AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -imelR_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 melR_melA 282 melR: regulator of melibiose operon, melA: alpha-galactosidase #2 melB 114 melibiose permease II Motif number 1 GCAGATCTCCTGGCTTGCTTGAATAAC 1 6 1 TCCCTGGCTG 0.990488 -277 TTCTGCAGATTCGCCTGCCATGATGAAGTTAT 1 33 0 TCCCTGCCTG 0.990488 -250 TCTGCAGAAAACCTCCGGCTTCCAGGTTGAGC 1 56 1 ACTCCGGCTC 0.986644 -227 ACTCGGAGAGTCCCCTCGCCCCTCTGGGAAGA 1 180 1 TCCCTCGCCC 0.977902 -103 AGCACGGTTTTCACCCTCTTCCCAGAGGGGCG 1 196 0 TCCCCTCTCC 0.9151 -87 CCACTCGCAGTCATCCTCCCTCACTCCTGCCA 1 229 1 TCTCCTCCTC 0.969816 -54 ATCCTCCCTCACTCCTGCCATAATTCTGATAT 1 241 1 ACCCTGCCTA 0.977619 -42 CCGGAATAAATCCCCCGGCGCAGTAGCGTTTA 2 19 0 TCCCCGGCCA 0.995808 -96 CCGGGGGATTTATTCCGGCGCACACCTCTGAC 2 33 1 TATCCGGCCA 0.855718 -82 GCTGTTACCAACGCCCGCCTTCTGTTATTGGT 2 68 0 ACCCCGCCTC 0.996196 -47 ** ****** ** Masking position 5 Map Score: 15.2046 Number of sites scoring better than the average of aligned sites = 2457 Number in coding regions = 2289 Number in noncoding regions = 168 Number of orfs with sites within 600 bp upstream = 156 Fraction of orfs with sites within 600 bp upstream = 0.0250562 Motif number 2 CAGGCGAATCTGCAGAAAACCTCCGGCTTCCAGGT 1 48 1 TCAAACTCCG 0.909111 -235 AGGTTGAGCATTCCCATAAACTCAGATCCTGCGTG 1 79 1 TCCAACTCAG 0.996398 -204 TCAGATTTACTGCTGCTTCACGCAGGATCTGAGTT 1 97 0 TCTTCCGCAG 0.965063 -186 AGGTAATTTATTCCCATAAACTCAGATTTACTGCT 1 118 0 TCCAACTCAG 0.996398 -165 TGGGAATAAATTACCTGAAAAGCAGAGTTTTCGGC 1 137 1 TACAAAGCAG 0.972289 -146 GTTTTCGGCCTCATGATACTCGGAGAGTCCCCTCG 1 163 1 TATACCGGAG 0.851035 -120 GTGAAAACCGTGCTCCCACTCGCAGTCATCCTCCC 1 214 1 TCTACCGCAG 0.994328 -69 ATGGCTCTCTTTCCTGGAATATCAGAATTATGGCA 1 256 0 TCCAAATCAG 0.989084 -27 CCTCTGACGATACCAATAACAGAAGGCGGGCGTTG 2 57 1 TCCAAAGAAG 0.952149 -58 * ** ** ***** Masking position 1 Map Score: 9.07805 Number of sites scoring better than the average of aligned sites = 1046 Number in coding regions = 990 Number in noncoding regions = 56 Number of orfs with sites within 600 bp upstream = 52 Fraction of orfs with sites within 600 bp upstream = 0.00835207 Motif number 3 TTTATGGGAATGCTCAACCTGGAAGCCGGAGGT 1 66 0 TGCTACTGGA 0.916061 -217 ACGCAGGATCTGAGTTTATGGGAATGCTCAACC 1 80 0 TGAGTAGGGA 0.987326 -203 GCAGTAAATCTGAGTTTATGGGAATAAATTACC 1 119 1 TGAGTAGGGA 0.987326 -164 CCGAAAACTCTGCTTTTCAGGTAATTTATTCCC 1 138 0 TGCTTCGGTA 0.989685 -145 TTCGGCCTCATGATACTCGGAGAGTCCCCTCGC 1 166 1 TGATTCGAGA 0.970666 -117 AGAGTCCCCTCGCCCCTCTGGGAAGAGGGTGAA 1 186 1 CGCCTCGGGA 0.978533 -97 GCCATAATTCTGATATTCCAGGAAAGAGAGCCA 1 257 1 TGATTCAGGA 0.974565 -26 TGAAATGCTCATAGGGTATCGGGTCGCT 2 97 0 TGCTTAGGTA 0.976655 -18 **** ** **** Masking position 13 Map Score: 7.94984 Number of sites scoring better than the average of aligned sites = 624 Number in coding regions = 575 Number in noncoding regions = 49 Number of orfs with sites within 600 bp upstream = 55 Fraction of orfs with sites within 600 bp upstream = 0.00883392 Motif number 4 GCATTCCCATAAACTCAGATCCTGCGTGAA 1 86 1 AAACTCAGAT 0.974946 -197 AACTCAGATTTACTGCTGCTTCACGCAGGA 1 105 0 TACTGCTGCT 0.894162 -178 TTATTCCCATAAACTCAGATTTACTGCTGC 1 116 0 AAACTCAGAT 0.974946 -167 ATGAGGCCGAAAACTCTGCTTTTCAGGTAA 1 147 0 AAACTCTGCT 0.990828 -136 ACTCCTGCCATAATTCTGATATTCCAGGAA 1 251 1 TAATTCTGAT 0.949605 -32 AACGCGACTAAACGCTACTGCGCCGGGGG 2 10 1 AAACGCTACT 0.952789 -105 TGAAATGCTCATAGGGTATCGG 2 103 0 AAATGCTCAT 0.923026 -12 ********** Masking position 2 Map Score: 6.02664 Number of sites scoring better than the average of aligned sites = 945 Number in coding regions = 869 Number in noncoding regions = 76 Number of orfs with sites within 600 bp upstream = 91 Fraction of orfs with sites within 600 bp upstream = 0.0146161 Motif number 5 AGATTTACTGCTGCTTCACGCAGGATCTGAG 1 99 0 CTGCTTCCGC 0.961293 -184 GCAGAGTTTTCGGCCTCATGATACTCGGAGA 1 158 1 CGGCCTCTGA 0.928472 -125 ACTCGGAGAGTCCCCTCGCCCCTCTGGGAAG 1 180 1 TCCCCTCCCC 0.959509 -103 GCACGGTTTTCACCCTCTTCCCAGAGGGGCG 1 196 0 CACCCTCTCC 0.983523 -87 GAAAACCGTGCTCCCACTCGCAGTCATCCTC 1 216 1 CTCCCACCGC 0.991146 -67 CGCAGTCATCCTCCCTCACTCCTGCCATAAT 1 234 1 CTCCCTCCTC 0.995059 -49 CTGTTACCAACGCCCGCCTTCTGTTATTGGT 2 68 0 CGCCCGCTTC 0.974675 -47 ******* *** Masking position 7 Map Score: 4.60406 Number of sites scoring better than the average of aligned sites = 831 Number in coding regions = 737 Number in noncoding regions = 94 Number of orfs with sites within 600 bp upstream = 91 Fraction of orfs with sites within 600 bp upstream = 0.0146161 Motif number 6 ATTCCCATAAACTCAGATCCTGCGTGAAGC 1 88 1 ACTCAGATCC 0.976222 -195 ATTCCCATAAACTCAGATTTACTGCTGCTT 1 114 0 ACTCAGATTT 0.988134 -169 GAGGCCGAAAACTCTGCTTTTCAGGTAATT 1 145 0 ACTCTGCTTT 0.979938 -138 TCCTGCCATAATTCTGATATTCCAGGAAAG 1 253 1 ATTCTGATAT 0.922395 -30 ********** Masking position 3 Map Score: 0.190112 Number of sites scoring better than the average of aligned sites = 72 Number in coding regions = 60 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 7 ********** No masking Map Score: 5.42445e-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: 5.42445e-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: 5.42445e-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