AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00350_ctra_reg_100.orf -o00350_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 ubiA 111 4-hydroxybenzoate octaphenyltransferase #3 yaeT 300 Omp85 Analog #4 CT242 68 (OmpH-Like Outer Membrane Protein) #5 lpxD 27 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase #6 CT355 300 hypothetical protein #7 CT389 181 hypothetical protein #8 aspC 89 Aspartate Aminotransferase #9 CT426 196 Fe-S oxidoreductase #10 lpxC 100 UDP-3-O-Acyl GlcNAc Deacetylase #11 cutE 63 Apolipoprotein N-Acetyltransferase #12 yciA 135 Acyl-CoA Thioester Hydrolase #13 tyrB 187 Aromatic AA Aminotransferase #14 ygcA 85 rRNA Methyltransferse #15 hctA 300 Histone-Like Developmental Protein Motif number 1 TATTGTAATCAGAAGGAGCTTTTCTTGCTG 2 49 0 AGAAGGAGCT 0.893211 -63 AGCAGGTTCGGGGGAGAACTCAGAGGGGGT 3 25 0 GGGGAGAACT 0.870007 -276 AAAAGAGAACAGAGAGAACTTTGAAAACAA 3 84 0 AGAGAGAACT 0.95372 -217 CTCTTTCTGGGAAGAGCACCATTCTTACTT 3 228 0 GAAGAGCACC 0.889179 -73 CTATAGGGGAGGAGGGACCCAGCCGTCAGA 6 122 0 GGAGGGACCC 0.958423 -179 TTATATTCTAAAAAAGAACCTACCCTCGTC 6 163 0 AAAAAGAACC 0.733509 -138 ATTTTTAGGAGAAGAGCGCTCGAGTGTCGG 7 106 0 GAAGAGCGCT 0.904426 -76 CGTAATTTTTAGAGAGCACTGAGAAAAG 8 9 0 AGAGAGCACT 0.967288 -81 CTTCCTAGTAGGAAAGACCCTATCAAAACA 9 85 0 GGAAAGACCC 0.936447 -112 CTTTCCTACTAGGAAGACCCCTATCTAAAG 9 99 1 AGGAAGACCC 0.857175 -98 AAACCCTGACAAAGAGACCCCGTATATTAT 10 78 0 AAAGAGACCC 0.909254 -23 TAAGCTAGTAAGGGAGCCCCTTTA 11 50 1 AGGGAGCCCC 0.947401 -14 TATAAAAAAGAGAAAGCGCTAAAATA 14 7 0 AGAAAGCGCT 0.945806 -79 TCTTTTTTATAGAGGGCACTTTTATCAACA 14 26 1 AGAGGGCACT 0.953145 -60 AGAAGAGGAAAGAGGGCCCTGTTGATAAAA 14 45 0 AGAGGGCCCT 0.970065 -41 AGAAAAGAAAGAAAGGAGCTTGTTCTCTTG 15 22 0 GAAAGGAGCT 0.666009 -279 TTCTTTTAATAGAAAGCGCTGAACCTTGTT 15 53 0 AGAAAGCGCT 0.945806 -248 ********** Masking position 6 Map Score: 19.1746 Number of sites scoring better than the average of aligned sites = 362 Number in coding regions = 361 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 TACGTAAAAGCTTCTTTATATAAAACGCTGT 1 38 0 CTTCTTTTAT 0.938513 -94 GATCACAAAGCTTCTTTCTGTAACTACTAGC 1 80 1 CTTCTTTTGT 0.92769 -52 AAAGTTCTCTCTGTTCTCTTTTCTTCCTATA 3 92 1 CTGTTCTTTT 0.865694 -209 CAGAAAAATACATTTTTGTTTCCTTTGGCTT 6 61 1 CATTTTTTTT 0.849939 -240 AGAATATAAGCTGCTTTGTTTGGGTGTTTGC 6 184 1 CTGCTTTTTT 0.978342 -117 TTCCTCCTCCCCTTTTTCTTTGGATCTTACC 6 232 0 CCTTTTTTTT 0.859437 -69 ATGAGAGTCTCATCTTTATATTACCGTCCAC 8 47 1 CATCTTTTAT 0.830519 -43 GCCTTCATGACTTCTTTATTTCTACTCGTCT 9 17 1 CTTCTTTTTT 0.986796 -180 GGGGACAAGACTTCTTTTTCTGACAGCAGTC 9 143 0 CTTCTTTTCT 0.92769 -54 GTATATTATCCTTTTTTTTTTTTAGCAAGCA 10 56 0 CTTTTTTTTT 0.946358 -45 ATTTTAGCGCTTTCTCTTTTTTATAGAGGGC 14 12 1 TTTCTCTTTT 0.829023 -74 TCATTGATCCCTTCTCTTTTTT 14 74 1 CTTCTCTTTT 0.978342 -12 AACAAGCTCCTTTCTTTCTTTTCTAAACAAG 15 28 1 TTTCTTTTTT 0.889157 -273 TCTCCTTGTACCGCTCTGTTTATCAATAGGT 15 149 0 CCGCTCTTTT 0.904424 -152 GATCCTAAAGCAGCTTTATTTGACATCTCCT 15 174 0 CAGCTTTTTT 0.935494 -127 ******* *** Masking position 5 Map Score: 15.6771 Number of sites scoring better than the average of aligned sites = 270 Number in coding regions = 270 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 TCTTGAGTAGTCTCTTCCTAATATGTGGGG 3 173 1 TCTCTTCCTA 0.641155 -128 AGGATGCTCTCCTTCTCCTTTCGGATT 4 8 0 CCTTCTCCTT 0.975906 -61 AGGAGAGCATCCTTCTCCTTTCACCTATTG 4 25 1 CCTTCTCCTT 0.975906 -44 CGGCTGGGTCCCTCCTCCCCTATAGCTTTT 6 127 1 CCTCCTCCCC 0.992779 -174 AAGAACCTACCCTCGTCCTAGGTAAAAGCT 6 150 0 CCTCGTCCTA 0.929897 -151 TTGGATCTTACCGCCTCCCTAGAGATGTGG 6 214 0 CCGCCTCCCT 0.942277 -87 TTGGGTTGTTCCTCCTCCCCTTTTTCTTTG 6 241 0 CCTCCTCCCC 0.992779 -60 ACTCGAGCGCTCTTCTCCTAAAAATCTTGT 7 111 1 TCTTCTCCTA 0.919541 -71 GAAAAAGAAGTCTTGTCCCCGTGAAAAGCA 9 154 1 TCTTGTCCCC 0.894406 -43 CAGGCCCACCTCTACTCCCCAGTCATCTCT 12 63 0 TCTACTCCCC 0.886553 -73 CTCATTGATCCCTTCTCTTTTTT 14 73 1 CCTTCTCTTT 0.761421 -13 ********** Masking position 6 Map Score: 11.1337 Number of sites scoring better than the average of aligned sites = 233 Number in coding regions = 231 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 4 GAACTTCAACGTACTTTTTTCAGCAAGAAAA 2 29 1 GTATTTTTTC 0.961953 -83 TTGCTTTTCGGGCTTTTTTTCGTTGTTTTCA 3 62 1 GGCTTTTTTC 0.895219 -239 TCTCTCTGTTCTCTTTTCTTCCTATATTTGT 3 97 1 CTCTTTCTTC 0.784369 -204 TAGGTCTTGAGTAGTCTCTTCCTAATATGTG 3 169 1 GTATCTCTTC 0.705935 -132 GTATTTTTCTGGAATTTTTTCACTTAAATAT 6 41 0 GGATTTTTTC 0.938581 -260 AAATTCTTAAGGTTTTTCTACCTAAAAACTA 6 270 1 GGTTTTCTAC 0.587512 -31 CCTTGATTTGTAGTTTTTAGGTAGAAAAAC 6 281 0 GTATTTTTAG 0.7003 -20 TCCTAAAAATCTTGTTTTTTCTCTACTTCCG 7 126 1 CTTTTTTTTC 0.800925 -56 TCTGTCCAGCGTAATTTTTAGAGAGCACTGA 8 17 0 GTATTTTTAG 0.700297 -73 GAACTAGGTAGTAATTTTTTGATATCGCTTG 10 27 1 GTATTTTTTG 0.896805 -74 TCCTCCAAGGAATTTCTTGATTTTCTTCT 12 9 1 GGATTTCTTG 0.797281 -127 ACATGATAACCTAGTTTCTTCCCTCGGGGTA 13 86 0 CTATTTCTTC 0.866784 -102 GCTGCTTACTGTCTTTTTTTCCAGTAAGATG 13 143 0 GTCTTTTTTC 0.933926 -45 TTATCAATAGGTTATTTTTCCTCTGTTAATA 15 130 0 GTTTTTTTCC 0.648644 -171 TTGTTTTAAACTATTTTTTTCAGTTTTAATT 15 260 0 CTATTTTTTC 0.896806 -41 ACAACTAGAGGATATTTTTTC 15 290 1 GATTTTTTTC 0.575502 -11 *** ******* Masking position 5 Map Score: 11.3577 Number of sites scoring better than the average of aligned sites = 307 Number in coding regions = 307 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 5 TAAAAGCTTCTTTATATAAAACGCTGTTTCA 1 34 0 TTATATAAAA 0.589498 -98 GGAGCTTTTCTTGCTGAAAAAAGTACGTTGA 2 34 0 TTCTGAAAAA 0.943652 -78 TTACTTCCTTTATCTAGAAAAGTCTGCGCTA 3 278 0 TACTAGAAAA 0.813444 -23 AATTCTTTCCTATAAAAATATAACCAA 4 52 0 TTCTATAAAA 0.878252 -17 AGTGAAAAAATTCCAGAAAAATACATTTTTG 6 48 1 TTCAGAAAAA 0.640779 -253 AGCAGCTTATATTCTAAAAAAGAACCTACCC 6 168 0 ATCTAAAAAA 0.879928 -133 TATCGCTTGCTTGCTAAAAAAAAAAAAGGAT 10 49 1 TTCTAAAAAA 0.957982 -52 AGCTGTCATCTTACTGGAAAAAAAGACAGTA 13 137 1 TTCTGGAAAA 0.940034 -51 CTTTCTTTCTTTTCTAAACAAGGTTCAGCGC 15 37 1 TTCTAAACAA 0.782373 -264 AGCACATAGTTTTATAAAAAATTTTTCTATT 15 103 1 TTATAAAAAA 0.819379 -198 TTTTCCTCTGTTAATAGAAAAATTTTTTATA 15 115 0 TTATAGAAAA 0.809533 -186 CCTTACCTAGATTCTAGAAAATGGTTGCATG 15 204 1 ATCTAGAAAA 0.872675 -97 TTAAAAATTAAAACTGAAAAAAATAGTTTAA 15 255 1 AACTGAAAAA 0.523616 -46 ** ******** Masking position 8 Map Score: 7.99924 Number of sites scoring better than the average of aligned sites = 208 Number in coding regions = 208 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 ATTATGGGATTATAGGTGTAAAAGATCTTGTA 2 77 0 TATAGGGTAA 0.660078 -35 GGGGAGAACTCAGAGGGGGTGCTGGTCACTAG 3 13 0 CAGAGGGGGC 0.973641 -288 CCGAACCTGCTAGAGGGGTTGCTTTTCGGGCT 3 44 1 TAGAGGGTGC 0.984349 -257 AAGCCAATCTCATAGGCGTCCCCACATATTAG 3 190 0 CATAGGGTCC 0.956783 -111 GCGAAGCTAGCCGAGGAGTGCCGT 5 14 1 CCGAGGGTCC 0.91539 -14 AAATATCGAAAAGAGGGGTAACTAAGAGCAAA 6 15 0 AAGAGGGTAC 0.915345 -286 ACCGCCTCCCTAGAGATGTGGCAAACACCCAA 6 203 0 TAGAGAGTGC 0.915772 -98 CCCTTCTCAGTATAGGAGTAACAGCTGTTTTG 9 60 1 TATAGGGTAC 0.956946 -137 GACTGGGGAGTAGAGGTGGGCCTGTAACTCTG 12 69 1 TAGAGGGGCC 0.978157 -67 TTCTCTTTTTTATAGAGGGCACTTTTATCAAC 14 23 1 TATAGAGGAC 0.732313 -63 ****** ** ** Masking position 4 Map Score: 6.216 Number of sites scoring better than the average of aligned sites = 76 Number in coding regions = 75 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 7 AAGTCTGCGCTAGGGATGAAGTTTTATTCT 3 260 0 TAGGGATGAA 0.88443 -41 TATATTTTTATAGGAAAGAATT 4 57 1 TAGGAAAGAA 0.874097 -12 CCTCAAGCCAAAGGAAACAAAAATGTATTT 6 66 0 AAGGAAACAA 0.744553 -235 AACTCGGAAGTAGAGAAAAAACAAGATTTT 7 131 0 TAGAGAAAAA 0.904376 -51 AACAGACGAGTAGAAATAAAGAAGTCATGA 9 21 0 TAGAAATAAA 0.520278 -176 CATTCAAGATGAGAGAAAAAGAATCCCCTT 11 20 0 GAGAGAAAAA 0.842657 -44 GTAGTCTCGATATAGAAGAAAATCAAGAAA 12 23 0 TATAGAAGAA 0.720805 -113 CTAATACCCCGAGGGAAGAAACTAGGTTAT 13 82 1 GAGGGAAGAA 0.924178 -106 AAAAAAGAGAAGGGATCAATGAGAAGAGG 14 67 0 AAGGGATCAA 0.76263 -19 ATCTTCTAACAAGAGAACAAGCTCCTTTCT 15 13 1 AAGAGAACAA 0.886377 -288 GAACCTTGTTTAGAAAAGAAAGAAAGGAGC 15 33 0 TAGAAAAGAA 0.857006 -268 TTCCTCTGTTAATAGAAAAATTTTTTATAA 15 114 0 AATAGAAAAA 0.473005 -187 ********** Masking position 6 Map Score: 3.73069 Number of sites scoring better than the average of aligned sites = 464 Number in coding regions = 463 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 CTTTGAAAACAACGAAAAAAAGCCCGAAAAG 3 65 0 AACAAAAAAA 0.697628 -236 GAACACTTTTAACAAAAAAGCGTTATATCCT 6 93 0 AACAAAAAGC 0.932899 -208 AGATGTGGCAAACACCCAAACAAAGCAGCTT 6 191 0 AACCCCAAAC 0.925857 -110 TCTACCTAAAAACTACAAATCAAGG 6 286 1 AACACAAATC 0.742689 -15 TGTGTGAGGAAACGTAAAAACG 7 2 0 AACTAAAAAC 0.835988 -180 ACAATTAACTAACCAACAAGCATACTCATTC 7 30 1 AACAACAAGC 0.95662 -152 TGAAAAGCAAAACTCACAAACTGATAACTAC 9 175 1 AACCACAAAC 0.95662 -22 CATGAATTTGAACAAACAAACTAATTAAAAA 15 231 1 AACAACAAAC 0.970389 -70 *** ******* Masking position 8 Map Score: 1.87381 Number of sites scoring better than the average of aligned sites = 68 Number in coding regions = 68 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 GACAGGCTCTACGTAAAAGCTTCTTTATATA 1 47 0 AGTAAAAGCT 0.921683 -85 GGGATTATAGGTGTAAAAGATCTTGTATTGT 2 73 0 GGTAAAAGAT 0.778778 -39 CCCTCGTCCTAGGTAAAAGCTATAGGGGAGG 6 140 0 AGTAAAAGCT 0.921617 -161 TTCTTTTTTAGAATATAAGCTGCTTTGTTTG 6 175 1 GATATAAGCT 0.905236 -126 AAGAGCGCTCGAGTGTCGGCTTCTTTCGGAT 7 94 0 GGTGTCGGCT 0.84629 -88 CTCAGTATAGGAGTAACAGCTGTTTTGATAG 9 65 1 GGTAACAGCT 0.972373 -132 CTCTCATCTTGAATGTAAGCTAGTAAGGGAG 11 35 1 GATGTAAGCT 0.887378 -29 TCTTCCCTCGGGGTATTAGCTCAGTTGGTAG 13 70 0 GGTATTAGCT 0.877855 -118 TTTTCCAGTAAGATGACAGCTTGTTGTCCTA 13 127 0 AATGACAGCT 0.753521 -61 * ********* Masking position 4 Map Score: 0.873039 Number of sites scoring better than the average of aligned sites = 82 Number in coding regions = 82 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: 2.7096e-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 AAAAAGCCCGAAAAGCAACCCCTCTAGCAGG 3 49 0 AAAAGAACCC 0.96239 -252 GAAAACAACGAAAAAAAGCCCGAAAAGCAAC 3 61 0 AAAAAAGCCC 0.775747 -240 CAGAAAGAGTAAGAATAAAACTTCATCCCTA 3 249 1 AAGAAAAAAC 0.764225 -52 TCTTTCCTATAAAAATATAACCAATAGGTGA 4 45 0 AAAAAATAAC 0.704329 -24 AGGGGTAACTAAGAGCAAAACAC 6 3 0 AAGAGAAAAC 0.864283 -298 CTTATATTCTAAAAAAGAACCTACCCTCGTC 6 163 0 AAAAAGAACC 0.714858 -138 TGTCCCCGTGAAAAGCAAAACTCACAAACTG 9 167 1 AAAAGAAAAC 0.936751 -30 AGATGAGAGAAAAAGAATCCCCTTAGAAGTT 11 13 0 AAAAGATCCC 0.889941 -51 GCTTTCTATTAAAAGAAACCCTATTCAGACC 15 66 1 AAAAGAACCC 0.96239 -235 AAACTAATTAAAAATTAAAACTGAAAAAAAT 15 248 1 AAAATAAAAC 0.696161 -53 ***** ***** Masking position 4 Map Score: 1.60464 Number of sites scoring better than the average of aligned sites = 136 Number in coding regions = 136 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: 2.7096e-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 ********** No masking Map Score: 2.7096e-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 14 ********** No masking Map Score: 2.7096e-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