AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -irpoN_ecoli_hinf_100.orf -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 glnP 138 glutamine high-affinity transport system; membrane component #2 glnH 300 periplasmic glutamine-binding protein; permease #3 pspF 151 psp operon transcriptional activator #4 hycB 124 probable small subunit of hydrogenase-3, iron-sulfur protein (part of formate hydrogenlyase (FHL) complex) #5 hycA_hypA 211 hycA: transcriptional repression of hyc and hyp operons, hypA: pleiotrophic effects on 3 hydrogenase isozymes #6 hypE 38 plays structural role in maturation of all 3 hydrogenases #7 glnL 285 histidine protein kinase sensor for GlnG regulator (nitrogen regulator II, NRII) #8 glnA 300 glutamine synthetase #9 fdhF 197 selenopolypeptide subunit of formate dehydrogenase H #10 HI0536 102 urease accessory protein (ureG) #11 HI0865 230 glutamine synthetase (glnA) #12 HI1079 67 amino acid ABC transporter, permease protein #13 HI1080 300 amino acid ABC transporter, periplasmic-binding protein Motif number 1 CTGTGTTGAGTGCACAATTTTAGCGCACCAGAT 2 115 1 TGCACAATTG 0.86609 -186 ACCATTCTGGGGCACCAATCTGGTGCGCTAAAA 2 132 0 GGCACCATTG 0.952401 -169 ACCCTGAAGATGCACCATTCTGGGGCACCAATC 2 145 0 TGCACCATTG 0.990676 -156 ATGAAAAAATCGTGCCAGTTTTGCAACTCCTTG 2 225 0 CGTGCCATTG 0.958481 -76 ATACAATTTGCGTGCCAATTTTTTATCTTTTTG 3 61 1 CGTGCCATTT 0.901707 -91 AAGCAATAATTGTGCCAGTGTTGATTATCCCTG 5 40 1 TGTGCCATTG 0.9786 -172 AAGCATTTTTTGTGCCAACTTTTAATTTATTGT 5 154 0 TGTGCCACTT 0.930283 -58 CTGAACAGGTTGCACCATTTTAGTGCATTATAG 7 252 0 TGCACCATTG 0.990676 -34 CAAAGGTCATTGCACCAACATGGTGCTTAATGT 8 80 1 TGCACCACTG 0.987345 -221 ATGTGAATGTTGCACCAATATAGTGCTTCAATG 8 116 0 TGCACCATTG 0.990676 -185 GCAAAAGGGCTGCACCACGATGTGAATGTTGCA 8 135 0 TGCACCAGTT 0.898013 -166 CGTTATCATGCGCACCATCGTGCAAAAGGGCTG 8 156 0 CGCACCACTC 0.851252 -145 AAGCGAAATCTGTGCCAACTTTTAAATTGCCCC 8 196 0 TGTGCCACTT 0.930283 -105 TGCAATTCATTGCGCCATTTTTTATGTAACAAT 11 51 0 TGCGCCATTT 0.980884 -180 ******* * * * Masking position 7 Map Score: 22.3854 Number of sites scoring better than the average of aligned sites = 651 Number in coding regions = 574 Number in noncoding regions = 77 Number of orfs with sites within 600 bp upstream = 60 Fraction of orfs with sites within 600 bp upstream = 0.00963701 Motif number 2 ATTTACTTAATCAGCTGGAGATAGCAGATGG 2 6 0 TCGCTGGTGA 0.773572 -295 GATTGTTTTTTCATCAGGTTTTACGCTAAATAATCA 2 79 1 TCTCAGTTCC 0.95589 -222 GAATGGTGCATCTTCAGGGTATTGCCCTATAAATCG 2 158 1 TCTCAGTTGC 0.99018 -143 TATAAATCGTGCATCACGTTTTTGCCGCATCTCGAA 2 185 1 GCTCAGTTGC 0.940841 -116 AATGTTGTCCTCTTGATTTCTGCGTTCAGGATT 3 8 1 TCTCTGTTTC 0.888203 -144 TGACATTTCATCGGCATGTTTTCGTCAAAAATGACA 4 80 1 TCGCAGTTGC 0.990361 -45 CAGGCATTCCTCAGGTGATTGTCATTTTTGACG 4 102 0 TCTCAGGTGC 0.980733 -23 AAGATGAATTTCGTCGCCGTGTCGACGTGTCATTTC 5 96 0 TCTCGCTTGC 0.880861 -116 GCCTACCACATCATCACCGTGTAGGCCGGATAAGAC 7 100 0 TCTCACTTGC 0.960045 -186 GTGAAGTTTGTCAGCTATCTGTAGCCCATCTCTGCA 7 161 1 TCGCTTTTGC 0.94058 -125 TAGGAAATCCTCTATGGTTAGTCTTATTAAGAT 11 208 0 TCTCTTGTGC 0.886902 -23 GATTACATACTCAGCTCGTTCTGCACTCATAAATGG 12 27 0 TCGCTGTTCC 0.956677 -41 GAGTATGTAATCAGCTCGTTTTGGCCT 12 51 1 TCGCTGTTGC 0.990361 -17 ** *** * * * * * Masking position 12 Map Score: 14.8998 Number of sites scoring better than the average of aligned sites = 381 Number in coding regions = 361 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 3 AAAATGACATTTCATCGGCATGTTTTCGTCAAA 4 76 1 TCACGGCATT 0.95163 -49 GGCGAAAAGTTTCCACGGCAACTAAAACAC 7 8 0 TCCCGGCAAT 0.93453 -278 AGCCCATCTCTGCATGGGCTTTTTTCTCCGTCA 7 183 1 TCAGGGCTTT 0.908804 -103 GATAACGCCTTTTAGGGGCAATTTAAAAGTTGG 8 182 1 TTAGGGCAAT 0.989666 -119 AGATTTTACTTGTAGGGGCAAATCACATTTGCC 10 30 1 TTAGGGCAAT 0.989666 -73 TCAACGAATGTTCAAGGGCAAATGTGATTTGCC 10 46 0 TCAGGGCAAT 0.99346 -57 TTCGTTGATATATAGGGGCAAATGTAACTTGCC 10 71 1 TTAGGGCAAT 0.989666 -32 GGGTGTAGGGGCAAGTTACATTTGCC 10 87 0 TTAGGGCAAT 0.989666 -16 * ** ****** * Masking position 1 Map Score: 10.671 Number of sites scoring better than the average of aligned sites = 31 Number in coding regions = 28 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 4 CAAACCCGCTCCGGGGCCATTAATTACCCTG 1 81 1 CCGGGGCCAT 0.964871 -58 ATAATCAAATTCAGGGTAATTAATGGCCCCG 1 92 0 TCAGGGTAAT 0.821604 -47 CGAAAAGTTTCCACGGCAACTAAAACAC 7 8 0 CCACGGCAAT 0.869971 -278 TAACGCCTTTTAGGGGCAATTTAAAAGTTGG 8 184 1 TAGGGGCAAT 0.990796 -117 ATTTTACTTGTAGGGGCAAATCACATTTGCC 10 32 1 TAGGGGCAAT 0.990796 -71 AACGAATGTTCAAGGGCAAATGTGATTTGCC 10 46 0 CAAGGGCAAT 0.976327 -57 CGTTGATATATAGGGGCAAATGTAACTTGCC 10 73 1 TAGGGGCAAT 0.990796 -30 GGGTGTAGGGGCAAGTTACATTTGCC 10 87 0 TAGGGGCAAT 0.990796 -16 ********* * Masking position 9 Map Score: 10.6524 Number of sites scoring better than the average of aligned sites = 128 Number in coding regions = 113 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 5 CGTGGATAGAAAAAAGGAAATGCT 2 287 1 AAAAAGGAAA 0.842195 -14 TTTATAAATCAAAAAGATAAAAAATTGGCA 3 73 0 AAAAAGATAA 0.948824 -79 TGTCGCCGTAAAAAAGATAAAGCGAAATCT 8 218 0 AAAAAGATAA 0.948824 -83 ACATTTGTCGAAAAGGAAAAATTATACATG 11 96 1 AAAAGGAAAA 0.842195 -135 GTCATAGCAGAAAAAGAAAAATACATGTAT 11 119 0 AAAAAGAAAA 0.958057 -112 CTATGACTAGAATAAGAAAAATAAATTTCA 11 142 1 AATAAGAAAA 0.922971 -89 GGTTAGTCTTATTAAGATAAGCGCACATTA 11 196 0 ATTAAGATAA 0.605236 -35 TTACTATCAAAATAAGAAAATAATCTACCG 13 164 0 AATAAGAAAA 0.922971 -137 CTTATGAAAAAAAAAGATTATTTATTTATG 13 232 0 AAAAAGATTA 0.745076 -69 ********** Masking position 4 Map Score: 7.31318 Number of sites scoring better than the average of aligned sites = 157 Number in coding regions = 89 Number in noncoding regions = 68 Number of orfs with sites within 600 bp upstream = 81 Fraction of orfs with sites within 600 bp upstream = 0.01301 Motif number 6 TGTGTTGAGTGCACAATTTTAGCGCACCAGATT 2 116 1 GCACATTTAC 0.90349 -185 AAAACGTGATGCACGATTTATAGGGCAATACCC 2 174 0 GCACATTTTG 0.949589 -127 TGCAAAACTGGCACGATTTTTTCATATATGTGA 2 233 1 GCACATTTTC 0.987411 -68 CATTTCATCGGCATGTTTTCGTCAAAAATGACA 4 83 1 GCATTTTTGC 0.798977 -42 ATCAACACTGGCACAATTATTGCTTGTAGCTGG 5 32 0 GCACATTATC 0.765091 -180 CCAGCTTTAAGCATTTTTTGTGCCAACTTTTAA 5 162 0 GCATTTTTTC 0.949281 -50 CTGATGCTTCGCGCTTTTTATCCGTAAAAAGCT 7 221 1 GCGCTTTTTC 0.952172 -65 GATATTACGGGCACTATTTATTCAAAACTCTGA 9 85 0 GCACATTTTC 0.986096 -113 ACTACAGTATGCATCTTTTATGCCACATTTTAT 9 133 0 GCATTTTTTC 0.95428 -65 TGGATAAGATGCAATTTTTATTGCATTGTTACA 11 27 1 GCAATTTTTG 0.604535 -204 GCAATTCATTGCGCCATTTTTTATGTAACAATG 11 50 0 GCGCATTTTA 0.705406 -181 AAAAATACATGTATAATTTTTCCTTTTCGACAA 11 100 0 GTATATTTTC 0.673293 -131 **** **** * * Masking position 7 Map Score: 9.36717 Number of sites scoring better than the average of aligned sites = 528 Number in coding regions = 452 Number in noncoding regions = 76 Number of orfs with sites within 600 bp upstream = 84 Fraction of orfs with sites within 600 bp upstream = 0.0134918 Motif number 7 GGACGATCCCCTGCGTGACATTCACATATA 2 257 0 CTGCGTGACA 0.822028 -44 TTTTTTCTATCCACGGGACGATCCCCTGCG 2 272 0 CCACGGGACG 0.850075 -29 GTTTGGGGATGGGCGTGTCGATGAGTGTCG 4 46 1 GGGCGTGTCG 0.986359 -79 TGAATTTCGTCGCCGTGTCGACGTGTCATT 5 98 0 CGCCGTGTCG 0.978734 -114 CCGCTACCGTGGGCGAGTTGGATATTAT 6 9 0 GGGCGAGTTG 0.763323 -30 GCGTCGCATCCGGCGTGATGTGCTTGCCAC 7 64 0 CGGCGTGATG 0.983079 -222 CAATTATTTTGGCCGTGTCGCCGTAAAAAA 8 233 0 GGCCGTGTCG 0.962445 -68 AATGTCTGCCGCGTGATGGCTGTCACGC 9 9 1 CCGCGTGATG 0.967692 -189 AAACGAAATACCGCGTGACAGCCATCACGC 9 21 0 CCGCGTGACA 0.948323 -177 TCGTCAGTTTTGACGTGACGAAACGAAATA 9 41 0 TGACGTGACG 0.858932 -157 ********** Masking position 4 Map Score: 7.50108 Number of sites scoring better than the average of aligned sites = 1515 Number in coding regions = 1469 Number in noncoding regions = 46 Number of orfs with sites within 600 bp upstream = 46 Fraction of orfs with sites within 600 bp upstream = 0.00738837 Motif number 8 TAAAGATTGTTTTTTCATCAGGTTTTACGCTAAA 2 75 1 TTTTTCTATT 0.952468 -226 CTGGCACGATTTTTTCATATATGTGAATGTCACG 2 240 1 TTTTTCTTGT 0.83437 -61 TTGTGCCAACTTTTAATTTATTGTTATTAAAGAG 5 144 0 TTTTAATAGT 0.657403 -68 CGACAGCCTGTTTTTCGTCAGAGTTTTGAATAAA 9 68 1 TTTTTCTAGT 0.969656 -130 GTGCGGTTATTTTTTATTGAGATTTTACTTGTAG 10 11 1 TTTTTATATT 0.895305 -92 GCCATGCTATTTTTTCATGAAATTTATTTTTCTT 11 155 0 TTTTTCTATT 0.952327 -76 GAAAGGCATTTTTTTACTGAAATTTTATAAGAGT 13 85 1 TTTTTATATT 0.895301 -216 AAAAAAAGATTATTTATTTATGGTTTATGAATTT 13 220 0 TATTTATAGT 0.657403 -81 ATAATCTTTTTTTTTCATAAGTTTGGTTTTTATA 13 241 1 TTTTTCTATT 0.952468 -60 TTTTTCTTCCTTGTGTTGTGTTTG 13 287 0 TTTTTCTCGT 0.881884 -14 ****** * * ** Masking position 8 Map Score: 5.04735 Number of sites scoring better than the average of aligned sites = 108 Number in coding regions = 78 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 9 GCTGAGGCTTTGCCCGTTTTGCAGGCGTT 4 10 1 TTGCCCGTTT 0.927877 -115 TGTCAGGTTACCCGTTTAACAGAGATG 5 195 0 TTACCCGTTT 0.834129 -17 TAAAATGGTGCAACCTGTTCAGGAGACTGC 7 263 1 CAACCTGTTC 0.819825 -23 GACCTTTGGATAACCCTTTTTATGCTCCGT 8 58 0 TAACCCTTTT 0.758567 -243 CATCGTGGTGCAGCCCTTTTGCACGATGGT 8 146 1 CAGCCCTTTT 0.953625 -155 AAACTGACGACAGCCTGTTTTTCGTCAGAG 9 61 1 CAGCCTGTTT 0.953623 -137 ATTACATACTCAGCTCGTTCTGCACTCATA 12 32 0 CAGCTCGTTC 0.920912 -36 AGTATGTAATCAGCTCGTTTTGGCCT 12 52 1 CAGCTCGTTT 0.953623 -16 ********** Masking position 8 Map Score: 2.78178 Number of sites scoring better than the average of aligned sites = 910 Number in coding regions = 848 Number in noncoding regions = 62 Number of orfs with sites within 600 bp upstream = 63 Fraction of orfs with sites within 600 bp upstream = 0.0101189 Motif number 10 TGTGGATACAAAAAATTTACTTAATCAGCTGGA 2 23 0 AAAAATCTTA 0.782395 -278 ATCGTTACATAAAGATTGTTTTTTCATCAGGTT 2 66 1 AAAGATTTTT 0.672523 -235 TTTTTAAGCTAAAGATGAATTTCGTCGCCGTGT 5 110 0 AAAGATTTTC 0.921579 -102 TCTTTAGCTTAAAAATCTCTTTAATAACAATAA 5 128 1 AAAAATTTTA 0.938843 -84 GCAGAAAAAGAAAAATACATGTATAATTTTTCC 11 110 0 AAAAATTGTA 0.80349 -121 CTAGAATAAGAAAAATAAATTTCATGAAAAAAT 11 148 1 AAAAATTTTC 0.955727 -83 ATTTCAGTAAAAAAATGCCTTTCTAAAGAAAGG 13 75 0 AAAAATTTTC 0.960492 -226 TTTCTTGTAGAAAAATACGTTTCTAAACAATGC 13 128 0 AAAAATTTTC 0.960492 -173 TTTAGTTATAAAAAATTAATATAAGTGATTACT 13 189 0 AAAAATTATA 0.733833 -112 ****** **** Masking position 6 Map Score: 2.19676 Number of sites scoring better than the average of aligned sites = 78 Number in coding regions = 49 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467 Motif number 11 AAAATTTACTTAATCAGCTGGAGATAGCAG 2 15 0 TAATCAGCTG 0.928124 -286 TAAAATTGTGCACTCAACACAGTGATTATT 2 107 0 CACTCAACAC 0.841651 -194 GTTGATTCTTCAATCAGATCTTTATAAATC 3 93 0 CAATCAGATC 0.914875 -59 TCAAAAATGACAATCACCTGAGGAATGCCT 4 104 1 CAATCACCTG 0.82522 -21 ACCGCAGGGATAATCAACACTGGCACAATT 5 47 0 TAATCAACAC 0.894136 -165 TCGCTCCAGTTAATCAAATCACGCATACGC 9 173 0 TAATCAAATC 0.840332 -25 GCTGATTACATACTCAGCTCGTTCTGCACT 12 36 0 TACTCAGCTC 0.953964 -32 GCTGAGTATGTAATCAGCTCGTTTTGGCCT 12 48 1 TAATCAGCTC 0.976955 -20 ACAATGCAATCAATCTACTCTTATAAAATT 13 105 0 CAATCTACTC 0.844345 -196 ********** Masking position 4 Map Score: 2.75574 Number of sites scoring better than the average of aligned sites = 728 Number in coding regions = 699 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 12 GCGTTTTACAGGTGTAGCGTTA 1 3 0 GGTGTAGCGT 0.858198 -136 TAGGGTGAGGGGCGCAAACCCGCTCCGGGG 1 67 1 GGCGCAAACC 0.894523 -72 TCCCCAAACAGGCGTAACGCCTGCAAAACG 4 25 0 GGCGTAACGC 0.942766 -100 GCACTAAAATGGTGCAACCTGTTCAGGAGA 7 259 1 GGTGCAACCT 0.972659 -27 GCACCATGTTGGTGCAATGACCTTTGGATA 8 76 0 GGTGCAATGA 0.898948 -225 GCACTATATTGGTGCAACATTCACATCGTG 8 123 1 GGTGCAACAT 0.899538 -178 TTCACATCGTGGTGCAGCCCTTTTGCACGA 8 142 1 GGTGCAGCCC 0.969392 -159 CATAAAAAATGGCGCAATGAATTGCACCCT 11 58 1 GGCGCAATGA 0.897115 -173 ********** Masking position 6 Map Score: 1.56444 Number of sites scoring better than the average of aligned sites = 1003 Number in coding regions = 952 Number in noncoding regions = 51 Number of orfs with sites within 600 bp upstream = 62 Fraction of orfs with sites within 600 bp upstream = 0.00995824 Motif number 13 TACCGTGGTGTAAATAATCAAATTCAGGGT 1 106 0 TAAATAATCA 0.929757 -33 ACCTGATGAAAAAACAATCTTTATGTAACG 2 68 0 AAAACAATCT 0.828856 -233 GGTTTTACGCTAAATAATCACTGTGTTGAG 2 95 1 TAAATAATCA 0.929757 -206 TTTAAGATTATAAATAAACTTGTAATGTCT 13 33 0 TAAATAAACT 0.859091 -268 TCAAAATAAGAAAATAATCTACCGCACTTT 13 158 0 AAAATAATCT 0.929757 -143 AAACCATAAATAAATAATCTTTTTTTTTCA 13 228 1 TAAATAATCT 0.961085 -73 ********** Masking position 6 Map Score: 1.92614 Number of sites scoring better than the average of aligned sites = 69 Number in coding regions = 48 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 14 ACGATTGTGTGATGATGTGGATACAAAAAA 2 41 0 GATGATGTGG 0.992391 -260 GAATAATGTCGATGATGTCGAAATGACACG 5 77 1 GATGATGTCG 0.986086 -135 CCTACACGGTGATGATGTGGTAGGCCGGAG 7 111 1 GATGATGTGG 0.992391 -175 ********** Masking position 5 Map Score: 1.34951 Number of sites scoring better than the average of aligned sites = 27 Number in coding regions = 25 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 15 GCGGGTTTGCGCCCCTCACCCTAATCCTCTC 1 59 0 GCCCTCACCC 0.96311 -80 AGACGCATTTGCGTCGCATCCGGCGTGATGT 7 73 0 GCGCGCATCC 0.985909 -213 CGACGCAAATGCGTCTTATCCGGCCTACACG 7 88 1 GCGCTTATCC 0.98171 -198 ACGTTGGAGAGCGACTCACCTGCTCCGGCCT 7 132 0 GCGCTCACCT 0.959429 -154 AATAAAAATTGCATCTTATCCAATTAAAGCA 11 18 0 GCACTTATCC 0.959717 -213 TAATAGAAAAGCAGCGTATCTAA 13 3 0 GCACGTATCT 0.869703 -298 *** ******* Masking position 8 Map Score: 0.980826 Number of sites scoring better than the average of aligned sites = 323 Number in coding regions = 192 Number in noncoding regions = 131 Number of orfs with sites within 600 bp upstream = 50 Fraction of orfs with sites within 600 bp upstream = 0.00803084