AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -ifis_ecoli_bsub_100.orf -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 queA 92 synthesis of queuine in tRNA; probably S-adenosylmethionine:tRNA ribosyltransferase-isomerase #2 tgt 55 tRNA-guanine transglycosylase #3 yajC 22 orf, hypothetical protein #4 secD 27 protein secretion; membrane protein, part of the channel #5 nrdA 300 ribonucleoside diphosphate reductase 1, alpha subunit, B1 #6 nrdB 233 ribonucleoside-diphosphate reductase 1, beta subunit, B2 #7 yhdG 300 putative dehydrogenase #8 fis 25 site-specific DNA inversion stimulation factor; DNA-binding protein; a trans activator for transcription #9 secF 125 protein-export membrane protein #10 yrbF 33 similar to hypothetical proteins #11 tgt 26 tRNA-guanine transglycosylase #12 queA 222 S-adenosylmethionine tRNA ribosyltransferase Motif number 1 TATTGAGATGCCGGATGCGGCGTAAACGCCTT 6 10 1 GCCGGATGCG 0.99963 -224 CGAGCCGTAGGCCGGATAAGGCGTTTACGCCGC 6 27 0 GCCGGATGCG 0.99963 -207 CGGTTTGTAGGCCTGATAAGACGCGCCAGCGTC 6 58 1 GCCTGATGCG 0.999134 -176 GGCACCCGGAGCCTGATGCGACGCTGGCGCGTC 6 77 0 GCCTGATGCG 0.999134 -157 GGCTCCGGGTGCCGGATGCAGCGTGAACGCCTT 6 97 1 GCCGGATACG 0.995786 -137 CGAGCCGTAGGCCGGATAAGGCGTTCACGCTGC 6 114 0 GCCGGATGCG 0.99963 -120 GGATTTGTAGGCCTGATAAGACGCGCCAGCGTC 6 146 1 GCCTGATGCG 0.999134 -88 CGCATCCTGTGCCTGATGCGACGCTGGCGCGTC 6 165 0 GCCTGATGCG 0.999134 -69 CGCATCAGGCACAGGATGCGGCGTAAAATGCCT 6 178 1 ACAGGATGCG 0.953804 -56 GGAGTTTAATGCCGGATAAGGCATTTTACGCCG 6 196 0 GCCGGATGCA 0.995786 -38 ******* * ** Masking position 7 Map Score: 43.8732 Number of sites scoring better than the average of aligned sites = 610 Number in coding regions = 74 Number in noncoding regions = 536 Number of orfs with sites within 600 bp upstream = 93 Fraction of orfs with sites within 600 bp upstream = 0.0149374 Motif number 2 AGTGTTCTAAGCAGCTTCCCGTACTACAGGTAGT 5 229 1 GCAGCTCCGC 0.934449 -72 TACGCCGCATCCGGCATCTCAATA 6 1 0 CCGGCTCTAA 0.854708 -233 GATGCCGGATGCGGCGTAAACGCCTTATCCGGCC 6 17 1 GCGGCTAACC 0.903925 -217 AACGCCTTATCCGGCCTACGGCTCGGTTTGTAGG 6 35 1 CCGGCTACGC 0.997224 -199 CGCGTCTTATCAGGCCTACAAACCGAGCCGTAGG 6 49 0 CAGGCTACAC 0.979488 -185 CACGCTGCATCCGGCACCCGGAGCCTGATGCGAC 6 88 0 CCGGCCCCGC 0.983737 -146 AACGCCTTATCCGGCCTACGGCTCGGATTTGTAG 6 122 1 CCGGCTACGC 0.997224 -112 CGCGTCTTATCAGGCCTACAAATCCGAGCCGTAG 6 137 0 CAGGCTACAC 0.979488 -97 GGCACAGGATGCGGCGTAAAATGCCTTATCCGGC 6 185 1 GCGGCTAAAC 0.962243 -49 AATGCCTTATCCGGCATTAAACTCCCAACAGGAC 6 204 1 CCGGCTTAAC 0.87794 -30 TGACTGCAAGGCGGCGTATATTACGCATTTTTTG 7 255 0 GCGGCTATTC 0.864069 -46 ATAAACATAACAGGCTTACAGAAAGGGGTGAAA 10 11 1 CAGGCTACGA 0.930302 -23 TTTTGATGAGGCCTCCTGTTCTCAAA 11 6 0 GAGGCTCCGC 0.983795 -21 AAAATATCTCCCGGCATCTTGCCGACAAAATGCA 12 67 0 CCGGCTCTGG 0.916132 -156 ***** *** * * Masking position 5 Map Score: 20.5332 Number of sites scoring better than the average of aligned sites = 1570 Number in coding regions = 1366 Number in noncoding regions = 204 Number of orfs with sites within 600 bp upstream = 99 Fraction of orfs with sites within 600 bp upstream = 0.0159011 Motif number 3 CAATTCCCTTAGGGAAAAATTTTAA 4 4 0 AGGAAAATTT 0.923974 -24 GTCAATGGGAAGAGAAAAATTTGTTAAAAATA 5 60 0 AGGAAAATTT 0.923974 -241 ATAACTCAGGAAGGAAAAAGTGGCTTTCGCGC 5 121 0 AAGAAAAGTG 0.948541 -180 TCACAAAAGGCACGTAAATTTGCCGATTATTT 7 28 1 CAGAAATTTG 0.967801 -273 AAAATTTTGGCACGCAAATTTGCGTAAATAAT 7 53 0 CAGAAATTTG 0.967825 -248 TTTCTTTATGAATGAAAATTTTGGCACGCAAA 7 67 0 AAGAAATTTT 0.956024 -234 TTTCATTCATAAAGAAAAATTGAGAACTTACT 7 82 1 AAGAAAATTG 0.979603 -219 AATTTACACTCAAAGAAATTTGAGTAAGTTCT 7 104 0 CAAAAATTTG 0.683356 -197 AATTTCTTTGAGTGTAAATTTTAGTCACTATT 7 116 1 AGGAAATTTT 0.923974 -185 TTGCCGACAAAATGCAAAACTGCTCCGATAAT 12 51 0 AAGAAAACTG 0.909223 -172 TTTTGTAAAAAAAGGAAATGTTACGTTTTTCT 12 98 1 AAGAAATGTT 0.892973 -125 CCAAAAAGATTAAGCAAAATTGATAATACCAC 12 159 0 TAGAAAATTG 0.88333 -64 ** * ******* Masking position 6 Map Score: 11.2213 Number of sites scoring better than the average of aligned sites = 340 Number in coding regions = 247 Number in noncoding regions = 93 Number of orfs with sites within 600 bp upstream = 92 Fraction of orfs with sites within 600 bp upstream = 0.0147767 Motif number 4 CTAGACTACCCGCCTCTTATTTTAGTCTGAG 1 64 1 CGCCTCTTTT 0.790238 -29 TTCCGCGGCGCTGGTTTAAAACGTTG 2 6 1 CGGCGCTGTT 0.995878 -50 ATCCGGCCTACGGCTCGGTTTGTAGGCCTGA 6 43 1 CGGCTCGGTT 0.990837 -191 GATGCGACGCTGGCGCGTCTTATCAGGCCTA 6 65 0 TGGCGCGTTT 0.97879 -169 ATCCGGCCTACGGCTCGGATTTGTAGGCCTG 6 130 1 CGGCTCGGTT 0.990837 -104 GATGCGACGCTGGCGCGTCTTATCAGGCCTA 6 153 0 TGGCGCGTTT 0.97879 -81 GACTGCAAGGCGGCGTATATTACGCATTTTT 7 257 0 CGGCGTATTT 0.828422 -44 ACGGTGCTGATCTAGTCGAAAA 9 2 1 CGGTGCTGTC 0.908444 -124 TTATGATTCTTGGTGCTGTTTTGCTTATTAT 12 25 1 TGGTGCTGTT 0.930673 -198 TGCTTATTATCGGAGCAGTTTTGCATTTTGT 12 46 1 CGGAGCAGTT 0.935321 -177 ******** ** Masking position 10 Map Score: 11.5667 Number of sites scoring better than the average of aligned sites = 1994 Number in coding regions = 1847 Number in noncoding regions = 147 Number of orfs with sites within 600 bp upstream = 127 Fraction of orfs with sites within 600 bp upstream = 0.0203983 Motif number 5 ACGTTTTAAACCAGCGCCGCGGAA 2 5 0 CCAGCGCCGC 0.995715 -51 AGGCCTACAAACCGAGCCGTAGGCCGGATA 6 42 0 ACCGAGCCGT 0.917017 -192 ATAAGACGCGCCAGCGTCGCATCAGGCTCC 6 73 1 CCAGCGTCGC 0.992569 -161 GGCCTACAAATCCGAGCCGTAGGCCGGATA 6 129 0 TCCGAGCCGT 0.97391 -105 ATAAGACGCGCCAGCGTCGCATCAGGCACA 6 161 1 CCAGCGTCGC 0.992569 -73 TTCGACTAGATCAGCACCGT 9 1 0 TCAGCACCGT 0.969864 -125 ATAAGTTTGTTTAGCGCCGTTTTCGACTAG 9 22 0 TTAGCGCCGT 0.969889 -104 ACCAAATTTATCAGCGTCTTTCAGCTTAAT 9 82 0 TCAGCGTCTT 0.926767 -44 ********** Masking position 4 Map Score: 10.3545 Number of sites scoring better than the average of aligned sites = 1951 Number in coding regions = 1838 Number in noncoding regions = 113 Number of orfs with sites within 600 bp upstream = 86 Fraction of orfs with sites within 600 bp upstream = 0.013813 Motif number 6 TATGCACTTGCAAGAGGGTCATTTTCACACTAT 5 162 1 CAAGGTCATT 0.980433 -139 ATTCTTTCCGCAATAGTTTCATGCAGACTACCT 5 256 0 CAATTTCATG 0.860351 -45 GCCAGCGTCGCATCAGGCTCCGGGTGCCGGATG 6 82 1 CAAGCTCCGG 0.913125 -152 GCCAGCGTCGCATCAGGCACAGGATGCGGCGTA 6 170 1 CAAGCACAGG 0.878307 -64 ATTTGCGTGCCAAAATTTTCATTCATAAAGAAA 7 66 1 CAATTTCATT 0.829102 -235 GTAATTATCGCACCACGCTCATTTTAAATGCAA 7 171 1 CAAGCTCATT 0.986441 -130 CTTGCAGTCACAGTATGGTCATTTCTTAACTC 7 279 1 CAAGGTCATT 0.982294 -22 TTAATCGTGACAATTGGCTCATTTGTTGTGCTA 9 54 0 CATGCTCATT 0.919958 -72 GTGAAGTGACCAAGAAGGTCATGAAA 9 110 1 CAAGGTCATG 0.95719 -16 ** * ******* Masking position 2 Map Score: 6.69836 Number of sites scoring better than the average of aligned sites = 249 Number in coding regions = 230 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 7 AAGGGGGTAAAGGTTGCAGGGAGAGCGCCCCG 1 29 1 AGTTGCGGGA 0.930863 -64 TCTTCCCATTGACTTTCCCGGACACCTTGTCT 5 79 1 GCTTTCCGGA 0.95275 -222 AGGAAAAAGTGGCTTTCGCGCACCTTAGGTCA 5 110 0 GCTTTCCGCA 0.961504 -191 TTTTCACACTATCTTGCAGTGAATCCCAAACA 5 183 1 ACTTGCGTGA 0.954974 -118 GAGTGTGTCCTGTTGGGAGTTTAATGCC 6 216 0 GCCTGTGGGA 0.845978 -18 GCCTTTTGTGAGCTTGCTCGCACTTCGC 7 7 0 ACTTGCCGCA 0.983379 -294 AATATACGCCGCCTTGCAGTCACAGTATGGTC 7 267 1 GCTTGCGTCA 0.971255 -34 ATCTCCCGGCATCTTGCCGACAAAATGCAAAA 12 64 0 ACTTGCGACA 0.937102 -159 ATTTTGCTTAATCTTTTTGGCAGAATGAAATA 12 171 1 ACTTTTGGCA 0.881133 -52 * ***** **** Masking position 5 Map Score: 3.60164 Number of sites scoring better than the average of aligned sites = 1105 Number in coding regions = 1027 Number in noncoding regions = 78 Number of orfs with sites within 600 bp upstream = 77 Fraction of orfs with sites within 600 bp upstream = 0.0123675 Motif number 8 TGCAACCTTTACCCCCTTTTGGATAGAATAT 1 16 0 ACCCCTTTTG 0.970902 -77 GCACTAGACTACCCGCCTCTTATTTTAGTCT 1 61 1 ACCCCCTCTT 0.949735 -32 GGTGCGCGAAAGCCACTTTTTCCTTCCTGAG 5 118 1 AGCCCTTTTT 0.854601 -183 GTATGTCGTACCTGTTTTTGGAATTCTTTC 5 281 0 ACCTTTTTTG 0.8477 -20 CGGCAAATTTACGTGCCTTTTGTGAGCTTGC 7 22 0 ACGTCCTTTT 0.858376 -279 TTATCGCACCACGCTCATTTTAAATGCAATT 7 175 1 ACGCCATTTT 0.871465 -126 GGCGTATATTACGCATTTTTTGCACGAGATG 7 246 0 ACGCTTTTTT 0.943253 -55 TTTCACCCCTTTCTGTAAGCCTGTT 10 19 0 ACCCTTTCTG 0.93337 -15 AGGAAATGTTACGTTTTTCTTCCCGGTTGTC 12 110 1 ACGTTTTCTT 0.817967 -113 **** ****** Masking position 8 Map Score: 1.99654 Number of sites scoring better than the average of aligned sites = 546 Number in coding regions = 474 Number in noncoding regions = 72 Number of orfs with sites within 600 bp upstream = 82 Fraction of orfs with sites within 600 bp upstream = 0.0131706 Motif number 9 CCGCAATAGTTTCATGCAGACTACCTGTAG 5 252 0 TTCATGCAGA 0.724317 -49 GTTTTTGGAATTCTTTCCGCAATAGTTTCA 5 268 0 TTCTTTCCGC 0.963102 -33 GGATAAGGCGTTTACGCCGCATCCGGCATC 6 17 0 TTTACGCCGC 0.789283 -217 GGATAAGGCGTTCACGCTGCATCCGGCACC 6 104 0 TTCACGCTGC 0.939255 -130 GATAAGGCATTTTACGCCGCATCCTGTGCC 6 185 0 TTTACGCCGC 0.789283 -49 TTACTCAAATTTCTTTGAGTGTAAATTTTA 7 109 1 TTCTTTGAGT 0.38352 -192 AGTTCTGTCAGCTCTTTATTTC 8 14 0 TTCTGTCAGC 0.937809 -12 ATTTATCAGCGTCTTTCAGCTTAATCGTGA 9 77 0 GTCTTTCAGC 0.833744 -49 TTTCACCCCTTTCTGTAAGCCTGTTATGTT 10 14 0 TTCTGTAAGC 0.596498 -20 ATCATTATGATTCTTGGTGCTGTTTTGCTT 12 21 1 TTCTTGGTGC 0.856252 -202 CTTTTGTTATTTCATTCTGCCAAAAAGATT 12 180 0 TTCATTCTGC 0.933194 -43 ********** Masking position 2 Map Score: 1.41471 Number of sites scoring better than the average of aligned sites = 3197 Number in coding regions = 2951 Number in noncoding regions = 246 Number of orfs with sites within 600 bp upstream = 202 Fraction of orfs with sites within 600 bp upstream = 0.0324446 Motif number 10 ********** No masking Map Score: 2.9725e-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 11 ********** No masking Map Score: 2.9725e-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: 2.9725e-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