AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00280_ctra_reg_300.orf -o00280_ctra_300.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 ybbP 274 hypothetical protein #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 pdhA/B 34 (pyruvate) Oxoisovalerate Dehydrogenase Alpha and Beta Fusion #7 dnaJ 28 Heat Shock Protein J #8 rs21 196 S21 Ribosomal Protein #9 CT343 300 O-Sialoglycoprotein Endopeptidase family #10 cutE 63 Apolipoprotein N-Acetyltransferase #11 yciA 135 Acyl-CoA Thioester Hydrolase #12 CT538 300 hypothetical protein #13 ldh 247 Leucine Dehydrogenase Motif number 1 GTTTTTCAACTGAAACAGCGTTTTATATAAAGAA 1 24 1 TGACAGTTTT 0.980961 -108 ACAGGCTCTACGTAAAAGCTTCTTTATATAAAAC 1 43 0 CGAAAGTCTT 0.763702 -89 CCTGTCTCGATCACAAAGCTTCTTTCTGTAACTA 1 72 1 TCAAAGTCTT 0.869465 -60 CACCAGTTGTTAAAACAGCCCTTTTCCACAAAAT 2 78 1 TAACAGCTTT 0.810345 -197 AGACAGTTAATGGCAAAGTATTTTGTGGAAAAGG 2 97 0 TGAAAGTTTT 0.973886 -178 TTCAAGGAGTTGGTACAGCTTCTTGTTTTGCTGA 2 209 1 TGACAGTCTT 0.962978 -66 TAACCCTAGCAGTTGAAGTGTTTTCATTATTTTC 2 241 0 AGGAAGTTTT 0.685596 -34 ACTTCATCCCTAGCGCAGACTTTTCTAGATAAAG 3 268 1 TAGCAGTTTT 0.93186 -33 GAAACACCACTAACAAAGATTTTTT 7 2 0 TAAAAGTTTT 0.951475 -27 CACGAGAAAGTATAGCAGGGTTTTTATCAATTGC 9 118 1 TAGCAGTTTT 0.93186 -183 CTCACTTCCTTGCAAAAGTATTTTTACAAAAAGC 12 167 0 TGAAAGTTTT 0.973886 -134 GATCACTCTCTATTAAAGTGTTTTATGCGCAATT 13 13 1 TAAAAGTTTT 0.951475 -235 GGCAATCCTTTCAGACAGGTTTTTTGTACGAAAG 13 179 1 TCACAGTTTT 0.947996 -69 ** **** **** Masking position 7 Map Score: 11.438 Number of sites scoring better than the average of aligned sites = 135 Number in coding regions = 135 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 TACAAATATAGGAAGAAAAGAGAACAGAGAG 3 98 0 GGAAGAAAGA 0.727189 -203 GCTCTTCCCAGAAAGAGTAAGAATAAAACTT 3 241 1 GAAAGAGAAG 0.904535 -60 AATCCGAAAGGAGAAGGAGAGCATCC 4 6 1 GAAAGGAAAG 0.951534 -63 ACCAATAGGTGAAAGGAGAAGGATGCTCTCC 4 26 0 GAAAGGAAAG 0.951534 -43 CAAAATCCTTGGAAGAGCAAGGGTTGTGTGC 9 24 1 GGAAGAGAAG 0.956901 -277 TAGTATATCGGTAAGAAGAAGTAATATTAAA 9 60 0 GTAAGAAAAG 0.928653 -241 CATTCAAGATGAGAGAAAAAGAATCCCCTTA 10 19 0 GAGAGAAAAG 0.945267 -45 GAGATGACTGGGGAGTAGAGGTGGGCCTGTA 11 64 1 GGGAGTAAGG 0.880813 -72 CTAGAGCATGGGGAGGTTAGGCCTGTTTTGC 12 138 1 GGGAGGTAGG 0.870495 -163 TTGCAAGGAAGTGAGAGTAGGTAGAGAACAG 12 186 1 GTGAGAGAGG 0.88312 -115 ACAGGGATATGGGCGGAAAGGCTTCCCTTTA 12 213 1 GGGCGGAAGG 0.937858 -88 ACTGAAAAAAGTAAGGATAAGT 12 289 1 GTAAGGAAAG 0.937803 -12 AAAACTATCTGGACGAATAAGCCGGATGCGC 13 52 0 GGACGAAAAG 0.926183 -196 ******* *** Masking position 9 Map Score: 11.839 Number of sites scoring better than the average of aligned sites = 277 Number in coding regions = 277 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 TTGGCTCTCCAAATCAAAAACTTCTAGTAT 2 13 1 AAATCAAAAA 0.915231 -262 TATTTTCAGCAAAACAAGAAGCTGTACCAA 2 218 0 AAAACAAGAA 0.809015 -57 TTGCTGAAAATAATGAAAACACTTCAACTG 2 236 1 TAATGAAAAC 0.779988 -39 AGGAAGAGACTACTCAAGACCTATCCAATT 3 162 0 TACTCAAGAC 0.557384 -139 TGTTGTCCCAAAAGGAAAACACT 8 4 0 AAAGGAAAAC 0.859562 -193 ACCAAACAAGTAAACAAAACTCTTGAAAAG 8 35 0 TAAACAAAAC 0.694088 -162 AGAGAAGTTGAATAGAAAAACTGTTATTTA 9 157 1 AATAGAAAAA 0.616286 -144 CGCTGTCGCCAAATCAAAACCGACTTTACT 9 210 0 AAATCAAAAC 0.924727 -91 AAACCGTTTTAATTCAAAAATTAATTCGCT 9 236 0 AATTCAAAAA 0.759605 -65 ATATAGAAGAAAATCAAGAAATTCCTTGGA 11 14 0 AAATCAAGAA 0.881334 -122 CTTTGAATTCAAATGAAAAACTTCTATGTC 12 30 0 AAATGAAAAA 0.905856 -271 TTCAAAGTCTTATTGAAAAACGTAATGAGC 12 53 1 TATTGAAAAA 0.47695 -248 ATTTTTACAAAAAGCAAAACAGGCCTAACC 12 152 0 AAAGCAAAAC 0.872901 -149 GCTGGTGATTAAAAGAAGAATCAGTTTGCC 12 251 1 AAAAGAAGAA 0.79058 -50 GCCATTAAGCAACTGAAAAAAGTAAGGATA 12 278 1 AACTGAAAAA 0.815768 -23 TTACTGCGAGAACAGAAGACTAAAACTATC 13 74 0 AACAGAAGAC 0.664058 -174 GACAAGAATAAAAGCAAAAAGAAAGGCTGC 13 120 0 AAAGCAAAAA 0.857873 -128 ********** Masking position 6 Map Score: 13.0848 Number of sites scoring better than the average of aligned sites = 353 Number in coding regions = 353 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 TGCTAGTGACCAGCACCCCCTCTGAGTTCTCC 3 9 1 ACAGCCCCCC 0.994562 -292 AAAAAGCCCGAAAAGCAACCCCTCTAGCAGGTTC 3 46 0 AAAGCCCCCC 0.991323 -255 AGCCAATCTCATAGGCGTCCCCACATATTAGGAA 3 187 0 AAGGCCCCCC 0.99314 -114 AGCAGCTCCCTCTCAGCTAAAAAG 6 21 0 ACAGCCCTCC 0.98938 -14 AGATGAGAGAAAAAGAATCCCCTTAGAAGTTAC 10 10 0 AAAGACCCCT 0.785523 -54 TAAAGGGGCTCCCTTACTAGCTTACAT 10 47 0 AGGGCCCTTC 0.944922 -17 ATATGGGCGGAAAGGCTTCCCTTTAGAAGGAGGC 12 219 1 AAGGCCCCTT 0.950071 -82 TCTTTTAATCACCAGCCTCCTTCTAAAGGGAAGC 12 233 0 ACAGCCCTTT 0.939252 -68 CTTTTATTTTATCGGCAGCCTTTCTTTTTGCTTT 13 106 1 ACGGCCCTTC 0.983869 -142 * **** **** * Masking position 1 Map Score: 9.22743 Number of sites scoring better than the average of aligned sites = 54 Number in coding regions = 54 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 CGTTTTATATAAAGAAGCTTTTACGTAGAG 1 42 1 AAAGAAGCTT 0.80725 -90 GTAGTTACAGAAAGAAGCTTTGTGATCGAG 1 77 0 AAAGAAGCTT 0.80725 -55 AAAAAGAATACTAGAAGTTTTTGATTTGGA 2 20 0 CTAGAAGTTT 0.928271 -255 GAACCGAAGTCAAGGAAGGTCTTAAGAAGG 2 166 0 CAAGGAAGGT 0.496566 -109 TAATAAGTTTCAAGGAGTTGGTACAGCTTC 2 201 1 CAAGGAGTTG 0.960125 -74 TTCAGCAAAACAAGAAGCTGTACCAACTCC 2 214 0 CAAGAAGCTG 0.91462 -61 TAAGATAACCCTAGCAGTTGAAGTGTTTTC 2 250 0 CTAGCAGTTG 0.82933 -25 AGCAACCCCTCTAGCAGGTTCGGGGGAGAA 3 37 0 CTAGCAGGTT 0.872668 -264 TTTATAATTCAAAGAAGGTTATACAACTTA 8 69 1 AAAGAAGGTT 0.846176 -128 CTTGCTCTTCCAAGGATTTTGAACTAGTTG 9 15 0 CAAGGATTTT 0.741034 -286 CTAAATCAATCTAGGAGTTTAGGCC 9 286 1 CTAGGAGTTT 0.953946 -15 TCCTCCAAGGAATTTCTTGATTTTC 11 6 1 CAAGGAATTT 0.878496 -130 CTTGCTCGACATAGAAGTTTTTCATTTGAA 12 23 1 ATAGAAGTTT 0.770373 -278 AATACTTTTGCAAGGAAGTGAGAGTAGGTA 12 179 1 CAAGGAAGTG 0.817636 -122 ********** Masking position 6 Map Score: 8.61805 Number of sites scoring better than the average of aligned sites = 371 Number in coding regions = 371 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 GCTAGTGACCAGCACCCCCTCTGAGTTCTCCC 3 12 1 AGCCCCCTCT 0.989858 -289 AAGCCCGAAAAGCAACCCCTCTAGCAGGTTCG 3 45 0 AGCCCCCTCT 0.989836 -256 CAATCTCATAGGCGTCCCCACATATTAGGAAG 3 186 0 GGCCCCCACA 0.985371 -115 AGCAGCTCCCTCTCAGCTAAAAAGA 6 20 0 AGCCCTCTCA 0.97319 -15 TAAAGGGGCTCCCTTACTAGCTTACATT 10 46 0 GGCCCTTACT 0.953622 -18 TGGGCGGAAAGGCTTCCCTTTAGAAGGAGGCT 12 222 1 GGCCCCTTTA 0.906754 -79 TTATTTTATCGGCAGCCTTTCTTTTTGCTTTT 13 109 1 GGCCCTTTCT 0.979278 -139 *** ******* Masking position 6 Map Score: 5.21022 Number of sites scoring better than the average of aligned sites = 48 Number in coding regions = 48 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 TGCTTTTCGGGCTTTTTTTCGTTGTTTTCA 3 63 1 GCTTTTTTTC 0.846267 -238 CTAGGGATGAAGTTTTATTCTTACTCTTTC 3 251 0 AGTTTTATTC 0.925842 -50 TTCACCTATTGGTTATATTTTTATAGGAAA 4 44 1 GGTTATATTT 0.776289 -25 TTGTAACACCACTTTTATTTAGGCTTCAAG 8 106 0 ACTTTTATTT 0.782915 -91 ATACGTAATTGGTTTTATTTAATAACGCGC 8 166 0 GGTTTTATTT 0.925842 -31 AGTATAGCAGGGTTTTTATCAATTGCAGCA 9 126 1 GGTTTTTATC 0.719876 -175 CGGTTTTAACGGTTATAATCCTTTGTCTAA 9 260 1 GGTTATAATC 0.71818 -41 TCGTCCAGATAGTTTTAGTCTTCTGTTCTC 13 67 1 AGTTTTAGTC 0.768306 -181 TCGCAGTAAAACTTTTATTTTATCGGCAGC 13 95 1 ACTTTTATTT 0.782915 -153 CTTTCTTTTTGCTTTTATTCTTGTCATTGT 13 125 1 GCTTTTATTC 0.951928 -123 ********** Masking position 6 Map Score: 4.31889 Number of sites scoring better than the average of aligned sites = 152 Number in coding regions = 152 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 TAGTATTCTTTTTAGTATATATACTATGCACG 2 37 1 TTTGTAATAT 0.630661 -238 TGGCAAAGTATTTTGTGGAAAAGGGCTGTTTT 2 89 0 TTTGTGAAAA 0.681973 -186 AGCTTCTTGTTTTGCTGAAAATAATGAAAACA 2 225 1 TTTCTGAAAT 0.916964 -50 TAGCGCAGACTTTTCTAGATAAAGGAAGTAAT 3 278 1 TTTCTAATAA 0.625542 -23 AATTCTTTCCTATAAAAATATAACCAA 4 52 0 TTTCTAAAAA 0.93903 -17 TTCTTACCGATATACTACAAAATCGCAACAAT 9 74 1 TATCTAAAAA 0.710724 -227 TCAACTTCTCTTTGCTGCAATTGATAAAAACC 9 136 0 TTTCTGAATT 0.583887 -165 CAAAACCGACTTTACTAAAAAAGCTCATTTAT 9 194 0 TTTCTAAAAA 0.93903 -107 CTGTTTTGCTTTTTGTAAAAATACTTTTGCAA 12 160 1 TTTGTAAAAT 0.860845 -141 CACTCTCGTCTTTCGTACAAAAAACCTGTCTG 13 190 0 TTTGTAAAAA 0.744341 -58 CGAGAGTGATTGTACTGCAAAATAATATGAGC 13 214 1 TGTCTGAAAA 0.795978 -34 *** *** **** Masking position 9 Map Score: 5.32817 Number of sites scoring better than the average of aligned sites = 81 Number in coding regions = 81 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 TATATACTATGCACGTTTCCCTGTCACCAGTT 2 54 1 GCACTTCCCT 0.976007 -221 CTTTGGGAAAGGACTCATCCCTAGTTTAGCTG 2 133 0 GGACCACCCT 0.969082 -142 TTAAACATGTGCACACAACCCTTGCTCTTCCA 9 33 0 GCACCACCCT 0.992738 -268 GTAGAGGTGGGCCTGTAACTCTGAGACTAGTC 11 78 1 GCCTTACTCT 0.861213 -58 GATTCAGGATGCCCCTACCCCTAGAGCATGGG 12 118 1 GCCCTACCCT 0.996158 -183 AAGCCTTTCCGCCCATATCCCTGTTCTCTACC 12 205 0 GCCCTACCCT 0.996158 -96 **** ** **** Masking position 12 Map Score: 3.98424 Number of sites scoring better than the average of aligned sites = 12 Number in coding regions = 12 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 AGTATGTGTTCCGTAAGGCTAGTATGACT 1 113 0 TCCGTAAGGC 0.976553 -19 ATGAGTCCTTTCCCAAAGGCCTTCTTAAGA 2 147 1 TCCCAAAGGC 0.980625 -128 CAGAAGCCAATCTCATAGGCGTCCCCACAT 3 195 0 TCTCATAGGC 0.901212 -106 AATCCGAAAGGAGAAGGAGAGC 4 3 1 TCCGAAAGGA 0.964476 -66 ATCATGATTTTCCGTTAGGCACAAGCTCAT 12 77 0 TCCGTTAGGC 0.947547 -224 AGGGATATGGGCGGAAAGGCTTCCCTTTAG 12 215 1 GCGGAAAGGC 0.927636 -86 AAAAAACCTGTCTGAAAGGATTGCCACAAG 13 174 0 TCTGAAAGGA 0.931157 -74 ********** Masking position 7 Map Score: 5.21201 Number of sites scoring better than the average of aligned sites = 42 Number in coding regions = 42 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 TTACGTAGAGCCTGTCTCGATCACAAAGCT 1 62 1 CCTGTCTCGA 0.963691 -70 ATAACGCGCGCCTAGCTCGAACGCACAAGA 8 145 0 CCTAGCTCGA 0.982504 -52 AATTAGTGCATCTAACACGAGAAAGTATAG 9 103 1 TCTAACACGA 0.756523 -198 GGCCTAAACTCCTAGATTGATTTAGACAAA 9 281 0 CCTAGATTGA 0.846411 -20 TTGATTTTCTTCTATATCGAGACTACTATC 11 27 1 TCTATATCGA 0.896913 -109 TCTAATAGCCTCTATCTTGACTAGTCTCAG 11 98 0 TCTATCTTGA 0.836216 -38 GAAATGATTTTCTTGCTCGACATAGAAGTT 12 12 1 TCTTGCTCGA 0.898981 -289 GTAGGGGCATCCTGAATCGACTACATGCTA 12 106 0 CCTGAATCGA 0.878725 -195 ********** Masking position 10 Map Score: 1.96116 Number of sites scoring better than the average of aligned sites = 60 Number in coding regions = 59 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 12 CTGTAACTACTAGCAAAGTCATACTAGCCT 1 97 1 TAGCAAAGTC 0.964938 -35 TTTTCGTTGTTTTCAAAGTTCTCTCTGTTC 3 78 1 TTTCAAAGTT 0.730284 -223 TTCCTTTATCTAGAAAAGTCTGCGCTAGGG 3 275 0 TAGAAAAGTC 0.962255 -26 AACAAAACTCTTGAAAAGTTGTTGTCCCAA 8 23 0 TTGAAAAGTT 0.941905 -174 TGAGCTTTTTTAGTAAAGTCGGTTTTGATT 9 199 1 TAGTAAAGTC 0.909826 -102 GTGAAAAATGTTGAAAAGTTACTTGTGGCA 13 153 1 TTGAAAAGTT 0.941905 -95 ********** Masking position 5 Map Score: 1.56648 Number of sites scoring better than the average of aligned sites = 47 Number in coding regions = 47 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 TATATACTATGCACGTTTCCCTGTCACCAGT 2 54 1 GCACTTTCCC 0.980678 -221 TGTTAAAACAGCCCTTTTCCACAAAATACTT 2 85 1 GCCCTTTCCA 0.925072 -190 CTTTGGGAAAGGACTCATCCCTAGTTTAGCT 2 134 0 GGACCATCCC 0.947361 -141 TTAAACATGTGCACACAACCCTTGCTCTTCC 9 34 0 GCACCAACCC 0.959777 -267 GATTCAGGATGCCCCTACCCCTAGAGCATGG 12 118 1 GCCCTACCCC 0.985311 -183 AAGCCTTTCCGCCCATATCCCTGTTCTCTAC 12 206 0 GCCCTATCCC 0.993329 -95 **** ****** Masking position 4 Map Score: 2.1975 Number of sites scoring better than the average of aligned sites = 19 Number in coding regions = 19 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 TCGATCACAAAGCTTCTTTCTGTAACTACTA 1 78 1 AGCTTCTTCT 0.803206 -54 TTCTGGGAAGAGCACCATTCTTACTTGGTCA 3 223 0 AGCACCTTCT 0.954255 -78 GGAGAAGGAGAGCATCCTTCTCCTTTCACCT 4 20 1 AGCATCTTCT 0.930634 -49 TGGTGTTACAATCCCCGGTCTCTTGTGCGTT 8 125 1 ATCCCCGTCT 0.971494 -72 AACGGTTATAATCCTTTGTCTAAATCAATCT 9 267 1 ATCCTTGTCT 0.747943 -34 CCCACCTCTACTCCCCAGTCATCTCTGTAAT 11 58 0 CTCCCCGTCA 0.688809 -78 TGAGTCTAATAGCCTCTATCTTGACTAGTCT 11 101 0 AGCCTCATCT 0.867539 -35 ATCACCCTTCTATATGAGTCT 11 125 0 ATCACCTTCT 0.930695 -11 CAGGCCTAACCTCCCCATGCTCTAGGGGTAG 12 132 0 CTCCCCTGCT 0.876237 -169 TTCCGCCCATATCCCTGTTCTCTACCTACTC 12 200 0 ATCCCTTTCT 0.83546 -101 TTTAATCACCAGCCTCCTTCTAAAGGGAAGC 12 233 0 AGCCTCTTCT 0.97331 -68 AATTATCCTGCGCATCCGGCTTATTCGTCCA 13 43 1 CGCATCGGCT 0.70851 -205 ****** **** Masking position 3 Map Score: 8.21455 Number of sites scoring better than the average of aligned sites = 163 Number in coding regions = 163 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: -1.26944e-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