AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i012_ecoli_mtub_300.orf -o012_ecoli_mtub_300.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 malP 300 maltodextrin phosphorylase #2 glgB 272 1,4-alpha-glucan branching enzyme #3 asd 192 aspartate-semialdehyde dehydrogenase #4 glgC 174 glgC #5 Rv1327c 30 hypothetical protein Rv1327c #6 glgX 38 glgX #7 Rv1565c 98 hypothetical protein Rv1565c #8 Rv1566c 239 hypothetical protein Rv1566c #9 Rv1567c 247 hypothetical protein Rv1567c #10 Rv1781c 263 hypothetical protein Rv1781c Motif number 1 TAAATCTGGGGCGCGATGCCGCCCCTGTTAG 2 22 1 GCGCGTGCCG 0.983969 -251 GCTATTCTTTAAGGGTGGCTGAATACATGAG 2 114 1 AAGGGGGCTG 0.891266 -159 AGATGTGCCAAGAGGAGACCGGCACATTTAT 3 140 1 AGAGGGACCG 0.734449 -53 CGTAGTGCGGTGACGGGGCGGCCCGCGTGGC 4 20 1 TGACGGGCGG 0.956485 -155 ACGGGGCGGCCCGCGTGGCGGGCCGAGGAGG 4 32 1 CCGCGGGCGG 0.96227 -143 CCGAGGAGGAGGCGGAGGCGGCACAGCACCC 4 54 1 GGCGGGGCGG 0.99008 -121 GGCCCCGTTCGACGGGTGCTGTGCCGCCTCC 4 67 0 GACGGTGCTG 0.924183 -108 AGCACCCGTCGAACGGGGCCAAACACCTTGA 4 78 1 GAACGGGCCA 0.812565 -97 CAGAGCAGTAGCCAGGGGCGGATTCCCCTTG 4 121 1 GCCAGGGCGG 0.908533 -54 GGCAGTGGTTTGCGGGGGCCGATAGGTTTGA 4 151 1 TGCGGGGCCG 0.97415 -24 GCGAGAAAGCAAGCGGGACCG 7 1 0 AAGCGGACCG 0.844957 -98 GCAGCGGGAAGCAGGAGGCGGGTTTGGGAGG 7 31 0 GCAGGGGCGG 0.986054 -68 AGCGCGCGAAGCAGGAGGCTGGTTTGGGTAA 7 64 1 GCAGGGGCTG 0.980834 -35 TCGCGCGTGACTGAAATCACAAC 8 3 1 GCGCGGACTG 0.960089 -237 ATCAAAGATTGAGCGCGGCAGTCACCGTCCG 8 39 1 GAGCGGGCAG 0.940703 -201 CTTTTTGCCGTAACGTGACCGGACGGTGACT 8 58 0 TAACGGACCG 0.844648 -182 GGCCAGCTATGGACGCGGCCGGCATCTGTTG 8 104 1 GGACGGGCCG 0.993701 -136 GGATGGGCCGTGGCGTGGCTGCATTACCCTC 9 18 0 TGGCGGGCTG 0.962298 -230 AGGTTTTGGCGACCGTTACTGGGATGGGCCG 9 39 0 GACCGTACTG 0.780867 -209 AAGACACTCAGCCCGATGCTGGCACCGAATC 9 115 1 GCCCGTGCTG 0.964304 -133 GAGTACCCGTGGGGGTGTCCGCTCGTCGGGC 9 164 0 GGGGGGTCCG 0.93119 -84 CCACGGGTACTCACGCTGCGGATAGCGCCCT 9 183 1 TCACGTGCGG 0.841859 -65 AGCGGCGAATGACCGAGTCCGCCTGTGGAAC 10 114 1 GACCGGTCCG 0.943127 -150 CTCGCCCGCACACGGGTGCCGGACGCAAGAT 10 236 1 CACGGTGCCG 0.810562 -28 ***** ***** Masking position 5 Map Score: 35.3318 Number of sites scoring better than the average of aligned sites = 4563 Number in coding regions = 4366 Number in noncoding regions = 197 Number of orfs with sites within 600 bp upstream = 189 Fraction of orfs with sites within 600 bp upstream = 0.0303566 Motif number 2 TCACATTTCCTTGCTCATCCCCGCAACTCCTCCC 1 184 1 TTGCTACCGC 0.765516 -117 CAACTCCTCCCTGCCTAATCCCCCGCAGGATGAG 1 207 1 CTGCCATCCC 0.972569 -94 CTAACAGGGGCGGCATCGCGCCCCAGATTTAATG 2 19 0 CGGCACCCCC 0.913689 -254 TGCATCCTCTCTGCGTCGTCCTCACTTCAGGTAA 2 156 0 CTGCGCTCCA 0.663803 -117 TTGACCTGAACGGCGCAGCACTCTGTGCATCCTC 2 181 0 CGGCGACCCT 0.942727 -92 CTCAAATTCCCTGATAATTGCCGCGGACTTTCTG 3 13 1 CTGATATCGC 0.459869 -180 AGTCGCATTACTGATGGCTTCGCTATCATTGATT 3 67 1 CTGATGTCCT 0.469425 -126 CCACGCGGGCCGCCCCGTCACCGCACTACGGTGC 4 16 0 CGCCCGCCGC 0.884486 -159 CCTCCGCCTCCTCCTCGGCCCGCCACGCGGGCCG 4 38 0 CTCCTGCCCC 0.96746 -137 GACGGGTGCTGTGCCGCCTCCGCCTCCTCCTCGG 4 54 0 GTGCCCTCCC 0.754064 -121 CCTTACCTTACTGAGGATGCCACCGC 5 15 1 CTGAGAGCCC 0.641487 -16 CGCCTACACCCGCCGGAGAACCTG 6 1 1 CGCCTCCCCC 0.960534 -38 GCTTTCTCGCCTCCCAAACCCGCCTCCTGCTTCC 7 22 1 CTCCCACCCC 0.97436 -77 AACCCGCCTCCTGCTTCCCGCTGCTCAGCGCGCG 7 38 1 CTGCTCCCGC 0.977888 -61 AACCAGCCTCCTGCTTCGCGCGCTGAGCAGCGGG 7 54 0 CTGCTCCCCT 0.975839 -45 CGGACGGTGACTGCCGCGCTCAATCTTTGATCGG 8 36 0 CTGCCCCCAT 0.700228 -204 CGTCCATAGCTGGCCAGATCCACCAGAAGTCTTT 8 85 0 TGGCCGTCCC 0.735024 -155 GCTATGGACGCGGCCGGCATCTGTTGTCAAAGTG 8 109 1 CGGCCGACGT 0.627325 -131 AAGTCACGTGCTGAGGCACACACCACCCGAGAGT 8 196 1 CTGAGCCCCC 0.949228 -44 GGGTTGTAACCTCCTTGGCACTCTCGGGTGGTGT 8 215 0 CTCCTGCCCT 0.892759 -25 AGCCACGCCACGGCCCATCCCAGTAACGGTCGCC 9 29 1 CGGCCACCGT 0.865777 -219 GGTACTCACGCTGCGGATAGCGCCCTGGGACGTG 9 188 1 CTGCGAACCC 0.95892 -60 ACCAGAAATACTGCCAATATCGCTACGGTACATA 9 223 0 CTGCCAACCT 0.893096 -25 ACCTTCCGGTCTGCTCAGAACACCTGGACATTGA 10 19 1 CTGCTAACCC 0.953521 -245 GTATTTGCCACTGCGCGGATCCCCCAAGGATTCG 10 58 1 CTGCGGACCC 0.963716 -206 AAGGCTCAGATTCCTGCGCTCGCCCGCACACGGG 10 218 1 TTCCTCCCCC 0.83378 -46 GTCGCCCATCTTGCGTCCGGCACCCGTGTGCGGG 10 240 0 TTGCGCGCCC 0.750961 -24 ***** * * * ** Masking position 11 Map Score: 29.4297 Number of sites scoring better than the average of aligned sites = 6359 Number in coding regions = 6014 Number in noncoding regions = 345 Number of orfs with sites within 600 bp upstream = 297 Fraction of orfs with sites within 600 bp upstream = 0.0477032 Motif number 3 TGAGGACGACGCAGAGAGGATGCACAGAGT 2 166 1 GCAGAGAGGA 0.65409 -107 AGAGTGCTGCGCCGTTCAGGTCAAAAAAAT 2 191 1 GCCGTTCAGG 0.654877 -82 TGAAAGATGTGCCAAGAGGAGACCGGCACA 3 136 1 GCCAAGAGGA 0.870876 -57 TCCTCGGCCCGCCACGCGGGCCGCCCCGTC 4 31 0 GCCACGCGGG 0.956948 -144 CGCGTGGCGGGCCGAGGAGGAGGCGGAGGC 4 43 1 GCCGAGGAGG 0.987996 -132 CGAGGAGGAGGCGGAGGCGGCACAGCACCC 4 55 1 GCGGAGGCGG 0.850604 -120 CACAGCACCCGTCGAACGGGGCCAAACACC 4 75 1 GTCGAACGGG 0.654511 -100 GCAAACCACTGCCAAGGGGAATCCGCCCCT 4 134 0 GCCAAGGGGA 0.975009 -41 TGCTCAGCGCGCGAAGCAGGAGGCTGGTTT 7 59 1 GCGAAGCAGG 0.921507 -40 GGCTGGAATGGCAGACGGTGAAGTCACGTG 8 176 1 GCAGACGGTG 0.70633 -64 ACCCGAGAGTGCCAAGGAGGTTACAACCCC 8 220 1 GCCAAGGAGG 0.976729 -20 CAAAACCTCTGCCATCGGGGAGCATGCATG 9 62 1 GCCATCGGGG 0.953409 -186 ATTCGGCGGTGCCATGCATGCATGCTCCCC 9 78 0 GCCATGCATG 0.634371 -170 CTCGTCTAGAGCCGACCGGGATTCGGTGCC 9 135 0 GCCGACCGGG 0.994009 -113 AGACGAGCCCGACGAGCGGACACCCCCACG 9 158 1 GACGAGCGGA 0.816351 -90 AGCGTGAGTACCCGTGGGGGTGTCCGCTCG 9 170 0 CCCGTGGGGG 0.827993 -78 GGTGTTCTGAGCAGACCGGAAGGTGATCTA 10 13 0 GCAGACCGGA 0.873591 -251 GAGGTAGACTGCGGAGCGGACAGTTCCACA 10 137 0 GCGGAGCGGA 0.955324 -127 TACGTTGCAGGTCAACGAGGTAGACTGCGG 10 153 0 GTCAACGAGG 0.637079 -111 GTGTTCGGTAGCCAACCGTGCTGTGCTGAC 10 186 1 GCCAACCGTG 0.914336 -78 ********** Masking position 1 Map Score: 22.226 Number of sites scoring better than the average of aligned sites = 3870 Number in coding regions = 3669 Number in noncoding regions = 201 Number of orfs with sites within 600 bp upstream = 183 Fraction of orfs with sites within 600 bp upstream = 0.0293929 Motif number 4 ATTTTCAAAAAGCGGAAGGTAACTCTATAA 1 53 0 AGCGGAAGGT 0.922649 -248 TTCATGATTTACCGGGAGTTAAATAGAGCA 2 81 1 ACCGGGAGTT 0.948645 -192 TCACAGCCTTACCTGAAGTGAGGACGACGC 2 148 1 ACCTGAAGTG 0.609723 -125 AAATGTCACAACCAGAAGTCAAAAATCCAA 2 217 1 ACCAGAAGTC 0.961479 -56 ACACAATAAAACAGGAAGACAAGC 2 259 1 ACAGGAAGAC 0.659296 -14 TAGTGCGGTGACGGGGCGGCCCGCGTGGCG 4 22 1 ACGGGGCGGC 0.762535 -153 AGCAGCGGGAAGCAGGAGGCGGGTTTGGGA 7 33 0 AGCAGGAGGC 0.91572 -66 CAGCGCGCGAAGCAGGAGGCTGGTTTGGGT 7 63 1 AGCAGGAGGC 0.91572 -36 CCGTAACGTGACCGGACGGTGACTGCCGCG 8 52 0 ACCGGACGGT 0.914422 -188 GGCCAGATCCACCAGAAGTCTTTTTGCCGT 8 78 0 ACCAGAAGTC 0.961479 -162 TGCCATTCCAGCCGGAAGTCACTTTATTCA 8 159 0 GCCGGAAGTC 0.973411 -81 CGCCGAATCAGCCTGAAGACACTCAGCCCG 9 100 1 GCCTGAAGAC 0.674295 -148 TCTAGAGCCGACCGGGATTCGGTGCCAGCA 9 131 0 ACCGGGATTC 0.80141 -117 TTCTGAGCAGACCGGAAGGTGATCTAGC 10 9 0 ACCGGAAGGT 0.976028 -255 GTGCTGTGCTGACGGAAGGCTCAGATTCCT 10 203 1 GACGGAAGGC 0.829966 -61 ********** Masking position 5 Map Score: 15.3623 Number of sites scoring better than the average of aligned sites = 1921 Number in coding regions = 1775 Number in noncoding regions = 146 Number of orfs with sites within 600 bp upstream = 136 Fraction of orfs with sites within 600 bp upstream = 0.0218439 Motif number 5 AAATCAATGCAATACAGCGCAGAAAATCTGTA 1 110 0 AATACGCCAG 0.787137 -191 CCGTCACCGCACTACGGTGCGGGGT 4 4 0 ACTACGTCGG 0.958268 -171 TCCGCCCCTGGCTACTGCTCTGACGGGCTGTC 4 111 0 GCTACGCCTG 0.920759 -64 GCCCCCGCAAACCACTGCCAAGGGGAATCCGC 4 138 0 ACCACGCAAG 0.889709 -37 CCTCCTGCTTCCCGCTGCTCAGCGCGCGAAGC 7 44 1 CCCGCGCCAG 0.847367 -55 GAGCGCGGCAGTCACCGTCCGGTCACGTTACG 8 49 1 GTCACGTCGG 0.925632 -191 GGTGGTGTGTGCCTCAGCACGTGACTTCACCG 8 191 0 GCCTCGCCGT 0.829944 -49 ATGCAGCCACGCCACGGCCCATCCCAGTAACG 9 25 1 GCCACGCCAT 0.970755 -223 TACGGTACATACCACGTCCCAGGGCGCTATCC 9 202 0 ACCACTCCAG 0.960041 -46 TGCCAATATCGCTACGGTACATACCACGTCCC 9 214 0 GCTACGTCAT 0.806313 -34 GCTAGATCACCTTCCGGTCTGCTCAGA 10 6 1 ATCACTTCGG 0.620246 -258 CTGGGTATTTGCCACTGCGCGGATCCCCCAAG 10 54 1 GCCACGCCGG 0.996062 -210 ACCGAACACCACTACGTTGCAGGTCAACGAGG 10 163 0 ACTACTTCAG 0.750819 -101 GCCTTCCGTCAGCACAGCACGGTTGGCTACCG 10 191 0 AGCACGCCGG 0.955321 -73 ***** ** *** Masking position 5 Map Score: 9.85355 Number of sites scoring better than the average of aligned sites = 2765 Number in coding regions = 2669 Number in noncoding regions = 96 Number of orfs with sites within 600 bp upstream = 93 Fraction of orfs with sites within 600 bp upstream = 0.0149374 Motif number 6 ACTCCTCCCTGCCTAATCCCCCGCAGGATGA 1 209 1 GCCTAATCCC 0.655383 -92 CATCGAGCCTGGCAAACTAGCGATAACGTTG 1 250 1 GGCAAACAGC 0.86174 -51 CACTAACAGGGGCGGCATCGCGCCCCAGATT 2 24 0 GGCGGCACGC 0.950239 -249 ACAAAAAGCAGCCAAAGTCGCAAGTGAAATT 3 101 0 GCCAAAGCGC 0.802769 -92 CTCCTCCTCGGCCCGCCACGCGGGCCGCCCC 4 34 0 GCCCGCCCGC 0.857213 -141 AGGAGGCGGAGGCGGCACAGCACCCGTCGAA 4 60 1 GGCGGCAAGC 0.931202 -115 CGTCGAACGGGGCCAAACACCTTGACGGACA 4 84 1 GGCCAAAACC 0.845409 -91 AGTAGCCAGGGGCGGATTCCCCTTGGCAGTG 4 127 1 GGCGGATCCC 0.97582 -48 GCCTACACCCGCCGGAGAACCTGGATAAGGT 6 12 1 GCCGGAGACC 0.917139 -27 GGGTTTGGGAGGCGAGAAAGCAAGCGGGACC 7 12 0 GGCGAGAAGC 0.781587 -87 GCATGGCACCGCCGAATCAGCCTGAAGACAC 9 91 1 GCCGAATAGC 0.953343 -157 CTCTAGACGAGCCCGACGAGCGGACACCCCC 9 154 1 GCCCGACAGC 0.903016 -94 TCCGCGCAGTGGCAAATACCCAGGTCAATGT 10 46 0 GGCAAATCCC 0.877723 -218 ACGAATCCTTGGGGGATCCGCGCAGTGGCAA 10 62 0 GGGGGATCGC 0.807428 -202 GCATGGTAGCGGCGAATGACCGAGTCCGCCT 10 107 1 GGCGAATACC 0.953506 -157 ******* *** Masking position 1 Map Score: 11.3612 Number of sites scoring better than the average of aligned sites = 3602 Number in coding regions = 3353 Number in noncoding regions = 249 Number of orfs with sites within 600 bp upstream = 166 Fraction of orfs with sites within 600 bp upstream = 0.0266624 Motif number 7 AGATACAGATTTTCTGCGCTGTATTGCATT 1 107 1 TTTCTGCGCT 0.878929 -194 TTTGATGCTAATCCTGTGGTTTGCACTAGC 1 139 1 ATCCTGTGGT 0.895349 -162 GACCTTCCTCATCCTGCGGGGGATTAGGCA 1 218 0 ATCCTGCGGG 0.981691 -83 GCTTGTCTTCCTGTTTTATTGTGTCAC 2 256 0 TTCCTGTTTT 0.537582 -17 TGCCGCGGACTTTCTGCGTGCTAACAAAGC 3 31 1 TTTCTGCGTG 0.879313 -162 AATGCGACTTATCCTGCTTTGTTAGCACGC 3 46 0 ATCCTGCTTT 0.845165 -147 TATCCAGGTTCTCCGGCGGGTGTAGGCG 6 9 0 CTCCGGCGGG 0.945049 -30 ATAAAGTGACTTCCGGCTGGAATGGCAGAC 8 162 1 TTCCGGCTGG 0.929929 -78 CTTCAGGCTGATTCGGCGGTGCCATGCATG 9 88 0 ATTCGGCGGT 0.908614 -160 AAGGCTCAGATTCCTGCGCTCGCCCGCACA 10 218 1 TTCCTGCGCT 0.962587 -46 ********** Masking position 2 Map Score: 6.42327 Number of sites scoring better than the average of aligned sites = 2178 Number in coding regions = 2058 Number in noncoding regions = 120 Number of orfs with sites within 600 bp upstream = 118 Fraction of orfs with sites within 600 bp upstream = 0.0189528 Motif number 8 ********** No masking Map Score: 6.83075e-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 9 TTGCGGGGATGAGCAAGGAAATGTGATCTCA 1 179 0 GAGAAGGAAA 0.91793 -122 CCCGCAGGATGAGGAAGGTCAACATCGAGCC 1 228 1 GAGAAGGTCA 0.890902 -73 CGTAATACAGGAGTAAGCGCAGATGTTTCAT 2 55 1 GAGAAGCGCA 0.96631 -218 CTGAATACATGAGTATTCACAGCCTTACCTG 2 132 1 GAGATTCACA 0.886546 -141 ACGACGCAGAGAGGATGCACAGAGTGCTGCG 2 171 1 GAGATGCACA 0.983672 -102 TTTGGGAGGCGAGAAAGCAAGCGGGACCG 7 9 0 GAGAAGCAAG 0.946911 -90 TGCCATCGGGGAGCATGCATGCATGGCACCG 9 71 1 GAGATGCATG 0.88595 -177 *** ******* Masking position 5 Map Score: 0.00710369 Number of sites scoring better than the average of aligned sites = 200 Number in coding regions = 178 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 10 ********** No masking Map Score: 6.83075e-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: 6.83075e-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: 6.83075e-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