AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i127_Transmembrane_Transport_1_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 ycjM 185 putative polysaccharide hydrolase #2 ycjQ 30 putative oxidoreductase #3 ugpA 21 sn-glycerol 3-phosphate transport system, integral membrane protein #4 BIME167 47 BIME #5 ugpB 238 sn-glycerol 3-phosphate transport system; periplasmic binding protein Motif number 1 TAAGGTGTGACAGAAAAAAAAACGGCGCAT 1 35 0 CAGAAAAAAA 0.985539 -151 CATTTTTTACCAGGGAAAAAGCGTATTTGT 1 97 0 CAGGGAAAAA 0.977432 -89 TTTAGTCACGCAGGAAATCATTTTTTACCA 1 115 0 CAGGAAATCA 0.979878 -71 GACTACTCCGCAGAAAATAAACTGTCAATT 1 157 0 CAGAAAATAA 0.981252 -29 ACAGTTCAGGAATTAACCGTA 3 7 1 CAGGAATTAA 0.957342 -15 CACGGATAAGCGGGAAAATATAGAAGGTCT 5 44 0 CGGGAAAATA 0.9587 -195 GCTCGAATTACAGAAAAATAACTTTTTTGT 5 151 0 CAGAAAAATA 0.973353 -88 ********** Masking position 6 Map Score: 10.3012 Number of sites scoring better than the average of aligned sites = 309 Number in coding regions = 240 Number in noncoding regions = 69 Number of orfs with sites within 600 bp upstream = 71 Fraction of orfs with sites within 600 bp upstream = 0.0114038 Motif number 2 AAAAAAACGGCGCATAAGCGCCGCTCATGG 1 20 0 CGCATAAGCG 0.82146 -166 TGAGCTGACGCAAATAATCTATGGGGATGT 1 68 0 CAAATAATCT 0.812628 -118 CGTCAGCTCACAAATACGCTTTTTCCCTGG 1 88 1 CAAATACGCT 0.975746 -98 AGTGTAATGTCGGATGCGTTTCGCTTATCT 4 13 1 CGGATGCGTT 0.919722 -35 GATGCCAGGTCAGATAAGCGAAACGCATCC 4 24 0 CAGATAAGCG 0.989879 -24 AGATGGGGCACGGATAAGCGGGAAAATATA 5 52 0 CGGATAAGCG 0.98788 -187 CTTGTTGTACCGAATGCGCGAATTCACGCG 5 208 0 CGAATGCGCG 0.990065 -31 ********** Masking position 4 Map Score: 8.58042 Number of sites scoring better than the average of aligned sites = 869 Number in coding regions = 737 Number in noncoding regions = 132 Number of orfs with sites within 600 bp upstream = 82 Fraction of orfs with sites within 600 bp upstream = 0.0131706 Motif number 3 TTTTTTTCTGTCACACCTTATTTACATCCCC 1 45 1 TCACCCTTAT 0.952272 -141 TGCGGAGTAGTCTCTCGTTTC 1 175 1 TCTCCGTTTC 0.988614 -11 CCGTGCCCCATCTCCCATTTTCCCTCACCCA 5 69 1 TCTCCATTTT 0.912968 -170 GTCACCGCCTTGTCATCTTTCTGACACCTTA 5 104 1 TGTCTCTTTC 0.940768 -135 GTCATCTTTCTGACACCTTACTATCTTACAA 5 115 1 TGACCCTTAC 0.951104 -124 AATTCGAGCATGTCATGTTACCCCGCGAGCA 5 172 1 TGTCTGTTAC 0.94125 -67 ATGCGCGAATTCACGCGTTTTATGCTCGCGG 5 194 0 TCACCGTTTT 0.971529 -45 CGTTTATCTCTCTTGTTGTACCGAATGCG 5 220 0 TCTCTGTTGT 0.906011 -19 **** ****** Masking position 8 Map Score: 6.55739 Number of sites scoring better than the average of aligned sites = 446 Number in coding regions = 380 Number in noncoding regions = 66 Number of orfs with sites within 600 bp upstream = 81 Fraction of orfs with sites within 600 bp upstream = 0.01301 Motif number 4 GTAAATAAGGTGTGACAGAAAAAAAAACGG 1 40 0 TGTGACAGAA 0.969186 -146 GTATTTGTGAGCTGACGCAAATAATCTATG 1 75 0 GCTGACGCAA 0.967565 -111 TGACGGCGTGGGTGAGGGAAAATGGGAGAT 5 78 0 GGTGAGGGAA 0.990569 -161 ATGACAAGGCGGTGACGGCGTGGGTGAGGG 5 90 0 GGTGACGGCG 0.986851 -149 AAGATAGTAAGGTGTCAGAAAGATGACAAG 5 112 0 GGTGTCAGAA 0.980349 -127 ********** Masking position 3 Map Score: 2.24499 Number of sites scoring better than the average of aligned sites = 822 Number in coding regions = 785 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467 Motif number 5 ACAAGGGTTTTAGTCACGCAGGAAATCATT 1 123 0 TAGTCACGCA 0.960522 -63 TTCTGCGGAGTAGTCTCTCGTTTC 1 172 1 TAGTCTCTCG 0.978629 -14 AGACCTTCTATATTTTCCCGCTTATCCGTG 5 44 1 TATTTTCCCG 0.923359 -195 TCACGCGTTTTATGCTCGCGGGGTAACATG 5 185 0 TATGCTCGCG 0.987 -54 CGAATGCGCGAATTCACGCGTTTTATGCTC 5 198 0 AATTCACGCG 0.972789 -41 ********** Masking position 2 Map Score: 1.15455 Number of sites scoring better than the average of aligned sites = 385 Number in coding regions = 348 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 47 Fraction of orfs with sites within 600 bp upstream = 0.00754899 Motif number 6 ********** No masking Map Score: -3.24418e-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: -3.24418e-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: -3.24418e-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