AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i034_Pyruvate_Synthase_2_ecoli_reg_300.orf -a/home/amcguire/alignace/lib/ORF_ecoli.txt -z/skink1/amcguire/genomes/ecoli.fna -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 ydbK 300 putative oxidoreductase, Fe-S subunit #2 cysJ 300 sulfite reductase (NADPH), flavoprotein beta subunit Motif number 1 AAAAAAATAGCCATAAAAAAGTAAAAATGCG 1 130 0 CCAAAAAAAG 0.894581 -171 AAACAGAGGGCAAAAAAATAGCCATAAAAAA 1 141 0 CAAAAAATAG 0.971162 -160 ATGAATGTTTTGATCAAACAGAGGGCAAAAA 1 156 0 TGACAAACAG 0.947911 -145 GACACAAAAGCGAAAATGCAGAAGAAAGCCA 1 202 1 CGAAATGCAG 0.896071 -99 CGATAAAACCGCCGTAGAGTA 2 1 1 CGAAAAACCG 0.991613 -300 TTAGATAATGCGAAAAAACAGCCTTTCCGGT 2 31 0 CGAAAAACAG 0.995366 -270 CGATTTTGCGCAACAAAGTCGTTTTAGATAA 2 54 0 CAAAAAGTCG 0.867032 -247 TAGTCTTTAACAACAAAATAGATTAACCAAC 2 130 0 CAAAAAATAG 0.97116 -171 TAAAGACTATTGCTAAAACAGGTTAGTCGAT 2 152 1 TGCAAAACAG 0.942637 -149 CGATAACTAATAACCAAATCGACTAACCTGT 2 169 0 TAACAAATCG 0.61466 -132 CTGTCAGCGCCCATAAAACAGAAGAGAAGGT 2 241 0 CCAAAAACAG 0.987011 -60 GCTGACAGGGCGCAGAAACAGCTTTGCTTAC 2 264 1 CGCGAAACAG 0.939483 -37 *** ******* Masking position 6 Map Score: 14.8547 Number of sites scoring better than the average of aligned sites = 1459 Number in coding regions = 1317 Number in noncoding regions = 142 Number of orfs with sites within 600 bp upstream = 149 Fraction of orfs with sites within 600 bp upstream = 0.0239319 Motif number 2 AGCTCTCGACGCCGCCCTCTGTGCTGCCTA 1 84 0 GCCGCCCTCT 0.974389 -217 GGCGTCGAGAGCTGTCCTGCGCGTTGCCCC 1 101 1 GCTGTCCTGC 0.969187 -200 TGTCCTGCGCGTTGCCCCGCATTTTTACTT 1 113 1 GTTGCCCCGC 0.991779 -188 TGGCTATTTTTTTGCCCTCTGTTTGATCAA 1 148 1 TTTGCCCTCT 0.957971 -153 TTTTCGCTTTTGTGTCCCCCACATCAGCGT 1 188 0 TGTGTCCCCC 0.967433 -113 AGCAATTTCGTGCGCCCCTCATTTGCGCAA 1 267 1 TGCGCCCCTC 0.949548 -34 ATTAGTTATCGCTATCCCGTCTTTAATCCA 2 189 1 GCTATCCCGT 0.825753 -112 ATCCACACCGTTTGCCCCGTTAACCTTACC 2 214 1 TTTGCCCCGT 0.986461 -87 AAGCTGTTTCTGCGCCCTGTCAGCGCCCAT 2 258 0 TGCGCCCTGT 0.979632 -43 ********** Masking position 6 Map Score: 9.87532 Number of sites scoring better than the average of aligned sites = 1610 Number in coding regions = 1452 Number in noncoding regions = 158 Number of orfs with sites within 600 bp upstream = 157 Fraction of orfs with sites within 600 bp upstream = 0.0252168 Motif number 3 ACACCCTACCCAAAACGCTGCTCGCATCTT 1 10 1 CCAAAAGCTG 0.973766 -291 AGATCAGAGGAAGAAAAGATGCGAGCAGCGT 1 25 0 AAGAAAGATG 0.847323 -276 CATAAAAAAGTAAAAATGCGGGGCAACGCGC 1 119 0 TAAAAAGCGG 0.915928 -182 ATGTGGGGGACACAAAAGCGAAAATGCAGAA 1 194 1 CACAAAGCGA 0.872457 -107 GAGGGGCGCACGAAATTGCTGCGCGCCCAGT 1 256 0 CGAAATGCTG 0.968584 -45 CCTTACATTGCGCAAATGAGGGGCGCACGAA 1 273 0 CGCAAAGAGG 0.930879 -28 CGTAGAGTACCGGAAAGGCTGTTTTTTCGCA 2 23 1 CGGAAAGCTG 0.991484 -278 CTTTGTTGCGCAAAATCGCTGATTTATCTTA 2 67 1 CAAAATGCTG 0.969414 -234 ATGTTCCAGTAAGCAAAGCTGTTTCTGCGCC 2 272 0 AAGCAAGCTG 0.862156 -29 ****** **** Masking position 5 Map Score: 4.77663 Number of sites scoring better than the average of aligned sites = 2656 Number in coding regions = 2490 Number in noncoding regions = 166 Number of orfs with sites within 600 bp upstream = 173 Fraction of orfs with sites within 600 bp upstream = 0.0277867 Motif number 4 GAAGAAAAGATGCGAGCAGCGTTTTGGGTA 1 17 0 TGCGAGCAGC 0.98508 -284 AGAGCTGTCCTGCGCGTTGCCCCGCATTTT 1 108 1 TGCGCGTTGC 0.972674 -193 ATTACTACTGGGCGCGCAGCAATTTCGTGC 1 250 1 GGCGCGCAGC 0.984206 -51 GCGCAAATGAGGGGCGCACGAAATTGCTGC 1 265 0 GGGGCGCACG 0.939653 -36 TTCTGTTTTATGGGCGCTGACAGGGCGCAG 2 249 1 TGGGCGCTGA 0.984706 -52 GGGCGCTGACAGGGCGCAGAAACAGCTTTG 2 260 1 AGGGCGCAGA 0.986238 -41 ********** Masking position 6 Map Score: 6.84045 Number of sites scoring better than the average of aligned sites = 1253 Number in coding regions = 1196 Number in noncoding regions = 57 Number of orfs with sites within 600 bp upstream = 52 Fraction of orfs with sites within 600 bp upstream = 0.00835207 Motif number 5 CTGATCTTCAAGCCAAACGACACCGCCATA 1 49 1 AGCCAAACGA 0.971516 -252 CCCCCACATCAGCGTAATGAATGTTTTGAT 1 173 0 AGCGTAATGA 0.966256 -128 TCGCTGATTTATCTTAATGATTGGCTAAAT 2 82 1 ATCTTAATGA 0.876287 -219 ACCTAATGAAAAACAAATGAATTTAGCCAA 2 102 0 AAACAAATGA 0.854986 -199 TAGATTAACCAACCTAATGAAAAACAAATG 2 113 0 AACCTAATGA 0.986132 -188 TGCTTACTGGAACATAACGACGC 2 288 1 AACATAACGA 0.93686 -13 ********** Masking position 6 Map Score: 2.2668 Number of sites scoring better than the average of aligned sites = 210 Number in coding regions = 174 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 45 Fraction of orfs with sites within 600 bp upstream = 0.00722775 Motif number 6 ATTATTTATGGCGGTGTCGTTTGGCTTGAA 1 55 0 GCGGTGTCGT 0.993972 -246 AGCACAGAGGGCGGCGTCGAGAGCTGTCCT 1 89 1 GCGGCGTCGA 0.987625 -212 GCGCAATGTAAGGGTGTCAT 1 291 1 AGGGTGTCAT 0.933578 -10 AACGGGGCAAACGGTGTGGATTAAAGACGG 2 205 0 ACGGTGTGGA 0.982342 -96 ********** Masking position 7 Map Score: 0.839887 Number of sites scoring better than the average of aligned sites = 354 Number in coding regions = 346 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 7 ********** No masking Map Score: 1.30983e-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 8 ********** No masking Map Score: 1.30983e-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 9 ********** No masking Map Score: 1.30983e-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