AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -imelR_ecoli_bsub_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 melR_melA 282 melR: regulator of melibiose operon, melA: alpha-galactosidase #2 melB 114 melibiose permease II #3 gutB 201 sorbitol dehydrogenase #4 ydjD 73 similar to H+-symporter #5 msmR 217 transcriptional regulator (LacI family) #6 msmE 33 multiple sugar-binding protein Motif number 1 TGCTTGAATAACTTCATCATGGCAGGCGAATCTGCAGA 1 26 1 ACTCTGGAGG 0.89223 -257 TCACGCAGGATCTGAGTTTATGGGAATGCTCAACCTGG 1 77 0 TCTAATGGAG 0.874354 -206 GTTTTCACCCTCTTCCCAGAGGGGCGAGGGGACTCTCC 1 184 0 TCTCAGGGGG 0.991085 -99 AGGGAGGATGACTGCGAGTGGGAGCACGGTTTTCACCC 1 212 0 ACTCGGGGAG 0.962972 -71 GGAATATCAGAATTATGGCAGGAGTGAGGGAGGATGAC 1 238 0 AATAAGGGGG 0.991022 -45 CTGTTATTGGTATCGTCAGAGGTGTGCGCCGGAATAAA 2 41 0 TATGAGGGGG 0.930444 -74 TGACGATACCAATAACAGAAGGCGGGCGTTGGTAACAG 2 61 1 AATAAGGGGG 0.991022 -54 ATAAAATAGTACTAATAGGAGGTGCAGGCTT 3 4 0 ACTAAGGGAG 0.989751 -198 CATTTTATTTTCTAAAGAAAGGAACTTGCCAA 3 180 1 TCTAAGGATG 0.82925 -22 GGAAATGAAAACGGATTCTTGGGGTGGGAAATG 4 51 1 ACGATGGGGG 0.942304 -23 GAAGTAAGCGAATAAGGAAGGGTGATGGG 5 2 0 AATAGGGGTG 0.90335 -216 TTAATATTTTACTAAATAGATGAGAGGGATACCC 5 194 1 ACTAATGGGG 0.979404 -24 *** * *** * * * Masking position 12 Map Score: 10.5622 Number of sites scoring better than the average of aligned sites = 526 Number in coding regions = 441 Number in noncoding regions = 85 Number of orfs with sites within 600 bp upstream = 81 Fraction of orfs with sites within 600 bp upstream = 0.01301 Motif number 2 ATCATGGCAGGCGAATCTGCAGAAAACCTCCGG 1 41 1 GGAACGCAGA 0.988379 -242 ATGCTCAACCTGGAAGCCGGAGGTTTTCTGCAG 1 57 0 TGAACGGAGG 0.955589 -226 CAGATCCTGCGTGAAGCAGCAGTAAATCTGAGT 1 101 1 GGAACGCAGT 0.962757 -182 TCGCCCCTCTGGGAAGAGGGTGAAAACCGTGCT 1 195 1 GGAAAGGTGA 0.963565 -88 TGTTGAACGTGTTAAAAAGCAGATAAAATGGGG 3 113 1 GTAAAGCAGA 0.953061 -89 GTGAACAGGGAGGATCTTCGTAT 4 1 1 GGAAAGGAGG 0.996256 -73 AAACAAGAGGGAGAATACGAAGATCCTCCCTGT 4 15 0 GGAAAGAAGA 0.962898 -59 TGTGAAGTAAGCGAATAAGGAAGGGTGATGGG 5 10 0 GGAAAGGAAG 0.963081 -208 GATTCATCACGATGATAAGGAGGAAAAG 6 16 1 GTGAAGGAGG 0.924484 -18 * *** * ***** Masking position 5 Map Score: 8.52928 Number of sites scoring better than the average of aligned sites = 532 Number in coding regions = 476 Number in noncoding regions = 56 Number of orfs with sites within 600 bp upstream = 62 Fraction of orfs with sites within 600 bp upstream = 0.00995824 Motif number 3 AAACGCTGGATTGATAAAATAGTACTAATAG 3 24 0 TTGAAAAATA 0.967942 -178 TTTTTTGTATATGAAAAAATAAAAGTACAGT 3 52 1 ATGAAAAATA 0.844028 -150 AGTTCCTTTCTTTAGAAAATAAAATGTAAGT 3 175 0 TTTAAAAATA 0.968558 -27 GTGATTTATGTTGGAAAAATAAAGGGGAACC 5 60 0 TTGGAAAATA 0.944749 -158 AATCACATCATTTACTAAATATTTAGTAAAT 5 85 1 TTTATAAATA 0.968558 -133 TTACTAAATATTTAGTAAATATTATGGAATA 5 96 1 TTTATAAATA 0.968558 -122 CTCATCTGTTTTTGATAAATTGATATTATCA 5 163 0 TTTGTAAATT 0.757651 -55 GAGTTAATATTTTACTAAATAGATGAGAGGG 5 191 1 TTTATAAATA 0.968558 -27 **** ****** Masking position 7 Map Score: 8.50011 Number of sites scoring better than the average of aligned sites = 79 Number in coding regions = 41 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 4 GCAGATCTCCTGGCTTGCTTGAAT 1 5 1 ATCTCCTGGC 0.84446 -278 ATCTGCAGAAAACCTCCGGCTTCCAGGTTG 1 55 1 AACCTCCGGC 0.974914 -228 ATAAACTCAGATCCTGCGTGAAGCAGCAGT 1 94 1 ATCCTGCGTG 0.888962 -189 TACTCGGAGAGTCCCCTCGCCCCTCTGGGA 1 179 1 GTCCCCTCGC 0.928127 -104 ACTCGCAGTCATCCTCCCTCACTCCTGCCA 1 231 1 ATCCTCCCTC 0.992739 -52 GCCGGAATAAATCCCCCGGCGCAGTAGCGT 2 22 0 ATCCCCCGGC 0.995318 -93 GAATACGAAGATCCTCCCTGTTCAC 4 6 0 ATCCTCCCTG 0.979746 -68 GGATCTTCGTATTCTCCCTCTTGTTTACTG 4 22 1 ATTCTCCCTC 0.938529 -52 ********** Masking position 2 Map Score: 6.90788 Number of sites scoring better than the average of aligned sites = 642 Number in coding regions = 567 Number in noncoding regions = 75 Number of orfs with sites within 600 bp upstream = 72 Fraction of orfs with sites within 600 bp upstream = 0.0115644 Motif number 5 TCACGCAGGATCTGAGTTTATGGGAATGCT 1 85 0 TCTGAGTTTA 0.911824 -198 CAGCAGTAAATCTGAGTTTATGGGAATAAA 1 117 1 TCTGAGTTTA 0.911824 -166 GGCCGAAAACTCTGCTTTTCAGGTAATTTA 1 143 0 TCTGCTTTTC 0.968247 -140 CTGCCATAATTCTGATATTCCAGGAAAGAG 1 255 1 TCTGATATTC 0.94626 -28 ACGCCCGCCTTCTGTTATTGGTATCGTCAG 2 60 0 TCTGTTATTG 0.962474 -55 CCCCATTTTATCTGCTTTTTAACACGTTCA 3 116 0 TCTGCTTTTT 0.917895 -86 TTTTGTTTTCTCTGTTACTGCCCCCATTTT 3 137 0 TCTGTTACTG 0.871997 -65 TATTAACTCATCTGTTTTTGATAAATTGAT 5 170 0 TCTGTTTTTG 0.976273 -48 ********** Masking position 3 Map Score: 6.46839 Number of sites scoring better than the average of aligned sites = 346 Number in coding regions = 292 Number in noncoding regions = 54 Number of orfs with sites within 600 bp upstream = 73 Fraction of orfs with sites within 600 bp upstream = 0.011725 Motif number 6 CCTCCTATTAGTACTATTTTATCAATCCAGCG 3 20 1 GTTATTTTAT 0.831837 -182 GACAGCGGCACTGTACTTTTATTTTTTCATAT 3 60 0 CTACTTTTAT 0.95946 -142 TACAGTGCCGCTGTCCTTTTATACAGCAGGAA 3 77 1 CTCCTTTTAT 0.985924 -125 TCTGTTACTGCCCCCATTTTATCTGCTTTTTA 3 125 0 CCCATTTTAT 0.958021 -77 AATGTATGCACTTACATTTTATTTTCTAAAGA 3 166 1 CTCATTTTAT 0.97132 -36 ACAGATCTGGGTTCCCCTTTATTTTTCCAACA 5 51 1 GTCCCTTTAT 0.942558 -167 TATTGTAACCGCTTACTTTTATATGATAATAT 5 140 1 GCACTTTTAT 0.923813 -78 ** ******** Masking position 11 Map Score: 2.38501 Number of sites scoring better than the average of aligned sites = 97 Number in coding regions = 59 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 7 AGGACAGCGGCACTGTACTTTTATTTTTTCA 3 63 0 CACTGTATTT 0.919132 -139 AGTACAGTGCCGCTGTCCTTTTATACAGCAG 3 75 1 CGCTGTCTTT 0.981444 -127 TAAGTGCATACATTTTTGTTTTCTCTGTTAC 3 149 0 CATTTTTTTT 0.723225 -53 AAAATGTATGCACTTACATTTTATTTTCTAA 3 164 1 CACTTACTTT 0.956017 -38 CCCAAGAATCCGTTTTCATTTCCAGTAAACA 4 43 0 CGTTTTCTTT 0.955441 -31 ATCTGGGTTCCCCTTTATTTTTCCAACATAA 5 55 1 CCCTTTATTT 0.908322 -163 TTATTGTAACCGCTTACTTTTATATGATAAT 5 139 1 CGCTTACTTT 0.971586 -79 ******* *** Masking position 4 Map Score: 2.66059 Number of sites scoring better than the average of aligned sites = 260 Number in coding regions = 208 Number in noncoding regions = 52 Number of orfs with sites within 600 bp upstream = 55 Fraction of orfs with sites within 600 bp upstream = 0.00883392 Motif number 8 AAGCCGGAGGTTTTCTGCAGATTCGCCTGC 1 47 0 TTTTCTGCAG 0.974058 -236 TAAACTCAGATTTACTGCTGCTTCACGCAG 1 107 0 TTTACTGCTG 0.978817 -176 GATGGCTCTCTTTCCTGGAATATCAGAATT 1 262 0 TTTCCTGGAA 0.968623 -21 TTCAACAGCCTTTCCTGCTGTATAAAAGGA 3 90 0 TTTCCTGCTG 0.986201 -112 CTCCCTCTTGTTTACTGGAAATGAAAACGG 4 35 1 TTTACTGGAA 0.952762 -39 ********** Masking position 6 Map Score: 3.18173 Number of sites scoring better than the average of aligned sites = 250 Number in coding regions = 220 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 9 ********** No masking Map Score: 1.37435e-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: 1.37435e-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: 1.37435e-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