AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i128_Transmembrane_Transport_2_ecoli_hinf_reg_100.orf -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -g0.46 -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 = 0.46 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 yaeC 39 putative lipoprotein #2 abc 187 ATP-binding component of a transporter #3 HI0620 300 28 kDa outer membrane protein (hlpA) #4 HI0621 175 ABC transporter, ATP-binding protein Motif number 1 TTCAACACAACATAAATAATTGAAGAAGGA 1 13 1 CATAAATAAT 0.964558 -27 TTAGTCGTGGCATCTCGAATGCCTGAAACG 2 144 0 CATCTCGAAT 0.889377 -44 TAATGACGATAATAAATAATCA 2 176 1 AATAAATAAT 0.870379 -12 GAGCTTCTGACAAATAGAATTTACGAACAA 3 15 0 CAAATAGAAT 0.863426 -286 ACGAATAGCACAATAATAATGGTTGCCACC 3 188 0 CAATAATAAT 0.660264 -113 TTTGGCTAATCATAACGAATAGCACAATAA 3 202 0 CATAACGAAT 0.947708 -99 AAAAGTGGATCATCGTTAATTAAACGCAAC 3 254 1 CATCGTTAAT 0.772921 -47 GCTTGGATTAAATAGATAATTTTTGTCAAT 4 35 0 AATAGATAAT 0.866659 -141 AAATATAAGTCATAACTAATCTGTCTAAAA 4 72 1 CATAACTAAT 0.950922 -104 ATCTGTCTAAAAAAGATAATCTGACATATT 4 90 1 AAAAGATAAT 0.724706 -86 GCAATCTAGACATCTAGAATACCAAAACAG 4 126 1 CATCTAGAAT 0.918653 -50 ********** Masking position 8 Map Score: 8.14446 Number of sites scoring better than the average of aligned sites = 592 Number in coding regions = 463 Number in noncoding regions = 129 Number of orfs with sites within 600 bp upstream = 152 Fraction of orfs with sites within 600 bp upstream = 0.0244137 Motif number 2 TAGCGTCACATGCCTTATTAAGGAGCTATAAAA 2 12 0 TGCTATTAGG 0.809403 -176 TCCAGACGTCTAAATCAATCAGGTTTATGCGAA 2 78 0 TAATAATAGG 0.861162 -110 GGCAACGCCGTCAATGAAATGGATGTTAAGGCA 2 111 0 TCATAAAGGA 0.878021 -77 GCATCTCGAATGCCTGAAACGGGCAACGCCGTC 2 132 0 TGCTAAAGGG 0.99157 -56 GGCGATACACTGGCTAAAAAAGTGGATCATCGT 3 237 1 TGCTAAAAGT 0.943808 -64 ACGCAACTCTTAACTTAAACAGGAAGGAAATCC 3 277 1 TACTAAAAGG 0.972664 -24 CAATTTGACATGTATAAAAGGTAAGAGA 4 6 0 TGATAAAGTA 0.765147 -170 GCTAATTGCTTGGATTAAATAGATAATTTTTGT 4 39 0 TGATAAAAGA 0.971754 -137 ATAACTAATCTGTCTAAAAAAGATAATCTGACA 4 83 1 TGCTAAAAGA 0.982192 -93 TTAAAAACAATAAATAAAAAGGGCTTAT 4 158 1 TAATAAAGGG 0.960277 -18 ** ** *** *** Masking position 7 Map Score: 7.51647 Number of sites scoring better than the average of aligned sites = 482 Number in coding regions = 404 Number in noncoding regions = 78 Number of orfs with sites within 600 bp upstream = 90 Fraction of orfs with sites within 600 bp upstream = 0.0144555 Motif number 3 ATTTAGACGTCTGGATGCCTTAACATCCAT 2 96 1 CTGGATGCCT 0.938026 -92 TTCAGGCATTCGAGATGCCACGACTAACTT 2 147 1 CGAGATGCCA 0.974053 -41 TTCGTAAATTCTATTTGTCAGAAGCTCTAC 3 18 1 CTATTTGTCA 0.936202 -283 GCGTATATCGCAATATGCCTTATGTAACTT 3 157 1 CAATATGCCT 0.976039 -144 TAATTTTTGTCAATTTGACATGTATAAAAG 4 19 0 CAATTTGACA 0.853107 -157 ATTGCTATGTCAATATGTCAGATTATCTTT 4 101 0 CAATATGTCA 0.971206 -75 TTTTGGTATTCTAGATGTCTAGATTGCTAT 4 123 0 CTAGATGTCT 0.969023 -53 ********** Masking position 6 Map Score: 4.83027 Number of sites scoring better than the average of aligned sites = 176 Number in coding regions = 156 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 4 GCATGTGACGCTAGTATCGCATGTTTCGACC 2 32 1 CTGTATCGCA 0.976035 -156 ATGCCTGAAACGGGCAACGCCGTCAATGAAA 2 125 0 CGGCAACGCC 0.993066 -63 GACTAGCGTAAGAGTAACGCCATTAATTAGC 3 52 0 AGGTAACGCC 0.9908 -249 CAACTACGGGCGTATATCGCAATATGCCTTA 3 148 1 CGATATCGCA 0.976035 -153 TTTTTTAGCCAGTGTATCGCCGAGTTTTTGG 3 227 0 AGGTATCGCC 0.995137 -74 ** ******** Masking position 6 Map Score: 3.5431 Number of sites scoring better than the average of aligned sites = 460 Number in coding regions = 440 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 5 ATAAGGCATGTGACGCTAGTATCGCATGTT 2 27 1 TGACGCTAGT 0.993247 -161 ATTATCGTCATTAAGTTAGTCGTGGCATCT 2 159 0 TTAAGTTAGT 0.867923 -29 ACTAACTTAATGACGATAATAAATAATCA 2 169 1 TGACGATAAT 0.942628 -19 GAAGCTCTACCTACGCTAATTAATGGCGTT 3 38 1 CTACGCTAAT 0.964581 -263 GGCGTTACTCTTACGCTAGTCACTTTAGTT 3 62 1 TTACGCTAGT 0.992713 -239 ********** Masking position 7 Map Score: 2.52464 Number of sites scoring better than the average of aligned sites = 56 Number in coding regions = 43 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 6 GAAACGGGCAACGCCGTCAATGAAATGGAT 2 120 0 ACGCCGTCAA 0.984504 -68 TTATTTATTATCGTCATTAAGTTAGTCGTG 2 165 0 TCGTCATTAA 0.972012 -23 CGTAAGAGTAACGCCATTAATTAGCGTAGG 3 47 0 ACGCCATTAA 0.982032 -254 TTAGGTAGCCTCGCTATCAACTACGGGCGT 3 131 1 TCGCTATCAA 0.94175 -170 AAAAAGTGGATCATCGTTAATTAAACGCAA 3 253 1 TCATCGTTAA 0.8778 -48 ********** Masking position 7 Map Score: 1.2529 Number of sites scoring better than the average of aligned sites = 790 Number in coding regions = 744 Number in noncoding regions = 46 Number of orfs with sites within 600 bp upstream = 54 Fraction of orfs with sites within 600 bp upstream = 0.00867331 Motif number 7 ********** No masking Map Score: -5.16264e-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: -5.16264e-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: -5.16264e-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