AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -ifis_ecoli_opreg_300.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 AAGGCGTTTACGCCGCATCCGGCATCTCAATA 6 10 0 CGCATCCGGC 0.999717 -224 GCGGCGTAAACGCCTTATCCGGCCTACGGCTCG 6 27 1 CGCATCCGGC 0.999717 -207 GACGCTGGCGCGTCTTATCAGGCCTACAAACCG 6 58 0 CGCATCAGGC 0.999337 -176 GACGCGCCAGCGTCGCATCAGGCTCCGGGTGCC 6 77 1 CGCATCAGGC 0.999337 -157 AAGGCGTTCACGCTGCATCCGGCACCCGGAGCC 6 97 0 CGTATCCGGC 0.99677 -137 GCAGCGTGAACGCCTTATCCGGCCTACGGCTCG 6 114 1 CGCATCCGGC 0.999717 -120 GACGCTGGCGCGTCTTATCAGGCCTACAAATCC 6 146 0 CGCATCAGGC 0.999337 -88 GACGCGCCAGCGTCGCATCAGGCACAGGATGCG 6 165 1 CGCATCAGGC 0.999337 -69 AGGCATTTTACGCCGCATCCTGTGCCTGATGCG 6 178 0 CGCATCCTGT 0.964236 -56 CGGCGTAAAATGCCTTATCCGGCATTAAACTCC 6 196 1 TGCATCCGGC 0.99677 -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 GGTAAAGGTTGCAGGGAGAGCGCCCCGGCACTAGAC 1 34 1 GCGGGAGGCC 0.991167 -59 TCTGACCTAAGGTGCGCGAAAGCCACTTTTTCCTTC 5 108 1 GGGCGAAGCC 0.997138 -193 GATGCCGGATGCGGCGTAAACGCCTTATCCGGCCTA 6 17 1 GCGCGAAGCT 0.679261 -217 GGCCTGATAAGACGCGCCAGCGTCGCATCAGGCTCC 6 67 1 GAGCGAGGCC 0.982892 -167 GGTGCCGGATGCAGCGTGAACGCCTTATCCGGCCTA 6 104 1 GCGCGAAGCT 0.99267 -130 GGCCTGATAAGACGCGCCAGCGTCGCATCAGGCACA 6 155 1 GAGCGAGGCC 0.982892 -79 GGCACAGGATGCGGCGTAAAATGCCTTATCCGGCAT 6 185 1 GCGCGAATCT 0.990678 -49 AAATGAGCGTGGTGCGATAATTACTCATAAAAATCA 7 159 0 GGGCGAATCC 0.992752 -142 TGACTGCAAGGCGGCGTATATTACGCATTTTTTGCA 7 253 0 GCGCGTATCC 0.979325 -48 ** *** ** * * * Masking position 14 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 GGACACCTTGTCTGACCTAAGGTGCGCGAAAGCCA 5 98 1 TCGACCAGGC 0.950778 -203 AAAGTTATGCACTTGCAAGAGGGTCATTTTCACAC 5 157 1 ACTGCAAGGC 0.851842 -144 TTTCACACTATCTTGCAGTGAATCCCAAACATACC 5 184 1 TCTGCAGAAC 0.936296 -117 AAACGCCTTATCCGGCCTACGGCTCGGTTTGTAGG 6 34 1 TCGGCCCGGC 0.997928 -200 GCGCGTCTTATCAGGCCTACAAACCGAGCCGTAGG 6 49 0 TCGGCCCAAC 0.994729 -185 TCACGCTGCATCCGGCACCCGGAGCCTGATGCGAC 6 88 0 TCGGCACGGC 0.997222 -146 GAACGCCTTATCCGGCCTACGGCTCGGATTTGTAG 6 121 1 TCGGCCCGGC 0.997928 -113 GCGCGTCTTATCAGGCCTACAAATCCGAGCCGTAG 6 137 0 TCGGCCCAAC 0.994729 -97 CAGCGTCGCATCAGGCACAGGATGCGGCGTAAAAT 6 172 1 TCGGCAGGAC 0.991217 -62 AAATGCCTTATCCGGCATTAAACTCCCAACAGGAC 6 203 1 TCGGCAAAAC 0.98622 -31 GCCTTTCATCTCGTGCAAAAAATGCGTAATATACG 7 240 1 TCTGCAAAAC 0.946605 -61 ** **** *** * Masking position 6 Map Score: 22.7157 Number of sites scoring better than the average of aligned sites = 650 Number in coding regions = 497 Number in noncoding regions = 153 Number of orfs with sites within 600 bp upstream = 57 Fraction of orfs with sites within 600 bp upstream = 0.00915516 Motif number 4 AGTGCCGGGGCGCTCTCCCTGCAACCTTTACC 1 34 0 CGCTTCCCGC 0.838781 -59 CAACGTTTTAAACCAGCGCCGCGGAA 2 5 0 AACCGCGCGC 0.929736 -51 GAAAAAGTGGCTTTCGCGCACCTTAGGTCAGA 5 108 0 CTTTGCGCCC 0.975759 -193 CCGGATAAGGCGTTTACGCCGCATCCGGCATC 6 17 0 CGTTACGCGC 0.992738 -217 CCTGATGCGACGCTGGCGCGTCTTATCAGGCC 6 67 0 CGCTGCGCTC 0.9762 -167 CCGGATAAGGCGTTCACGCTGCATCCGGCACC 6 104 0 CGTTACGCGC 0.992738 -130 CCTGATGCGACGCTGGCGCGTCTTATCAGGCC 6 155 0 CGCTGCGCTC 0.9762 -79 CGGATAAGGCATTTTACGCCGCATCCTGTGCC 6 185 0 ATTTACGCGC 0.958847 -49 ATAATCGGCAAATTTACGTGCCTTTTGTGAGC 7 26 0 AATTACGTCC 0.834358 -275 TATTTACGCAAATTTGCGTGCCAAAATTTTCA 7 55 1 AATTGCGTCC 0.889291 -246 TTTTATGAGTAATTATCGCACCACGCTCATTT 7 163 1 AATTTCGCCC 0.940374 -138 AAAAATGCGTAATATACGCCGCCTTGCAGTCA 7 257 1 AATAACGCGC 0.87188 -44 **** **** ** Masking position 7 Map Score: 10.7281 Number of sites scoring better than the average of aligned sites = 4147 Number in coding regions = 3706 Number in noncoding regions = 441 Number of orfs with sites within 600 bp upstream = 243 Fraction of orfs with sites within 600 bp upstream = 0.0390299 Motif number 5 TAAATTTCCCTCATTATTAATA 3 11 0 AAATTTCCTC 0.860186 -12 TTAAAATTTTTCCCTAAGGGAATT 4 4 1 AAATTTTCCC 0.930491 -24 TATTTTTAACAAATTTTTCTCTTCCCATTGA 5 60 1 AAATTTTCTC 0.931775 -241 GCAAGTGCATAACTTTGTGGATAACTCAGGA 5 142 0 AACTTTGGGA 0.877542 -159 AAAGGCACGTAAATTTGCCGATTATTTACGC 7 33 1 AAATTTGCGA 0.943394 -268 TTTGGCACGCAAATTTGCGTAAATAATCGGC 7 49 0 AAATTTGGTA 0.96119 -252 TTATGAATGAAAATTTTGGCACGCAAATTTG 7 63 0 AAATTTTGCA 0.925127 -238 ACACTCAAAGAAATTTGAGTAAGTTCTCAAT 7 100 0 AAATTTGGTA 0.96119 -201 CTTTGAGTGTAAATTTTAGTCACTATTTTCT 7 121 1 AAATTTTGTC 0.931775 -180 TGAAAGGCCAAACTTTGACCAATCCTCTGAG 7 217 0 AACTTTGCCA 0.912574 -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 6 GGCCTACAAACCGAGCCGTAGGCCGGATAA 6 41 0 CCGAGCCGTA 0.994601 -193 ATCCGGCACCCGGAGCCTGATGCGACGCTG 6 84 0 CGGAGCCTGA 0.99011 -150 GCCTACAAATCCGAGCCGTAGGCCGGATAA 6 128 0 CCGAGCCGTA 0.994601 -106 ACGCCGCATCCTGTGCCTGATGCGACGCTG 6 172 0 CTGTGCCTGA 0.963946 -62 ********** Masking position 10 Map Score: 2.31367 Number of sites scoring better than the average of aligned sites = 65 Number in coding regions = 61 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 7 AACCTTTACCCCCTTTTGGATAGAATATAA 1 14 0 CCCTTTTGGA 0.921397 -79 GGCAATTCCCTTAGGGAAAAATTTTAA 4 11 0 CCCTTAGGGA 0.949162 -17 GCACCCGGAGCCTGATGCGACGCTGGCGCG 6 79 0 CCTGATGCGA 0.981451 -155 GCATCCTGTGCCTGATGCGACGCTGGCGCG 6 167 0 CCTGATGCGA 0.981451 -67 GAGTGTGTCCTGTTGGGAGTTTAATGCC 6 216 0 CCTGTTGGGA 0.993091 -18 AATTTACGTGCCTTTTGTGAGCTTGCTCGC 7 18 0 CCTTTTGTGA 0.958367 -283 ********** Masking position 10 Map Score: 4.95024 Number of sites scoring better than the average of aligned sites = 269 Number in coding regions = 141 Number in noncoding regions = 128 Number of orfs with sites within 600 bp upstream = 45 Fraction of orfs with sites within 600 bp upstream = 0.00722775 Motif number 8 TCAAGAAATCGCCGAACAGTTATTTTTAAC 5 40 1 GCCGAACAGT 0.964132 -261 TTTTCACACTATCTTGCAGTGAATCCCAAA 5 183 1 ATCTTGCAGT 0.845469 -118 AGGCCTACAAACCGAGCCGTAGGCCGGATA 6 42 0 ACCGAGCCGT 0.988726 -192 GGCCTACAAATCCGAGCCGTAGGCCGGATA 6 129 0 TCCGAGCCGT 0.982512 -105 AATATACGCCGCCTTGCAGTCACAGTATGG 7 267 1 GCCTTGCAGT 0.977848 -34 ********** Masking position 10 Map Score: 0.761562 Number of sites scoring better than the average of aligned sites = 418 Number in coding regions = 396 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 9 ********** 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 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