AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -ifhlA_ecoli_opreg_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 Motif number 1 TTTTCGACACTCATCGACACGCCCATCCCCA 1 49 0 TCTCGACACG 0.938344 -76 AAATGACATTTCATCGGCATGTTTTCGTCAA 1 77 1 TCTCGGCATG 0.977913 -48 ATTCCTCAGGTGATTGTCATTTTTGACGAAA 1 99 0 TGTTGTCATT 0.613189 -26 CATTTCGACATCATCGACATTATTCACCGCA 2 71 0 TCTCGACATT 0.893788 -141 AAGATGAATTTCGTCGCCGTGTCGACGTGTC 2 101 0 TCTCGCCGTG 0.979617 -111 CGCCTGGCCGCCGCTACCGTGGGCG 3 24 0 TGCCGCCGCT 0.973105 -15 AATGTCTGCCGCGTGATGGCTGT 4 3 1 TGCTGCCGCG 0.932728 -195 TGCCGCGTGATGGCTGTCACGCGGTATTTCG 4 17 1 TGCTGTCACG 0.777003 -181 CGCGCTCAACTCCCTGCCATTACCGGTGGTC 5 15 1 TCCTGCCATT 0.940458 -126 GCACGCGACCTGGTCGCCGCTCGCTTAACTC 5 70 0 TGTCGCCGCT 0.967502 -71 AGTTGCACGGTCTGCGGCACGCGACCTGGTC 5 86 0 TCGCGGCACG 0.95998 -55 TTTTTGAGTTGCATCGCCATGCGAGAGAGAA 6 27 0 GCTCGCCATG 0.892673 -274 ATGCTCATTATCTCCGGCAATCCCGGTGATC 6 94 1 TCCCGGCAAT 0.840643 -207 GCAATCCCGGTGATCGGCGCTTATTATCCCA 6 110 1 TGTCGGCGCT 0.949663 -191 AGCTGGTTTTTCTGCGCCATTGCCAGCCTTA 6 140 1 TCGCGCCATT 0.954402 -161 CTTTTTGCTCTCTACGCCATGCTGTTCTGGC 6 248 1 TCACGCCATG 0.916765 -53 CATGCTGTTCTGGCTGGCATTTTTCTAATCT 6 265 1 TGCTGGCATT 0.875969 -36 ** ******** Masking position 6 Map Score: 23.9445 Number of sites scoring better than the average of aligned sites = 4334 Number in coding regions = 4139 Number in noncoding regions = 195 Number of orfs with sites within 600 bp upstream = 194 Fraction of orfs with sites within 600 bp upstream = 0.0311597 Motif number 2 GCTGAGGCTTTGCCCGTTTTGCAGGCGTTA 1 11 1 TGCCCGTTTT 0.911258 -114 GCAGGCGTTACGCCTGTTTGGGGATGGGCG 1 31 1 CGCCTGTTTG 0.643825 -94 CATTAACTATTGCCAGCTACAAGCAATAAT 2 20 1 TGCCAGCTAC 0.940479 -192 GCAATAATTGTGCCAGTGTTGATTATCCCT 2 42 1 TGCCAGTGTT 0.896454 -170 GTGTTGATTATCCCTGCGGTGAATAATGTC 2 57 1 TCCCTGCGGT 0.858963 -155 GCATTTTTTGTGCCAACTTTTAATTTATTG 2 155 0 TGCCAACTTT 0.911717 -57 TTAACAGAGATGCCAGCTTTAAGCATTTTT 2 177 0 TGCCAGCTTT 0.987233 -35 ATATCCAACTCGCCCACGGTAGCGGCGGCC 3 14 1 CGCCCACGGT 0.676221 -25 GAATAAATAGTGCCCGTAATATCAGGGAAT 4 95 1 TGCCCGTAAT 0.682794 -103 CGCGCTCAACTCCCTGCCATTACCGGTGGT 5 15 1 TCCCTGCCAT 0.691129 -126 CATGAAAGAACGCCAGCAGCCTGACCACCG 5 38 0 CGCCAGCAGC 0.838658 -103 CTGGGTAGGCTGCCTGCTGGTGATTCTGAT 5 117 1 TGCCTGCTGG 0.977068 -24 TTTAATATGCCAACAGTTCTCTCTCGC 6 8 1 TGCCAACAGT 0.85491 -293 GCGCTTATTATCCCAGCTGGTTTTTCTGCG 6 126 1 TCCCAGCTGG 0.955365 -175 TCTGCGCCATTGCCAGCCTTATTTTGACGC 6 150 1 TGCCAGCCTT 0.97739 -151 GATTGATATTTGCCCGCTGAATAACTCGCC 6 189 0 TGCCCGCTGA 0.912701 -112 TTCCGACAAATGCCAGATTGATATTTGCCC 6 204 0 TGCCAGATTG 0.794491 -97 ATTAGAAAAATGCCAGCCAGAACAGCATGG 6 264 0 TGCCAGCCAG 0.954408 -37 ********** Masking position 4 Map Score: 20.2537 Number of sites scoring better than the average of aligned sites = 7879 Number in coding regions = 7546 Number in noncoding regions = 333 Number of orfs with sites within 600 bp upstream = 287 Fraction of orfs with sites within 600 bp upstream = 0.046097 Motif number 3 CTGAGGCTTTGCCCGTTTTGCAGGCGTTACGCC 1 12 1 GCCGTTTTAG 0.794516 -113 CATTTCATCGGCATGTTTTCGTCAAAAATGACA 1 83 1 GCTGTTTTTC 0.977159 -42 CCAGCTTTAAGCATTTTTTGTGCCAACTTTTAA 2 162 0 GCTTTTTTGC 0.951332 -50 TGGCTGTCACGCGGTATTTCGTTTCGTCACGTC 4 27 1 GCGTATTTTT 0.76207 -171 ACTGACGACAGCCTGTTTTTCGTCAGAGTTTTG 4 63 1 GCTGTTTTGT 0.886123 -135 GATATTACGGGCACTATTTATTCAAAACTCTGA 4 85 0 GCCTATTTTC 0.928173 -113 ACTACAGTATGCATCTTTTATGCCACATTTTAT 4 133 0 GCTCTTTTGC 0.838675 -65 GAGCGCGTATGCGTGATTTGATTAACTGGAGCG 4 169 1 GCTGATTTTT 0.846064 -29 CAGGCTGCTGGCGTTCTTTCATGAAGAGTTAAG 5 45 1 GCTTCTTTTG 0.866725 -96 CCTGGTCGCCGCTCGCTTAACTCTTCATGAAAG 5 60 0 GCCGCTTATC 0.696409 -81 AATTATCCAGGCTGTTTTTTTGAGTTGCATCGC 6 41 0 GCGTTTTTGA 0.642177 -260 TATTATCCCAGCTGGTTTTTCTGCGCCATTGCC 6 131 1 GCGGTTTTTG 0.939699 -170 GCCATTGCCAGCCTTATTTTGACGCTCATCACG 6 155 1 GCTTATTTAC 0.774295 -146 TATTTATACCGCCCTTTTTGCTCTCTACGCCAT 6 235 1 GCCTTTTTTC 0.961435 -66 TGCTGTTCTGGCTGGCATTTTTCTAATCTATTT 6 267 1 GCGGCATTTC 0.696413 -34 ** ****** ** Masking position 8 Map Score: 9.93377 Number of sites scoring better than the average of aligned sites = 2074 Number in coding regions = 1816 Number in noncoding regions = 258 Number of orfs with sites within 600 bp upstream = 248 Fraction of orfs with sites within 600 bp upstream = 0.039833 Motif number 4 GAGGCTTTGCCCGTTTTGCAGGCGTTACGCCTGTTT 1 14 1 CCGTTCGCGT 0.911598 -111 CAGGCATTCCTCAGGTGATTGTCATT 1 109 0 CAGCACCAGT 0.990183 -16 TGACGAAAAACAGGCTGTCGTCAGTTTTGACGTGAC 4 52 0 CAGCTCCAGT 0.996384 -146 CGGTCTCGCTCCAGTTAATCAAATCA 4 182 0 CGGCTCCAGT 0.995641 -16 AGAACGCCAGCAGCCTGACCACCGGTAATGGCAGGG 5 26 0 CAGCTCCCGT 0.993631 -115 CACCAGCAGGCAGCCTACCCAGAGTTGCACGGTCTG 5 103 0 CAGCTCGAGT 0.994129 -38 CGCCGATCACCGGGATTGCCGGAGATAATGAGCATC 6 93 0 CGGATCGAGT 0.947945 -208 ATAAATAATTCCGACAAATGCCAGATTGATATTTGC 6 206 0 CCGCATCAGT 0.903267 -95 *** ** * *** * Masking position 16 Map Score: 8.34621 Number of sites scoring better than the average of aligned sites = 412 Number in coding regions = 391 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 5 CTGTAGTCGAGAGCGCGTATGCGTGATTTG 4 159 1 GAGCGCGTAT 0.95963 -39 TGATTAACTGGAGCGAGACCG 4 187 1 GAGCGAGACC 0.988178 -11 TGAGCGCGCTCAACTCCCTGC 5 2 1 GAGCGCGCTC 0.499813 -139 ACGGTCTGCGGCACGCGACCTGGTCGCCGC 5 81 0 GCACGCGACC 0.923729 -60 ATCGCCATGCGAGAGAGAACTGTTGGCATA 6 16 0 GAGAGAGAAC 0.888358 -285 GAGCGCGTCTCAAATAGATT 6 291 0 GAGCGCGTCT 0.974301 -10 ********** Masking position 5 Map Score: 2.95507 Number of sites scoring better than the average of aligned sites = 560 Number in coding regions = 535 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 6 CCACGGTAGCGGCGGCCAGGCG 3 27 1 GGCGGCCAGG 0.969198 -12 CAAAACTGACGACAGCCTGTTTTTCGTCAG 4 59 1 GACAGCCTGT 0.978413 -139 AAAGAACGCCAGCAGCCTGACCACCGGTAA 5 34 0 AGCAGCCTGA 0.978417 -107 ACTCTGGGTAGGCTGCCTGCTGGTGATTCT 5 114 1 GGCTGCCTGC 0.969775 -27 AACTCAAAAAAACAGCCTGGATAATTCCCG 6 48 1 AACAGCCTGG 0.991345 -253 TGCCAGCCAGAACAGCATGGCGTAGAGAGC 6 254 0 AACAGCATGG 0.946581 -47 ********** Masking position 5 Map Score: 4.1236 Number of sites scoring better than the average of aligned sites = 817 Number in coding regions = 777 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 7 CCTGTTTGGGGATGGGCGTGTCGATGAGTG 1 43 1 GATGGGCGTG 0.981511 -82 TGGGCGTGTCGATGAGTGTCGAAAATGACA 1 55 1 GATGAGTGTC 0.988678 -70 TCTGCCGCGTGATGGCTGTCACGCGGTATT 4 15 1 GATGGCTGTC 0.941682 -183 TGCCGGAGATAATGAGCATCCCGAAACCAT 6 83 0 AATGAGCATC 0.875251 -218 CTCGCCTCGTGATGAGCGTCAAAATAAGGC 6 165 0 GATGAGCGTC 0.985681 -136 ********** Masking position 3 Map Score: 3.44311 Number of sites scoring better than the average of aligned sites = 400 Number in coding regions = 381 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 8 GATGAAATGTCATTTTCGACACTCATCGACA 1 61 0 CATTTCGACA 0.972633 -64 AGGTGATTGTCATTTTTGACGAAAACATGCC 1 92 0 CATTTTGACG 0.95918 -33 CTGCGGTGAATAATGTCGATGATGTCGAAAT 2 70 1 TATGTCGATG 0.708453 -142 TGTCGACGTGTCATTTCGACATCATCGACAT 2 82 0 TCTTTCGACA 0.95793 -130 AATTTCGTCGCCGTGTCGACGTGTCATTTCG 2 95 0 CCTGTCGACG 0.967252 -117 AGCTAAAGATGAATTTCGTCGCCGTGTCGAC 2 106 0 GATTTCGTCG 0.867984 -106 ACGCGGTATTTCGTTTCGTCACGTCAAAACT 4 35 1 TCTTTCGTCA 0.863566 -163 AGGCTGTCGTCAGTTTTGACGTGACGAAACG 4 46 0 CATTTTGACG 0.95918 -152 ATTGCCAGCCTTATTTTGACGCTCATCACGA 6 158 1 TTTTTTGACG 0.791197 -143 GCGGTATAAATAATTCCGACAAATGCCAGAT 6 216 0 TATTCCGACA 0.852006 -85 ** ******** Masking position 4 Map Score: 6.75819 Number of sites scoring better than the average of aligned sites = 807 Number in coding regions = 761 Number in noncoding regions = 46 Number of orfs with sites within 600 bp upstream = 57 Fraction of orfs with sites within 600 bp upstream = 0.00915516 Motif number 9 ********** No masking Map Score: -1.07759e-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 10 ********** No masking Map Score: -1.07759e-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: -1.07759e-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