AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i164_NIF1_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 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 b2532 118 putative ATP synthase beta subunit #7 HI0376 56 conserved hypothetical protein #8 HI0377 59 iscU protein (iscU) #9 HI0378 60 nifS protein (nifS) #10 HI0379 52 conserved hypothetical protein #11 HI0380 300 conserved hypothetical protein Motif number 1 TTTTACGGTAAAGCCCCTGCGTTTGCTGGG 1 215 1 AAGCCCCTGC 0.775314 -86 GATTATCAGTTCAACCCAGCAAACGCAGGG 1 229 0 TCAACCCAGC 0.943854 -72 GCGCATACCGATAACCCCACCGTGGTCGCC 2 12 1 ATAACCCCAC 0.974803 -84 AATGTCAGACTTGACCCTGCTATGCAATAC 5 102 1 TTGACCCTGC 0.912884 -76 CTGCTATGCAATACCCCCACTTTTACAATA 5 118 1 ATACCCCCAC 0.965995 -60 CACCTCAAACTCGCCCCTGCCCGGGGTTTT 5 149 0 TCGCCCCTGC 0.9249 -29 GCGGTCAAAATTGACCGCACTTTTTCACAT 7 13 0 TTGACCGCAC 0.848717 -44 CTATCCCCCAACACCGCTAAAA 7 45 0 ATCCCCCAAC 0.845708 -12 TATGCTAAATATAACCGCACTTTTTTATTA 9 33 0 ATAACCGCAC 0.883333 -28 GACTGAGCTAACGACCCCACTGTATTAAAT 11 13 0 ACGACCCCAC 0.990011 -288 CGAATCCTTCACGACCCACCACTCTCTGAT 11 81 1 ACGACCCACC 0.96813 -220 AACTGAGCTAACAACCCAACTGGACAACTA 11 112 0 ACAACCCAAC 0.974892 -189 CTAGTCTCTCACAACCCACCATTTTTATTA 11 180 1 ACAACCCACC 0.949949 -121 ********** Masking position 5 Map Score: 15.7269 Number of sites scoring better than the average of aligned sites = 856 Number in coding regions = 780 Number in noncoding regions = 76 Number of orfs with sites within 600 bp upstream = 69 Fraction of orfs with sites within 600 bp upstream = 0.0110826 Motif number 2 GAGATAGGTAAAAAAGTGCAGCGTTCAGAA 1 28 0 AAAAAGTGCA 0.876106 -273 CGCCACGATAAAAAAATGGCACTGAAGGTT 5 23 1 AAAAAATGGC 0.85193 -155 TTTTTTATTGTAAAAGTGGGGGTATTGCAT 5 123 0 TAAAAGTGGG 0.93566 -55 CTTTTACAATAAAAAACCCCGGGCAGGGGC 5 137 1 AAAAAACCCC 0.767648 -41 ACTGGATGTTAAAGAACGGGAAAACGGCGC 6 22 1 AAAGAACGGG 0.757121 -97 TCATGTGAAAAAGTGCGGTCAATTTTG 7 8 1 AAAAAGTGCG 0.984454 -49 CCAACACCGCTAAAAATGCGGTCAAAATTG 7 30 0 TAAAAATGCG 0.951528 -27 TTTTTTAATAAAAAAGTGCGGTTATATTTA 9 28 1 AAAAAGTGCG 0.984454 -33 AAAGAATCCCTAAAAATTAA 10 43 0 AAAGAATCCC 0.843543 -10 ACCAACGGATTAAAAGTCCGCTGCTCTACC 11 43 0 TAAAAGTCCG 0.956059 -258 ACTGACGGATTAAGAGTCCGCTACTCTACC 11 142 0 TAAGAGTCCG 0.931635 -159 ********** Masking position 5 Map Score: 10.5502 Number of sites scoring better than the average of aligned sites = 938 Number in coding regions = 748 Number in noncoding regions = 190 Number of orfs with sites within 600 bp upstream = 190 Fraction of orfs with sites within 600 bp upstream = 0.0305172 Motif number 3 GAGCATTAAGGCTGTGATGAAAAAGAAAAA 1 82 0 GCTGTGATGA 0.851585 -219 TCACTAACATGCTGTTATACGCTGAAAGCG 1 263 1 GCTGTTATAC 0.960023 -38 GCTGCGATCCGCCGCGATAACGGCGAATCA 2 64 0 GCCGCGATAA 0.961763 -32 CATTCTCAGGGCTGCGATCCGCCGCGATAA 2 74 0 GCTGCGATCC 0.979688 -22 AGGTACAAACGCCACGATAAAAAAATGGCA 5 14 1 GCCACGATAA 0.832017 -164 CAGACTTGACCCTGCTATGCAATACCCCCA 5 107 1 CCTGCTATGC 0.909372 -71 TGCCGATCTCGCTGCTATACTCTGCGCCGT 6 45 0 GCTGCTATAC 0.991866 -74 TTAAAAGTCCGCTGCTCTACCGACTGAGCT 11 34 0 GCTGCTCTAC 0.983469 -267 TTAAGAGTCCGCTACTCTACCAACTGAGCT 11 133 0 GCTACTCTAC 0.921495 -168 ********** Masking position 8 Map Score: 8.06515 Number of sites scoring better than the average of aligned sites = 1048 Number in coding regions = 994 Number in noncoding regions = 54 Number of orfs with sites within 600 bp upstream = 61 Fraction of orfs with sites within 600 bp upstream = 0.00979762 Motif number 4 ACTATTTAAGAGATAGGTAAAAAAGTGCAG 1 37 0 AGATAGGTAA 0.812528 -264 GGTATCTCATTGTTAGATAATGGTTATTAT 1 117 0 TGTTAGATAA 0.707254 -184 GCACGCTAAGAATTAGGTATCTCATTGTTA 1 132 0 AATTAGGTAT 0.784346 -169 AAAGCGATGAAGTGAGGTAAATCG 1 287 1 AGTGAGGTAA 0.947556 -14 GATAACGGCGAATCAGGTAAAACAAACCCC 2 49 0 AATCAGGTAA 0.942019 -47 TGACTGATTTAGTCGGGTATTTAACCTTCA 5 45 0 AGTCGGGTAT 0.965038 -133 CGACTAAATCAGTCAAGTAAATAGTTGACC 5 60 1 AGTCAAGTAA 0.891435 -118 TGAATGCCATTGTCAGATAATGGCAACTAA 8 14 0 TGTCAGATAA 0.880547 -46 CTAAATTAGTCAGATATGTAAGTATTG 10 8 1 AGTCAGATAT 0.94768 -45 CTTAAATTTTAGTCGGGTATCATT 11 287 1 AGTCGGGTAT 0.965038 -14 ********** Masking position 8 Map Score: 7.90839 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 5 CAGGCACGCTAAGAATTAGGTATCTCATTG 1 135 0 AAGAATTAGG 0.93315 -166 CGCGATAACGGCGAATCAGGTAAAACAAAC 2 52 0 GCGAATCAGG 0.980872 -44 TCGGTATCGGAATCAGGAGAATTTATA 3 8 1 CGGAATCAGG 0.994217 -20 AAAAAGAATTCAGAATCAGGCCGGAGTGCT 4 12 1 CAGAATCAGG 0.991128 -76 TCAATGCAAGGAATCAGGCTACCGGCTG 4 70 0 AGGAATCAGG 0.991207 -18 ********** Masking position 5 Map Score: 5.24839 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 6 TACCTATCTCTTAAATAGTCATTTTCAATAC 1 48 1 TTAAATGTCA 0.93848 -253 AATACCCGACTAAATCAGTCAAGTAAATAGT 5 54 1 TAAATCGTCA 0.977783 -124 CATTCCCGAGTAAATTGGTCAACTATTTACT 5 75 0 TAAATTGTCA 0.981521 -103 CTAAATTAGTCAGATATGTAAG 10 2 1 TAAATTGTCA 0.981509 -51 TAGCGGACTCTTAATCCGTCAGTCGAGAGTT 11 149 1 TTAATCGTCA 0.959351 -152 AATAACCGCTAAAAATAGTCAAGAATTTAAG 11 243 0 AAAAATGTCA 0.875363 -58 ****** **** Masking position 4 Map Score: 5.02908 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 7 GGGTATTTAACCTTCAGTGCCATTTTTTTATC 5 29 0 CCTCAGGCCA 0.919933 -149 GGTTAAATACCCGACTAAATCAGTCAAGTAAA 5 49 1 CCACTAATCA 0.786646 -129 CAGACTTGACCCTGCTATGCAATACCCCCACT 5 107 1 CCGCTAGCAA 0.891345 -71 CTATCCCCCAACACCGCTAAAAATGCGGT 7 38 0 CCACACGCTA 0.938673 -19 AGCTAACGACCCCACTGTATTAAATGG 11 6 0 CCACTGATTA 0.942206 -295 CGCTGCTCTACCGACTGAGCTAACGACCCCAC 11 23 0 CCACTGGCTA 0.994546 -278 AGCTAACAACCCAACTGGACAACTAAATCAGA 11 105 0 CCACTGACAA 0.974491 -196 CGCTACTCTACCAACTGAGCTAACAACCCAAC 11 122 0 CCACTGGCTA 0.994546 -179 ** **** **** Masking position 12 Map Score: 3.36964 Number of sites scoring better than the average of aligned sites = 473 Number in coding regions = 456 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 8 CCGTGGTCGCCTGCGCGTGGGGTTTGTTTT 2 31 1 CTGCGCGTGG 0.863763 -65 CGGCGGATCGCAGCCCTGAGAATGTT 2 80 1 CAGCCCTGAG 0.96297 -16 AATTCAGAATCAGGCCGGAGTGCTAAATAC 4 18 1 CAGGCCGGAG 0.978703 -70 GTCGTACATCCAGCCGGTAGCCTGATTCCT 4 60 1 CAGCCGGTAG 0.986142 -28 AAACTCGCCCCTGCCCGGGGTTTTTTATTG 5 143 0 CTGCCCGGGG 0.970835 -35 AACGGGAAAACGGCGCAGAGTATAGCAGCG 6 36 1 CGGCGCAGAG 0.832933 -83 GTCGTTAGCTCAGTCGGTAGAGCAGCGGAC 11 28 1 CAGTCGGTAG 0.969479 -273 GTTGTTAGCTCAGTTGGTAGAGTAGCGGAC 11 127 1 CAGTTGGTAG 0.806924 -174 CTTAATCCGTCAGTCGAGAGTTCTAGTCTC 11 158 1 CAGTCGAGAG 0.935244 -143 ********** Masking position 1 Map Score: 6.79885 Number of sites scoring better than the average of aligned sites = 1279 Number in coding regions = 1202 Number in noncoding regions = 77 Number of orfs with sites within 600 bp upstream = 61 Fraction of orfs with sites within 600 bp upstream = 0.00979762 Motif number 9 GGTATCGGAATCAGGAGAATTTATA 3 13 1 TAGAATTATA 0.896437 -15 TAAAAAGAATTCAGAATCAGGCCGG 4 1 1 TAGAATTAGA 0.978341 -87 GGGGCGAGTTTGAGGTGAAGTAAGAC 5 162 1 TAGAAGTAGA 0.986235 -16 CGGTCTCTCTCACTGGATGTTAAAGAACGGGAAA 6 10 1 TAGATGTAAA 0.861436 -109 CATCTTATCATAAAACGAAGACAGATGCCGATCTC 6 65 0 TAGAAGAAGA 0.963275 -54 TGAATAATCTTTAGATGAAGAAAGACA 6 102 1 TAGAAGAAGA 0.963275 -17 ACAATGGCATTCACTAGAATTGAAAAAAGGAAAGT 8 31 1 TAGAATTAAA 0.956276 -29 TTTAAGCTAATTAAAGAAATTTAAAATATTAGGGA 11 214 0 TAAAATTAAA 0.7095 -87 * * ***** *** Masking position 8 Map Score: 2.3944 Number of sites scoring better than the average of aligned sites = 68 Number in coding regions = 51 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 10 TCAGTCGGTAGAGCAGCGGACTTTTAATCC 11 37 1 GAGCAGCGGA 0.9921 -264 TCGAACCTTCGACCAACGGATTAAAAGTCC 11 54 0 GACCAACGGA 0.987833 -247 TCAGTTGGTAGAGTAGCGGACTCTTAATCC 11 136 1 GAGTAGCGGA 0.987833 -165 TAGAACTCTCGACTGACGGATTAAGAGTCC 11 153 0 GACTGACGGA 0.968542 -148 ********** Masking position 2 Map Score: 1.95177 Number of sites scoring better than the average of aligned sites = 66 Number in coding regions = 64 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 1 Fraction of orfs with sites within 600 bp upstream = 0.000160617 Motif number 11 ********** No masking Map Score: -3.03101e-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 12 ********** No masking Map Score: -3.03101e-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 13 ********** No masking Map Score: -3.03101e-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