AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i127_Transmembrane_Transport_1_ecoli_hinf_reg_300.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 pspA 151 phage shock protein, inner membrane protein #2 pspB 53 phage shock protein #3 pspE 74 phage shock protein #4 ycjM 185 putative polysaccharide hydrolase #5 ycjQ 30 putative oxidoreductase #6 ugpA 21 sn-glycerol 3-phosphate transport system, integral membrane protein #7 BIME167 47 BIME #8 ugpB 238 sn-glycerol 3-phosphate transport system; periplasmic binding protein #9 BIME168 126 BIME #10 livH 47 high-affinity branched-chain amino acid transport system; membrane component #11 livK 300 high-affinity leucine-specific transport system; periplasmic binding protein Motif number 1 TAATTCGCTAACTCATCCTGGCATGTTGCTGT 1 20 1 ACTCATCTGC 0.814124 -132 ACGCGCCGCCGCTCATCGTCTAAGGAGTACTT 2 32 1 GCTCATCTTA 0.907357 -22 TAAATCTCAGGCGTATAATGGATGGCAATTTT 3 32 1 GCGTATATGA 0.70397 -43 AAAAAAAACGGCGCATAAGCGCCGCTCATGGT 4 19 0 GCGCATAGGC 0.692437 -167 CAGGGAAAAAGCGTATTTGTGAGCTGACGCAA 4 85 0 GCGTATTGGA 0.922175 -101 AAACCCTTGTGCTCAATTGACAGTTTATTTTC 4 143 1 GCTCAATGCA 0.696226 -43 GATAAGCGAAACGCATCCGACATTACACTGA 7 10 0 ACGCATCGCA 0.938414 -38 GATGCGTTTCGCTTATCTGACCTGGCATCGCG 7 25 1 GCTTATCGCC 0.979379 -23 TCTACAGATTGCTCATCGTTTCAT 8 3 0 GCTCATCTTC 0.931184 -236 ATATTTTCCCGCTTATCCGTGCCCCATCTCCC 8 53 1 GCTTATCGGC 0.979522 -186 GCGTGAATTCGCGCATTCGGTACAACAAGAGA 8 209 1 GCGCATTGTA 0.921016 -30 GATAAGCGCAGCGCATCAGGCAATTTTACATT 9 61 0 GCGCATCGCA 0.991765 -66 GATGCGCTGCGCTTATCAGGCCTACTGGGTGA 9 76 1 GCTTATCGCC 0.979532 -51 ******* * ** Masking position 5 Map Score: 12.5368 Number of sites scoring better than the average of aligned sites = 2773 Number in coding regions = 2469 Number in noncoding regions = 304 Number of orfs with sites within 600 bp upstream = 142 Fraction of orfs with sites within 600 bp upstream = 0.0228076 Motif number 2 TAAGGTGTGACAGAAAAAAAAACGGCGCAT 4 35 0 CAGAAAAAAA 0.977083 -151 CATTTTTTACCAGGGAAAAAGCGTATTTGT 4 97 0 CAGGGAAAAA 0.881775 -89 TTTAGTCACGCAGGAAATCATTTTTTACCA 4 115 0 CAGGAAATCA 0.931366 -71 GACTACTCCGCAGAAAATAAACTGTCAATT 4 157 0 CAGAAAATAA 0.964595 -29 ACAGTTCAGGAATTAACCGTA 6 7 1 CAGGAATTAA 0.747114 -15 CACGGATAAGCGGGAAAATATAGAAGGTCT 8 44 0 CGGGAAAATA 0.81473 -195 GCTCGAATTACAGAAAAATAACTTTTTTGT 8 151 0 CAGAAAAATA 0.961742 -88 CCTTTGTCAGCATAAAATAACGGCACAAAG 11 71 0 CATAAAATAA 0.775132 -230 GATAGATAAACAGAAAAAAGTGCCTTTGTC 11 93 0 CAGAAAAAAG 0.870546 -208 TCAATAAATTCAGAATATTATCTGTTCTTA 11 121 1 CAGAATATTA 0.630917 -180 TCTTAATCGACTGAAAAATAGGGATTTTAA 11 146 1 CTGAAAAATA 0.744358 -155 CTTAATCAGACAGGCAAAAACAGTGCAGTA 11 207 1 CAGGCAAAAA 0.881775 -94 TTTGTTAACACATAAAAACAAAGCAACACA 11 256 1 CATAAAAACA 0.725039 -45 ********** Masking position 1 Map Score: 10.2953 Number of sites scoring better than the average of aligned sites = 965 Number in coding regions = 784 Number in noncoding regions = 181 Number of orfs with sites within 600 bp upstream = 199 Fraction of orfs with sites within 600 bp upstream = 0.0319627 Motif number 3 TAAATCAAAAAGATAAAAAATTGGCACGCAAATTG 1 74 1 AGTAAAATGC 0.969006 -78 TCCTGAACGCAGAAATCAAGAGGACAACATT 1 131 1 AGAAAAGGGC 0.955899 -21 CGTCCTTCTATGGATGAAAATTGCCATCCATTATA 3 45 0 TGATAAATGC 0.942529 -30 AAGGTGTGACAGAAAAAAAAACGGCGCATAAGCGC 4 29 0 AGAAAAACGC 0.96334 -157 TCTATGGGGATGTAAATAAGGTGTGACAGAAAAAA 4 46 0 TGAAAAGTGG 0.861494 -140 ACTACTCCGCAGAAAATAAACTGTCAATTGAGCAC 4 151 0 AGAAAAATGC 0.989994 -35 TAAAACTCCTTGTAAAGAAACTGGCCGCT 5 5 0 TGAAAAATGC 0.981096 -26 TACATTTGTAAGATAGTAAGGTGTCAGAAAGATGA 8 116 0 AGTAAAGTGC 0.96267 -123 AACATTAGAGAATGAAAAATGTCCAGCATAATC 11 9 1 AGATAAATGC 0.969006 -292 ** ** *** ** * Masking position 8 Map Score: 8.27019 Number of sites scoring better than the average of aligned sites = 189 Number in coding regions = 155 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 4 AGCGCCGCTCATGGTGAATTCTT 4 4 0 ATGGTGAATT 0.981729 -182 CAAATAATCTATGGGGATGTAAATAAGGTG 4 58 0 ATGGGGATGT 0.968645 -128 GAGTGGCAATATGTTGAATTTGCACGATCT 9 106 1 ATGTTGAATT 0.892617 -21 CCCCTGAATGATAGTGAATTATTCCGCCCT 11 43 1 ATAGTGAATT 0.947797 -258 CGACTGAAAAATAGGGATTTTAATCGCTAT 11 153 1 ATAGGGATTT 0.966157 -148 AACATCACGAATGGGGATTTTTGACT 11 285 1 ATGGGGATTT 0.988303 -16 ********** Masking position 7 Map Score: 5.16033 Number of sites scoring better than the average of aligned sites = 98 Number in coding regions = 78 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 5 CGCTTATCCGTGCCCCATCTCCCATTTTCCCTCA 8 62 1 TCCCATCCCA 0.97814 -177 CCATCTCCCATTTTCCCTCACCCACGCCGTCACC 8 76 1 TTCCCTCCCA 0.981163 -163 GCATGTCATGTTACCCCGCGAGCATAAAACGCGT 8 179 1 TCCCCGCACA 0.988807 -60 ATTTTACATTTGTCACCTGTCTCAAAGGAGTCTT 9 37 0 TCACCTGCCA 0.944689 -90 ATTCAACATATTGCCACTCACCCAGTAGGCCTGA 9 91 0 TCCACTCCCA 0.978188 -36 TCATCCCACCGCCCGTAAAATGCGGGC 10 4 1 TCACCGCCTA 0.909535 -44 GTAACCTTTCTAAACCCGCCCGCATTTTACGGGC 10 21 0 TACCCGCCCA 0.980785 -27 AATACTGCGCTAACCCCTTAATCAGACAGGCAAA 11 191 1 TCCCCTTACA 0.922556 -110 * ****** * ** Masking position 14 Map Score: 4.3737 Number of sites scoring better than the average of aligned sites = 408 Number in coding regions = 335 Number in noncoding regions = 73 Number of orfs with sites within 600 bp upstream = 79 Fraction of orfs with sites within 600 bp upstream = 0.0126887 Motif number 6 TTTATAAATCAAAAAGATAAAAAATTGGCAC 1 70 1 AAAAGATAAA 0.794306 -82 AAATAAGGTGTGACAGAAAAAAAAACGGCGC 4 37 0 TGAAGAAAAA 0.690466 -149 GTAAGGTGTCAGAAAGATGACAAGGCGGTGA 8 105 0 AGAAGATGAC 0.966349 -134 CTCGAATTACAGAAAAATAACTTTTTTGTTA 8 149 0 AGAAAATAAC 0.83254 -90 CGGTACAACAAGAGAGATAAACG 8 226 1 AGAAGATAAA 0.975241 -13 GACTCCTTTGAGACAGGTGACAAATGTAAAA 9 39 1 AGAAGGTGAC 0.959492 -88 GGGCGGGTTTAGAAAGGTTACCTT 10 34 1 AGAAGGTTAC 0.896738 -14 CTGAATTTATTGATAGATAAACAGAAAAAAG 11 103 0 TGAAGATAAA 0.925637 -198 CCCCTTAATCAGACAGGCAAAAACAGTGCAG 11 204 1 AGAAGGCAAA 0.896154 -97 *** ******* Masking position 5 Map Score: 3.68038 Number of sites scoring better than the average of aligned sites = 278 Number in coding regions = 221 Number in noncoding regions = 57 Number of orfs with sites within 600 bp upstream = 64 Fraction of orfs with sites within 600 bp upstream = 0.0102795 Motif number 7 CGGCGTCCGAACGCGCCGCCGCTCATCGTC 2 22 1 ACGCGCCGCC 0.994575 -32 AACGGCGCATAAGCGCCGCTCATGGTGAAT 4 15 0 AAGCGCCGCT 0.984192 -171 CAGGTCAGATAAGCGAAACGCATCCGACAT 7 19 0 AAGCGAAACG 0.903268 -29 ACGCGATGCCAGGTCAGATA 7 38 0 ACGCGATGCC 0.967566 -10 TAGGCCTGATAAGCGCAGCGCATCAGGCAA 9 70 0 AAGCGCAGCG 0.990974 -57 ********** Masking position 1 Map Score: 1.73768 Number of sites scoring better than the average of aligned sites = 734 Number in coding regions = 690 Number in noncoding regions = 44 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 8 GGCGCGTTCGGACGCCGCCTGGATGTTA 2 9 0 GACGCCGCCT 0.986 -45 GTCCGAACGCGCCGCCGCTCATCGTCTAAG 2 26 1 GCCGCCGCTC 0.994822 -28 ACGGCGCATAAGCGCCGCTCATGGTGAATT 4 14 0 AGCGCCGCTC 0.963335 -172 CACCCACGCCGTCACCGCCTTGTCATCTTT 8 94 1 GTCACCGCCT 0.969001 -145 TCATCCCACCGCCCGTAAAATGCG 10 5 1 CCCACCGCCC 0.986238 -43 ********** Masking position 5 Map Score: 1.70669 Number of sites scoring better than the average of aligned sites = 759 Number in coding regions = 736 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 9 TGACACCTTACTATCTTACAAATGTAACAA 8 125 1 CTATCTTACA 0.965987 -114 TTTTGACTCCCTATCAATCAACGTGTTA 9 9 0 CTATCAATCA 0.938346 -118 GCGCATCAGGCAATTTTACATTTGTCACCT 9 53 0 CAATTTTACA 0.703047 -74 GAATAATTCACTATCATTCAGGGGATTATG 11 37 0 CTATCATTCA 0.965987 -264 TTTTTTCTGTTTATCTATCAATAAATTCAG 11 104 1 TTATCTATCA 0.814576 -197 ATTAAAATCCCTATTTTTCAGTCGATTAAG 11 147 0 CTATTTTTCA 0.947105 -154 ********** Masking position 4 Map Score: 1.01837 Number of sites scoring better than the average of aligned sites = 121 Number in coding regions = 99 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 10 GTGCCAATTTTTTATCTTTTTGATTTATAAA 1 70 0 TTTTCTTTTT 0.664519 -82 GATTGTCCTGCTGAACTGTTAATACAATTTG 1 102 0 CTGACTGTTA 0.922802 -50 CGCTTATGCGCCGTTTTTTTTTCTGTCACAC 4 30 1 CCGTTTTTTT 0.688893 -156 AGAAAAATAACTTTTTTGTTACATTTGTAAG 8 139 0 CTTTTTGTTA 0.760695 -100 GGGGATTATGCTGGACATTTTTCATTCTCTA 11 16 0 CTGACATTTT 0.613186 -285 CAAAGGCACTTTTTTCTGTTTATCTATCAAT 11 95 1 TTTTCTGTTT 0.822743 -206 TTTTTTTATACTGCACTGTTTTTGCCTGTCT 11 214 0 CTGACTGTTT 0.963502 -87 ACAAATCAGACTGTTCTTTTTTTATACTGCA 11 230 0 CTGTCTTTTT 0.961361 -71 AAAGAACAGTCTGATTTGTTAACACATAAAA 11 242 1 CTGTTTGTTA 0.918473 -59 TGATGTTGTGTTGCTTTGTTTTTATGTGTTA 11 261 0 TTGTTTGTTT 0.875314 -40 *** ******* Masking position 9 Map Score: 2.92794 Number of sites scoring better than the average of aligned sites = 988 Number in coding regions = 847 Number in noncoding regions = 141 Number of orfs with sites within 600 bp upstream = 157 Fraction of orfs with sites within 600 bp upstream = 0.0252168 Motif number 11 ********** No masking Map Score: -1.72419e-12 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 12 ********** No masking Map Score: -1.72419e-12 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 13 ********** No masking Map Score: -1.72419e-12 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