AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -imodE_ecoli_hinf_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 HI1047 253 anaerobic dimethyl sulfoxide reductase, chain A (dmsA) #6 HI1675 91 molybdenum cofactor biosynthesis protein C (moaC) #7 HI1676 300 molybdenum cofactor biosynthesis protein A (moaA) #8 HI1692 173 molybdenum ABC transporter, permease protein (modB) #9 HI1693 137 molybdenum ABC transporter, periplasmic-binding protein (modA) Motif number 1 TTGCTAACCTTTGTGAGGTAGATAAGAAAAAATATC 1 71 0 TTATAATAAG 0.92321 -96 AGTCGTTATATTGTCGCCTACATAACGTTACATTAA 1 131 1 TTGTAATAAC 0.939695 -36 TTTCGCTATGTAATCATGTATATAGCGTCATGATCG 2 103 0 TTATAATAGC 0.986294 -198 ATTCGATGTATACAAGCCTATATAGCGAACTGCTAT 4 124 1 TAGTAATAGC 0.848208 -177 CCGTATTGTGTAATTATTTCTATAGCAGTTCGCTAT 4 145 0 TTATCATAGC 0.96145 -156 TGCTAACGGATTTTTAAATCCATAGTCAATTTGTTA 5 73 1 TTATCATAGT 0.811725 -181 TTTATGGTTATTAATATAAATAGGATTAATTATC 7 9 1 TTATAATAGG 0.9506 -292 ATCAATTATATAAAAAAATACATAATGAATATAAGA 7 58 0 TAATAATAAT 0.63523 -243 GCAAAATGAATCCTTATCTAAATAGCCTCTCTTTAA 8 113 0 TTATAATAGC 0.986294 -61 AAAAATTATTTAGTAAAATATATAACGCTTAGGCTT 9 40 0 TTATAATAAC 0.978243 -98 CTTGATTATATATTGAAATAAATAACAATCATATAG 9 82 0 TTATAATAAC 0.978243 -56 TTTCAATATATAATCAAGTAAATAACGTTTAATCGT 9 100 1 TTATAATAAC 0.978243 -38 * * * ** ***** Masking position 12 Map Score: 12.6214 Number of sites scoring better than the average of aligned sites = 36 Number in coding regions = 26 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 2 ATTTTCCCTTATTCTGTAGCGAAATAGCACGATCAT 2 74 1 ATTTAGAAAA 0.968814 -227 CTATATAGCGAACTGCTATAGAAATAATTACACAAT 4 141 1 AAGTATAAAA 0.769802 -160 GAAAAGATCCTCTAGTTAATAATAGTTAAACT 5 7 1 ATTTAGAATA 0.767762 -247 TTGTTATTCCAAAGTTTATTAAAACATCAATCTACT 5 103 1 AATTATAAAA 0.951173 -151 GCTCAAGTAAAACTTCTATACAAAGATTATAATTAA 5 184 1 AATTATAAAA 0.951158 -70 TTAAAAATCAATTATATAAAAAAATACATAATGAAT 7 64 0 ATTTAAAAAA 0.827757 -237 TTGATTTTTAAGAATTTAGGAAAATACTGATTTTCA 7 89 1 AGTTAGAAAA 0.891906 -212 TGTTTAGCCTAAGTTTCATAGAAATACGGTGGCAAG 7 203 1 AATCATAAAA 0.754251 -98 GAGAGGTAAGATGCTCTATAATAACAAAAGGGCAGA 8 45 0 ATTTATTAAA 0.740521 -129 AAGCAAAATGAATCCTTATCTAAATAGCCTCTCTTT 8 115 0 AACTATAAAA 0.769807 -59 CAAAAGAAAAATTATTTAGTAAAATATATAACGCTT 9 46 0 ATTTAGAAAA 0.968814 -92 ATAAATAACAATCATATAGCAAAAGAAAAATTATTT 9 65 0 ATTTAGAAAA 0.968814 -73 TATTTACTTGATTATATATTGAAATAAATAACAATC 9 88 0 ATTTATAAAA 0.964046 -50 ** * *** *** * Masking position 8 Map Score: 7.827 Number of sites scoring better than the average of aligned sites = 62 Number in coding regions = 33 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 3 AACTGCTGGGAAAATTCCGAGTTAGTCGTTATATTG 1 108 1 ATTCGGTTAT 0.961383 -59 GGTTATGCCGATACTAGCGTGTAAATGAGATTTTTA 2 149 0 ATACGGTAAT 0.988238 -152 ACTCGAAAGTAGTATTACGTGTAAGTGAGGAGTAAT 4 56 0 ATTCGGTAAT 0.965192 -245 CCAGTAACAAACCGTATTGTGTAATTATTTCTATAG 4 156 0 ATATGGTAAT 0.891752 -145 ATCCGTTAGCATAGTGGCGTGTTAGTTTATCTAATA 5 48 0 ATGCGGTTAT 0.954517 -206 TTGAAAAATAACTAAAACGAGTTAATTATAATCTTT 5 205 0 AAACGGTTAT 0.933309 -49 CGAAAAATCAAATTTAACGCATAACTCCGAGCTTGT 7 170 1 ATACGATAAT 0.885161 -131 ATCCCTGAATAACGTAGCGCGTTATTGGCTTGCCAC 7 231 0 ATACGGTTAT 0.985549 -70 TTATTTCAATATATAATCAAGTAAATAACGTTTAAT 9 97 1 AAACAGTAAT 0.722403 -41 * ** ** **** * Masking position 12 Map Score: 4.75976 Number of sites scoring better than the average of aligned sites = 101 Number in coding regions = 79 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 4 AGGAAGTTGAGAAAAAGAAAATGCCCGACTA 1 28 0 GAAAAAGAAA 0.898442 -139 ATGATGTATATCAAAGTAAAACCGCCATTTT 2 48 1 TCAAAGTAAA 0.796524 -253 TGCCACCAGGGCGAAGGAAGAAATGACTTCG 2 256 1 GCGAAGGAGA 0.854988 -45 AACGTCAAAAGGAGAGATCAG 3 5 1 TCAAAAGAGA 0.900146 -17 TTGTTCGGTATCAAAGGGAGACAAAAAAAGC 4 23 0 TCAAAGGAGA 0.881178 -278 AGATTTTCACTCGAAAGTAGTATTACGTGTA 4 69 0 TCGAAAGAGT 0.477627 -232 GAGCCATTATGAAAACGAAAATCCCTGATGC 4 216 1 GAAAACGAAA 0.673942 -85 AAAGCAAAGTGAGATGAATGGTAA 6 4 1 GCAAAGTAGA 0.909406 -88 CCTAAATTCTTAAAAATCAATTATATAAAAA 7 78 0 TAAAAATAAT 0.377749 -223 TTAGAATGACGAAAAATCAAATTTAACGCAT 7 161 1 GAAAAATAAA 0.826343 -140 AATTGGGTAAGCAAAATGAATCCTTATCTAA 8 128 0 GCAAAATAAT 0.793578 -46 GCGTCAGATTGAAAAATGAAAAAAATTGGGT 8 151 0 GAAAAATAAA 0.826343 -23 CAATCATATAGCAAAAGAAAAATTATTTAGT 9 62 0 GCAAAAGAAA 0.957012 -76 ******* *** Masking position 5 Map Score: 5.39011 Number of sites scoring better than the average of aligned sites = 988 Number in coding regions = 827 Number in noncoding regions = 161 Number of orfs with sites within 600 bp upstream = 189 Fraction of orfs with sites within 600 bp upstream = 0.0303566 Motif number 5 TTCCCTGAATGCCCGCTTAG 1 1 1 TTCCCTGAAT 0.955449 -166 TGGTAACCCCTTAATGTAACGTTAT 1 152 0 ACCCCTTAAT 0.856409 -15 CACGCTATGCCTCCCTGATGATGTATATCA 2 31 1 CTCCCTGATG 0.940478 -270 AACCGCCATTTTCCCTTATTCTGTAGCGAA 2 67 1 TTCCCTTATT 0.931164 -234 GAAAACGAAAATCCCTGATGCGGTATTGGC 4 226 1 ATCCCTGATG 0.972274 -75 TTTCCAGCGTATCCCTGAATAACGTAGCGC 7 247 0 ATCCCTGAAT 0.975274 -54 CTCTCTTTAAATCCCTTGTTTATGGGAATA 8 93 0 ATCCCTTGTT 0.885909 -81 ********** Masking position 6 Map Score: 3.13823 Number of sites scoring better than the average of aligned sites = 143 Number in coding regions = 109 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 42 Fraction of orfs with sites within 600 bp upstream = 0.0067459 Motif number 6 AAAAAATATCGGCAGGAAAAGCAGGAAGTT 1 51 0 GGCAGGAAAA 0.963135 -116 TACATCATCAGGGAGGCATAGCGTGCATCG 2 26 0 GGGAGGCATA 0.987437 -275 TTCCAGATACGGGAGGCGAAGTCATTTCTT 2 273 0 GGGAGGCGAA 0.984885 -28 CGGTATCAAAGGGAGACAAAAAAAGCGCCC 4 19 0 GGGAGACAAA 0.963713 -282 TTACGTGTAAGTGAGGAGTAATTATTGTTC 4 48 0 GTGAGGAGTA 0.865062 -253 ATAACAAAAGGGCAGAAATATCCGCCCTTC 8 31 0 GGCAGAAATA 0.898249 -143 ********** Masking position 4 Map Score: 2.12062 Number of sites scoring better than the average of aligned sites = 148 Number in coding regions = 125 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 7 CCCGCTTAGTCGGGCATTTTCTTTTTCTCAA 1 22 1 CGGCATTTTC 0.974251 -145 GGAGGCATAGCGTGCATCGTCCTTTAGAGGT 2 14 0 CGGCATCGTC 0.975836 -287 GCGTCATGATCGTGCTATTTCGCTACAGAAT 2 84 0 CGGCTATTTC 0.956935 -217 CAACTGATACGGTGCTTTGGCCGTGACAATG 2 214 1 GGGCTTTGGC 0.900469 -87 GCAATCTTTACGAGCATTGTCACGGCCAAAG 2 228 0 CGGCATTGTC 0.98361 -73 GCGCCTGCGGGCGCTTTTTTTGTCTCCCTT 4 10 1 GGGCTTTTTT 0.893551 -291 CGCATAACTCCGAGCTTGTTTAGCCTAAGTT 7 187 1 CGGCTTGTTT 0.896644 -114 AAGCCAATAACGCGCTACGTTATTCAGGGAT 7 236 1 CGGCTACGTT 0.902635 -65 ** ******** Masking position 5 Map Score: 2.79313 Number of sites scoring better than the average of aligned sites = 670 Number in coding regions = 613 Number in noncoding regions = 57 Number of orfs with sites within 600 bp upstream = 60 Fraction of orfs with sites within 600 bp upstream = 0.00963701 Motif number 8 ATACATCATCAGGGAGGCATAGCGTGCATCGTCC 2 23 0 AGGGAGGACG 0.872372 -278 GGTATTGGCTGCTGAGGTGAGTCGCCGTGGTTTG 4 247 1 GCTGAGGGCG 0.958994 -54 GTTTTAATAAACTTTGGAATAACAAATTGACTAT 5 94 0 ACTTTGGACA 0.966933 -160 TTTCAATCTGACTGTGGGGGAACGATATA 5 235 1 ACTGTGGACG 0.978477 -19 TTTCTATGAAACTTAGGCTAAACAAGCTCGGAGT 7 193 0 ACTTAGGACA 0.97912 -108 TCATAGAAATACGGTGGCAAGCCAATAACGCGCT 7 218 1 ACGGTGGGCA 0.936999 -83 ACTTAGGATTACTTAGGAACAGCAAA 9 3 0 ACTTAGGACA 0.979128 -135 AATATATAACGCTTAGGCTTACCACTTAGGATTA 9 26 0 GCTTAGGACA 0.963714 -112 ******* * ** Masking position 7 Map Score: 1.70909 Number of sites scoring better than the average of aligned sites = 201 Number in coding regions = 193 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 9 AATAAGGGAAAATGGCGGTTTTACTTTGAT 2 57 0 AATGGCGGTT 0.946852 -244 TACATAGCGAAAGTGTGGATGGTAAAAATC 2 127 1 AAGTGTGGAT 0.919481 -174 AATATAATAAAAGTGCGGTTAAAATATTGA 6 72 0 AAGTGCGGTT 0.974793 -20 AATAGTCATGAAGGGCGGATATTTCTGCCC 8 22 1 AAGGGCGGAT 0.992583 -152 ATAATAACAAAAGGGCAGAAATATCCGCCC 8 34 0 AAGGGCAGAA 0.886621 -140 ********** Masking position 2 Map Score: 0.732657 Number of sites scoring better than the average of aligned sites = 165 Number in coding regions = 136 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 10 TTTTTCTTATCTACCTCACAAAGGTTAGCA 1 76 1 CTACCTCACA 0.711807 -91 TCTACCTCTAAAGGACGATGC 2 2 1 CTACCTCTAA 0.858576 -299 AATGAGATTTTTACCATCCACACTTTCGCT 2 132 0 TTACCATCCA 0.819829 -169 AGTATCGGCATAACCACTAAACACTCTAGC 2 170 1 TAACCACTAA 0.933854 -131 CCAAATCAATTAATCATTAATAGGTATATT 5 155 0 TAATCATTAA 0.510188 -99 CAGATGAATATTACCATTCATCTCACTTTG 6 15 0 TTACCATTCA 0.944847 -77 TTTATATTAATAACCATAAA 7 1 0 TAACCATAAA 0.655653 -300 ATAGGATTAATTATCACTAATGAGCTAGTC 7 30 1 TTATCACTAA 0.843499 -271 ATAGAGCATCTTACCTCTCATCAATGTGGG 8 62 1 TTACCTCTCA 0.947855 -112 ACGCTTAGGCTTACCACTTAGGATTACTTA 9 22 0 TTACCACTTA 0.884952 -116 ********** Masking position 3 Map Score: 0.755434 Number of sites scoring better than the average of aligned sites = 458 Number in coding regions = 392 Number in noncoding regions = 66 Number of orfs with sites within 600 bp upstream = 78 Fraction of orfs with sites within 600 bp upstream = 0.0125281 Motif number 11 ********** No masking Map Score: -5.52559e-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: -5.52559e-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: -5.52559e-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