AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -imelR_ecoli_bsub_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 #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 AGGATCTGAGTTTATGGGAATGCTCAACCTGGAAGCC 1 72 0 TTTGAATTAA 0.926956 -211 TAAATCTGAGTTTATGGGAATAAATTACCTGAAAAGC 1 123 1 TTTGAATATA 0.89554 -160 ATGGCTCTCTTTCCTGGAATATCAGAATTATGGCAGG 1 254 0 TCTGATAAAA 0.80211 -29 CAATCCAGCGTTTTTTGTATATGAAAAAATAAAAGTA 3 42 1 TTTGATAAAA 0.95536 -160 CAAGTTCCTTTCTTTAGAAAATAAAATGTAAGTGCAT 3 171 0 TTTGAAAAAT 0.955602 -31 CTCCCTCTTGTTTACTGGAAATGAAAACGGATTCTTG 4 35 1 TTCGAAAAAA 0.942312 -39 AACCCAGATCTGTCTCGTAAATGTGAAGTAAGCGAAT 5 27 0 TTTGAAATAA 0.980823 -191 TGATGTGATTTATGTTGGAAAAATAAAGGGGAACCCA 5 58 0 TTTGAAATAA 0.980822 -160 ATTTACTAAATATTTAGTAAATATTATGGAATATTTC 5 94 1 TTTGAAATAT 0.926955 -124 TATTATGGAATATTTCGAAAACAATTATTGTAACCGC 5 115 1 TTTGAAAATA 0.971869 -103 CCCTCTCATCTATTTAGTAAAATATTAACTCATCTGT 5 185 0 TTTGAAAATA 0.971872 -33 * * * * *** * ** Masking position 9 Map Score: 10.1084 Number of sites scoring better than the average of aligned sites = 88 Number in coding regions = 62 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 2 TGCTCAACCTGGAAGCCGGAGGTTTTCTGCA 1 58 0 GGAAGCGGAG 0.978649 -225 CCCTCTTCCCAGAGGGGCGAGGGGACTCTCC 1 184 0 AGAGGGCGAG 0.968274 -99 CGCCCCTCTGGGAAGAGGGTGAAAACCGTGC 1 196 1 GGAAGGGGTG 0.98496 -87 GAGGATGACTGCGAGTGGGAGCACGGTTTTC 1 216 0 GCGAGGGGAG 0.978403 -67 CAGAATTATGGCAGGAGTGAGGGAGGATGAC 1 238 0 GCAGGGTGAG 0.989856 -45 TGGTATCGTCAGAGGTGTGCGCCGGAATAAA 2 41 0 AGAGGGTGCG 0.967173 -74 ACCAATAACAGAAGGCGGGCGTTGGTAACAG 2 68 1 GAAGGGGGCG 0.972662 -47 TTTCCAGTAAACAAGAGGGAGAATACGAAGA 4 25 0 ACAAGGGGAG 0.984507 -49 AAGCGAATAAGGAAGGGTGATGGG 5 4 0 GGAAGGTGAT 0.923597 -214 ***** ***** Masking position 5 Map Score: 9.82982 Number of sites scoring better than the average of aligned sites = 555 Number in coding regions = 485 Number in noncoding regions = 70 Number of orfs with sites within 600 bp upstream = 76 Fraction of orfs with sites within 600 bp upstream = 0.0122069 Motif number 3 TTCACGCAGGATCTGAGTTTATGGGAATGC 1 86 0 ATCTGAGTTT 0.974363 -197 GCAGCAGTAAATCTGAGTTTATGGGAATAA 1 116 1 ATCTGAGTTT 0.974363 -167 AGGCCGAAAACTCTGCTTTTCAGGTAATTT 1 144 0 CTCTGCTTTT 0.93742 -139 CCCCCATTTTATCTGCTTTTTAACACGTTC 3 117 0 ATCTGCTTTT 0.979872 -85 CACCCCAAGAATCCGTTTTCATTTCCAGTA 4 47 0 ATCCGTTTTC 0.86696 -27 TACGAGACAGATCTGGGTTCCCCTTTATTT 5 45 1 ATCTGGGTTC 0.955548 -173 ATATTAACTCATCTGTTTTTGATAAATTGA 5 171 0 ATCTGTTTTT 0.969205 -47 ********** Masking position 8 Map Score: 7.08877 Number of sites scoring better than the average of aligned sites = 177 Number in coding regions = 151 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 4 ACTGCTGCTTCACGCAGGATCTGAGTTTATGGGAA 1 89 0 CAGGGATCTG 0.995479 -194 CCCAGAGGGGCGAGGGGACTCTCCGAGTATCATGA 1 173 0 CGGGACTCTG 0.98662 -110 AGGATGACTGCGAGTGGGAGCACGGTTTTCACCCT 1 211 0 CGGGGAGCAG 0.983275 -72 GTGAACAGGGAGGATCTTCGTATTCTCCCT 4 6 1 CAGGGATCTG 0.994775 -68 TTCACATTTACGAGACAGATCTGGGTTCCCCTTTA 5 37 1 CGGAGATCTG 0.990179 -181 TCCTTATCATCGTGATGAATCTTTGC 6 2 0 CGGGAATCTG 0.995479 -32 ** * ****** * Masking position 11 Map Score: 6.20356 Number of sites scoring better than the average of aligned sites = 84 Number in coding regions = 80 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 5 GAAGCCGGAGGTTTTCTGCAGATTCGCCTGC 1 47 0 GTTTTCGCAG 0.919486 -236 GAAAAGCAGAGTTTTCGGCCTCATGATACTC 1 153 1 GTTTTCGCCT 0.993902 -130 TGGGAGCACGGTTTTCACCCTCTTCCCAGAG 1 201 0 GTTTTCCCCT 0.995806 -82 ATACATTTTTGTTTTCTCTGTTACTGCCCCC 3 142 0 GTTTTCCTGT 0.912521 -60 GAGGATCTTCGTATTCTCCCTCTTGTTTACT 4 20 1 GTATTCCCCT 0.983214 -54 CTTTTCCTCCTTATCATCGTG 6 23 0 CTTTTCTCCT 0.931979 -11 ****** **** Masking position 5 Map Score: 2.23905 Number of sites scoring better than the average of aligned sites = 322 Number in coding regions = 281 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 48 Fraction of orfs with sites within 600 bp upstream = 0.0077096 Motif number 6 ATTCAAGCAAGCCAGGAGATCTGC 1 5 0 GCCAGGAGAT 0.817863 -278 CAACCTGGAAGCCGGAGGTTTTCTGCAGAT 1 55 0 GCCGGAGGTT 0.969828 -228 ACTGCTGCTTCACGCAGGATCTGAGTTTAT 1 94 0 CACGCAGGAT 0.868792 -189 TCCCAGAGGGGCGAGGGGACTCTCCGAGTA 1 179 0 GCGAGGGGAC 0.914386 -104 TGGCAGGAGTGAGGGAGGATGACTGCGAGT 1 231 0 GAGGGAGGAT 0.991234 -52 ACGCTACTGCGCCGGGGGATTTATTCCGGC 2 22 1 GCCGGGGGAT 0.994344 -93 GTGAACAGGGAGGATCTTCGTATTC 4 6 1 CAGGGAGGAT 0.975614 -68 CAGTAAACAAGAGGGAGAATACGAAGATCC 4 22 0 GAGGGAGAAT 0.926619 -52 ********** Masking position 9 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 7 GACGATACCAATAACAGAAGGCGGGCGTTGGTAA 2 62 1 ATAACAGGCG 0.946103 -53 CGCTGGATTGATAAAATAGTACTAATAGGAGGTG 3 18 0 ATAAAATACA 0.861875 -184 ATATGAAAAAATAAAAGTACAGTGCCGCTGTCCT 3 60 1 ATAAAAGAGG 0.98414 -142 TTCCTGCTGTATAAAAGGACAGCGGCACTGTACT 3 75 0 ATAAAAGAGG 0.98414 -127 TAAAAAGCAGATAAAATGGGGGCAGTAACAGAGA 3 125 1 ATAAAATGGA 0.908234 -77 TCTTTAGAAAATAAAATGTAAGTGCATACATTTT 3 164 0 ATAAAATAGG 0.967788 -38 ATATTATCATATAAAAGTAAGCGGTTACAATAAT 5 138 0 ATAAAAGGCG 0.982773 -80 ******* ** * Masking position 6 Map Score: 2.99316 Number of sites scoring better than the average of aligned sites = 86 Number in coding regions = 70 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 8 AGTTATTCAAGCAAGCCAGGAGATCTGC 1 7 0 GCAAGCGGAG 0.843315 -276 ATCATGGCAGGCGAATCTGCAGAAAACCTCCG 1 41 1 GCGAACGCAG 0.992174 -242 ATGCTCAACCTGGAAGCCGGAGGTTTTCTGCA 1 58 0 TGGAACGGAG 0.932813 -225 CAGATCCTGCGTGAAGCAGCAGTAAATCTGAG 1 101 1 GTGAACGCAG 0.987749 -182 TCGCCCCTCTGGGAAGAGGGTGAAAACCGTGC 1 195 1 GGGAAAGGTG 0.945477 -88 TGTTGAACGTGTTAAAAAGCAGATAAAATGGG 3 113 1 GTTAAAGCAG 0.874908 -89 GTGAACAGGGAGGATCTTCGTA 4 1 1 GTGAAAGGAG 0.990282 -73 AAACAAGAGGGAGAATACGAAGATCCTCCCTG 4 16 0 GAGAAAGAAG 0.861859 -58 TGTGAAGTAAGCGAATAAGGAAGGGTGATGGG 5 11 0 GCGAAAGGAA 0.940149 -207 ***** * **** Masking position 4 Map Score: 4.949 Number of sites scoring better than the average of aligned sites = 982 Number in coding regions = 908 Number in noncoding regions = 74 Number of orfs with sites within 600 bp upstream = 88 Fraction of orfs with sites within 600 bp upstream = 0.0141343 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