AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00260_ctra_reg_300.orf -o00260_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 dapB 176 Dihydrodipicolinate Reductase #2 CT365 169 hypothetical protein #3 glyA 300 Serine Hydroxymethyltransferase #4 CT552 300 hypothetical protein #5 fmu 124 RNA Methyltransferase #6 brnQ 149 Amino Acid (Branched) Transport #7 CT555 174 SWI/SNF family helicase #8 CT556 177 hypothetical protein #9 lpdA 208 Lipoamide Dehydrogenase #10 thrS 229 Threonyl tRNA Synthetase #11 psdD 266 Phosphatidylserine Decarboxylase #12 serS 41 Seryl tRNA Synthetase #13 glyQ 300 Glycyl tRNA Synthetase #14 pssA 300 CDP-diacylglycerol-serine-O-phosphatidyltransferase Motif number 1 CGCAAACTTGCTCTTTTTCCTAATTTATTTA 1 47 0 CCTTTTTCCT 0.983643 -130 AAGCTTTTTTCCTAGTAGGAAGC 3 3 1 GTTTTTTCCT 0.921191 -298 GGAAGCATCGTTTCTTTTTCTTATAGTTATA 3 137 1 TTCTTTTTCT 0.797391 -164 AAAATAAATCCTCTTTCTCCTAGAAAGTTTA 3 171 1 CCTTTCTCCT 0.965125 -130 CTACCCACTCTCCCTTATCCTTTATGGGAAT 3 224 0 TCCTTATCCT 0.912365 -77 TGCAGAGGCACTCTTTATCCTCTACCCACTC 3 245 0 CCTTTATCCT 0.971057 -56 TAGAACTTACGTTCTTATCCTACTCTTTGTT 4 81 1 GTCTTATCCT 0.82151 -220 CGCACGAGGTTGCTTTTTCCTACGATAGATC 4 114 0 TCTTTTTCCT 0.963557 -187 CTTTTTCTAACCCTTTTTTCTCTTAACTCTC 4 152 1 CCTTTTTTCT 0.953329 -149 ACTTTTTTTCCGCTTTTTTCTAAGATTTCCT 4 204 1 CCTTTTTTCT 0.953329 -97 TTAGAGAAAGTCTTTTTTCCTGTCCCGTTCT 4 240 1 TTTTTTTCCT 0.942584 -61 GCTACACGGTTGCTTTCTCCTATTGGGGAAG 5 59 0 TCTTTCTCCT 0.924055 -66 TTCTAATTCATCCTTTATTCTTTCCAAAGAA 6 69 1 TCTTTATTCT 0.833629 -81 AAATGATTGACCTTTTATTCTTCTTTTTACG 8 17 1 CTTTTATTCT 0.876176 -161 GTATTACCTTGATTTTTTCCTCCTAGGAACT 8 47 1 GTTTTTTCCT 0.921191 -131 TCTTACGTTCCTATTTTTTCTCTCCTGCTAC 9 14 1 CATTTTTTCT 0.758856 -195 TCTCCTGCTACCACTTCTCCTCATTGAGATT 9 34 1 CACTTCTCCT 0.750557 -175 CTGAAGGACCTCTCTTTTCCTTTCCTAGAAA 9 103 1 TTCTTTTCCT 0.920549 -106 CTCAGATTCTCATTTTATCCTTTATAAAACC 10 181 1 CTTTTATCCT 0.954195 -49 CCGTAAGGCTCTTCTTTTTCTCAGATATCCA 13 271 1 CTCTTTTTCT 0.899509 -30 * ********* Masking position 6 Map Score: 27.3546 Number of sites scoring better than the average of aligned sites = 266 Number in coding regions = 266 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 GCCATTTTCTAAGAGGATCCTATAGGTTCCA 1 147 1 AAGAGGTCCT 0.948688 -30 TAGTCTTCGGAAGAGTTTTTTGCATGATATT 2 51 1 AAGAGTTTTT 0.689168 -119 TTTTGTTATGAAAAGGATTTTATTTTGTTGT 2 113 1 AAAAGGTTTT 0.929331 -57 AGCAAAAGTCAAGAAGCTTCCTACTAGGAAA 3 18 0 AAGAAGTTCC 0.83795 -283 TTCTAGGAGAAAGAGGATTTATTTTAACTAT 3 165 0 AAGAGGTTTA 0.890322 -136 AAAGGGTTAGAAAAAGTTTTTGTCGCACGAG 4 137 0 AAAAAGTTTT 0.800221 -164 TATCTGAGGGAAGAGGATTCTCCTTCCAAGC 9 135 0 AAGAGGTTCT 0.984539 -74 AATCTCCTAAAAGAAGCTCCTCCGAACTCAG 10 155 1 AAGAAGTCCT 0.894173 -75 GGAACTAAGCAAAAGGGTTTTATAAAGGATA 10 196 0 AAAAGGTTTT 0.929331 -34 TTTTTAAATAAAGAAGCTTTTTTTAGGAGTT 11 124 1 AAGAAGTTTT 0.899563 -143 AAGAACTATAAAGAAGTTTCTCTTTCTCAAA 11 179 0 AAGAAGTTCT 0.967291 -88 CTTTGTGTGTAAAAGGCTTCTATAGGAAGAG 11 214 1 AAAAGGTTCT 0.953446 -53 AAGTTTTTGAAAAAGGATTTAGAATGTATTT 13 75 0 AAAAGGTTTA 0.741894 -226 AAGCCATAAAAAGAAGCTTCTCAACAAAAAA 14 225 1 AAGAAGTTCT 0.966642 -76 ****** **** Masking position 4 Map Score: 19.6101 Number of sites scoring better than the average of aligned sites = 255 Number in coding regions = 255 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 TCCTAATTTATTTAGAGAAAGAACTTTAGATG 1 29 0 TTGAGAAAGA 0.936875 -148 TTTTAGCCATTTTCTAAGAGGATCCTATAGGT 1 142 1 TTTAAGAGGA 0.72067 -35 AAGCTTTTTTCCTAGTAGGAAGCTTCTTGA 3 9 1 TCTAGTAGGA 0.729544 -292 CGCTAAAGATTTCTTAGATAGAGAGTTAAGAG 4 171 0 TCTAGATAGA 0.599747 -130 GAACAAAAGCTCTTGAGAAAGAACGGGACAGG 4 258 0 TTGAGAAAGA 0.93626 -43 TTGTTCGGATTGCGTAAAAGGACTCCT 4 284 1 TCTAAAAGGA 0.850027 -17 TGCTTTCTCCTATTGGGGAAGAGAATAAACTA 5 48 0 TTGGGGAAGA 0.815961 -77 TCACAGAAGTTCTTTGGAAAGAATAAAGGATG 6 77 0 TTTGGAAAGA 0.787222 -73 ATCAAGGTAATACGTAAAAAGAAGAATAAAAG 8 28 0 TCTAAAAAGA 0.832813 -150 CGAATTATAGTTCCTAGGAGGAAAAAATCAAG 8 54 0 TCTAGGAGGA 0.94576 -124 TCCAAGCCTTTCTAGGAAAGGAAAAGAGAGGT 9 110 0 TTGGAAAGGA 0.621131 -99 CTAAATAAAGTGCTGAAAAGGAAATGATTATA 11 28 1 TCGAAAAGGA 0.89052 -239 TAGCCCTTCTTGCTTAGAAAGATCATCCAAAA 11 61 0 TCTAGAAAGA 0.949088 -206 GGGTTTGTGTTTTTGAGAAAGAGAAACTTCTT 11 168 1 TTGAGAAAGA 0.936869 -99 GTAAAAGGCTTCTATAGGAAGAGCAAATCAGC 11 222 1 TTTAGGAAGA 0.89465 -45 ATCAGCCGCTTGCAGAGCAGGAGATAAGC 11 248 1 TCGAGCAGGA 0.851592 -19 TTTCCGCGATTCCTGAGGAAGAT 14 288 1 TCGAGGAAGA 0.956488 -13 * * ******** Masking position 1 Map Score: 16.405 Number of sites scoring better than the average of aligned sites = 290 Number in coding regions = 290 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 CATCTAAAGTTCTTTCTCTAAATAAATTAG 1 29 1 TCTTTCTCTA 0.902899 -148 CAAAATAAAATCCTTTTCATAACAAAAAAA 2 110 0 TCCTTTTCAT 0.683236 -60 AAGCATCGTTTCTTTTTCTTATAGTTATAG 3 139 1 TCTTTTTCTT 0.511919 -162 CCTGTCCCGTTCTTTCTCAAGAGCTTTTGT 4 258 1 TCTTTCTCAA 0.958861 -43 TAGTTTATTCTCTTCCCCAATAGGAGAAAG 5 48 1 TCTTCCCCAA 0.901334 -77 CATCCTTTATTCTTTCCAAAGAACTTCTGT 6 77 1 TCTTTCCAAA 0.825121 -73 GGGCATATCATCCTTCCCAAGTCACAGAAG 6 100 0 TCCTTCCCAA 0.940078 -50 ACCTCTCTTTTCCTTTCCTAGAAAGGCTTG 9 110 1 TCCTTTCCTA 0.66507 -99 AAGAGGATTCTCCTTCCAAGCCTTTCTAGG 9 126 0 TCCTTCCAAG 0.807664 -83 AACATTTCCTCTTCAATGAGTGTTTA 9 193 0 TCCTCTTCAA 0.743476 -16 TATAATCATTTCCTTTTCAGCACTTTATTT 11 30 0 TCCTTTTCAG 0.868095 -237 TTTTGGATGATCTTTCTAAGCAAGAAGGGC 11 61 1 TCTTTCTAAG 0.861852 -206 AAGAAGTTTCTCTTTCTCAAAAACACAAAC 11 170 0 TCTTTCTCAA 0.958861 -97 GCTGATTTGCTCTTCCTATAGAAGCCTTTT 11 224 0 TCTTCCTATA 0.522916 -43 TTATCGCCAGTCTTTCCCATCTATATTTGG 13 42 1 TCTTTCCCAT 0.871771 -259 AAGGCTCTTCTTTTTCTCAGATATCCAGGA 13 275 1 TTTTTCTCAG 0.541485 -26 TTGAGAAGCTTCTTTTTATGGCTTGAATTT 14 219 0 TCTTTTTATG 0.441224 -82 ATCTTCCTCAGGAATCGCGGA 14 290 0 TCTTCCTCAG 0.923541 -11 ********** Masking position 4 Map Score: 13.7479 Number of sites scoring better than the average of aligned sites = 628 Number in coding regions = 628 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 CAGAGAGCGATATCCTCCCTACTTTAAAGC 4 10 1 ATACCTCCCT 0.803654 -291 CGTACTTTAAAGAGCATCCCTCTCTTGGCTC 5 92 1 AGACATCCCT 0.97974 -33 CAATTGTTTGAAGCCATCCCTTACTGAATAA 7 23 1 AAGCATCCCT 0.919773 -152 TCCGGGCAAAAGAACATCCCTTACTTATTCA 7 47 0 AGACATCCCT 0.982076 -128 GAGATCACCTCTTTAACAGTCT 8 166 0 AGACACCTCT 0.903167 -12 ATTTGTCTGAAGGACCTCTCTTTTCCTTTCC 9 97 1 AGGCCTCTCT 0.968992 -112 GATCTATTGTAGGGCATCTCTTGAAAAAAAC 10 88 1 AGGCATCTCT 0.97974 -142 TCTTATAAACAGGGCATTTCTCGCCTTGTTC 13 139 1 AGGCATTTCT 0.859243 -162 *** ******* Masking position 1 Map Score: 5.572 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 6 TCTTTCTCCTAGAAAGTTTAGACTTTCTCAT 3 182 1 AGAAAGTTAG 0.788544 -119 AGGATAAGGGAGAGTGGGTAGAGGATAAAGA 3 234 1 AGAGTGGTAG 0.724196 -67 TTTCTTAGATAGAGAGTTAAGAGAAAAAAGG 4 163 0 AGAGAGTAAG 0.906093 -138 CTTCGAGCCAAGAGAGGGATGCTCTTTAAAG 5 96 0 AGAGAGGATG 0.981111 -29 TTACTTATTCAGTAAGGGATGGCTTCAAACA 7 27 0 AGTAAGGATG 0.896607 -148 TTACTGAATAAGTAAGGGATGTTCTTTTGCC 7 43 1 AGTAAGGATG 0.896607 -132 TGACCTAGGCAGAAAGGAACGAGTGTTTAGG 7 118 0 AGAAAGGACG 0.922536 -57 AAAAAGAAATGATTGACCTTTTATT 8 5 1 AGAAATGTTG 0.736086 -173 TTCCTTTCCTAGAAAGGCTTGGAAGGAGAAT 9 119 1 AGAAAGGTTG 0.952548 -90 AGATAGCGAGAGAGATGCAAGG 12 30 1 AGAGATGAAG 0.858617 -12 GTGAAATGATAGAGAGGTAAGCT 14 3 0 AGAGAGGAAG 0.977633 -298 GAAAACCCACAGATAGTTATGGTTATTGCGT 14 49 0 AGATAGTATG 0.639485 -252 ******* *** Masking position 1 Map Score: 8.49284 Number of sites scoring better than the average of aligned sites = 140 Number in coding regions = 140 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 CTTTCTCCTAGAAAGTTTAGACTTTCTCAT 3 183 1 GAAAGTTTAG 0.717175 -118 GGATAAGGGAGAGTGGGTAGAGGATAAAGA 3 235 1 GAGTGGGTAG 0.953262 -66 TAAGTTCTATAAGTGGTAAGCATACGAAGA 4 60 0 AAGTGGTAAG 0.80088 -241 TTCTTAGATAGAGAGTTAAGAGAAAAAAGG 4 163 0 GAGAGTTAAG 0.95782 -138 TTCGAGCCAAGAGAGGGATGCTCTTTAAAG 5 96 0 GAGAGGGATG 0.78518 -29 AGAAAGGAACGAGTGTTTAGGAGTAGATAG 7 109 0 GAGTGTTTAG 0.95782 -66 CCTCTTCAATGAGTGTTTAGGATTGCAACG 9 182 0 GAGTGTTTAG 0.95782 -27 TGAAATGATAGAGAGGTAAGCT 14 3 0 GAGAGGTAAG 0.972986 -298 ********** Masking position 2 Map Score: 4.1013 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 8 CATCTAAAGTTCTTTCTCTAAATAAATTAG 1 29 1 TCTTTCTCTA 0.39 -148 AAATAAGTTCTATTTTTTTGTTATGAAAAG 2 98 1 TATTTTTTTG 0.917846 -72 AAAAGGATTTTATTTTGTTGTTATAATTAA 2 123 1 TATTTTGTTG 0.810889 -47 GGGAATCTAATCTTTTGATGAGAAAGTCTA 3 200 0 TCTTTTGATG 0.645187 -101 CTTATCCTACTCTTTGTTTGGATCTATCGT 4 94 1 TCTTTGTTTG 0.925188 -207 CCGGGAAATGTATTTGTCTGAAGGACCTCT 9 86 1 TATTTGTCTG 0.818331 -123 AATAGATCCTTATTTTTTTAGTGCACAGCT 10 66 0 TATTTTTTTA 0.632515 -164 ATTTTTTACATCTTTCTTTGTGAAGCCTAA 14 117 0 TCTTTCTTTG 0.894627 -184 AGGAGATGTATATTTGTTTGCATAAATGCA 14 190 1 TATTTGTTTG 0.902108 -111 TTGAGAAGCTTCTTTTTATGGCTTGAATTT 14 219 0 TCTTTTTATG 0.825719 -82 GGGCTTAGTTTATTTTTTTGTTGAGAAGCT 14 239 0 TATTTTTTTG 0.917846 -62 ********** Masking position 5 Map Score: 5.07304 Number of sites scoring better than the average of aligned sites = 188 Number in coding regions = 188 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 GAACTTATTTCCCTCGTATGATCTTAAATATCAT 2 74 0 CCTGAGATCT 0.960872 -96 AAGAATCAATCTCTGTTACGTTCCCATGCTTGCG 7 151 0 CCTTAGTTCC 0.982685 -24 CACTCTTACGTTCCTATTTTTTCT 9 1 1 CCTTAGTTCC 0.982685 -208 AATGATTATACTTTTGGATGATCTTTCTAAGCAA 11 50 1 CTTGAGATCT 0.761069 -217 AAAACACAAACCCTTTCAGGATACCGAACTCCTA 11 147 0 CCTTAGATAC 0.849704 -120 ATACAGCTTCCACTAGTATGTTCCTCTAGGAATA 13 175 1 CCTGAGTTCC 0.991541 -126 GTCCTTTTGGCACTAGAAAGTTCCAAGTCAAAGG 14 159 1 CCTGAGTTCC 0.991541 -142 * ** * * ***** Masking position 8 Map Score: 3.5692 Number of sites scoring better than the average of aligned sites = 10 Number in coding regions = 10 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 CAAAAATATTCAGGTGCACATCTAAAGTTCTTT 1 10 1 TCAGTACATT 0.972972 -167 GAAGACTACATTAGCTATTCATTTTTAACCTTTT 2 25 0 TTAGTTCATT 0.91228 -145 CATTGCAGCTTCAGTTGATCATATTCTTACAGCA 3 45 0 TCAGTTCATT 0.985343 -256 TTCGCTTCCATCATCTCTACATTTTGCTCGATAG 5 17 1 TCATTACATT 0.847872 -108 TCCTCTTCCCTCAGATAATCATCTCATATGGATC 9 149 1 TCAGTTCATT 0.985343 -60 TCCTCCGAACTCAGATTCTCATTTTATCCTTTAT 10 172 1 TCAGTTCATT 0.985343 -58 **** * **** * Masking position 6 Map Score: 2.27404 Number of sites scoring better than the average of aligned sites = 5 Number in coding regions = 5 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 AAAAAGCGGAAAAAAAGTCCGCTAAAGATT 4 192 0 AAAAAAGTCC 0.802608 -109 ATGAATTAGAAGAAACGTCCGTTAGCCCTC 6 50 0 AGAAACGTCC 0.96594 -100 AAGCAACCCAAAAAACGCCTTTAGAAGACA 7 78 1 AAAAACGCCT 0.662666 -97 TGGAAGCCATAAAAAGGCCCAAAGACTGTT 8 144 1 AAAAAGGCCC 0.96244 -34 GGAAAGGAAAAGAGAGGTCCTTCAGACAAA 9 98 0 AGAGAGGTCC 0.959018 -111 GTTTTTTTCAAGAGATGCCCTACAATAGAT 10 89 0 AGAGATGCCC 0.942773 -141 GAACAAGGCGAGAAATGCCCTGTTTATAAG 13 140 0 AGAAATGCCC 0.966756 -161 TTTTGGCACTAGAAAGTTCCAAGTCAAAGG 14 163 1 AGAAAGTTCC 0.821648 -138 ********** Masking position 5 Map Score: 2.03535 Number of sites scoring better than the average of aligned sites = 71 Number in coding regions = 71 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 TATACTATACTGCTGCAGTGGTTTCTTTTAGC 1 117 1 TGCTCAGTGT 0.901365 -60 GATCAACTGAAGCTGCAATGGTATTAAAGCAC 3 59 1 AGCTCAATGT 0.933961 -242 ATTTCCACCTCCACTGATTAAACCTTGC 3 283 0 ACCTCACTGT 0.974784 -18 TAAAGTACGCAGCTACACGGTTGCTTTCTCCT 5 69 0 AGCTCACGGT 0.984036 -56 GTCCTATAGTACCTGCACTGATGGTTTAAGAT 6 18 0 ACCTCACTGT 0.974774 -132 CGCAGATCCGTGCGACACGGTTC 10 2 0 TGCGCACGGT 0.907467 -228 AAATAAACTAAGCCCCACTGATTTCTGTAATA 14 254 1 AGCCCACTGT 0.970983 -47 **** ***** * Masking position 7 Map Score: 0.969601 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 13 CCTACTTTAAAGCAACGAATTCTTTTAATGAGTC 4 28 1 ACAACGATTT 0.902811 -273 TTTCTCTAACAACCAGGAAATCTTAGAAAAAAGC 4 215 0 ACCAGGATTT 0.983151 -86 TCGTCTTGCAAACAAGGGGATGTTGCGAGAAGAC 8 95 1 ACAAGGGTTT 0.967294 -83 GCACTAAAAAAATAAGGATCTATTGTAGGGCATC 10 72 1 ATAAGGATTT 0.862393 -158 AACTTTTTTCAACCTGGGTTTTTTTCAAGAGATG 10 102 0 ACCTGGGTTT 0.89073 -128 CTCTAGGAATATCAAGGATTTCTTAATCCTTGTT 13 198 1 ACAAGGATTT 0.979722 -103 TTTCTCAGATATCCAGGAGTTTTT 13 287 1 ACCAGGATTT 0.983151 -14 * ****** * ** Masking position 1 Map Score: 1.10905 Number of sites scoring better than the average of aligned sites = 26 Number in coding regions = 26 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: -2.03683e-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: -2.03683e-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