AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00190_ctra_reg_300.orf -o00190_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 atpK 41 ATP Synthase Subunit K #2 CT309 166 hypothetical protein #3 atpE 108 ATP Synthase Subunit E #4 sdhB 236 Succinate Dehydrogenase #5 sdhC 25 Succinate Dehydrogenase #6 CT593.1 221 hypothetical protein-possible frameshift with CT593 #7 ycfH 84 PHP superfamily hydrolase #8 dsbD 152 Thio:disulfide Interchange Protein #9 CT663 300 hypothetical protein #10 CT665 43 hypothetical protein #11 CT666 26 hypothetical protein #12 fliI 73 Flagellum-specific ATP Synthase #13 fliF 272 Flagellar M-Ring Protein #14 pgm 296 Phosphoglycerate Mutase #15 ppa 247 Inorganic Pyrophosphatase Motif number 1 TAAATATTCAAAATAAATGTCTCTTTCAAATTAGCC 4 171 0 AAAACTCTTT 0.649734 -66 CTGAAGAGAAAAAATTCTCTCTCCC 5 2 0 AAAACTCTCC 0.978883 -24 TCCTGCCCTTCCATAAAGAGCCCTCCTCAAACATCA 6 88 0 CAAACCCTCC 0.989421 -134 GGGAGATAGTACAAAAATCTTCCTACATTCGTTTCA 6 164 1 AAAATCCTAC 0.706266 -58 GCCCTTTTAGCGGAAAATGTTTCTACTTGAATCGTT 7 11 0 CGAATTCTAC 0.736549 -74 ACATTTTCCGCTAAAAGGGCTTCTTCCTTCATGATC 7 27 1 CAAATTCTTC 0.903583 -58 AATTGCAAAAACAAAAACAACTCTTCTGTTGTTTGA 8 95 1 AAAACTCTTC 0.923466 -58 AAACACAACACTCTCTCCGGTTTAGCAA 8 135 0 AAAACTCTCC 0.978968 -18 AAGACATCTCCCAAAACACATTTTCCCGGCACAAAT 9 36 0 CAAATTTTCC 0.84785 -265 AAAGAGAAAACAGAAAAGGCTCCTCTATCGAGATGA 9 147 1 CGAATCCTCT 0.751986 -154 AGCTCTGGGTCCGAAATACTCCCTCCCTAGCTATTG 9 248 0 CGAACCCTCC 0.981111 -53 TTCTTGTTCACAAGAAGAAGCCTTCTTTTTCATCCT 13 159 1 CAAACCTTCT 0.688709 -114 GCGACTATCTAAGAAACCTTCTCTCCGAAACAACAC 14 61 1 AGAACTCTCC 0.962755 -236 AAGGGTAAAAATAAAAACGACCCTCCATCATATCAA 14 116 1 AAAACCCTCC 0.978539 -181 AGTAGAGAGTCCAGAAGAAGTTCTCCTCTCAAAGAG 14 158 1 CAAATTCTCC 0.97295 -139 GAAAGGATTGCCACAAGTAACTTTTCAACATTTTTC 15 78 1 CAAACTTTTC 0.79197 -170 * * ** ****** Masking position 6 Map Score: 16.0849 Number of sites scoring better than the average of aligned sites = 499 Number in coding regions = 499 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 CGTTATTGGGAAAATTCGTTGACGATGGAAGCTCCGCAAAC 2 46 1 AATGTAGAAG 0.876162 -121 AGTGCGCTGTTCATCATGATGTTTGAGGAGGGCTCTTTATG 6 72 1 TAAGAGGAGG 0.757763 -150 TGAATACATCATATAATGAAACGAATGTAGGAAGATTTTTG 6 175 0 AAAGAAGAGG 0.985283 -47 AATCTTTCTCAATCAAAGATCATGAAGGAAGAAGCCCTTTT 7 39 0 ATAGAAGAAG 0.946702 -46 TTTGATTGAGAAAGATTGATTATGAGGGAAGT 7 63 1 AATGAAGAAG 0.966119 -22 CTTTTGTACTTTAAATTGAAAGGGATGAAAGAGAAAACAGA 9 120 1 TATGAAGAAG 0.876162 -181 GCTATTAAAAACAATAGGTTATCTAAGAAAGATTTCGATAG 13 35 0 AAAGTAGAAG 0.946702 -238 TATCCTACAAAGAAAAGGATGAAAAAGAAGGCTTCTTCTTG 13 169 0 AAAGAAGAGG 0.985283 -104 AGAGAGCAAGATTTAAGGATGATTACGAAAGGCTTCATCTT 14 266 0 ATAGAAGAAG 0.946702 -31 GTACTGCAAAATAATATGAGCCGGACGTAGGAT 15 3 0 AAAGAAGAGG 0.985283 -245 CACAATGACAAGAATAAAAGCAAAAAGAAAGGCTGCCGATA 15 113 1 AAAAAAGAAG 0.849413 -135 * * * ** * * *** Masking position 19 Map Score: 7.84409 Number of sites scoring better than the average of aligned sites = 74 Number in coding regions = 74 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 ATAGCGGGTATCTACTTTCTTATATGAAATTTCTGGCT 4 41 0 TCTACTAGAA 0.879222 -196 AAATTAGCCTCCTATATCGGGAAATGAATATTCGCTGG 4 142 0 CCTATTAGAA 0.914068 -95 CCCAGGAACGCCTCTATAAATATTCAAAATAAATGTCT 4 185 0 CCTCTTAAAA 0.932663 -52 TTTTGTACTATCTCCCTCCTCATATGAACGCCTCCTTA 6 142 0 TCTCCTAGAA 0.967087 -80 TTTTCTCTTTCATCCCTTTCAATTTAAAGTACAAAAGA 9 119 0 CATCCTAAAA 0.754974 -182 AGAAAAGGCTCCTCTATCGAGATGAGAAATCGTTTTTC 9 158 1 CCTCTTAGAA 0.977243 -143 TATGCCAATACCTACTTTAAAAAGAAAAACGATTTCTC 9 181 0 CCTACTAAAA 0.914058 -120 CGAAATACTCCCTCCCTAGCTATTGGAATGGGCCCCGC 9 235 0 CCTCCTAGAA 0.992545 -66 TTTTTAATAGCCTCTTTTTGTTACAGAAGACAAAAGGG 13 65 1 CCTCTTTGAA 0.905851 -208 ATGCTAATTTTCTTCTTGTTCACAAGAAGAAGCCTTCT 13 147 1 TCTTCTAGAA 0.742351 -126 TAAAAACGACCCTCCATCATATCAAGATTTCAGTAGAG 14 127 1 CCTCCTTGAT 0.775539 -170 GAGTTCCCCCCCTCCCTTATAAGGTAAAAAATCTTTGC 14 207 1 CCTCCTAAAA 0.977216 -90 ***** * * *** Masking position 17 Map Score: 9.80475 Number of sites scoring better than the average of aligned sites = 120 Number in coding regions = 120 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 ATCTTTGGCTTAAGGGGCTATGTTGGTTAAAT 2 14 1 TAGGGCTATG 0.799729 -153 CACCTTCAACTAAGAAACTCTCTAGACAGCTC 2 133 0 TAGAACTCTC 0.766122 -34 TGATCTAACCTTAGGGGCTAACCGGATCATAA 3 42 1 TAGGGCTAAC 0.865167 -67 CTGGATTCACATAGCGGGTATCTACTTTCTTA 4 57 0 AAGGGGTATC 0.961016 -180 ACGTTAACAAACAGCAGCTATATCCCTCAACT 6 32 0 AAGAGCTATA 0.690466 -190 CAACTCATTCAGAGCAGCTCTCGTA 9 4 0 AAGAGCTCTC 0.966497 -297 TTTTCTTTTTAAAGTAGGTATTGGCATAACTC 9 191 1 AAGAGGTATT 0.617939 -110 AAACGGTAAAAGAGAGGGTATCT 11 14 1 AAGGGGTATC 0.961016 -13 CCTTGGTTTTTTAGGATCTCTCGTACGTAATG 12 29 0 TAGATCTCTC 0.564543 -45 TCTGTAACAAAAAGAGGCTATTAAAAACAATA 13 60 0 AAGGGCTATT 0.892817 -213 GAGAAGCTCAAAAGGGACTCTCAATTAAAAGA 13 104 0 AAGGACTCTC 0.924027 -169 AGTTCACTAATAAGCGACTATCTAAGAAACCT 14 48 1 TAGGACTATC 0.871921 -249 GTTGTTTCGGAGAGAAGGTTTCTTAGATAGTC 14 63 0 AAGAGGTTTC 0.647276 -234 TTCTCCTCTCAAAGAGGCTCACAAATGAAGAG 14 178 1 AAGGGCTCAC 0.919769 -119 * ** ******* Masking position 3 Map Score: 8.60511 Number of sites scoring better than the average of aligned sites = 300 Number in coding regions = 300 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 GGGAGAGAGAATTTTTTCTC 5 1 1 GGGAGAGAGA 0.965677 -25 GAAGCCTTTCAGTTGAGGGATATAGCTGCT 6 22 1 AGTTGAGGGA 0.73744 -200 CGTTCATATGAGGAGGGAGATAGTACAAAA 6 150 1 AGGAGGGAGA 0.959475 -72 TTTGCTAAACCGGAGAGAGTGTTGTGTTT 8 134 1 CGGAGAGAGT 0.907787 -19 CCAATAGCTAGGGAGGGAGTATTTCGGACC 9 247 1 GGGAGGGAGT 0.974062 -54 TAAACGGTAAAAGAGAGGGTATCT 11 13 1 AAGAGAGGGT 0.834505 -14 CCATGTACGTGGTTGGGGGATTCCTTGGTT 12 53 0 GGTTGGGGGA 0.796648 -21 TCAAGATTTCAGTAGAGAGTCCAGAAGAAG 14 148 1 AGTAGAGAGT 0.919934 -149 TACCTTATAAGGGAGGGGGGGAACTCTTCA 14 203 0 GGGAGGGGGG 0.937015 -94 AAAACACTTTAATAGAGAGTGATCTT 15 232 1 AATAGAGAGT 0.66513 -16 ********** Masking position 5 Map Score: 5.7467 Number of sites scoring better than the average of aligned sites = 242 Number in coding regions = 242 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 TCTCAACGCATACAAAAAAACTCCGAGTTTGC 2 81 0 TACAAAAACT 0.960484 -86 AGGGAGATAGTACAAAAATCTTCCTACATTCG 6 163 1 TACAAAAATT 0.925213 -59 CTTGGTTCTATACAAGAAATTTGTTAGGATCG 8 43 0 TACAAGAATT 0.858098 -110 CAATTTAAAGTACAAAAGAATTTTAGAAAAAA 9 106 0 TACAAAAGTT 0.960484 -195 TGTTACAGAAGACAAAAGGGCTCTTTTAATTG 13 83 1 GACAAAAGCT 0.958919 -190 AGTAAGTTCTTACAAAAGCTCTACGTATAGGT 13 242 0 TACAAAAGCT 0.979489 -31 GCAGTCGAAAGACAAGAGGACTGGC 14 4 0 GACAAGAGCT 0.919419 -293 TAAGGATGATTACGAAAGGCTTCATCTTCCTT 14 262 0 TACGAAAGTT 0.850276 -35 TCGTCTTTCGTACAAAAAACCTGTCTGAAAGG 15 52 1 TACAAAAACT 0.960484 -196 ******** ** Masking position 7 Map Score: 7.97496 Number of sites scoring better than the average of aligned sites = 34 Number in coding regions = 34 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 ATTCATTTCCCGATATAGGAGGCTAATTTGA 4 151 1 CGAATAGGAG 0.941199 -86 TGAGGGACAGCGAATAAGGAGGCGTTCATAT 6 128 1 CGATAAGGAG 0.908906 -94 AGGAGGCGTTCATATGAGGAGGGAGATAGTA 6 144 1 CATTGAGGAG 0.843467 -78 AATCATCAAACAACAGAAGAGTTGTTTTTGT 8 105 0 CAAAGAAGAG 0.942194 -48 TTTCTCATCTCGATAGAGGAGCCTTTTCTGT 9 156 0 CGAAGAGGAG 0.991962 -145 ATTAAGCAGTCGAAAGACAAGAGGACTGGC 14 10 0 CGAAGACAAG 0.878087 -287 AAGAGGCTCACAAATGAAGAGTTCCCCCCCT 14 189 1 CAATGAAGAG 0.910395 -108 GTTTTTTGTACGAAAGACGAGAGTGATTGTA 15 41 0 CGAAGACGAG 0.984733 -207 *** ******* Masking position 7 Map Score: 4.61022 Number of sites scoring better than the average of aligned sites = 57 Number in coding regions = 57 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 GTTAAATCGTTATTGGGAAAATTCGTTGAC 2 39 1 TATTGGGAAA 0.935375 -128 TAGCCTCCTATATCGGGAAATGAATATTCG 4 146 0 TATCGGGAAA 0.971175 -91 ATAGAGGCGTTCCTGGGAAATAATATTGGG 4 206 1 TCCTGGGAAA 0.785592 -31 TGGGAAATAATATTGGGAAAGTTTTGAG 4 219 1 TATTGGGAAA 0.935375 -18 ATTCATTCCGTATCGGGATGT 6 211 1 TATCGGGATG 0.910658 -11 CATGATCTTTGATTGAGAAAGATTGATTAT 7 56 1 GATTGAGAAA 0.63717 -29 AGTTGATTTGTGCCGGGAAAATGTGTTTTG 9 31 1 TGCCGGGAAA 0.895678 -270 AAGGCTCCTCTATCGAGATGAGAAATCGTT 9 162 1 TATCGAGATG 0.741813 -139 GATTTATTCCTACCTGGAAGAATTAAATAA 10 23 0 TACCTGGAAG 0.776698 -21 CATCCGGGATGACCGAGAAGCTCAAAAGGG 13 120 0 GACCGAGAAG 0.828477 -153 ********** Masking position 8 Map Score: 3.08353 Number of sites scoring better than the average of aligned sites = 113 Number in coding regions = 113 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 CATATTCTGTAGATGAGCCAGAAATTTCATA 4 26 1 AGATGGCCAG 0.876554 -211 TCATCATGATGTTTGAGGAGGGCTCTTTATG 6 82 1 GTTTGGGAGG 0.862446 -140 GGCTCTTTATGGAAGGGCAGGAACCATGAGG 6 102 1 GGAAGGCAGG 0.945353 -120 GGAGGCGTTCATATGAGGAGGGAGATAGTAC 6 145 1 ATATGGGAGG 0.851986 -77 GAATGAGTTGATTTGTGCCGGGAAAATGTGT 9 26 1 ATTTGGCCGG 0.959096 -275 AGAACGAGTCGTTCGTGCCCGATTTTTTTCT 9 83 1 GTTCGGCCCG 0.836553 -218 TCTCAGTTAGAGATGAGCACGTGAATAC 9 283 1 AGATGGCACG 0.946498 -18 ATAGAGCAAGGGTAGAGCCCGCTAAGTATCC 13 205 0 GGTAGGCCCG 0.906636 -68 CTGCAAAATAATATGAGCCGGACGTAGGAT 15 10 0 ATATGGCCGG 0.971694 -238 CGAATAAGCCGGATGCGCAGGATAATTGCGC 15 199 1 GGATGGCAGG 0.982061 -49 ***** ***** Masking position 5 Map Score: 5.75374 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 10 GGTTGATGTGCGTTTTTTTGAAAAAAATAGA 1 19 1 CGTTTTTTGA 0.969049 -23 TGATTTTAAACGTTGTTATGATCTAACCTTA 3 24 1 CGTTTTATGA 0.942606 -85 CATAATTGATCGTTTTTTTAAGATAAACGTT 3 69 1 CGTTTTTTAA 0.857133 -40 TTAAGATAAACGTTGTTTTTCTTGGTATCAG 3 86 1 CGTTTTTTTC 0.950854 -23 AATAAGGAGGCGTTCATATGAGGAGGGAGAT 6 140 1 CGTTATATGA 0.721372 -82 ACGAACGACTCGTTCTTTTGATTTCTAAAGA 9 68 0 CGTTTTTTGA 0.969049 -233 CGTTCGTGCCCGATTTTTTTCTAAAATTCTT 9 92 1 CGATTTTTTC 0.753085 -209 CAAGAAGAAGCCTTCTTTTTCATCCTTTTCT 13 169 1 CCTTTTTTTC 0.737614 -104 GATGGAGGGTCGTTTTTATTTTTACCCTTGA 14 114 0 CGTTTTATTT 0.718662 -183 **** ****** Masking position 7 Map Score: 2.93771 Number of sites scoring better than the average of aligned sites = 77 Number in coding regions = 77 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 CCGAGTTTGCGGAGCTTCCATCGTCAACGA 2 61 0 GGAGCTTCCA 0.701417 -106 AACTCTCTAGACAGCTCTCCAGAGATAGTT 2 120 0 ACAGCTCTCC 0.960566 -47 CCTTCCATAAAGAGCCCTCCTCAAACATCA 6 88 0 AGAGCCCTCC 0.906128 -134 CTCATTCAGAGCAGCTCTCGTA 9 3 0 GCAGCTCTCG 0.952596 -298 ATTTCTAAAGACATCTCCCAAAACACATTT 9 49 0 ACATCTCCCA 0.688573 -252 TTTCGGACCCAGAGCTCTCAGTTAGAGATG 9 268 1 AGAGCTCTCA 0.958084 -33 TGGTTTTTTAGGATCTCTCGTACGTAATGT 12 28 0 GGATCTCTCG 0.870869 -46 TGAATCTAAGAGAGTTCCCGGTGTTGTTTC 14 87 0 AGAGTTCCCG 0.916742 -210 GAGTCCAGAAGAAGTTCTCCTCTCAAAGAG 14 164 1 GAAGTTCTCC 0.651746 -133 TCACAAATGAAGAGTTCCCCCCCTCCCTTA 14 196 1 AGAGTTCCCC 0.935272 -101 ********** Masking position 3 Map Score: 3.51729 Number of sites scoring better than the average of aligned sites = 284 Number in coding regions = 283 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 AGGATCTTTGGCTTAAGGGG 2 1 1 AGGATCTTTG 0.979617 -166 GCTGTTCATCATGATGTTTGAGGAGGGCTC 6 77 1 ATGATGTTTG 0.910778 -145 CGAATGTAGGAAGATTTTTGTACTATCTCC 6 165 0 AAGATTTTTG 0.827782 -57 TTCTTCCTTCATGATCTTTGATTGAGAAAG 7 47 1 ATGATCTTTG 0.978032 -38 CATACCAAAAAGGATCTTGGTTCTATACAA 8 60 0 AGGATCTTGG 0.936661 -93 TATAAGGTAAAAAATCTTTGCAAAGATAAT 14 224 1 AAAATCTTTG 0.827776 -73 TTGTTTGCGGATTATCTTTGCAAAGATTTT 14 234 0 ATTATCTTTG 0.873216 -63 ********** Masking position 4 Map Score: 3.01073 Number of sites scoring better than the average of aligned sites = 46 Number in coding regions = 46 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: 5.57309e-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: 5.57309e-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: 5.57309e-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