AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i164_NIF1_ecoli_hinf_reg_100.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 ydiC 300 orf, hypothetical protein #2 yfhE 95 orf, hypothetical protein #3 b2529 27 orf, hypothetical protein #4 yfhO 87 putative aminotransferase #5 b2531 177 orf, hypothetical protein #6 HI0376 56 conserved hypothetical protein #7 HI0377 59 iscU protein (iscU) #8 HI0378 60 nifS protein (nifS) #9 HI0379 52 conserved hypothetical protein #10 HI0380 300 conserved hypothetical protein Motif number 1 TTTTACGGTAAAGCCCCTGCGTTTGCTGGG 1 215 1 AAGCCCCTGC 0.814327 -86 GATTATCAGTTCAACCCAGCAAACGCAGGG 1 229 0 TCAACCCAGC 0.939558 -72 GCGCATACCGATAACCCCACCGTGGTCGCC 2 12 1 ATAACCCCAC 0.979799 -84 TCAGGTAAAACAAACCCCACGCGCAGGCGA 2 37 0 CAAACCCCAC 0.787372 -59 AATGTCAGACTTGACCCTGCTATGCAATAC 5 102 1 TTGACCCTGC 0.893212 -76 CTGCTATGCAATACCCCCACTTTTACAATA 5 118 1 ATACCCCCAC 0.969844 -60 CACCTCAAACTCGCCCCTGCCCGGGGTTTT 5 149 0 TCGCCCCTGC 0.898754 -29 GCGGTCAAAATTGACCGCACTTTTTCACAT 6 13 0 TTGACCGCAC 0.847872 -44 CTATCCCCCAACACCGCTAAAA 6 45 0 ATCCCCCAAC 0.817892 -12 TATGCTAAATATAACCGCACTTTTTTATTA 8 33 0 ATAACCGCAC 0.897054 -28 GACTGAGCTAACGACCCCACTGTATTAAAT 10 13 0 ACGACCCCAC 0.990763 -288 CGAATCCTTCACGACCCACCACTCTCTGAT 10 81 1 ACGACCCACC 0.960392 -220 AACTGAGCTAACAACCCAACTGGACAACTA 10 112 0 ACAACCCAAC 0.976086 -189 CTAGTCTCTCACAACCCACCATTTTTATTA 10 180 1 ACAACCCACC 0.946093 -121 ********** Masking position 5 Map Score: 17.0181 Number of sites scoring better than the average of aligned sites = 866 Number in coding regions = 765 Number in noncoding regions = 101 Number of orfs with sites within 600 bp upstream = 95 Fraction of orfs with sites within 600 bp upstream = 0.0152586 Motif number 2 GAGATAGGTAAAAAAGTGCAGCGTTCAGAA 1 28 0 AAAAAGTGCA 0.949453 -273 TTTTTTATTGTAAAAGTGGGGGTATTGCAT 5 123 0 TAAAAGTGGG 0.973155 -55 TCATGTGAAAAAGTGCGGTCAATTTTG 6 8 1 AAAAAGTGCG 0.993142 -49 CCAACACCGCTAAAAATGCGGTCAAAATTG 6 30 0 TAAAAATGCG 0.96072 -27 TTTTTTAATAAAAAAGTGCGGTTATATTTA 8 28 1 AAAAAGTGCG 0.993142 -33 ACCAACGGATTAAAAGTCCGCTGCTCTACC 10 43 0 TAAAAGTCCG 0.987588 -258 ACTGACGGATTAAGAGTCCGCTACTCTACC 10 142 0 TAAGAGTCCG 0.960758 -159 ********** Masking position 5 Map Score: 10.997 Number of sites scoring better than the average of aligned sites = 98 Number in coding regions = 76 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 3 ACTATTTAAGAGATAGGTAAAAAAGTGCAG 1 37 0 AGATAGGTAA 0.84256 -264 GGTATCTCATTGTTAGATAATGGTTATTAT 1 117 0 TGTTAGATAA 0.748939 -184 GCACGCTAAGAATTAGGTATCTCATTGTTA 1 132 0 AATTAGGTAT 0.81788 -169 AAAGCGATGAAGTGAGGTAAATCG 1 287 1 AGTGAGGTAA 0.957099 -14 GATAACGGCGAATCAGGTAAAACAAACCCC 2 49 0 AATCAGGTAA 0.952519 -47 TGACTGATTTAGTCGGGTATTTAACCTTCA 5 45 0 AGTCGGGTAT 0.971496 -133 CGACTAAATCAGTCAAGTAAATAGTTGACC 5 60 1 AGTCAAGTAA 0.910223 -118 TGAATGCCATTGTCAGATAATGGCAACTAA 7 14 0 TGTCAGATAA 0.90101 -46 CTAAATTAGTCAGATATGTAAGTATTG 9 8 1 AGTCAGATAT 0.957201 -45 CTTAAATTTTAGTCGGGTATCATT 10 287 1 AGTCGGGTAT 0.971496 -14 ********** Masking position 8 Map Score: 8.84197 Number of sites scoring better than the average of aligned sites = 445 Number in coding regions = 386 Number in noncoding regions = 59 Number of orfs with sites within 600 bp upstream = 76 Fraction of orfs with sites within 600 bp upstream = 0.0122069 Motif number 4 AACATTCTCAGGGCTGCGATCCGCCG 2 80 0 CTCAGGGCTG 0.975559 -16 GTATTTAGCACTCCGGCCTGATTCTGAATT 4 18 0 CTCCGGCCTG 0.989716 -70 AGGAATCAGGCTACCGGCTGGATGTACGAC 4 60 0 CTACCGGCTG 0.98986 -28 CAATAAAAAACCCCGGGCAGGGGCGAGTTT 5 143 1 CCCCGGGCAG 0.942238 -35 GTCCGCTGCTCTACCGACTGAGCTAACGAC 10 28 0 CTACCGACTG 0.989877 -273 GTCCGCTACTCTACCAACTGAGCTAACAAC 10 127 0 CTACCAACTG 0.931195 -174 GAGACTAGAACTCTCGACTGACGGATTAAG 10 158 0 CTCTCGACTG 0.970494 -143 ********** Masking position 8 Map Score: 7.57965 Number of sites scoring better than the average of aligned sites = 475 Number in coding regions = 443 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 5 GTATTGAAAATGACTATTTAAGAGATAGGTA 1 48 0 TGACATTTAA 0.948523 -253 ACTATTTACTTGACTGATTTAGTCGGGTATT 5 54 0 TGACGATTTA 0.981533 -124 AGTAAATAGTTGACCAATTTACTCGGGAATG 5 75 1 TGACAATTTA 0.984653 -103 CTTACATATCTGACTAATTTAG 9 2 0 TGACAATTTA 0.984639 -51 AACTCTCGACTGACGGATTAAGAGTCCGCTA 10 149 0 TGACGATTAA 0.966113 -152 CTTAAATTCTTGACTATTTTTAGCGGTTATT 10 243 1 TGACATTTTT 0.89456 -58 **** ****** Masking position 8 Map Score: 5.58892 Number of sites scoring better than the average of aligned sites = 42 Number in coding regions = 33 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 6 ACCTAATTCTTAGCGTGCCTGTTAACCCACA 1 144 1 TAGCGTCCTG 0.968999 -157 TGTTTTACGGTAAAGCCCCTGCGTTTGCTGG 1 213 1 TAAAGCCCTG 0.856959 -88 GATTCGCCGTTATCGCGGCGGATCGCAGCCC 2 65 1 TATCGCGCGG 0.990571 -31 ACGGAGTATTTAGCACTCCGGCCTGATTCTG 4 22 0 TAGCACCCGG 0.968456 -66 GCCATTTTTTTATCGTGGCGTTTGTACCTGT 5 12 0 TATCGTGCGT 0.868383 -166 GCTCAGTCGGTAGAGCAGCGGACTTTTAATC 10 35 1 TAGAGCGCGG 0.993401 -266 GCTCAGTTGGTAGAGTAGCGGACTCTTAATC 10 134 1 TAGAGTGCGG 0.986465 -167 ****** **** Masking position 2 Map Score: 3.80711 Number of sites scoring better than the average of aligned sites = 915 Number in coding regions = 873 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 53 Fraction of orfs with sites within 600 bp upstream = 0.00851269 Motif number 7 CTTAAGGGTTTTCTTATTTCTG 1 2 1 TTAAGGGTTT 0.945853 -299 TAACAGCATGTTAGTGATAATGATTATCAGT 1 249 0 TTAGTGATAT 0.855939 -52 GACCGCATTTTTAGCGGTGTTGGGGGATAG 6 37 1 TTAGCGGTTT 0.97099 -20 CAATTAATTTTTAGGGATTCTTT 9 40 1 TTAGGGATCT 0.947883 -13 ATTTAAAATATTAGGGATGAATAATAAAAAT 10 200 0 TTAGGGATAA 0.865538 -101 TTGACTATTTTTAGCGGTTATTGTGGTAGAA 10 252 1 TTAGCGGTAT 0.970903 -49 CGACTAAAATTTAAGGGTATTCTACCACAAT 10 271 0 TTAAGGGTTT 0.945857 -30 ******** ** Masking position 3 Map Score: 2.06748 Number of sites scoring better than the average of aligned sites = 109 Number in coding regions = 93 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 8 AGGTAAAAAAGTGCAGCGTTCAGAAATAAGA 1 22 0 GGCAGCGTTC 0.98337 -279 CAAACCCCACGCGCAGGCGACCACGGTGGGG 2 26 0 GGCAGGCGAC 0.981533 -70 AACATTCTCAGGGCTGCGATCCGCCGCGATA 2 75 0 GGCTGCGATC 0.936003 -21 AAAAAACCCCGGGCAGGGGCGAGTTTGAGGT 5 147 1 GGCAGGGGCG 0.968922 -31 TCAGTCGGTAGAGCAGCGGACTTTTAATCCG 10 37 1 GGCAGCGGAC 0.997715 -264 TCAGTTGGTAGAGTAGCGGACTCTTAATCCG 10 136 1 GGTAGCGGAC 0.985633 -165 * ********* Masking position 6 Map Score: 3.26298 Number of sites scoring better than the average of aligned sites = 289 Number in coding regions = 276 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 9 CATCACAGCCTTAATGCTCCTTAGATAATAACC 1 93 1 TAATGCTTTA 0.977946 -208 CACATCAGGGTCTATGCTTATTAAAAGCAGGCA 1 173 1 TTATGCTTTA 0.959622 -128 TATAAATTCTCCTGATTCCGATACC 3 13 0 TAATTCTTGA 0.958972 -15 GGCCTGATTCTGAATTCTTTTTA 4 1 0 TAATTCTTTA 0.965687 -87 TTTCCTTTTTTCAATTCTAGTGAATGCCATTGT 7 31 0 TAATTCTTGA 0.958827 -29 TAGTCAAGAATTTAAGCTAATTAAAGAAATTTA 10 226 0 TTAAGCTTTA 0.8543 -75 * ****** *** Masking position 8 Map Score: 1.04954 Number of sites scoring better than the average of aligned sites = 39 Number in coding regions = 30 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 10 CAGGCACGCTAAGAATTAGGTATCTCATTG 1 135 0 AAGAATTAGG 0.927262 -166 CGCGATAACGGCGAATCAGGTAAAACAAAC 2 52 0 GCGAATCAGG 0.979105 -44 TCGGTATCGGAATCAGGAGAATTTATA 3 8 1 CGGAATCAGG 0.993686 -20 AAAAAGAATTCAGAATCAGGCCGGAGTGCT 4 12 1 CAGAATCAGG 0.990307 -76 TCAATGCAAGGAATCAGGCTACCGGCTG 4 70 0 AGGAATCAGG 0.990379 -18 ********** Masking position 5 Map Score: 5.71498 Number of sites scoring better than the average of aligned sites = 72 Number in coding regions = 55 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 11 ********** No masking Map Score: -2.2713e-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 12 ********** No masking Map Score: -2.2713e-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 13 ********** No masking Map Score: -2.2713e-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