AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00150_ecoli_reg_100.orf -o00150_ecoli_100.ace -a/home/amcguire/alignace/lib/ORF_ecoli.txt -z/skink1/amcguire/genomes/ecoli.fna -g0.51 -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 = 0.51 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 surA 52 survival protein #2 imp 254 organic solvent tolerance #3 mhpA 76 3-(3-hydroxyphenyl)propionate hydroxylase #4 potF 300 periplasmic putrescine-binding protein; permease protein #5 ybjO 59 orf, hypothetical protein #6 ybjF 40 putative enzyme #7 ygcA 56 putative enzyme #8 pepP 25 proline aminopeptidase P II #9 ygfB 161 orf, hypothetical protein #10 yhdT 108 orf, hypothetical protein #11 aslA 300 arylsulfatase #12 yigN 140 putative alpha helix chain #13 ubiE 94 2-octaprenyl-6-methoxy-1,4-benzoquinone --> 2-octaprenyl-3-methyl-6-methoxy-1,4-benzoquinone Motif number 1 CATACCTGTCATTCAATGCCGTGCCTAACAC 2 123 1 ATTAATGCCG 0.963753 -132 CACGACTCGGACAAAATGTCGTTGCGCGCAC 3 46 0 ACAAATGTCG 0.947959 -31 CAACCTGGCTACATAATGCCGCGCATGTCGC 5 27 1 ACAAATGCCG 0.994647 -33 GAAAACAATGCCGCGACATGCGC 5 47 0 AAAAATGCCG 0.980653 -13 TGCTAAAGCGTCAAAAGGCCGGATTTTCCGG 10 14 1 TCAAAGGCCG 0.986944 -95 CCCCAGTAATAAAAAAGGCCGGAAAATCCGG 10 32 0 AAAAAGGCCG 0.984907 -77 TAACACATATATTAATTGCCGTTAAAACTAA 11 53 1 ATTATTGCCG 0.807377 -248 TCTTCTCCTGTCTGAAGGCCGACGCGTTCGG 12 14 1 TCTAAGGCCG 0.975402 -127 ACGCAAAAATACAAAAGGCCGAACGCGTCGG 12 32 0 ACAAAGGCCG 0.995837 -109 *** ******* Masking position 5 Map Score: 14.4601 Number of sites scoring better than the average of aligned sites = 287 Number in coding regions = 246 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 2 GTCAATTGTGGGACATCGCCTATAATTTGC 2 88 1 GGACATCGCC 0.911708 -167 CTGTCATTCAATGCCGTGCCTAACACCACT 2 128 1 ATGCCGTGCC 0.864388 -127 TGCGCGCACAGTACAGCGCAACTTATTTTG 3 25 0 GTACAGCGCA 0.913311 -52 TGTACTGTGCGCGCAACGACATTTTGTCCG 3 40 1 GCGCAACGAC 0.75838 -37 CGCTATATAAAAGCATCGCAAGAATAACTT 4 152 0 AAGCATCGCA 0.804343 -149 CTCTTTTCTTACACCGCGCCGATAAAAAAT 4 206 1 ACACCGCGCC 0.960314 -95 TGGCTACATAATGCCGCGCATGTCGCGGCA 5 32 1 ATGCCGCGCA 0.977029 -28 GAAAACAATGCCGCGACATGCGCGGCA 5 43 0 ATGCCGCGAC 0.952467 -17 CTAAAGACGAAGGCAGCGCAGTCAATCAGC 9 22 0 AGGCAGCGCA 0.974537 -140 TTTTTGCGTAGCGCCTCGCAGGAAATGCCT 12 54 1 GCGCCTCGCA 0.967121 -87 TAGAAATCTAGGGCATCGACGCCCAATCTG 13 35 1 GGGCATCGAC 0.911709 -60 ********** Masking position 4 Map Score: 7.88842 Number of sites scoring better than the average of aligned sites = 4078 Number in coding regions = 3891 Number in noncoding regions = 187 Number of orfs with sites within 600 bp upstream = 178 Fraction of orfs with sites within 600 bp upstream = 0.0285898 Motif number 3 CCTGATATCCGTGTGTCGATTTGGGGAATAT 2 7 0 GTGTCTTGGG 0.992708 -248 TGCTTTTACCGTTTTCCGGCTGCGGTCAATTGTGG 2 64 1 GTTTCTGCGG 0.851122 -191 GTTGATTTTATTGTTCCATCATCGGTAACGTTGCG 2 228 0 TTGTCATCGG 0.944902 -27 TTCACTTCTCTTGTGTCGATTTGGCTTTATCACAT 4 47 1 TTGTCTTGGC 0.962965 -254 GGAGTTCCGTTATGGGACAATTAAGG 7 2 1 GAGTCATGGG 0.896625 -55 GGTAGCTATAGTGTCGCCCCTTCGCAGACCATGGG 9 53 0 GTGTCTTCGC 0.948445 -109 AAAGCGGGGATTGTACCTTATGGGGGTTGTCGATC 10 62 0 TTGTCTGGGG 0.989303 -47 TTTTTGTCCCTGATGGGTGAAGAAAGCG 10 91 0 TTGTCTGGGT 0.911721 -18 TGCGGGTAAGTTGTTGCGTCAGGAGGCGTT 12 121 1 TTGTCAGGAG 0.785349 -20 TGTTCCAGAAGTGTAACAGATTGGGCGTCGATGCC 13 46 0 GTGTCTTGGG 0.992708 -49 **** * ***** Masking position 4 Map Score: 7.48209 Number of sites scoring better than the average of aligned sites = 262 Number in coding regions = 235 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 4 TAATCGTCGCCCCTGATGATGTGAAGGTCA 6 17 1 CCCTGATGAT 0.948829 -24 GGAGTTCCGTTATGGGACAATTAAGG 7 7 1 CCGTTATGGG 0.951201 -50 ACTATAGCTACCCTGATGAGAAGAGACAAG 9 76 1 CCCTGATGAG 0.991411 -86 CCACTTTGGGCCCTGGTGGACCAGAAAAGG 9 107 0 CCCTGGTGGA 0.954357 -55 CGGGGATTGTACCTTATGGGGGTTGTCGAT 10 63 0 ACCTTATGGG 0.905969 -46 TTTTTGTCCCTGATGGGTGAAGAAAGC 10 92 0 CCCTGATGGG 0.985775 -17 AGATCCCTCTCCCTGACAGGATGATTACAT 11 223 0 CCCTGACAGG 0.945737 -78 ********** Masking position 4 Map Score: 6.26579 Number of sites scoring better than the average of aligned sites = 308 Number in coding regions = 282 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 5 TTGAGACTATAGCTCGGATTAAAAAACGGT 4 112 0 AGCTCGGATT 0.92303 -189 GAATAACTTTAGCCAGGGTTTGAGACTATA 4 131 0 AGCCAGGGTT 0.959544 -170 GGCATTATGTAGCCAGGTTGGCAAATTTTA 5 17 0 AGCCAGGTTG 0.952171 -43 TCGTCGTCAAAGGGAGGAATATTCATGATA 9 142 0 AGGGAGGAAT 0.875523 -20 AAGCGTCAAAAGGCCGGATTTTCCGGCCTT 10 19 1 AGGCCGGATT 0.972519 -90 GGGTGAAGAAAGCGGGGATTGTACCTTATG 10 75 0 AGCGGGGATT 0.948855 -34 TTGATATGTAAGGCAGGTTTATTATATCGC 11 104 0 AGGCAGGTTT 0.970483 -197 ACTGCGCCAGAGGTAGGATTGAAAACGCTC 11 133 1 AGGTAGGATT 0.93502 -168 GGAGTAGTTAAGCCGGGTAGAAATCTAGGG 13 18 1 AGCCGGGTAG 0.808916 -77 ********** Masking position 1 Map Score: 6.05274 Number of sites scoring better than the average of aligned sites = 448 Number in coding regions = 388 Number in noncoding regions = 60 Number of orfs with sites within 600 bp upstream = 66 Fraction of orfs with sites within 600 bp upstream = 0.0106007 Motif number 6 AAAGATTATTTCACTTCTCTTGTGTCGATTT 4 38 1 TCACTTCTCT 0.963804 -263 GGGAGAAAGTTCTCTTTTCTTACACCGCGCC 4 195 1 TCTCTTTTCT 0.985641 -106 ATCTCTTTCCTTCTGAAAGTTC 4 289 0 TCTCTTTCCT 0.968673 -12 AACACTCTCCTTACGTTTTTTGTTT 8 10 0 TCTCCTTACT 0.884104 -16 AAAGGGCTTGTCTCTTCTCATCAGGGTAGCT 9 81 0 TCTCTTCTCT 0.99082 -81 TTCTCTTCTCCTGTCTGAAGGC 12 2 1 TCTCTTCTCT 0.99082 -139 ********* * Masking position 6 Map Score: 5.68361 Number of sites scoring better than the average of aligned sites = 43 Number in coding regions = 26 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 7 AGAGATGACGAGTACGTTAGTCTCTGACCGT 2 189 1 AGACGTTAGT 0.893099 -66 CGTTAGTCTCTGACCGTTTGTCACGCGCAAC 2 203 1 TGCCGTTTGT 0.980466 -52 ATAAAAAATATGCACGTTTATTGCATATCTT 4 227 1 TGACGTTTAT 0.945165 -74 TGACAACTTTTGTTCGTTTGTTAACGAACTT 4 264 1 TGTCGTTTGT 0.971318 -37 TCTTTCCTTCTGAAAGTTCGTTAACAAACGA 4 277 0 TGAAGTTCGT 0.885901 -24 CCTTTCCAACTGGACGTTTGTACAGCACAAT 12 81 1 TGACGTTTGT 0.991105 -60 ** ******** Masking position 7 Map Score: 2.20857 Number of sites scoring better than the average of aligned sites = 65 Number in coding regions = 56 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 8 TAATTTGCATTATCATACCTGTCATTCAATGCC 2 110 1 TCATACCTGC 0.919475 -145 TCTACGCTAGTGTTAATCCTGTCCGAATAGCGT 2 159 0 TTAATCCTGC 0.975711 -96 AAATACCGTTTTTTAATCCGAGCTATAGTCTCA 4 108 1 TTAATCCGAC 0.838786 -193 ACACTAAAATTTGCCAACCTGGCTACATAATGC 5 13 1 TCCAACCTGC 0.984241 -47 CAACGCGATATAATAAACCTGCCTTACATATCA 11 100 1 TTAAACCTGC 0.975711 -201 AGGAGAGCGTTTTCAATCCTACCTCTGGCGCAG 11 134 0 TCAATCCTAC 0.935789 -167 ATTATTTATGTAATCATCCTGTCAGGGAGAGGG 11 216 1 TTCATCCTGC 0.975232 -85 AGGAAATGCCTTTCCAACTGGACGTTTGTACAG 12 73 1 TCCAACTGGC 0.79795 -68 * ******** * Masking position 1 Map Score: 2.97645 Number of sites scoring better than the average of aligned sites = 338 Number in coding regions = 303 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 9 ATATTCCCCAAATCGACACACGGATAT 2 8 1 CCAAATCGAC 0.977014 -247 CAGAGACTAACGTACTCGTCATCTCTACGC 2 185 0 CGTACTCGTC 0.918829 -70 TGTGATAAAGCCAAATCGACACAAGAGAAG 4 51 0 CCAAATCGAC 0.977014 -250 GACTGCTAAAGCGTCAAAAGGCCGG 10 6 1 CTAAAGCGTC 0.898674 -103 TACAAAAGGCCGAACGCGTCGGCCTTCAGA 12 24 0 CGAACGCGTC 0.974385 -117 AAATGCCTTTCCAACTGGACGTTTGTACAG 12 76 1 CCAACTGGAC 0.938742 -65 ********** Masking position 4 Map Score: 1.84019 Number of sites scoring better than the average of aligned sites = 203 Number in coding regions = 190 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 10 TTTGCATTATCATACCTGTCATTCAATGCC 2 113 1 CATACCTGTC 0.90283 -142 ACGCTAGTGTTAATCCTGTCCGAATAGCGT 2 159 0 TAATCCTGTC 0.92586 -96 CTAAAATTTGCCAACCTGGCTACATAATGC 5 16 1 CCAACCTGGC 0.958632 -44 GCCACCTTCCTGCTGATTGACTGC 9 5 1 CCTTCCTGCT 0.72672 -157 ATATCATGAATATTCCTCCCTTTGACGACG 9 141 1 TATTCCTCCC 0.842916 -21 CCATAAGGTACAATCCCCGCTTTCTTCACC 10 74 1 CAATCCCCGC 0.803969 -35 CGCGATATAATAAACCTGCCTTACATATCA 11 103 1 TAAACCTGCC 0.946286 -198 AGAGCGTTTTCAATCCTACCTCTGGCGCAG 11 134 0 CAATCCTACC 0.821208 -167 ATTTATGTAATCATCCTGTCAGGGAGAGGG 11 219 1 TCATCCTGTC 0.931175 -82 GCCCTAGATTTCTACCCGGCTTAACTACTC 13 19 0 TCTACCCGGC 0.810168 -76 ********** Masking position 5 Map Score: 2.50849 Number of sites scoring better than the average of aligned sites = 1999 Number in coding regions = 1842 Number in noncoding regions = 157 Number of orfs with sites within 600 bp upstream = 158 Fraction of orfs with sites within 600 bp upstream = 0.0253774 Motif number 11 ATTTACCACGTAATCCGCAGTGCGGTTAAT 1 18 1 TAATCCGCAG 0.893533 -35 GAAAAGGTTAAAAACAGCAGATAAT 4 6 0 AAAACAGCAG 0.97621 -295 GCAGCGCAGTCAATCAGCAGGAAGGTGGC 9 10 0 CAATCAGCAG 0.971444 -152 GTTAAAACTAAAAACAGCATCAATAATCAA 11 73 1 AAAACAGCAT 0.841835 -228 ATGAATTGGAAAATCAGGAGAGCGTTTTCA 11 152 0 AAATCAGGAG 0.959988 -149 TTGATGACATGAAACCGGAGCATTTTGC 11 283 1 GAAACCGGAG 0.924988 -18 CGTCGGCCTTCAGACAGGAGAAGAGAA 12 8 0 CAGACAGGAG 0.912103 -133 ********** Masking position 2 Map Score: 2.01458 Number of sites scoring better than the average of aligned sites = 649 Number in coding regions = 593 Number in noncoding regions = 56 Number of orfs with sites within 600 bp upstream = 63 Fraction of orfs with sites within 600 bp upstream = 0.0101189 Motif number 12 CACTAGCGTAGAGATGACGAGTACGTTAGT 2 180 1 GAGATGACGA 0.89625 -75 CACATCATCAGGGGCGACGATTATACACA 6 10 0 GGGGCGACGA 0.993655 -31 ATTCCTCCCTTTGACGACGA 9 152 1 TTGACGACGA 0.879841 -10 TACCTTATGGGGGTTGTCGATCCCCAGTAA 10 54 0 GGGTTGTCGA 0.931912 -55 TTGTCCCTGATGGGTGAAGAAAGCGGGGAT 10 86 0 TGGGTGAAGA 0.909055 -23 TGTAACAGATTGGGCGTCGATGCCCTAGAT 13 40 0 TGGGCGTCGA 0.977574 -55 ********** Masking position 10 Map Score: 0.533098 Number of sites scoring better than the average of aligned sites = 435 Number in coding regions = 419 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 13 ********** No masking Map Score: 2.43208e-15 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: 2.43208e-15 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 ********** No masking Map Score: 2.43208e-15 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