AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i146_ecoli_mtub_100.orf -o146_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 nuoN 186 NADH dehydrogenase I chain N #2 nuoM 89 NADH dehydrogenase I chain M #3 BIME110 38 BIME #4 nuoG 46 NADH dehydrogenase I chain G #5 nuoC 93 NADH dehydrogenase I chain C, D #6 nuoA 300 NADH dehydrogenase I chain A #7 hyfA 213 hydrogenase 4 Fe-S subunit #8 hycB 124 probable small subunit of hydrogenase-3, iron-sulfur protein (part of formate hydrogenlyase (FHL) complex) #9 Rv0079 300 hypothetical protein Rv0079 #10 Rv0081 94 hypothetical protein Rv0081 #11 nuoA 300 nuoA #12 nuoH 115 nuoH Motif number 1 GCTCTCCATTGCGTGGCGACGCAATCATTT 1 91 1 GCGTGGCGAC 0.940146 -96 AGCGCCCGCCTGGCCAACAAACCAG 1 172 0 CCGCCTGGCC 0.872648 -15 TGTAAAAGTCCCGTCAGGACCGGATTTTCA 2 54 0 CCGTCAGGAC 0.618624 -36 TTGTGGGATTGCCCCTGGGCATATAAGAAC 3 19 1 GCCCCTGGGC 0.515252 -20 TTTGCGCCTGTCGGCAAAGGGATTT 5 6 1 GCCTGTCGGC 0.987254 -88 GGTCCGTGGTGACTGTCGGCGCAGTAAGCT 5 67 0 GACTGTCGGC 0.890309 -27 TTGCTCCATTCCGTGCTGGCTGCGCTTGCG 7 16 1 CCGTGCTGGC 0.808423 -198 GGTATGCTGGCCGCAAGCGCAGCCAGCACG 7 27 0 CCGCAAGCGC 0.769915 -187 CCCCAAACAGGCGTAACGCCTGCAAAACGG 8 24 0 GCGTAACGCC 0.959403 -101 TCATCGACACGCCCATCCCCAAACAGGCGT 8 40 0 GCCCATCCCC 0.782738 -85 CTCAGCTTCTGCGCAGCGACGGAAACTGCC 9 80 1 GCGCAGCGAC 0.79858 -221 CTAGTCCGCGGCCCAACGGCGGCATTTCGT 9 156 0 GCCCAACGGC 0.95709 -145 GGACTTTCGGCCCTGTCCGCGTCCGTGTCG 9 226 1 CCCTGTCCGC 0.927098 -75 CTGTCCGCGTCCGTGTCGGCCAGACAAGCT 9 238 1 CCGTGTCGGC 0.988536 -63 CGTGCGGGCCGCCCGCGGCCAATCGG 10 7 0 GCCCGCGGCC 0.781346 -88 TAGTGCGGATGCGTGCGGGCCGCCCGCGGC 10 18 0 GCGTGCGGGC 0.826097 -77 TGGGGATTGCGCGTCCCGGCGAATTGTATG 11 68 0 GCGTCCCGGC 0.977098 -233 GCTTCGCAGCGACCGACGCCGGACCCAGCC 11 103 1 GACCGACGCC 0.82166 -198 GTATGCACCAGCCTGACCCCGGGAATGTGG 11 158 1 GCCTGACCCC 0.939364 -143 CAACATAGTCGCGCAACGGCCACCCCACAT 11 182 0 GCGCAACGGC 0.981096 -119 TTGAAGGTCACTGTGACGGCCCGAAGCCCC 11 209 1 CTGTGACGGC 0.847071 -92 AAGCCCCGGTTCGTCACGGCAGCCCGGTCA 11 232 1 TCGTCACGGC 0.76963 -69 GGGGCCGCCAGCGCGGCGGCCGGGCGGTGA 11 259 0 GCGCGGCGGC 0.942835 -42 GCGTCTCCCCTTGCCGCGAG 12 1 1 GCGTCTCCCC 0.917834 -115 TCTCCCCTTGCCGCGAGCGCGCGTGTTCCC 12 14 1 CCGCGAGCGC 0.936084 -102 CCGCGAGCGCGCGTGTTCCCCCGCAAGCGG 12 24 1 GCGTGTTCCC 0.695955 -92 ATCAAAATCGGTGTGTCGGCGTACTGGGGG 12 60 0 GTGTGTCGGC 0.925551 -56 GCCACTCCTTGCGCGAGGGTCCGCACTGGT 12 92 0 GCGCGAGGGT 0.764362 -24 CTCGCGCAAGGAGTGGCGGCC 12 105 1 GAGTGGCGGC 0.922024 -11 ********** Masking position 10 Map Score: 41.3224 Number of sites scoring better than the average of aligned sites = 9486 Number in coding regions = 9085 Number in noncoding regions = 401 Number of orfs with sites within 600 bp upstream = 356 Fraction of orfs with sites within 600 bp upstream = 0.0571796 Motif number 2 CACCGTCAAGCCGACGATCAGCAACGGTAG 1 50 0 CCGACGATCA 0.756738 -137 TGGGCTTAACGCGGCGCTGGTTTCGCTCTG 1 145 1 GCGGCGCTGG 0.941427 -42 TGGTTTGTTGGCCAGGCGGGCGCT 1 173 1 GCCAGGCGGG 0.923521 -14 TTCTTATATGCCCAGGGGCAATCCCACAAT 3 18 0 CCCAGGGGCA 0.833281 -21 AATCCCTTTGCCGACAGGCGCAAA 5 5 0 CCGACAGGCG 0.962839 -89 GCTTACTGCGCCGACAGTCACCACGGACCA 5 68 1 CCGACAGTCA 0.784008 -26 AGGTATGCTGGCCGCAAGCGCAGCCAGCAC 7 28 0 GCCGCAAGCG 0.97663 -186 GCTTTCCCCTGCGACACGGGTGTCGAATCC 7 86 1 GCGACACGGG 0.952104 -128 TCACGACCCAGCCTCATGCGCTGCATCTGC 9 20 1 GCCTCATGCG 0.713888 -281 GACGGAAACTGCCACACTCAAAGCCTACTG 9 97 1 GCCACACTCA 0.927454 -204 TCGACTCGTTGCCACACGTGCGCCCAGTAG 9 121 0 GCCACACGTG 0.809969 -180 GCTTGTCTGGCCGACACGGACGCGGACAGG 9 237 0 CCGACACGGA 0.841414 -64 TTGGGCATTGGCCACAATCGGGCCACAATC 9 268 1 GCCACAATCG 0.933533 -33 CCACAATCGGGCCACAATCGAAAGCCGAGC 9 279 1 GCCACAATCG 0.933533 -22 CCGATTGGCCGCGGGCGGCCCGCACGC 10 8 1 GCCGCGGGCG 0.989129 -87 CCGCGGGCGGCCCGCACGCATCCGCACTAT 10 19 1 CCCGCACGCA 0.969895 -76 ATACAATTCGCCGGGACGCGCAATCCCCAG 11 69 1 CCGGGACGCG 0.943801 -232 GCTGGGTCCGGCGTCGGTCGCTGCGAAGCA 11 102 0 GCGTCGGTCG 0.876684 -199 GAAGCAGAACCCGTGGCTGGGTCCGGCGTC 11 117 0 CCGTGGCTGG 0.514969 -184 ACCCCACATTCCCGGGGTCAGGCTGGTGCA 11 161 0 CCCGGGGTCA 0.746886 -140 CCGCCCGGCCGCCGCGCTGGCGGCCCCGTA 11 262 1 GCCGCGCTGG 0.956718 -39 GTCTCCCCTTGCCGCGAGCGCGCGTGTTCC 12 13 1 GCCGCGAGCG 0.981547 -103 CGCGTGTTCCCCCGCAAGCGGGAGGTGCCC 12 33 1 CCCGCAAGCG 0.971483 -83 CCAGTGCGGACCCTCGCGCAAGGAGTGGCG 12 93 1 CCCTCGCGCA 0.925017 -23 ********** Masking position 2 Map Score: 35.2187 Number of sites scoring better than the average of aligned sites = 8210 Number in coding regions = 7827 Number in noncoding regions = 383 Number of orfs with sites within 600 bp upstream = 306 Fraction of orfs with sites within 600 bp upstream = 0.0491487 Motif number 3 AAACCTGATCGCACTGCTACCGTTGCTGATCG 1 34 1 GCCTGCACCG 0.972957 -153 AACGCTACGCTCTCGGTTATTGGGCTTAACGC 1 125 1 TCCGGTATTG 0.682706 -62 GCTTAACGCGGCGCTGGTTTCGCTCTGGTTTG 1 148 1 GCCTGGTTCG 0.92632 -39 TTCGATTAACGCTCAGTCTCTGACTGAGAAAA 4 17 1 GCCAGTTCTG 0.939878 -30 AGTGAATCTGGCGCTACTTTTGATGAGTAAGC 6 278 1 GCCTACTTTG 0.627731 -23 CCAGCCTCATGCGCTGCATCTGCTCGCCAACC 9 27 1 GCCTGCTCTG 0.986075 -274 CCAGAGCGAGCCTCAGCTTCTGCGCAGCGACG 9 69 1 CCCAGCTCTG 0.944057 -232 CTGCTCGGCTTTCGATTGTGGCCC 9 287 0 GCCGGCTTCG 0.989958 -14 TTGTTGTTAATCTCGGCATTTGCC 11 3 0 TCCGGCTTTG 0.958874 -298 CCCCTGATAAGCGCAGCATTTGTTGTTAATCT 11 22 0 GCCAGCTTTG 0.967534 -279 CAGTTTTGCTTCGCAGCGACCGACGCCGGACC 11 96 1 TCCAGCACCG 0.911831 -205 CCGGACCCAGCCACGGGTTCTGCTTCGACTCG 11 121 1 CCCGGGTCTG 0.940982 -180 CACCCCACATTCCCGGGGTCAGGCTGGTGCAT 11 160 0 TCCGGGTCAG 0.751967 -141 CGTCACGGCAGCCCGGTCACCGCCCGGCCGCC 11 243 1 GCCGGTACCG 0.955787 -58 GGGGCCGCCAGCGCGGCGGCCGGGCGGTGACC 11 257 0 GCCGGCGCCG 0.977833 -44 ** **** **** Masking position 4 Map Score: 19.8776 Number of sites scoring better than the average of aligned sites = 2158 Number in coding regions = 2065 Number in noncoding regions = 93 Number of orfs with sites within 600 bp upstream = 94 Fraction of orfs with sites within 600 bp upstream = 0.015098 Motif number 4 CGCACTGCTACCGTTGCTGATCGTCGGCTTGA 1 43 1 CCGTTGCTAC 0.938371 -144 GTGATGCTCTCCATTGCGTGGCGACGCAATCA 1 86 1 CCATTGCGGC 0.991654 -101 GCCCAATAACCGAGAGCGTAGCGTTGAGGAAA 1 118 0 CGAGAGCGAC 0.797449 -69 GGCCAACAAACCAGAGCGAAACCAGCGCCGCG 1 154 0 CCAGAGCGAC 0.977598 -33 TTTTCCATTGCTTCACAACGGACACG 6 5 1 CCATTGCTCC 0.95423 -296 TCGTACATGTCCAGAGCGAGCCTCAGCTTCTG 9 59 1 CCAGAGCGGC 0.990315 -242 GTGGCAGTTTCCGTCGCTGCGCAGAAGCTGAG 9 80 0 CCGTCGCTCC 0.834028 -221 CGAAATGCCGCCGTTGGGCCGCGGACTAGCCG 9 157 1 CCGTTGGGCC 0.893664 -144 GACTTTCGGCCCTGTCCGCGTCCGTGTCGGCC 9 227 1 CCTGTCCGGC 0.872025 -74 TGGCCAATGCCCAAAGCTTGTCTGGCCGACAC 9 250 0 CCAAAGCTGC 0.747488 -51 CTGGTGCATACCTGTGCGAGTCGAAGCAGAAC 11 137 0 CCTGTGCGGC 0.985876 -164 TGTGGGGTGGCCGTTGCGCGACTATGTTGAAG 11 183 1 CCGTTGCGGC 0.992787 -118 GCCCGAAGCCCCGGTTCGTCACGGCAGCCCGG 11 227 1 CCGGTTCGCC 0.919406 -74 TTTTGATGTACCAGTGCGGACCCTCGCGCAAG 12 83 1 CCAGTGCGAC 0.989503 -33 ******** * * Masking position 1 Map Score: 18.8532 Number of sites scoring better than the average of aligned sites = 1313 Number in coding regions = 1252 Number in noncoding regions = 61 Number of orfs with sites within 600 bp upstream = 65 Fraction of orfs with sites within 600 bp upstream = 0.0104401 Motif number 5 TGCTCTCCATTGCGTGGCGACGCAATCATT 1 90 1 TGCGTGGCGA 0.984393 -97 TTTGCGCCTGTCGGCAAAGGGATT 5 5 1 CGCCTGTCGG 0.753487 -89 TGCAAATGGTCCGTGGTGACTGTCGGCGC 5 75 0 TCCGTGGTGA 0.740296 -19 CCCTGCGACACGGGTGTCGAATCCATTTTT 7 92 1 CGGGTGTCGA 0.969796 -122 TTTGGGGATGGGCGTGTCGATGAGTGTCGA 8 47 1 GGCGTGTCGA 0.962877 -78 GGCGTGTCGATGAGTGTCGAAAATGACATT 8 57 1 TGAGTGTCGA 0.859275 -68 CGCATGAGGCTGGGTCGTGAACGGCCCAA 9 10 0 TGGGTCGTGA 0.675935 -291 CCTCAGCTTCTGCGCAGCGACGGAAACTGC 9 79 1 TGCGCAGCGA 0.828273 -222 ATGCCGCCGTTGGGCCGCGGACTAGCCGAA 9 161 1 TGGGCCGCGG 0.915599 -140 CCGAATTTTCCGGGTGGTGACACAGCCCAC 9 186 1 CGGGTGGTGA 0.929354 -115 CCTGTCCGCGTCCGTGTCGGCCAGACAAGC 9 237 1 TCCGTGTCGG 0.910085 -64 AGACAAGCTTTGGGCATTGGCCACAATCGG 9 259 1 TGGGCATTGG 0.473939 -42 GTGGCTGGGTCCGGCGTCGGTCGCTGCGAA 11 105 0 CCGGCGTCGG 0.880776 -196 TGCATACCTGTGCGAGTCGAAGCAGAACCC 11 135 0 TGCGAGTCGA 0.789868 -166 CCGGGAATGTGGGGTGGCCGTTGCGCGACT 11 176 1 GGGGTGGCCG 0.815043 -125 GCGCGGCGGCCGGGCGGTGACCGGGCTGCC 11 249 0 CGGGCGGTGA 0.915037 -52 CGGGGCCGCCAGCGCGGCGGCCGGGCGGTG 11 260 0 AGCGCGGCGG 0.913721 -41 CATCAAAATCGGTGTGTCGGCGTACTGGGG 12 61 0 GGTGTGTCGG 0.787144 -55 CCTCGCGCAAGGAGTGGCGGCC 12 104 1 GGAGTGGCGG 0.920917 -12 ********** Masking position 4 Map Score: 18.5779 Number of sites scoring better than the average of aligned sites = 5503 Number in coding regions = 5296 Number in noncoding regions = 207 Number of orfs with sites within 600 bp upstream = 212 Fraction of orfs with sites within 600 bp upstream = 0.0340508 Motif number 6 AGCGCCCGCCTGGCCAACAAAC 1 175 0 GCGCCGCCTG 0.985541 -12 ACTACCCCCAGTCCGAAGAGA 2 1 1 ACTCCCCCAG 0.964127 -89 TCCTTGTAAAAGTCCCGTCAGGACCGGATTT 2 57 0 AGTCCGTCAG 0.788064 -33 AATCGATGTGGCGTCCATCTGCCGTGAAGAG 6 246 1 GCGCCATCTG 0.772786 -55 ACTCATCAAAAGTAGCGCCAGATTCACTGCT 6 275 0 AGTGCGCCAG 0.778342 -26 TCACATTCTCGCTTTCCCCTGCGACACGGGT 7 76 1 GCTTCCCCTG 0.946856 -138 CAGGCATTCCTCAGGTGATTGTCA 8 111 0 GCATCCTCAG 0.873525 -14 CATGTCCAGAGCGAGCCTCAGCTTCTGCGCA 9 64 1 GCGGCCTCAG 0.93902 -237 GCCGGGACGCGCAATCCCCAGTTTTGCTTCG 11 78 1 GCATCCCCAG 0.955384 -223 GCACAGGTATGCACCAGCCTGACCCCGGGAA 11 152 1 GCACAGCCTG 0.703087 -149 TCCGTCGTACGGGGCCGCCAGCGCGGCGGCC 11 268 0 GGGCCGCCAG 0.985344 -33 GCAAGCGGGAGGTGCCCCCAGTACGCCGACA 12 46 1 GGTCCCCCAG 0.984199 -70 *** ******* Masking position 9 Map Score: 9.76927 Number of sites scoring better than the average of aligned sites = 2924 Number in coding regions = 2816 Number in noncoding regions = 108 Number of orfs with sites within 600 bp upstream = 107 Fraction of orfs with sites within 600 bp upstream = 0.017186 Motif number 7 CTGCTACCGTTGCTGATCGTCGGCTTGACG 1 47 1 TGCTGATCGT 0.974997 -140 TGCAAATGGTCCGTGGTGAC 5 84 0 TGCAAATGGT 0.862134 -10 GGGCATTAAATGCTAATGGTGTTGATATTA 6 86 1 TGCTAATGGT 0.934958 -215 ATCCATTTTTTGCTGAACGTTAATGACCAT 7 112 1 TGCTGAACGT 0.980686 -102 ATTAACTGGATTCTGAACGGTACAAAAATG 7 142 0 TTCTGAACGG 0.815905 -72 GCGTAACGCCTGCAAAACGGGCAAAGCCTC 8 14 0 TGCAAAACGG 0.878003 -111 TGCGCGACTATGTTGAAGGTCACTGTGACG 11 197 1 TGTTGAAGGT 0.833731 -104 ********** Masking position 6 Map Score: 1.37456 Number of sites scoring better than the average of aligned sites = 755 Number in coding regions = 721 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 8 TCGGTTATTGGGCTTAACGCGGCGCTGGTT 1 137 1 GGCTTAACGC 0.839569 -50 TAAGGATTGTGGGATTGCCCCTGGGCATAT 3 13 1 GGGATTGCCC 0.969046 -26 GCTGAGGCTTTGCCCGTTTTGCAGG 8 6 1 GGCTTTGCCC 0.987353 -119 CCGTTTTGCAGGCGTTACGCCTGTTTGGGG 8 24 1 GGCGTTACGC 0.884314 -101 GCGCCCAGTAGGCTTTGAGTGTGGCAGTTT 9 102 0 GGCTTTGAGT 0.789164 -199 GCCCAACGGCGGCATTTCGTGTGGATCGAC 9 146 0 GGCATTTCGT 0.763164 -155 ACAAGCTTTGGGCATTGGCCACAATCGGGC 9 261 1 GGCATTGGCC 0.974775 -40 TGTTAATCTCGGCATTTGCC 11 1 0 GGCATTTGCC 0.846244 -300 GCTTATCAGGGGGTTAGACCAACATTCATA 11 42 1 GGGTTAGACC 0.683576 -259 AGCAAAACTGGGGATTGCGCGTCCCGGCGA 11 76 0 GGGATTGCGC 0.97635 -225 GACGAACCGGGGCTTCGGGCCGTCACAGTG 11 217 0 GGCTTCGGGC 0.927421 -84 ********** Masking position 5 Map Score: 8.23981 Number of sites scoring better than the average of aligned sites = 1864 Number in coding regions = 1764 Number in noncoding regions = 100 Number of orfs with sites within 600 bp upstream = 98 Fraction of orfs with sites within 600 bp upstream = 0.0157404 Motif number 9 GGTTTTGTGGAGTTATTGTCATGGCGAT 1 9 0 AGTTATTGTC 0.852135 -178 GCTTGACGGTGGTGGTTGTGATGCTCTCCA 1 69 1 GGTGGTTGTG 0.950586 -118 CTACGCTCTCGGTTATTGGGCTTAACGCGG 1 129 1 GGTTATTGGG 0.866672 -58 AATGGTCCGTGGTGACTGTCGGCGCAGTAA 5 70 0 GGTGACTGTC 0.976782 -24 GAATTTCTACAGTGATTGTAAGGTTTTTTT 6 202 1 AGTGATTGTA 0.811059 -99 GCATTCCTCAGGTGATTGTCATTTTTGACG 8 102 0 GGTGATTGTC 0.984257 -23 CTATGTTGAAGGTCACTGTGACGGCCCGAA 11 204 1 GGTCACTGTG 0.92277 -97 ********** Masking position 7 Map Score: 1.58561 Number of sites scoring better than the average of aligned sites = 423 Number in coding regions = 392 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 10 TTTGCGCCTGTCGGCAAAGGGATTTTTCTT 5 11 1 TCGGCAAAGG 0.879757 -83 TAAATCTATTTCGCGAAGCTTACTGCGCCG 5 51 1 TCGCGAAGCT 0.876723 -43 TGAGGCTGGGTCGTGAACGGCCCAA 9 6 0 TCGTGAACGG 0.946504 -295 CTGCATCTGCTCGCCAACCTCGTACATGTC 9 40 1 TCGCCAACCT 0.935544 -261 ATTCTTCAACTCGTCAACCGATGTAACGCT 10 56 1 TCGTCAACCG 0.947307 -39 TTCAACATAGTCGCGCAACGGCCACCCCAC 11 184 0 TCGCGCAACG 0.967645 -117 GTGCGGACCCTCGCGCAAGGAGTGGCGGCC 12 96 1 TCGCGCAAGG 0.957909 -20 ********** Masking position 7 Map Score: 0.933375 Number of sites scoring better than the average of aligned sites = 807 Number in coding regions = 790 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 11 ********** No masking Map Score: 4.50727e-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: 4.50727e-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: 4.50727e-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