AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i135_Transmembrane_Transport_9_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 cydA 300 cytochrome d terminal oxidase, polypeptide subunit I #2 ybgE 127 orf, hypothetical protein #3 ybgC 149 orf, hypothetical protein #4 tolA 64 membrane spanning protein, required for outer membrane integrity #5 tolB 132 periplasmic protein involved in the tonb-independent uptake of group A colicins #6 pal 34 peptidoglycan-associated lipoprotein #7 HI0381 23 peptidoglycan-associated outer membrane lipoprotein (pal) #8 HI0382 41 colicin tolerance protein (tolB) #9 HI0384 71 colicin transport protein (tolR) #10 HI0386 300 conserved hypothetical protein Motif number 1 ATTTATAGCTAAATTACCGCCTTTCAGCCAATT 1 31 0 AATACCGCTT 0.892807 -270 AAATACCACATTTTTAGCTCCTTAC 2 3 0 TTTAGCTCTT 0.759184 -125 TCGTTTGGGGTAATCACCGCGCTGGCGCTTGAA 2 67 1 TATACCGCCT 0.984274 -61 CAGATGTCTTCTTGACCGGCTTTGCCTGATTC 2 106 0 TTTACCGGTT 0.878883 -22 GCCCATAAATTTTTACGCTCCCTTAACTTGCCC 3 48 1 TTTCGCTCCT 0.847017 -102 CGCTCCCTTAACTTGCCCTCATTCCCAAACCTC 3 63 1 ATTCCCTCTT 0.790117 -87 ACTGTTCGCCTGTTACCCGCTCTCTTTCAAGCA 4 27 0 TTTCCCGCCT 0.989942 -38 CGGTGCCTGATGTTGACCGTCCGAACAGTCAAC 5 18 0 TTTACCGTCG 0.871597 -115 ATATAGGGAAAATTGACCGCACTTTGAAGAAAA 9 12 1 ATTACCGCCT 0.989042 -60 TTTTAACTTATTTTTACCGCACTTTTTCTTCAA 9 35 0 TTTACCGCCT 0.994897 -37 TCTATTCAAAACATAACCGTTCTTTAAAAATAG 10 88 0 AATACCGTCT 0.864801 -213 GACAAATCATTTTTAACCTTTCTCATTGAGTAA 10 123 0 TTTACCTTCT 0.92521 -178 ACATCTAAAATTTTTACCGCACTTTTAGCCTGA 10 176 0 TTTACCGCCT 0.994897 -125 * ** ***** ** Masking position 4 Map Score: 18.595 Number of sites scoring better than the average of aligned sites = 944 Number in coding regions = 868 Number in noncoding regions = 76 Number of orfs with sites within 600 bp upstream = 90 Fraction of orfs with sites within 600 bp upstream = 0.0144555 Motif number 2 CATGTTTGCAACCTTTCTTTACGCCGTTTT 1 166 1 ACCTTTCTTT 0.91888 -135 TCGCCTGTTACCCGCTCTCTTTCAAGCAAG 4 25 0 CCCGCTCTCT 0.966635 -40 GGGAAAATTGACCGCACTTTGAAGAAAAAG 9 17 1 ACCGCACTTT 0.995388 -55 ACTTATTTTTACCGCACTTTTTCTTCAAAG 9 33 0 ACCGCACTTT 0.995388 -39 TCAAAACATAACCGTTCTTTAAAAATAGCC 10 86 0 ACCGTTCTTT 0.986501 -215 TAAAATTTTTACCGCACTTTTAGCCTGACT 10 174 0 ACCGCACTTT 0.995388 -127 ********** Masking position 8 Map Score: 10.4163 Number of sites scoring better than the average of aligned sites = 75 Number in coding regions = 66 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 3 ATAAACAGGTTTTTGTTGAAGCAAATTTGCATTTTTCGA 1 73 0 TTTTTATTTG 0.973653 -228 ACAAAAACCTGTTTATTGTAAGGATTTTGCGGCGTAATA 1 96 1 GTTTTATTTG 0.985972 -205 ATCAATTTGAGTTTTTATTAACATGTTTGCAACCTTTCT 1 145 1 GTTTTTTTTG 0.899301 -156 TAAAAATGTGGTATTTCGCATGGATTCTGGGAACGCTTC 2 20 1 GTATTATCTG 0.916126 -108 CGGCCCATAATTTTTTAAAGAGAATTCTGAT 3 3 0 TTTTTATCTG 0.958584 -147 GTTCTGGTAGTTTTGTGTATTTTAGTTTGTTAACATTCT 5 62 1 TTTTTATTTG 0.973653 -71 AAATTTTAACTTATTTTTACCGCACTTTTTCTTCAAAGT 9 32 0 TTATTATTTT 0.585508 -40 GATATTTAGCGTTTCTATGCGACAATCTTTGCGGTTATT 10 11 0 GTTTTATCTT 0.871498 -290 CCACCAGTATTTTTATTCTTGATATTTAGCGTTTCTATG 10 31 0 TTTTTATTAG 0.838705 -270 ATCTTATTGAGTTTTTCATAGATAGCTTGCTTATCCCAA 10 224 1 GTTTTACTTG 0.929757 -77 AGAATACACGGTTTATTGCGACCAATTGGGTGAGAAT 10 274 1 GTTTTATTGG 0.936135 -27 **** * * **** Masking position 6 Map Score: 6.23398 Number of sites scoring better than the average of aligned sites = 223 Number in coding regions = 171 Number in noncoding regions = 52 Number of orfs with sites within 600 bp upstream = 60 Fraction of orfs with sites within 600 bp upstream = 0.00963701 Motif number 4 CTGGAGCGGCCCATAATTTTTTAAAGAGAAT 3 17 0 CCATAATTTT 0.947704 -133 CGCTCCAGGCCCATAAATTTTTACGCTCCCT 3 40 1 CCATAATTTT 0.947706 -110 CGTTTAAAAGCTCTAACTTTTGTTGCATTAC 3 118 1 CTCTAATTTT 0.963501 -32 TAAAATTTAACAATAAATTTTTCTAAAGAA 8 10 0 CAATAATTTT 0.921358 -32 TTTGTTACCTTTAAAATTTAACAATAAAT 8 23 0 CTTTAAATTT 0.869183 -19 ATATTCCTCTAAAATTTTAACTTATTT 9 55 0 CTCTAAATTT 0.963501 -17 ATTTTAAAACATCTAAAATTTTTACCGCACT 10 186 0 ATCTAAATTT 0.746696 -115 ATGAAAAACTCAATAAGATTTTATTCATTTT 10 212 0 CAATAAATTT 0.921297 -89 ****** **** Masking position 6 Map Score: 5.39498 Number of sites scoring better than the average of aligned sites = 92 Number in coding regions = 66 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 5 AGATAAATTGTTCTCGATCAAATTG 1 5 1 AAATTGTTCC 0.987247 -296 ATTTAGCTATAAATTGATCACCGTCGAAAAA 1 50 1 AAATTGATCC 0.991065 -251 ATAAAAACTCAAATTGATCCCACGTATATAT 1 132 0 AAATTGATCC 0.991065 -169 CGGTTTCCAAAAACTGTTCGCCTGTTACCCG 4 41 0 AAACTGTTCC 0.965876 -24 AATATAGGGAAAATTGACCGCACTTTGAAGA 9 11 1 AAATTGACCC 0.975937 -61 ATTCTCACCCAATTGGTCGCAATAAACCGT 10 281 0 CAATTGGTCC 0.959662 -20 ********* * Masking position 5 Map Score: 7.2692 Number of sites scoring better than the average of aligned sites = 48 Number in coding regions = 41 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 6 ATTTCGCATGGATTCTGGGAACGCTTCTTG 2 32 1 GATTCTGGGA 0.907306 -96 TTGCCTGTTCGTTTGGGGTAATCACCGCGC 2 59 1 GTTTGGGGTA 0.916023 -69 GCGCGATTGAGGTTTGGGAATGAGGGCAAG 3 74 0 GGTTTGGGAA 0.966932 -76 CAGGCGAACAGTTTTTGGAAACCGAGA 4 48 1 GTTTTTGGAA 0.961095 -17 GTTGCCACGGGGTTCTGGTAGTTTTGTGTA 5 51 1 GGTTCTGGTA 0.972991 -82 GGTTCTGGTAGTTTTGTGTATTTTAGTTTG 5 61 1 GTTTTGTGTA 0.758501 -72 TCTAGAACCAGTTTTTGGGATAAGCAAGCT 10 247 0 GTTTTTGGGA 0.963857 -54 CCCAAAAACTGGTTCTAGAATACACGGTTT 10 258 1 GGTTCTAGAA 0.823721 -43 ********** Masking position 10 Map Score: 3.71211 Number of sites scoring better than the average of aligned sites = 407 Number in coding regions = 377 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 7 CATGTTAATAAAAACTCAAATTGATCCCAC 1 140 0 AAAACTCAAA 0.962118 -161 CCTCATTCCCAAACCTCAATCGCGCGCGTA 3 79 1 AAACCTCAAT 0.974121 -71 AAAACTCATTTAGGAGAAAT 7 1 1 AAAACTCATT 0.962116 -23 CTATCTATGAAAAACTCAATAAGATTTTAT 10 219 0 AAAACTCAAT 0.984656 -82 ********** Masking position 6 Map Score: 2.15705 Number of sites scoring better than the average of aligned sites = 13 Number in coding regions = 12 Number in noncoding regions = 1 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 8 CTCGATCAAATTGGCTGAAAGGCGGTAATTTAGCT 1 23 1 TTGCTGAGGG 0.99328 -278 TGAAGCAAATTTGCATTTTTCGACGGTGATCAATT 1 61 0 TTGATTTCGG 0.868575 -240 GGAACGCTTCTTGCCTGTTCGTTTGGGGTAATCAC 2 49 1 TTGCTGTGTG 0.977127 -79 TTGACCGGCTTTGCCTGATTCGACGTGTTCAAGCG 2 92 0 TTGCTGTCGG 0.996392 -36 TCGCGATGTTGACTGTTCGGACGGTCAACATCA 5 9 1 TTGCTGTGGG 0.996392 -124 CATATCTCCCTTATCTGGACCGATGGCCCACGATA 5 108 0 TTACTGACGG 0.958153 -25 *** *** * ** * Masking position 6 Map Score: 1.87131 Number of sites scoring better than the average of aligned sites = 176 Number in coding regions = 122 Number in noncoding regions = 54 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 9 TATTAACATGTTTGCAACCTTTCTTTACGCCGT 1 160 1 TTTGCCTTTC 0.987177 -141 TTACGCCGTTTTTGTGTGCATTCACATGGTATG 1 184 1 TTTGGCATTC 0.97054 -117 TAGAAATTTGTTTGAACACTTTCATCATACCAT 1 209 0 TTTGACTTTC 0.979983 -92 AAGCTCTAACTTTTGTTGCATTACCGGGATGTA 3 125 1 TTTTGCATTA 0.746535 -25 TTCTGGTAGTTTTGTGTATTTTAGTTTGTTAAC 5 63 1 TTTGATTTTA 0.681224 -70 TGTATTTTAGTTTGTTAACATTCTGCTAAATTA 5 77 1 TTTGACATTC 0.968272 -56 TTTGTTACCTTTAAAATTTAACA 8 29 0 TTTGCCTTTA 0.967837 -13 TGACAAATCATTTTTAACCTTTCTCATTGAGTA 10 124 0 TTTTCCTTTC 0.946259 -177 **** ****** Masking position 3 Map Score: 4.38663 Number of sites scoring better than the average of aligned sites = 251 Number in coding regions = 221 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 10 ********** No masking Map Score: -2.10077e-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 11 ********** No masking Map Score: -2.10077e-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 ATAAATTGATCACCGTCGAAAAATGCAAATTT 1 58 1 CACCGTAAAA 0.955665 -243 CACACGCATGCCCCAATAGAAATTTGTTTGAA 1 226 0 CCCCAAGAAA 0.939889 -75 CGAGAGTGAACCCCGTTAGAAAGGGTCACACG 1 252 0 CCCCGTGAAA 0.992467 -49 GCGGTGATTACCCCAAACGAACAGGCAAGAAG 2 55 0 CCCCAAGAAC 0.949698 -73 CGTATAGTAGCAGCGTTTAAAAGCTCTAACTT 3 105 1 CAGCGTAAAA 0.805598 -45 GCCTGATGTTGACCGTCCGAACAGTCAACATC 5 15 0 GACCGTGAAC 0.936744 -118 ACTACCAGAACCCCGTGGCAACCGGTGCCTGA 5 41 0 CCCCGTCAAC 0.978349 -92 ****** **** Masking position 10 Map Score: 0.14358 Number of sites scoring better than the average of aligned sites = 333 Number in coding regions = 298 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 13 ********** No masking Map Score: -2.10077e-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 14 ********** No masking Map Score: -2.10077e-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 15 ********** No masking Map Score: -2.10077e-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