AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i216_ecoli_bsub_300.orf -o216_ecoli_bsub_300.ace -a/home/amcguire/alignace/lib/ORF_ecoli.txt -z/skink1/amcguire/genomes/ecoli.fna -g0.47 -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 = 0.47 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 rpsB 300 30S ribosomal subunit protein S2 #2 tsf 257 protein chain elongation factor EF-Ts #3 pyrH 146 uridylate kinase #4 frr 291 ribosome releasing factor #5 yaeM 91 putative ATP-binding component of a transport system #6 yaeS 185 orf, hypothetical protein #7 cdsA 120 CDP-diglyceride synthetase #8 yaeT 29 orf, hypothetical protein #9 hlpA 121 histone-like protein, located in outer membrane or nucleoid #10 fabZ 104 (3R)-hydroxymyristol acyl carrier protein dehydratase #11 rplS 41 50S ribosomal subunit protein L19 #12 trmD 30 tRNA methyltransferase; tRNA (guanine-7-)-methyltransferase #13 rpsP 248 30S ribosomal subunit protein S16 #14 ffh 91 GTP-binding export factor binds to signal sequence, GTP and RNA #15 ylxM 176 similar to hypothetical proteins #16 rpsP 105 ribosomal protein S16 (BS17) #17 ylqD 121 ylqD #18 rplS 130 ribosomal protein L19 #19 ylqF 142 similar to hypothetical proteins #20 rnh 70 ribonuclease H Motif number 1 CGACCCCAAAGGGCACCCCGGAATATGTGCCG 1 225 0 GGCCCCCGGA 0.813831 -76 GAATTCTCGAGCTTGCCGCCTTTCTGCAACTC 2 41 0 GCTCCGCCTT 0.701795 -217 ATCTTCGCTCGCTCATCCCGGTCACTTACTGA 2 86 0 GCCTCCCGGT 0.981359 -172 GTCTATAAGGGCTCTCCCCCTTCATATTTCGC 2 132 0 GCCCCCCCTT 0.988905 -126 GGGGCCATATGCAGGCCCCCTAACCAAACGTG 2 173 0 GCGCCCCCTA 0.776638 -85 TCGGAGATGTGATCTGCCCGGCATTAAACCGC 2 226 0 GACGCCCGGC 0.763724 -32 CGGTTGCTGCGCGCTGGCCGTGACCAAACTGC 4 94 0 GCCGGCCGTG 0.8069 -198 ACGTACTTTTGTACGCTCCGGTTGCTGCGCGC 4 112 0 GTCCTCCGGT 0.924169 -180 AGGATGGCGAGCACTGCCCGGGGCCAAAATGG 4 145 1 GCCGCCCGGG 0.962086 -147 TTGCGGATCGGCTGGCGGCGTTTTGCTTTTTA 5 46 1 GCGCGGCGTT 0.835213 -46 CGTTGTTTCTGTTGCCGCCGGTGGGGTTCGCC 7 78 1 GTGCGCCGGT 0.802394 -43 GCAGTTCTTTGCGTGGCCCGGCGATCTTATAT 9 64 0 GCTGCCCGGC 0.73852 -58 GCAAAGAACTGCACCCTCCGGTGCAAATGGGA 9 84 1 GCCCTCCGGT 0.989823 -38 AGGATGACGAGCACATCCCGGTGCCAAAATGG 13 28 0 GCCTCCCGGT 0.981359 -221 CGTACTGCGTGTACGCTCCGGTGACTGCGCGC 13 62 1 GTCCTCCGGT 0.924169 -187 CGGTGACTGCGCGCACTCCGGCACCAAACTGG 13 80 1 GCCCTCCGGC 0.970638 -169 GCTGTAAAAGGCCGTCGGCGGTGCAGCCAGTT 13 106 0 GCGCGGCGGT 0.906327 -143 TTGAGCTCTCCCCTTTGTTAAGTCAA 15 161 0 GCCCCCCTTT 0.953243 -16 GGAGGTGCCGGCCCTCTCCCTT 17 1 0 GCCCTCCCTT 0.956509 -121 GAGAGGGCCGGCACCTCCCCTTTTTTTACACG 17 15 1 GCCTCCCCTT 0.922507 -107 CGCACCAAGCTCCCCGCTTTTAAAACTTTT 17 102 0 GCCCCGCTTT 0.860244 -20 GTGACACGAACACCGCCTTTATCTTCAGT 19 124 0 GACCCGCCTT 0.701795 -19 ** * ******* Masking position 9 Map Score: 25.4561 Number of sites scoring better than the average of aligned sites = 2165 Number in coding regions = 2026 Number in noncoding regions = 139 Number of orfs with sites within 600 bp upstream = 125 Fraction of orfs with sites within 600 bp upstream = 0.0200771 Motif number 2 ACAGCATCAGACGTCGAATTTTCTATTATAGA 1 63 0 ACGCGATTTT 0.739284 -238 ATTGGTGTCCACGACGTATTTGTGGTATAAAG 1 112 1 ACGCGTTTTG 0.960221 -189 TTCATATTTCGCGCCGCAGATGCGTTATCTTC 2 112 0 GCGCGCGATG 0.78775 -146 CCGCCCTCAGGCGGCTCCTTTTTGATAA 3 7 0 GCGCTCTTTT 0.9367 -140 CCGCCTGAGGGCGGCTTCTTTTTGTGCCCATC 3 25 1 GCGCTTTTTT 0.947334 -122 GCGACATTGTACGTCGCTTTTCAGCGCAGCCC 3 81 0 ACGCGCTTTC 0.893384 -66 GATCTACTGAGCGGCGTTTTTGTCGTTCAAGA 5 13 0 GCGCGTTTTG 0.988232 -79 GGATCGGCTGGCGGCGTTTTGCTTTTTATTCT 5 50 1 GCGCGTTTGC 0.848233 -42 GTGGTTTTACACGGCTTTTTTTTGTATAGGCT 6 118 1 ACGCTTTTTT 0.837937 -68 TGGGGGTCGCTTTTGCTGAAGTATC 7 4 1 GGGCGCTTTG 0.870871 -117 CGTCGTCATCGCGGCGTTGTTTCTGTTGCCGC 7 64 1 GCGCGTGTTT 0.969316 -57 AGCGCCGTCTTTTACCGTTTATC 12 18 0 GCGCGTTTTT 0.984271 -13 TAACATGAAGGCGTCTTTGTTGTT 14 3 0 GCGCTTGTTG 0.924162 -89 *** *** **** Masking position 5 Map Score: 13.9215 Number of sites scoring better than the average of aligned sites = 1120 Number in coding regions = 1012 Number in noncoding regions = 108 Number of orfs with sites within 600 bp upstream = 113 Fraction of orfs with sites within 600 bp upstream = 0.0181497 Motif number 3 TCAGAATGATTCTCAATTTGCCCG 1 2 0 TCTCATTCCC 0.942381 -299 TGAGAATCATTCTGAATTTCGCCAAACGTGCCA 1 20 1 TCTGATTGCC 0.864026 -281 TATATAAAAGTTGGGGTTATGCCTCCACGTATC 1 266 0 TTGGGTTGCC 0.877435 -35 GCTATTTTATTTGCCATTTTGGCCCCGGGCAGT 4 157 0 TTGCATTGGC 0.95296 -135 CGCGGCGTTGTTTCTGTTGCCGCCGGTGGGGTT 7 73 1 TTTCGTTCGC 0.924126 -48 TGTCTCATTCTTACGATTGCGGCAGGCCGTGTT 10 44 1 TTACATTGGC 0.846778 -61 GCCCCCGAGATATCAGTTTACCCAGGATAAGAG 11 11 1 TATCGTTCCC 0.878087 -31 CCTGGCTTGTTTGCCATTTTGGCACCGGGATGT 13 15 1 TTGCATTGGC 0.95296 -234 CAACTGTTGATTGCAATTCCCGCAAAAATGAGT 13 146 1 TTGCATTCGC 0.931719 -103 CGACACATCATCAGTATTTTGCCGCAGTATAAC 14 31 0 TCAGATTGCC 0.638515 -61 TGATGATGTGTCGCGATTGCGGCCAACCGTTTC 14 51 1 TCGCATTGGC 0.943394 -41 CCTAAGCTTCTATCAGTTTACCCTTTTTTTGCG 17 45 0 TATCGTTCCC 0.878087 -77 CGTCCAGGCTTTTCTATTTTGCCTAAGCTTCTA 17 66 0 TTTCATTGCC 0.967231 -56 TTACTGTATGTATCGGTTCAGCCAAGAAAAAAT 20 35 0 TATCGTTGCC 0.914481 -36 TTTCTCTTCTCCCTTACTGTATG 20 58 0 TTTCCTTCCC 0.805679 -13 **** *** *** Masking position 7 Map Score: 12.8457 Number of sites scoring better than the average of aligned sites = 763 Number in coding regions = 700 Number in noncoding regions = 63 Number of orfs with sites within 600 bp upstream = 69 Fraction of orfs with sites within 600 bp upstream = 0.0110826 Motif number 4 CGAAATGGATCGGAAGTCCGGCGCGCTTTA 1 139 0 CGGAAGTCCG 0.819712 -162 TCGTATACACAGACTGGACGGAAGCGACAA 1 166 1 AGACTGGACG 0.877609 -135 TTCGAGTTGCAGAAAGGCGGCAAGCTCGAG 2 38 1 AGAAAGGCGG 0.758115 -220 CCTTGCGGATCGGCTGGCGGCGTTTTGCTT 5 44 1 CGGCTGGCGG 0.96751 -48 CGTAAGAATGAGACAGGCCGTAAAGTTTGG 10 29 0 AGACAGGCCG 0.978693 -76 CTTACGATTGCGGCAGGCCGTGTTATTATT 10 53 1 CGGCAGGCCG 0.687565 -52 ATGGCAAACAAGCCAGGCCGA 13 2 0 AGCCAGGCCG 0.986244 -247 CTGCTGTAAAAGGCCGTCGGCGGTGCAGCC 13 110 0 AGGCCGTCGG 0.80584 -139 GGGGTGGAAACGGTTGGCCGCAATCGCGAC 14 60 0 CGGTTGGCCG 0.910149 -32 AAAATAGAAAAGCCTGGACGAGTAAAAGTT 17 79 1 AGCCTGGACG 0.918532 -43 TATTTTACGATGCCTGTCCGGCATTTTCAA 19 67 0 TGCCTGTCCG 0.790054 -76 ********** Masking position 6 Map Score: 9.37429 Number of sites scoring better than the average of aligned sites = 1632 Number in coding regions = 1557 Number in noncoding regions = 75 Number of orfs with sites within 600 bp upstream = 68 Fraction of orfs with sites within 600 bp upstream = 0.0109219 Motif number 5 TTGTGGTATAAAGCGCGCCGGACTTCCGAT 1 131 1 AAGCGCGCCG 0.984994 -170 GGGAATTCTCGAGCTTGCCGCCTTTCTGCA 2 45 0 GAGCTTGCCG 0.930709 -213 TTACTGATGTAAGCTCCCGGGAATTCTCGA 2 63 0 AAGCTCCCGG 0.772081 -195 TGGTCACGGCCAGCGCGCAGCAACCGGAGC 4 100 1 CAGCGCGCAG 0.833794 -192 CTTACGATCAGATGGCGCAGACTATATCAC 6 60 0 GATGGCGCAG 0.6673 -126 CGATCAATATAAGATCGCCGGGCCACGCAA 9 58 1 AAGATCGCCG 0.830705 -64 ATTTGCACCGGAGGGTGCAGTTCTTTGCGT 9 82 0 GAGGGTGCAG 0.8631 -40 TGGTGCCGGAGTGCGCGCAGTCACCGGAGC 13 76 0 GTGCGCGCAG 0.877527 -173 CGCACCAAGCTCCCCGCTTTTAAAAC 17 106 0 AAGCTCCCCG 0.92262 -16 CATCGTTTTCAAGCTTGCAGCGGATAAGCC 18 65 0 AAGCTTGCAG 0.919637 -66 AGGCGCGCAGAAATGCGGGT 20 1 1 AGGCGCGCAG 0.890233 -70 ********** Masking position 8 Map Score: 7.55413 Number of sites scoring better than the average of aligned sites = 1556 Number in coding regions = 1491 Number in noncoding regions = 65 Number of orfs with sites within 600 bp upstream = 71 Fraction of orfs with sites within 600 bp upstream = 0.0114038 Motif number 6 TGGTCTATAAGGGCTCTCCCCCTTCATATT 2 136 0 GGGCTCTCCC 0.968506 -122 GCCCCGGGCAGTGCTCGCCATCCTCACGTA 4 139 0 GTGCTCGCCA 0.992013 -153 GCCGCCGGTGGGGTTCGCCATTGTAACGCT 7 91 1 GGGTTCGCCA 0.980538 -30 GTGTTCTCCACAAAGGAATG 9 1 1 GTGTTCTCCA 0.967903 -121 GTTCCATCTTTTGTTCGCCAAACTTTACGG 10 12 1 TTGTTCGCCA 0.889836 -93 GCACCGGGATGTGCTCGTCATCCTCACGTA 13 36 1 GTGCTCGTCA 0.943449 -213 TTGAGCTCTCCCCTTTGTTAAG 15 165 0 GAGCTCTCCC 0.927123 -12 ********** Masking position 5 Map Score: 6.03181 Number of sites scoring better than the average of aligned sites = 245 Number in coding regions = 237 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 7 TAAGATTCCGCGTAAGTATCGCGGGGGCGTAAG 4 34 1 CGTAATCGCG 0.98698 -258 TACAAAAGTACGTGAGGATGGCGAGCACTGCCC 4 131 1 CGTAATGGCG 0.949823 -161 CAACTACTTACGATCAGATGGCGCAGACTATAT 6 63 0 CGACATGGCG 0.960225 -123 TGTTAATACCCGTCGTCATCGCGGCGTTGTTTC 7 54 1 CGTGATCGCG 0.901628 -67 AGACCACCAGCGTTACAATGGCGAACCCCACCG 7 96 0 CGTAATGGCG 0.991105 -25 ACACGCAGTACGTGAGGATGACGAGCACATCCC 13 41 0 CGTAATGACG 0.666429 -208 *** * ****** Masking position 8 Map Score: 4.85676 Number of sites scoring better than the average of aligned sites = 119 Number in coding regions = 112 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 8 TTACGCGGAATCTTACCCTTATTTATCCATCACGG 4 14 0 TCTTCCTTTA 0.714262 -278 TGAGCGGCGTTTTTGTCGTTCAAGAAA 5 3 0 TTTTTCTTAA 0.870218 -89 GCGTTTTGCTTTTTATTCTGTCTCAACTCTGGATG 5 63 1 TTTTTTTGTA 0.716141 -29 GCCGTGTTATTATTGTCGTTTCTTATATTTTGACA 10 69 1 TATTTCTTTA 0.75105 -36 AATTTAATCTCTTATCCTGGGTAAACTGATATCT 11 18 0 TCTTTCTGTA 0.957979 -24 ACTGTCAAGTTTTTATCTTGTCAAAGCGGCGATTA 15 87 0 TTTTTCTGAA 0.927291 -90 TTAACAACGGTTTTATCATGTATAACCGA 16 5 0 TTTTTCTGTA 0.969713 -101 TTACAAACACTTTTATCATTGTTAATATACTATCT 16 51 1 TTTTTCTTTA 0.943929 -55 GTTTACCCTTTTTTTGCGTGTAAAAAAAGGGGAGG 17 28 0 TTTTGCTGAA 0.726726 -94 GGTAACAAGCTCTTTTCGTTCGTTATCA 19 4 0 TCTTTCTTTA 0.922995 -139 CGGGTCTTTATTTTTTCTTGGCTGAACCGATACAT 20 26 1 TTTTTCTGTA 0.969714 -45 **** ** ** * * Masking position 15 Map Score: 4.61582 Number of sites scoring better than the average of aligned sites = 179 Number in coding regions = 126 Number in noncoding regions = 53 Number of orfs with sites within 600 bp upstream = 67 Fraction of orfs with sites within 600 bp upstream = 0.0107613 Motif number 9 ACGTATTTGTGGTATAAAGCGCGCCGGACT 1 125 1 GGTATAAAGC 0.941358 -176 TTTTGGGGGAGTTATCAAGCCTTA 2 5 0 GTTATCAAGC 0.952199 -253 CGTAAGTCTGGTTATAAGGCGTTATTGTTG 4 61 1 GTTATAAGGC 0.898935 -231 CATATCTGACCTTATAAAGCCAACTACTTA 6 86 0 CTTATAAAGC 0.706027 -100 CACAAAAGCAGATATCAGGCGATACTTCAG 7 26 0 GATATCAGGC 0.777751 -95 CTAACTCTGCTGTAAAAGGCCGTCGGCGGT 13 116 0 TGTAAAAGGC 0.719383 -133 CGAGTAAAAGTTTTAAAAGCGGGGAGCTTG 17 97 1 TTTTAAAAGC 0.437381 -25 GCGGAACATCGTTTTCAAGCTTGCAGCGGA 18 71 0 GTTTTCAAGC 0.846891 -60 GCTTGTTACAGGTAACAAGCTCTTTTCGTT 19 19 0 GGTAACAAGC 0.946002 -124 GCTTGTTACCTGTAACAAGCTCTTTTTTTA 19 29 1 TGTAACAAGC 0.851671 -114 ********** Masking position 7 Map Score: 2.70172 Number of sites scoring better than the average of aligned sites = 376 Number in coding regions = 342 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 42 Fraction of orfs with sites within 600 bp upstream = 0.0067459 Motif number 10 GGACGGAAGCGACAATCTCACTTTGTGTAA 1 181 1 GACAATCTCA 0.966209 -120 TTCAATCGTTGACAGTCTCAGGAAAGAAAC 3 127 1 GACAGTCTCA 0.988321 -20 AGTCAGACCAGACAGTCACACACAGTGGAA 4 246 0 GACAGTCACA 0.954289 -46 AGATGGCGCAGACTATATCACTGAAGCCCT 6 51 0 GACTATATCA 0.74598 -135 AAACTTTACGGCCTGTCTCATTCTTACGAT 10 31 1 GCCTGTCTCA 0.943129 -74 ATAAAAACTTGACAGTGTCATTAAAACCGT 15 106 1 GACAGTGTCA 0.960054 -71 ********** Masking position 6 Map Score: 2.72636 Number of sites scoring better than the average of aligned sites = 58 Number in coding regions = 49 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 11 AGCTTACATCAGTAAGTGACCGGGATGAGC 2 78 1 AGTAAGTGAC 0.953113 -180 AGCGTACAAAAGTACGTGAGGATGGCGAGC 4 127 1 AGTACGTGAG 0.988271 -165 GCGTACACGCAGTACGTGAGGATGACGAGC 13 48 0 AGTACGTGAG 0.988271 -201 CGATACATACAGTAAGGGAGAAGAGAAA 20 53 1 AGTAAGGGAG 0.969664 -18 ********** Masking position 4 Map Score: 0.791524 Number of sites scoring better than the average of aligned sites = 17 Number in coding regions = 11 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 12 GCGCCAACAATTATTGGTGTCCACGACGTA 1 100 1 TTATTGGTGT 0.825591 -201 TGAGGGCGGCTTCTTTTTGTGCCCATCTTG 3 30 1 TTCTTTTTGT 0.867646 -117 CTGAGCGGCGTTTTTGTCGTTCAAGAAA 5 9 0 TTTTTGTCGT 0.932457 -83 TTTACACGGCTTTTTTTTGTATAGGCTTCA 6 123 1 TTTTTTTTGT 0.844444 -63 GAGGGTGCAGTTCTTTGCGTGGCCCGGCGA 9 72 0 TTCTTTGCGT 0.881564 -50 GGCCGTGTTATTATTGTCGTTTCTTATATT 10 68 1 TTATTGTCGT 0.91381 -37 CATGAAGGCGTCTTTGTTGTT 14 2 0 TCTTTGTTGT 0.788241 -90 AGTTTACCCTTTTTTTGCGTGTAAAAAAAG 17 34 0 TTTTTTGCGT 0.860409 -88 AGGTAACAAGCTCTTTTCGTTCGTTATCA 19 10 0 CTCTTTTCGT 0.685552 -133 TATGCATGATTCATTGTTGTCCTTTATGTA 19 95 0 TCATTGTTGT 0.740845 -48 ********** Masking position 5 Map Score: 2.32414 Number of sites scoring better than the average of aligned sites = 335 Number in coding regions = 259 Number in noncoding regions = 76 Number of orfs with sites within 600 bp upstream = 84 Fraction of orfs with sites within 600 bp upstream = 0.0134918 Motif number 13 ********** No masking Map Score: -3.3087e-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 14 CTTCAGTGGCACGTTTGGCGAAATTCAGAA 1 29 0 ACGTTTGGCG 0.966127 -272 AGAAAATTCGACGTCTGATGCTGTACACAG 1 71 1 ACGTCTGATG 0.713623 -230 AATGGATCGGAAGTCCGGCGCGCTTTATAC 1 136 0 AAGTCCGGCG 0.833488 -165 CAGGTAGTACACGTTTGGTTAGGGGGCCTG 2 164 1 ACGTTTGGTT 0.877776 -94 GCGGGGGCGTAAGTCTGGTTATAAGGCGTT 4 54 1 AAGTCTGGTT 0.858026 -238 TTGTTGCAGGCAGTTTGGTCACGGCCAGCG 4 85 1 CAGTTTGGTC 0.899486 -207 CTGTGTGTGACTGTCTGGTCTGACTGAGAC 4 251 1 CTGTCTGGTC 0.705177 -41 ACAGGCCGTAAAGTTTGGCGAACAAAAGAT 10 17 0 AAGTTTGGCG 0.956811 -88 GCGGTGCAGCCAGTTTGGTGCCGGAGTGCG 13 91 0 CAGTTTGGTG 0.93573 -158 TGGGGTGGAAACGGTTGGCCGCAATCGCGA 14 61 0 ACGGTTGGCC 0.785226 -31 ********** Masking position 7 Map Score: 1.36631 Number of sites scoring better than the average of aligned sites = 1163 Number in coding regions = 1118 Number in noncoding regions = 45 Number of orfs with sites within 600 bp upstream = 56 Fraction of orfs with sites within 600 bp upstream = 0.00899454 Motif number 15 ********** No masking Map Score: -3.3087e-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