AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i009_Nucleotide_Biosynthes_ecoli_reg_300.orf -a/home/amcguire/alignace/lib/ORF_ecoli.txt -z/skink1/amcguire/genomes/ecoli.fna -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 fixA 300 probable flavoprotein subunit, carnitine metabolism #2 fixC 50 flavoprotein; electron transport #3 yaaU 56 putative transport protein #4 yabF 107 putative NAD(P)H oxidoreductase #5 folA 191 dihydrofolate reductase type I; trimethoprim resistance #6 lgt 150 phosphatidylglycerol-prolipoprotein diacylglyceryl transferase; a major membrane phospholipid #7 ygdP 300 putative invasion protein Motif number 1 CTGATTATTAATCAAAATTAACGAAAAAAC 1 56 0 ATCAAAATTA 0.882338 -245 ACATCTGACTTTCAATATTGGTGATCCATA 1 116 1 TTCAATATTG 0.993063 -185 AAAAGAAATTTTCAATATTGTTTTATGGAT 1 139 0 TTCAATATTG 0.993063 -162 ACGCCGTGTTTTCAATATTGGTGAGGAACT 1 173 1 TTCAATATTG 0.993063 -128 AAATCCAACTTTCAATATTGTTAAGTTCCT 1 196 0 TTCAATATTG 0.993063 -105 GTGTGACATTTTCAATATTGGTGATTAAAG 1 232 1 TTCAATATTG 0.993063 -69 AAAGTTTTATTTCAAAATTAAAGGGCGTGA 1 258 1 TTCAAAATTA 0.953454 -43 TCTTTTCTGAATCAATATTATTGACTATAA 4 27 1 ATCAATATTA 0.953454 -81 ********** Masking position 5 Map Score: 19.8676 Number of sites scoring better than the average of aligned sites = 31 Number in coding regions = 25 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 2 AAAAACGCCCTCTATTCACCCGAAACAAAA 1 32 0 TCTATTCACC 0.961215 -269 GATGTTATTTTTTACTCACAACAGAGCATA 1 91 0 TTTACTCACA 0.950308 -210 ATATTGTTAAGTTCCTCACCAATATTGAAA 1 182 0 GTTCCTCACC 0.963393 -119 GAAATAAAACTTTAATCACCAATATTGAAA 1 241 0 TTTAATCACC 0.895686 -60 TACGCCTTTGTTTTCCCACAAAGTGTAGTC 4 72 0 TTTTCCCACA 0.738689 -36 AATATAAAATTTTCCTCAACATCATCCTCG 5 107 1 TTTCCTCAAC 0.763552 -85 TAATTCCGTAGTTCTTCACAACTCTATCCA 7 108 1 GTTCTTCACA 0.897158 -193 TCTTCACAACTCTATCCACAGAAAAGGTGA 7 120 1 TCTATCCACA 0.882771 -181 GATAGCCGTTTTTATTCACCTTTTCTGTGG 7 135 0 TTTATTCACC 0.972073 -166 AATAAAAACGGCTATCCACCCCTTCCTCTG 7 149 1 GCTATCCACC 0.926274 -152 ********** Masking position 3 Map Score: 8.07224 Number of sites scoring better than the average of aligned sites = 745 Number in coding regions = 667 Number in noncoding regions = 78 Number of orfs with sites within 600 bp upstream = 92 Fraction of orfs with sites within 600 bp upstream = 0.0147767 Motif number 3 TCAAAATTAACGAAAAAACGCCCTCTATTCACCC 1 41 0 CGAAACGCCT 0.991352 -260 TGTTAATTACAGATATCACGCCCTTTAATTTTGA 1 269 0 AGAAACGCCT 0.936985 -32 TGGTTTGATACGTAACGCCGCACTGACTCTCATT 3 14 1 CGTACCGCCT 0.987516 -43 AGGTAGCCCGCGTGATTACGCCTTTGTTTTCCCA 4 84 0 CGTAACGCTT 0.923655 -24 CTCTCTCCCTGGACTCGCCGCATTACAATGAAAC 5 56 0 GGATCCGCTT 0.843593 -136 ATTCTGCTGGCGAGTCCACGCTCTCTCCCTGGAC 5 76 0 CGATACGCCT 0.983632 -116 TGAATAAAAACGGCTATCCACCCCTTCCTCTGTT 7 147 1 CGGTCCACCC 0.877319 -154 ACTCTCTGCAGGGCATTACACACTAATAACAATT 7 211 0 GGGAACACCT 0.941344 -90 TCCAGGAAGACGGTAAACCACTCTCTGCAGGGCA 7 230 0 CGGACCACCT 0.983168 -71 *** * **** ** Masking position 9 Map Score: 5.84144 Number of sites scoring better than the average of aligned sites = 802 Number in coding regions = 755 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 46 Fraction of orfs with sites within 600 bp upstream = 0.00738837 Motif number 4 TGACTTTCAATATTGGTGATCCATAAAACA 1 121 1 TATTGGTGAT 0.981102 -180 GTGTTTTCAATATTGGTGAGGAACTTAACA 1 178 1 TATTGGTGAG 0.977596 -123 ACATTTTCAATATTGGTGATTAAAGTTTTA 1 237 1 TATTGGTGAT 0.981102 -64 GCTTTACGTATAGTGGCGACAATTTTTTTT 5 158 1 TAGTGGCGAC 0.975032 -34 TAACAAGAACTTGTGGTGACAG 6 139 1 TTGTGGTGAC 0.963435 -12 ********** Masking position 4 Map Score: 3.95467 Number of sites scoring better than the average of aligned sites = 80 Number in coding regions = 75 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 5 TCTATTCACCCGAAACAAAAATGTGATACCA 1 21 0 CGAAAAAAAA 0.96608 -280 TCAAAATTAACGAAAAAACGCCCTCTATTCA 1 44 0 CGAAAAACGC 0.677525 -257 CCTTTAATTTTGAAATAAAACTTTAATCACC 1 251 0 TGAAAAAAAC 0.952888 -50 TGACTCTCATTGCAAAAAACAGGAATAACC 3 37 1 TGCAAAAACA 0.72554 -20 TCAATAATATTGATTCAGAAAAGAGAGAAAT 4 20 0 TGATTAGAAA 0.522647 -88 CGCATTACAATGAAACAAAAACAAACAGTTA 5 41 0 TGAAAAAAAA 0.960917 -151 TGAGATTTCCCGATAAAAAAAATTGTCGCCA 5 171 0 CGATAAAAAA 0.910119 -21 GTTATTTCGCTGAAAGAGAACAGCGATTGAA 6 112 0 TGAAAAGAAC 0.918748 -39 TCTCTTTCAGCGAAATAACAAGAACTTGTGG 6 124 1 CGAAAAACAA 0.916184 -27 TGAATAAGCCCGATATAGACATTTTAAAATA 7 54 0 CGATAAGACA 0.780002 -247 ACAGAAAAGGTGAATAAAAACGGCTATCCAC 7 137 1 TGAATAAAAC 0.819226 -164 TCCTGGAGTATGAAACAATCATTCGTATATA 7 257 1 TGAAAAATCA 0.684122 -44 ***** ***** Masking position 7 Map Score: 4.09725 Number of sites scoring better than the average of aligned sites = 674 Number in coding regions = 525 Number in noncoding regions = 149 Number of orfs with sites within 600 bp upstream = 150 Fraction of orfs with sites within 600 bp upstream = 0.0240925 Motif number 6 CCAAAATGCAGCCCTGCCAGAGTGGA 2 7 0 GCCCTGCCAG 0.989629 -44 CTGCATTTTGGCCCTGCCGCTGACAGGGAG 2 26 1 GCCCTGCCGC 0.991324 -25 CAGGTTTCAGGCGCTCCAAAGGTGCGAATA 6 72 0 GCGCTCCAAA 0.917645 -79 ATTGAAATGCGCGCCGCAGGTTTCAGGCGC 6 88 0 GCGCCGCAGG 0.983873 -63 AGTGTGTAATGCCCTGCAGAGAGTGGTTTA 7 221 1 GCCCTGCAGA 0.992293 -80 ********** Masking position 4 Map Score: 1.91532 Number of sites scoring better than the average of aligned sites = 480 Number in coding regions = 456 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 7 AGGTAGCCCGCGTGATTACG 4 98 0 AGGTAGCCCG 0.991986 -10 TATCTTTTAACGGTATCCGGCAACCAGCCA 6 26 1 CGGTATCCGG 0.883706 -125 GAGCATTCTGAATAAGCCCGATATAGACAT 7 63 0 AATAAGCCCG 0.874699 -238 GTTTTCCCGTAGTAATTCCGTAGTTCTTCA 7 96 1 AGTAATTCCG 0.865332 -205 TTCATACTCCAGGAAGACGGTAAACCACTC 7 241 0 AGGAAGACGG 0.945762 -60 CTTTATTTTGAGGTAGTCCG 7 291 1 AGGTAGTCCG 0.977326 -10 ********** Masking position 5 Map Score: 0.695087 Number of sites scoring better than the average of aligned sites = 442 Number in coding regions = 397 Number in noncoding regions = 45 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 8 CATATATTCACGCGGCTTATAGTCAATAAT 4 43 0 CGCGGCTTAT 0.968382 -65 TCGACTGGTGCGAGGATGATGTTGAGGAAA 5 117 0 CGAGGATGAT 0.934995 -75 CGCGGATCATATACATATCT 6 1 1 CGCGGATCAT 0.990581 -150 TACGGGAAAACCCGGAGCATTCTGAATAAG 7 77 0 CCCGGAGCAT 0.987332 -224 TTACCGTCTTCCTGGAGTATGAAACAATCA 7 248 1 CCTGGAGTAT 0.926912 -53 ********** Masking position 9 Map Score: 0.0803236 Number of sites scoring better than the average of aligned sites = 247 Number in coding regions = 229 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 9 CATTTTTGTTTCGGGTGAATAGAGGGCGTT 1 29 1 TCGGGTGAAT 0.974959 -272 TGACTATAAGCCGCGTGAATATATGACTAC 4 48 1 CCGCGTGAAT 0.994909 -60 AGGTAGCCCGCGTGATTACGCCTTTGT 4 91 0 CCGCGTGATT 0.991058 -17 ********** Masking position 8 Map Score: 0.00962032 Number of sites scoring better than the average of aligned sites = 44 Number in coding regions = 39 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 10 ********** No masking Map Score: -9.71011e-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: -9.71011e-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: -9.71011e-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