AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ctra.txt -z/home/amcguire/genomes/ctra.fna -iflhCD_ctra_opreg_300.orf -g0.413 -x5 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 = 0.413 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 flhA 181 Flagellar Secretion Protein #2 fliA 107 Sigma-28/WhiG Family #3 yscU 256 YopS Translocation Protein U #4 CT102 134 hypothetical protein #5 CT552 300 hypothetical protein #6 fmu 124 RNA Methyltransferase #7 brnQ 149 Amino Acid (Branched) Transport #8 CT555 174 SWI/SNF family helicase #9 CT556 177 hypothetical protein #10 lpdA 208 Lipoamide Dehydrogenase #11 yscJ 103 Yop Translocation J #12 yscL 275 Yop Translocation L #13 CT663 300 hypothetical protein #14 CT665 43 hypothetical protein #15 CT666 26 hypothetical protein #16 CT670 22 hypothetical protein Motif number 1 GGACTCCAGAAGGAAAAAGAAAAGATTAGT 1 12 1 AGGAAAAAGA 0.923137 -170 TATACTAGACAAGAGAAAGATACTGTAA 1 164 1 AAGAGAAAGA 0.72622 -18 TGTTAGCCTTAAGAAAAAGCTGTACAACTT 3 19 0 AAGAAAAAGC 0.9 -238 TTTATTATTAAGGAAAAAGAAATTCTAAAG 3 56 1 AGGAAAAAGA 0.923137 -201 AGAAATTCTAAAGAAAAAGCAAGATTAGTG 3 73 1 AAGAAAAAGC 0.9 -184 AACGCTCTTTAAAAAAAATATTCCGTTCTC 3 113 1 AAAAAAAATA 0.715949 -144 GTTTTTCTCAAGAAAGAAGGTGGCAGATGC 3 180 0 AGAAAGAAGG 0.924733 -77 AGTATTTTTTAGAAAAGAGGGAGTATGCCA 4 16 1 AGAAAAGAGG 0.899842 -119 GATCTATCGTAGGAAAAAGCAACCTCGTGC 5 114 1 AGGAAAAAGC 0.950769 -187 GAGAGTTAAGAGAAAAAAGGGTTAGAAAAA 5 153 0 AGAAAAAAGG 0.977623 -148 AGGAAATCTTAGAAAAAAGCGGAAAAAAAG 5 205 0 AGAAAAAAGC 0.967055 -96 GAACGGGACAGGAAAAAAGACTTTCTCTAA 5 240 0 GGAAAAAAGA 0.789642 -61 AAAGCTCTTGAGAAAGAACGGGACAGGAAA 5 255 0 AGAAAGAACG 0.695119 -46 CTTCCCCAATAGGAGAAAGCAACCGTGTAG 6 59 1 AGGAGAAAGC 0.901505 -66 AGGATGAATTAGAAGAAACGTCCGTTAGCC 7 53 0 AGAAGAAACG 0.793492 -97 TTCTTTGGAAAGAATAAAGGATGAATTAGA 7 70 0 AGAATAAAGG 0.728684 -80 AAAAAGAAATGATTGACCTTT 9 2 1 AAAAGAAATG 0.740864 -176 GGTAATACGTAAAAAGAAGAATAAAAGGTC 9 25 0 AAAAAGAAGA 0.70521 -153 GTTCCTAGGAGGAAAAAATCAAGGTAATAC 9 47 0 GGAAAAAATC 0.64138 -131 GTAGCAGGAGAGAAAAAATAGGAACGTAAG 10 15 0 AGAAAAAATA 0.843959 -194 CTAGGAAAGGAAAAGAGAGGTCCTTCAGAC 10 101 0 AAAAGAGAGG 0.66491 -108 CATTCTCTGCAGAAAAAATGTTCCCGATTG 11 35 1 AGAAAAAATG 0.928288 -69 CCATATATACAAAAAAAAGAAGCACCAAAT 12 43 1 AAAAAAAAGA 0.894813 -233 TAGCCATCGGAGAAAAAATCTACAATGCTA 12 72 0 AGAAAAAATC 0.896876 -204 TCTCTGTGTAAAAAAGAATGCGATCCTTGT 12 142 1 AAAAAGAATG 0.629138 -134 AAGAATTTTAGAAAAAAATCGGGCACGAAC 13 93 0 GAAAAAAATC 0.454582 -208 CTACTTTAAAAAGAAAAACGATTTCTCATC 13 178 0 AAGAAAAACG 0.713127 -123 TGTAAACGGTAAAAGAGAGGGTATCT 15 11 1 AAAAGAGAGG 0.66491 -16 ********** Masking position 4 Map Score: 29.0842 Number of sites scoring better than the average of aligned sites = 855 Number in coding regions = 855 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 TTACAGTATCTTTCTCTTGTCTAGTAT 1 165 0 AAATCTTTCT 0.862351 -17 TCCGTTCTCTAAAGAACCCCTTACTCTTTGTTTAT 3 134 1 AAACCCCTCT 0.986253 -123 AAAAGACCTCTTCCTCGCCGGATCC 4 120 0 AAACCTCTCT 0.928605 -15 TAAAGTAGGGAGGATATCGCTCTCTG 5 2 0 AGATCGCTCT 0.904306 -299 CTCTCTATCTAAGAAATCTTTAGCGGACTTTTTTT 5 178 1 AGATCTTTCG 0.598967 -123 CGTACTTTAAAGAGCATCCCTCTCTTGGCTCGAAG 6 92 1 AAATCCCTCT 0.990841 -33 ATAAGAGGGCATATCATCCTTCCCAAGTCACAGAA 7 101 0 AAATCCTTCA 0.786204 -49 CAATTGTTTGAAGCCATCCCTTACTGAATAAGTAA 8 23 1 AGATCCCTCT 0.988872 -152 TCCGGGCAAAAGAACATCCCTTACTTATTCAGTAA 8 43 0 AAATCCCTCT 0.990842 -132 AAACGCCTTTAGAAGACACCTATCTACTCCTAAAC 8 90 1 AAACACCTCT 0.802342 -85 TGTTTGCAAGACGATACCCCTCCCGAATTATAGTT 9 74 0 AGACCCCTCG 0.944762 -104 GTAAAAAAGAATGCGATCCTTGTCTGGCTATCCCT 12 149 1 AGATCCTTCT 0.965965 -127 TGGCTTTGCCAAAGGATCCCTACCTCGTCAGAAGG 12 251 1 AAATCCCTCT 0.990842 -25 TCATCTCGATAGAGGAGCCTTTTCTGTTTTCTCTT 13 148 0 AAAGCCTTCT 0.865277 -153 TCTGGGTCCGAAATACTCCCTCCCTAGCTATTGGA 13 246 0 AACTCCCTCT 0.936224 -55 * * ****** ** Masking position 1 Map Score: 19.5999 Number of sites scoring better than the average of aligned sites = 105 Number in coding regions = 105 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 CCCTCTACTCCGATTCTTAACTAATCTTTTCT 1 29 0 CGATTCTTCT 0.839311 -153 CAATATGCTAACTTCCTTAGCTCCTACTTTTT 1 128 0 ACTTCCTTCT 0.730414 -54 ACTTTAAAGAGCATCCCTCTCTTGGCTCGAAG 6 95 1 GCATCCCTCT 0.982206 -30 TTGTTTGAAGCCATCCCTTACTGAATAAGTAA 8 26 1 CCATCCCTCT 0.985037 -149 GGGCAAAAGAACATCCCTTACTTATTCAGTAA 8 43 0 ACATCCCTCT 0.937725 -132 ATCTCTGTTACGTTCCCATGCTTGCGCATGAC 8 145 0 CGTTCCCACT 0.905729 -30 GCCTTTTTATGGCTTCCATACTGCCATCTGTA 9 130 0 GGCTTCCACT 0.615779 -48 AAAAAGAATGCGATCCTTGTCTGGCTATCCCT 12 152 1 CGATCCTTCT 0.976349 -124 CAGGGAACCTCGCTCCTTTGCTCGTTACTTTA 12 214 0 CGCTCCTTCT 0.967098 -62 AAAGGAGCGAGGTTCCCTGCCTGTTGGCTTTG 12 227 1 GGTTCCCTCT 0.975273 -49 CTTTGCCAAAGGATCCCTACCTCGTCAGAAGG 12 254 1 GGATCCCTCT 0.98865 -22 TCTCGATAGAGGAGCCTTTTCTGTTTTCTCTT 13 148 0 GGAGCCTTCT 0.845185 -153 CCGAAATACTCCCTCCCTAGCTATTGGAATGG 13 242 0 CCCTCCCTCT 0.979112 -59 ******** ** Masking position 12 Map Score: 15.3179 Number of sites scoring better than the average of aligned sites = 85 Number in coding regions = 85 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 GGGAGCAATAGGTCGGGGGTTCGAATCCCTC 1 56 0 GTCGGGGGTT 0.953492 -126 TAAACAAAGAGTAAGGGGTTCTTTAGAGAAC 3 137 0 GAAGGGGTTC 0.70743 -120 TTATTGATTAGAACAAGGGCTCTTGATTAAT 4 50 1 GACAAGGGCT 0.769376 -85 GATCCGGCGAGGAAGAGGTCTTTT 4 121 1 GAAGAGGTCT 0.863016 -14 AGTTTTTGTCGCACGAGGTTGCTTTTTCCTA 5 123 0 GACGAGGTTG 0.928941 -178 AGGTACTATAGGACGAGGGCTAACGGACGTT 7 36 1 GACGAGGGCT 0.980638 -114 AGGCAGAAAGGAACGAGTGTTTAGGAGTAGA 8 112 0 GACGAGTGTT 0.868566 -63 ATTATCTGAGGGAAGAGGATTCTCCTTCCAA 10 137 0 GAAGAGGATT 0.72152 -72 GTGAAAAGGTGTGCGTGGGTT 11 93 1 GGCGTGGGTT 0.861714 -11 AAACGAGAGCGATCGAGGGTCAGGAAAACCT 12 108 1 GTCGAGGGTC 0.970641 -168 TTTACACAGAGATCGAGGTTTTCCTGACCCT 12 123 0 GTCGAGGTTT 0.973653 -153 ACGAGCAAAGGAGCGAGGTTCCCTGCCTGTT 12 221 1 GGCGAGGTTC 0.944796 -55 GCAGTTCGAGGTTTATTTAATTCT 14 4 1 GTCGAGGTTT 0.973656 -40 * ********* Masking position 7 Map Score: 11.3654 Number of sites scoring better than the average of aligned sites = 73 Number in coding regions = 72 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 ATGTGTTAGTTGTGTAAGGGTAGATATTGTTTAA 2 32 1 TTTAGGGAGA 0.961537 -76 ACTCTTTGTTTATAAATGGGATGAGCATCTGCCA 3 156 1 TTAAGGGTGA 0.980539 -101 AAGGAACGAGTGTTTAGGAGTAGATAGGTGTCTT 8 102 0 TTTAGAGAGA 0.940034 -73 GCCCAAAGACTGTTAAAGAGGTGATCTC 9 160 1 TTAAGAGTGA 0.96932 -18 GTGGATAAAATCTCAATGAGGAGAAGTGGTAGCA 10 39 0 TTAAGAGAGA 0.963751 -170 ATGAGATGATTATCTGAGGGAAGAGGATTCTCCT 10 142 0 TTTGGGGAGA 0.824801 -67 ATTGCAACGATCCATATGAGATGATTATCTGAGG 10 157 0 TCTAGAGTGA 0.921057 -52 CACTCACCATAGCAAATGGGGAGATTAGTGCCAA 11 62 0 ACAAGGGAGA 0.868231 -42 GTTACTTTATTCCCAACGCGATGAGGCATGTCAT 12 189 0 TCAAGCGTGA 0.878575 -87 CGAGAGCTGCTCTGAATGAGTTGATTTGTGCCGG 13 13 1 TTAAGAGTGA 0.96932 -288 TGTACTTTAAATTGAAAGGGATGAAAGAGAAAAC 13 124 1 ATAAGGGTGA 0.925934 -177 * * ** *** *** Masking position 14 Map Score: 8.4623 Number of sites scoring better than the average of aligned sites = 58 Number in coding regions = 58 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 TAAACAATATCTACCCTTACACAACTAACA 2 35 0 CTACCCTTAC 0.903527 -73 CTTTAAAGAGCATCCCTCTCTTGGCTCGAA 6 96 1 CATCCCTCTC 0.975353 -29 TGTTTGAAGCCATCCCTTACTGAATAAGTA 8 27 1 CATCCCTTAC 0.985892 -148 GGCAAAAGAACATCCCTTACTTATTCAGTA 8 44 0 CATCCCTTAC 0.985892 -131 CTTCTCGCAACATCCCCTTGTTTGCAAGAC 9 97 0 CATCCCCTTG 0.867844 -81 ATTCTCCTTCCAAGCCTTTCTAGGAAAGGA 10 120 0 CAAGCCTTTC 0.808947 -89 GGAGAATCCTCTTCCCTCAGATAATCATCT 10 143 1 CTTCCCTCAG 0.836745 -66 TTTTCTCTTTCATCCCTTTCAATTTAAAGT 13 127 0 CATCCCTTTC 0.985892 -174 ********** Masking position 5 Map Score: 7.60019 Number of sites scoring better than the average of aligned sites = 62 Number in coding regions = 62 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 CTATTGCTCCCAAAGCAACCGCGCTAACCA 1 76 1 CAAAGCAACC 0.955801 -106 CTCCCTACTTTAAAGCAACGAATTCTTTTA 5 25 1 TAAAGCAACG 0.912633 -276 CAAAGAGTAGGATAAGAACGTAAGTTCTAT 5 80 0 GATAAGAACG 0.683503 -221 TATCGTAGGAAAAAGCAACCTCGTGCGACA 5 118 1 AAAAGCAACC 0.855058 -183 CCCAATAGGAGAAAGCAACCGTGTAGCTGC 6 63 1 GAAAGCAACC 0.955801 -62 CTTTTGCCCGGAAAGCAACCCAAAAAACGC 8 66 1 GAAAGCAACC 0.955801 -109 GACCTAGGCAGAAAGGAACGAGTGTTTAGG 8 118 0 GAAAGGAACG 0.978012 -57 CATGCGCAAGCATGGGAACGTAACAGAGAT 8 147 1 CATGGGAACG 0.745722 -28 GGAGAGAAAAAATAGGAACGTAAGAGTG 10 9 0 AATAGGAACG 0.835319 -200 GAGTGTTTAGGATTGCAACGATCCATATGA 10 172 0 GATTGCAACG 0.629936 -37 GCGTTGGGAATAAAGTAACGAGCAAAGGAG 12 204 1 TAAAGTAACG 0.575363 -72 AAGTAACGAGCAAAGGAGCGAGGTTCCCTG 12 216 1 CAAAGGAGCG 0.875239 -60 TTGGCTTTGCCAAAGGATCCCTACCTCGTC 12 250 1 CAAAGGATCC 0.727752 -26 CTTTAGAAATCAAAAGAACGAGTCGTTCGT 13 69 1 CAAAAGAACG 0.83782 -232 ********** Masking position 7 Map Score: 10.8334 Number of sites scoring better than the average of aligned sites = 154 Number in coding regions = 154 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 TTTAGTTTGTAAAAGAAATTTTTTTT 2 92 1 AAAAGATTTT 0.853746 -16 CTTAATAATAAAAAGGCTGTGTTAGCCTTAAGA 3 35 0 AAAAGTGTTT 0.754077 -222 TTATTAAGGAAAAAGAAATTCTAAAGAAAAAGC 3 60 1 AAAAGATTTA 0.560796 -197 ATTTTTTTTAAAGAGCGTTTTTCATGAAGCACT 3 99 0 AAGAGTTTTC 0.918999 -158 TACCGTATATAAATGTTTTTCTCAAGAAAGAAG 3 191 0 AAATGTTTTC 0.888687 -66 CCTAAAGTATTTTTTAGAAAAGAGG 4 3 1 TAAAGTTTTT 0.673889 -132 AAGACTCATTAAAAGAATTCGTTGCTTTAAAGT 5 31 0 AAAAGTTCTT 0.754098 -270 AAGGGTTAGAAAAAGTTTTTGTCGCACGAGGTT 5 134 0 AAAAGTTTTC 0.975054 -167 GGGACAGGAAAAAAGACTTTCTCTAACAACCAG 5 233 0 AAAAGTTTTC 0.975005 -68 GTTCTTTCTCAAGAGCTTTTGTTCGGATTGCGT 5 266 1 AAGAGTTTTT 0.859209 -35 GGTGTCTTCTAAAGGCGTTTTTTGGGTTGCTTT 8 77 0 AAAGGTTTTT 0.78303 -98 ACAACCCGGGAAATGTATTTGTCTGAAGGACCT 10 81 1 AAATGTTTTC 0.888687 -128 GACATCTCCCAAAACACATTTTCCCGGCACAAA 13 37 0 AAAACATTTC 0.671945 -264 TTTAAAAAGAAAAACGATTTCTCATCTCGATAG 13 171 0 AAAACTTTTC 0.875344 -130 ***** *** ** Masking position 2 Map Score: 7.25536 Number of sites scoring better than the average of aligned sites = 263 Number in coding regions = 263 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 AGTATCTTTCTCTTGTCTAGTATATAGGCA 1 158 0 TCTTGTCTAG 0.854284 -24 AAGAGTTATTGATTAGGAGTTATGTG 2 7 1 TATTGATTAG 0.957482 -101 TAAGGGTAGATATTGTTTAAAAATTTTATT 2 46 1 TATTGTTTAA 0.837417 -62 GATTTAGCCTTATTTTTTAGTTTGTAAAAG 2 77 1 TATTTTTTAG 0.837417 -31 CCTAAAGTATTTTTTAGAAAAGAGGGA 4 8 1 TATTTTTTAG 0.837417 -127 TGCCAAAGCTTATTGATTAGAACAAGGGCT 4 41 1 TATTGATTAG 0.957482 -94 GAACAAGGGCTCTTGATTAATAAGCTTTGG 4 60 1 TCTTGATTAA 0.834673 -75 GAGGGACATATCTTGATTAGGATCCGGCGA 4 101 1 TCTTGATTAG 0.956659 -34 ********** Masking position 9 Map Score: 4.77226 Number of sites scoring better than the average of aligned sites = 40 Number in coding regions = 40 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 TTCCTTAGCTCCTACTTTTTTAAATCGGAG 1 118 0 CCTACTTTTT 0.972863 -64 TAAAGAACCCCTTACTCTTTGTTTATAAAT 3 143 1 CTTACTCTTT 0.6618 -114 CGATATCCTCCCTACTTTAAAGCAACGAAT 5 18 1 CCTACTTTAA 0.880244 -283 ACGTTCTTATCCTACTCTTTGTTTGGATCT 5 89 1 CCTACTCTTT 0.946014 -212 AAATCTTTAGCGGACTTTTTTTCCGCTTTT 5 191 1 CGGACTTTTT 0.824412 -110 CGTGTAGCTGCGTACTTTAAAGAGCATCCC 6 82 1 CGTACTTTAA 0.691246 -43 CTCTTACGTTCCTATTTTTTCTCTCCTGCT 10 13 1 CCTATTTTTT 0.86106 -196 TCGTTCGTGCCCGATTTTTTTCTAAAATTC 13 91 1 CCGATTTTTT 0.72713 -210 TATGCCAATACCTACTTTAAAAAGAAAAAC 13 189 0 CCTACTTTAA 0.880244 -112 ACAATCCTACTATTTTCCAGAC 16 8 0 CCTACTATTT 0.865311 -15 ********** Masking position 6 Map Score: 5.40603 Number of sites scoring better than the average of aligned sites = 66 Number in coding regions = 66 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 CCCCGACCTATTGCTCCCAAAGCAACCGCGC 1 69 1 TTGCTCCCAA 0.802123 -113 ATAGTTTATTCTCTTCCCCAATAGGAGAAAG 6 47 1 CTCTTCCCAA 0.965396 -78 TCATCCTTTATTCTTTCCAAAGAACTTCTGT 7 76 1 TTCTTTCCAA 0.876575 -74 GGGCATATCATCCTTCCCAAGTCACAGAAGT 7 99 0 TCCTTCCCAG 0.972913 -51 CAAGACGATACCCCTCCCGAATTATAGTTCC 9 72 0 CCCCTCCCAA 0.978832 -106 ACCTCTCTTTTCCTTTCCTAGAAAGGCTTGG 10 110 1 TCCTTTCCAG 0.921702 -99 GAAGAGGATTCTCCTTCCAAGCCTTTCTAGG 10 126 0 CTCCTTCCAG 0.938101 -83 AAGGAGAATCCTCTTCCCTCAGATAATCATC 10 141 1 CTCTTCCCCA 0.866992 -68 TCCGAAATACTCCCTCCCTAGCTATTGGAAT 13 244 0 TCCCTCCCAG 0.978832 -57 ******** ** Masking position 5 Map Score: 6.00466 Number of sites scoring better than the average of aligned sites = 93 Number in coding regions = 93 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: 3.17856e-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: 3.17856e-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: 3.17856e-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