AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i256_ecoli_bsub_300.orf -o256_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 hslV 92 heat shock protein hslVU, proteasome-related peptidase subunit #2 ftsN 91 essential cell division protein #3 cytR 155 regulator for deo operon, udp, cdd, tsx, nupC, and nupG #4 priA 202 primosomal protein N'(= factor Y)(putative helicase) #5 ylxM 176 similar to hypothetical proteins #6 rpsP 105 ribosomal protein S16 (BS17) #7 ylqD 121 ylqD #8 rplS 130 ribosomal protein L19 #9 ylqF 142 similar to hypothetical proteins #10 rnh 70 ribonuclease H #11 ylqG 31 ylqG #12 sucC 172 succinyl-CoA synthetase (beta subunit) #13 sucD 28 succinyl-CoA synthetase (alpha subunit) #14 smf 60 DNA processing Smf protein homolog #15 topA 187 DNA topoisomerase I #16 gid 75 glucose-inhibited division protein #17 codV 67 integrase/recombinase Motif number 1 TCTGTATTCGTAACCAAGGGGTCAGCTC 1 75 1 TAACCAAGGG 0.821421 -18 AAATCCTCCTTAAAATAGGGTTCATATACA 5 13 1 TAAAATAGGG 0.911915 -164 GGATTTGACTTAACAAAGGGGAGAGCTCAA 5 157 1 TAACAAAGGG 0.966847 -20 TTTTTGCGTGTAAAAAAAGGGGAGGTGCCG 7 23 0 TAAAAAAAGG 0.976643 -99 TTTTACACGCAAAAAAAGGGTAAACTGATA 7 38 1 AAAAAAAGGG 0.948841 -84 GTAAAAGTTTTAAAAGCGGGGAGCTTGGTG 7 100 1 TAAAAGCGGG 0.954837 -22 AAATTCTGTATAAAAAAAGAGCTTGTTACA 9 39 0 TAAAAAAAGA 0.733623 -104 AACATAAATTTCAAAGAAGGATGGGGAATA 12 17 0 TCAAAGAAGG 0.93866 -156 TAAAAAAGGGACAGCCGTCA 14 1 1 TAAAAAAGGG 0.982984 -60 CTTTTGTTAGAAAAAGCAGGAACAGCCTTG 14 29 0 AAAAAGCAGG 0.830877 -32 CTGCTTTTTCTAACAAAAGGAGGTCAATCT 14 40 1 TAACAAAAGG 0.954769 -21 CTTTTAACACACAAAGAAGGTGAGCAAGAC 16 22 0 ACAAAGAAGG 0.830877 -54 CTTTGTGTGTTAAAAGAAGGCCTTGAATAA 16 36 1 TAAAAGAAGG 0.979772 -40 ********** Masking position 3 Map Score: 16.5949 Number of sites scoring better than the average of aligned sites = 248 Number in coding regions = 160 Number in noncoding regions = 88 Number of orfs with sites within 600 bp upstream = 73 Fraction of orfs with sites within 600 bp upstream = 0.011725 Motif number 2 ATGCAATTATAGATGGGGGGGATTTTGAGGG 1 13 0 AGATGGGGGG 0.94985 -80 ATTCGTAACCAAGGGGTCAGCTC 1 80 1 AAGGGGCAGC 0.947332 -13 CATGTTACTTAAGCGGCGGGCCTTTGACCAG 2 35 0 AAGCGGGGGC 0.97886 -57 CGCTTAAGTAACATGGCGGGCTGACGAACGA 2 51 1 ACATGGGGGC 0.884921 -41 TGACTTAACAAAGGGGAGAGCTCAA 5 162 1 AAGGGGGAGC 0.981067 -15 AAGGGAGAGGGCCGGCACCTCCCCTT 7 6 1 AGAGGGCGGC 0.977103 -116 TGCGTGTAAAAAAAGGGGAGGTGCCGGCCCT 7 18 0 AAAAGGGAGG 0.952776 -104 AAAGTTTTAAAAGCGGGGAGCTTGGTGCG 7 103 1 AAGCGGGAGC 0.956266 -19 TAAATTTCAAAGAAGGATGGGGAATATTTTA 12 12 0 AGAAGGTGGG 0.870254 -161 TACATAAGTTAGGAGGATGGGAA 12 160 1 AGGAGGTGGG 0.859168 -13 GAAAGAATGAAAGGCAGGGGACCAAATA 13 10 1 AAAGGCGGGG 0.860084 -19 TAAAAAAGGGACAGCCGTCAAGGCT 14 5 1 AAAGGGCAGC 0.951867 -56 TTTTTCTAACAAAAGGAGGTCAATCTA 14 44 1 AAAAGGGGTC 0.821597 -17 TAACACACAAAGAAGGTGAGCAAGACCCTGC 16 17 0 AGAAGGGAGC 0.973265 -59 ****** **** Masking position 1 Map Score: 14.2073 Number of sites scoring better than the average of aligned sites = 783 Number in coding regions = 679 Number in noncoding regions = 104 Number of orfs with sites within 600 bp upstream = 104 Fraction of orfs with sites within 600 bp upstream = 0.0167041 Motif number 3 AACCCTCAAAATCCCCCCCATCTATAAT 1 7 1 CAAATCCCCC 0.900816 -86 ACTCACTCCTCGCCTGGCACGTC 3 143 0 CCACTCCCGC 0.919457 -13 GCCCTAACGCCAGACACCACGCGATGTTAAAA 4 47 1 CGACACCCGC 0.98886 -156 TTTACTAGCACCTCCGAAAATATTTC 6 90 0 CAGCACCCCG 0.982897 -16 AGGGAGAGGGCCGGCACCTCCCCTTTTTTTAC 7 12 1 CGGCACCCCC 0.995241 -110 CGCACCAAGCTCCCCGCTTTTAAAACT 7 105 0 CAGCTCCCGC 0.98031 -17 GCCACAAAAACCGGCACAGCGGAACATCGTTT 8 87 0 CGGCACACGG 0.896455 -44 GTGACACGAACACCGCCTTTATCTTCAG 9 125 0 CAACACCCCT 0.958845 -18 TTAGAAAAAGCAGGAACAGCCTTGACGGCTGT 14 21 0 CGGAACACCT 0.619522 -40 GCCTAATACCTCCCCAGGAAGGGC 17 54 0 CAATACCCCC 0.919191 -14 * ****** *** Masking position 7 Map Score: 7.15025 Number of sites scoring better than the average of aligned sites = 936 Number in coding regions = 905 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 4 CAATATTCATCACACTTTTCATGAAAATTC 3 43 1 CACACTTTTC 0.933061 -113 AAAATTCTGTAACCGTTTTCACGCGCTATC 3 66 1 AACCGTTTTC 0.751933 -90 TCACATCGGCAACATTTTTAGCAGATAGCG 3 89 0 AACATTTTTA 0.820591 -67 ATGACACTGTCAAGTTTTTATCTTGTCAAA 5 97 0 CAAGTTTTTA 0.759623 -80 ACTTAGTTTACACGGTTTTAATGACACTGT 5 117 0 CACGGTTTTA 0.946269 -60 TTTTCTTAACAACGGTTTTATCATGTATAA 6 15 0 AACGGTTTTA 0.902528 -91 ACACTTTACAAACACTTTTATCATTGTTAA 6 46 1 AACACTTTTA 0.921267 -60 TTTACTCGTCCAGGCTTTTCTATTTTGCCT 7 75 0 CAGGCTTTTC 0.74812 -47 CCCCGCTTTTAAAACTTTTACTCGTCCAGG 7 91 0 AAAACTTTTA 0.767522 -31 GACAAGGAGGCACCTTTTTAAA 11 20 1 CACCTTTTTA 0.854098 -12 TCTAAACATTCAAACTTTTACTTTATTAAA 12 47 0 CAAACTTTTA 0.862622 -126 ********** Masking position 2 Map Score: 4.76378 Number of sites scoring better than the average of aligned sites = 549 Number in coding regions = 443 Number in noncoding regions = 106 Number of orfs with sites within 600 bp upstream = 136 Fraction of orfs with sites within 600 bp upstream = 0.0218439 Motif number 5 AGCAGATAGCGCGTGAAAACGGTTACAGAATTTTC 3 65 0 GCGTAAGTTA 0.819628 -91 TAAAAGTATAGCTTCAATACGATCATTTCGTACGA 4 74 1 GCTTAAGTCA 0.971185 -129 GTTAATCGCCGCTTTGACAAGATAAAAACTTGACA 5 85 1 GCTTAAGTAA 0.985704 -92 TCGGTTATACATGATAAAACCGTTGTT 6 3 1 GGTTAAGTAA 0.889531 -103 TTTTGCCTAAGCTTCTATCAGTTTACCCTTTTTTT 7 48 0 GCTTACGTTA 0.959361 -74 TCGTTTTCAAGCTTGCAGCGGATAAGCCCGCTTAA 8 58 0 GCTTACGTAA 0.986791 -73 TAAAAAAAGAGCTTGTTACAGGTAACAAGCTCTTT 9 24 0 GCTTTCGTAA 0.948811 -119 AATGAATCATGCATACTGAAGATAAAGGCGGTGTT 9 110 1 GCATTAGTAA 0.706513 -33 AATAGACTGCGCTTTCATTCTATAATAATACTGGA 12 115 0 GCTTATTTAA 0.688022 -58 TCTTTATTTGGCTTTCAACATTTCATTCTTTATCA 15 99 0 GCTTACTTCA 0.849069 -89 CCCAGGAAGGGCTTTTAAATGGTATCACAAATCGC 17 31 0 GCTTAAGTAT 0.897553 -37 **** * * * *** Masking position 4 Map Score: 5.13862 Number of sites scoring better than the average of aligned sites = 243 Number in coding regions = 214 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 6 TGACGAACGAATAAATACAGCGAAACGATA 2 72 1 ATAAATACAG 0.901856 -20 GCGCGAAATCATACAGAAATTAACCAGCGT 4 111 1 ATACAGAAAT 0.902301 -92 CTCTTTTTTTATACAGAATTTGAAAATGCC 9 48 1 ATACAGAATT 0.744799 -95 GCATCGTAAAATACATAAAGGACAACAATG 9 84 1 ATACATAAAG 0.956309 -59 TCAGCCAAGAAAAAATAAAGACCCGCATTT 10 21 0 AAAAATAAAG 0.778785 -50 GGCTGAACCGATACATACAGTAAGGGAGAA 10 45 1 ATACATACAG 0.947517 -26 ACTTTATTAAAAACATAAATTTCAAAGAAG 12 28 0 AAACATAAAT 0.693895 -145 GACGTTCATGATAAAGAATGAAATGTTGAA 15 91 1 ATAAAGAATG 0.819247 -97 TGAAAGCCAAATAAAGACAGCTGCAAAAAT 15 117 1 ATAAAGACAG 0.922061 -71 ********** Masking position 5 Map Score: 2.95828 Number of sites scoring better than the average of aligned sites = 231 Number in coding regions = 164 Number in noncoding regions = 67 Number of orfs with sites within 600 bp upstream = 73 Fraction of orfs with sites within 600 bp upstream = 0.011725 Motif number 7 TACTTAAGCGGCGGGCCTTTGACCAGTCAC 2 31 0 GCGGGCCTTT 0.985432 -61 AAGTAACATGGCGGGCTGACGAACGAATAA 2 56 1 GCGGGCTGAC 0.960208 -36 AAGGGGAGGTGCCGGCCCTCTCCCTT 7 7 0 GCCGGCCCTC 0.721008 -115 TGTGGCTTAAGCGGGCTTATCCGCTGCAAG 8 52 1 GCGGGCTTAT 0.961466 -79 GTTCCGCTGTGCCGGTTTTTGTGGCCAAGA 8 94 1 GCCGGTTTTT 0.922557 -37 GCGCAGAAATGCGGGTCTTTATTTTTTCTT 10 15 1 GCGGGTCTTT 0.949729 -56 GAACAGCCTTGACGGCTGTCCCTTTTTTA 14 10 0 GACGGCTGTC 0.739725 -51 ********** Masking position 5 Map Score: 2.76951 Number of sites scoring better than the average of aligned sites = 577 Number in coding regions = 511 Number in noncoding regions = 66 Number of orfs with sites within 600 bp upstream = 66 Fraction of orfs with sites within 600 bp upstream = 0.0106007 Motif number 8 GCGGATCAGTTTGCATACGCTGGTTAATTTC 4 126 0 TTGCATAGCT 0.990046 -77 CTTTTCTATTTTGCCTAAGCTTCTATCAGTT 7 60 0 TTGCCTAGCT 0.978168 -62 ATTTTATTGCATAGGCTATGAAATTGT 8 7 1 TTGCATAGCT 0.990046 -124 TTTAGTTTTGTTACATAAGTTAGGAGGATGG 12 149 1 TTACATAGTT 0.827498 -24 GGATTTAAAGTTGCATATTGTTTTCTATTTA 15 54 1 TTGCATATGT 0.876692 -134 ******* *** Masking position 6 Map Score: 0.040301 Number of sites scoring better than the average of aligned sites = 32 Number in coding regions = 27 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 9 ********** No masking Map Score: 1.98485e-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 10 CACGATGCGAGGCGGATCGAAAAATTCAATAT 3 17 1 GGCGGTGAAA 0.933217 -139 CATTTCGTACGAAGGCGCGAAATCATACAGAA 4 97 1 GAAGGGGAAA 0.983555 -106 AGAAAAGCCTGGACGAGTAAAAGTTTTAAAAG 7 84 1 GGACGGAAAA 0.770747 -38 ATACAGTAAGGGAGAAGAGAAA 10 59 1 GGAGAGGAAA 0.958572 -12 AAATTTCAAAGAAGGATGGGGAATATTTTAG 12 10 0 GAAGGTGGGA 0.801095 -163 TGAATGTTTAGAAGGATTAAAAGATTTTGCAT 12 65 1 GAAGGTAAAA 0.857026 -108 ACATAAGTTAGGAGGATGGGAA 12 161 1 GGAGGTGGAA 0.97132 -12 AACACACAAAGAAGGTGAGCAAGACCCTGCTC 16 15 0 GAAGGGGCAA 0.948461 -61 TAATAAACTAGGAGATGTGAAAG 16 63 1 GGAGAGGAAA 0.958572 -13 ***** * **** Masking position 12 Map Score: 3.4258 Number of sites scoring better than the average of aligned sites = 415 Number in coding regions = 365 Number in noncoding regions = 50 Number of orfs with sites within 600 bp upstream = 64 Fraction of orfs with sites within 600 bp upstream = 0.0102795 Motif number 11 ********** No masking Map Score: 1.98485e-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: 1.98485e-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 13 CCCCGTACAAAAGTACGGGGCATAATGCAA 1 38 0 AAGTACGGGG 0.936624 -55 CCGATACATACAGTAAGGGAGAAGAGAAA 10 52 1 CAGTAAGGGA 0.923496 -19 AATTTCAAAGAAGGATGGGGAATATTTTAG 12 11 0 AAGGATGGGG 0.981145 -162 CATAAGTTAGGAGGATGGGAA 12 162 1 GAGGATGGGA 0.931258 -11 GAAAGAATGAAAGGCAGGGGACCAAATA 13 11 1 AAGGCAGGGG 0.964619 -18 AATACCTCCCCAGGAAGGGCTTTTAAATGG 17 44 0 CAGGAAGGGC 0.967769 -24 ********** Masking position 2 Map Score: 0.446674 Number of sites scoring better than the average of aligned sites = 207 Number in coding regions = 178 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 14 ********** No masking Map Score: 1.98485e-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 ********** No masking Map Score: 1.98485e-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