AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00500_ctra_reg_300.orf -o00500_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 sycE 37 Secretion Chaperone #2 yscU 256 YopS Translocation Protein U #3 glgP 155 Glycogen Phosphorylase #4 dut 36 dUTP Nucleotidohydrolase #5 accD 71 AcCoA Carboxylase/Transferase Beta #6 sodM 131 Superoxide Dismutase (Mn) #7 yhxB 151 Phosphomannomutase #8 CT296 108 hypothetical protein #9 valS 126 Valyl tRNA Synthetase #10 atpK 41 ATP Synthase Subunit K #11 CT309 166 hypothetical protein #12 atpE 108 ATP Synthase Subunit E #13 pgi 112 Glucose-6-P Isomerase #14 phnP 28 predicted metal dependent hydrolase (histidinic triad) #15 artJ 68 Arginine Binding Protein #16 aroG 136 phospho-2-dehydro-3-deoxyheptonate aldolase #17 CT382.1 182 hypothetical protein #18 glgC 192 Glucose-1-P Adenyltransferase #19 uvrD 80 DNA Helicase #20 zntA 23 Metal Transport P-type ATPase #21 CT728 36 hypothetical protein #22 serS 41 Seryl tRNA Synthetase #23 glgA 300 Glycogen Synthase #24 CT865 248 hypothetical protein Motif number 1 GCTGTGTTAGCCTTAAGAAAAAGCTGTACAAC 2 21 0 CCTTAAAAAA 0.830416 -236 AAAAAGAAATTCTAAAGAAAAAGCAAGATTAG 2 69 1 TCTAAAAAAA 0.767656 -188 TGAAAAACGCTCTTTAAAAAAAATATTCCGTT 2 108 1 TCTTAAAAAA 0.951437 -149 CCACCTTCTTTCTTGAGAAAAACATTTATATA 2 187 1 TCTTAAAAAA 0.980397 -70 CATAGGAGGCTCTTCAAAAAGAGGGCCTTCT 4 16 1 TCTTAAAAGA 0.872937 -21 AAAACCATCCTCTTTACAAAAAATTGAGCAAT 5 50 0 TCTTAAAAAA 0.951437 -22 AGCCATCCTAAAAAATAAGGTTACTAT 6 115 0 TCCTAAAATA 0.926139 -17 TTAAGCAAGTTTTTTACAAAAACAGAAGCCTG 7 46 1 TTTTAAAAAA 0.792569 -106 GATTTTGTATTCTTAAAAAATAGTT 8 4 0 TCTTAAAATA 0.950002 -105 TTTCTATTTTTTTCAAAAAAACGCACATCAA 10 21 0 TTTTAAAAAA 0.938571 -21 ACAACGTTTATCTTAAAAAAACGATCAATTAT 12 70 0 TCTTAAAAAC 0.939027 -39 CCAACATGATTCTTAAAAAAAATAAGAAT 15 8 0 TCTTAAAAAA 0.980397 -61 AACAAATAGATCTTAAAAAATAAAATTAAATT 17 121 0 TCTTAAAATA 0.950002 -62 ATTTTCTCACAAAACACAATAGTTT 17 168 0 TTCTAAAAAC 0.762359 -15 AATTATCTAATTTTGACAAAAAACGGACCCAT 18 49 0 TTTTAAAAAA 0.938571 -144 TAAAAAATAATTTTAAAAAATAAATTATTAAA 18 156 0 TTTTAAAATA 0.857052 -37 GTAGAGAAATTTCTCAAAAATCAAAGTTTTTT 23 123 1 TTCTAAAATC 0.543463 -178 TAATTATTTCTTTTAACAAAAATAATCAAGAT 23 241 0 TTTTAAAAAA 0.938571 -60 TTGCAAATATTCCTAATAAACAAA 24 3 0 TCCTAAAACA 0.820928 -246 AAAATGTTTATCCTTATAAAAAATTGCTCGTG 24 43 0 TCCTAAAAAA 0.942138 -206 GCGTATTTCCTCCTGACAAAATAAGATTTCTT 24 89 1 TCCTAAAAAT 0.718889 -160 **** * ***** Masking position 6 Map Score: 35.1617 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 2 GCTTTTTCTTTAGAATTTCTTTTTCCTTAATAA 2 60 0 TAATTTTTTT 0.769739 -197 TAGAGAACGGAATATTTTTTTTAAAGAGCGTTT 2 112 0 AAATTTTTTA 0.597624 -145 TTGAGAATAGAAATCTTTCTTTTAATATTAATA 3 89 1 AATTTTTTTT 0.90424 -67 TTCTCATGTAAAGAGTTTGTTTGCTTGTGAATA 3 127 0 AAATTTTTTG 0.885726 -29 AAAATTGAGCAATAATTTTATTGTAATTTTTTT 5 30 0 AAATTTATTG 0.828744 -42 ATTGACTCTCAAGATTTTGTATTCTTAAAAAAT 8 15 0 AAATTTTATT 0.857557 -94 AAGGTTTAGTATTTGATTTTAAACGTTGT 12 7 1 TATTTTATTT 0.516011 -102 TTTCATTGAAAAATCTTTCTATTTCTTTTCTCT 16 54 1 AATTTTTATT 0.754598 -83 ATTTTAACAAAAGTTTTTCTTTGTCTTCAATGA 17 54 1 AATTTTTTTG 0.798362 -129 TTCAAATGAAAACAATTTAATTTAAAACCATTA 17 90 0 AAATTTATTT 0.920288 -93 TCATTTGAATTTAATTTTATTTTTTAAGATCTA 17 114 1 TTATTTTTTT 0.630677 -69 ATTTTTTAAGATCTATTTGTTTTAGTTTTATAA 17 132 1 ATTTTTTTTT 0.82834 -51 CACAAAACACAATAGTTTCTATTATAAAACTAA 17 153 0 AAATTTTATT 0.857542 -30 TCAAAATTAGATAATTTTTATTTTTCAAACATC 18 65 1 ATATTTATTT 0.855024 -128 TGGCTTTTTTAATAATTTATTTTTTAAAATTAT 18 149 1 AAATTTTTTT 0.948679 -44 ATTTTTTAAAATTATTTTTTATGGTGGCGGGGA 18 167 1 ATATTTTATG 0.563137 -26 TTAAATGTAAAAAACTTTGATTTTTGAGAAATT 23 130 0 AAATTTATTT 0.920262 -171 GTTATATTTAATTACTTTTATTTAATGGATAGT 23 202 0 ATATTTATTT 0.855024 -99 AAAACTCATTAATTATTTCTTTTAACAAAAATA 23 249 0 AATTTTTTTT 0.904262 -52 GAAATAATTAATGAGTTTTATTTAATTAACGAA 23 263 1 ATATTTATTT 0.855024 -38 ACAAAATAAGATTTCTTTTAATTACGAGTGTAG 24 104 1 ATTTTTAATT 0.495166 -145 ** * *** **** Masking position 7 Map Score: 16.615 Number of sites scoring better than the average of aligned sites = 265 Number in coding regions = 265 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 TTCTCAAGAAAGAAGGTGGCAGATGCTCAT 2 176 0 AGAAGGTGGC 0.987672 -81 ACGATACTGCAGAGGGTCTTGATATTCGGT 3 56 0 AGAGGGTCTT 0.958724 -100 CTCTTCAAAAAGAGGGCCTTCT 4 25 1 AGAGGGCCTT 0.908986 -12 TTTTTTGTAAAGAGGATGGTTTT 5 59 1 AGAGGATGGT 0.826244 -13 TAGAAAATAGAGAAGGTGGCGAGGATAGTA 6 91 1 AGAAGGTGGC 0.987672 -41 GTAAAAAGAAAGAAGGTCTCTCGTATCACA 13 74 1 AGAAGGTCTC 0.971582 -39 CTTCAAGAGAAGAGGGCGTTTTTTTCATTG 16 32 1 AGAGGGCGTT 0.908986 -105 TCATACTCTTAGTAGGTGGCCT 20 12 1 AGTAGGTGGC 0.926629 -12 TTCTGCTCATAGAAGGTCGTTGTGGTGGTA 23 172 0 AGAAGGTCGT 0.980483 -129 TTACGAGTGTAGGAGGTCGCTATGTTGATA 24 125 1 AGGAGGTCGC 0.949285 -124 ********** Masking position 1 Map Score: 10.6978 Number of sites scoring better than the average of aligned sites = 53 Number in coding regions = 53 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 AAAAAAAATATTCCGTTCTCTAAAGAACCCCTT 2 123 1 TTCCTTCTCA 0.90211 -134 AAAGAAAGATTTCTATTCTCAACAGACGATACT 3 78 0 TTCTTTCTCC 0.989663 -78 AAAATAAGGTTACTATCCTCGCCACCTTCTCTA 6 98 0 TACTTCCTCC 0.961473 -34 TTTGCGGAGCTTCCATCGTCAACGAATTTTCCC 11 53 0 TTCCTCGTCC 0.84869 -114 GAGATAGTTCTTCTTTTCTCAACGCATACAAAA 11 96 0 TTCTTTCTCC 0.989663 -71 TCATTAAACGTTCTCTTCTCTTCAAGAGAAGAG 16 13 1 TTCTTTCTCC 0.989663 -124 ATCTTTCTATTTCTTTTCTCTTCCCTGTGTGTA 16 66 1 TTCTTTCTCC 0.989663 -71 ATACGCTTTCTTCTATTCTAAAAATGTTTATCC 24 62 0 TTCTTTCTAA 0.64891 -187 AGCGCCTTTGTACTATCCTCTCCAGACCTTATA 24 217 0 TACTTCCTCC 0.961473 -32 **** ***** * Masking position 6 Map Score: 9.64813 Number of sites scoring better than the average of aligned sites = 60 Number in coding regions = 60 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 GTGCTTCATGAAAAACGCTCTTTAAAAAAAAT 2 100 1 AAAACGCTTT 0.730282 -157 GTTACCGTATATAAATGTTTTTCTCAAGAAAG 2 194 0 AAAATGTTTT 0.745448 -63 CTATGTTGGTTAAATCGTTATTGGGAAAATTC 11 31 1 TAATCGTTTT 0.949415 -136 GTATTTGATTTTAAACGTTGTTATGATCTAAC 12 19 1 TAAACGTTTT 0.963306 -90 CGGATCATAATTGATCGTTTTTTTAAGATAAA 12 64 1 TGATCGTTTT 0.743631 -45 TTTTTTTAAGATAAACGTTGTTTTTCTTGGTA 12 81 1 AAAACGTTTT 0.951108 -28 TTTTTGTAGAACAATCGATCTTTTCATCTA 13 9 0 AAATCGATTT 0.794243 -104 ATAAGGCCCCTTAATCGTTTTCTAAAA 14 6 0 TAATCGTTTC 0.902468 -23 CATCATTAAACGTTCTCTTCTCTTCAA 16 6 1 TAAACGTTTC 0.924169 -131 AAAAATTTTAACAAAAGTTTTTCTTTGTCTTC 17 50 1 AAAAAGTTTT 0.650175 -133 GGTTTTAAATTAAATTGTTTTCATTTGAATTT 17 94 1 TAATTGTTTC 0.539467 -89 GCATGAATAATAAATCGATTTTATTTTTAGAT 18 95 0 TAATCGATTT 0.732028 -98 TTTTATAAGGATAAACATTTTTAGAATAGAAG 24 54 1 AAAACATTTT 0.579767 -195 GGTACCTTTTAGAAACGTTATTATCAACATAG 24 144 0 AAAACGTTTT 0.951108 -105 * ******* ** Masking position 4 Map Score: 9.18586 Number of sites scoring better than the average of aligned sites = 160 Number in coding regions = 159 Number in noncoding regions = 1 Number of orfs with sites within 600 bp upstream = 1 Fraction of orfs with sites within 600 bp upstream = 0.000160617 Motif number 6 AAGTTTTTTACAAAAACAGAAGCCTGACGT 7 52 1 CAAAAACAGA 0.955564 -100 CACGCTCTACCAAATACAGATACAAGCGAG 7 98 0 CAAATACAGA 0.772206 -54 GTTTTTTTGAAAAAAATAGAAA 10 30 1 AAAAAATAGA 0.782001 -12 GGAAGCTCCGCAAACTCGGAGTTTTTTTGT 11 72 1 CAAACTCGGA 0.781531 -95 GATTGTTCTACAAAAATGGAATCGCGAAAG 13 25 1 CAAAAATGGA 0.856834 -88 GATTCTTAAAAAAAATAAGAAT 15 3 0 AAAAATAAGA 0.714566 -66 TAATTTTGACAAAAAACGGACCCATGCCCT 18 44 0 AAAAAACGGA 0.867269 -149 CGTTTTTTGTCAAAATTAGATAATTTTTAT 18 56 1 CAAAATTAGA 0.893681 -137 ACTCAACCTGAAAAATCAGATAGCGAGAGA 22 13 1 AAAAATCAGA 0.901739 -29 TTCCTCCTGACAAAATAAGATTTCTTTTAA 24 95 1 CAAAATAAGA 0.854359 -154 ********** Masking position 4 Map Score: 4.36876 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 TAAAAACTGTAATAAAAAGAGCGCACTTCC 1 15 1 AATAAAAAGA 0.921197 -23 TGTTAGCCTTAAGAAAAAGCTGTACAACTT 2 19 0 AAGAAAAAGC 0.892945 -238 TTTCCTTAATAATAAAAAGGCTGTGTTAGC 2 42 0 AATAAAAAGG 0.817736 -215 TTTATTATTAAGGAAAAAGAAATTCTAAAG 2 56 1 AGGAAAAAGA 0.916467 -201 AGAAATTCTAAAGAAAAAGCAAGATTAGTG 2 73 1 AAGAAAAAGC 0.892945 -184 TAGGCACAAAAATCCAAAGAA 7 2 0 AATCCAAAGA 0.748422 -150 ATAGCCCCTTAAGCCAAAGATCCT 11 5 0 AAGCCAAAGA 0.846878 -162 ATCTGATACCAAGAAAAACAACGTTTATCT 12 89 0 AAGAAAAACA 0.679649 -20 AGATAGTACAAGTAAAAAGAAAGAAGGTCT 13 63 1 AGTAAAAAGA 0.8551 -50 GGGAAGAGAAAAGAAATAGAAAGATTTTTC 16 61 0 AAGAAATAGA 0.698136 -76 AAATTCATTGAAGACAAAGAAAAACTTTTG 17 61 0 AAGACAAAGA 0.941032 -122 CTACACTCGTAATTAAAAGAAATCTTATTT 24 107 0 AATTAAAAGA 0.597638 -142 TGGAGAGGATAGTACAAAGGCGCTGGGAGT 24 226 1 AGTACAAAGG 0.624501 -23 ********** Masking position 6 Map Score: 8.39402 Number of sites scoring better than the average of aligned sites = 307 Number in coding regions = 307 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 TGCTTCATGAAAAACGCTCTTTAAAAAAAA 2 101 1 AAAACGCTCT 0.895538 -156 CGTTCTCTAAAGAACCCCTTACTCTTTGTT 2 136 1 AGAACCCCTT 0.851404 -121 TTTTTAGTTAAGGAGGCTTT 3 1 0 AGGAGGCTTT 0.789805 -155 ACCGAATATCAAGACCCTCTGCAGTATCGT 3 56 1 AAGACCCTCT 0.860093 -100 TCTTTACATGAGAAGCCTCT 3 146 1 AGAAGCCTCT 0.948905 -10 AAGATCATAGGAGGCTCTTCAAAAAGAG 4 9 1 AGGAGGCTCT 0.935654 -28 AGAAGGCCCTCTTTTTGAAG 4 27 0 AGAAGGCCCT 0.956848 -10 CTAGCTAGATAGATCCCTCTAGATTATCAA 6 57 0 AGATCCCTCT 0.878749 -75 TTCAATGAAAAAAACGCCCTCTTCTCTTGA 16 34 0 AAAACGCCCT 0.903538 -103 TGTGGTGGTAAGATGCCCCTTAAATGTAAA 23 152 0 AGATGCCCCT 0.891018 -149 ********** Masking position 1 Map Score: 7.85472 Number of sites scoring better than the average of aligned sites = 143 Number in coding regions = 143 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 TCTCAAGAAAGAAGGTGGCAGATGCTCATC 2 175 0 GAAGGTGGCA 0.973196 -82 AGAAAATAGAGAAGGTGGCGAGGATAGTAA 6 92 1 GAAGGTGGCG 0.968271 -40 GTTCTGATCGGAAGGTTGTCTT 7 140 1 GAAGGTTGTC 0.838103 -12 ATCCAGAAGGTTGATGTGCGTTTTT 10 6 1 GAAGGTTGAT 0.861961 -36 TTTCTTAGTTGAAGGTGTAAGAGCGGATT 11 148 1 GAAGGTGTAA 0.661054 -19 TAAAAAGAAAGAAGGTCTCTCGTATCACAT 13 75 1 GAAGGTCTCT 0.910352 -38 CATACTCTTAGTAGGTGGCCT 20 13 1 GTAGGTGGCC 0.90962 -11 TCTGCTCATAGAAGGTCGTTGTGGTGGTAA 23 171 0 GAAGGTCGTT 0.933639 -130 TACGAGTGTAGGAGGTCGCTATGTTGATAA 24 126 1 GGAGGTCGCT 0.931965 -123 ********** Masking position 6 Map Score: 3.11657 Number of sites scoring better than the average of aligned sites = 65 Number in coding regions = 65 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 TCTAAAGAAAAAGCAAGATTAGTGCTTCAT 2 79 1 AAGCAAGATT 0.914115 -178 TGTTTTTCTCAAGAAAGAAGGTGGCAGATG 2 181 0 AAGAAAGAAG 0.873379 -76 TATAGCGCTTAAGCAACTGGCCATCT 2 241 1 AAGCAACTGG 0.616844 -16 TTAATATTAAAAGAAAGATTTCTATTCTCA 3 90 0 AAGAAAGATT 0.797051 -66 TTTTATTGATAATCTAGAGGGATCTATCTA 6 52 1 AATCTAGAGG 0.67967 -80 TTTCTAAGTTAAGCAAGTTTTTTACAAAAA 7 38 1 AAGCAAGTTT 0.72617 -114 GATTATGATCAAGCAAGAGGTGCC 9 5 0 AAGCAAGAGG 0.982319 -122 TACAAGTAAAAAGAAAGAAGGTCTCTCGTA 13 69 1 AAGAAAGAAG 0.873379 -44 GTGAGATAGAAAGCTAGAGGAGCGGCACG 21 18 1 AAGCTAGAGG 0.932357 -19 TAACAAAAATAATCAAGATGTTTTTGTTAT 23 230 0 AATCAAGATG 0.868989 -71 ATCCTACTGAAAGAAAGATGATTAAATATA 24 191 1 AAGAAAGATG 0.940672 -58 ********** Masking position 6 Map Score: 7.90658 Number of sites scoring better than the average of aligned sites = 215 Number in coding regions = 215 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 GAGTAAGGGGTTCTTTAGAGAACGGAATAT 2 130 0 TTCTTTAGAG 0.745144 -127 CTGCAGTATCGTCTGTTGAGAATAGAAATC 3 74 1 GTCTGTTGAG 0.883065 -82 ATGTGGATAGCTCTTGACAGTGAATATTTT 6 26 1 CTCTTGACAG 0.789583 -106 AGAATACAAAATCTTGAGAGTCAATCGGGT 8 23 1 ATCTTGAGAG 0.889778 -86 AGAACATATTGCCTTTAGAGCTTGATTATG 9 28 0 GCCTTTAGAG 0.812405 -99 GAAGAACTATCTCTGGAGAGCTGTCTAGAG 11 116 1 CTCTGGAGAG 0.926589 -51 CTGGAGAGCTGTCTAGAGAGTTTCTTAGTT 11 128 1 GTCTAGAGAG 0.948922 -39 AAACTATTGTGTTTTGTGAGAAAAT 17 168 1 GTTTTGTGAG 0.860731 -15 GACCCATGCCCTTTATAGAGATAAGAACTC 18 26 0 CTTTATAGAG 0.48428 -167 CGATAAAAAGGTTTTGTGAGGTACACTCGG 23 93 0 GTTTTGTGAG 0.860731 -208 TAAATATAAGGTCTGGAGAGGATAGTACAA 24 213 1 GTCTGGAGAG 0.980316 -36 ********** Masking position 9 Map Score: 5.14789 Number of sites scoring better than the average of aligned sites = 168 Number in coding regions = 168 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 TTAACCAACATAGCCCCTTAAGCCAAAGAT 11 14 0 TAGCCCCTTA 0.974818 -153 ATGATCCGGTTAGCCCCTAAGGTTAGATCA 12 42 0 TAGCCCCTAA 0.921667 -67 AATAAGGCCCCTTAATCGTTTTCT 14 15 0 AGGCCCCTTA 0.979001 -14 AAACGGACCCATGCCCTTTATAGAGATAAG 18 31 0 ATGCCCTTTA 0.91401 -162 TGGTGGTAAGATGCCCCTTAAATGTAAAAA 23 150 0 ATGCCCCTTA 0.982291 -151 ********** Masking position 8 Map Score: 1.79776 Number of sites scoring better than the average of aligned sites = 9 Number in coding regions = 9 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: -5.74586e-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: -5.74586e-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: -5.74586e-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