AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i081_PTS_cellobiose_specific_Transport_ecoli_reg_100.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 celC 50 PEP-dependent phosphotransferase enzyme III for cellobiose, arbutin, and salicin #2 celB 84 PEP-dependent phosphotransferase enzyme II for cellobiose, arbutin, and salicin #3 celA 298 PEP-dependent phosphotransferase enzyme IV for cellobiose, arbutin, and salicin Motif number 1 GATGCCGGTACGGGTAATCGTGCCGGTAAGA 1 13 1 CGGGTAATGT 0.785179 -38 GGTAATCGTGCCGGTAAGAAAAGAGAGGAAC 1 25 1 CCGGTAAGAA 0.844472 -26 TTTAAATTTTCCCGTCAAAGAGTTATTTCAT 2 16 1 CCCGTCAAGA 0.941495 -69 ACAACGGAAACCGGCCATTGCGCCGGTTTTT 3 35 1 CCGGCCATGC 0.976927 -264 ATTAAGAACTCAGGCCAAAAAAAACCGGCGC 3 54 0 CAGGCCAAAA 0.978856 -245 CTTCACATTTCGGGCAAATAATTCGCGAAGA 3 87 0 CGGGCAAAAA 0.927556 -212 AAATGTGAAGAGGGTCATAACCACAGGTCAA 3 108 1 AGGGTCATAC 0.845577 -191 GTCATAACCACAGGTCAAGGAGAAACAATTT 3 121 1 CAGGTCAAGA 0.992937 -178 AACAATTTATAAGGTCAAAGAAATACTATTG 3 144 1 AAGGTCAAGA 0.955867 -155 TACTATTGCTCAGGTCTATACCGTATACTCC 3 167 1 CAGGTCTAAC 0.910517 -132 AGCATGGAAGCAGGTTAAGGCTTGCGGAGTG 3 242 1 CAGGTTAAGC 0.944472 -57 ******** ** Masking position 4 Map Score: 8.97882 Number of sites scoring better than the average of aligned sites = 3478 Number in coding regions = 3241 Number in noncoding regions = 237 Number of orfs with sites within 600 bp upstream = 217 Fraction of orfs with sites within 600 bp upstream = 0.0348538 Motif number 2 CGGGTAATCGTGCCGGTAAGAAAAGAGAGG 1 23 1 TGCCGGTAAG 0.975084 -28 TCAATTCGTCTGAAAGCTTGAGTAAC 3 7 1 CGTCTGAAAG 0.973152 -292 GCGAATTATTTGCCCGAAATGTGAAGAGGG 3 92 1 TGCCCGAAAT 0.961049 -207 ACTTTTTTTGTGGCTGAAAGGAGTATACGG 3 187 0 TGGCTGAAAG 0.995465 -112 GCGGAGTGTCTGGCTGACAGATAATCGTCG 3 265 1 TGGCTGACAG 0.989988 -34 ********** Masking position 9 Map Score: 3.55408 Number of sites scoring better than the average of aligned sites = 352 Number in coding regions = 321 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 3 CACGATTACCCGTACCGGCATCGA 1 5 0 CGTACCGGCA 0.977306 -46 CCTCTCTTTTCTTACCGGCACGATTACCCG 1 23 0 CTTACCGGCA 0.966728 -28 TTCATAAATCAATACCGCAATATTTAAATT 2 42 1 AATACCGCAA 0.983997 -43 AATACCCTTAAAAACCGCAATTTAAATATT 2 60 0 AAAACCGCAA 0.977227 -25 AAGCTTGAGTAACAACGGAAACCGGCCATT 3 24 1 AACAACGGAA 0.918755 -275 CAGGCCAAAAAAAACCGGCGCAATGGCCGG 3 45 0 AAAACCGGCG 0.954427 -254 GTCAGCCAGACACTCCGCAAGCCTTAACCT 3 253 0 CACTCCGCAA 0.943313 -46 ********** Masking position 6 Map Score: 4.73026 Number of sites scoring better than the average of aligned sites = 1765 Number in coding regions = 1681 Number in noncoding regions = 84 Number of orfs with sites within 600 bp upstream = 81 Fraction of orfs with sites within 600 bp upstream = 0.01301 Motif number 4 AATTAAGAACTCAGGCCAAAAAAAACCGGC 3 56 0 TCAGGCCAAA 0.927093 -243 TGACTTTTTTTGTGGCTGAAAGGAGTATAC 3 189 0 TGTGGCTGAA 0.980207 -110 GCTTCCATGCTCTGGGTAACTTGCGAAACC 3 223 0 TCTGGGTAAC 0.981117 -76 TTGCGGAGTGTCTGGCTGACAGATAATCGT 3 263 1 TCTGGCTGAC 0.995319 -36 ********** Masking position 9 Map Score: 0.597715 Number of sites scoring better than the average of aligned sites = 457 Number in coding regions = 427 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 5 ********** No masking Map Score: -5.51791e-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 6 ********** No masking Map Score: -5.51791e-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 7 ********** No masking Map Score: -5.51791e-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