AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i050_ecoli_mtub_100.orf -o050_ecoli_mtub_100.ace -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -g0.58 -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 = 0.58 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 yaiM 93 putative esterase (EC 3.1.1.1) #2 adhC 34 alcohol dehydrogenase class III; formaldehyde dehydrogenase, glutathione-dependent #3 yaiN 166 putative alpha helix chain #4 yeiG 257 putative esterase (EC 3.1.1.-). #5 adhB 98 adhB #6 Rv0767c 201 hypothetical protein Rv0767c #7 Rv1284 206 hypothetical protein Rv1284 #8 cysD 93 cysD #9 Rv1287 53 hypothetical protein Rv1287 #10 Rv1288 57 hypothetical protein Rv1288 #11 Rv3083 77 hypothetical protein Rv3083 #12 adhD 30 adhD Motif number 1 CGCCTGAAGTGGACGGGGTAAACCTGCGGG 1 14 0 GGACGGGGTA 0.907015 -80 GTCCACTTCAGGCGGGGGTTCTTAATACTC 1 30 1 GGCGGGGGTT 0.859086 -64 CCGGACGGCTGCCCGGGGAGAGTATTAAGA 1 49 0 GCCCGGGGAG 0.860381 -45 GGTTAATCCCCCGGACGGCTGCCCGGGGAG 1 59 0 CCGGACGGCT 0.617249 -35 GCCCCGGATAGCGGGCGGCAGAAGGAA 3 8 0 GCGGGCGGCA 0.971927 -159 GCCCGCTATCCGGGGCGGCCTTCCCTGCCG 3 22 1 CGGGGCGGCC 0.825505 -145 GGGGGCTAATCGGCAGGGAAGGCCGCCCCG 3 32 0 CGGCAGGGAA 0.655223 -135 AGAGGAAAGGGGGGGGGGCTAATCGGCAGG 3 45 0 GGGGGGGGCT 0.961688 -122 CCCCACGCAGGGCGGAGGCGTCACACCTGC 4 25 0 GGCGGAGGCG 0.971387 -233 CTCCGCCCTGCGTGGGGGCAAAGTTATTAA 4 38 1 CGTGGGGGCA 0.940256 -220 TGATTATTGTGCGTGAGGCGGCGCACATAA 4 82 1 GCGTGAGGCG 0.869823 -176 GCTGATGAAAGGCAGCGGCAATTACAATAA 4 132 0 GGCAGCGGCA 0.919812 -126 AGGTCAACGGCGCTAGGGCGT 5 2 0 CGCTAGGGCG 0.849436 -97 TCGGCGTTCCGGCCGAGGCTAGGGACCACT 5 44 1 GGCCGAGGCT 0.926232 -55 CGGAGAAGTTGGGAGCGGTAG 6 2 0 GGGAGCGGTA 0.772183 -200 GATACGGTCTCGATGAGGCAATATCGGACA 6 55 0 CGATGAGGCA 0.749462 -147 GAGACCGTATCCGCAAGGCCGCTACACCGT 6 74 1 CCGCAAGGCC 0.759289 -128 GACCGATGCACCAGGGGCCACGTCGCGTCG 6 107 1 CCAGGGGCCA 0.806902 -95 GGCCACGTCGCGTCGCGGACAGTCCCATGT 6 122 1 CGTCGCGGAC 0.551416 -80 GCTATCGGATGGTCGCGGCAGGAGGCAAGC 6 174 0 GGTCGCGGCA 0.948311 -28 TGTCCCAATGCGACGCGGTGGTTGGGC 7 8 0 CGACGCGGTG 0.893061 -199 CGTCGCATTGGGACAGGGTAGCGAGCCCGG 7 23 1 GGACAGGGTA 0.629906 -184 GGCACGCCATCGCCGGGCTCGCTACCCTGT 7 35 0 CGCCGGGCTC 0.894833 -172 GGCGCGCTGGCGGCACGCCATCGCCGGGCT 7 46 0 CGGCACGCCA 0.845898 -161 CCCCATCAACCGGCGCGCTGGCGGCACGCC 7 57 0 CGGCGCGCTG 0.736565 -150 GGATGGTTCCGCTCGGGCCGATTCTGATGC 7 100 1 GCTCGGGCCG 0.846513 -107 CTCAGATCGACGCCGCGGTGAATTTTAACA 7 150 0 CGCCGCGGTG 0.663618 -57 CCGCGATACCCGAGGAGGCCCGC 7 194 1 CGAGGAGGCC 0.868949 -13 CAGCCCGAGCCGTCAGCCTAGG 8 3 1 GCCCGAGCCG 0.908177 -91 CGAGCCGTCAGCCTAGGGCGCACTGGCGCA 8 16 1 GCCTAGGGCG 0.742604 -78 GGCGGGCTGCCGGTGCGCCAGTGCGCCCTA 8 29 0 CGGTGCGCCA 0.895609 -65 AGCCCCATCTCGGCGGGCTGCCGGTGCGCC 8 40 0 CGGCGGGCTG 0.935991 -54 TCCCTGGCAAGCGGGTGGCACAATCCTGAA 9 32 1 GCGGGTGGCA 0.695243 -22 CCGCCAGAGCCATCGGCAGGGC 10 3 1 GCCAGAGCCA 0.505919 -55 CCAGAGCCATCGGCAGGGCCTGCCTGAGCC 10 14 1 CGGCAGGGCC 0.927744 -44 GGCAGGGCCTGCCTGAGCCAGGTGCAACCG 10 25 1 GCCTGAGCCA 0.661248 -33 GTCAATACGTGGCGGGGGTCCTCCACCATG 11 50 1 GGCGGGGGTC 0.943143 -28 ********** Masking position 7 Map Score: 45.1518 Number of sites scoring better than the average of aligned sites = 17687 Number in coding regions = 16591 Number in noncoding regions = 1096 Number of orfs with sites within 600 bp upstream = 699 Fraction of orfs with sites within 600 bp upstream = 0.112271 Motif number 2 TTAAGAACCCCCGCCTGAAGTGGACGGGGTAAACCTG 1 18 0 CCGCCTGGCG 0.701603 -76 ATCCCCCGGACGGCTGCCCGGGGAGAGTATTAAGAAC 1 47 0 CGGCTGGGGG 0.951544 -47 CCTTCTGCCGCCCGCTATCCGGGGCGGCCTTCCCTGC 3 13 1 CCCGCGGGCG 0.554395 -154 TAAAATTTATCCGGTGAATGTGGTCGGAAAACAAAGA 3 72 0 CCGGTTGGCG 0.941165 -95 TGTGACGCCTCCGCCCTGCGTGGGGGCAAAGTTATTA 4 30 1 CCGCCTGGGC 0.61478 -228 ATTGTAATTGCCGCTGCCTTTCATCAGCAGATGTTAA 4 134 1 CCGCTTCACG 0.5408 -124 CGTTGAACTTCGGCTACGAGTGGTCCCTAGCCTCGGC 5 55 0 CGGCTTGGCC 0.97017 -44 GATGCACCAGGGGCCACGTCGCGTCGCGGACAGTCCC 6 111 1 GGGCCGCGCC 0.80802 -91 GCTAAACATGCAGCTAACATGGGACTGTCCGCGACGC 6 131 0 CAGCTGGGCG 0.950209 -71 CCCAACCACCGCGTCGCATTGGGACAGGGTAGCGAGC 7 12 1 GCGTCGGGCG 0.861512 -195 GGTAGCGAGCCCGGCGATGGCGTGCCGCCAGCGCGCC 7 39 1 CCGGCCGTCG 0.57011 -168 CGCCAGCGCGCCGGTTGATGGGGTCACCCGTGATCCG 7 64 1 CCGGTGGGCC 0.989477 -143 GCGGGCCTCCTCGGGTATCGCGGTGTGGA 7 188 0 GGGCCGGGAC 0.764099 -19 CAGCCCGAGCCGTCAGCCTAGGGCGCACTGGCGCAC 8 10 1 CCGTCAGGCC 0.539375 -84 CACCGGCAGCCCGCCGAGATGGGGCTGCGTTGACAGC 8 44 1 CCGCCGGGCG 0.555977 -50 GCCGGCCTGGTTGCTCTGCTGTCCCTGG 9 2 1 CCGGCTGCCG 0.932416 -52 ATTGTGCCACCCGCTTGCCAGGGACAGCAGAGCAACC 9 19 0 CCGCTGGGCG 0.99682 -35 GCCATCGGCAGGGCCTGCCTGAGCCAGGTGCAACCGA 10 19 1 GGGCCGAGCG 0.835578 -39 TGGAGGACCCCCGCCACGTATTGACACTTTGCGACAG 11 38 0 CCGCCTTGCC 0.911194 -40 ***** *** * * Masking position 3 Map Score: 30.1069 Number of sites scoring better than the average of aligned sites = 2677 Number in coding regions = 2505 Number in noncoding regions = 172 Number of orfs with sites within 600 bp upstream = 146 Fraction of orfs with sites within 600 bp upstream = 0.02345 Motif number 3 TTTCCCGCAGGTTTACCCCGTCCACT 1 7 1 GCAGGTTTAC 0.786038 -87 GGCCTTCCCTGCCGATTAGCCCCCCCCCCT 3 38 1 GCCGATTAGC 0.84618 -129 GATTTCTCCTGCAGGTGTGACGCCTCCGCC 4 15 1 GCAGGTGTGA 0.859743 -243 TTGCCCCCACGCAGGGCGGAGGCGTCACAC 4 29 0 GCAGGGCGGA 0.906867 -229 CGGCCGGAACGCCGACTGGCTGAGTGTAGG 5 29 0 GCCGACTGGC 0.677873 -70 AACGATGAAAGCAGGTTTGCG 5 88 1 GCAGGTTTGC 0.909867 -11 TGCATGTTTAGCAGACTGGCTTGCCTCCTG 6 156 1 GCAGACTGGC 0.673676 -46 TCGCATTGGGACAGGGTAGCGAGCCCGGCG 7 25 1 ACAGGGTAGC 0.683269 -182 TCGGCGGGCTGCCGGTGCGCCAGTGCGCCC 8 31 0 GCCGGTGCGC 0.897946 -63 CGATAGGGAAGCCTGGTTGCATAG 8 80 1 GCCTGGTTGC 0.971883 -14 GCCGGCCTGGTTGCTCTGCTGTCC 9 5 1 GCCTGGTTGC 0.971883 -49 CATCGGCAGGGCCTGCCTGAGCCAGGTGCA 10 21 1 GCCTGCCTGA 0.686348 -37 GGCTCCAGCATGGTGGAGGACCCCCGC 11 61 0 GCATGGTGGA 0.888984 -17 ********** Masking position 2 Map Score: 10.8159 Number of sites scoring better than the average of aligned sites = 4381 Number in coding regions = 4183 Number in noncoding regions = 198 Number of orfs with sites within 600 bp upstream = 179 Fraction of orfs with sites within 600 bp upstream = 0.0287504 Motif number 4 CAGTCATTATCTCAGGGTTAATCCCCC 1 77 0 TATCTCAGGG 0.871743 -17 TGCCGCCCGCTATCCGGGGCGGCCTTCCCT 3 18 1 TATCCGGGGC 0.88854 -149 TGTTATATACTATAGGGGGGTATGCATTGA 3 117 1 TATAGGGGGG 0.972578 -50 GCAATATACTATAGGGGGGTATTCTATAT 3 148 0 TATAGGGGGG 0.972578 -19 TTACAATAATTATCGCTGTGAATACTGGAT 4 111 0 TATCGCTGTG 0.951338 -147 ATGTCCAAGCTATCGGATGGTCGCGGCAGG 6 182 0 TATCGGATGG 0.858301 -20 GGCGGCACGCCATCGCCGGGCTCGCTACCC 7 38 0 CATCGCCGGG 0.957167 -169 CCTCCTCGGGTATCGCGGTGTGGACTTTGC 7 182 0 TATCGCGGTG 0.982849 -25 CGCAGCCCCATCTCGGCGGGCTGCCGGTGC 8 43 0 TCTCGGCGGG 0.957201 -51 CAGGCTTCCCTATCGCTGTCAACGCAGCCC 8 65 0 TATCGCTGTC 0.839506 -29 ********** Masking position 3 Map Score: 7.31495 Number of sites scoring better than the average of aligned sites = 1093 Number in coding regions = 1015 Number in noncoding regions = 78 Number of orfs with sites within 600 bp upstream = 82 Fraction of orfs with sites within 600 bp upstream = 0.0131706 Motif number 5 TGAAGTGGACGGGGTAAACCTGCGGGAAA 1 10 0 GGGGTAAACC 0.376506 -84 CTCTCCCCGGGCAGCCGTCCGGGGGATTAA 1 57 1 GCAGCCGTCC 0.785785 -37 AGCCGTCCGGGGGATTAACCCTGAGATAAT 1 69 1 GGGATTAACC 0.435957 -25 GCTATCCGGGGCGGCCTTCCCTGCCGATTA 3 26 1 GCGGCCTTCC 0.86112 -141 GAAAGGGGGGGGGGCTAATCGGCAGGGAAG 3 41 0 GGGGCTAATC 0.713771 -126 TATACTATAGGGGGGTATGCATTGACATAT 3 122 1 GGGGGTATGC 0.911438 -45 TATACTATAGGGGGGTATTCTATATGTCAA 3 143 0 GGGGGTATTC 0.696346 -24 AACACAACAAGGAGCCACGC 4 248 1 GGAGCCACGC 0.975973 -10 GCCGAGGCTAGGGACCACTCGTAGCCGAAG 5 55 1 GGGACCACTC 0.89594 -44 GGACGGTGTAGCGGCCTTGCGGATACGGTC 6 76 0 GCGGCCTTGC 0.86925 -126 CGATGCACCAGGGGCCACGTCGCGTCGCGG 6 110 1 GGGGCCACGT 0.83088 -92 CAGCTAACATGGGACTGTCCGCGACGCGAC 6 128 0 GGGACTGTCC 0.642606 -74 GGTCGCGGCAGGAGGCAAGCCAGTCTGCTA 6 164 0 GGAGGCAAGC 0.883273 -38 GCCTCCTGCCGCGACCATCCGATAGCTTGG 6 178 1 GCGACCATCC 0.935695 -24 CCGGCGCGCTGGCGGCACGCCATCGCCGGG 7 48 0 GGCGGCACGC 0.807357 -159 GCCGGTTGATGGGGTCACCCGTGATCCGGA 7 73 1 GGGGTCACCC 0.955764 -134 CGGCCCGAGCGGAACCATCCGGATCACGGG 7 90 0 GGAACCATCC 0.923941 -117 CGATACCCGAGGAGGCCCGC 7 197 1 GGAGGCCCGC 0.478253 -10 CTATGCAACCAGGCTTCCCTATCG 8 80 0 GCAACCAGGC 0.656369 -14 GGACAGCAGAGCAACCAGGCCGGC 9 5 0 GCAACCAGGC 0.656369 -49 ATACGTGGCGGGGGTCCTCCACCATGCTGG 11 54 1 GGGGTCCTCC 0.725096 -24 ********** Masking position 1 Map Score: 20.3656 Number of sites scoring better than the average of aligned sites = 2546 Number in coding regions = 2353 Number in noncoding regions = 193 Number of orfs with sites within 600 bp upstream = 184 Fraction of orfs with sites within 600 bp upstream = 0.0295535 Motif number 6 CAGGGAAGGCCGCCCCGGATAGCGGGCGGC 3 19 0 CGCCCCGGAT 0.916053 -148 CAATAATTATCGCTGTGAATACTGGATTAT 4 108 0 CGCTGTGAAT 0.684922 -150 ACGCCCTAGCGCCGTTGACCTACACTCAG 5 10 1 CGCCGTTGAC 0.918707 -89 TCCCTAGCCTCGGCCGGAACGCCGACTGGC 5 39 0 CGGCCGGAAC 0.924636 -60 CTACCGCTCCCAACTTCTCCGACT 6 5 1 CGCTCCCAAC 0.753763 -197 CTTGCGGATACGGTCTCGATGAGGCAATAT 6 61 0 CGGTCTCGAT 0.881258 -141 CCTGGTGCATCGGTCAGGACGGTGTAGCGG 6 92 0 CGGTCAGGAC 0.919822 -110 GTCCGCGACGCGACGTGGCCCCTGGTGCAT 6 112 0 CGACGTGGCC 0.703945 -90 GGCCACGTCGCGTCGCGGACAGTCCCATGT 6 122 1 CGTCGCGGAC 0.836866 -80 GGCTTGCCTCCTGCCGCGACCATCCGATAG 6 173 1 CTGCCGCGAC 0.671736 -29 GTAGCGAGCCCGGCGATGGCGTGCCGCCAG 7 40 1 CGGCGATGGC 0.50949 -167 TCAACCGGCGCGCTGGCGGCACGCCATCGC 7 52 0 CGCTGGCGGC 0.867355 -155 CGGATGGTTCCGCTCGGGCCGATTCTGATG 7 99 1 CGCTCGGGCC 0.896341 -108 AAATTCACCGCGGCGTCGATCTGAGTAGCA 7 155 1 CGGCGTCGAT 0.937602 -52 TCGGGTATCGCGGTGTGGACTTTGCTACTC 7 177 0 CGGTGTGGAC 0.978863 -30 GCTTCCCTATCGCTGTCAACGCAGCCCCAT 8 62 0 CGCTGTCAAC 0.84578 -32 GCCGGCCTGGTTGCTCTGCTGT 9 3 1 CGGCCTGGTT 0.679047 -51 ********** Masking position 1 Map Score: 13.4462 Number of sites scoring better than the average of aligned sites = 6160 Number in coding regions = 5861 Number in noncoding regions = 299 Number of orfs with sites within 600 bp upstream = 225 Fraction of orfs with sites within 600 bp upstream = 0.0361388 Motif number 7 GGCTAATCGGCAGGGAAGGCCGCCCCGGATAG 3 27 0 CAGGGAAGCG 0.967381 -140 GGAAAACAAAGAGGAAAGGGGGGGGGGCTAAT 3 52 0 GAGGAAAGGG 0.977814 -115 AACATCTGCTGATGAAAGGCAGCGGCAATTAC 4 137 0 GATGAAAGCG 0.993129 -121 GAAGTTCAACGATGAAAGCAGGTTTGCG 5 81 1 GATGAAAGAG 0.949361 -18 TCCAATCGATGATGAGAGTCGGAGAAGTTGGG 6 19 0 GATGAGAGCG 0.974613 -183 GTCGCGGCAGGAGGCAAGCCAGTCTGCTAAAC 6 161 0 GAGGCAAGCG 0.988189 -41 TTGACAGCGATAGGGAAGCCTGGTTGCATAG 8 73 1 TAGGGAAGCG 0.952391 -21 GTCGGAAAATGATAAAAGGCTGTCGCAAAGTG 11 19 1 GATAAAAGCG 0.941658 -59 ******** * * Masking position 7 Map Score: 8.22098 Number of sites scoring better than the average of aligned sites = 224 Number in coding regions = 202 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 8 TTTCCTCTTTGTTTTCCGACCACATTCACC 3 67 1 GTTTTCCGAC 0.973979 -100 CCGCTCCCAACTTCTCCGACTCTCATCATC 6 14 1 CTTCTCCGAC 0.944016 -188 CGCGGTGTGGACTTTGCTACTCAGATCGAC 7 169 0 ACTTTGCTAC 0.900618 -38 GCCTTTTATCATTTTCCGACAGGAGGTG 11 9 0 ATTTTCCGAC 0.984571 -69 ACGTATTGACACTTTGCGACAGCCTTTTAT 11 30 0 ACTTTGCGAC 0.979293 -48 ********** Masking position 5 Map Score: 0.617803 Number of sites scoring better than the average of aligned sites = 69 Number in coding regions = 62 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 9 GGCTGAGTGTAGGTCAACGGCGCTAGGGCG 5 12 0 AGGTCAACGG 0.9724 -87 TCGTAGCCGAAGTTCAACGATGAAAGCAGG 5 73 1 AGTTCAACGA 0.796 -26 CGTGGCCCCTGGTGCATCGGTCAGGACGGT 6 99 0 GGTGCATCGG 0.956935 -103 CCGGTTGATGGGGTCACCCGTGATCCGGAT 7 74 1 GGGTCACCCG 0.984984 -133 CGTGAAAACTGGGTAACCGGTTGTTAAAAT 7 129 1 GGGTAACCGG 0.954071 -78 AGGGCGCACTGGCGCACCGGCAGCCCGCCG 8 30 1 GGCGCACCGG 0.981055 -64 GCCTGAGCCAGGTGCAACCGAAGGAGTCAA 10 35 1 GGTGCAACCG 0.962776 -23 GCAACCGAAGGAGTCAACGA 10 48 1 GAGTCAACGA 0.797348 -10 ********** Masking position 6 Map Score: 4.86215 Number of sites scoring better than the average of aligned sites = 981 Number in coding regions = 941 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 10 ********** No masking Map Score: -3.12396e-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: -3.12396e-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: -3.12396e-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