AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i064_ecoli_bsub_300.orf -o064_ecoli_bsub_300.ace -a/home/amcguire/alignace/lib/ORF_ecoli.txt -z/skink1/amcguire/genomes/ecoli.fna -g0.47 -x5 -e 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 = 0.47 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 hisL 255 his operon leader peptide #2 hisG 145 ATP phosphoribosyltransferase #3 hisZ 250 histidyl-tRNA synthetase Motif number 1 CAGCACACATCGCCTGAAAGA 2 2 0 CGCCTGAAAG 0.98686 -144 CGTTCATGCACCACTGGAAGATCTGAATGT 2 36 0 CCACTGGAAG 0.994049 -110 CATGAGAAAGCCCCCGGAAGATCACCTTCC 2 66 1 CCCCCGGAAG 0.977419 -80 AATAAAAAAGCCCCCGGAAGGTGATCTTCC 2 81 0 CCCCCGGAAG 0.977419 -65 ********** Masking position 8 Map Score: 7.14946 Number of sites scoring better than the average of aligned sites = 65 Number in coding regions = 59 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 2 TTCATTAAACAAATCCATTGCCATAAAATA 1 155 1 AAATCCATTG 0.884037 -101 AATATATAAAAAAGCCCTTGCTTTCTAACG 1 181 1 AAAGCCCTTG 0.993158 -75 AAAAGTCTCTGTGAATGTTTA 1 245 0 AAAGTCTCTG 0.944995 -11 AACGCATGAGAAAGCCCCCGGAAGATCACC 2 62 1 AAAGCCCCCG 0.997404 -84 GCGCAATAAAAAAGCCCCCGGAAGGTGATC 2 85 0 AAAGCCCCCG 0.997404 -61 ********** Masking position 3 Map Score: 5.88116 Number of sites scoring better than the average of aligned sites = 260 Number in coding regions = 232 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 3 CAATGATGAGCGTTAATTAACTATTTATTAATT 1 15 1 CGTTAATATA 0.978235 -241 CTCCTTTCCCCGCTCATTCATTAAACAAATCCA 1 139 1 CGCTCATATA 0.984243 -117 CTTTCTCATGCGTTCATGCACCACTGGAAGATC 2 43 0 CGTTCATACA 0.966174 -103 TATTACGTACCTTTAATACATTATTCATGATTT 3 73 1 CTTTAATATA 0.938223 -178 GATTTTCATTCTTTCATCTGCTAACATATTATC 3 164 1 CTTTCATGTA 0.974279 -87 TCCTTTAGTTCGCTAATATGATAATATGTTAGC 3 183 0 CGCTAATGTA 0.97335 -68 TCGGAATTTTCCTTCATAAGATAACAGCGGAGG 3 217 1 CCTTCATGTA 0.969547 -34 ******* * ** Masking position 6 Map Score: 4.82218 Number of sites scoring better than the average of aligned sites = 97 Number in coding regions = 82 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 4 TTAATTAACGCTCATCATTGTACA 1 5 0 CTCATCATTG 0.93845 -251 TAAGAGGACTGTCCTCTTAGCTGATGGCAC 1 104 0 GTCCTCTTAG 0.987588 -152 TAAGAGGACAGTCCTCTTAGCCCCCTCCTT 1 115 1 GTCCTCTTAG 0.987588 -141 TTTGTTATTCCTCTTTAAACCTGTCTG 2 129 0 TTCCTCTTTA 0.948854 -17 AAATATCCTTCTCCTCATTATGAAAAAATC 3 101 0 CTCCTCATTA 0.972463 -150 ********** Masking position 5 Map Score: 2.66852 Number of sites scoring better than the average of aligned sites = 91 Number in coding regions = 61 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 5 TGAGCGTTAATTAACTATTTATTAATTAGT 1 21 1 TTAACTATTT 0.907363 -235 TAACTATTTATTAATTAGTTTGTAGATCAA 1 32 1 TTAATTAGTT 0.830064 -224 AAATCCAGGCTTCGCTATTTTTGGTGCCAT 1 81 1 TTCGCTATTT 0.930858 -175 AAGGGCTTTTTTATATATTTTATGGCAATG 1 170 0 TTATATATTT 0.711422 -86 TATCTCCTTGTTCTCTATTTGATTTGTATT 3 14 1 TTCTCTATTT 0.967622 -237 ATATCTCAAATTCTTTATGTTTGGCATGCT 3 46 0 TTCTTTATGT 0.876906 -205 TAATACATTATTCATGATTTTTTCATAATG 3 86 1 TTCATGATTT 0.876906 -165 AGCGTTGATTTTCATTCTTTCATCTGCTAA 3 158 1 TTCATTCTTT 0.876906 -93 AAATTCCGAATCCTTTAGTTCGCTAATATG 3 196 0 TCCTTTAGTT 0.776894 -55 ********** Masking position 1 Map Score: 2.57679 Number of sites scoring better than the average of aligned sites = 424 Number in coding regions = 321 Number in noncoding regions = 103 Number of orfs with sites within 600 bp upstream = 121 Fraction of orfs with sites within 600 bp upstream = 0.0194346 Motif number 6 TTTTTAGTTCAAATATCCTTCTCCTCATTA 3 111 0 AAATATCCTT 0.98354 -140 TTTGAACTAAAAATATCCTTACTGAAGTTA 3 128 1 AAATATCCTT 0.98354 -123 AAGGATTCGGAATTTTCCTTCATAAGATAA 3 211 1 AATTTTCCTT 0.959795 -40 ********** Masking position 2 Map Score: 1.2702 Number of sites scoring better than the average of aligned sites = 18 Number in coding regions = 13 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 7 CCTCTTAGCCCCCTCCTTTCCCCGCTCATT 1 127 1 CCCTCCTTTC 0.970174 -129 ATAAAAAAGCCCTTGCTTTCTAACGTGAAA 1 186 1 CCTTGCTTTC 0.986154 -70 GGGGGCTTTCTCATGCGTTCATGCACCACT 2 51 0 TCATGCGTTC 0.971527 -95 GCGTTGATTTTCATTCTTTCATCTGCTAAC 3 159 1 TCATTCTTTC 0.953348 -92 AATTCCGAATCCTTTAGTTCGCTAATATGA 3 195 0 CCTTTAGTTC 0.904985 -56 ********** Masking position 4 Map Score: 0.660091 Number of sites scoring better than the average of aligned sites = 248 Number in coding regions = 222 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 8 ********** No masking Map Score: -1.36892e-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 9 ********** No masking Map Score: -1.36892e-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 10 ********** No masking Map Score: -1.36892e-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