AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i228_6_1_1_17_ecoli_hinf_reg_300.orf -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -g0.46 -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 = 0.46 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 gltX 258 glutamate tRNA synthetase, catalytic subunit #2 HI0274 300 glutamyl-tRNA synthetase (gltX) Motif number 1 GGAGTCGCATTATAGGGAGAGTTCAAAATG 1 20 1 TATAGGGAGA 0.959727 -239 TTGAGGAATCAGGCGGGAGTGATAGAATAT 1 176 1 AGGCGGGAGT 0.983934 -83 TGGAAAAATTAAGTGGGCGATATTCTATCA 1 195 0 AAGTGGGCGA 0.991604 -64 AAGTTTGACCAAGCGGGCGATTAGC 2 6 0 AAGCGGGCGA 0.992192 -295 TTTAGAGAAGTGGTGGGCGATACCGGTCTC 2 55 1 TGGTGGGCGA 0.991508 -246 CTCCCTTACAAGGAGGGGGTCACTGGTTCG 2 84 0 AGGAGGGGGT 0.962383 -217 CGATTAGCTCAGTTGGGAGAGCACCTCCCT 2 108 0 AGTTGGGAGA 0.983776 -193 GGGTTGGCATTATAGGGAGAATGCATTTTC 2 151 1 TATAGGGAGA 0.959727 -150 ********** Masking position 5 Map Score: 13.5455 Number of sites scoring better than the average of aligned sites = 510 Number in coding regions = 471 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 2 TGTTCGTTCGTCGTAAATTTAAGCAAGATGATC 1 74 1 TGTAAATAAG 0.996626 -185 CGGCAAATCCTGGAAAAATTAAGTGGGCGATAT 1 202 0 TGAAAATAAG 0.988986 -57 GTCGGCATCTTTCTAAACGTAAGGCCATTTC 1 238 1 TCTAAATAAG 0.988222 -21 TGGTCAAACTTAGTAAAATTAAGAAAACTTTTT 2 25 1 TGTAAATAAG 0.996626 -276 TGTTTAATTGTCGTAAAAATAAGCATAAAATCC 2 205 1 TGTAAATAAG 0.996626 -96 * ***** **** Masking position 7 Map Score: 8.59725 Number of sites scoring better than the average of aligned sites = 10 Number in coding regions = 7 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 3 GCTGTGTGGAGTCGCATTATAGGGAGAGTT 1 13 1 GTCGCATTAT 0.961502 -246 AAAATGCGTTGACTCATTTTGAACTCTCCC 1 34 0 GACTCATTTT 0.893025 -225 AAAATGAGTCAACGCATTTTCTAAAGAAAT 1 44 1 AACGCATTTT 0.985765 -215 CAGACCGTGTTGCGCAATTTGTCAACGAAA 1 113 1 TGCGCAATTT 0.911414 -146 GTTTCTACCTTACGCATTATTGTTTTCGTT 1 136 0 TACGCATTAT 0.977359 -123 ATGTTGTGGGTTGGCATTATAGGGAGAATG 2 144 1 TTGGCATTAT 0.81644 -157 TTATAGGGAGAATGCATTTTCAGTCAATAC 2 160 1 AATGCATTTT 0.899824 -141 TAAATAAAAAAGCGGATTTTATGCTTATTT 2 221 0 AGCGGATTTT 0.90478 -80 ********** Masking position 6 Map Score: 4.94445 Number of sites scoring better than the average of aligned sites = 914 Number in coding regions = 765 Number in noncoding regions = 149 Number of orfs with sites within 600 bp upstream = 167 Fraction of orfs with sites within 600 bp upstream = 0.026823 Motif number 4 ATTTAAGCAAGATGATCGCAAAACAGACCG 1 90 1 GATGATCGCA 0.976055 -169 GGGAGTGATAGAATATCGCCCACTTAATTT 1 190 1 GAATATCGCC 0.977389 -69 GCTAATCGCCCGCTTGGTCA 2 1 1 GCTAATCGCC 0.996492 -300 TCCCAACTGAGCTAATCGCCCTTAATGTTG 2 120 1 GCTAATCGCC 0.996492 -181 ********** Masking position 5 Map Score: 4.0621 Number of sites scoring better than the average of aligned sites = 387 Number in coding regions = 377 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 5 ACGCATTTTCTAAAGAAATTGTTCGTTCGTC 1 55 1 TAAAGAAATG 0.926986 -204 GTCGTAAATTTAAGCAAGATGATCGCAAAAC 1 83 1 TAAGCAAGTG 0.976644 -176 GGCCTTACGTTTAGAAAGATGCCGACAACCG 1 233 0 TTAGAAAGTG 0.951544 -26 TTAGTAAAATTAAGAAAACTTTTTAGAGAAG 2 34 1 TAAGAAAATT 0.904803 -267 AGAAAACTTTTTAGAGAAGTGGTGGGCGATA 2 46 1 TTAGAGAATG 0.881736 -255 CCCCTCCTTGTAAGGGAGGTGCTCTCCCAAC 2 96 1 TAAGGGAGTG 0.953358 -205 AAACAAAATTTAATAAAAAGGTATTGACTGA 2 179 0 TAATAAAAGG 0.784944 -122 TTACGACAATTAAACAAAATTTAATAAAAAG 2 190 0 TAAACAAATT 0.714286 -111 GACTTCTAAATAAAAAAGCGGATTTTATGCT 2 226 0 TAAAAAAGGG 0.92232 -75 ******** ** Masking position 7 Map Score: 2.92274 Number of sites scoring better than the average of aligned sites = 869 Number in coding regions = 707 Number in noncoding regions = 162 Number of orfs with sites within 600 bp upstream = 173 Fraction of orfs with sites within 600 bp upstream = 0.0277867 Motif number 6 TATAATGCGACTCCACACAGCGG 1 4 0 CTCCACACAG 0.980405 -255 GCAAGATGATCGCAAAACAGACCGTGTTGC 1 96 1 CGCAAAACAG 0.981093 -163 TGACAAATTGCGCAACACGGTCTGTTTTGC 1 107 0 CGCAACACGG 0.966609 -152 AGAAAGATGCCGACAACCGGCAAATCCTGG 1 222 0 CGACAACCGG 0.952249 -37 AGACCGGTATCGCCCACCACTTCTCTAAAA 2 54 0 CGCCCACCAC 0.959985 -247 CGATACCGGTCTCGAACCAGTGACCCCCTC 2 72 1 CTCGAACCAG 0.962198 -229 GGGAGGTGCTCTCCCAACTGAGCTAATCGC 2 109 1 CTCCCAACTG 0.9383 -192 ********** Masking position 8 Map Score: 4.25805 Number of sites scoring better than the average of aligned sites = 2802 Number in coding regions = 2695 Number in noncoding regions = 107 Number of orfs with sites within 600 bp upstream = 104 Fraction of orfs with sites within 600 bp upstream = 0.0167041 Motif number 7 ********** No masking Map Score: 8.40873e-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 8 ********** No masking Map Score: 8.40873e-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 ********** No masking Map Score: 8.40873e-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