AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00650_ctra_reg_300.orf -o00650_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 221 Pyruvate Dehydrogenase Alpha #7 lpxC 100 UDP-3-O-Acyl GlcNAc Deacetylase #8 cutE 63 Apolipoprotein N-Acetyltransferase #9 yciA 135 Acyl-CoA Thioester Hydrolase #10 CT538 300 hypothetical protein #11 sdhB 236 Succinate Dehydrogenase #12 sdhC 25 Succinate Dehydrogenase #13 CT593.1 221 hypothetical protein-possible frameshift with CT593 #14 ycfH 84 PHP superfamily hydrolase #15 dsbD 152 Thio:disulfide Interchange Protein Motif number 1 GGCTCTACGTAAAAGCTTCTTTATATAAAACG 1 42 0 AAAAGCTTTT 0.550044 -90 ATTTTGTGGAAAAGGGCTGTTTTAACAACTGG 2 80 0 AAAGGGTTTT 0.905595 -195 GTCCTTTCCCAAAGGCCTTCTTAAGACCTTCC 2 151 1 AAAGGCTCTT 0.976879 -124 GGAGAACTCAGAGGGGGTGCTGGTCACTAGCA 3 11 0 GAGGGGTCTG 0.937949 -290 GAACCTGCTAGAGGGGTTGCTTTTCGGGCTTT 3 46 1 GAGGGGTCTT 0.967137 -255 AAAGGAGAAGGAGAGCATCCTTCTCCTTTCAC 4 17 1 GAGAGCTCTT 0.789456 -52 TCTCTTGGATAAAGGGTTCCTGAAAAATTCTA 6 196 0 AAAGGGTCTG 0.960949 -26 GTAACTTCTAAGGGGATTCTTTTTCTCTCAT 8 10 1 AAGGGGTCTT 0.977136 -54 TAAAGGGGCTCCCTTACTAGCTTA 8 50 0 AAGGGGTCCT 0.943528 -14 CTCTAGGGGTAGGGGCATCCTGAATCGACTAC 10 112 0 AGGGGCTCTG 0.909569 -189 ATATGGGCGGAAAGGCTTCCCTTTAGAAGGAG 10 219 1 AAAGGCTCCT 0.947497 -82 GAATATTTATAGAGGCGTTCCTGGGAAATAAT 11 198 1 AGAGGCTCCT 0.902608 -39 CCCTCAACTGAAAGGCTTCCATCCCTAATT 13 9 0 AAAGGCTCAT 0.88904 -213 TGATGTTTGAGGAGGGCTCTTTATGGAAGGGC 13 88 1 GGAGGGTTTT 0.772203 -134 CAGCGAATAAGGAGGCGTTCATATGAGGAGGG 13 135 1 GGAGGCTCAT 0.738962 -87 TTTTCCGCTAAAAGGGCTTCTTCCTTCATGAT 14 30 1 AAAGGGTCTT 0.979317 -55 TTACATACCAAAAAGGATCTTGGTTCTATACA 15 61 0 AAAAGGTTTG 0.41335 -92 ****** * *** Masking position 8 Map Score: 20.3454 Number of sites scoring better than the average of aligned sites = 267 Number in coding regions = 265 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 2 AGCCCTACAAATATAGGAAGAAAAGAGAAC 3 104 0 ATATAGGAAG 0.826033 -197 CGTCCCCACATATTAGGAAGAGACTACTCA 3 176 0 TATTAGGAAG 0.759004 -125 ACTTTTCTAGATAAAGGAAGTAATA 3 286 1 ATAAAGGAAG 0.826033 -15 AATCCGAAAGGAGAAGGAGAGCATCCT 4 8 1 AAGGAGAAGG 0.884264 -61 CAATAGGTGAAAGGAGAAGGATGCTCTCCT 4 25 0 AAGGAGAAGG 0.884264 -44 TATTAGACTCATATAGAAGGGTGAT 9 121 1 ATATAGAAGG 0.734899 -15 GGCTTCCCTTTAGAAGGAGGCTGGTGATTA 10 232 1 TAGAAGGAGG 0.8854 -69 AGAAATTTCATATAAGAAAGTAGATACCCG 11 45 1 TATAAGAAAG 0.501466 -192 TCATTTCCCGATATAGGAGGCTAATTTGAA 11 153 1 ATATAGGAGG 0.896691 -84 CATCATGATGTTTGAGGAGGGCTCTTTATG 13 83 1 TTTGAGGAGG 0.912564 -139 AGGGACAGCGAATAAGGAGGCGTTCATATG 13 130 1 AATAAGGAGG 0.917886 -92 GAGGCGTTCATATGAGGAGGGAGATAGTAC 13 146 1 TATGAGGAGG 0.901778 -76 AATGAAACGAATGTAGGAAGATTTTTGTAC 13 172 0 ATGTAGGAAG 0.903184 -50 ATCAAAGATCATGAAGGAAGAAGCCCTTTT 14 39 0 ATGAAGGAAG 0.903184 -46 ATGATCTTTGATTGAGAAAGATTGATTATG 14 57 1 ATTGAGAAAG 0.779764 -28 ********** Masking position 5 Map Score: 12.6905 Number of sites scoring better than the average of aligned sites = 370 Number in coding regions = 368 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 3 ATTTGGCTCTCCAAATCAAAAACTTCTAGTAT 2 10 1 TCAACAAAAA 0.916305 -265 ATTATTTTCAGCAAAACAAGAAGCTGTACCAAC 2 217 0 GCAAAAGAAG 0.795278 -58 CCAAGTCTATGCTACAAAAAAAAACTTTTCGGC 6 53 0 GCAAAAAAAA 0.970532 -169 TAGCAAGCAAGCGATATCAAAAAATTACTACCT 7 32 0 GCAACAAAAA 0.977875 -69 TCGCTTGCTTGCTAAAAAAAAAAAAGGATAATA 7 51 1 GCAAAAAAAA 0.970532 -50 TAGTAGTCTCGATATAGAAGAAAATCAAGAAAT 9 22 0 GAAAAAGAAA 0.836325 -114 TTGCCATTAAGCAACTGAAAAAAGTAAGGATAA 10 276 1 GCATAAAAAA 0.890971 -25 TGAGGAGGGAGATAGTACAAAAATCTTCCTACA 13 158 1 GAATCAAAAA 0.730927 -64 GGATCTTGGTTCTATACAAGAAATTTGTTAGGA 15 46 0 TCAAAAGAAA 0.836325 -107 TGCAATTCATTACATACCAAAAAGGATCTTGGT 15 69 0 TAAACAAAAA 0.730598 -84 GTAATGAATTGCAAAAACAAAAACAACTCTTCT 15 89 1 GCAACAAAAA 0.977875 -64 ** * * ****** Masking position 9 Map Score: 7.97035 Number of sites scoring better than the average of aligned sites = 110 Number in coding regions = 110 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 ATATAAAGAAGCTTTTACGTAGAGCCTGTC 1 48 1 GCTTTTACGT 0.78366 -84 TTAAAACAGCCCTTTTCCACAAAATACTTT 2 87 1 CCTTTTCCAC 0.79636 -188 TAGAGGGGTTGCTTTTCGGGCTTTTTTTCG 3 54 1 GCTTTTCGGG 0.931657 -247 ACAAAAAAAAACTTTTCGGCACTACCCAGA 6 43 0 ACTTTTCGGC 0.926623 -179 CGAAGGCCGGACCTTTCCGGTTACTTTTCC 6 111 1 ACCTTTCCGG 0.925692 -111 CTTTCCGGTTACTTTTCCGCGCCGGCCTTG 6 123 1 ACTTTTCCGC 0.97645 -99 ATGCTATCATGATTTTCCGTTAGGCACAAG 10 82 0 GATTTTCCGT 0.87757 -219 CTAAAGGGAAGCCTTTCCGCCCATATCCCT 10 215 0 GCCTTTCCGC 0.98693 -86 AGGGATGGAAGCCTTTCAGTTGAGGGATAT 13 15 1 GCCTTTCAGT 0.767244 -207 CAAGTAGAAACATTTTCCGCTAAAAGGGCT 14 18 1 CATTTTCCGC 0.885555 -67 ********** Masking position 5 Map Score: 5.5126 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 5 TAAGGCTAGTATGACTTTGCTAGTAGTTACAGAAA 1 94 0 ACTTTGCATA 0.976257 -38 TTGTTAAAACAGCCCTTTTCCACAAAATACTTTGC 2 84 1 ACTTTTCAAA 0.821161 -191 TTTTCCACAAAATACTTTGCCATTAACTGTCTTCC 2 99 1 ACTTTGCATA 0.976257 -176 ACTAGGGATGAGTCCTTTCCCAAAGGCCTTCTTAA 2 140 1 ACTTTCCAAG 0.937435 -135 GAGAACAGAGAGAACTTTGAAAACAACGAAAAAAA 3 75 0 ACTTTGAACA 0.715816 -226 AGACTACTCAAGACCTATCCAATTACAATAGAGAA 3 151 0 ACTATCCATA 0.905023 -150 ATATGTGGGGACGCCTATGAGATTGGCTTCTGACC 3 193 1 ACTATGAATG 0.570214 -108 AATTCTTTCCTATAAAAATATAACC 4 54 0 ACTTTCCAAA 0.967406 -15 GCTGGGCGCCAAGTCTATGCTACAAAAAAAAACTT 6 59 0 ACTATGCAAA 0.929581 -163 AAATTCTAGAATGTCTTTCAAATAAATCTTTTGAA 6 169 0 ACTTTCAAAA 0.855262 -53 ACCTACTCTCACTTCCTTGCAAAAGTATTTTTACA 10 173 0 ACCTTGCAAG 0.766023 -128 TAAAAGAAGAATCAGTTTGCCATTAAGCAACTGAA 10 260 1 AGTTTGCATA 0.800557 -41 CTCAAAACTTTCCCAATATTATTTCCCA 11 219 0 ACTTTCCATA 0.967406 -18 * ****** * ** Masking position 12 Map Score: 6.46864 Number of sites scoring better than the average of aligned sites = 197 Number in coding regions = 197 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 TTTTTGATTTGGAGAGCCAAAT 2 3 0 GGAGAGCCAA 0.932296 -272 GAAGAAAAGAGAACAGAGAGAACTTTGAAA 3 88 0 GAACAGAGAG 0.928194 -213 CACATATTAGGAAGAGACTACTCAAGACCT 3 170 0 GAAGAGACTA 0.814011 -131 TTACATTCAAGATGAGAGAAAAAGAATCCC 8 23 0 GATGAGAGAA 0.898012 -41 CTTTTGCAAGGAAGTGAGAGTAGGTAGAGA 10 183 1 GAAGTGAGAG 0.808313 -118 ATATTCTGTAGATGAGCCAGAAATTTCATA 11 27 1 GATGAGCCAG 0.773585 -210 GGGAGAGAGAATTTTTTCTCT 12 2 1 GGAGAGAGAA 0.970749 -24 CTGAAGAGAAAAAATTCTCTCT 12 14 0 GAAGAGAAAA 0.798501 -12 ACATCATGATGAACAGCGCACTTAATCGCG 13 64 0 GAACAGCGCA 0.751256 -158 GAACCATGAGGGACAGCGAATAAGGAGGCG 13 122 1 GGACAGCGAA 0.923599 -100 TTGCTAAACCGGAGAGAGTGTTGTGTTT 15 135 1 GGAGAGAGTG 0.896132 -18 ********** Masking position 6 Map Score: 4.61091 Number of sites scoring better than the average of aligned sites = 377 Number in coding regions = 377 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 GGGAAAGGACTCATCCCTAGTTTAGCTGGA 2 131 0 TCATCCCTAG 0.985401 -144 TGACTTCGGTTCATCCGTAATAAGTTTCAA 2 184 1 TCATCCGTAA 0.909134 -91 GAATAAAACTTCATCCCTAGCGCAGACTTT 3 261 1 TCATCCCTAG 0.985401 -40 CAAACCAACTTCATCTCTATCCATTTTTCT 6 16 1 TCATCTCTAT 0.936487 -206 TACTCCCCAGTCATCTCTGTAATGGATAGT 9 51 0 TCATCTCTGT 0.843538 -85 TGAAAGGCTTCCATCCCTAATT 13 3 0 CCATCCCTAA 0.94102 -219 ********** Masking position 4 Map Score: 2.10966 Number of sites scoring better than the average of aligned sites = 18 Number in coding regions = 18 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 TGTGATCGAGACAGGCTCTACGTAAAAGCTT 1 56 0 ACGGCTCTAC 0.891071 -76 GCAAAGTCATACTAGCCTTACGGAACACATA 1 109 1 ACAGCCTTAC 0.978356 -23 GGATAATTTGACTAGCCCTACAAATATAGGA 3 116 0 ACAGCCCTAC 0.988865 -185 TGGGAAGAGCACCATTCTTACTTGGTCAGAA 3 220 0 ACATTCTTAC 0.592231 -81 TCTCAGAGTTACAGGCCCACCTCTACTCCCC 9 73 0 ACGGCCCACC 0.949451 -63 AAAAAGCAAAACAGGCCTAACCTCCCCATGC 10 143 0 ACGGCCTAAC 0.951357 -158 AAACTACGATCGCTACATATTCTGTA 11 6 1 ACATCGCTAC 0.828102 -231 CCCTTCCATAAAGAGCCCTCCTCAAACATCA 13 88 0 AAAGCCCTCC 0.809734 -134 GAGTTCCTAGACGATCCTAACAAATTTCTTG 15 32 1 ACATCCTAAC 0.885993 -121 ** ******** Masking position 1 Map Score: 2.9326 Number of sites scoring better than the average of aligned sites = 79 Number in coding regions = 79 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 GCAAAACCCTGACAAAGAGACCCCGTAT 7 83 0 CCTGACAAGA 0.940115 -18 GGATAGTAGTCTCGATATAGAAGAAAATCAA 9 27 0 CTCGATAAGA 0.976214 -109 GATTTTCTTGCTCGACATAGAAGTTTTTCAT 10 17 1 CTCGACAAGA 0.984741 -284 CGAGATTACACTCGACAGGGAGCAAAAGATG 11 94 1 CTCGACAGGA 0.981652 -143 ATATTCATTTCCCGATATAGGAGGCTAATTT 11 149 1 CCCGATAAGG 0.959325 -88 ACATCCCGATACGGAATGAATACAT 13 207 0 CCCGATAGGA 0.981519 -15 ******* *** Masking position 5 Map Score: 3.56601 Number of sites scoring better than the average of aligned sites = 17 Number in coding regions = 17 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 AAGGCCTTTGGGAAAGGACTCATCCCTAGT 2 140 0 GGAAAGGACT 0.92418 -135 TATTGTAATTGGATAGGTCTTGAGTAGTCT 3 156 1 GGATAGGTCT 0.968547 -145 TAACCGGAAAGGTCCGGCCTTCGCAAATAT 6 104 0 GGTCCGGCCT 0.936553 -118 AGCATGGGGAGGTTAGGCCTGTTTTGCTTT 10 142 1 GGTTAGGCCT 0.985795 -159 GGATATGGGCGGAAAGGCTTCCCTTTAGAA 10 217 1 GGAAAGGCTT 0.882254 -84 GGAACTCGTTGGTTAGGTCTACGTCCTT 15 9 0 GGTTAGGTCT 0.96855 -144 ********** Masking position 10 Map Score: 2.33264 Number of sites scoring better than the average of aligned sites = 20 Number in coding regions = 20 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 3 27 1 TTCTCCCCCG 0.887436 -274 AAGAATGGTGCTCTTCCCAGAAAGAGTAAG 3 232 1 CTCTTCCCAG 0.960191 -69 AACTTTTCGGCACTACCCAGAAAAATGGAT 6 34 0 CACTACCCAG 0.974807 -188 ATCAAAAAATTACTACCTAGTTCTAAAACA 7 20 0 TACTACCTAG 0.89734 -81 GGCCCACCTCTACTCCCCAGTCATCTCTGT 9 61 0 TACTCCCCAG 0.980223 -75 TACCTACTCTCACTTCCTTGCAAAAGTATT 10 179 0 CACTTCCTTG 0.788646 -122 TTCCCAATATTATTTCCCAGGAACGCCTCT 11 208 0 TATTTCCCAG 0.856227 -29 ********** Masking position 4 Map Score: 1.5085 Number of sites scoring better than the average of aligned sites = 69 Number in coding regions = 68 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 12 ACCCAGAAAAATGGATAGAGATGAAGTTGG 6 20 0 ATGGATAGAG 0.901487 -202 CCCATGCTCTAGGGGTAGGGGCATCCTGAA 10 120 0 AGGGGTAGGG 0.958929 -181 GGTAGAGAACAGGGATATGGGCGGAAAGGC 10 205 1 AGGGATATGG 0.975967 -96 CTTTCAGTTGAGGGATATAGCTGCTGTTTG 13 27 1 AGGGATATAG 0.974106 -195 AGGAACCATGAGGGACAGCGAATAAGGAGG 13 120 1 AGGGACAGCG 0.93987 -102 TCATATGAGGAGGGAGATAGTACAAAAATC 13 153 1 AGGGAGATAG 0.944279 -69 ********** Masking position 7 Map Score: 1.44274 Number of sites scoring better than the average of aligned sites = 50 Number in coding regions = 50 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: -1.68155e-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 TTTTATATAAAGAAGCTTTTACGTAGAGCC 1 44 1 AGAAGCTTTT 0.875956 -88 AAAGAATACTAGAAGTTTTTGATTTGGAGA 2 18 0 AGAAGTTTTT 0.941381 -257 GAAGGTCTTAAGAAGGCCTTTGGGAAAGGA 2 152 0 AGAAGGCCTT 0.853111 -123 CCGAAGTCAAGGAAGGTCTTAAGAAGGCCT 2 163 0 GGAAGGTCTT 0.96792 -112 GAAAAATTCTAGAATGTCTTTCAAATAAAT 6 177 0 AGAATGTCTT 0.901254 -45 TCCTCCAAGGAATTTCTTGATTTTCTTC 9 9 1 GGAATTTCTT 0.86177 -127 TGCTCGACATAGAAGTTTTTCATTTGAATT 10 25 1 AGAAGTTTTT 0.941381 -276 AATAATATTGGGAAAGTTTTGAG 11 224 1 GGAAAGTTTT 0.783182 -13 GGGAGAGAGAATTTTTTCTCTTCAG 12 8 1 AGAATTTTTT 0.841253 -18 AACGAATGTAGGAAGATTTTTGTACTATCT 13 167 0 GGAAGATTTT 0.842151 -55 ********** Masking position 4 Map Score: 6.15051 Number of sites scoring better than the average of aligned sites = 296 Number in coding regions = 296 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: -1.68155e-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