AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i182_ecoli_bsub_100.orf -o182_ecoli_bsub_100.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 ybaD 90 orf, hypothetical protein #2 ribH 88 riboflavin synthase, beta chain #3 ribA 169 GTP cyclohydrolase II #4 ribE 214 riboflavin synthase, alpha chain #5 ribB 300 3,4 dihydroxy-2-butanone-4-phosphate synthase #6 ribH 32 riboflavin synthase (beta subunit) #7 ypuE 258 ypuE Motif number 1 TCTCCCGGCTCGAAAGGGAAGCAGCGCACGAAA 2 11 1 CGAAGGGAGA 0.900717 -78 GAGTATGGCCCCGCAGGGGGGCGGATTTTAGCA 2 49 0 CCGCGGGGGG 0.99426 -40 ATACTCGAACCCGAAGGAAGAAA 2 76 1 CCGAGGAGAA 0.915623 -13 AAAAGCCGCCTGAATGGGCAGCAAAAAGAAGAA 4 47 1 TGAAGGGAGA 0.72282 -168 CCCTTACCAGTGAAGGGGTAAGAATGGCTATTT 4 132 0 TGAAGGGAAA 0.648787 -83 CTTATTCTCAGGGCGGGGCGAAATTCCCCACCG 5 60 1 GGGCGGGGAA 0.959456 -241 AGTTGATTTACCGCCGGTGGGGAATTTCGCCCC 5 74 0 CCGCGGTGGA 0.976412 -227 AATTCCGGGGCCGACGGTTAGAGTCCGGATGGG 5 164 1 CCGAGGTAGG 0.945835 -137 GGTTAGAGTCCGGATGGGAGAGAGTAACGATTC 5 179 1 CGGAGGGGAA 0.991797 -122 ACCCTTCGATCCGAAAGGTGATGTTTT 7 5 0 CCGAAGGGAG 0.941303 -254 ACCTTTCGGATCGAAGGGTGATGTTTTGTTTTT 7 19 1 TCGAGGGGAG 0.977244 -240 TGTATCTTCGGGGCAGGGTGGAAATCCCGACCG 7 130 1 GGGCGGGGGA 0.970936 -129 TGCTTTACTACCGCCGGTCGGGATTTCCACCCT 7 144 0 CCGCGGTGGA 0.976412 -115 TAAGCTGAAGCCGACAGTGAAAGTCTGGATGGG 7 230 1 CCGAAGTAAG 0.570402 -29 AGTGAAAGTCTGGATGGGAGAAGG 7 245 1 TGGAGGGGAG 0.974161 -14 **** *** ** * Masking position 7 Map Score: 19.1944 Number of sites scoring better than the average of aligned sites = 2635 Number in coding regions = 2454 Number in noncoding regions = 181 Number of orfs with sites within 600 bp upstream = 171 Fraction of orfs with sites within 600 bp upstream = 0.0274655 Motif number 2 TCTCCCGGCTCGAAAGGGAAGCA 2 3 1 TCCCGGTCGA 0.992008 -86 TTTCTTCCTTCGGGTTCGAGTATGGCCCC 2 70 0 TTCGGGTCGA 0.992182 -19 TTTGTGCCATTCCGTGAACGATCGACGCGTC 3 78 1 TCCGTGACGA 0.965787 -92 CCGCGAGCGCTTTGGGTGCGAACTCAAAGGA 5 118 1 TTTGGGGCGA 0.953071 -183 CCGGTGTAATTCCGGGGCCGACGGTTAGAGT 5 157 1 TCCGGGCCGA 0.996215 -144 CGTGAGCGGGTCCATGCCCGACAGAATCGTT 5 204 0 TCCATGCCGA 0.930489 -97 AAACATCACCTTTCGGATCGAAGGGTGATGT 7 12 1 TTTCGGTCGA 0.947632 -247 ****** **** Masking position 11 Map Score: 6.36372 Number of sites scoring better than the average of aligned sites = 260 Number in coding regions = 239 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 3 CTATTTTACCCTGAACTGACGATACAACAAAGG 1 37 0 CTGAACGAGT 0.978982 -54 ACGGCGTCCTGACCAGGTGGTTAACGGAAAT 1 70 0 CTGACCGGGT 0.991261 -21 CAATTTTTCCTGGAACTGGCGTTTTCAGTTATG 3 40 0 TGGAACGGGT 0.798225 -130 TGCTATTGTGCTGAACAGAATGTCTTAACTGAT 4 176 1 CTGAACGATT 0.927042 -39 GAATTTCGCCCCGCCCTGAGAATAAGCGGATTC 5 53 0 CCGCCCGAAT 0.970587 -248 GGGCGAAATTCCCCACCGGCGGTAAATCAACTC 5 75 1 CCCCACGGGT 0.920099 -226 CTCTAACCGTCGGCCCCGGAATTACACCGGATC 5 154 0 CGGCCCGGAT 0.977007 -147 ACTCCTAAGACTGCCCTGATTCTGGTAACCATA 5 256 1 CTGCCCGATT 0.980018 -45 GATTTCCACCCTGCCCCGAAGATACAATCTTTA 7 123 0 CTGCCCGAGT 0.994468 -136 ****** ** * * Masking position 13 Map Score: 7.27604 Number of sites scoring better than the average of aligned sites = 1197 Number in coding regions = 1130 Number in noncoding regions = 67 Number of orfs with sites within 600 bp upstream = 59 Fraction of orfs with sites within 600 bp upstream = 0.00947639 Motif number 4 GATTTGTGCCATTCCGTGAACGATCGACGCGT 3 76 1 ATTCCGGACG 0.988879 -94 TTATTTTGCCATAACGAGAAGGGGTTCACCTA 3 114 0 ATAACGGAGG 0.947844 -56 CTCAGTTGAAAGCCCGCGAGCGCTTTGGGTGC 5 105 1 AGCCCGGACG 0.986493 -196 ATCCGGTGTAATTCCGGGGCCGACGGTTAGAG 5 155 1 ATTCCGGGCG 0.983556 -146 TATAGCCAAAATAACGTGAGCGGGTCCATGCC 5 217 0 ATAACGGACG 0.977307 -84 TTTGCTTTAGAGCCCGTGACCCGTGTGCATAA 7 179 1 AGCCCGGACC 0.978945 -80 CGTGTGCATAAGCACGCGGTGGATTCAGTTTA 7 200 1 AGCACGGGGG 0.970351 -59 ****** ** ** Masking position 1 Map Score: 6.0802 Number of sites scoring better than the average of aligned sites = 257 Number in coding regions = 243 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 5 GTATCGTCAGTTCAGGGTAAAATAGATTTC 1 45 1 TTCAGGGTAA 0.759685 -46 TCCGCCCCCCTGCGGGGCCATACTCGAACC 2 57 1 TGCGGGGCCA 0.990481 -32 TTTCTTCCTTCGGGTTCGAGTATGGCCC 2 71 0 TTCGGGTTCG 0.921954 -18 AAAAAGAAGAAGCAGGGGAAATTCAGTCTA 4 69 1 AGCAGGGGAA 0.784627 -146 CCTGAGAATAAGCGGATTCACTATAACGCT 5 42 0 AGCGGATTCA 0.715578 -259 CTCAAAGGACAGCAGATCCGGTGTAATTCC 5 140 1 AGCAGATCCG 0.839338 -161 CCGGTGTAATTCCGGGGCCGACGGTTAGAG 5 157 1 TCCGGGGCCG 0.97439 -144 AAATAACGTGAGCGGGTCCATGCCCGACAG 5 211 0 AGCGGGTCCA 0.977976 -90 GGTTACCAGAATCAGGGCAGTCTTAGGAGT 5 256 0 ATCAGGGCAG 0.938956 -45 AGATTGTATCTTCGGGGCAGGGTGGAAATC 7 126 1 TTCGGGGCAG 0.973005 -133 ********** Masking position 3 Map Score: 6.00014 Number of sites scoring better than the average of aligned sites = 2130 Number in coding regions = 1965 Number in noncoding regions = 165 Number of orfs with sites within 600 bp upstream = 160 Fraction of orfs with sites within 600 bp upstream = 0.0256987 Motif number 6 CGATCCTTTATCTCAAAAGCG 1 1 1 CATCCTTTAT 0.979556 -90 GGCCTCTCCTTTTTGATAAGTCCC 3 4 1 CCTCCTTTTT 0.986114 -166 ATGATTCCCATCCTTTTTTGTGATATTT 6 15 0 CATCCTTTTT 0.993697 -18 GTTATTATAGCGATCCTTTTTAAAGTACGCA 7 75 0 CATCCTTTTT 0.993697 -184 CCCGAAGATACAATCTTTATTCATTTGTCCT 7 111 0 CATCTTTATT 0.901784 -148 * ********* Masking position 7 Map Score: 4.41787 Number of sites scoring better than the average of aligned sites = 20 Number in coding regions = 13 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 7 GGCGTTTTCAGTTATGATTGTGGGACTTAT 3 26 0 GTTATGATTG 0.846182 -144 GTCTATTGTAGCGAGGATTTATTAATTCTC 4 94 1 GCGAGGATTT 0.928583 -121 CATAATTTTAGTGAGGTTTTTTTACC 5 285 1 GTGAGGTTTT 0.985152 -16 ATCCTTTTTTGTGATATTTGTGA 6 4 0 GTGATATTTG 0.911222 -29 GATCCGAAAGGTGATGTTTT 7 1 0 GTGATGTTTT 0.987659 -258 GGATCGAAGGGTGATGTTTTGTTTTTCTCA 7 26 1 GTGATGTTTT 0.987659 -233 ********** Masking position 4 Map Score: 3.91238 Number of sites scoring better than the average of aligned sites = 314 Number in coding regions = 272 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 55 Fraction of orfs with sites within 600 bp upstream = 0.00883392 Motif number 8 GAAATTCTCCAGATAATGCT 3 160 0 GAAATTCTCC 0.96221 -10 ACAATAGACTGAATTTCCCCTGCTTCTTCT 4 73 0 GAATTTCCCC 0.989332 -142 AGGGCGGGGCGAAATTCCCCACCGGCGGTA 5 69 1 GAAATTCCCC 0.992534 -232 CGTCGGCCCCGGAATTACACCGGATCTGCT 5 150 0 GGAATTACAC 0.924267 -151 CCGCCGGTCGGGATTTCCACCCTGCCCCGA 7 137 0 GGATTTCCAC 0.977993 -122 ********** Masking position 5 Map Score: 3.67512 Number of sites scoring better than the average of aligned sites = 117 Number in coding regions = 99 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 9 ATATTATGCTAAAATCCGCCCCCCTGCGGG 2 43 1 AAAATCCGCC 0.977712 -46 TGAGAGACTAAAAAGCCGCCTGAATGGGCA 4 37 1 AAAAGCCGCC 0.98571 -178 AGCGTTATAGTGAATCCGCTTATTCTCAGG 5 42 1 TGAATCCGCT 0.938615 -259 TATTTTGGCTATATGCCGCCACTCCTAAGA 5 236 1 ATATGCCGCC 0.906108 -65 CAGCTTAAACTGAATCCACCGCGTGCTTAT 7 207 0 TGAATCCACC 0.938616 -52 CAGTTTAAGCTGAAGCCGACAGTGAAAGTC 7 225 1 TGAAGCCGAC 0.960069 -34 ********** Masking position 3 Map Score: 2.81039 Number of sites scoring better than the average of aligned sites = 728 Number in coding regions = 680 Number in noncoding regions = 48 Number of orfs with sites within 600 bp upstream = 51 Fraction of orfs with sites within 600 bp upstream = 0.00819146 Motif number 10 TCCTTTATCTCAAAAGCGTTGCGCCTTTGTTGTAT 1 14 1 CAAGTGCGCC 0.979187 -77 GGAAAACGCCCTTACCAGTGAAGGGGTAAGAATGG 4 138 0 CTACTAAGGG 0.84861 -77 CACTATAACGCTAATGATTAGCGGCAGCAACGCAT 5 19 0 CTAGTGCGGC 0.99515 -282 AGTTCGCACCCAAAGCGCTCGCGGGCTTTCAACTG 5 107 0 CAACTGCGGG 0.990762 -194 TCAGGGCAGTCTTAGGAGTGGCGGCATATAGCCAA 5 240 0 CTAGTGCGGC 0.99515 -61 CGTGCTTATGCACACGGGTCACGGGCTCTAAAGCA 7 181 0 CAAGTACGGG 0.985721 -78 ** * * * ***** Masking position 9 Map Score: 1.08057 Number of sites scoring better than the average of aligned sites = 188 Number in coding regions = 173 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 11 TCCTGACCAGGTGGTTAACGGAAATCTATTT 1 64 0 GTGGTTACGG 0.961031 -27 ACGGCGTCCTGACCAGGTGGTTAACG 1 75 0 GTCCTGACAG 0.990374 -16 CGATCGACGCGTCGTGATTAGGTGAACCCCT 3 96 1 GTCGTGATAG 0.94658 -74 GGTGGAAAACGCCCTTACCAGTGAAGGGGTA 4 145 0 GCCCTTACAG 0.946279 -70 ACCTGCTATTGTGCTGAACAGAATGTCTTAA 4 173 1 GTGCTGACAG 0.984773 -42 GACGGTTAGAGTCCGGATGGGAGAGAGTAAC 5 176 1 GTCCGGAGGG 0.863172 -125 CACTAAAATTATGGTTACCAGAATCAGGGCA 5 267 0 ATGGTTACAG 0.736775 -34 TTATTCATTTGTCCTTATTGGTTATTATAGC 7 95 0 GTCCTTATGG 0.946852 -164 ******* *** Masking position 7 Map Score: 3.13568 Number of sites scoring better than the average of aligned sites = 721 Number in coding regions = 671 Number in noncoding regions = 50 Number of orfs with sites within 600 bp upstream = 57 Fraction of orfs with sites within 600 bp upstream = 0.00915516 Motif number 12 GTCAGTTCAGGGTAAAATAGATTTCCGTTAAC 1 50 1 GGAAAATAGT 0.918186 -41 GCCAGTTCCAGGAAAAATTGACAGATTTGTGC 3 53 1 GGAAAATTGC 0.939373 -117 TTCTCGTTATGGCAAAATAAGCCAATACAGAA 3 126 1 GGAAAATAAC 0.981397 -44 ATAAATCCTCGCTACAATAGACTGAATTTCCC 4 84 0 GCACAATAGC 0.952983 -131 ATTCTCCAGTGAAAAAATAGCCATTCTTACCC 4 118 1 GAAAAATAGC 0.943082 -97 GCGGCATATAGCCAAAATAACGTGAGCGGGTC 5 223 0 GCAAAATAAG 0.888675 -78 GGTAAAAAAACCTCACTAAAAT 5 289 0 GGAAAAAAAC 0.907102 -12 AAAAAGGATCGCTATAATAACCAATAAGGACA 7 85 1 GCATAATAAC 0.89599 -174 ** ******* * Masking position 6 Map Score: 2.3843 Number of sites scoring better than the average of aligned sites = 349 Number in coding regions = 307 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 49 Fraction of orfs with sites within 600 bp upstream = 0.00787022 Motif number 13 ********** No masking Map Score: 3.38462e-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 ********** No masking Map Score: 3.38462e-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: 3.38462e-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