AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00500_ctra_reg_100.orf -o00500_ctra_100.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 valS 126 Valyl tRNA Synthetase #8 pgi 112 Glucose-6-P Isomerase #9 glgC 192 Glucose-1-P Adenyltransferase #10 uvrD 80 DNA Helicase #11 zntA 23 Metal Transport P-type ATPase #12 CT728 36 hypothetical protein #13 serS 41 Seryl tRNA Synthetase #14 glgA 300 Glycogen Synthase #15 CT865 248 hypothetical protein Motif number 1 TGTGTTAGCCTTAAGAAAAAGCTGTACAAC 2 21 0 TTAAGAAAAA 0.834797 -236 TTCTTTTTCCTTAATAATAAAAAGGCTGTG 2 47 0 TTAATAATAA 0.735274 -210 AAAGAAATTCTAAAGAAAAAGCAAGATTAG 2 71 1 TAAAGAAAAA 0.693711 -186 AAAACGCTCTTTAAAAAAAATATTCCGTTC 2 111 1 TTAAAAAAAA 0.96623 -146 AAAGCCTCCTTAACTAAAAAAGGCGAACAT 3 11 1 TAACTAAAAA 0.479039 -145 AATATTAATATTAAAAGAAAGATTTCTATT 3 94 0 TTAAAAGAAA 0.926091 -62 TATTGATTGGTTAAAAAAAATTACAATAAA 5 17 1 TTAAAAAAAA 0.96623 -55 TTAAAAAAAATTACAATAAAATTATTGCTC 5 27 1 TTACAATAAA 0.534071 -45 ACCATCCTCTTTACAAAAAATTGAGCAATA 5 49 0 TTACAAAAAA 0.90583 -23 AGCCATCCTAAAAAATAAGGTTACTATC 6 114 0 TAAAAAATAA 0.873687 -18 ATAGTACAAGTAAAAAGAAAGAAGGTCTCT 8 65 1 TAAAAAGAAA 0.849517 -48 TATCTAATTTTGACAAAAAACGGACCCATG 9 48 0 TGACAAAAAA 0.755216 -145 TTTAGATGTTTGAAAAATAAAAATTATCTA 9 72 0 TGAAAAATAA 0.831255 -121 TTCAAACATCTAAAAATAAAATCGATTTAT 9 88 1 TAAAAATAAA 0.606299 -105 AATTATTGCATGAATAATAAATCGATTTTA 9 104 0 TGAATAATAA 0.511016 -89 AAAAAATAAATTATTAAAAAAGCCAGACAA 9 144 0 TTATTAAAAA 0.40766 -49 AAAATAATTTTAAAAAATAAATTATTAAAA 9 155 0 TAAAAAATAA 0.873687 -38 CCCGCCACCATAAAAAATAATTTTAAAAAA 9 168 0 TAAAAAATAA 0.873687 -25 AAGATGCCCCTTAAATGTAAAAAACTTTGA 14 143 0 TTAAATGTAA 0.558551 -158 AAACTATCCATTAAATAAAAGTAATTAAAT 14 200 1 TTAAATAAAA 0.876871 -101 ATAAAAGTAATTAAATATAACAAAAACATC 14 214 1 TTAAATATAA 0.756617 -87 ATTATTTTTGTTAAAAGAAATAATTAATGA 14 247 1 TTAAAAGAAA 0.926091 -54 GTTTCGTTAATTAAATAAAACTCATTAATT 14 268 0 TTAAATAAAA 0.876871 -33 ATGTTTATCCTTATAAAAAATTGCTCGTGC 15 42 0 TTATAAAAAA 0.764805 -207 ACACTCGTAATTAAAAGAAATCTTATTTTG 15 105 0 TTAAAAGAAA 0.926091 -144 AGAAAGATGATTAAATATAAGGTCTGGAGA 15 202 1 TTAAATATAA 0.756617 -47 ********** Masking position 1 Map Score: 31.4613 Number of sites scoring better than the average of aligned sites = 417 Number in coding regions = 417 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 GAAGTGCGCTCTTTTTATTACAGTTTTTAC 1 14 0 CTTTTTATTA 0.861451 -24 AGTTGTACAGCTTTTTCTTAAGGCTAACAC 2 20 1 CTTTTTCTTA 0.882469 -237 CTAACACAGCCTTTTTATTATTAAGGAAAA 2 43 1 CTTTTTATTA 0.861451 -214 TTTCTTTAGAATTTCTTTTTCCTTAATAAT 2 59 0 ATTTCTTTTT 0.88207 -198 ACTAATCTTGCTTTTTCTTTAGAATTTCTT 2 72 0 CTTTTTCTTT 0.862798 -185 AGAACGGAATATTTTTTTTAAAGAGCGTTT 2 112 0 ATTTTTTTTA 0.887986 -145 TAAAGAACCCCTTACTCTTTGTTTATAAAT 2 143 1 CTTACTCTTT 0.625126 -114 GAATAGAAATCTTTCTTTTAATATTAATAT 3 93 1 CTTTCTTTTA 0.961362 -63 TTTTATTGTAATTTTTTTTAACCAATCAAT 5 18 0 ATTTTTTTTA 0.887986 -54 GGATAGTAACCTTATTTTTTAGGATGGCT 6 113 1 CTTATTTTTT 0.813233 -19 GAGAGACCTTCTTTCTTTTTACTTGTACTA 8 66 0 CTTTCTTTTT 0.95421 -47 AAATTAGATAATTTTTATTTTTCAAACATC 9 68 1 ATTTTTATTT 0.651461 -125 TAATAAATCGATTTTATTTTTAGATGTTTG 9 90 0 ATTTTATTTT 0.609813 -103 ATTTTTTAAAATTATTTTTTATGGTGGCGG 9 167 1 ATTATTTTTT 0.609813 -26 GCTCCTCTAGCTTTCTATCTCACTATAAGG 12 11 0 CTTTCTATCT 0.507894 -26 TATTTAATTACTTTTATTTAATGGATAGTT 14 201 0 CTTTTATTTA 0.838682 -100 CTCATTAATTATTTCTTTTAACAAAAATAA 14 248 0 ATTTCTTTTA 0.899301 -53 ATTGCTCGTGCTTTTATCTTGCAAATATTC 15 23 0 CTTTTATCTT 0.433764 -226 AGGAAATACGCTTTCTTCTATTCTAAAAAT 15 70 0 CTTTCTTCTA 0.814035 -179 ACAAAATAAGATTTCTTTTAATTACGAGTG 15 104 1 ATTTCTTTTA 0.899301 -145 ATTTAATCATCTTTCTTTCAGTAGGATGGA 15 188 0 CTTTCTTTCA 0.814035 -61 CTCTCCAGACCTTATATTTAATCATCTTTC 15 203 0 CTTATATTTA 0.550314 -46 ********** Masking position 3 Map Score: 23.3655 Number of sites scoring better than the average of aligned sites = 676 Number in coding regions = 676 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 0.990557 -81 ACGATACTGCAGAGGGTCTTGATATTCGGT 3 56 0 AGAGGGTCTT 0.947031 -100 CTCTTCAAAAAGAGGGCCTTCT 4 25 1 AGAGGGCCTT 0.806849 -12 TTTTTTGTAAAGAGGATGGTTTT 5 59 1 AGAGGATGGT 0.811944 -13 TAGAAAATAGAGAAGGTGGCGAGGATAGTA 6 91 1 AGAAGGTGGC 0.990557 -41 GTAAAAAGAAAGAAGGTCTCTCGTATCACA 8 74 1 AGAAGGTCTC 0.977057 -39 TCATACTCTTAGTAGGTGGCCT 11 12 1 AGTAGGTGGC 0.949493 -12 TTCTGCTCATAGAAGGTCGTTGTGGTGGTA 14 172 0 AGAAGGTCGT 0.985105 -129 TTACGAGTGTAGGAGGTCGCTATGTTGATA 15 125 1 AGGAGGTCGC 0.971841 -124 ********** Masking position 1 Map Score: 12.3218 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 4 ACACAGCCTTTTTATTATTAAGGAAAAAGA 2 46 1 TTTATTATTA 0.77433 -211 TTCTTTAGAATTTCTTTTTCCTTAATAATA 2 58 0 TTTCTTTTTC 0.924739 -199 AGCACTAATCTTGCTTTTTCTTTAGAATTT 2 75 0 TTGCTTTTTC 0.909842 -182 AACATTTTACTTGATTTTTTACCGAATATC 3 36 1 TTGATTTTTT 0.876922 -120 AATATTAATATTTCTTATTCACAAGCAAAC 3 112 1 TTTCTTATTC 0.863541 -44 TTTTATTATTGATTGGTTAAA 5 2 1 TTTATTATTG 0.787417 -70 GGATAGTAACCTTATTTTTTAGGATGGCT 6 113 1 CTTATTTTTT 0.699595 -19 AGAGACCTTCTTTCTTTTTACTTGTACTAT 8 65 0 TTTCTTTTTA 0.801072 -48 TTAGATAATTTTTATTTTTCAAACATCTAA 9 71 1 TTTATTTTTC 0.953112 -122 ATAAATCGATTTTATTTTTAGATGTTTGAA 9 88 0 TTTATTTTTA 0.869489 -105 ATAAAATCGATTTATTATTCATGCAATAAT 9 103 1 TTTATTATTC 0.912812 -90 TTTTTAATAATTTATTTTTTAAAATTATTT 9 154 1 TTTATTTTTT 0.89664 -39 CTCTCGCTATCTGATTTTTCAGGTTGAGTA 13 12 0 CTGATTTTTC 0.817587 -30 GTAAAAAACTTTGATTTTTGAGAAATTTCT 14 127 0 TTGATTTTTG 0.855216 -174 CAAAAACATCTTGATTATTTTTGTTAAAAG 14 234 1 TTGATTATTT 0.785849 -67 ********** Masking position 5 Map Score: 18.7228 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 5 GTAAGGGGTTCTTTAGAGAACGGAATATTTTTT 2 125 0 CTTTGGAAGG 0.879351 -132 GCAGTATCGTCTGTTGAGAATAGAAATCTTTCT 3 76 1 CTGTGGAAAG 0.977848 -80 TCTAGCTAGCCTGTAGAAAATAGAGAAGGTGGC 6 78 1 CTGTGAAAAG 0.816889 -54 AATAGAGAAGGTGGCGAGGATAGTAACCTTATT 6 96 1 GTGGGGGAAG 0.989076 -36 GTTAATTAGAGATGCGAGAATAGTCACAACATA 7 92 1 GATGGGAAAG 0.70424 -35 GATTCTCCTTTTGAGGAAATGTGATACGAG 8 93 0 CTTTGGGAAT 0.741664 -20 ATTTTTTATGGTGGCGGGGACAG 9 180 1 GTGGGGGAAG 0.989044 -13 CTGGGGTGGAAGGATTCGAACCT 14 1 1 CTGGGGGAGG 0.98849 -300 AATATAAGGTCTGGAGAGGATAGTACAAAGGCG 15 215 1 CTGGGGGAAG 0.994339 -34 **** * *** ** Masking position 10 Map Score: 6.45638 Number of sites scoring better than the average of aligned sites = 78 Number in coding regions = 78 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 TCTCAAGAAAGAAGGTGGCAGATGCTCATC 2 175 0 GAAGGTGGCA 0.98163 -82 AGAAAATAGAGAAGGTGGCGAGGATAGTAA 6 92 1 GAAGGTGGCG 0.987531 -40 TAAAAAGAAAGAAGGTCTCTCGTATCACAT 8 75 1 GAAGGTCTCT 0.954274 -38 CATACTCTTAGTAGGTGGCCT 11 13 1 GTAGGTGGCC 0.960115 -11 TCTGCTCATAGAAGGTCGTTGTGGTGGTAA 14 171 0 GAAGGTCGTT 0.954308 -130 TACGAGTGTAGGAGGTCGCTATGTTGATAA 15 126 1 GGAGGTCGCT 0.983813 -123 ********** Masking position 6 Map Score: 3.70896 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 7 GGCTGTGTTAGCCTTAAGAAAAAGCTGTAC 2 24 0 GCCTTAAGAA 0.715422 -233 ATCTTGCTTTTTCTTTAGAATTTCTTTTTC 2 68 0 TTCTTTAGAA 0.870447 -189 GAGTAAGGGGTTCTTTAGAGAACGGAATAT 2 130 0 TTCTTTAGAG 0.937917 -127 GCCACCTTCTTTCTTGAGAAAAACATTTAT 2 186 1 TTCTTGAGAA 0.855619 -71 CTGCAGTATCGTCTGTTGAGAATAGAAATC 3 74 1 GTCTGTTGAG 0.880896 -82 AGAAGGCCCTCTTTTTGAAGAGCCTCCTA 4 18 0 TCTTTTTGAA 0.607164 -19 TATCTAGCTAGCCTGTAGAAAATAGAGAAG 6 76 1 GCCTGTAGAA 0.92176 -56 AGAACATATTGCCTTTAGAGCTTGATTATG 7 28 0 GCCTTTAGAG 0.956839 -99 GCGATTCCATTTTTGTAGAACAATCGATCT 8 20 0 TTTTGTAGAA 0.706242 -93 GATTCTCCTTTTGAGGAAATGTGAT 8 98 0 TCCTTTTGAG 0.881359 -15 CGATAAAAAGGTTTTGTGAGGTACACTCGG 14 93 0 GTTTTGTGAG 0.704299 -208 AAAACTTTGATTTTTGAGAAATTTCTCTAC 14 123 0 TTTTTGAGAA 0.728762 -178 TAAATATAAGGTCTGGAGAGGATAGTACAA 15 213 1 GTCTGGAGAG 0.92927 -36 ********** Masking position 9 Map Score: 9.40051 Number of sites scoring better than the average of aligned sites = 372 Number in coding regions = 372 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 TTTTTTTTAAAGAGCGTTTTTCATGAAGCA 2 101 0 AGAGCGTTTT 0.886858 -156 AACAAAGAGTAAGGGGTTCTTTAGAGAACG 2 136 0 AAGGGGTTCT 0.921039 -121 AAAGCCTCCTTAACTAAAAA 3 1 1 AAAGCCTCCT 0.903926 -155 ACGATACTGCAGAGGGTCTTGATATTCGGT 3 56 0 AGAGGGTCTT 0.876996 -100 AGAGGCTTCTCATGTAAAGA 3 146 0 AGAGGCTTCT 0.945308 -10 CTCTTTTTGAAGAGCCTCCTATGATCTT 4 9 0 AGAGCCTCCT 0.944595 -28 CTTCAAAAAGAGGGCCTTCT 4 27 1 AGGGCCTTCT 0.944595 -10 TTGATAATCTAGAGGGATCTATCTAGCTAG 6 57 1 AGAGGGATCT 0.914214 -75 GCGAGTCAGAAAAGAGTTCTTATCTCTATA 9 13 1 AAAGAGTTCT 0.727871 -180 TTTACATTTAAGGGGCATCTTACCACCACA 14 152 1 AGGGGCATCT 0.897492 -149 ********** Masking position 1 Map Score: 9.22977 Number of sites scoring better than the average of aligned sites = 228 Number in coding regions = 228 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 CTTGTAAAAACTGTAATAAAAAGAGCGC 1 8 1 AAACGTAATA 0.720381 -30 TTCTTGAGAAAAACATTTATATACGGTAACT 2 196 1 AAACTTTATA 0.939615 -61 ATATTAAAAGAAAGATTTCTATTCTCAACAG 3 86 0 AAAGTTTCTA 0.793877 -70 TGTGAATAAGAAATATTAATATTAAAAGAAA 3 104 0 AAATTTAATA 0.600087 -52 GTACCTCACAAAACCTTTTTATCGGTAGAGA 14 99 1 AAACTTTTTA 0.952967 -202 CTCAAAAATCAAAGTTTTTTACATTTAAGGG 14 135 1 AAAGTTTTTA 0.895284 -166 TTATAAGGATAAACATTTTTAGAATAGAAGA 15 56 1 AAACTTTTTA 0.952964 -193 TACCTTTTAGAAACGTTATTATCAACATAGC 15 143 0 AAACTTATTA 0.926633 -106 **** ****** Masking position 3 Map Score: 1.90116 Number of sites scoring better than the average of aligned sites = 44 Number in coding regions = 44 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 ********** No masking Map Score: 1.37378e-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 11 ********** No masking Map Score: 1.37378e-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 12 ********** No masking Map Score: 1.37378e-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