AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -ifhlA_ecoli_bsub_300.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 hycB 124 probable small subunit of hydrogenase-3, iron-sulfur protein (part of formate hydrogenlyase (FHL) complex) #2 hycA_hypA 211 hycA: transcriptional repression of hyc and hyp operons, hypA: pleiotrophic effects on 3 hydrogenase isozymes #3 hypE 38 plays structural role in maturation of all 3 hydrogenases #4 fdhF 197 selenopolypeptide subunit of formate dehydrogenase H #5 yjcQ 140 putative enzyme #6 yjcR 300 putative membrane protein #7 yufT 300 similar to NADH dehydrogenase Motif number 1 CATTAACTATTGCCAGCTACAAGCAATAAT 2 20 1 TGCCAGCTAC 0.943554 -192 TCGACATTATTCACCGCAGGGATAATCAAC 2 59 0 TCACCGCAGG 0.572552 -153 GCATTTTTTGTGCCAACTTTTAATTTATTG 2 155 0 TGCCAACTTT 0.798493 -57 TTAACAGAGATGCCAGCTTTAAGCATTTTT 2 177 0 TGCCAGCTTT 0.967395 -35 CGCCTGGCCGCCGCTACCGTGGGC 3 25 0 TGGCCGCCGC 0.87951 -14 AAATACCGCGTGACAGCCATCACGCGGCAG 4 16 0 TGACAGCCAT 0.861104 -182 TCAAAACTGACGACAGCCTGTTTTTCGTCA 4 58 1 CGACAGCCTG 0.808096 -140 CGCGCTCAACTCCCTGCCATTACCGGTGGT 5 15 1 TCCCTGCCAT 0.529949 -126 GCCAGCAGCCTGACCACCGGTAATGGCAGG 5 27 0 TGACCACCGG 0.751185 -114 CATGAAAGAACGCCAGCAGCCTGACCACCG 5 38 0 CGCCAGCAGC 0.818921 -103 CTGGGTAGGCTGCCTGCTGGTGATTCTGAT 5 117 1 TGCCTGCTGG 0.961492 -24 TTTAATATGCCAACAGTTCTCTCTCGC 6 8 1 TGCCAACAGT 0.769717 -293 GCGCTTATTATCCCAGCTGGTTTTTCTGCG 6 126 1 TCCCAGCTGG 0.96545 -175 TCTGCGCCATTGCCAGCCTTATTTTGACGC 6 150 1 TGCCAGCCTT 0.976682 -151 GATTGATATTTGCCCGCTGAATAACTCGCC 6 189 0 TGCCCGCTGA 0.878702 -112 TTCCGACAAATGCCAGATTGATATTTGCCC 6 204 0 TGCCAGATTG 0.745853 -97 ATTAGAAAAATGCCAGCCAGAACAGCATGG 6 264 0 TGCCAGCCAG 0.983762 -37 GTTCGAAGCGTGGCAGCTTGCAGAAAAGTG 7 114 1 TGGCAGCTTG 0.91862 -187 ********** Masking position 4 Map Score: 18.5365 Number of sites scoring better than the average of aligned sites = 7243 Number in coding regions = 6902 Number in noncoding regions = 341 Number of orfs with sites within 600 bp upstream = 271 Fraction of orfs with sites within 600 bp upstream = 0.0435271 Motif number 2 TTTTCGACACTCATCGACACGCCCATCCCCAAA 1 47 0 TCTCGCACGC 0.986269 -78 AAATGACATTTCATCGGCATGTTTTCGTCAAAA 1 77 1 TCTCGCATGT 0.983799 -48 CATTTCGACATCATCGACATTATTCACCGCAGG 2 69 0 TCTCGCATTT 0.923601 -143 AAGATGAATTTCGTCGCCGTGTCGACGTGTCAT 2 99 0 TCTCGCGTGC 0.957341 -113 AATGTCTGCCGCGTGATGGCTGTCACGCGG 4 8 1 GCGCGGATGC 0.976049 -190 GCGGTATTTCGTTTCGTCACGTCAAAACTGACG 4 37 1 GTTCGCACGC 0.902543 -161 AGTTGCACGGTCTGCGGCACGCGACCTGGTCGC 5 84 0 TCGCGCACGG 0.958652 -57 TTTTTGAGTTGCATCGCCATGCGAGAGAGAACT 6 25 0 GCTCGCATGG 0.986794 -276 CGTCTTCATGGTTTCGGGATGCTCATTATCTCC 6 76 1 GTTCGGATGT 0.781154 -225 TAAGCGCCGATCACCGGGATTGCCGGAGATAAT 6 100 0 TCCCGGATTC 0.751099 -201 AGCTGGTTTTTCTGCGCCATTGCCAGCCTTATT 6 140 1 TCGCGCATTC 0.946631 -161 TGAATAACTCGCCTCGTGATGAGCGTCAAAATA 6 169 0 GCTCGGATGG 0.971484 -132 CTTTTTGCTCTCTACGCCATGCTGTTCTGGCTG 6 248 1 TCACGCATGT 0.905414 -53 ** *** **** * Masking position 5 Map Score: 16.3555 Number of sites scoring better than the average of aligned sites = 1459 Number in coding regions = 1397 Number in noncoding regions = 62 Number of orfs with sites within 600 bp upstream = 66 Fraction of orfs with sites within 600 bp upstream = 0.0106007 Motif number 3 GTAACGCCTGCAAAACGGGCAAAGCCTCAG 1 12 0 CAAAACGGGC 0.973898 -113 ACGCCCATCCCCAAACAGGCGTAACGCCTG 1 32 0 CCAAACAGGC 0.926943 -93 CGATGAGTGTCGAAAATGACATTTCATCGG 1 64 1 CGAAAATGAC 0.757693 -61 CATTTTTGACGAAAACATGCCGATGAAATG 1 83 0 GAAAACATGC 0.767855 -42 ATGTTTTCGTCAAAAATGACAATCACCTGA 1 95 1 CAAAAATGAC 0.80682 -30 CAGGGATAATCAACACTGGCACAATTATTG 2 43 0 CAACACTGGC 0.878212 -169 AAAGTTGGCACAAAAAATGCTTAAAGCTGG 2 165 1 CAAAAAATGC 0.957356 -47 TTCGTCACGTCAAAACTGACGACAGCCTGT 4 49 1 CAAAACTGAC 0.826153 -149 AACTCTGACGAAAAACAGGCTGTCGTCAGT 4 63 0 AAAAACAGGC 0.9632 -135 TGCAACTCAAAAAAACAGCCTGGATAATTC 6 45 1 AAAAACAGCC 0.702506 -256 GATGAGCGTCAAAATAAGGCTGGCAATGGC 6 155 0 AAAATAAGGC 0.648827 -146 TAAATAATTCCGACAAATGCCAGATTGATA 6 211 0 CGACAAATGC 0.796865 -90 GCGTAGAGAGCAAAAAGGGCGGTATAAATA 6 235 0 CAAAAAGGGC 0.970407 -66 CAAATAGATTAGAAAAATGCCAGCCAGAAC 6 271 0 AGAAAAATGC 0.856166 -30 GGCAGCTTGCAGAAAAGTGCGATATAATTT 7 125 1 AGAAAAGTGC 0.750308 -176 CGTTCTCAATTGAAAAATGCGCTATGTATA 7 181 0 TGAAAAATGC 0.721408 -120 TAAAAGCAAATAAAAAAGGCGATAAAATAG 7 249 0 TAAAAAAGGC 0.90915 -52 ********** Masking position 3 Map Score: 16.2872 Number of sites scoring better than the average of aligned sites = 2730 Number in coding regions = 2350 Number in noncoding regions = 380 Number of orfs with sites within 600 bp upstream = 383 Fraction of orfs with sites within 600 bp upstream = 0.0615162 Motif number 4 CGCCTGTTTGGGGATGGGCGTGTCGATGAG 1 41 1 GGGATGGGCG 0.996397 -84 ACTCGCCCACGGTAGCGGCGGCCAGGCG 3 21 1 GGTAGCGGCG 0.960224 -18 TGTCTGCCGCGTGATGGCTGTCACGCGGTA 4 13 1 GTGATGGCTG 0.905901 -185 GAAGAGTTAAGCGAGCGGCGACCAGGTCGC 5 67 1 GCGAGCGGCG 0.985801 -74 GCCGATCACCGGGATTGCCGGAGATAATGA 6 98 0 GGGATTGCCG 0.967077 -203 GGCAATCCCGGTGATCGGCGCTTATTATCC 6 109 1 GTGATCGGCG 0.994347 -192 AACTCGCCTCGTGATGAGCGTCAAAATAAG 6 167 0 GTGATGAGCG 0.95801 -134 ********** Masking position 4 Map Score: 7.32974 Number of sites scoring better than the average of aligned sites = 672 Number in coding regions = 648 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 5 TAACGCCTGCAAAACGGGCAAAGCCTCAGC 1 10 0 AAAACGGGAA 0.841249 -115 CCCATCCCCAAACAGGCGTAACGCCTGCAAA 1 28 0 AACAGGCGAA 0.934693 -97 GTTGGCACAAAAAATGCTTAAAGCTGGCATC 2 168 1 AAAATGCTAA 0.791062 -44 TAGAGAGCAAAAAGGGCGGTATAAATAATTC 6 231 0 AAAGGGCGTA 0.973608 -70 AGTCTAACAAAAAAGAGGTTATTTGTATATT 7 42 0 AAAAGAGGTA 0.819053 -259 AGCTTGCAGAAAAGTGCGATATAATTTGGAC 7 128 1 AAAGTGCGTA 0.958776 -173 TCTCAATTGAAAAATGCGCTATGTATAAAAT 7 177 0 AAAATGCGTA 0.979416 -124 AAGCAAATAAAAAAGGCGATAAAATAGCAAG 7 245 0 AAAAGGCGTA 0.986923 -56 CCTTCTTGGCAAAATACGCAAAAAGA 7 285 1 AAAATACGAA 0.883786 -16 ******** ** Masking position 2 Map Score: 6.21245 Number of sites scoring better than the average of aligned sites = 704 Number in coding regions = 595 Number in noncoding regions = 109 Number of orfs with sites within 600 bp upstream = 132 Fraction of orfs with sites within 600 bp upstream = 0.0212014 Motif number 6 CAAATCACGCATACGCGCTCTCGACTACAG 4 159 0 ATACGCGCTC 0.947874 -39 CGGTCTCGCTCCAGTTAATCA 4 187 0 GGTCTCGCTC 0.98789 -11 TGAGCGCGCTCAACTCCCTGC 5 2 1 GAGCGCGCTC 0.498948 -139 GCGGCGACCAGGTCGCGTGCCGCAGACCGT 5 81 1 GGTCGCGTGC 0.929331 -60 TATGCCAACAGTTCTCTCTCGCATGGCGAT 6 16 1 GTTCTCTCTC 0.879867 -285 AATCTATTTGAGACGCGCTC 6 291 1 AGACGCGCTC 0.96373 -10 AAGACCTCCTTTTCTCGTTCTCAATTGAAA 7 196 0 TTTCTCGTTC 0.74696 -105 ********** Masking position 6 Map Score: 1.41241 Number of sites scoring better than the average of aligned sites = 778 Number in coding regions = 740 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 7 CCTGCAAAACGGGCAAAGCCTCAGC 1 6 0 GGGCAAAGCC 0.917571 -119 CCCCAAACAGGCGTAACGCCTGCAAAACGG 1 24 0 GCGTAACGCC 0.986626 -101 CACAAAAAATGCTTAAAGCTGGCATCTCTG 2 173 1 GCTTAAAGCT 0.909766 -39 TGAGCGCGCTCAACTCCCTGCCATTAC 5 8 1 GCTCAACTCC 0.979131 -133 GTCGCCGCTCGCTTAACTCTTCATGAAAGA 5 59 0 GCTTAACTCT 0.949939 -82 GCCGCAGACCGTGCAACTCTGGGTAGGCTG 5 99 1 GTGCAACTCT 0.899906 -42 ********** Masking position 5 Map Score: 0.454513 Number of sites scoring better than the average of aligned sites = 1363 Number in coding regions = 1289 Number in noncoding regions = 74 Number of orfs with sites within 600 bp upstream = 75 Fraction of orfs with sites within 600 bp upstream = 0.0120463 Motif number 8 ********** No masking Map Score: -1.88842e-14 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: -1.88842e-14 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 10 CCGTGGGCGAGTTGGATATTAT 3 1 0 GTGGAATTAT 0.916123 -38 TGATATTACGGGCACTATTTATTCAAAACTCT 4 87 0 GCACTTTTAT 0.850251 -111 CATCTTTTATGCCACATTTTATGTGGGGTCAT 4 123 0 GCACATTTAT 0.711818 -75 TAGGCTGCCTGCTGGTGATTCTGATCTCG 5 122 1 GTGGTATTCT 0.934285 -19 AAACCATGAAGACGGGAATTATCCAGGCTGTT 6 58 0 GCGGGATTAT 0.935738 -243 ATGGTTTCGGGATGCTCATTATCTCCGGCAAT 6 83 1 GTGCTATTAT 0.961696 -218 CCCGGTGATCGGCGCTTATTATCCCAGCTGGT 6 115 1 GCGCTATTAT 0.975504 -186 TATTATCCCAGCTGGTTTTTCTGCGCCATTGC 6 131 1 GTGGTTTTCT 0.898604 -170 * **** ***** Masking position 9 Map Score: 0.550515 Number of sites scoring better than the average of aligned sites = 747 Number in coding regions = 676 Number in noncoding regions = 71 Number of orfs with sites within 600 bp upstream = 79 Fraction of orfs with sites within 600 bp upstream = 0.0126887 Motif number 11 ********** No masking Map Score: -1.88842e-14 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: -1.88842e-14 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: -1.88842e-14 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