AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i216_Ribosomal_Operon_3_ecoli_reg_300.orf -a/home/amcguire/alignace/lib/ORF_ecoli.txt -z/skink1/amcguire/genomes/ecoli.fna -g0.5 -x5 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 = 0.5 maxlen = 30 weight = 0.8 exclude = 0 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 Motif number 1 CATTTCGTATACACAGACTGGACGGAAGCGACAATCTCACT 1 162 1 ACCCTGGAAA 0.918216 -139 ATCTTCGCTCGCTCATCCCGGTCACTTACTGATGTAAGCTC 2 77 0 GCCCCGGTTG 0.981924 -181 AACCAAACGTGTACTACCTGGTCTATAAGGGCTCTCCCCCT 2 143 0 GTCCTGGTAG 0.788926 -115 TCGGAGATGTGATCTGCCCGGCATTAAACCGCACAGATATA 2 217 0 GACCCGGAAG 0.989626 -41 CGGTTGCTGCGCGCTGGCCGTGACCAAACTGCCTGCAACAA 4 85 0 GCCCCGTAAG 0.980392 -207 CGGCCAGCGCGCAGCAACCGGAGCGTACAAAAGTACGTGAG 4 106 1 GCGCCGGTAA 0.963182 -186 AGGATGGCGAGCACTGCCCGGGGCCAAAATGGCAAATAAAA 4 145 1 GCCCCGGAAG 0.998784 -147 GATATAGTCTGCGCCATCTGATCGTAAGTAGTTGGCTTTAT 6 62 1 GCCCTGAAAG 0.900641 -124 AGTACCGTAAACCCTGTCAGGGAATAAAAAACGC 6 162 1 ACCCAGGAAA 0.816294 -24 TACAATGGCGAACCCCACCGGCGGCAACAGAAACAACGCCG 7 75 0 AACCCGGAAA 0.877939 -46 GCAAAGAACTGCACCCTCCGGTGCAAATGGGATGGTAAGGA 9 84 1 GCCCCGGAAG 0.998784 -38 AGGATGACGAGCACATCCCGGTGCCAAAATGGCAAACAAGC 13 19 0 GCCCCGGAAG 0.998784 -230 CGGAGTGCGCGCAGTCACCGGAGCGTACACGCAGTACGTGA 13 59 0 GCGCCGGTAG 0.987939 -190 CGGTGACTGCGCGCACTCCGGCACCAAACTGGCTGCACCGC 13 80 1 GCCCCGGAAG 0.998784 -169 CCATCGAGGAACGGAGTCCGGTGTCATATTAAAAGCCCGAA 13 185 0 ACGCCGGATA 0.737713 -64 ** * **** ** * Masking position 10 Map Score: 28.4112 Number of sites scoring better than the average of aligned sites = 563 Number in coding regions = 503 Number in noncoding regions = 60 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 2 GGCCTGCATATGGCCCCCTTTTTCACTTTTAT 2 188 1 TGGCCCTTTT 0.891246 -70 CGCCCTCAGGCGGCTCCTTTTTGATAA 3 6 0 CGGCTCTTTT 0.980469 -141 CGCCTGAGGGCGGCTTCTTTTTGTGCCCATCT 3 26 1 CGGCTCTTTT 0.980469 -121 TCTGGTTATAAGGCGTTATTGTTGCAGGCAGT 4 67 1 AGGCGTTTGT 0.962784 -225 CTGGATTATTAGGCTATTTTATTTGCCATTTT 4 170 0 AGGCTTTTAT 0.858048 -122 ATCTACTGAGCGGCGTTTTTGTCGTTCAAGAA 5 12 0 CGGCGTTTGT 0.985997 -80 GCGGATCGGCTGGCGGCGTTTTGCTTTTTATT 5 48 1 TGGCGCTTTT 0.964164 -44 TGGTTTTACACGGCTTTTTTTTGTATAGGCTT 6 119 1 CGGCTTTTTT 0.973215 -67 GTCGTCATCGCGGCGTTGTTTCTGTTGCCGCC 7 65 1 CGGCGTTTTC 0.939753 -56 TTGCGTGGCCCGGCGATCTTATATTGATCGCC 9 56 0 CGGCGTTTAT 0.978157 -66 CGATTGCGGCAGGCCGTGTTATTATTGTCGTT 10 57 1 AGGCCTTTAT 0.833645 -48 GCTGCACCGCCGACGGCCTTTTACAGCAGAGT 13 111 1 CGACGCTTTT 0.899995 -138 TATAACATGAAGGCGTCTTTGTTGTT 14 5 0 AGGCGCTTGT 0.972783 -87 ***** * **** Masking position 9 Map Score: 18.5269 Number of sites scoring better than the average of aligned sites = 860 Number in coding regions = 718 Number in noncoding regions = 142 Number of orfs with sites within 600 bp upstream = 121 Fraction of orfs with sites within 600 bp upstream = 0.0194346 Motif number 3 ACGAAATGGATCGGAAGTCCGGCGCGCTTTATA 1 137 0 TCGAGTCGGC 0.961291 -164 GTTACACAAAGTGAGATTGTCGCTTCCGTCCAG 1 179 0 GTGATTTCGC 0.782745 -122 CCGGGAATTCTCGAGCTTGCCGCCTTTCTGCAA 2 44 0 TCGCTTCCGC 0.850597 -214 CGCCGCAGATGCGTTATCTTCGCTCGCTCATCC 2 100 0 GCGATCTCGC 0.975133 -158 GTAAGATTCCGCGTAAGTATCGCGGGGGCGTAA 4 33 1 GCGAGTTCGC 0.937135 -259 TATCGCGGGGGCGTAAGTCTGGTTATAAGGCGT 4 50 1 GCGAGTTGGT 0.671816 -242 TGGTTATAAGGCGTTATTGTTGCAGGCAGTTTG 4 69 1 GCGATTTTGC 0.885631 -223 CGGGCAGTGCTCGCCATCCTCACGTACTTTTGT 4 132 0 TCGATCTCAC 0.836708 -160 GCTATTTTATTTGCCATTTTGGCCCCGGGCAGT 4 157 0 TTGATTTGGC 0.933689 -135 GGTCGCTTTTGCTGAAGTATCGCCTGATATCTG 7 15 1 GCTAGTTCGC 0.619276 -106 TTAATACCCGTCGTCATCGCGGCGTTGTTTCTG 7 56 1 TCGATCCGGC 0.949067 -65 CCGGTGGGGTTCGCCATTGTAACGCTGGTGGTC 7 95 1 TCGATTTAAC 0.632971 -26 AAGGAATGTAGTGGTAGTGTAGCGATGACTTTA 9 23 1 GTGAGTTAGC 0.709148 -99 CCTGGCTTGTTTGCCATTTTGGCACCGGGATGT 13 15 1 TTGATTTGGC 0.933689 -234 CGGGATGTGCTCGTCATCCTCACGTACTGCGTG 13 40 1 TCGATCTCAC 0.836708 -209 CAACTGTTGATTGCAATTCCCGCAAAAATGAGT 13 146 1 TTGATTCCGC 0.927539 -103 TGATGATGTGTCGCGATTGCGGCCAACCGTTTC 14 51 1 TCGATTCGGC 0.973169 -41 *** *** **** Masking position 6 Map Score: 17.91 Number of sites scoring better than the average of aligned sites = 3175 Number in coding regions = 2928 Number in noncoding regions = 247 Number of orfs with sites within 600 bp upstream = 204 Fraction of orfs with sites within 600 bp upstream = 0.0327658 Motif number 4 GTGGTATAAAGCGCGCCGGACTTCCGATCC 1 133 1 GCGCGCCGGA 0.925328 -168 ACCCCAAAGGGCACCCCGGAATATGTGCCG 1 225 0 GCACCCCGGA 0.968089 -76 ACTGATGTAAGCTCCCGGGAATTCTCGAGC 2 61 0 GCTCCCGGGA 0.95557 -197 TTCATATTTCGCGCCGCAGATGCGTTATCT 2 114 0 GCGCCGCAGA 0.96451 -144 GCGGTTTAATGCCGGGCAGATCACATCTCC 2 226 1 GCCGGGCAGA 0.63514 -32 CCAGACTTACGCCCCCGCGATACTTACGCG 4 42 0 GCCCCCGCGA 0.987605 -250 TGCCATTTTGGCCCCGGGCAGTGCTCGCCA 4 149 0 GCCCCGGGCA 0.952845 -143 TTCAGCAAAAGCGACCCCCA 7 1 0 GCGACCCCCA 0.590719 -120 TTCTTTGCGTGGCCCGGCGATCTTATATTG 9 62 0 GGCCCGGCGA 0.956149 -60 CATCCCATTTGCACCGGAGGGTGCAGTTCT 9 88 0 GCACCGGAGG 0.731224 -34 GCCCCCGAGATATCAGTTTA 11 1 1 GCCCCCGAGA 0.982371 -41 TGGCAAACAAGCCAGGCCGA 13 1 0 GCCAGGCCGA 0.853779 -248 TTGCCATTTTGGCACCGGGATGTGCTCGTC 13 25 1 GGCACCGGGA 0.787456 -224 CTGCGTGTACGCTCCGGTGACTGCGCGCAC 13 66 1 GCTCCGGTGA 0.805936 -183 CAAACTGGCTGCACCGCCGACGGCCTTTTA 13 104 1 GCACCGCCGA 0.971746 -145 ********** Masking position 1 Map Score: 17.3804 Number of sites scoring better than the average of aligned sites = 1674 Number in coding regions = 1576 Number in noncoding regions = 98 Number of orfs with sites within 600 bp upstream = 98 Fraction of orfs with sites within 600 bp upstream = 0.0157404 Motif number 5 CGTATACACAGACTGGACGGAAGCGACAATC 1 167 1 GACTGACGGA 0.611495 -134 TCGAGTTGCAGAAAGGCGGCAAGCTCGAGAA 2 39 1 GAAAGCGGCA 0.619951 -219 TAAGTGACCGGGATGAGCGAGCGAAGATAAC 2 90 1 GGATGGCGAG 0.751639 -168 AAAAGGAGCCGCCTGAGGGCGGCTTCTTTTT 3 17 1 GCCTGGGGCG 0.963227 -130 ACCCTTGTGGGGCTGCGCTGAAAAGCGACGT 3 72 1 GGCTGGCTGA 0.872841 -75 TTTGGTCACGGCCAGCGCGCAGCAACCGGAG 4 98 1 GCCAGGCGCA 0.959685 -194 TTTGGCCCCGGGCAGTGCTCGCCATCCTCAC 4 142 0 GGCAGGCTCG 0.959834 -150 CTTGCGGATCGGCTGGCGGCGTTTTGCTTTT 5 45 1 GGCTGCGGCG 0.982653 -47 GAGTTAGTTAGGAAGAACGCATAATAACG 8 11 1 GGAAGACGCA 0.736747 -19 GTAAGAATGAGACAGGCCGTAAAGTTTGGCG 10 27 0 GACAGCCGTA 0.674269 -78 TTACGATTGCGGCAGGCCGTGTTATTATTGT 10 54 1 GGCAGCCGTG 0.920504 -51 TTTGGCACCGGGATGTGCTCGTCATCCTCAC 13 32 1 GGATGGCTCG 0.892743 -217 ACGCTCCGGTGACTGCGCGCACTCCGGCACC 13 74 1 GACTGGCGCA 0.96676 -175 TGCTGTAAAAGGCCGTCGGCGGTGCAGCCAG 13 108 0 GGCCGCGGCG 0.91948 -141 GGGTGGAAACGGTTGGCCGCAATCGCGACAC 14 58 0 GGTTGCCGCA 0.845849 -34 TGTCTCTCGCCTGGGGTGGAAACGGTTGG 14 73 0 GCCTGGGTGG 0.639901 -19 ***** ***** Masking position 5 Map Score: 9.8073 Number of sites scoring better than the average of aligned sites = 4979 Number in coding regions = 4771 Number in noncoding regions = 208 Number of orfs with sites within 600 bp upstream = 188 Fraction of orfs with sites within 600 bp upstream = 0.030196 Motif number 6 TATACCACAAATACGTCGTGGACACCAATAA 1 110 0 ATACGCGTGG 0.959599 -191 GTATCGGCACATATTCCGGGGTGCCCTTTGG 1 221 1 ATATTCGGGG 0.98564 -80 GCGGCGCGAAATATGAAGGGGGAGAGCCCTT 2 127 1 ATATGAGGGG 0.923383 -131 TTCCGCGTAAGTATCGCGGGGGCGTAAGTCT 4 39 1 GTATCCGGGG 0.976721 -253 CTGATTAAACATATTACGGGTAATCGTCTGG 4 198 0 ATATTCGGGT 0.940115 -94 ATAAGGTCAGATATGCCGTGGTTTTACACGG 6 101 1 ATATGCGTGG 0.976839 -85 GGGTAAACTGATATCTCGGGGGC 11 3 0 ATATCCGGGG 0.986683 -39 TCATCCTCACGTACTGCGTGTACGCTCCGGT 13 53 1 GTACTCGTGT 0.662993 -196 ***** ***** Masking position 3 Map Score: 6.18312 Number of sites scoring better than the average of aligned sites = 124 Number in coding regions = 102 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 7 ATCCCATATTACCGACCCCAAAGGGCACCCC 1 238 0 ACCGACCCAA 0.933664 -63 ATACGTGGAGGCATAACCCCAACTTTTATAT 1 267 1 GCATACCCCA 0.932789 -34 ATATGAAGGGGGAGAGCCCTTATAGACCAGG 2 137 1 GGAGACCCTT 0.780881 -121 GGGGCCATATGCAGGCCCCCTAACCAAACGT 2 174 0 GCAGGCCCCT 0.968669 -84 TTAATGCCGGGCAGATCACATCTCCGAGGAT 2 231 1 GCAGACACAT 0.710021 -27 AACGCCGCCAGCCGATCCGCAAGGATCTACT 5 37 0 GCCGACCGCA 0.970413 -55 CTTCAGCAAAAGCGACCCCCA 7 1 0 AGCGACCCCA 0.969381 -120 GCGTTACAATGGCGAACCCCACCGGCGGCAA 7 89 0 GGCGACCCCA 0.991176 -32 GCAGACCACCAGCGTTACAAT 7 110 0 GCAGACACCA 0.964864 -11 GAATAAAACAACCGGACCCCATCGAGGAACG 13 213 0 ACCGGCCCCA 0.968418 -36 ***** ***** Masking position 7 Map Score: 7.9798 Number of sites scoring better than the average of aligned sites = 550 Number in coding regions = 522 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 8 CTTCAGTGGCACGTTTGGCGAAATTCAGAA 1 29 0 ACGTTTGGCG 0.918775 -272 GACACCAATAATTGTTGGCGCTGTGTACAG 1 91 0 ATTGTTGGCG 0.929633 -210 CAACTCGAACTATTTTGGGGGAGTTATCAA 2 17 0 TATTTTGGGG 0.692233 -241 TCCTTGCGGATCGGCTGGCGGCGTTTTGCT 5 43 1 TCGGCTGGCG 0.807639 -49 AGCGCGACTCTCTGTAGCCGGATTATCC 6 9 0 TCTGTAGCCG 0.894945 -177 AGTCGCGCTATTTGTTAGCGTAGGGCTTCA 6 30 1 TTTGTTAGCG 0.723443 -156 CGGCGTTGTTTCTGTTGCCGCCGGTGGGGT 7 75 1 TCTGTTGCCG 0.976586 -46 TGTAGCGATGACTTTAGGCGATCAATATAA 9 40 1 ACTTTAGGCG 0.820675 -82 ACAGGCCGTAAAGTTTGGCGAACAAAAGAT 10 17 0 AAGTTTGGCG 0.787561 -88 AGCGCCGTCTTTTACCGTTTATCCGGT 12 14 0 TCTTTTACCG 0.792515 -17 GTGCAGCCAGTTTGGTGCCGGAGTGCGCGC 13 88 0 TTTGGTGCCG 0.753429 -161 AATTTTACTCATTTTTGCGGGAATTGCAAT 13 155 0 ATTTTTGCGG 0.617026 -94 ACATCATCAGTATTTTGCCGCAGTATAACA 14 30 0 TATTTTGCCG 0.908207 -62 ********** Masking position 10 Map Score: 5.42257 Number of sites scoring better than the average of aligned sites = 2945 Number in coding regions = 2738 Number in noncoding regions = 207 Number of orfs with sites within 600 bp upstream = 221 Fraction of orfs with sites within 600 bp upstream = 0.0354963 Motif number 9 TCTGAATTTCGCCAAACGTGCCACTGAAGG 1 30 1 GCCAAACGTG 0.983202 -271 AGGCCCCCTAACCAAACGTGTACTACCTGG 2 163 0 ACCAAACGTG 0.958123 -95 GCTGGCCGTGACCAAACTGCCTGCAACAAT 4 84 0 ACCAAACTGC 0.894617 -208 ACTGCCCGGGGCCAAAATGGCAAATAAAAT 4 157 1 GCCAAAATGG 0.955878 -135 TCTTTTGTTCGCCAAACTTTACGGCCTGTC 10 18 1 GCCAAACTTT 0.942164 -87 ACATCCCGGTGCCAAAATGGCAAACAAGCC 13 18 0 GCCAAAATGG 0.955878 -231 GCACTCCGGCACCAAACTGGCTGCACCGCC 13 92 1 ACCAAACTGG 0.973701 -157 CGCGATTGCGGCCAACCGTTTCCACCCCAG 14 62 1 GCCAACCGTT 0.809198 -30 ********** Masking position 5 Map Score: 7.10854 Number of sites scoring better than the average of aligned sites = 713 Number in coding regions = 679 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 10 GCCGCCCTCAGGCGGCTCCTTTTTGATAA 3 10 0 GGCGGCTCCT 0.940754 -137 GCCGCCTGAGGGCGGCTTCTTTTTGTGCCC 3 24 1 GGCGGCTTCT 0.985471 -123 GGATCTACTGAGCGGCGTTTTTGTCGTTCA 5 16 0 AGCGGCGTTT 0.973314 -76 CGGATCGGCTGGCGGCGTTTTGCTTTTTAT 5 49 1 GGCGGCGTTT 0.99264 -43 CGTGGTTTTACACGGCTTTTTTTTGTATAG 6 117 1 CACGGCTTTT 0.879492 -69 CCGTCGTCATCGCGGCGTTGTTTCTGTTGC 7 63 1 CGCGGCGTTG 0.930056 -58 AGCGCCGTCTTTTACCGTTT 12 21 0 AGCGCCGTCT 0.873279 -10 CTGCACCGCCGACGGCCTTTTACAGCAGAG 13 112 1 GACGGCCTTT 0.909966 -137 AGTATAACATGAAGGCGTCTTTGTTGTT 14 9 0 GAAGGCGTCT 0.847642 -83 ********** Masking position 6 Map Score: 8.04435 Number of sites scoring better than the average of aligned sites = 1083 Number in coding regions = 1025 Number in noncoding regions = 58 Number of orfs with sites within 600 bp upstream = 60 Fraction of orfs with sites within 600 bp upstream = 0.00963701 Motif number 11 TTTTGGGGGAGTTATCAAGCCTTA 2 2 0 GTTATAGCTT 0.98614 -256 CGTAAGTCTGGTTATAAGGCGTTATTGTTGCAG 4 61 1 GTTATAGCTT 0.98614 -231 AATCGTCTGGATTATTAGGCTATTTTATTTGCC 4 175 0 ATTATAGCAT 0.904895 -117 CACAAAAGCAGATATCAGGCGATACTTCAGCAA 7 23 0 GATATAGCAT 0.937856 -98 CGTTATTATGCGTTCTTCCTAACT 8 16 0 GTTATAGCTT 0.98614 -14 ***** * ** ** Masking position 7 Map Score: 0.414401 Number of sites scoring better than the average of aligned sites = 27 Number in coding regions = 20 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 12 GGATAATCCGGCTACAGAGAGTCGCGCTA 6 10 1 GGCTACAGAG 0.983033 -176 GTTAGCGTAGGGCTTCAGTGATATAGTCTG 6 43 1 GGCTTCAGTG 0.983033 -143 TTTTTGTATAGGCTTCAGTATTCCTGAGTA 6 136 1 GGCTTCAGTA 0.974001 -50 CCCCACCGGCGGCAACAGAAACAACGCCGC 7 74 0 GGCAACAGAA 0.936835 -47 ********** Masking position 7 Map Score: 0.252246 Number of sites scoring better than the average of aligned sites = 27 Number in coding regions = 23 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 13 ********** No masking Map Score: 3.45567e-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: 3.45567e-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: 3.45567e-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