AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i054_ecoli_mtub_300.orf -o054_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 cstC 300 acetylornithine delta-aminotransferase #2 argG 300 argininosuccinate synthetase #3 argD 85 acetylornithine delta-aminotransferase #4 pabA 31 p-aminobenzoate synthetase, component II #5 yhfG 104 orf, hypothetical protein #6 ppiA 270 peptidyl-prolyl cis-trans isomerase A (rotamase A) #7 argC 153 N-acetyl-gamma-glutamylphosphate reductase #8 argH 60 argininosuccinate lyase #9 ppa 300 inorganic pyrophosphatase #10 argI 161 ornithine carbamoyltransferase 1 #11 argC 193 argC #12 argH 79 argH #13 ppa 137 ppa Motif number 1 GATTTGGTGTACCGAGACGGGACGTAAAATC 2 18 1 ACGAGACGGG 0.918601 -283 GGCGGCTCCGGTACAAAAGAAC 4 20 0 GCGCTCCGGT 0.98535 -12 GCAAATCCGGGTTACGCCGGGAGAGCAGAAG 5 41 0 GTACGCCGGG 0.868297 -64 TGTTGACACACCTCTGGTCATGATAGTA 7 8 1 ACCCTCTGGT 0.752562 -146 CCGGAAAGCTGCGCCTCCGGCCAACAAAAC 8 10 0 GCCCTCCGGC 0.953954 -51 AATAATAACTACCCCGACGAG 9 1 0 ACCCGACGAG 0.912706 -300 TATGAAAAATGCGGCTACGGTTATGGATTTT 9 152 1 GCGCTACGGT 0.965908 -149 ATGTCCACTAGCTGCGCCGAGTCGAAGGGGG 11 17 0 GCGCGCCGAG 0.983344 -177 CCGCCGGGCGGCGCCGATGGGACTCGAAGTT 11 117 0 GCCCGATGGG 0.961308 -77 GGGACTTGACACACCGCCGGGCGGCGCCGAT 11 130 0 ACCCGCCGGG 0.995698 -64 TTCCGCGGTGACTGCGCCGGGACTTGACACA 11 148 0 ACGCGCCGGG 0.995682 -46 GCAGAATCGCACGCCGACGGGCGTGGCGGTG 12 40 0 ACCCGACGGG 0.989838 -40 TGGCAGCGTCGCCCGGCCGGTTCGGCAGAAT 13 35 0 GCCGGCCGGT 0.956802 -103 GCCGGGCGACGCTGCCACGGTACCGGCTCGA 13 49 1 GCGCCACGGT 0.927222 -89 GGACACCCTAGTCGAGCCGGTACCGTGGCAG 13 60 0 GTGAGCCGGT 0.76339 -78 ** ******** Masking position 9 Map Score: 21.9518 Number of sites scoring better than the average of aligned sites = 2929 Number in coding regions = 2775 Number in noncoding regions = 154 Number of orfs with sites within 600 bp upstream = 138 Fraction of orfs with sites within 600 bp upstream = 0.0221651 Motif number 2 CGAAATTTACTGGAAATTACTGCGCCATTCTGA 1 12 0 TGAAATTTGC 0.951247 -289 ATTTTACTTCTGCATAACATTGCGTTTTTTATT 1 70 1 TGATAACTGC 0.732723 -231 GCATATAAAGTGAATACGTTTGCGATGTGGGTG 1 112 0 TGATACGTGC 0.958214 -189 GAAAGTGAACTGGATATTCATTCACATGATTAG 2 95 0 TGATATTTTC 0.910486 -206 TTTCATTTGTTGAATACTTTTGCCTTCTCCTGC 2 124 1 TGATACTTGC 0.974318 -177 GTGTGTTTTTTGTAAAATAATGCGCTTAAGGGA 2 159 0 TGAAAATTGC 0.828803 -142 CCGCTCTCACTGAATTTTTATGCAAAATAAATG 2 235 0 TGATTTTTGC 0.975113 -66 TGCCATTTAGTGATTTTTTATGCATATTTTGTG 3 19 1 TGTTTTTTGC 0.855318 -67 AATGTTTTATTGCAATCGGTTGCTAAATTGCAT 6 93 1 TGAATCGTGC 0.934783 -178 AAATACTGCATGAATATTGATACTATCATGACC 7 26 0 TGATATTTAC 0.715046 -128 TCAACGTTAGTGTATTTTTATTCATAAATACTG 7 51 0 TGATTTTTTC 0.919325 -103 TTCCTTATTTTGAAATTCAATGCCGGAAAGCTG 8 30 0 TGAATTCTGC 0.873515 -31 ATCACAAGTTTGTAATCGCTTTCATCTCACTAT 9 122 1 TGAATCGTTC 0.80653 -179 GCTACGGTTATGGATTTTCCTGCTCTGTATACC 9 165 1 TGATTTTTGC 0.975113 -136 TGTCTTCGCTTGTTTTCGTCTTCATTTTCCTTT 9 215 0 TGTTTCGTTC 0.529942 -86 CCATATAAATTGAATTTTAATTCATTGAGGCGT 10 121 1 TGATTTTTTC 0.919325 -41 GGAATGAGTTTGCAAACTGTTGCATAACG 11 175 1 TGAAACTTGC 0.954886 -19 ** ***** *** Masking position 11 Map Score: 19.5532 Number of sites scoring better than the average of aligned sites = 402 Number in coding regions = 347 Number in noncoding regions = 55 Number of orfs with sites within 600 bp upstream = 64 Fraction of orfs with sites within 600 bp upstream = 0.0102795 Motif number 3 GCAGATTTTACGTCCCGTCTCGGTACACCAA 2 21 0 CGTCCCGTCC 0.893951 -280 CTTTTGCCTTCTCCTGCTCTCCCTTAAGCGC 2 140 1 CTCCTGCTCC 0.978669 -161 ACACTAAACTCTTCCTGTCTCCGATAAAAGA 2 188 1 CTTCCTGTCC 0.891917 -113 TGAGCCTGGATTTCCGCTCTCACTGAATTTT 2 250 0 TTTCCGCTCC 0.981993 -51 CTTGCCCGCGCTTCTGCTCTCCCGGCGTAAC 5 31 1 CTTCTGCTCC 0.990069 -74 CACCTAAAATCGCCCGCTCGCGGCATATCCC 6 45 0 CGCCCGCTCC 0.984754 -226 AAAAAGTGATCGTCAGGTTACATATATTTCA 6 153 1 CGTCAGGTTC 0.715218 -118 ACTTGCTTTTTTTCTGCTCTGTTTGTTAAGG 6 243 1 TTTCTGCTCG 0.894268 -28 CACCTTCTTATGTCTGGTTGCCAGGTTAAAC 7 123 0 TGTCTGGTTC 0.789603 -31 TTGTAATCGCTTTCATCTCACTATGAAAAAT 9 131 1 TTTCATCTCC 0.653054 -170 GTTATGGATTTTCCTGCTCTGTATACCGTCT 9 171 1 TTCCTGCTCG 0.795593 -130 TGCGATTCTGCGTCTGCTCGCGGGAGAACCG 12 11 0 CGTCTGCTCC 0.991814 -69 TGCGATTCTGCGTCTGCTCGCCACAGAAAA 12 60 1 CGTCTGCTCC 0.991814 -20 CTCTCCTGCCTTTCCGGTCCCATTCTGCCGA 13 14 1 TTTCCGGTCC 0.968552 -124 ********* * Masking position 8 Map Score: 18.754 Number of sites scoring better than the average of aligned sites = 927 Number in coding regions = 874 Number in noncoding regions = 53 Number of orfs with sites within 600 bp upstream = 65 Fraction of orfs with sites within 600 bp upstream = 0.0104401 Motif number 4 AAGTGCATAAACGGCGGAGGCTAACTGGAAA 1 181 0 ACGGCGAGGC 0.937714 -120 TTCTTTTGTACCGGAGCCGCC 4 21 1 CCGGAGCGCC 0.893111 -11 TTCTGCTCTCCCGGCGTAACCCGGATTTGCC 5 42 1 CCGGCGAACC 0.842498 -63 ACAAGTATAAGCGGCAAATCCGGGTTACGCC 5 54 0 GCGGCAATCC 0.938633 -51 TCGCCCGCTCGCGGCATATCCCGCTATGCCA 6 36 0 GCGGCAATCC 0.938633 -235 ATGCCGGAAAGCTGCGCCTCCGGCCAACAAA 8 13 0 GCTGCGCTCC 0.979344 -48 CCCCTTCGACTCGGCGCAGCTAGTGGACATG 11 18 1 TCGGCGAGCT 0.751738 -176 TCGAGTCCCATCGGCGCCGCCCGGCGGTGTG 11 121 1 TCGGCGCGCC 0.992931 -73 AACTCATTCCGCGGTGACTGCGCCGGGACTT 11 154 0 GCGGTGCTGC 0.943604 -40 GCGGTGCGATTCTGCGTCTGCTCGCGGGAGA 12 15 0 TCTGCGCTGC 0.919525 -65 GGCGTGCGATTCTGCGTCTGCTCGCCACAGA 12 56 1 TCTGCGCTGC 0.919525 -24 CGGTACCGTGGCAGCGTCGCCCGGCCGGTTC 13 43 0 GCAGCGCGCC 0.962833 -95 CGACGCTGCCACGGTACCGGCTCGACTAGGG 13 55 1 ACGGTACGGC 0.493734 -83 GCGTCGGCTCCTTCAGATCAG 13 127 0 GCGTCGCTCC 0.935458 -11 ****** **** Masking position 2 Map Score: 14.9849 Number of sites scoring better than the average of aligned sites = 3630 Number in coding regions = 3504 Number in noncoding regions = 126 Number of orfs with sites within 600 bp upstream = 104 Fraction of orfs with sites within 600 bp upstream = 0.0167041 Motif number 5 AATAGCGCGGTTCTTTTGTA 4 1 1 AATAGCGCGG 0.959452 -31 TGATTTCTCGCGCGGGCAATCTTGC 5 6 1 TCTCGCGCGG 0.909886 -99 CCGGGAGAGCAGAAGCGCGGGCAAGATTGC 5 26 0 AGAAGCGCGG 0.810835 -79 AATCACCTAAAATCGCCCGCTCGCGGCATA 6 49 0 AATCGCCCGC 0.948395 -222 TAAGAAGGTGAATAGCCCCG 7 144 1 AATAGCCCCG 0.917577 -10 ATTATAGCCAACTCGCGCCGAATGTCTTCG 9 240 0 ACTCGCGCCG 0.973398 -61 GTCCCATCGGCGCCGCCCGGCGGTGTGTCA 11 125 1 CGCCGCCCGG 0.898834 -69 GCAGACGCAGAATCGCACCGCCACGCCCGT 12 25 1 AATCGCACCG 0.938218 -55 GCAGACGCAGAATCGCACGCCGACGGGCGT 12 47 0 AATCGCACGC 0.861303 -33 ACCGTGGCAGCGTCGCCCGGCCGGTTCGGC 13 40 0 CGTCGCCCGG 0.976906 -98 TGGACACCCTAGTCGAGCCGGTACCGTGGC 13 62 0 AGTCGAGCCG 0.849553 -76 ********** Masking position 8 Map Score: 8.54103 Number of sites scoring better than the average of aligned sites = 1548 Number in coding regions = 1492 Number in noncoding regions = 56 Number of orfs with sites within 600 bp upstream = 61 Fraction of orfs with sites within 600 bp upstream = 0.00979762 Motif number 6 AACATTGCGTTTTTTATTCTTTTTATTCACCCAC 1 85 1 TTTTCTTTTT 0.791922 -216 GCCTCCGCCGTTTATGCACTTTTATCACTGGCTG 1 191 1 TTTTCTTTTA 0.791922 -110 CAGGAAGAGTTTAGTGTGTTTTTTGTAAAATAAT 2 171 0 TTATTTTTTT 0.926671 -130 GAGTTTTCATTTAATCATCTTTTATCGGAGACAG 2 202 0 TTATCTTTTA 0.931932 -99 ATTTCCGCTCTCACTGAATTTTTATGCAAAATAA 2 238 0 TCATTTTTTA 0.899977 -63 TGATTGCCATTTAGTGATTTTTTATGCATATTTT 3 15 1 TTATTTTTTA 0.926671 -71 TAGAATCTCTTCACTTGCTTTTTTTCTGCTCTGT 6 231 1 TCATTTTTTT 0.899977 -40 ACGCTCAACGTTAGTGTATTTTTATTCATAAATA 7 54 0 TTATTTTTTA 0.926671 -100 GATTAACGTTTTATTTACTTTTTTGAAGTGTGAT 9 91 0 TTATTTTTTT 0.926671 -210 GTTTTCGTCTTCATTTTCCTTTTTCACCAGTTTT 9 203 0 TCATCTTTTT 0.906962 -98 *** * ****** Masking position 5 Map Score: 6.31884 Number of sites scoring better than the average of aligned sites = 120 Number in coding regions = 62 Number in noncoding regions = 58 Number of orfs with sites within 600 bp upstream = 78 Fraction of orfs with sites within 600 bp upstream = 0.0125281 Motif number 7 TCGCAAACGTATTCACTTTATATGCACTTT 1 120 1 ATTCACTTTA 0.970415 -181 TTCACTTTATATGCACTTTAAATGCATATG 1 131 1 ATGCACTTTA 0.969834 -170 TCCGCCGTTTATGCACTTTTATCACTGGCT 1 194 1 ATGCACTTTT 0.888038 -107 TGAATATCCAGTTCACTTTCATTTGTTGAA 2 108 1 GTTCACTTTC 0.854278 -193 ACCTCTTAAAATGCAATTTAGCAACCGATT 6 106 0 ATGCAATTTA 0.88029 -165 AACGTAAAACATTCACCTTACGGCTGGTGG 7 96 0 ATTCACCTTA 0.948911 -58 CGGGGCTATTCACCTTCTTATGTCTGG 7 137 0 ATTCACCTTC 0.925918 -17 ATGAATTAAAATTCAATTTATATGGATGAT 10 116 0 ATTCAATTTA 0.882384 -46 ********** Masking position 5 Map Score: 6.117 Number of sites scoring better than the average of aligned sites = 106 Number in coding regions = 79 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 8 CGTTTATGCACTTTTATCACTGGCTGGCACGAA 1 199 1 CTTTTCACGG 0.989393 -102 TGAACGTGTCCATTTGCCACAAGTATAAGCGGC 5 70 0 CTTTCCACAG 0.975818 -35 GTAAATAAAACGTTAATCACAAGTTTGTAATCG 9 107 1 CTTATCACAG 0.969701 -194 TCTTCATTTTCCTTTTTCACCAGTTTTAAGACG 9 197 0 CTTTTCACAG 0.983421 -104 TTCATTGAGGCGTTAGCCACAGGAGGGATCT 10 141 1 CTTACCACGG 0.976381 -21 AGCTAGTGGACATGTGTCACGGGAAATTCAGCC 11 35 1 CTGTTCACGG 0.964782 -159 * *** **** ** Masking position 9 Map Score: 3.98231 Number of sites scoring better than the average of aligned sites = 50 Number in coding regions = 46 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 9 ACGAAATTTACTGGAAATTACTGCGCCATT 1 16 0 CTGGAAATTA 0.795271 -285 AAATATAATTCTGGAATTGTGATCATTGAC 1 44 0 CTGGAATTGT 0.784147 -257 CGGAGGCTAACTGGAAATCAAGGAGTTATA 1 168 0 CTGGAAATCA 0.859315 -133 TGAAAGTGAACTGGATATTCATTCACATGA 2 99 0 CTGGATATTC 0.920637 -202 GATGATGAGCCTGGATTTCCGCTCTCACTG 2 256 0 CTGGATTTCC 0.892002 -45 CCGGCGTAACCCGGATTTGCCGCTTATACT 5 52 1 CCGGATTTGC 0.914042 -53 AATGGCATAGCGGGATATGCCGCGAGCGGG 6 34 1 CGGGATATGC 0.941596 -237 AAATTCAATGCCGGAAAGCTGCGCCTCCGG 8 21 0 CCGGAAAGCT 0.720226 -40 ACATGTGTCACGGGAAATTCAGCCTAGTTG 11 44 1 CGGGAAATTC 0.919538 -150 CAGAATGGGACCGGAAAGGCAGGAGAGCTC 13 11 0 CCGGAAAGGC 0.936642 -127 ********** Masking position 5 Map Score: 3.4291 Number of sites scoring better than the average of aligned sites = 1160 Number in coding regions = 1098 Number in noncoding regions = 62 Number of orfs with sites within 600 bp upstream = 64 Fraction of orfs with sites within 600 bp upstream = 0.0102795 Motif number 10 ATTTCCAGTTAGCCTCCGCCGTTTATGCAC 1 180 1 AGCCTCCGCC 0.97649 -121 CGGGCAAGATTGCCCGCGCGAGAAATCA 5 9 0 TGCCCGCGCG 0.776282 -96 TTGATGCCTCCCTGAACGTGTCCA 5 91 0 TGCCTCCCTG 0.888351 -14 CGGAAAGCTGCGCCTCCGGCCAACAAAAC 8 10 0 CGCCTCCGGC 0.853614 -51 CCACTGACATTGCCTCCACCTTTGTGACAA 10 56 1 TGCCTCCACC 0.936765 -106 GACTCGAAGTTGCGTCCGCGAAAACGTGCG 11 98 0 TGCGTCCGCG 0.991429 -96 GGTGCGATTCTGCGTCTGCTCGCGGGAGAA 12 14 0 TGCGTCTGCT 0.898195 -66 CGTGCGATTCTGCGTCTGCTCGCCACAGAA 12 58 1 TGCGTCTGCT 0.898195 -22 GTACCGTGGCAGCGTCGCCCGGCCGGTTCG 13 42 0 AGCGTCGCCC 0.678785 -96 GCAGGTCCAATGCGTCCGTGGACACCCTAG 13 80 0 TGCGTCCGTG 0.963111 -58 ********** Masking position 3 Map Score: 3.65506 Number of sites scoring better than the average of aligned sites = 1013 Number in coding regions = 951 Number in noncoding regions = 62 Number of orfs with sites within 600 bp upstream = 68 Fraction of orfs with sites within 600 bp upstream = 0.0109219 Motif number 11 GCCGCTTATACTTGTGGCAAATGGACACGT 5 70 1 CTTGTGGCAA 0.929631 -35 CATGACCAGAGGTGTGTCAACA 7 3 0 GGTGTGTCAA 0.972538 -151 CCTTTAAAAATATGTGGCAAACAAGTGCCG 9 273 0 TATGTGGCAA 0.92739 -28 ATGTCAGTGGTGTGTGACAATAAGAGTATC 10 36 0 TGTGTGACAA 0.970419 -126 TGCCTCCACCTTTGTGACAAAGATTTATGC 10 66 1 TTTGTGACAA 0.935733 -96 GCCGCCCGGCGGTGTGTCAAGTCCCGGCGC 11 136 1 GGTGTGTCAA 0.972538 -58 ********** Masking position 5 Map Score: 2.6849 Number of sites scoring better than the average of aligned sites = 49 Number in coding regions = 44 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 12 GTTTTTTATTCTTTTTATTCACCCACATCG 1 93 1 CTTTTTATTC 0.941726 -208 AACGTATTCACTTTATATGCACTTTAAATG 1 125 1 CTTTATATGC 0.943359 -176 TTTATATGCACTTTAAATGCATATGGTTTG 1 136 1 CTTTAAATGC 0.897295 -165 CTCTCACTGAATTTTTATGCAAAATAAATG 2 235 0 ATTTTTATGC 0.925433 -66 CATTTAGTGATTTTTTATGCATATTTTGTG 3 22 1 TTTTTTATGC 0.830847 -64 AAAATCACCTCTTAAAATGCAATTTAGCAA 6 112 0 CTTAAAATGC 0.579346 -159 CTGACGATCACTTTTTATTCCGTGATCAAA 6 139 0 CTTTTTATTC 0.941726 -132 ACGTTAGTGTATTTTTATTCATAAATACTG 7 51 0 ATTTTTATTC 0.863329 -103 TATAAATTGAATTTTAATTCATTGAGGCGT 10 124 1 ATTTTAATTC 0.768174 -38 ********** Masking position 7 Map Score: 6.91514 Number of sites scoring better than the average of aligned sites = 152 Number in coding regions = 110 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 51 Fraction of orfs with sites within 600 bp upstream = 0.00819146 Motif number 13 CTCATGATCACCCTGTTACGCA 3 74 0 CATGATCACC 0.800951 -12 GGCTCCGGTACAAAAGAACCGCGCTATT 4 9 0 CAAAAGAACC 0.67939 -23 GAAGCGCGGGCAAGATTGCCCGCGCGAGAA 5 15 0 CAAGATTGCC 0.831635 -90 CAAAATCACCTAAAATCGCCCGCTCGCGGC 6 52 0 TAAAATCGCC 0.884226 -219 AAACAGATCACAAAATCACCTAAAATCGCC 6 62 0 CAAAATCACC 0.975401 -209 ATTCCGTGATCAAAATCACCTCTTAAAATG 6 123 0 CAAAATCACC 0.975401 -148 TGAAGAGATTCTAAATAGCCTTCAAGAACA 6 214 0 CTAAATAGCC 0.737466 -57 CGAGCAGACGCAGAATCGCACCGCCACGCC 12 22 1 CAGAATCGCA 0.896769 -58 CGAGCAGACGCAGAATCGCACGCCGACGGG 12 50 0 CAGAATCGCA 0.896769 -30 ********** Masking position 5 Map Score: 2.24672 Number of sites scoring better than the average of aligned sites = 1336 Number in coding regions = 1244 Number in noncoding regions = 92 Number of orfs with sites within 600 bp upstream = 92 Fraction of orfs with sites within 600 bp upstream = 0.0147767 Motif number 14 ********** No masking Map Score: 3.98147e-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 TGGCTGGCACGAACCCTGCAATCTACATTTA 1 219 1 GACCCTGCAA 0.939909 -82 AGCGACCTCTACAGTAAATAATTC 1 287 0 GACTCTACAG 0.892237 -14 CGGTACACCAAATCCCAGCAG 2 1 0 AACCCAGCAG 0.962121 -300 GGATCACTATAATGCCTGCAGATTTTACGTC 2 38 0 AAGCCTGCAG 0.918197 -263 GAGCGTAATAAAACCCACCAGCCGTAAGGTG 7 82 1 AACCCACCAG 0.962121 -72 AGATCCCTCCTGTGGCTAACGC 10 150 0 GACCCTCCTG 0.981294 -12 GAGCTCTCCTGCCTTTCCGGT 13 1 1 GACTCTCCTG 0.93468 -137 ** ******** Masking position 2 Map Score: 0.0813513 Number of sites scoring better than the average of aligned sites = 294 Number in coding regions = 269 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727