AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00950_ecoli_reg_100.orf -o00950_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 fabZ 104 (3R)-hydroxymyristol acyl carrier protein dehydratase #4 mhpA 76 3-(3-hydroxyphenyl)propionate hydroxylase #5 potF 300 periplasmic putrescine-binding protein; permease protein #6 ybjO 59 orf, hypothetical protein #7 ybjF 40 putative enzyme #8 aspC 184 aspartate aminotransferase #9 hemA 213 enzyme in alternate path of synthesis of 5-aminolevulinate #10 prfA 41 peptide chain release factor RF-1 #11 ubiX 94 3-octaprenyl-4-hydroxybenzoate carboxy-lyase #12 purF 36 amidophosphoribosyltransferase = PRPP amidotransferase #13 cvpA 165 membrane protein required for colicin V production #14 ygcA 56 putative enzyme #15 pepP 25 proline aminopeptidase P II #16 ygfB 161 orf, hypothetical protein #17 yhdT 108 orf, hypothetical protein #18 yigN 140 putative alpha helix chain #19 ubiE 94 2-octaprenyl-6-methoxy-1,4-benzoquinone --> 2-octaprenyl-3-methyl-6-methoxy-1,4-benzoquinone #20 tyrB 192 tyrosine aminotransferase, tyrosine repressible Motif number 1 ATCGTAAGAATGAGACAGGCCGTAAAGTTTGG 3 29 0 TAACAGGCCG 0.944843 -76 TTCTTACGATTGCGGCAGGCCGTGTTATTATT 3 51 1 TCGCAGGCCG 0.975367 -54 TCACGACTCGGACAAAATGTCGTTGCGCGCAC 4 46 0 GCAAATGTCG 0.815857 -31 CCAACCTGGCTACATAATGCCGCGCATGTCGC 6 26 1 TCTAATGCCG 0.859364 -34 CACACCTCTTTGTTAAATGCCGAAAAAACAGG 8 14 1 TTAAATGCCG 0.879951 -171 TTGGAGTAATTGCCGAAAGCCGTTAGATTCTG 9 104 0 TCGAAAGCCG 0.880655 -110 CGGCAATTACTCCAAAAGGGGGCGCTCTCTTT 9 121 1 TCAAAGGGGG 0.842337 -93 CCCCGAACAGGATGACAGGGCGTAAAATCGTG 13 136 1 GTACAGGGCG 0.693454 -30 ACCCATGGTCTGCGAAGGGGCGACACTATAGC 16 52 1 TCAAGGGGCG 0.902849 -110 CTGCTAAAGCGTCAAAAGGCCGGATTTTCCGG 17 13 1 GCAAAGGCCG 0.991936 -96 TCCCCAGTAATAAAAAAGGCCGGAAAATCCGG 17 32 0 TAAAAGGCCG 0.975913 -77 CTCTTCTCCTGTCTGAAGGCCGACGCGTTCGG 18 13 1 GCGAAGGCCG 0.982641 -128 TACGCAAAAATACAAAAGGCCGAACGCGTCGG 18 32 0 TCAAAGGCCG 0.99511 -109 TTTCATGCTCTTATAAAGGTCGTGCCTCTGGC 20 42 1 TAAAAGGTCG 0.849154 -151 CTCACTCTGTTGCTAATTGCCGTTCGCTCCTG 20 95 1 TCAATTGCCG 0.83851 -98 * * ******** Masking position 9 Map Score: 16.7187 Number of sites scoring better than the average of aligned sites = 585 Number in coding regions = 531 Number in noncoding regions = 54 Number of orfs with sites within 600 bp upstream = 51 Fraction of orfs with sites within 600 bp upstream = 0.00819146 Motif number 2 TGACCGCAGCCGGAAAACGGTAAAAGCACCTTT 2 59 0 CGGAAACGAA 0.852963 -196 ACGTTGCGCGTGACAAACGGTCAGAGACTAACG 2 203 0 TGAAAACGCA 0.847941 -52 TGTCAAAATATAAGAAACGACAATAATAACACG 3 71 0 TAAAAACGAA 0.959337 -34 AAATAATCTTTAAGAAAAGGTTAAAAACAGCAG 5 16 0 TAAAAAAGTA 0.571223 -285 CAAATCGACACAAGAGAAGTGAAATAATCTTTA 5 37 0 CAAAGAAGAA 0.822006 -264 TAGCTCGGATTAAAAAACGGTATTTAACAAATT 5 100 0 TAAAAACGAT 0.698978 -201 CGGCGCGGTGTAAGAAAAGAGAACTTTCTCCCG 5 194 0 TAAAAAAGAA 0.920012 -107 GAAAGATATGCAATAAACGTGCATATTTTTTAT 5 227 0 CAAAAACGCA 0.958213 -74 GAAAGTTCGTTAACAAACGAACAAAAGTTGTCA 5 264 0 TAAAAACGCA 0.934471 -37 TGCGTAAGATCAATAAAAGAGAGCGCCCCCTTT 9 135 0 CAAAAAAGAG 0.832359 -79 ATGCACCCTGTAAAAAAAGAAAATGATGTACTG 10 11 0 TAAAAAAGAA 0.920012 -31 CGCATTCTAACAGAAAAAGAAAACGTTTGCGTA 13 103 0 CAGAAAAGAA 0.878528 -63 AAACAAAAAACGTAAGGAGAGTGTT 15 4 1 CAAAAACGAG 0.91059 -22 GGCCTTCAGACAGGAGAAGAGAA 18 1 0 CAGAGAAGAA 0.643606 -140 GTGAGACTCATGACAAACGTACATCCGCCAGAG 20 67 0 TGAAAACGCA 0.847941 -126 GGTTAAAACACAATAAACCGGAAGAAGGCGAAG 20 141 0 CAAAAACCAA 0.748239 -52 *** ***** ** Masking position 7 Map Score: 10.5514 Number of sites scoring better than the average of aligned sites = 561 Number in coding regions = 433 Number in noncoding regions = 128 Number of orfs with sites within 600 bp upstream = 142 Fraction of orfs with sites within 600 bp upstream = 0.0228076 Motif number 3 AACAAAAGTTGTCACACTGAAAGATATGCA 5 248 0 GTCACACTGA 0.918543 -53 TAAATCTCCCGTTACCCTGATAGCGGACTT 8 136 1 GTTACCCTGA 0.935064 -49 TCCAAAAGGGGGCGCTCTCTTTTATTGATC 9 131 1 GGCGCTCTCT 0.608103 -83 ATTGATCTTACGCATCCTGTATGATGCAAG 9 154 1 CGCATCCTGT 0.799602 -60 AGGCGTAAATGCACCCTGTAAAAAAAGAA 10 23 0 TGCACCCTGT 0.913259 -19 GTGCCAGACCGGCACCCTCAGCGAAGGCA 11 10 0 GGCACCCTCA 0.949529 -85 GTGCCGGTCTGGCACCCTGACTTGCAACTC 11 25 1 GGCACCCTGA 0.988705 -70 AAATAGTTGCCCTGTCAGACTTGCA 11 80 0 GTTGCCCTGT 0.872939 -15 TTTACGCCCTGTCATCCTGTTCGGGGCGCA 13 132 0 GTCATCCTGT 0.925799 -34 GACAATTAAGGTCACACTGTTAAATTGAGA 14 26 1 GTCACACTGT 0.939481 -31 CGACACTATAGCTACCCTGATGAGAAGAGA 16 72 1 GCTACCCTGA 0.815865 -90 TGTCATGAGTCTCACTCTGTTGCTAATTGC 20 85 1 CTCACTCTGT 0.787204 -108 ********** Masking position 8 Map Score: 9.36045 Number of sites scoring better than the average of aligned sites = 882 Number in coding regions = 821 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 4 AAGCACCTTTATATTGTGGGAGATAGCCCTGAT 2 36 0 AATTGGGAGA 0.790922 -219 CGGCTGCGGTCAATTGTGGGACATCGCCTATAA 2 80 1 CATTGGGACA 0.990388 -175 ACACCACTGACGCTATTCGGACAGGATTAACAC 2 150 1 CCTTCGGACA 0.975098 -105 GCAACGTTACCGATGATGGAACAATAAAATCAA 2 229 1 CATTGGAACA 0.974265 -26 TTCAGTACCTCACGACTCGGACAAAATGTCGTT 4 54 0 CCGTCGGACA 0.880586 -23 CCTTCTGTAACCATAATGGAACCTCGTC 8 167 1 CATTGGAACC 0.876988 -18 ACAGGGCGTAAAATCGTGGGACACAT 13 150 1 AATTGGGACA 0.940739 -16 GGAGTTCCGTTATGGGACAATTAAGGTCA 14 7 1 CGTTGGGACA 0.974144 -50 CCACTTTGGGCCCTGGTGGACCAGAAAAGGGCT 16 104 0 CCTTGGACCA 0.926418 -58 TTTTTGTCCCTGATGGGTGAAGAAAGCGGG 17 89 0 CCTTGGGTGA 0.846387 -20 CAATCTGTTACACTTCTGGAACAATTTTTTGAT 19 58 1 CCTTGGAACA 0.983706 -37 * ** ******* Masking position 7 Map Score: 8.30184 Number of sites scoring better than the average of aligned sites = 153 Number in coding regions = 133 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 5 TCACGCGCAACGTTACCGATGATGGAACAATA 2 223 1 CTTACCGAGA 0.67694 -32 ATCTCTTTCCTTCTGAAAGTTCGTTA 5 285 0 CTTCCTTCGA 0.897375 -16 GTATAATCGTCGCCCCTGATGATGTGAAGGTC 7 14 1 CCCCCTGAGA 0.933995 -27 TTTTTTTATACCTTCCAGAGCAATCTCACGTC 8 59 1 CTTCCAGACA 0.809049 -126 CGTTGGTATTATTTCCCGCAGAC 9 201 1 ATTCCCGCGA 0.940963 -13 CCTGACTTGCAACTCCCGCCGAAATCCTGCAA 11 40 1 ACTCCCGCGA 0.929139 -55 GTAGGGATTTCCTTCCCGCGCATCAATAAAAA 13 74 0 CTTCCCGCCA 0.985697 -92 GCCACCTTCCTGCTGATTGACTGCGC 16 5 1 CTTCCTGCGA 0.985737 -157 GCTATAGTGTCGCCCCTTCGCAGACCATGGGT 16 52 0 CCCCCTTCCA 0.795033 -110 GACACTATAGCTACCCTGATGAGAAGAGACAA 16 73 1 CACCCTGAGA 0.730571 -89 GACGCAACAACTTACCCGCACAAAATAGAATT 18 109 0 CTACCCGCCA 0.91572 -32 CTCAATGCCTGCTCATCAAAAAATT 19 80 0 ATGCCTGCCA 0.734582 -15 AATTGCCGTTCGCTCCTGAACATCCACTCGAT 20 109 1 CCTCCTGACA 0.951096 -84 * ******* ** Masking position 12 Map Score: 7.12784 Number of sites scoring better than the average of aligned sites = 1377 Number in coding regions = 1268 Number in noncoding regions = 109 Number of orfs with sites within 600 bp upstream = 133 Fraction of orfs with sites within 600 bp upstream = 0.021362 Motif number 6 TCCATTTCAATTAACCGCACTGCGGATTAC 1 27 0 TTAACCGCAC 0.933289 -26 TGTCCCACAATTGACCGCAGCCGGAAAACG 2 73 0 TTGACCGCAG 0.965419 -182 CAAAATGTCGTTGCGCGCACAGTACAGCGC 4 36 0 TTGCGCGCAC 0.891241 -41 GTTGGTATTATTTCCCGCAGAC 9 202 1 TTTCCCGCAG 0.96272 -12 CCTGTCAGACTTGCAGGCAGACTTTGCAGG 11 65 0 TTGCAGGCAG 0.888914 -30 ACGCAACAACTTACCCGCACAAAATAGAAT 18 110 0 TTACCCGCAC 0.97972 -31 TTCTCCAGGTTTACGGGCAGGTGGTTAAAA 20 166 0 TTACGGGCAG 0.931972 -27 ********** Masking position 9 Map Score: 4.50034 Number of sites scoring better than the average of aligned sites = 367 Number in coding regions = 344 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 7 TTATATTGTGGGAGATAGCCCTGATATCCGTGTG 2 27 0 GAGATAGCGA 0.962986 -228 GCAAATTATAGGCGATGTCCCACAATTGACCGCA 2 84 0 GCGATGTCCA 0.796459 -171 CAGGGTTTGAGACTATAGCTCGGATTAAAAAACG 5 114 0 GCTATAGCGA 0.892192 -187 CTTGAACATAGACGATAGCGGACGGTAACGCTAG 9 57 0 GCGATAGCCG 0.923526 -157 TGGAGTAATTGCCGAAAGCCGTTAGATTCTGGCA 9 101 0 GCGAAAGCTA 0.896534 -113 GGCATAAAAAGTCGATGGCGTTGAATATTTTTTC 13 33 1 GCGATGGCGA 0.994065 -133 TGGGTCTAAAGACGAAGGCAGCGCAGTCAATCAG 16 23 0 GCGAAGGCGC 0.97053 -139 CCTGATGGGTGAAGAAAGCGGGGATTGTACCTTA 17 77 0 GAGAAAGCGA 0.95632 -32 AATACAAAAGGCCGAACGCGTCGGCCTTCAGACA 18 22 0 GCGAACGCGG 0.932869 -119 CAGATTGGGCGTCGATGCCCTAGATTTCTACCCG 19 31 0 GCGATGCCGA 0.955925 -64 CAATAAACCGGAAGAAGGCGAAGATCGAGTGGAT 20 130 0 GAGAAGGCGA 0.972156 -63 * ******* ** Masking position 5 Map Score: 7.62952 Number of sites scoring better than the average of aligned sites = 1264 Number in coding regions = 1234 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 8 ACAATATAAAGGTGCTTTTACCGTTTTCCG 2 52 1 GGTGCTTTTA 0.832044 -203 TTACATGTTTTTAACAAAATAAG 4 4 1 CATGTTTTTA 0.914991 -73 ATTATCTGCTGTTTTTAACCTTTTCTT 5 8 1 GCTGTTTTTA 0.954847 -293 TTATTCTTGCGATGCTTTTATATAGCGAGC 5 155 1 GATGCTTTTA 0.916646 -146 GGACCAAAGTCCTGTTTTTTCGGCATTTAA 8 26 0 CCTGTTTTTT 0.914105 -159 GGACTTTGGTCCTGTTTTTTTTATACCTTC 8 44 1 CCTGTTTTTT 0.914105 -141 GAAAACGCAGGCTGTTTTTGCAAGACGTGA 8 84 0 GCTGTTTTTG 0.885483 -101 TCAATAAGTTGATGTTCTTTCATGCTCTTA 20 25 1 GATGTTCTTT 0.802461 -168 GATGTTCTTTCATGCTCTTATAAAGGTCGT 20 35 1 CATGCTCTTA 0.812722 -158 ********** Masking position 6 Map Score: 3.46612 Number of sites scoring better than the average of aligned sites = 423 Number in coding regions = 328 Number in noncoding regions = 95 Number of orfs with sites within 600 bp upstream = 113 Fraction of orfs with sites within 600 bp upstream = 0.0181497 Motif number 9 TACGATTGCGGCAGGCCGTGTTATTATTGT 3 55 1 GCAGGCCGTG 0.934553 -50 CTTTTATATAGCGAGCAGTGCTGGCCGGGA 5 169 1 GCGAGCAGTG 0.929863 -132 GTCTGCGGGAAATAATACCAACGT 9 200 0 GCGGGAAATA 0.85604 -14 CAGGATTTCGGCGGGAGTTGCAAGTCAGGG 11 39 0 GCGGGAGTTG 0.942479 -56 CTTTGCGGCATCGGGCAATGCGT 13 4 0 TCGGGCAATG 0.924707 -162 GGTGAAGAAAGCGGGGATTGTACCTTATGG 17 74 0 GCGGGGATTG 0.968978 -35 GTAGCGCCTCGCAGGAAATGCCTTTCCAAC 18 61 1 GCAGGAAATG 0.95416 -80 TTTTTGATGAGCAGGCATTGAG 19 83 1 GCAGGCATTG 0.977267 -12 ********** Masking position 9 Map Score: 3.53311 Number of sites scoring better than the average of aligned sites = 1182 Number in coding regions = 1134 Number in noncoding regions = 48 Number of orfs with sites within 600 bp upstream = 52 Fraction of orfs with sites within 600 bp upstream = 0.00835207 Motif number 10 AACGAACTTTCAGAAGGAAAGAGAT 5 286 1 CAGAGGAAAG 0.990882 -15 ATAAAAAAAACAGGACCAAAGTCCTGTTTTT 8 37 0 CAGACCAAAG 0.928688 -148 ATTATGGTTACAGAAGGGAAGTCCGCTATCA 8 153 0 CAGAGGGAAG 0.989022 -32 CGCAGTCAATCAGCAGGAAGGTGGC 16 5 0 CAGAGGAAGG 0.97545 -157 TACAAACGTCCAGTTGGAAAGGCATTTCCTG 18 72 0 CAGTGGAAAG 0.96404 -69 AGTGGATGTTCAGGAGCGAACGGCAATTAGC 20 106 0 CAGAGCGAAC 0.915229 -87 *** ******* Masking position 9 Map Score: 2.16602 Number of sites scoring better than the average of aligned sites = 121 Number in coding regions = 109 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 11 TAGAGCAAATATGCATAAAAATTTGTTAAAT 5 81 1 ATGATAAAAA 0.928791 -220 TTGCTCTGGAAGGTATAAAAAAAACAGGACC 8 51 0 AGGATAAAAA 0.974748 -134 GATGCCGCAAAGGCATAAAAAGTCGATGGCG 13 22 1 AGGATAAAAA 0.974748 -144 CTTCCCGCGCATCAATAAAAATGGCGCTGAA 13 64 0 ATCATAAAAA 0.787432 -102 GTCGATCCCCAGTAATAAAAAAGGCCGGAAA 17 38 0 AGTATAAAAA 0.880906 -71 TTCACCCATCAGGGACAAAAA 17 98 1 AGGACAAAAA 0.933836 -11 *** ******* Masking position 5 Map Score: 1.83467 Number of sites scoring better than the average of aligned sites = 52 Number in coding regions = 33 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 12 ACTGACGCTATTCGGACAGGATTAACACTA 2 155 1 TTCGGACAGG 0.949318 -100 GTTTCTTATATTTTGACAGGAAGAGTATC 3 86 1 TTTTGACAGG 0.963561 -19 CAAGAATAACTTTAGCCAGGGTTTGAGACT 5 134 0 TTTAGCCAGG 0.971222 -167 CGCGGCATTATGTAGCCAGGTTGGCAAATT 6 20 0 TGTAGCCAGG 0.899639 -40 TCATTTTCTTTTTTTACAGGGTGCATTTAC 10 18 1 TTTTTACAGG 0.74702 -24 CTGCCTGCAAGTCTGACAGGGCAACTATTT 11 75 1 GTCTGACAGG 0.894531 -20 CGCGTCGGCCTTCAGACAGGAGAAGAGAA 18 10 0 TTCAGACAGG 0.976515 -131 TTGGGAGTAGTTAAGCCGGGTAGAAATCTA 19 15 1 TTAAGCCGGG 0.731512 -80 ********** Masking position 7 Map Score: 3.50567 Number of sites scoring better than the average of aligned sites = 298 Number in coding regions = 259 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 54 Fraction of orfs with sites within 600 bp upstream = 0.00867331 Motif number 13 CCTAACACCACTGACGCTATTCGGACAGGA 2 146 1 CTGACGCTAT 0.757317 -109 ATAACACGGCCTGCCGCAATCGTAAGAATG 3 49 0 CTGCCGCAAT 0.97411 -56 TGGCTACATAATGCCGCGCATGTCGCGGCA 6 32 1 ATGCCGCGCA 0.919306 -28 GAAAACAATGCCGCGACATGCGCGGCA 6 43 0 ATGCCGCGAC 0.975586 -17 TCTTTGTTAAATGCCGAAAAAACAGGACTT 8 20 1 ATGCCGAAAA 0.852782 -165 GCATTGCCCGATGCCGCAAAGGCATAAAAA 13 13 1 ATGCCGCAAA 0.978094 -153 AACGCCTCCTGACGCAACAACTTACCCG 18 123 0 CTGACGCAAC 0.940764 -18 ********** Masking position 2 Map Score: 2.07243 Number of sites scoring better than the average of aligned sites = 845 Number in coding regions = 799 Number in noncoding regions = 46 Number of orfs with sites within 600 bp upstream = 59 Fraction of orfs with sites within 600 bp upstream = 0.00947639 Motif number 14 TCATCGGTAACGTTGCGCGTGACAAACGGT 2 215 0 CGTTGCGCGT 0.986395 -40 GACAAAATGTCGTTGCGCGCACAGTACAGC 4 38 0 CGTTGCGCGC 0.970295 -39 TGTGTATAATCGTCGCCCCTGATGATGTGA 7 11 1 CGTCGCCCCT 0.991066 -30 GTAGCTATAGTGTCGCCCCTTCGCAGACCA 16 57 0 TGTCGCCCCT 0.95545 -105 TGTATTTTTGCGTAGCGCCTCGCAGGAAAT 18 50 1 CGTAGCGCCT 0.983513 -91 ********** Masking position 3 Map Score: 1.91572 Number of sites scoring better than the average of aligned sites = 133 Number in coding regions = 125 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 15 ATATTCCCCAAATCGACACACGGATATC 2 7 1 CCCAAACGCA 0.973173 -248 CGTTGCGCGTGACAAACGGTCAGAGACTAACG 2 203 0 GACAAAGGCA 0.874233 -52 ATGTGATAAAGCCAAATCGACACAAGAGAAGT 5 50 0 GCCAAACGCA 0.993719 -251 GCATTATGTAGCCAGGTTGGCAAATTTTAGTG 6 14 0 GCCAGGTGCA 0.901865 -46 AAGTCAGGGTGCCAGACCGGCACCCTCAGCGA 11 16 0 GCCAGACGCA 0.992433 -79 GACTGCTAAAGCGTCAAAAGGCCGGA 17 5 1 GCTAAACGCA 0.960746 -104 ****** ** ** Masking position 4 Map Score: 0.520676 Number of sites scoring better than the average of aligned sites = 499 Number in coding regions = 476 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542