AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i154_Hydrogenase_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 hyaA 300 hydrogenase-1 small subunit #2 b2997 188 putative hydrogenase subunit #3 b2998 118 orf, hypothetical protein #4 b3000 205 orf, hypothetical protein Motif number 1 TACTCGTTTAGCAACCGGCTAAACATCCCCACCG 1 26 1 GCAACGCTAC 0.902307 -275 ATTGTTTTGTGCAAAAGTTTCACTACGCTTTATT 1 120 1 GCAAAGTTCT 0.954432 -181 CTCACGTGAAGCGATGGTTTGCCTTGCTACAGGG 1 212 1 GCGAGGTTCT 0.966788 -89 CTTATGGTCGGCAAGCGACGTCCCTGTAGCAAGG 1 233 0 GCAACGCGCC 0.993321 -68 CCGACCATAAGCGCCCGGTGTCCTGCCGGTGTCG 1 256 1 GCGCCGTGCT 0.974592 -45 ATCGCACGTCTCTCCTCCTTGCGAC 1 286 0 TCGCCGCTCC 0.804729 -15 AATCAATAATGCGATCGATGCGCCATTTACCACA 2 114 0 GCGACGTGCC 0.994388 -75 CCAGGTCTTCGCAACGGAATAACTATAA 2 171 1 GCAAGGATCT 0.82438 -18 AATAGCGTGCGCAAAAGTCGTTCTTTGCCTAAAA 3 55 1 GCAAAGCGCT 0.963336 -64 TTAGCGATTCGCCAGCGCGTATCCCGTAGTCTGG 4 55 1 GCCACGGTCC 0.972769 -151 GGTTAAACGCGGCATCGTTGCACTCCTCAGTTGG 4 148 0 GGCACGTGCT 0.899633 -58 GCGTTTAACCGCCAAAGATTTCCCACAAGAGTTG 4 172 1 GCCAAGTTCC 0.96929 -34 **** ** ** ** Masking position 7 Map Score: 9.7664 Number of sites scoring better than the average of aligned sites = 2907 Number in coding regions = 2802 Number in noncoding regions = 105 Number of orfs with sites within 600 bp upstream = 119 Fraction of orfs with sites within 600 bp upstream = 0.0191134 Motif number 2 CTTTTACTCGTTTAGCAACCGGCTAAACAT 1 22 1 TTTAGCAACC 0.880275 -279 GGATTTATCTTTTAGCGATAAAAATGGACC 1 79 0 TTTAGCGATA 0.959079 -222 GTAGTGAAACTTTTGCACAAAACAATACAA 1 116 0 TTTTGCACAA 0.577948 -185 TTCCCTTCGTTTTAGCGCCCCGCCGCAGTA 2 57 1 TTTAGCGCCC 0.968132 -132 GCAAAATCAATAATGCGATCGATGCGCCAT 2 122 0 TAATGCGATC 0.7339 -67 GCATTATTGATTTTGCGATTGAGGCAAAAT 2 136 1 TTTTGCGATT 0.952382 -53 AAAGAACGACTTTTGCGCACGCTATTTTTT 3 51 0 TTTTGCGCAC 0.950397 -68 TATTGTCATATATAGCGATATTTTAGGCAA 3 79 0 TATAGCGATA 0.918583 -40 TATGACAATATATAGCGAATGAGGTGAACG 3 99 1 TATAGCGAAT 0.895601 -20 ATGTTTCTAGTTTAGCGATTCGCCAGCGCG 4 44 1 TTTAGCGATT 0.968169 -162 ********** Masking position 1 Map Score: 9.05264 Number of sites scoring better than the average of aligned sites = 1009 Number in coding regions = 892 Number in noncoding regions = 117 Number of orfs with sites within 600 bp upstream = 143 Fraction of orfs with sites within 600 bp upstream = 0.0229682 Motif number 3 ACATCCCCACCGCCCGGCCAAAAGAAAAATAGGTCCA 1 48 1 CGCCGCAAAA 0.98343 -253 TACTTTCTGGCGACGTGCGCCAGTGCAGAAGGATGAG 1 159 1 CGACGCCAGA 0.96381 -142 AGCGATGGTTTGCCTTGCTACAGGGACGTCGCTTGCC 1 221 1 TGCCGCCAGC 0.89068 -80 GGACGTCGCTTGCCGACCATAAGCGCCCGGTGTCCTG 1 244 1 TGCCCCAAGC 0.975929 -57 CACGTCTCTCCTCCTTGCGACACCGGCAGGACACCGG 1 270 0 CTCCGCCAGC 0.985599 -31 TTCGTTTTAGCGCCCCGCCGCAGTATCATGATATCGA 2 62 1 CGCCGCCAAC 0.995865 -127 TACGTGCTTATGCTTTGCTTAAAAAAACACCAACTGA 4 119 1 TGCTGCAAAA 0.80691 -87 AGTGCAACGATGCCGCGTTTAACCGCCAAAGATTTCC 4 158 1 TGCCGTAAGC 0.964726 -48 **** ** ** * * Masking position 12 Map Score: 5.15683 Number of sites scoring better than the average of aligned sites = 1459 Number in coding regions = 1413 Number in noncoding regions = 46 Number of orfs with sites within 600 bp upstream = 54 Fraction of orfs with sites within 600 bp upstream = 0.00867331 Motif number 4 TTTTGGCCGGGCGGTGGGGATGTTTAGCCGG 1 40 0 GCGGGGGGAT 0.989206 -261 AACAATACAAACTGTGTGGATTTATCTTTTA 1 95 0 ACTGGTGGAT 0.828149 -206 CCGGTGTCGCAAGGAGGAGAGACGTGCGAT 1 281 1 AAGGGGAGAG 0.969092 -20 GGGCGCTAAAACGAAGGGAAGAAGCATTAGT 2 46 0 ACGAGGGAAG 0.946424 -143 TCATGATACTGCGGCGGGGCGCTAAAACGAA 2 62 0 GCGGGGGGCG 0.991925 -127 TCGAAATTGAACGGTGGAAAGGAGAGGTC 4 9 0 ACGGGGAAAG 0.985061 -197 AAAAACACCAACTGAGGAGTGCAACGATGCC 4 141 1 ACTGGGAGTG 0.942089 -65 **** ****** Masking position 6 Map Score: 2.82829 Number of sites scoring better than the average of aligned sites = 918 Number in coding regions = 846 Number in noncoding regions = 72 Number of orfs with sites within 600 bp upstream = 73 Fraction of orfs with sites within 600 bp upstream = 0.011725 Motif number 5 TTTATCTTTTAGCGATAAAAATGGACCTATTTTT 1 72 0 AGCAAAAAGG 0.966349 -229 TTTTGCACAAAACAATACAAACTGTGTGGATTTA 1 102 0 AACAACAATG 0.926131 -199 ACGCTTTATTAACAATACTTTCTGGCGACGTGCG 1 144 1 AACAACTTTG 0.905911 -157 AATTAATTAAAGCAAGATAATACGTATGTTTGA 2 10 0 AGCAATAACG 0.780124 -179 TGATATCGATAACCATAATAAATGTGTGGTAAAT 2 90 1 AACAAATATG 0.942912 -99 TTTGCGATTGAGGCAAAATATATGCCAGGTCTTC 2 147 1 AGGAAATATG 0.839999 -42 TGTCATATATAGCGATATTTTAGGCAAAGAACGA 3 72 0 AGCAATTTGG 0.905607 -47 CGAATCGCTAAACTAGAAACATTGTTTCGAAATT 4 32 0 AACAAAACTG 0.721181 -174 TCACTCTGTGAGCCAGACTACGGGATACGCGCTG 4 67 0 AGCAACTAGG 0.984303 -139 CGAAAAACTGGGCAAAAATACGTGCTTATGCTTT 4 101 1 GGCAAATATG 0.894358 -105 AGTAATCCAGCAACTCTTGTGGGAAATCTTTG 4 184 0 AGCATCTTGG 0.782971 -22 *** * **** ** Masking position 5 Map Score: 2.62989 Number of sites scoring better than the average of aligned sites = 844 Number in coding regions = 746 Number in noncoding regions = 98 Number of orfs with sites within 600 bp upstream = 110 Fraction of orfs with sites within 600 bp upstream = 0.0176678 Motif number 6 ********** No masking Map Score: -9.56801e-13 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 7 ********** No masking Map Score: -9.56801e-13 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 8 ********** No masking Map Score: -9.56801e-13 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