AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -imodE_ecoli_bsub_100.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 modA 166 molybdate-binding periplasmic protein; permease #2 moaA 300 molybdopterin biosynthesis, protein A #3 moaB 21 molybdopterin biosynthesis, protein B #4 dmsA 300 anaerobic dimethyl sulfoxide reductase subunit A #5 ydiG 125 similar to molybdopterin precursor biosynthesis #6 mobA 136 molybdopterin-guanine dinucleotide biosynthesis protein A #7 moeB 50 molybdopterin biosynthesis protein #8 yoaE 300 similar to formate dehydrogenase #9 moaB 84 molybdopterin precursor biosynthesis protein B #10 ackA 300 acetate kinase #11 yvgL 110 alternate gene name: yvsD; similar to molybdate-binding protein #12 yvgM 103 alternate gene name: yvsC; similar to molybdenum transport permease #13 narQ 245 alternate gene name: narAA #14 yyaE 300 similar to formate dehydrogenase Motif number 1 TTGAGAAAAAGAAAATGCCCGACTAAGCGGGC 1 21 0 GAAAATCCGA 0.915718 -146 AATATCGGCAGGAAAAGCAGGAAGTTGAGAAA 1 45 0 GGAAAACAGA 0.880069 -122 ATAACTGCTGGGAAAATTCCGAGTTAGTCGTT 1 106 1 GGAAAATCGA 0.944034 -61 GTATATCAAAGTAAAACCGCCATTTTCCCTTA 2 53 1 GTAAAACGCA 0.876273 -248 AGTGTGGATGGTAAAAATCTCATTTACACGCT 2 138 1 GTAAAATCCA 0.846179 -163 TTATGAAAACGAAAATCCCTGATGCGGTATTG 4 222 1 GAAAATCCGA 0.915718 -79 CCGTGGTTTGGTAAAAACGACAGCGATCGGCG 4 271 1 GTAAAACGCA 0.876273 -30 CGTCAATTCTGAAAAAAAGAGATTGACATCAA 8 220 0 GAAAAAAGGA 0.697549 -81 AAATACAGAGGGAAAAACCGCAAATTGTAAGC 10 71 1 GGAAAACCCA 0.969773 -230 AAGTTGACTTGAAAAGCCGACATGACAATGTT 10 176 1 GAAAAGCGCA 0.737149 -125 ATGTTTAAATGGAAAAGTCAGATATTTTTCGG 10 203 1 GGAAAATCGA 0.944034 -98 CAACGGGTGTGAAAAATTCTGAAGCGCTTATG 12 11 0 GAAAAATCGA 0.953498 -93 CTCAGAATTCGACAAAATCCGAGGAGTGTGAA 13 185 1 GACAAATCGA 0.735591 -61 TCGTAGAAATGAAAAAACCGCATCCATGCGGA 14 85 1 GAAAAACCCA 0.974999 -216 CCTTCTATATGAAAAAGCATGAGTGTCGGCCT 14 263 0 GAAAAACAGA 0.899193 -38 ****** ** ** Masking position 5 Map Score: 13.8172 Number of sites scoring better than the average of aligned sites = 521 Number in coding regions = 445 Number in noncoding regions = 76 Number of orfs with sites within 600 bp upstream = 79 Fraction of orfs with sites within 600 bp upstream = 0.0126887 Motif number 2 GCTTGTCTGTTTATTAAAGAGGAATAGCTGTT 6 58 0 TTTTAAGAGG 0.924965 -79 GGAAAGAGATTCATATATAGGCGCGCTCTGT 8 10 1 TTATAATAGG 0.961115 -291 AAGCGCTAGCTTGAAAGATAGGAAAGCAAGGT 8 63 0 TTAAAATAGG 0.776695 -238 GAATACGTTTATCATAAAGAAGACTCAGATTG 8 191 1 ATATAAGAAG 0.808057 -110 TTTGAAACACAAAATACAGAGGGAAAAACCGC 10 60 1 AAATAAGAGG 0.774096 -241 AACGAAGTTGTTGATACAGAGTATAAAGGAGC 10 272 1 TTATAAGAGT 0.884446 -29 AGTCCTTTATACAGAGGTGTCTCAGCG 13 6 1 TTATAAGAGG 0.988714 -240 GTAAAAGCCCTTTATATAGAGGGCTCTTTTTG 13 150 1 TTATAAGAGG 0.988711 -96 AGGAGCCTACTTCATAAATAGGCCGACACTCA 14 244 1 TTATAATAGG 0.961118 -57 CTCATGCTTTTTCATATAGAAGGTAAGGAGAA 14 272 1 TTATAAGAAG 0.938057 -29 ** *** ***** Masking position 6 Map Score: 9.7593 Number of sites scoring better than the average of aligned sites = 58 Number in coding regions = 37 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 3 AGTTGACCCAGGTGCAGAGGCTAGAGTGTTTAGT 2 185 0 GTGGAGGTAG 0.629599 -116 ACCTTTCCAGATACGGGAGGCGAAGTCATTTCTT 2 273 0 AACGAGGGAA 0.93351 -28 AGTATTACGTGTAAGTGAGGAGTAATTATTGTTC 4 48 0 GAAGAGGGTA 0.817036 -253 TGCGGTATTGGCTGCTGAGGTGAGTCGCCGTGGT 4 244 1 GTGGAGGGAG 0.967784 -57 TTAACTTATTATAGCAGAGGTGAAATAAT 5 6 0 AAGGAGGGAA 0.98131 -120 GCTTTTAACGAAACTAGAGGTGAGATGAT 6 118 1 AACGAGGGAG 0.962498 -19 AGATGACATAAAAGATAAGGAGAACAGGTTTG 7 29 1 AAGAAGGGAA 0.904935 -22 TTTTCTATCCAGAGAGGTGGAGGGACTGGCCCTA 8 130 0 AAGGTGGGGG 0.752789 -171 GACAGAAAACATAAAAGAGGTGGGCCA 9 68 1 AAAGAGGGGG 0.914741 -17 AAAAGGTATAATAAAATAGGAGAGTGATGATG 11 9 0 AAATAGGGAG 0.689562 -102 AGTTATATCTAATGATAAGGGGTGCAATC 11 92 1 ATGAAGGGTG 0.680398 -19 GAATTCGACAAAATCCGAGGAGTGTGAAAAAATA 13 189 1 AATGAGGGTG 0.751296 -57 AGGCAGGAACATTGCGGAGGGGAAGAGACA 13 226 1 ATGGAGGGAA 0.952401 -20 CAGCAGTTTAGGAAAAGAGGTGAAGGGTCTTGGC 14 25 1 GAAGAGGGAA 0.932928 -276 TTTTCATATAGAAGGTAAGGAGAAGACGGCG 14 280 1 GAGAAGGGAA 0.886599 -21 * ** **** *** Masking position 9 Map Score: 9.56217 Number of sites scoring better than the average of aligned sites = 367 Number in coding regions = 305 Number in noncoding regions = 62 Number of orfs with sites within 600 bp upstream = 67 Fraction of orfs with sites within 600 bp upstream = 0.0107613 Motif number 4 TTCCTGCTTTTCCTGCCGATATTTTTTCTTATCT 1 54 1 TCGCCGTTTT 0.907791 -113 TCCTTCGCCCTGGTGGCAATCTTTACGAGCATTG 2 240 0 TGGGCATTTT 0.902271 -61 GCGCCTGCGGGCGCTTTTTTTGTCTCCCT 4 6 1 TGGGCGTTTT 0.989493 -295 TGCTGAGGTGAGTCGCCGTGGTTTGGTAAAAACG 4 256 1 AGGCCGGTTT 0.957136 -45 GGCACAATAATGTTGCCGAGGTTTCATAGGGCCA 8 104 1 TGGCCGGTTT 0.970319 -197 GCTTACAATAAGAAGTCGTTATTTTCAGACACAT 10 129 0 AGGTCGTTTT 0.908685 -172 CTAAGCATTTAGCCGCCGTTCCTTTTATAACACG 13 82 0 AGGCCGTCTT 0.91547 -164 CAGGATGTGATGACGGCGGTGTTTAGGCAGGACG 13 117 0 TGGGCGTTTT 0.989492 -129 CCCTTTATATAGAGGGCTCTTTTTGTGTCTCAGA 13 157 1 AGGGCTTTTT 0.863127 -89 TCGCTCCGCATGGATGCGGTTTTTTCATTTCTAC 14 87 0 TGTGCGTTTT 0.891631 -214 ** **** * *** Masking position 13 Map Score: 7.38072 Number of sites scoring better than the average of aligned sites = 513 Number in coding regions = 471 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 5 CTTCCTGCTTTTCCTGCCGATATTTTTTCTT 1 53 1 TTCCTGCCGT 0.897744 -114 ATGCACGCTATGCCTCCCTGATGATGTATAT 2 28 1 TGCCTCCCTA 0.826909 -273 GCGCTTTTTTTGTCTCCCTTTGATACCGAAC 4 21 1 TGTCTCCCTT 0.958195 -280 ATACACTATTTTCTTCTCTATGTCTTATATG 5 81 0 TTCTTCTCTT 0.78735 -45 TCAACGCTACTGCTTGTCTGTTTATTAAAGA 6 70 0 TGCTTGTCTT 0.855946 -67 TTTATACCGGCGTCTGCCTGTAACAGAGCGC 8 33 0 CGTCTGCCTT 0.769772 -268 GTATAAACCTTGCTTTCCTATCTTTCAAGCT 8 57 1 TGCTTTCCTT 0.839808 -244 GGCCCAGTTCCTCTCTCTAGTTAGATAT 8 283 0 TTCCTCTCTT 0.886889 -18 TCTTTTATGTTTTCTGTCTGTCACTATCATG 9 55 0 TTTCTGTCTT 0.78735 -30 CAATTTGCGGTTTTTCCCTCTGTATTTTGTG 10 67 0 TTTTTCCCTT 0.870875 -234 TTTTCGTACTTTTTTCCCGGTGAATATCAAC 10 242 0 TTTTTCCCGT 0.661896 -59 ACACCCGTTGTGCTTTCCTTTCAGGTGGCGG 12 33 1 TGCTTTCCTT 0.839808 -71 CTCCGCAATGTTCCTGCCTTTATATTTTTTC 13 214 0 TTCCTGCCTT 0.967996 -32 AAAGCATGAGTGTCGGCCTATTTATGAAGTA 14 251 0 TGTCGGCCTT 0.769772 -50 ********* * Masking position 8 Map Score: 8.40114 Number of sites scoring better than the average of aligned sites = 681 Number in coding regions = 581 Number in noncoding regions = 100 Number of orfs with sites within 600 bp upstream = 117 Fraction of orfs with sites within 600 bp upstream = 0.0187922 Motif number 6 TATCGGCAGGAAAAGCAGGAAGTTGAGAAA 1 45 0 AAAAGCAGGA 0.809429 -122 GAATAATTTGAAAATCAAAGAGATAGGTAG 4 98 0 AAAATCAAAG 0.584944 -203 AAAGCATAGCAAAAGCAAAGGCTCAACGCT 6 93 0 AAAAGCAAAG 0.941626 -44 TAGTTTCGTTAAAAGCATAGCAAAAGCAAA 6 104 0 AAAAGCATAG 0.941626 -33 TGAAAGATAGGAAAGCAAGGTTTATACCGG 8 54 0 GAAAGCAAGG 0.891038 -247 ATCGCATGAAAGCACATTCTCTTGAAT 9 8 1 GAAAGCACAT 0.859203 -77 GCATCAACAAAAAAGCACATTCAAGAGAAT 9 26 0 AAAAGCACAT 0.895515 -59 TCCGGTCTTCAAAAGCATAAATAAAAGCA 10 10 0 AAAAGCATAA 0.910473 -291 CACCTGAAAGGAAAGCACAACGGGTGTGAA 12 30 0 GAAAGCACAA 0.919263 -74 TTCTATATGAAAAAGCATGAGTGTCGGCCT 14 263 0 AAAAGCATGA 0.878655 -38 ********** Masking position 4 Map Score: 4.91066 Number of sites scoring better than the average of aligned sites = 345 Number in coding regions = 265 Number in noncoding regions = 80 Number of orfs with sites within 600 bp upstream = 96 Fraction of orfs with sites within 600 bp upstream = 0.0154192 Motif number 7 AGGGAGGCATAGCGTGCATCGTCCTTTAGA 2 17 0 AGCGTGCATC 0.936455 -284 AAGCCTATATAGCGAACTGCTATAGAAATA 4 137 1 AGCGAACTGC 0.940372 -164 TAAAAACGACAGCGATCGGCGGCCTGGCA 4 282 1 AGCGATCGGC 0.970941 -19 GACAAGCAGTAGCGTTGAGCCTTTGCTTTT 6 83 1 AGCGTTGAGC 0.944592 -54 GCAAATTGTAAGCGTTCATCAATACAAAAC 10 90 1 AGCGTTCATC 0.961719 -211 ATCCATGCGGAGCGAACAGCTGGAAAATTA 14 106 1 AGCGAACAGC 0.98109 -195 ********** Masking position 1 Map Score: 1.96767 Number of sites scoring better than the average of aligned sites = 415 Number in coding regions = 398 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 8 GCGCCTGCGGGCGCTTTTTTT 4 1 1 GCGCTGCGGG 0.988751 -300 AAAAACGACAGCGATCGGCGGCCTGGCA 4 283 1 GCGACGGCGG 0.929843 -18 TCTGTTACAGGCAGACGCCGGTATAAACCTT 8 37 1 GCAGCGCCGG 0.980932 -264 TTTCAAGCTAGCGCTTGCTGGAATTGGCACA 8 79 1 GCGCTGCTGG 0.982772 -222 TCAGGTGGCGGCAGTTGCCGGAATTGTTGTC 12 53 1 GCAGTGCCGG 0.977078 -51 TATTCTCGGAACACTTGCTGGAGCATGG 12 86 1 ACACTGCTGG 0.882916 -18 TGCATTGACAACGAACGCGGGGTTTGTCGAC 13 39 0 ACGACGCGGG 0.928123 -207 **** ****** Masking position 7 Map Score: 1.98049 Number of sites scoring better than the average of aligned sites = 1100 Number in coding regions = 1044 Number in noncoding regions = 56 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 9 CGAAGGAAGAAATGACTTCGCCTCCCGTAT 2 267 1 AATGACTTCG 0.814145 -34 AAAAAAAGAGATTGACATCAATCTGAGTCT 8 211 0 ATTGACATCA 0.777041 -90 TAACATTTCCGATGATAACGTCAATTCTGA 8 240 0 GATGATAACG 0.867838 -61 CAACTTGCGTATTGATAACGCTTACAATAA 10 152 0 ATTGATAACG 0.939065 -149 AGTTATATCTAATGATAAGGGGTGCAATC 11 92 1 AATGATAAGG 0.803605 -19 TTCCGAGAATAATGACAACAATTCCGGCAA 12 67 0 AATGACAACA 0.899691 -37 ACCAATGTGCATTGACAACGAACGCGGGGT 13 47 0 ATTGACAACG 0.960698 -199 CTTTGGCCTGAATGATATCGTAGAAATGAA 14 68 1 AATGATATCG 0.939065 -233 ********** Masking position 5 Map Score: 1.76522 Number of sites scoring better than the average of aligned sites = 329 Number in coding regions = 302 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 10 CAAACCTGTTCTCCTTATCTTTTATGT 7 34 0 TTTCTCCTTA 0.870954 -17 GTCAATCTCTTTTTTTCAGAATTGACGTTAT 8 225 1 TTTTTCAGAA 0.697507 -76 GAATTGACGTTATCATCGGAAATGTTATAAT 8 243 1 TTCATCGGAA 0.548304 -58 AATATCAACATCTTCTCCGAAAAATATCTGA 10 220 0 TTTCTCCGAA 0.984887 -81 TTATTATACCTTTTCGCCGAATGTAAAAAAA 11 29 1 TTTCGCCGAA 0.93837 -82 TTGTTGTCATTATTCTCGGAACACTTGCTGG 12 76 1 TTTCTCGGAA 0.975642 -28 ACCCTTCACCTCTTTTCCTAAACTGCTGTAT 14 22 0 TTTTTCCTAA 0.830077 -279 TTTCAAATTCTCTTCTCGGAATCATAACACT 14 183 0 TTTCTCGGAA 0.975642 -118 CGCCGTCTTCTCCTTACCTTCTATAT 14 285 0 TTTCTCCTTA 0.870954 -16 * ********* Masking position 3 Map Score: 3.00701 Number of sites scoring better than the average of aligned sites = 165 Number in coding regions = 133 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 11 ********** No masking Map Score: -6.40666e-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: -6.40666e-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: -6.40666e-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