AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -ifis_ecoli_opreg_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 Motif number 1 TATTGAGATGCCGGATGCGGCGTAAACGCCTT 6 10 1 GCCGGATGCG 0.999726 -224 CGAGCCGTAGGCCGGATAAGGCGTTTACGCCGC 6 27 0 GCCGGATGCG 0.999726 -207 CGGTTTGTAGGCCTGATAAGACGCGCCAGCGTC 6 58 1 GCCTGATGCG 0.999359 -176 GGCACCCGGAGCCTGATGCGACGCTGGCGCGTC 6 77 0 GCCTGATGCG 0.999359 -157 GGCTCCGGGTGCCGGATGCAGCGTGAACGCCTT 6 97 1 GCCGGATACG 0.996878 -137 CGAGCCGTAGGCCGGATAAGGCGTTCACGCTGC 6 114 0 GCCGGATGCG 0.999726 -120 GGATTTGTAGGCCTGATAAGACGCGCCAGCGTC 6 146 1 GCCTGATGCG 0.999359 -88 CGCATCCTGTGCCTGATGCGACGCTGGCGCGTC 6 165 0 GCCTGATGCG 0.999359 -69 CGCATCAGGCACAGGATGCGGCGTAAAATGCCT 6 178 1 ACAGGATGCG 0.96539 -56 GGAGTTTAATGCCGGATAAGGCATTTTACGCCG 6 196 0 GCCGGATGCA 0.996878 -38 ******* * ** Masking position 7 Map Score: 47.0743 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 GTCTAGTGCCGGGGCGCTCTCCCTGCAACCTTTACC 1 34 0 GGCCTCCCGC 0.991167 -59 GAAGGAAAAAGTGGCTTTCGCGCACCTTAGGTCAGA 5 108 0 GGCTTCGCCC 0.997138 -193 TAGGCCGGATAAGGCGTTTACGCCGCATCCGGCATC 6 17 0 AGCTTCGCGC 0.679261 -217 GGAGCCTGATGCGACGCTGGCGCGTCTTATCAGGCC 6 67 0 GGCCTCGCTC 0.982892 -167 TAGGCCGGATAAGGCGTTCACGCTGCATCCGGCACC 6 104 0 AGCTTCGCGC 0.99267 -130 TGTGCCTGATGCGACGCTGGCGCGTCTTATCAGGCC 6 155 0 GGCCTCGCTC 0.982892 -79 ATGCCGGATAAGGCATTTTACGCCGCATCCTGTGCC 6 185 0 AGATTCGCGC 0.990678 -49 TGATTTTTATGAGTAATTATCGCACCACGCTCATTT 7 159 1 GGATTCGCCC 0.992752 -142 TGCAAAAAATGCGTAATATACGCCGCCTTGCAGTCA 7 253 1 GGATACGCGC 0.979325 -48 * * * ** *** ** Masking position 11 Map Score: 20.6133 Number of sites scoring better than the average of aligned sites = 685 Number in coding regions = 410 Number in noncoding regions = 275 Number of orfs with sites within 600 bp upstream = 100 Fraction of orfs with sites within 600 bp upstream = 0.0160617 Motif number 3 AGGCGGGTAGTCTAGTGCCGGGGCGCTCTCCC 1 47 0 TCGTGCCGGG 0.981452 -46 TATTGAGATGCCGGATGCGGCGTAA 6 4 1 TGATGCCGGA 0.984446 -230 ACAAACCGAGCCGTAGGCCGGATAAGGCGTTT 6 34 0 CCAGGCCGGA 0.996608 -200 ACGGCTCGGTTTGTAGGCCTGATAAGACGCGC 6 52 1 TTAGGCCTGA 0.978559 -182 GCATCAGGCTCCGGGTGCCGGATGCAGCGTGA 6 91 1 CCGTGCCGGA 0.992759 -143 CAAATCCGAGCCGTAGGCCGGATAAGGCGTTC 6 121 0 CCAGGCCGGA 0.996608 -113 CGGCTCGGATTTGTAGGCCTGATAAGACGCGC 6 140 1 TTAGGCCTGA 0.978559 -94 TTACGCCGCATCCTGTGCCTGATGCGACGCTG 6 172 0 TCGTGCCTGA 0.981252 -62 CTGTTGGGAGTTTAATGCCGGATAAGGCATTT 6 203 0 TTATGCCGGA 0.99084 -31 ** ******** Masking position 8 Map Score: 18.2329 Number of sites scoring better than the average of aligned sites = 400 Number in coding regions = 211 Number in noncoding regions = 189 Number of orfs with sites within 600 bp upstream = 72 Fraction of orfs with sites within 600 bp upstream = 0.0115644 Motif number 4 TATTAATAATGAGGGAAATTTA 3 11 1 GAGGAAATTT 0.894362 -12 AATTCCCTTAGGGAAAAATTTTAA 4 4 0 GGGAAAATTT 0.94851 -24 TCAATGGGAAGAGAAAAATTTGTTAAAAATA 5 60 0 GAGAAAATTT 0.949479 -241 TCCTGAGTTATCCACAAAGTTATGCACTTGC 5 142 1 TCCCAAAGTT 0.907929 -159 GCGTAAATAATCGGCAAATTTACGTGCCTTT 7 33 0 TCGCAAATTT 0.958218 -268 GCCGATTATTTACGCAAATTTGCGTGCCAAA 7 49 1 TACCAAATTT 0.971495 -252 CAAATTTGCGTGCCAAAATTTTCATTCATAA 7 63 1 TGCAAAATTT 0.944454 -238 ATTGAGAACTTACTCAAATTTCTTTGAGTGT 7 100 1 TACCAAATTT 0.971495 -201 AGAAAATAGTGACTAAAATTTACACTCAAAG 7 121 0 GACAAAATTT 0.949479 -180 CTCAGAGGATTGGTCAAAGTTTGGCCTTTCA 7 217 1 TGGCAAAGTT 0.934913 -84 *** ******* Masking position 6 Map Score: 9.30665 Number of sites scoring better than the average of aligned sites = 149 Number in coding regions = 128 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 5 TTCCGCGGCGCTGGTTTAAAACGT 2 5 1 GCGGCGCTGG 0.989724 -51 TGGCTTTCGCGCACCTTAGGTCAGACAAGG 5 103 0 GCACCTTAGG 0.612485 -198 TATTGAGATGCCGGATGCGGCGTA 6 5 1 GAGATGCCGG 0.519684 -229 GATGCCGGATGCGGCGTAAACGCCTTATCC 6 17 1 GCGGCGTAAA 0.937921 -217 CCTACAAACCGAGCCGTAGGCCGGATAAGG 6 39 0 GAGCCGTAGG 0.98317 -195 GGAGCCTGATGCGACGCTGGCGCGTCTTAT 6 73 0 GCGACGCTGG 0.983285 -161 CTACAAATCCGAGCCGTAGGCCGGATAAGG 6 126 0 GAGCCGTAGG 0.98317 -108 TGTGCCTGATGCGACGCTGGCGCGTCTTAT 6 161 0 GCGACGCTGG 0.983285 -73 GGCACAGGATGCGGCGTAAAATGCCTTATC 6 185 1 GCGGCGTAAA 0.937921 -49 TGACTGCAAGGCGGCGTATATTACGCATTT 7 259 0 GCGGCGTATA 0.89539 -42 ********** Masking position 1 Map Score: 10.6528 Number of sites scoring better than the average of aligned sites = 3616 Number in coding regions = 3450 Number in noncoding regions = 166 Number of orfs with sites within 600 bp upstream = 121 Fraction of orfs with sites within 600 bp upstream = 0.0194346 Motif number 6 CTAACCTATTATGCCGTTCAAGAAATCGCC 5 23 1 ATGCCGTTCA 0.841636 -278 AGGTGCGCGAAAGCCACTTTTTCCTTCCTG 5 117 1 AAGCCACTTT 0.906097 -184 GTAGTACGGGAAGCTGCTTAGAACACTATA 5 226 0 AAGCTGCTTA 0.856262 -75 TAGGCCGGATAAGGCGTTTACGCCGCATCC 6 23 0 AAGGCGTTTA 0.980316 -211 TAGGCCGGATAAGGCGTTCACGCTGCATCC 6 110 0 AAGGCGTTCA 0.971115 -124 AATGCCGGATAAGGCATTTTACGCCGCATC 6 192 0 AAGGCATTTT 0.913048 -42 AAGCTCACAAAAGGCACGTAAATTTGCCGA 7 24 1 AAGGCACGTA 0.899728 -277 ********** Masking position 1 Map Score: 1.21179 Number of sites scoring better than the average of aligned sites = 945 Number in coding regions = 668 Number in noncoding regions = 277 Number of orfs with sites within 600 bp upstream = 165 Fraction of orfs with sites within 600 bp upstream = 0.0265018 Motif number 7 CAAGAGGGTCATTTTCACACTATCTTGCAG 5 172 1 ATTTTCACAC 0.888154 -129 TTTCCGCAATAGTTTCATGCAGACTACCTG 5 255 0 AGTTTCATGC 0.976438 -46 TCCTGTTGGGAGTTTAATGCCGGATAAGGC 6 207 0 AGTTTAATGC 0.843143 -27 TAATCGGCAAATTTACGTGCCTTTTGTGAG 7 27 0 ATTTACGTGC 0.956916 -274 ATTTACGCAAATTTGCGTGCCAAAATTTTC 7 56 1 ATTTGCGTGC 0.949157 -245 GCGTGCCAAAATTTTCATTCATAAAGAAAA 7 70 1 ATTTTCATTC 0.954148 -231 AGTGACTAAAATTTACACTCAAAGAAATTT 7 115 0 ATTTACACTC 0.882422 -186 ********** Masking position 1 Map Score: 1.69056 Number of sites scoring better than the average of aligned sites = 422 Number in coding regions = 356 Number in noncoding regions = 66 Number of orfs with sites within 600 bp upstream = 81 Fraction of orfs with sites within 600 bp upstream = 0.01301 Motif number 8 ********** No masking Map Score: -9.4259e-13 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 9 TTTCTCCACTACGTCAGAAAAACAGTCCAACG 2 32 0 ACGTAGAAAA 0.838315 -24 TTTCTGACGTAGTGGAGAAAAA 2 44 1 AGTGAGAAAA 0.791898 -12 ACGGCATAATAGGTTAGATAAATTGATAT 5 8 0 AGGTAGAAAA 0.98152 -293 GGAAAGTCAATGGGAAGAGAAAAATTTGTTAA 5 65 0 TGGGAGAAAA 0.761939 -236 CGCGCACCTTAGGTCAGACAAGGTGTCCGGGA 5 94 0 AGGTAGAAAG 0.986555 -207 GTCTGACCTAAGGTGCGCGAAAGCCACTTTTT 5 107 1 AGGTCGCAAA 0.825896 -194 TGGATAACTCAGGAAGGAAAAAGTGGCTTTCG 5 124 0 AGGAGGAAAA 0.900942 -177 TTCCAAAAACAGGTACGACATAC 5 288 1 AGGTCGAATA 0.859999 -13 ACCGAGCCGTAGGCCGGATAAGGCGTTTACGC 6 30 0 AGGCGGAAAG 0.984979 -204 CTCGGTTTGTAGGCCTGATAAGACGCGCCAGC 6 56 1 AGGCTGAAAG 0.966782 -178 TCCGAGCCGTAGGCCGGATAAGGCGTTCACGC 6 117 0 AGGCGGAAAG 0.984979 -117 TCGGATTTGTAGGCCTGATAAGACGCGCCAGC 6 144 1 AGGCTGAAAG 0.966782 -90 GAGTTAAGAAATGACCATACTGT 7 288 0 AGTTAGAATG 0.654728 -13 **** *** *** Masking position 10 Map Score: 14.1644 Number of sites scoring better than the average of aligned sites = 747 Number in coding regions = 281 Number in noncoding regions = 466 Number of orfs with sites within 600 bp upstream = 148 Fraction of orfs with sites within 600 bp upstream = 0.0237713 Motif number 10 ********** No masking Map Score: -9.4259e-13 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: -9.4259e-13 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: -9.4259e-13 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