AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00330_ctra_reg_300.orf -o00330_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 gatC 200 Glu-tRNA Gln Amidotransferase (C subunit) #2 dhnA 300 Predicted 1,6-Fructose biphosphate aldolase (dehydrin family) #3 ydaO 153 PP-Loop Superfamily ATPase #4 surE 100 SurE-like Acid Phosphatase #5 ubiA 111 4-hydroxybenzoate octaphenyltransferase #6 CT389 181 hypothetical protein #7 aspC 89 Aspartate Aminotransferase #8 proS 200 Prolyl tRNA Synthetase #9 yaeS 300 YaeS family #10 lpxC 100 UDP-3-O-Acyl GlcNAc Deacetylase #11 cutE 63 Apolipoprotein N-Acetyltransferase #12 yciA 135 Acyl-CoA Thioester Hydrolase #13 CT538 300 hypothetical protein #14 greA 113 Transcription Elongation Factor G #15 tyrB 187 Aromatic AA Aminotransferase Motif number 1 TAATAAAGTCTTTTTTTGTTCTCTCTATTA 1 68 1 TTTTTTTGTT 0.921937 -133 AACTATTTTCTCTTTTTAATTTTTA 2 6 1 TTTTCTCTTT 0.793365 -295 CTCTTTTTAATTTTTATTCTGCACACATTG 2 20 1 TTTTTATTCT 0.732369 -281 ATCGCAGAGTCTTTCATTTTCTTTACCTCA 2 96 1 CTTTCATTTT 0.612768 -205 GAAATAAATGTTTGCATGCTAAGAAAGATT 2 189 1 TTTGCATGCT 0.739385 -112 AAAGAAGCTCTTTTCTTTCTAAGACTTACC 3 38 1 TTTTCTTTCT 0.907065 -116 CTTGGTTTATTTTTCTTATTATTTTAAAAA 4 53 1 TTTTCTTATT 0.706931 -48 CAGAAGGAGCTTTTCTTGCTGAAAAAAGTA 5 40 0 TTTTCTTGCT 0.94574 -72 CGTTTTTACGTTTCCTCACACA 6 3 1 TTTTTACGTT 0.657812 -179 AAAAATCTTGTTTTTTCTCTACTTCCGAGT 6 130 1 TTTTTTCTCT 0.723924 -52 TGATGTTTCTTTTGTTTGTTTCTTAAAATT 8 49 0 TTTGTTTGTT 0.823455 -152 ATCTCTGTGATTTTTTTGTTCTTATTGGAT 8 114 0 TTTTTTTGTT 0.921937 -87 AAAATAAAAATTTTTATATTTGAAGTTTTG 9 44 0 TTTTTATATT 0.403449 -257 AATATAAAAATTTTTATTTTGCTGATGCTT 9 54 1 TTTTTATTTT 0.731595 -247 TTTGATATCGCTTGCTTGCTAAAAAAAAAA 10 44 1 CTTGCTTGCT 0.73108 -57 TATTATCCTTTTTTTTTTTTAGCAAGCAAG 10 54 0 TTTTTTTTTT 0.868653 -47 TAAGGGGATTCTTTTTCTCTCATCTTGAAT 11 19 1 CTTTTTCTCT 0.508743 -45 AGAAATGATTTTCTTGCTCGACATAGAA 13 9 1 TTTTCTTGCT 0.94574 -292 TTAGGCCTGTTTTGCTTTTTGTAAAAATAC 13 154 1 TTTGCTTTTT 0.793365 -147 ATAATAAAATTTTTCTTGTTTTTTGTGATG 14 36 1 TTTTCTTGTT 0.945537 -78 TAATATTGCTCTTTTTTGTTATTCGGCGTA 14 66 1 CTTTTTTGTT 0.823455 -48 ********** Masking position 3 Map Score: 19.718 Number of sites scoring better than the average of aligned sites = 500 Number in coding regions = 500 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 ATGCTAAGAAAGATTTATAGACAATCTGCCA 2 204 1 AGATTATAGA 0.951098 -97 GATTTGACTAAGAATTTTAGGAGGCAATGAA 6 66 0 AGATTTTAGG 0.980194 -116 AGAAAAAACAAGATTTTTAGGAGAAGAGCGC 6 117 0 AGATTTTAGG 0.980194 -65 TGCTTAAAATAGATTTTTAGAAGAACTGGTT 9 79 1 AGATTTTAGA 0.968945 -222 CTGTTCTCTGAGAATTATAGGGATCCATATC 9 244 0 AGATTATAGG 0.968602 -57 CAGCCACTATAGAATATCAGACTGCGT 9 284 1 AGATATCAGA 0.759975 -17 GATAGCAAGTGTTTTAGAACTAGGTAGT 10 8 1 AGTTTTTAGA 0.848287 -93 GACTAGTCTCAGAGTTACAGGCCCACCTCTA 12 79 0 AGATTACAGG 0.945855 -57 *** ******* Masking position 9 Map Score: 7.05663 Number of sites scoring better than the average of aligned sites = 33 Number in coding regions = 33 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 ATGGTGAAAACCCAAAAAAGCGCAACACAC 2 258 0 CCCAAAAAAG 0.918367 -43 ATTCTTTTGCACAGAAAAGGGCTTTGTAA 3 10 1 CACAGAAAAG 0.907492 -144 GCTTTTCTTGCTGAAAAAAGTACGTTGAAG 5 32 0 CTGAAAAAAG 0.94758 -80 TTAGTCAAATCCGAAAGAAGCCGACACTCG 6 86 1 CCGAAAGAAG 0.947386 -96 TTAGAGAGCACTGAGAAAAG 7 1 0 CTGAGAAAAG 0.972614 -89 GTTCTTAGAACTCAGAGCAGGGATGGTACC 9 150 0 CTCAGAGCAG 0.88066 -151 CTATAATTCTCAGAGAACAGCCAAATCTCC 9 255 1 CAGAGAACAG 0.902955 -46 CATTAAGCAACTGAAAAAAGTAAGGATAAG 13 280 1 CTGAAAAAAG 0.94758 -21 AGCTAATACCCCGAGGGAAGAAACTAGGTT 15 80 1 CCGAGGGAAG 0.892074 -108 ********** Masking position 4 Map Score: 6.30748 Number of sites scoring better than the average of aligned sites = 89 Number in coding regions = 89 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 GACAGCAAAACGCATCTTTAATAGAGAGAA 1 86 0 CGCATCTTTA 0.885239 -115 TTTAATATAACTGATCTTTAGAACGGGGAA 2 64 1 CTGATCTTTA 0.953035 -237 TAAAATTTCCCTCATGTTTACACTACAATG 3 91 1 CTCATGTTTA 0.963839 -63 AGATGAGAGTCTCATCTTTATATTACCGTC 7 45 1 CTCATCTTTA 0.970601 -45 TTTTATTTTGCTGATGCTTAAAATAGATTT 9 65 1 CTGATGCTTA 0.931096 -236 TTCTTTTTCTCTCATCTTGAATGTAAGCTA 11 27 1 CTCATCTTGA 0.885239 -37 ACTTATCCTTACTTTTTTCAG 13 290 0 CTTATCCTTA 0.808167 -11 AAACTAGGTTATCATGTTTACACGATTTAG 15 100 1 ATCATGTTTA 0.723222 -88 CTATAGCGCACTGCTGCTTACTGTCTTTTT 15 156 0 CTGCTGCTTA 0.759455 -32 ********** Masking position 5 Map Score: 4.14188 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 5 CTCATGTTTACACTACAATGTAGTCCTCCAT 3 101 1 CACTACATGT 0.683187 -53 GTTTTTTCTCTACTTCCGAGTTATAACGCGG 6 139 1 TACTTCCAGT 0.910683 -43 ACCATTTTGACTCTCCCGTGTTTC 7 76 1 CTCTCCCTGT 0.933231 -14 CAATATAAAGCACTTCCTTCCCT 8 188 1 CACTTCCTCC 0.877809 -13 GAGTCGCCACCTCTTCCTACTAGCGATATGG 9 189 1 CTCTTCCACT 0.943527 -112 ATCAAAAAATTACTACCTAGTTCTAAAACAC 10 19 0 TACTACCAGT 0.910683 -82 GGCCCACCTCTACTCCCCAGTCATCTCTGTA 12 60 0 TACTCCCAGT 0.894212 -76 TACCTACTCTCACTTCCTTGCAAAAGTATTT 13 178 0 CACTTCCTGC 0.91389 -123 TATCCCTGTTCTCTACCTACTCTCACTTCCT 13 191 0 CTCTACCACT 0.943527 -110 CATTGTTGCGCTCTACCAACTGAGCTAATAC 15 58 1 CTCTACCACT 0.943527 -130 ******* *** Masking position 4 Map Score: 3.95921 Number of sites scoring better than the average of aligned sites = 90 Number in coding regions = 90 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 TAACTCTGACTTTTAATCTTTTTTGCAATT 1 38 1 TTTTAATCTT 0.528783 -163 TAAAGTCTTTTTTTGTTCTCTCTATTAAAG 1 71 1 TTTTGTTCTC 0.802935 -130 GTACGAAGGATTTTATTCTGCATAAGATCA 1 156 1 TTTTATTCTG 0.729306 -45 TCTTTTTAATTTTTATTCTGCACACATTGA 2 21 1 TTTTATTCTG 0.729306 -280 GGTTTATTTTTCTTATTATTTTAAAAAGAT 4 56 1 TCTTATTATT 0.54121 -45 CTCCTAAAAATCTTGTTTTTTCTCTACTTC 6 125 1 TCTTGTTTTT 0.880566 -57 TTTTTGCAAATTTTGTTTTTAAATCTCC 8 9 0 TTTTGTTTTT 0.939147 -192 TTGATGTTTCTTTTGTTTGTTTCTTAAAAT 8 50 0 TTTTGTTTGT 0.63384 -151 TCTGTGATTTTTTTGTTCTTATTGGATTTT 8 111 0 TTTTGTTCTT 0.933498 -90 ATATTTGAAGTTTTGTTTTGATGGTTGCGG 9 29 0 TTTTGTTTTG 0.895514 -272 ATATAAAAATTTTTATTTTGCTGATGCTTA 9 55 1 TTTTATTTTG 0.747611 -246 GGTAGTAATTTTTTGATATCGCTTGCTTGC 10 33 1 TTTTGATATC 0.324183 -68 ATATTATCCTTTTTTTTTTTTAGCAAGCAA 10 55 0 TTTTTTTTTT 0.52547 -46 CCAAGGAATTTCTTGATTTTCTTCTATATC 12 15 1 TCTTGATTTT 0.630366 -121 GTTAGGCCTGTTTTGCTTTTTGTAAAAATA 13 153 1 TTTTGCTTTT 0.676789 -148 ACAAGAAAAATTTTATTATTAAATAAAAGA 14 25 0 TTTTATTATT 0.711755 -89 ATAAAATTTTTCTTGTTTTTTGTGATGTAA 14 39 1 TCTTGTTTTT 0.880566 -75 TATTGCTCTTTTTTGTTATTCGGCGTATAT 14 69 1 TTTTGTTATT 0.877219 -45 ********** Masking position 4 Map Score: 13.3257 Number of sites scoring better than the average of aligned sites = 374 Number in coding regions = 374 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 CGTTTTGCTGTCGCAAAAGACGCTTCAGTAAG 1 104 1 TCGCAAAGAG 0.935978 -97 CTAGTTAAAATCCAATAAGAACAAAAAAATCA 8 105 1 TCCATAAGAC 0.764287 -96 AGAAAAAGAATCCCCTTAGAAGTTAC 11 5 0 TCCCTTAGAG 0.968559 -59 GATAGTAGTCTCGATATAGAAGAAAATCAAGA 12 25 0 TCGAATAGAG 0.959884 -111 CTGAGACTAGTCAAGATAGAGGCTATTAGACT 12 98 1 TCAAATAGAG 0.857599 -38 ATTTTCTTGCTCGACATAGAAGTTTTTCATTT 13 18 1 TCGAATAGAG 0.959884 -283 CGGAAAGGCTTCCCTTTAGAAGGAGGCTGGTG 13 226 1 TCCCTTAGAG 0.968558 -75 TGTCTTTTTTTCCAGTAAGATGACAGCTTGTT 15 133 0 TCCATAAGAG 0.951435 -55 **** ***** * Masking position 8 Map Score: 3.57553 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 8 AGTTAAGTATACATCTACGTTGGAGAAACGTC 1 9 0 AATTACGGGA 0.984773 -192 TTTAGTGTAAAAAAGTACGAAGGATTTTATTCTG 1 142 1 AAATACGGGA 0.984773 -59 TTATCTGTACGTTGAAACGAACTTCA 5 3 1 ACTTACGGAA 0.93765 -109 TCTTGCTGAAAAAAGTACGTTGAAGTTCGTTTCA 5 23 0 AAATACGGAA 0.976263 -89 GTGCTCTCTAAAAATTACGCTGGACAGATGAGAG 7 20 1 AAATACGGGA 0.984773 -70 TTTAGTCCGGAAATATACGCCGAATAACAAAAAA 14 77 0 AATTACGGAA 0.976263 -37 * ** **** *** Masking position 7 Map Score: 3.06481 Number of sites scoring better than the average of aligned sites = 7 Number in coding regions = 7 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 ACGCGGCTGTCTCATAACCCACACTAAC 6 164 1 CTCATAACCC 0.9402 -18 AGAAACCATCCCCATATCGCTAGTAGGAAG 9 201 0 CCCATATCGC 0.964197 -100 ATTATAGGGATCCATATCCCCCTCATTTCT 9 232 0 TCCATATCCC 0.947882 -69 ATTCAGGATGCCCCTACCCCTAGAGCATGG 13 119 1 CCCCTACCCC 0.978905 -182 AGCCTTTCCGCCCATATCCCTGTTCTCTAC 13 206 0 CCCATATCCC 0.991564 -95 ACCAACTGAGCTAATACCCCGAGGGAAGAA 15 72 1 CTAATACCCC 0.869012 -116 ********** Masking position 5 Map Score: 2.81228 Number of sites scoring better than the average of aligned sites = 23 Number in coding regions = 23 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 CTTTATTAAATTGCAAAAAAGATTAAAAGT 1 46 0 TTGCAAAAAA 0.95245 -155 CGTTTTGCTGTCGCAAAAGACGCTTCAGTA 1 104 1 TCGCAAAAGA 0.819031 -97 AGTGTTTTTAGTGTAAAAAAGTACGAAGGA 1 136 1 GTGTAAAAAA 0.858879 -65 GCCCTTTTCTGTGCAAAAGAAT 3 3 0 GTGCAAAAGA 0.939216 -151 GAAAAGGGCTTTGTAAAGAAGCTCTTTTCT 3 24 1 TTGTAAAGAA 0.640625 -130 GGGATTATAGGTGTAAAAGATCTTGTATTG 5 74 0 GTGTAAAAGA 0.868317 -38 AAAACAAAATTTGCAAAAACGCTTAAATTA 8 20 1 TTGCAAAAAC 0.84178 -181 TATCGCTTGCTTGCTAAAAAAAAAAAAGGA 10 49 1 TTGCTAAAAA 0.738102 -52 GTTTTGCTTTTTGTAAAAATACTTTTGCAA 13 162 1 TTGTAAAAAT 0.729824 -139 TCTCACTTCCTTGCAAAAGTATTTTTACAA 13 172 0 TTGCAAAAGT 0.872738 -129 ********** Masking position 6 Map Score: 3.88212 Number of sites scoring better than the average of aligned sites = 146 Number in coding regions = 146 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 AACTAAAGACTCCAGGAAAGATCGTTTATC 2 142 1 TCCAGGAAAG 0.94957 -159 ATGTTTGCATGCTAAGAAAGATTTATAGAC 2 196 1 GCTAAGAAAG 0.900105 -105 TCCAGGTAAGTCTTAGAAAGAAAAGAGCTT 3 42 0 TCTTAGAAAG 0.858746 -112 GAATTAGAAATCCAGGTAAGTCTTAGAAAG 3 52 0 TCCAGGTAAG 0.771395 -102 TTTATTTAAATCTAGGAAAGGA 4 3 0 TCTAGGAAAG 0.970804 -98 TTAAATTAATTTTAAGAAACAAACAAAAGA 8 42 1 TTTAAGAAAC 0.699559 -159 TGCTCTGAGTTCTAAGAACCCTCTACCAGA 9 161 1 TCTAAGAACC 0.847053 -140 CCCCCTCATTTCTAAGAAACCATCCCCATA 9 215 0 TCTAAGAAAC 0.954236 -86 ********** Masking position 8 Map Score: 1.63383 Number of sites scoring better than the average of aligned sites = 99 Number in coding regions = 99 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 TAGAAGAACTGGTTTCTCTATTCAGAGGAGA 9 96 1 GGTTCTCTAT 0.917358 -205 GATAATATACGGGGTCTCTTTGTCAGGGTTT 10 77 1 GGGTCTCTTT 0.973892 -24 ACTTCTAAGGGGATTCTTTTTCTCTCATCTT 11 14 1 GGTTCTTTTT 0.874385 -50 AGCTAGTAAGGGAGCCCCTTTA 11 52 1 GGGCCCCTTT 0.97985 -12 TGGGCGGAAAGGCTTCCCTTTAGAAGGAGGC 13 222 1 GGTTCCCTTT 0.986063 -79 GATGGCTCCCCTTTTTAGTCCGGA 14 100 0 GGTCCCCTTT 0.983237 -14 ** ******** Masking position 9 Map Score: 2.97509 Number of sites scoring better than the average of aligned sites = 40 Number in coding regions = 40 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: -6.88983e-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: -6.88983e-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: -6.88983e-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