135 Acyl-CoA Thioester Hydrolase #9 sdhB 236 Succinate Dehydrogenase #10 sdhC 25 Succinate Dehydrogenase #11 CT593.1 221 hypothetical protein-possible frameshift with CT593 Motif number 1 TTTGCTAGTAGTTACAGAAAGAAGCTTTGTG 1 83 0 GTTAAGAAAG 0.790686 -49 TAGCCCTACAAATATAGGAAGAAAAGAGAAC 2 104 0 AATAAGGAAG 0.929908 -197 GCGTCCCCACATATTAGGAAGAGACTACTCA 2 176 0 ATATAGGAAG 0.907586 -125 GCTCTTCCCAGAAAGAGTAAGAATAAAACTT 2 241 1 GAAAAGTAAG 0.675504 -60 GACTTTTCTAGATAAAGGAAGTAATA 2 285 1 GATAAGGAAG 0.948266 -16 AATCCGAAAGGAGAAGGAGAGCATCCT 3 7 1 AAAGAGAAGG 0.870352 -62 CCAATAGGTGAAAGGAGAAGGATGCTCTCCT 3 25 0 AAAGAGAAGG 0.870352 -44 CAGAAATTTCATATAAGAAAGTAGATACCCG 9 44 1 ATATAGAAAG 0.760057 -193 TTCATTTCCCGATATAGGAGGCTAATTTGAA 9 152 1 GATAAGGAGG 0.962012 -85 TCATCATGATGTTTGAGGAGGGCTCTTTATG 11 82 1 GTTTAGGAGG 0.941799 -140 GAGGGACAGCGAATAAGGAGGCGTTCATATG 11 129 1 GAATAGGAGG 0.967037 -93 GGAGGCGTTCATATGAGGAGGGAGATAGTAC 11 145 1 ATATAGGAGG 0.931359 -77 TAATGAAACGAATGTAGGAAGATTTTTGTAC 11 172 0 AATGAGGAAG 0.928592 -50 **** ****** Masking position 6 Map Score: 12.4117 Number of sites scoring better than the average of aligned sites = 301 Number in coding regions = 300 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 2 GCTAGTGACCAGCACCCCCTCTGAGTTCTCC 2 12 1 AGCACCCCTC 0.986482 -289 AAGCCCGAAAAGCAACCCCTCTAGCAGGTTC 2 46 0 AGCACCCCTC 0.986482 -255 AAGGAGAAGGATGCTCTCCTTCTCCTTTCGG 3 14 0 ATGCCTCCTT 0.863693 -55 ACGGCACTCCTCGGCTAGCTTC 4 16 0 CGGCCTCCTC 0.958864 -12 AGAATTTTTCAGGAACCCTTTATCCAAGAGA 5 197 1 AGGACCCTTT 0.887646 -25 TGAGAGAAAAAGAATCCCCTTAGAAGTTAC 7 10 0 AGAACCCCTT 0.907662 -54 AAGCTAGTAAGGGAGCCCCTTTA 7 51 1 GGGACCCCTT 0.977323 -13 TCAGAGTTACAGGCCCACCTCTACTCCCCAG 8 71 0 AGGCCACCTC 0.975299 -65 ATTATTTCCCAGGAACGCCTCTATAAATATT 9 199 0 AGGACGCCTC 0.991391 -38 CTTCCATAAAGAGCCCTCCTCAAACATCATG 11 86 0 GAGCCTCCTC 0.807846 -136 CCCTCCTCATATGAACGCCTCCTTATTCGCT 11 136 0 ATGACGCCTC 0.95217 -86 **** ****** Masking position 10 Map Score: 11.0752 Number of sites scoring better than the average of aligned sites = 124 Number in coding regions = 123 Number in noncoding regions = 1 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 3 CGTTTTATATAAAGAAGCTTTTACGTAGAGC 1 42 1 AAAGAACTTT 0.776714 -90 GTAGTTACAGAAAGAAGCTTTGTGATCGAGA 1 76 0 AAAGAACTTT 0.776714 -56 AAAAGCCCGAAAAGCAACCCCTCTAGCAGGT 2 48 0 AAAGCACCCC 0.872475 -253 AAAAGAGAACAGAGAGAACTTTGAAAACAAC 2 83 0 AGAGAGACTT 0.913791 -218 CATATTAGGAAGAGACTACTCAAGACCTATC 2 167 0 AGAGACACTC 0.712327 -134 CTTTCTGGGAAGAGCACCATTCTTACTTGGT 2 225 0 AGAGCACATT 0.701941 -76 AAGGAGAAGGAGAGCATCCTTCTCCTTTCAC 3 18 1 AGAGCACCTT 0.909989 -51 AAACCCTGACAAAGAGACCCCGTATATTATC 6 77 0 AAAGAGCCCC 0.953378 -24 GATGAGAGAAAAAGAATCCCCTTAGAAGTTA 7 12 0 AAAGAACCCC 0.935796 -52 TAAGCTAGTAAGGGAGCCCCTTTA 7 50 1 AGGGAGCCCT 0.782385 -14 ATGTCGTGCTAGAGAATATTCCAGCGAATAT 9 122 1 AGAGAAATTC 0.750548 -115 GGCTAATTTGAAAGAGACATTTATTTTGAAT 9 171 1 AAAGAGCATT 0.814247 -66 GGGAGAGAGAATTTTTTCTCTTCA 10 4 1 AGAGAGATTT 0.773512 -22 GCCCTTCCATAAAGAGCCCTCCTCAAACATC 11 89 0 AAAGAGCCTC 0.968603 -133 ****** **** Masking position 1 Map Score: 9.12831 Number of sites scoring better than the average of aligned sites = 593 Number in coding regions = 592 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 4 GGGTTGCTTTTCGGGCTTTTTTTCGTTGTTTTCA 2 59 1 TCGGTTTTTC 0.899237 -242 CAATAGAGAATCGAGGATAATTTGACTAGCCCTA 2 127 0 TCGGTATTTG 0.946291 -174 ATTGGATAGGTCTTGAGTAGTCTCTTCCTAATAT 2 163 1 TCTGTATCTC 0.991386 -138 ACTTCCTTTATCTAGAAAAGTCTGCGCTAGGGAT 2 273 0 TCTGAATCTG 0.879475 -28 TTCTTCTATATCGAGACTACTATCCATTACAGAG 8 33 1 TCGGTATATC 0.965795 -103 ATAGCCTCTATCTTGACTAGTCTCAGAGTTACAG 8 90 0 TCTGTATCTC 0.991386 -46 TTGCTCCCTGTCGAGTGTAATCTCGTAATTCTGG 9 85 0 TCGGTATCTC 0.994551 -152 ATGAATATTCGCTGGAATATTCTCTAGCACGACA 9 123 0 GCTGTATCTC 0.968322 -114 *** * ** **** Masking position 11 Map Score: 6.19972 Number of sites scoring better than the average of aligned sites = 32 Number in coding regions = 31 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 TGCTAGTGACCAGCACCCCCTCTGAGTTCT 2 11 1 CAGCACCCCC 0.974435 -290 AAAGCCCGAAAAGCAACCCCTCTAGCAGGT 2 48 0 AAGCAACCCC 0.985388 -253 CCAATCTCATAGGCGTCCCCACATATTAGG 2 189 0 AGGCGTCCCC 0.974738 -112 AACCCTGACAAAGAGACCCCGTATATTATC 6 77 0 AAGAGACCCC 0.985387 -24 ATGAGAGAAAAAGAATCCCCTTAGAAGTTA 7 12 0 AAGAATCCCC 0.977204 -52 CCCTTCCATAAAGAGCCCTCCTCAAACATC 11 89 0 AAGAGCCCTC 0.941575 -133 ********** Masking position 7 Map Score: 4.76769 Number of sites scoring better than the average of aligned sites = 36 Number in coding regions = 36 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 6 TCTCTCTGTTCTCTTTTCTTCCTATATTTGT 2 97 1 CTCTTTCTTC 0.935976 -204 AGGAGAAGGATGCTCTCCTTCTCCTTTCGGA 3 13 0 TGCTTCCTTC 0.893551 -56 CCAACTTCATCTCTATCCATTTTTCTGGGTA 5 20 1 CTCTTCCATT 0.874232 -202 CAAACAGCAGCTATATCCCTCAACTGAAAGG 11 26 0 CTATTCCCTC 0.970535 -196 CGATTAAGTGCGCTGTTCATCATGATGTTTG 11 66 1 CGCTTTCATC 0.946392 -156 CCTCCTTATTCGCTGTCCCTCATGGTTCCTG 11 119 0 CGCTTCCCTC 0.993189 -103 GATTTTTGTACTATCTCCCTCCTCATATGAA 11 152 0 CTATTCCCTC 0.970535 -70 **** ****** Masking position 6 Map Score: 4.28221 Number of sites scoring better than the average of aligned sites = 121 Number in coding regions = 121 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 TTTTCTTCCTATATTTGTAGGGCTAGTCAA 2 110 1 ATATTTGTAG 0.956502 -191 TATTGGTTATATTTTTATAGGAAAGAATT 3 50 1 ATTTTTATAG 0.947942 -19 CGAAAAGTTTTTTTTTGTAGCATAGACTTG 5 55 1 TTTTTTGTAG 0.956504 -167 TTATCCTTTTTTTTTTTTAGCAAGCAAGCG 6 52 0 TTTTTTTTAG 0.846977 -49 TTTATTTTGAATATTTATAGAGGCGTTCCT 9 190 1 ATATTTATAG 0.907008 -47 ATGTAGGAAGATTTTTGTACTATCTCCCTC 11 162 0 ATTTTTGTAC 0.903918 -60 ********** Masking position 5 Map Score: 1.67152 Number of sites scoring better than the average of aligned sites = 92 Number in coding regions = 92 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 AAGTCTGCGCTAGGGATGAAGTTTTATTCT 2 260 0 TAGGGATGAA 0.96636 -41 TATATTTTTATAGGAAAGAATT 3 57 1 TAGGAAAGAA 0.829112 -12 GAAAAATGGATAGAGATGAAGTTGGTTTGA 5 15 0 TAGAGATGAA 0.932925 -207 GTAGTCTCGATATAGAAGAAAATCAAGAAA 8 23 0 TATAGAAGAA 0.897633 -113 ATTAGACTCATATAGAAGGGTGAT 8 122 1 TATAGAAGGG 0.876932 -14 AATTAGGGATGGAAGCCTTTCAG 11 4 1 TAGGGATGGA 0.971981 -218 GAGGGCTCTTTATGGAAGGGCAGGAACCAT 11 99 1 TATGGAAGGG 0.936374 -123 ********** Masking position 6 Map Score: 3.14425 Number of sites scoring better than the average of aligned sites = 158 Number in coding regions = 158 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 TTTTATATAAAGAAGCTTTTACGTAGAGCC 1 44 1 AGAAGCTTTT 0.936927 -88 AGTTACAGAAAGAAGCTTTGTGATCGAGAC 1 75 0 AGAAGCTTTG 0.841428 -57 TAATATGTGGGGACGCCTATGAGATTGGCT 2 191 1 GGACGCCTAT 0.903551 -110 TTACTTGGTCAGAAGCCAATCTCATAGGCG 2 204 0 AGAAGCCAAT 0.890095 -97 GAATTTTTCAGGAACCCTTTATCCAAGAGA 5 198 1 GGAACCCTTT 0.89401 -24 TAGTCAAGATAGAGGCTATTAGACTCATAT 8 105 1 AGAGGCTATT 0.87122 -31 TCCCGATATAGGAGGCTAATTTGAAAGAGA 9 158 1 GGAGGCTAAT 0.875384 -79 AATTAGGGATGGAAGCCTTTCAGTTGAGGG 11 11 1 GGAAGCCTTT 0.982584 -211 AACGAATGTAGGAAGATTTTTGTACTATCT 11 167 0 GGAAGATTTT 0.815513 -55 ********** Masking position 3 Map Score: 4.22206 Number of sites scoring better than the average of aligned sites = 303 Number in coding regions = 303 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 AAGCTTTTACGTAGAGCCTGTCTCGATCACA 1 56 1 GAGAGCCTGT 0.982375 -76 TATGTGTTCCGTAAGGCTAGTATGACTTTGC 1 109 0 GAAGGCTAGT 0.913724 -23 TCCTATATTTGTAGGGCTAGTCAAATTATCC 2 116 1 GAGGGCTAGT 0.982211 -185 CGCCGGCCTTGCATAGCCAGAGTGAAATTCA 5 142 1 GATAGCCAGA 0.914408 -80 GGGGAGTAGAGGTGGGCCTGTAACTCTGAGA 8 73 1 GTGGGCCTGT 0.978829 -63 ATATTCTGTAGATGAGCCAGAAATTTCATAT 9 27 1 GTGAGCCAGA 0.967614 -210 * ********* Masking position 6 Map Score: 0.496095 Number of sites scoring better than the average of aligned sites = 43 Number in coding regions = 43 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 CCCCTCTGAGTTCTCCCCCGAACCTGCTAG 2 27 1 TTCTCCCCCG 0.955468 -274 AAGAATGGTGCTCTTCCCAGAAAGAGTAAG 2 232 1 CTCTTCCCAG 0.969183 -69 AACTTTTCGGCACTACCCAGAAAAATGGAT 5 34 0 CACTACCCAG 0.983244 -188 ATCAAAAAATTACTACCTAGTTCTAAAACA 6 20 0 TACTACCTAG 0.916316 -81 GGCCCACCTCTACTCCCCAGTCATCTCTGT 8 61 0 TACTCCCCAG 0.990949 -75 TTCCCAATATTATTTCCCAGGAACGCCTCT 9 208 0 TATTTCCCAG 0.916316 -29 ********** Masking position 4 Map Score: 3.75452 Number of sites scoring better than the average of aligned sites = 49 Number in coding regions = 49 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: 1.26009e-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 CGAAAAAAAGCCCGAAAAGCAACCCCTCTA 2 54 0 CCCGAAAAGC 0.965523 -247 CTTCCTTTATCTAGAAAAGTCTGCGCTAGG 2 276 0 CTAGAAAAGT 0.884153 -25 TCGGCACTACCCAGAAAAATGGATAGAGAT 5 28 0 CCAGAAAAAT 0.941353 -194 TCTGGGTAGTGCCGAAAAGTTTTTTTTTGT 5 43 1 GCCGAAAAGT 0.974622 -179 GGAAAAGTAACCGGAAAGGTCCGGCCTTCG 5 111 0 CCGGAAAGGT 0.965523 -111 CAAGGCCGGCGCGGAAAAGTAACCGGAAAG 5 123 0 GCGGAAAAGT 0.974622 -99 ATAAAGGGTTCCTGAAAAATTCTAGAATGT 5 190 0 CCTGAAAAAT 0.901016 -32 ********** Masking position 5 Map Score: 3.75056 Number of sites scoring better than the average of aligned sites = 31 Number in coding regions = 31 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 14 ********** No masking Map Score: 1.26009e-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 15 ********** No masking Map Score: 1.26009e-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