AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00720_ctra_reg_300.orf -o00720_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 mdhC 190 Malate Dehyrogenase #2 ltuA 114 hypothetical protein #3 pgi 112 Glucose-6-P Isomerase #4 phnP 28 predicted metal dependent hydrolase (histidinic triad) #5 artJ 68 Arginine Binding Protein #6 aroG 136 phospho-2-dehydro-3-deoxyheptonate aldolase #7 CT382.1 182 hypothetical protein #8 sdhB 236 Succinate Dehydrogenase #9 sdhC 25 Succinate Dehydrogenase #10 CT593.1 221 hypothetical protein-possible frameshift with CT593 #11 ycfH 84 PHP superfamily hydrolase #12 dsbD 152 Thio:disulfide Interchange Protein #13 sucC 69 Succinyl-CoA Synthetase, Beta #14 fumC 52 Fumarate Hydratase Motif number 1 TAGATGAGCTTTTTTTTGCCAAAAGCTTTTA 1 49 1 TTTTTTTCCA 0.472706 -142 AAGCCACCCTCTCTTTACTTTTACAAAACG 1 171 0 TCTCTTTCTT 0.94198 -20 CTAGGCAAAGTTTTTTTGTTTGCAGAGTTTT 2 31 1 TTTTTTTTTT 0.841963 -84 GAACAATCGATCTTTTCATCTA 3 2 0 TCTTTTCTCT 0.912342 -111 AGACCTTCTTTCTTTTTACTTGTACTATCTT 3 62 0 TCTTTTTCTT 0.95535 -51 CATTAAACGTTCTCTTCTCTTCAAGAGAAGA 6 14 1 TCTCTTCCTT 0.977863 -123 AAAAAAACGCCCTCTTCTCTTGAAGAGAAGA 6 26 0 CCTCTTCCTT 0.824071 -111 AAGAGGGCGTTTTTTTCATTGAAAAATCTTT 6 41 1 TTTTTTCTTG 0.771847 -96 TCTTTCTATTTCTTTTCTCTTCCCTGTGTGT 6 67 1 TCTTTTCCTT 0.983113 -70 GTTTTCCTTGTTTCTTCTCTTAACTCATGAA 6 109 0 TTTCTTCCTT 0.964876 -28 TAGATTTGTTTTCCTTGTTTCTTCTCT 6 120 0 TGTTTTCTTG 0.67937 -17 TTTGTTAAAATTTTTTCGCTATACCGCAAAA 7 34 0 TTTTTTCCTA 0.845259 -149 AACAAAAGTTTTTCTTTGTCTTCAATGAATT 7 59 1 TTTCTTTTCT 0.643506 -124 TAAATTAAATTGTTTTCATTTGAATTTAATT 7 99 1 TGTTTTCTTT 0.900781 -84 GGAGAGAGAATTTTTTCTCTTCAG 9 12 1 TTTTTTCCTT 0.973121 -14 ACAGAAGAGTTGTTTTTGTTTTTGCAATTCA 12 93 0 TGTTTTTTTT 0.769416 -60 CTTTTATTATTCTTTTTACTTCAATCAACTT 13 21 0 TCTTTTTCTT 0.95535 -49 CATGAAGTCGTTTTTTCTATTTTT 14 4 0 TTTTTTCATT 0.722041 -49 ATGCTCTCTTCCCCTATGATTCTTC 14 38 0 TCTCTTCCCT 0.951748 -15 ******* *** Masking position 6 Map Score: 21.7606 Number of sites scoring better than the average of aligned sites = 634 Number in coding regions = 634 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 AAGCCCCTAAAAAAACGATTTTAAGAGAGAAG 2 92 0 AAAAACTTTT 0.743717 -23 ATGTGATACGAGAGACCTTCTTTCTTTTTACT 3 73 0 AGAGACTCTT 0.929109 -40 CTTCAAGAGAAGAGGGCGTTTTTTTCATTGAA 6 32 1 AGAGGGTTTT 0.914011 -105 GAAAAGAAATAGAAAGATTTTTCAATGAAAAA 6 52 0 AGAAAGTTTT 0.964972 -85 GAAGACAAAGAAAAACTTTTGTTAAAATTTTT 7 50 0 AAAAACTTGT 0.685745 -133 GTTTTATAATAGAAACTATTGTGTTTTGTGAG 7 156 1 AGAAACTTGT 0.931395 -27 CTAATTTGAAAGAGACATTTATTTTGAATATT 8 173 1 AGAGACTTAT 0.831914 -64 GGGAGAGAGAATTTTTTCTCTTCAG 9 4 1 AGAGAGTTTT 0.961777 -22 ATGATGTTTGAGGAGGGCTCTTTATGGAAGGG 10 87 1 AGGAGGTCTT 0.757199 -135 AAACGAATGTAGGAAGATTTTTGTACTATCTC 10 166 0 AGGAAGTTTT 0.926347 -56 CGATTCAAGTAGAAACATTTTCCGCTAAAAGG 11 13 1 AGAAACTTTC 0.784857 -72 TCATGAAGGAAGAAGCCCTTTTAGCGGAAAAT 11 29 0 AGAAGCTTTT 0.866694 -56 ATTACATACCAAAAAGGATCTTGGTTCTATAC 12 62 0 AAAAAGTCTT 0.722623 -91 GCTAAACCGGAGAGAGTGTTGTGTTT 12 137 1 AGAGAGTTGT 0.927023 -16 GACTTCATGAAGGAAGAATCATAGGGGAAGAG 14 26 1 AGGAAGTCAT 0.636929 -27 ****** **** Masking position 1 Map Score: 12.1796 Number of sites scoring better than the average of aligned sites = 481 Number in coding regions = 481 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 CTCCTCAAACATCATGATGAACAGCGCACTT 10 71 0 ATATGATGAA 0.791807 -151 ATCATGATGTTTGAGGAGGGCTCTTTATGGA 10 84 1 TTAGGAGGGC 0.911599 -138 AAGGGCAGGAACCATGAGGGACAGCGAATAA 10 114 1 ACATGAGGGA 0.966315 -108 AGGCGTTCATATGAGGAGGGAGATAGTACAA 10 147 1 ATAGGAGGGA 0.990659 -75 TCAATCAAAGATCATGAAGGAAGAAGCCCTT 11 41 0 ATATGAAGGA 0.967217 -44 AGAAAGATTGATTATGAGGGAAGT 11 71 1 ATATGAGGGA 0.990842 -14 ATAATAAAAGATAAGGAGGAAAAATTAAAGG 13 42 1 ATAGGAGGAA 0.960407 -28 AAAAAACGACTTCATGAAGGAAGAATCATAG 14 19 1 TTATGAAGGA 0.914998 -34 ** ******** Masking position 7 Map Score: 7.25084 Number of sites scoring better than the average of aligned sites = 54 Number in coding regions = 54 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 GGTACTTGATTCTTTTATCATCCAAACGTATG 1 92 1 TCTTTTAATC 0.961386 -99 TTATTTTAAATATGTTATAATCTGTCTATTAC 2 61 1 TATGTTAATC 0.889603 -54 CTATTACTTCTCTCTTAAAATCGTTTTTTTAG 2 86 1 TCTCTTAATC 0.900919 -29 ATTCTTATTTTTTTTAAGAATCATGTTGGGTA 5 11 1 TTTTTAAATC 0.809444 -58 AAGAAAAACTTTTGTTAAAATTTTTTCGCTAT 7 43 0 TTTGTTAATT 0.870331 -140 TTTAATTTTATTTTTTAAGATCTATTTGTTTT 7 123 1 TTTTTTAATC 0.96789 -60 ATAGCTGCTGTTTGTTAACGTCGCGATTAAGT 10 43 1 TTTGTTAGTC 0.890171 -179 GTAGGAAGATTTTTGTACTATCTCCCTCCTCA 10 158 0 TTTTGTAATC 0.862932 -64 ATACAAGAAATTTGTTAGGATCGTCTAGGAAC 12 34 0 TTTGTTAATC 0.974914 -119 TTCCTCCTTATCTTTTATTATTCTTTTTACTT 13 31 0 TCTTTTAATT 0.811484 -39 ******* *** Masking position 7 Map Score: 5.87704 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 5 AGTTAAAGTCGGCTCATCTATTGAAAAATA 1 21 1 GGCTCATCTA 0.995402 -170 GGCAAAAAAAAGCTCATCTATTTTTCAATA 1 39 0 AGCTCATCTA 0.981979 -152 TGAAATTTCTGGCTCATCTACAGAATATGT 8 25 0 GGCTCATCTA 0.995402 -212 AAATTTGTTAGGATCGTCTAGGAACTCGTT 12 29 0 GGATCGTCTA 0.969663 -124 ********** Masking position 4 Map Score: 3.91876 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 6 AATAAGGCCCCTTAATCGTTTTCTAAAA 4 6 0 CCTTACGTTC 0.978982 -23 CATCATTAAACGTTCTCTTCTCTTCAA 6 4 1 CATTACGTTC 0.985759 -133 GCCTCGCAATCATTTTGCGGTATAGCGAAAAAAT 7 22 1 CATTTCGTTA 0.977787 -161 AGCGAATATTCATTTCCCGATATAGGAGGCTAAT 8 144 1 CATTTCGTTA 0.977783 -93 ATGAACGCCTCCTTATTCGCTGTCCCTCATGGTT 10 123 0 CCTTACGTTC 0.978982 -99 ACATTCGTTTCATTATATGATGTATTCATTCCGT 10 188 1 CATTATGTTA 0.881443 -34 CAAGTAGAAACATTTTCCGCTAAAAGGGCTTCTT 11 18 1 CATTTCGTAA 0.901369 -67 ***** ** * ** Masking position 4 Map Score: 3.83045 Number of sites scoring better than the average of aligned sites = 19 Number in coding regions = 19 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 TGCAAACAAAAAAACTTTGCCTAGCCGTCTC 2 24 0 AAAACTTTCC 0.970655 -91 ATTTAAAATAAAAACTCTGCAAACAAAAAAA 2 41 0 AAAACTCTCA 0.821698 -74 TTTTTCATTGAAAAATCTTTCTATTTCTTTT 6 52 1 AAAAATCTTC 0.941126 -85 AACTTTTGTTAAAATTTTTTCGCTATACCGC 7 38 0 AAAATTTTTC 0.875126 -145 AAATTTTAACAAAAGTTTTTCTTTGTCTTCA 7 52 1 AAAAGTTTTC 0.854625 -131 CTCAAAACTTTCCCAATATTATTT 8 223 0 AAAACTTTCC 0.970655 -14 CTGAAGAGAAAAAATTCTCTCTCCC 9 5 0 AAAATTCTTC 0.917876 -21 GAGATAGTACAAAAATCTTCCTACATTCGTT 10 166 1 AAAAATCTCC 0.962317 -56 ATTCAAGTAGAAACATTTTCCGCTAAAAGGG 11 15 1 AAACATTTCC 0.769582 -70 AAACACAACACTCTCTCCGGTTTAGCA 12 136 0 AACACTCTTC 0.873388 -17 ******** ** Masking position 6 Map Score: 7.12108 Number of sites scoring better than the average of aligned sites = 186 Number in coding regions = 186 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 AGAATCAAGTACCTAGATTCCTTAGTAAAAGCT 1 72 0 ACCTAATCTT 0.956493 -119 TAATTTTGGTCCCAACATACGTTTGGATGATAA 1 106 0 CCCAAATCTT 0.987572 -85 GTATGTTGGGACCAAAATTAGTTAGTTGCAAAC 1 119 1 ACCAAATATT 0.960691 -72 AGGGACTATACCCAACATGATTCTTAAAAAAAA 5 18 0 CCCAAATATC 0.922112 -51 TCAAAACTTTCCCAATATTATTTCCCAGGAACG 8 213 0 CCCAAATATT 0.974668 -24 ACAAAAATCTTCCTACATTCGTTTCATTATATG 10 174 1 TCCTAATCTT 0.896918 -48 CTTGTATAGAACCAAGATCCTTTTTGGTATGTA 12 59 1 ACCAAATCTT 0.980597 -94 ***** ** * ** Masking position 7 Map Score: 4.18679 Number of sites scoring better than the average of aligned sites = 29 Number in coding regions = 29 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 CATCTATTGAAAAATAGATGAGCTTTTTTT 1 35 1 AAAATAGATG 0.246949 -156 AAACGATTTTAAGAGAGAAGTAATAGACAG 2 82 0 AAGAGAGAAG 0.97305 -33 TACAAGTAAAAAGAAAGAAGGTCTCTCGTA 3 69 1 AAGAAAGAAG 0.968914 -44 TGATTCTTAAAAAAAATAAGAAT 5 4 0 AAAAAATAAG 0.82015 -65 TCTTCTCTTGAAGAGAAGAGAACGTTTAAT 6 15 0 AAGAGAAGAG 0.844158 -122 TCTTCTCTTCAAGAGAAGAGGGCGTTTTTT 6 26 1 AAGAGAAGAG 0.844158 -111 ACACACAGGGAAGAGAAAAGAAATAGAAAG 6 68 0 AAGAGAAAAG 0.933834 -69 GAGTTAAGAGAAGAAACAAGGAAAACAAAT 6 114 1 AAGAAACAAG 0.877251 -23 AATAGATCTTAAAAAATAAAATTAAATTCA 7 119 0 AAAAAATAAA 0.230982 -64 AATTTCATATAAGAAAGTAGATACCCGCTA 8 48 1 AAGAAAGTAG 0.885501 -189 AAAGATCATGAAGGAAGAAGCCCTTTTAGC 11 36 0 AAGGAAGAAG 0.830971 -49 GGTTCTATACAAGAAATTTGTTAGGATCGT 12 42 0 AAGAAATTTG 0.445667 -111 AAAGAATAATAAAAGATAAGGAGGAAAAAT 13 37 1 AAAAGATAAG 0.840828 -33 ********** Masking position 6 Map Score: 7.60175 Number of sites scoring better than the average of aligned sites = 475 Number in coding regions = 475 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 AATAAGGCCCCTTAATCGTTTTCTAAAA 4 9 0 CCCTAATGTT 0.857889 -20 GTCTTCAATGAATTTAATGGTTTTAAATTAAA 7 76 1 AATTAATGTT 0.960224 -107 AATGGTTTTAAATTAAATTGTTTTCATTTGAA 7 91 1 AATTAATGTT 0.95965 -92 TTTCTCACAAAACACAATAGTTTCTATTATAA 7 159 0 AACAAATGTT 0.89645 -24 AAATGTTTCTACTTGAATCGTT 11 1 0 ACTTAATGTT 0.942017 -84 ATCATCAAACAACAGAAGAGTTGTTTTTGTTT 12 103 0 AACAAAGGTT 0.8924 -50 AAGGAGGAAAAATTAAAGGGTTATTT 13 54 1 AATTAAGGTT 0.941941 -16 **** *** *** Masking position 6 Map Score: 0.823648 Number of sites scoring better than the average of aligned sites = 22 Number in coding regions = 22 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 TACAAAAATGGAATCGCGAAAGATCACGAA 3 33 1 GAATCGCGAA 0.964392 -80 CTTAACTCATGAACAGCAAATCATACACAC 6 92 0 GAACAGCAAA 0.969646 -45 TCATTTTGCGGTATAGCGAAAAAATTTTAA 7 31 1 GTATAGCGAA 0.948116 -152 ACATCATGATGAACAGCGCACTTAATCGCG 10 64 0 GAACAGCGCA 0.971884 -158 GAACCATGAGGGACAGCGAATAAGGAGGCG 10 122 1 GGACAGCGAA 0.977058 -100 GGTATGTAATGAATTGCAAAAACAAAAACA 12 84 1 GAATTGCAAA 0.860621 -69 ********** Masking position 3 Map Score: 2.46796 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 12 ********** No masking Map Score: 1.64379e-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 13 ********** No masking Map Score: 1.64379e-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: 1.64379e-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