AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00630_ctra_reg_300.orf -o00630_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 folD 117 Methylene Tetrahydrofolate Dehydrogenase #2 CT079 276 hypothetical protein #3 def 274 Polypeptide Deformylase #4 CT355 300 hypothetical protein #5 mdhC 190 Malate Dehyrogenase #6 ltuA 114 hypothetical protein #7 pgi 112 Glucose-6-P Isomerase #8 phnP 28 predicted metal dependent hydrolase (histidinic triad) #9 artJ 68 Arginine Binding Protein #10 aroG 136 phospho-2-dehydro-3-deoxyheptonate aldolase #11 CT382.1 182 hypothetical protein Motif number 1 AACCAGAATAATTTATTTCAAAATCTATTCTAA 2 18 1 ATTTATAAAA 0.900798 -259 TCTATTCTAATTTTAAATTAAAAAATTGTTTTT 2 41 1 TTTTAAAAAA 0.499205 -236 ATAACCTGTAATTTATGTCAGAAGACGCTAGGG 3 182 1 ATTTATAGAA 0.766327 -93 TCTTTTCGATATTTAAGTGAAAAAATTCCAGAA 4 33 1 ATTTAAAAAA 0.942758 -268 GTCAGAACACTTTTAACAAAAAAGCGTTATATC 4 95 0 TTTTAAAAAA 0.544576 -206 GCAGCTTATATTCTAAAAAAGAACCTACCCTCG 4 165 0 TTCTAAAGAA 0.590825 -136 AGGCGGTAAGATCCAAAGAAAAAGGGGAGGAGG 4 228 1 ATCCAAAAAA 0.910154 -73 TCTTAAGGTTTTTCTACCTAAAAACTACAAATC 4 274 1 TTTCTAAAAA 0.813649 -27 AAGTCGGCTCATCTATTGAAAAATAGATGAGCT 5 26 1 ATCTATAAAA 0.889937 -165 AGATGAGCTTTTTTTTGCCAAAAGCTTTTACTA 5 50 1 TTTTTTAAAA 0.778 -141 AGTACCTAGATTCCTTAGTAAAAGCTTTTGGCA 5 65 0 TTCCTTAAAA 0.657667 -126 ATTATAACATATTTAAAATAAAAACTCTGCAAA 6 49 0 ATTTAAAAAA 0.81189 -66 AAAAAAACGATTTTAAGAGAGAAGTAATAGACA 6 83 0 TTTTAAAGAA 0.757745 -32 CCCAACATGATTCTTAAAAAAAATAAGAAT 9 8 0 TTCTTAAAAA 0.566821 -61 TAGAAAGATTTTTCAATGAAAAAAACGCCCTCT 10 42 0 TTTCAAAAAA 0.935849 -95 AATGAAAACAATTTAATTTAAAACCATTAAATT 11 86 0 ATTTAAAAAA 0.739861 -97 ATAAAATTAAATTCAAATGAAAACAATTTAATT 11 101 0 ATTCAAAAAA 0.924955 -82 ACACAATAGTTTCTATTATAAAACTAAAACAAA 11 147 0 TTCTATAAAA 0.520693 -36 ****** **** Masking position 2 Map Score: 21.3657 Number of sites scoring better than the average of aligned sites = 224 Number in coding regions = 224 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 GAGAGGTCTAGACTCTTTCCCTCTAAACAA 1 65 1 GACTCTTTCC 0.817948 -53 TTGAGGCCTATATTCCTCTCCGCAATATTC 2 192 1 TATTCCTCTC 0.88515 -85 CTCTCCGCAATATTCCTTTCCCAACGCTCA 2 207 1 TATTCCTTTC 0.772137 -70 TCTCCCAAGCCACTCTACTCCTAGTCTCT 2 258 1 CACTCTACTC 0.738529 -19 GAAAGAGAAGTCTTCCTTTCGCTGAATAGC 3 20 0 TCTTCCTTTC 0.865682 -255 AAAGGAAGACTTCTCTTTCCAAATATCTTC 3 31 1 TTCTCTTTCC 0.932936 -244 TTTCCAAATATCTTCTTTTCCATCACAATG 3 46 1 TCTTCTTTTC 0.903562 -229 GATTTCATAGCACTCTTCTCGGTGTTTGTA 3 94 1 CACTCTTCTC 0.97235 -181 GAATGAAACTTTTTCTTCACTTTGACGATA 3 125 1 TTTTCTTCAC 0.748934 -150 TCTTAGTTACCCCTCTTTTCGATATTTAAG 4 20 1 CCCTCTTTTC 0.967114 -281 ACGGCTGGGTCCCTCCTCCCCTATAGCTTT 4 126 1 CCCTCCTCCC 0.974219 -175 TTTGGGTTGTTCCTCCTCCCCTTTTTCTTT 4 242 0 TCCTCCTCCC 0.972094 -59 AAGCCACCCTCTCTTTACTTTTACAAAA 5 173 0 CTCTCTTTAC 0.804562 -18 TCATTAAACGTTCTCTTCTCTTCAAGAGAA 10 13 1 TTCTCTTCTC 0.974698 -124 GAAAAAAACGCCCTCTTCTCTTGAAGAGAA 10 28 0 CCCTCTTCTC 0.985269 -109 TCTATTTCTTTTCTCTTCCCTGTGTGTATG 10 71 1 TTCTCTTCCC 0.969362 -66 TGTTTTCCTTGTTTCTTCTCTTAACTCATG 10 111 0 GTTTCTTCTC 0.836329 -26 ********** Masking position 4 Map Score: 22.1856 Number of sites scoring better than the average of aligned sites = 522 Number in coding regions = 521 Number in noncoding regions = 1 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 3 TTCTAATTTTAAATTAAAAAATTGTTTTTCA 2 45 1 AAATAAAAAA 0.880487 -232 TTCGATATTTAAGTGAAAAAATTCCAGAAAA 4 37 1 AAGGAAAAAA 0.774895 -264 ATCCTCAAGCCAAAGGAAACAAAAATGTATT 4 67 0 CAAGGAAACA 0.86219 -234 CGGTAAGATCCAAAGAAAAAGGGGAGGAGGA 4 231 1 CAAGAAAAAG 0.950121 -70 AAAAACTCTGCAAACAAAAAAACTTTGCCTA 6 32 0 CAACAAAAAA 0.879982 -83 TAACATATTTAAAATAAAAACTCTGCAAACA 6 47 0 AAATAAAAAC 0.760065 -68 AAAGATAGTACAAGTAAAAAGAAAGAAGGTC 7 61 1 CAATAAAAAG 0.874975 -52 AAAGATTTTTCAATGAAAAAAACGCCCTCTT 10 41 0 CAAGAAAAAA 0.977925 -96 AGAGAAGAAACAAGGAAAACAAATCTA 10 120 1 CAAGAAAACA 0.973294 -17 TCATTGAAGACAAAGAAAAACTTTTGTTAAA 11 56 0 CAAGAAAAAC 0.950121 -127 AATTAAATTCAAATGAAAACAATTTAATTTA 11 99 0 AAAGAAAACA 0.942845 -84 TTCTATTATAAAACTAAAACAAATAGATCTT 11 139 0 AAATAAAACA 0.858372 -44 *** ******* Masking position 7 Map Score: 9.57348 Number of sites scoring better than the average of aligned sites = 217 Number in coding regions = 217 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 ATAGAGGGATAACGGCAAGGATTGTTAATA 2 109 0 AACGGCAAGG 0.987309 -168 TATGTCAGAAGACGCTAGGGAATTTTTTAG 3 195 1 GACGCTAGGG 0.955544 -80 AAAGTGTTCTGACGGCTGGGTCCCTCCTCC 4 115 1 GACGGCTGGG 0.996379 -186 TTTCTACGGAGACGGCTAGGCAAAGTTTTT 6 16 1 GACGGCTAGG 0.991892 -99 TCAATGGTCTAACGGCAGGGACTATACCCA 9 37 0 AACGGCAGGG 0.994321 -32 ********** Masking position 2 Map Score: 5.3587 Number of sites scoring better than the average of aligned sites = 6 Number in coding regions = 6 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 TTCTCTTTCAGTCTTCTAGTT 1 1 1 TTCTCTTTAG 0.97061 -117 AAATCATTCTATCTTTTATAGTCCGGCGATG 2 147 1 ATCTTTTAAG 0.815921 -130 GGAACGGCCTATCTTTTTGAGACTTTGTATA 3 239 1 ATCTTTTTAG 0.955257 -36 CGAGGGTAGGTTCTTTTTTAGAATATAAGCT 4 165 1 TTCTTTTTAG 0.983142 -136 GTTCTTATTCAGTTAAAGTCGG 5 2 1 TTCTTATTAG 0.912674 -189 ATTCTTATTTTTTTTAAGAATCATGTTG 9 8 1 TTTTTTTTAG 0.930261 -61 AAACGCCCTCTTCTCTTGAAGAGAAGAGAAC 10 22 0 TTCTCTTGAG 0.910408 -115 AATTTAATTTTATTTTTTAAGATCTATTTGT 11 121 1 TATTTTTTAG 0.705057 -62 ******** ** Masking position 10 Map Score: 3.3582 Number of sites scoring better than the average of aligned sites = 181 Number in coding regions = 180 Number in noncoding regions = 1 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 6 TCACATAGGTTGTTTAGAGGGAAAGAGTCTAGA 1 71 0 TGTAGGGGAA 0.935556 -47 AATTGTTTTATGGTTTATGAAAAACAATTTTTT 2 60 0 TGTTAGAAAA 0.889903 -217 TGTTTTGATGAGCGTTGGGAAAGGAATATTGCG 2 212 0 AGTTGGAAAG 0.864005 -65 AGGAGTAGAGTGGCTTGGGAGAGATTCTCGAAG 2 247 0 TGTTGGAGAG 0.969753 -30 TTCCTTTCGCTGAATAGCGAAAACCTT 3 5 0 TGTAGGAAAA 0.954898 -270 TTGTTTCCTTTGGCTTGAGGATATAACGCTTTT 4 76 1 TGTTGGGATA 0.848225 -225 TTGCAAACGTAGTGTTGAGAGTATGTGCGTTTT 5 144 1 AGTTGGAGTA 0.867548 -47 TTGCTGTTCATGAGTTAAGAGAAGAAACAAGGA 10 103 1 TGTTAGAGAA 0.928005 -34 ATCATTTTGCGGTATAGCGAAAAAATTTTAACA 11 30 1 GGTAGGAAAA 0.849019 -153 GAAACTATTGTGTTTTGTGAGAAAAT 11 167 1 TGTTGGAGAA 0.986766 -16 ** *** ***** Masking position 5 Map Score: 3.95025 Number of sites scoring better than the average of aligned sites = 149 Number in coding regions = 149 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 TCTTTCAGTCTTCTAGTTTTAAAAATTCAT 1 14 1 TTCTAGTTTT 0.854835 -104 TCAAAATCTATTCTAATTTTAAATTAAAAA 2 35 1 TTCTAATTTT 0.791969 -242 CTGTAAATCATTCTATCTTTTATAGTCCGG 2 143 1 TTCTATCTTT 0.924137 -134 TACCCCTCTTTTCGATATTTAAGTGAAAAA 4 27 1 TTCGATATTT 0.564527 -274 GGAAACAAAAATGTATTTTTCTGGAATTTT 4 54 0 ATGTATTTTT 0.653829 -247 CCTTGATTTGTAGTTTTTAGGTAGAAA 4 284 0 TTGTAGTTTT 0.476118 -17 AAAAAAGCTCATCTATTTTTCAATAGATGA 5 34 0 ATCTATTTTT 0.92446 -157 CTCTCTTAAAATCGTTTTTTTAGGGGCTTT 6 95 1 ATCGTTTTTT 0.687576 -20 TTGTAGAACAATCGATCTTTTCATCTA 7 8 0 ATCGATCTTT 0.790545 -105 TCTTTCGCGATTCCATTTTTGTAGAACAAT 7 26 0 TTCCATTTTT 0.775771 -87 TTTTTACTTGTACTATCTTTCGTGATCTTT 7 51 0 TACTATCTTT 0.494547 -62 ACGAGAGACCTTCTTTCTTTTTACTTGTAC 7 68 0 TTCTTTCTTT 0.797761 -45 AGGCCCCTTAATCGTTTTCTAAAA 8 5 0 ATCGTTTTCT 0.354641 -24 ATTCTTATTTTTTTTAAGAAT 9 2 1 TTCTTATTTT 0.552124 -67 TGAAAAATCTTTCTATTTCTTTTCTCTTCC 10 60 1 TTCTATTTCT 0.845612 -77 TTGAATTTAATTTTATTTTTTAAGATCTAT 11 118 1 TTTTATTTTT 0.553802 -65 ATTTTTTAAGATCTATTTGTTTTAGTTTTA 11 132 1 ATCTATTTGT 0.624125 -51 ********** Masking position 8 Map Score: 5.91093 Number of sites scoring better than the average of aligned sites = 527 Number in coding regions = 527 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 AACCTATGTGAAACCATTTAACTAAGTATT 1 93 1 AAACCATTTA 0.951284 -25 GGTTTATGAAAAACAATTTTTTAATTTAAA 2 52 0 AAACAATTTT 0.752437 -225 ATAAACCATAAAACAATTGATAGGAACATT 2 75 1 AAACAATTGA 0.937487 -202 TGCTGACACTAACCCATTGAGGCCTATATT 2 176 1 AACCCATTGA 0.878419 -101 CCGTTCCGATAAACCTATGATCTAAAAAAT 3 216 0 AAACCTATGA 0.382484 -59 GCCCCTAAAAAAACGATTTTAAGAGAGAAG 6 92 0 AAACGATTTT 0.766453 -23 TTTTAGAAAACGATTAAGGGGCCTTAT 8 8 1 AAACGATTAA 0.81537 -21 CCCTGCCGTTAGACCATTGAGTCGGAGTGA 9 47 1 AGACCATTGA 0.878419 -22 ATTTAATTTAAAACCATTAAATTCATTGAA 11 79 0 AAACCATTAA 0.912785 -104 ATTCAAATGAAAACAATTTAATTTAAAACC 11 94 0 AAACAATTTA 0.884163 -89 TTTATAATAGAAACTATTGTGTTTTGTGAG 11 158 1 AAACTATTGT 0.702729 -25 ********** Masking position 1 Map Score: 5.39721 Number of sites scoring better than the average of aligned sites = 109 Number in coding regions = 109 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 TCTCGAAGAATGTTTTGATGAGCGTTGGGA 2 225 0 TGTTTTGATG 0.943467 -52 CTCTTCTCGGTGTTTGTATGAATGAAACTT 3 106 1 TGTTTGTATG 0.974782 -169 TAAGCTGCTTTGTTTGGGTGTTTGCCACAT 4 190 1 TGTTTGGGTG 0.975145 -111 TCCCAACATACGTTTGGATGATAAAAGAAT 5 100 0 CGTTTGGATG 0.975144 -91 TTCTCTTCCCTGTGTGTATGATTTGCTGTT 10 81 1 TGTGTGTATG 0.94569 -56 ********** Masking position 5 Map Score: 1.61335 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 10 ********** No masking Map Score: 1.9209e-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: 1.9209e-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: 1.9209e-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