AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -imodE_ecoli_bsub_300.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 b0762 128 orf, hypothetical protein #2 modA 166 molybdate-binding periplasmic protein; permease #3 moaA 300 molybdopterin biosynthesis, protein A #4 moaB 21 molybdopterin biosynthesis, protein B #5 dmsA 300 anaerobic dimethyl sulfoxide reductase subunit A #6 ydiG 125 similar to molybdopterin precursor biosynthesis #7 mobA 136 molybdopterin-guanine dinucleotide biosynthesis protein A #8 moeB 50 molybdopterin biosynthesis protein #9 yoaE 300 similar to formate dehydrogenase #10 moaB 84 molybdopterin precursor biosynthesis protein B #11 ackA 300 acetate kinase #12 yvgL 110 alternate gene name: yvsD; similar to molybdate-binding protein #13 yvgM 103 alternate gene name: yvsC; similar to molybdenum transport permease #14 narQ 245 alternate gene name: narAA #15 ywmE 93 ywmE #16 ywmD 300 similar to hypothetical proteins from B. subtilis #17 yyaE 300 similar to formate dehydrogenase Motif number 1 GCTTTGCGTGGCGTTCGTTTTCCGTCACAATAAGACT 1 28 0 GCTTTTCTCA 0.78966 -101 GCCCGCTTAGTCGGGCATTTTCTTTTTCTCAACTTCC 2 21 1 TCTTTTCTTT 0.910936 -146 TCAAAGTAAAACCGCCATTTTCCCTTATTCTGTAGCG 3 58 1 ACTTTTCTTA 0.604599 -243 TCTACCTATCTCTTTGATTTTCAAATTATTCGATGTA 5 97 1 TCTTTTCATT 0.918874 -204 CAATACCGCATCAGGGATTTTCGTTTTCATAATGGCT 5 217 0 TCTTTTCTTT 0.910936 -84 TTGATGTCAATCTCTTTTTTTCAGAATTGACGTTATC 9 220 1 TCTTTTCAAT 0.781623 -81 GGCCCACCTCTTTTATGTTTTCTGTCTGTCACTATCA 10 57 0 TTTTTTCTCT 0.928705 -28 CGCTTACAATTTGCGGTTTTTCCCTCTGTATTTTGTG 11 67 0 TTTTTTCTCT 0.928705 -234 ACAATAAGAAGTCGTTATTTTCAGACACATTCACTAT 11 122 0 GTTTTTCACA 0.699525 -179 TCCGAAAAATATCTGACTTTTCCATTTAAACATTGTC 11 199 0 ATTTTTCTTT 0.569851 -102 TGTATCAACAACTTCGTTTTTCGTACTTTTTTCCCGG 11 253 0 ACTTTTCACT 0.856294 -48 CATAAGCGCTTCAGAATTTTTCACACCCGTTGTGCTT 13 11 1 TCTTTTCACC 0.815578 -93 GTTCCTGCCTTTATATTTTTTCACACTCCTCGGATTT 14 199 0 TTTTTTCACT 0.935172 -47 TAGTAGCAGATTTCCGTTTTTCTGTCATAATCAAGGC 16 68 1 TTTTTTCTCA 0.893835 -233 TCCTATATCTTTTTGCATTTTCGTATTCTAGCATAAA 16 223 1 TTTTTTCATT 0.863807 -78 TTCCTTTCTTTTTCATATTTTCCAACTATATGTTGGA 16 266 0 TTTTTTCACT 0.935172 -35 CCAAGACCCTTCACCTCTTTTCCTAAACTGCTGTATC 17 21 0 TCTTTTCAAA 0.698193 -280 ACTAGTACTTTTTTTAGTTTTCTTTCAAATTCTCTTC 17 199 0 TTTTTTCTCA 0.893835 -102 AGGCCGACACTCATGCTTTTTCATATAGAAGGTAAGG 17 263 1 TCTTTTCATA 0.879817 -38 ** ***** *** Masking position 9 Map Score: 15.1843 Number of sites scoring better than the average of aligned sites = 329 Number in coding regions = 267 Number in noncoding regions = 62 Number of orfs with sites within 600 bp upstream = 75 Fraction of orfs with sites within 600 bp upstream = 0.0120463 Motif number 2 AACAGCTATTCCTCTTTAATAAACAGACAAGC 7 58 1 CCTCTTAAAA 0.902817 -79 ACAGAGCGCGCCTATATATGAATCTCTTTCC 9 10 0 CCTATTATAA 0.947672 -291 ACCTTGCTTTCCTATCTTTCAAGCTAGCGCTT 9 63 1 CCTATTTTAA 0.817971 -238 CAATCTGAGTCTTCTTTATGATAAACGTATTC 9 191 0 CTTCTTATAT 0.736481 -110 GCGGTTTTTCCCTCTGTATTTTGTGTTTCAAA 11 60 0 CCTCTTATTT 0.81822 -241 GCTCCTTTATACTCTGTATCAACAACTTCGTT 11 272 0 ACTCTTATAA 0.85209 -29 CGCTGAGACACCTCTGTATAAAGGACT 14 6 0 CCTCTTATAA 0.986507 -240 CAAAAAGAGCCCTCTATATAAAGGGCTTTTAC 14 150 0 CCTCTTATAA 0.986506 -96 AGCCTCTTTTTGTATGTAACAAAA 16 3 1 CCTCTTTTTA 0.81822 -298 TGAGTGTCGGCCTATTTATGAAGTAGGCTCCT 17 244 0 CCTATTATAA 0.947673 -57 TTCTCCTTACCTTCTATATGAAAAAGCATGAG 17 272 0 CTTCTTATAA 0.918458 -29 ***** *** ** Masking position 7 Map Score: 9.61781 Number of sites scoring better than the average of aligned sites = 115 Number in coding regions = 84 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 3 CAGAAAAGCACTCCCCTTTTGTGCGGTCAGCTTT 1 60 0 CTCCCTTTGC 0.865058 -69 AAGAAATGACTTCGCCTCCCGTATCTGGAAAGGT 3 273 1 TTCCCTCTAT 0.969642 -28 GAACAATAATTACTCCTCACTTACACGTAATACT 5 48 1 TACCCTCTAC 0.88476 -253 ACCACGGCGACTCACCTCAGCAGCCAATACCGCA 5 244 0 CTCCCTCAGC 0.829567 -57 ATTATTTCACCTCTGCTATAATAAGTTAA 6 6 1 TTCCCTCTAT 0.969642 -120 ATCATCTCACCTCTAGTTTCGTTAAAAGC 7 118 0 CTCCCTCTTT 0.970373 -19 CAAACCTGTTCTCCTTATCTTTTATGTCATCT 8 29 0 TTCCCTTTTT 0.891499 -22 TGGCCCACCTCTTTTATGTTTTCTGTC 10 68 0 CCCCCTCTAT 0.88559 -17 CATCATCACTCTCCTATTTTATTATACCTTTT 12 9 1 CTCCCTATAT 0.797544 -102 GATTGCACCCCTTATCATTAGATATAACT 12 92 0 CACCCTTATT 0.477196 -19 TATTTTTTCACACTCCTCGGATTTTGTCGAATTC 14 189 0 CACCCTCTTT 0.905532 -57 TGTCTCTTCCCCTCCGCAATGTTCCTGCCT 14 226 0 TTCCCTCAAT 0.895707 -20 TCATTCTTTTTTCGCCTTGATTATGACAGAAAAA 16 84 0 TTCCCTTTAT 0.918773 -217 GCCAAGACCCTTCACCTCTTTTCCTAAACTGCTG 17 25 0 TTCCCTCTCC 0.874494 -276 CGCCGTCTTCTCCTTACCTTCTATATGAAAA 17 280 0 TTCCCTTTTC 0.870942 -21 *** **** *** Masking position 7 Map Score: 10.79 Number of sites scoring better than the average of aligned sites = 165 Number in coding regions = 115 Number in noncoding regions = 50 Number of orfs with sites within 600 bp upstream = 60 Fraction of orfs with sites within 600 bp upstream = 0.00963701 Motif number 4 AAAAGGGGAGTGCTTTTCTGTGCTTAGCGGT 1 74 1 TGCTTTTCTT 0.897706 -55 TTTTCTCAACTTCCTGCTTTTCCTGCCGATA 2 44 1 TTCCTGCTTT 0.775847 -123 ATGCACGCTATGCCTCCCTGATGATGTATAT 3 28 1 TGCCTCCCTA 0.786912 -273 GCGCTTTTTTTGTCTCCCTTTGATACCGAAC 5 21 1 TGTCTCCCTT 0.903407 -280 ATACACTATTTTCTTCTCTATGTCTTATATG 6 81 0 TTCTTCTCTT 0.912127 -45 TCAACGCTACTGCTTGTCTGTTTATTAAAGA 7 70 0 TGCTTGTCTT 0.93331 -67 GTATAAACCTTGCTTTCCTATCTTTCAAGCT 9 57 1 TGCTTTCCTT 0.933826 -244 GGCCCAGTTCCTCTCTCTAGTTAGATAT 9 283 0 TTCCTCTCTT 0.943475 -18 CTCTTGAATGTGCTTTTTTGTTGATGCATGA 10 29 1 TGCTTTTTTT 0.574427 -56 TCTTTTATGTTTTCTGTCTGTCACTATCATG 10 55 0 TTTCTGTCTT 0.752028 -30 CAATTTGCGGTTTTTCCCTCTGTATTTTGTG 11 67 0 TTTTTCCCTT 0.783412 -234 ACACCCGTTGTGCTTTCCTTTCAGGTGGCGG 13 33 1 TGCTTTCCTT 0.933826 -71 CTCCGCAATGTTCCTGCCTTTATATTTTTTC 14 214 0 TTCCTGCCTT 0.957454 -32 ACTAATTAGCTGTCTGCCTGTAGCATAGTAG 16 43 1 TGTCTGCCTT 0.8869 -258 ATATGTTGGATTCTTCTTTATGCTAGAATAC 16 245 0 TTCTTCTTTT 0.614869 -56 ATGATTACTTCCTTTCTTTTTCATATTTT 16 282 0 TTCCTTTCTT 0.897706 -19 ********* * Masking position 5 Map Score: 13.8491 Number of sites scoring better than the average of aligned sites = 496 Number in coding regions = 408 Number in noncoding regions = 88 Number of orfs with sites within 600 bp upstream = 105 Fraction of orfs with sites within 600 bp upstream = 0.0168648 Motif number 5 AGGGAGGCATAGCGTGCATCGTCCTTTAGAGGTAGA 3 10 0 AGCTGACCTT 0.825702 -291 GCGCCTGCGGGCGCTTTTTTTGTCTCCC 5 2 1 CGCTGGGCTT 0.991673 -299 ATCGTGAGCAAGCTTGAGTGAGCCATTATGAAAACGA 5 197 1 AGCTGGGCTT 0.988857 -104 ATCGCATGAAAGCACATTCTCTTGAATGT 10 3 1 CGCTGAGCTC 0.964794 -82 ATAAAAAAGGCGCCTGGGGGAGCGCCTGATCTTTAGG 15 15 0 CGCTGGGCCT 0.991101 -79 AAGCATAAACAGCTTGTGTGATCATTCATTCTTTTTT 16 106 0 AGCTGGGCTC 0.982326 -195 TGTCCAAAATCGCTTGAAATGCCGTTCATTTTTAGCC 16 156 0 CGCTGATCTC 0.728742 -145 CTGTTCGCTCCGCATGGATGCGGTTTTTTCATTTCTA 17 88 0 CGCTGAGGTT 0.944574 -213 ATTCGAATTAAGTGTGAGGGATGCTCTCACAGTGTTA 17 153 1 AGTTGGGGCT 0.718071 -148 GTACTAGTCAAGCATGAGGAGCCTACTTCATAAATAG 17 228 1 AGCTGGACCT 0.890529 -73 TATATGAAAAAGCATGAGTGTCGGCCTATTTATGAAG 17 253 0 AGCTGGGGCT 0.969989 -48 *** ** * * * ** Masking position 5 Map Score: 6.47345 Number of sites scoring better than the average of aligned sites = 485 Number in coding regions = 456 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 6 TATATCAAAGTAAAACCGCCATTTTCCCTT 3 54 1 TAAAACCGCC 0.94814 -247 AGGGAGACAAAAAAAGCGCCCGCAGGCGC 5 10 0 AAAAAGCGCC 0.984303 -291 ATACAGAGGGAAAAACCGCAAATTGTAAGC 11 73 1 AAAAACCGCA 0.958906 -228 AGTTGACTTGAAAAGCCGACATGACAATGT 11 177 1 AAAAGCCGAC 0.865795 -124 CGTCCTGCCTAAACACCGCCGTCATCACAT 14 117 1 AAACACCGCC 0.964409 -129 TCTGAGACACAAAAAGAGCCCTCTATATAA 14 161 0 AAAAAGAGCC 0.875038 -85 AAACCAATAAAAAAGGCGCCTGGGGGAGCG 15 28 0 AAAAGGCGCC 0.972609 -66 GTAGAAATGAAAAAACCGCATCCATGCGGA 17 87 1 AAAAACCGCA 0.958906 -214 ********** Masking position 3 Map Score: 8.13665 Number of sites scoring better than the average of aligned sites = 425 Number in coding regions = 338 Number in noncoding regions = 87 Number of orfs with sites within 600 bp upstream = 68 Fraction of orfs with sites within 600 bp upstream = 0.0109219 Motif number 7 AGTTGACCCAGGTGCAGAGGCTAGAGTGTTTA 3 187 0 GGTGCAGGCT 0.988072 -114 TATCCAGAGAGGTGGAGGGACTGGCCCTATGA 9 127 0 GGTGGAGGCT 0.993483 -174 ACATTGCGGAGGGGAAGAGACA 14 234 1 GGGGAAGGCA 0.970004 -12 AAAGGCGCCTGGGGGAGCGCCTGATCTTTAGG 15 15 0 GGGGGAGGCT 0.993959 -79 TAGGAAAAGAGGTGAAGGGTCTTGGCGGATAA 17 33 1 GGTGAAGGCT 0.989956 -268 ******* * ** Masking position 6 Map Score: 3.14332 Number of sites scoring better than the average of aligned sites = 26 Number in coding regions = 22 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 8 TCGTTTTTACCAAACCACGGCGACTCACCTC 5 260 0 CAAACCCGGC 0.94715 -41 AAAACGACAGCGATCGGCGGCCTGGCA 5 284 1 CGATCGCGGC 0.819821 -17 GCTTATGAACCAGAAGTCAGCAAACAATACA 6 45 1 CAGAAGCAGC 0.887813 -81 CTGTTACAGGCAGACGCCGGTATAAACCTTG 9 38 1 CAGACGCGGT 0.888293 -263 CTGGCCCTATGAAACCTCGGCAACATTATTG 9 108 0 GAAACCCGGC 0.937602 -193 AAGTTGACTTGAAAAGCCGACATGACAATGT 11 176 1 GAAAAGCGAC 0.716615 -125 GCTTTCCTTTCAGGTGGCGGCAGTTGCCGGA 13 44 1 CAGGTGCGGC 0.851666 -60 TGTTATAAAAGGAACGGCGGCTAAATGCTTA 14 84 1 GGAACGCGGC 0.964429 -162 TTTACAGGATGTGATGACGGCGGTGTTTAGG 14 124 0 GTGATGCGGC 0.784432 -122 GAAAGCAGCACAAAAGGCAGCATGTCCTATA 16 199 1 CAAAAGCAGC 0.85501 -102 AGAAGGTAAGGAGAAGACGGCG 17 289 1 GAGAAGCGGC 0.977308 -12 ****** **** Masking position 8 Map Score: 2.78036 Number of sites scoring better than the average of aligned sites = 1172 Number in coding regions = 1113 Number in noncoding regions = 59 Number of orfs with sites within 600 bp upstream = 55 Fraction of orfs with sites within 600 bp upstream = 0.00883392 Motif number 9 ACGACTAACTCGGAATTTTCCCAGCAGTTA 2 107 0 CGGAATTTTC 0.876018 -60 ATCCCTGATGCGGTATTGGCTGCTGAGGTG 5 236 1 CGGTATTGGC 0.946893 -65 TAGCGCTTGCTGGAATTGGCACAATAATGT 9 87 1 TGGAATTGGC 0.917426 -214 CTCTTTTTTTCAGAATTGACGTTATCATCG 9 231 1 CAGAATTGAC 0.831395 -70 ACGTTATCATCGGAAATGTTATAATTCTTA 9 249 1 CGGAAATGTT 0.841221 -52 TTTTGAAGACCGGACTTGACGAATTGAATC 11 26 1 CGGACTTGAC 0.921436 -275 CGGCAGTTGCCGGAATTGTTGTCATTATTC 13 61 1 CGGAATTGTT 0.935367 -43 GCTTTCTGGGCGGAAATGGCTAAAAATGAA 16 139 1 CGGAAATGGC 0.973278 -162 ********** Masking position 7 Map Score: 1.96074 Number of sites scoring better than the average of aligned sites = 571 Number in coding regions = 543 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 10 AATATCAACATCTTCTCCGAAAAATATCTGA 11 220 0 TTTCTCCGAA 0.921865 -81 TTATTATACCTTTTCGCCGAATGTAAAAAAA 12 29 1 TTTCGCCGAA 0.960579 -82 TTGTTGTCATTATTCTCGGAACACTTGCTGG 13 76 1 TTTCTCGGAA 0.96547 -28 TTAAAAACAGTTTGGGCGGGAATGATACCCT 15 56 1 TTGGGCGGGA 0.900973 -38 GTTTATGCTTTCTGGGCGGAAATGGCTAAAA 16 133 1 TTGGGCGGAA 0.967288 -168 AGGTGAAGGGTCTTGGCGGATAAAGACTTTG 17 42 1 TTTGGCGGAT 0.90126 -259 TTTCAAATTCTCTTCTCGGAATCATAACACT 17 183 0 TTTCTCGGAA 0.96547 -118 * ********* Masking position 3 Map Score: 1.24218 Number of sites scoring better than the average of aligned sites = 139 Number in coding regions = 129 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 11 TTATTGCTAACCTTTGTGAGGTAGATAAGAAAA 2 77 0 CCTTTGAGTA 0.904904 -90 GCGTGCATCGTCCTTTAGAGGTAGA 3 3 0 TCCTAGAGTA 0.777314 -298 CGCTATGCCTCCCTGATGATGTATATCAAAGTA 3 33 1 CCCTTGAGTA 0.988395 -268 CCGCCATTTTCCCTTATTCTGTAGCGAAATAGC 3 69 1 CCCTTTCGTA 0.916911 -232 CTGATCTCTCCTTTTGACGTT 4 1 0 TCCTTGAGTT 0.923947 -21 AAACGAAAATCCCTGATGCGGTATTGGCTGCTG 5 228 1 CCCTTGCGTA 0.979691 -73 CGAACCATCTCCCTCATGATGTTAACACTACAA 7 12 1 CCCTTGAGTT 0.981522 -125 ATGTTCAACCCCTTTTTAGGGTATCATTCCCG 15 72 0 CCCTTTAGGT 0.763415 -22 **** *** *** Masking position 4 Map Score: 1.71059 Number of sites scoring better than the average of aligned sites = 119 Number in coding regions = 103 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 12 CCGTCACAATAAGACTTTTGCCAGGACATTGT 1 12 0 AAACTTTGCC 0.985403 -117 ATAACCACTAAACACTCTAGCCTCTGCACCTG 3 179 1 AAACTCTGCC 0.968165 -122 GTCAGCAAACAATACATTGGCCATATAAGACA 6 60 1 AAACATTGCC 0.943358 -66 GAATTGGCACAATAATGTTGCCGAGGTTTCAT 9 99 1 AAAATGTGCC 0.911317 -202 CAGGACGCCTAAGCATTTAGCCGCCGTTCCTT 14 92 0 AACATTTGCC 0.892944 -154 TTGGCGGATAAAGACTTTGGCCTGAATGATAT 17 54 1 AAACTTTGCC 0.985403 -247 ** ***** *** Masking position 8 Map Score: 1.10754 Number of sites scoring better than the average of aligned sites = 50 Number in coding regions = 46 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 13 ********** No masking Map Score: -6.3214e-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 14 GTCGGGCATTTTCTTTTTCTCAACTTCCTGCT 2 30 1 TTCTTTTCTA 0.765088 -137 GTAATTATTGTTCGGTATCAAAGGGAGACAAA 5 29 0 TTCGGTTCAA 0.944639 -272 ACCTATCTCTTTGATTTTCAAATTATTCGATG 5 100 1 TTGATTTCAA 0.641472 -201 ATCAGGGATTTTCGTTTTCATAATGGCTCACT 5 213 0 TTCGTTTCAA 0.948053 -88 GTTTGCTGACTTCTGGTTCATAAGCTACACTT 6 38 0 TTCTGGTCAA 0.818655 -88 AATCTGAGTCTTCTTTATGATAAACGTATTCT 9 190 0 TTCTTTTGAA 0.749588 -111 CCTCTGTATTTTGTGTTTCAAAGCTGGATTCA 11 50 0 TTGTGTTCAA 0.90326 -251 AAACCCCGCGTTCGTTGTCAATGCACATTGGT 14 45 1 TTCGTTTCAT 0.698699 -201 AGGGCTCTTTTTGTGTCTCAGAATTCGACAAA 14 169 1 TTGTGTTCAA 0.90326 -77 ATTACTTCCTTTCTTTTTCATATTTTCCAACT 16 276 0 TTCTTTTCAA 0.962452 -25 CCGACACTCATGCTTTTTCATATAGAAGGTAA 17 266 1 TGCTTTTCAA 0.82839 -35 ****** *** * Masking position 8 Map Score: 2.83549 Number of sites scoring better than the average of aligned sites = 111 Number in coding regions = 88 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 15 ********** No masking Map Score: -6.3214e-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