AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i180_molybdopterin_biosyntesis_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 talB 278 transaldolase B #2 mog 114 required for the efficient incorporation of molybdate into molybdoproteins #3 moaA 300 molybdopterin biosynthesis, protein A #4 moaB 21 molybdopterin biosynthesis, protein B #5 moeA 203 molybdopterin biosynthesis #6 HI0329 37 conserved hypothetical protein #7 HI0330 98 opacity associated protein (oapA) #8 HI0331 59 opacity associated protein (oapB) #9 HI0334 77 GTP pyrophosphokinase (relA) #10 HI0336 82 molybdopeterin biosynthesis protein (mog) #11 HI1448 137 molybdopterin biosynthesis protein (moeA) #12 HI1675 91 molybdenum cofactor biosynthesis protein C (moaC) #13 HI1676 300 molybdenum cofactor biosynthesis protein A (moaA) Motif number 1 TTGATATCGCCCGCCATTTTTATACAAAAC 1 123 0 CCGCCATTTT 0.979972 -156 CAAAGTAAAACCGCCATTTTCCCTTATTCT 3 59 1 CCGCCATTTT 0.979972 -242 CTGATCTCTCCTTTTGACGTT 4 6 0 TCTCCTTTTG 0.667194 -16 TAAGGGTGGTTCGCCACTTTTGCTATAAAT 5 24 1 TCGCCACTTT 0.917956 -180 TCAAACCATCTCTCATTTTTAGGATATTTC 6 15 0 TCTCATTTTT 0.861635 -23 AATTTTTTCGCCGCACTTTTGAGCTTCTCA 7 30 1 CCGCACTTTT 0.987109 -69 CTTTTGAGCTTCTCAATTTTGTGGCTAATT 7 45 1 TCTCAATTTT 0.909008 -54 GGGCGAGTAATCGCCCCTTTTTCTTTTTAA 8 17 1 TCGCCCCTTT 0.946928 -43 TAAAAACTTACCGCACTTTTGGAGGG 10 7 0 CCGCACTTTT 0.987109 -76 TAAGTTTTTACCGCATTTTTGATTTATCCA 10 27 1 CCGCATTTTT 0.96767 -56 TCATTCAAATTTGCAATTTTTCTCATTTTA 11 65 0 TTGCAATTTT 0.695968 -73 TTACCATTCATCTCACTTTGCTTT 12 5 0 TCTCACTTTG 0.834247 -87 AATATTTTAACCGCACTTTTATTATATT 12 74 1 CCGCACTTTT 0.987109 -18 ********** Masking position 8 Map Score: 20.2309 Number of sites scoring better than the average of aligned sites = 825 Number in coding regions = 709 Number in noncoding regions = 116 Number of orfs with sites within 600 bp upstream = 132 Fraction of orfs with sites within 600 bp upstream = 0.0212014 Motif number 2 ATACATGAGGTTTTGTATAAAAATGGCGGGCG 1 114 1 TTTTTATAAA 0.753874 -165 CTCCCTGATGATGTATATCAAAGTAAAACCGC 3 41 1 ATGTTATAAA 0.824591 -260 AAATTCTGATATTTATAGCAAAAGTGGCGAAC 5 32 0 ATTTTAGAAA 0.816959 -172 AAATATCAGAATTTTTATGAATTACTCATTCA 5 50 1 ATTTTATAAT 0.902021 -154 GCTTGTTCTTATTTATATTAATTAGCCACAAA 7 62 0 ATTTTATAAT 0.688254 -37 ATTTTTCCTTATTTTTATAAATGATTTTGACG 10 61 0 ATTTTATAAT 0.547382 -22 AGCCGATTATTTTTTTAGGAAAGACTATT 11 8 0 TTTTTAGAAA 0.650324 -130 AAAATTGCAAATTTGAATGAATTAGGCTTTAG 11 75 1 ATTTAATAAT 0.776778 -63 ATAGCTGACAAATTTTATCAAATAAGGATTTT 11 114 1 AATTTATAAA 0.85981 -24 AATTAATCCTATTTATATTAATAACCATAAA 13 10 0 ATTTTATAAT 0.688254 -291 CTTAAAAATCAATTATATAAAAAAATACATAA 13 69 0 AATTTATAAA 0.771164 -232 TATATAATTGATTTTTAAGAATTTAGGAAAAT 13 82 1 ATTTTAAAAT 0.736583 -219 GAAAATACTGATTTTCATCAATATTATTGATT 13 108 1 ATTTCATAAT 0.836368 -193 TTGCCACCGTATTTCTATGAAACTTAGGCTAA 13 206 0 ATTTTATAAA 0.932765 -95 **** *** *** Masking position 7 Map Score: 16.2591 Number of sites scoring better than the average of aligned sites = 91 Number in coding regions = 53 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 51 Fraction of orfs with sites within 600 bp upstream = 0.00819146 Motif number 3 CAGGAAAGTCATCGCGACCGGCAATAAGAG 1 19 0 ATCGCGACCG 0.974335 -260 GTTATCGCCAGGCGAGACTGTTTCGGATTT 1 164 0 GGCGAGACTG 0.931953 -115 ACGCAACGTCAGCGCAACCGCCGACAAGAC 1 195 0 AGCGCAACCG 0.964793 -84 TCATTCTTAGCGTGACCGGGAAGTCGGT 2 9 1 AGCGTGACCG 0.991654 -106 CAGAAGAGGTAGCGTGACCGACTTCCCGGT 2 25 0 AGCGTGACCG 0.991654 -90 CACTGCGAAGGGAGTGACAGACAGGCTTCA 2 53 0 GGAGTGACAG 0.847029 -62 CATTCTGTTTAACGAGACTGTTTAAACGGA 2 86 1 AACGAGACTG 0.916333 -29 ATGTCAGAAAAACGCCACAGACTGTATGCC 5 145 0 AACGCCACAG 0.884882 -59 ACCCAAAATAAAAGCGACAGGAAGTTGCTT 9 34 1 AAAGCGACAG 0.901433 -44 ********** Masking position 7 Map Score: 7.82063 Number of sites scoring better than the average of aligned sites = 838 Number in coding regions = 798 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 4 TCTTATTGCCGGTCGCGATGACTTTCCTGT 1 20 1 GGTCGCGATG 0.826527 -259 ACATCATCAGGGAGGCATAGCGTGCATCGT 3 25 0 GGAGGCATAG 0.942514 -276 CCTTCGCCCTGGTGGCAATCTTTACGAGCA 3 243 0 GGTGGCAATC 0.984668 -58 TCCAGATACGGGAGGCGAAGTCATTTCTTC 3 272 0 GGAGGCGAAG 0.97716 -29 TTATAGCAAAAGTGGCGAACCACCCTTAAT 5 22 0 AGTGGCGAAC 0.944078 -182 CTACGCCCGAGGTGGCATACAGTCTGTGGC 5 132 1 GGTGGCATAC 0.970358 -72 ACACTCCTGCGGAGGCAAAATCGAATTTGC 5 180 0 GGAGGCAAAA 0.92887 -24 AACAAGCATCAGAGGCAATCCA 7 87 1 AGAGGCAATC 0.911982 -12 ATAGAAATACGGTGGCAAGCCAATAACGCG 13 220 1 GGTGGCAAGC 0.974237 -81 ********** Masking position 6 Map Score: 8.89255 Number of sites scoring better than the average of aligned sites = 998 Number in coding regions = 944 Number in noncoding regions = 54 Number of orfs with sites within 600 bp upstream = 68 Fraction of orfs with sites within 600 bp upstream = 0.0109219 Motif number 5 TGCGTAGCATACATGAGGTTTTGTATAAAAATG 1 106 1 AATAGTTTTG 0.921814 -173 ACTAGCGTGTAAATGAGATTTTTACCATCCACA 3 140 0 AATAGTTTTT 0.949087 -161 TTTGCTATAAATATCAGAATTTTTATGAATTAC 5 42 1 AATAGATTTT 0.940608 -162 CATAATAGGCAAATTCGATTTTGCCTCCGCAGG 5 172 1 AATCGTTTTG 0.811503 -32 GGCGAAAAAATTATGTGTATTTTATCGGATC 7 9 0 TATTGATTTT 0.668078 -90 CCTTATTTTTATAAATGATTTTGACGTGATTGG 10 54 0 AAATGTTTTG 0.745196 -29 TAATTCATTCAAATTTGCAATTTTTCTCATTTT 11 66 0 AATTGAATTT 0.666752 -72 AAATTTTATCAAATAAGGATTTTCT 11 123 1 AATAGATTTT 0.937181 -15 ATTTTTTTATATAATTGATTTTTAAGAATTTAG 13 75 1 AAATGTTTTT 0.822153 -226 ATATTGATGAAAATCAGTATTTTCCTAAATTCT 13 99 0 AATAGATTTT 0.940156 -202 GTTATGCGTTAAATTTGATTTTTCGTCATTCTA 13 162 0 AATTGTTTTT 0.941642 -139 * ** ** ***** Masking position 3 Map Score: 6.75189 Number of sites scoring better than the average of aligned sites = 115 Number in coding regions = 75 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 49 Fraction of orfs with sites within 600 bp upstream = 0.00787022 Motif number 6 GATGACTTTCCTGTGTAAACGTTACCAATTG 1 36 1 CTTGTAAACG 0.932092 -243 AGCGTATATACTTCTTAAACAATTGGTAACG 1 55 0 CTCTTAAACA 0.972459 -224 GATAGTATTTCTCTTTAAACAGCTTGTTAGG 1 258 0 CTTTTAAACA 0.966931 -21 TTTAAACAGTCTCGTTAAACAGAATGATACA 2 81 0 CTGTTAAACA 0.929439 -34 TTTAACGAGACTGTTTAAACGGAAAAATCTT 2 93 1 CTTTTAAACG 0.943023 -22 CACACTTTCGCTATGTAATCATGTATATAGC 3 113 0 CTTGTAATCA 0.812879 -188 GTTGCTTGCTCTTCATCAACAAGGGGGTATT 9 57 1 CTCATCAACA 0.834067 -21 AAAGATTTCACTCCATAAACACAATCAATAA 13 131 0 CTCATAAACA 0.949811 -170 ** ******** Masking position 8 Map Score: 4.29821 Number of sites scoring better than the average of aligned sites = 106 Number in coding regions = 88 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 7 ACATAATTTTTTCGCCGCACTTTTGAGCTTC 7 26 1 TTGCCGCACT 0.98639 -73 GCGGTAAAAACTTACCGCACTTTTGGAGGG 10 10 0 CTACCGCACT 0.986391 -73 GCGGTAAGTTTTTACCGCATTTTTGATTTAT 10 23 1 TTACCGCATT 0.968586 -60 AATATTACCATTCATCTCACTTTGCTTT 12 8 0 TTATCTCACT 0.855251 -84 ATTCAATATTTTAACCGCACTTTTATTATAT 12 70 1 TTACCGCACT 0.993824 -22 ** ******** Masking position 9 Map Score: 2.17057 Number of sites scoring better than the average of aligned sites = 98 Number in coding regions = 90 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 8 ACCGCCATTTTCCCTTATTCTGTAGCGAAA 3 68 1 TCCCTTATTC 0.961788 -233 CTCGGTTATTCGGTACAATAT 9 2 1 TCGGTTATTC 0.985944 -76 AAAAAAATAATCGGCTATTCTAGCAAAGGA 11 24 1 TCGGCTATTC 0.983095 -114 ATAAAATTTGTCAGCTATTCTATATCTAAA 11 102 0 TCAGCTATTC 0.936048 -36 CTTCCTTTTGTCGCTTATTTAAAACATTCA 12 45 1 TCGCTTATTT 0.850116 -47 AATAACGCGCTACGTTATTCAGGGATACGC 13 241 1 TACGTTATTC 0.881654 -60 ********** Masking position 6 Map Score: 2.05644 Number of sites scoring better than the average of aligned sites = 65 Number in coding regions = 55 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 9 GCATATCCCTCTTATTGCCGGTC 1 3 1 ATATCCTCTT 0.986921 -276 CTCGTAGCGTATATACTTCTTAAACAATTGG 1 60 0 ATATACTCTT 0.971006 -219 TCGCCTGGCGATAACCGTCTTGTCGGCGGTT 1 179 1 ATAACCTCTT 0.94901 -100 TTTTACTTTGATATACATCATCAGGGAGGCA 3 38 0 ATATACTCAT 0.892031 -263 TTTACATGCCATATCCATCTTTCTATATTCA 5 87 0 ATATCCTCTT 0.986921 -117 ATGAATGGTAATATTCATCTGCTTCCTTTTG 12 24 1 ATATTCTCTG 0.874125 -68 ****** **** Masking position 8 Map Score: 3.59933 Number of sites scoring better than the average of aligned sites = 24 Number in coding regions = 18 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 10 CAAGTACCTCGTAGCGTATATACTTCTTAA 1 68 0 GTAGCGTATA 0.942201 -211 TTCAGAAGAGGTAGCGTGACCGACTTCCCG 2 27 0 GTAGCGTGAC 0.762599 -88 CACTCCCTTCGCAGTGTATCATTCTGTTTA 2 67 1 GCAGTGTATC 0.840346 -48 TATGCCGATACTAGCGTGTAAATGAGATTT 3 152 0 CTAGCGTGTA 0.865463 -149 CACGGCCAAAGCACCGTATCAGTTGACCCA 3 209 0 GCACCGTATC 0.97745 -92 ATGACTTCGCCTCCCGTATCTGGAAAGGTG 3 278 1 CTCCCGTATC 0.863957 -23 GGTGGATATTGTACCGAATAACCGAG 9 7 0 GTACCGAATA 0.674758 -71 TATTGGCTTGCCACCGTATTTCTATGAAAC 13 215 0 CCACCGTATT 0.844082 -86 TAAACCGTTTCCAGCGTATCCCTGAATAAC 13 254 0 CCAGCGTATC 0.97745 -47 ********** Masking position 6 Map Score: 2.06026 Number of sites scoring better than the average of aligned sites = 1091 Number in coding regions = 1032 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 11 AGTCGGTCACGCTACCTCTTCTGAAGCCTG 2 32 1 GCTACCTCTT 0.969674 -83 TGCCTCTGATGCTTGTTCTTATTTATATTA 7 74 0 GCTTGTTCTT 0.953128 -25 ACAGGAAGTTGCTTGCTCTTCATCAACAAG 9 50 1 GCTTGCTCTT 0.987774 -28 ATATTCATCTGCTTCCTTTTGTCGCTTATT 12 34 1 GCTTCCTTTT 0.953128 -58 ********** Masking position 7 Map Score: 0.145995 Number of sites scoring better than the average of aligned sites = 24 Number in coding regions = 19 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 12 GACTGTTTAAACGGAAAAATCTTG 2 101 1 ACGGAAAAAT 0.908371 -14 GCTACAGAATAAGGGAAAATGGCGGTTTTA 3 64 0 AAGGGAAAAT 0.841248 -237 GAAAGTGTGGATGGTAAAAATCTCATTTAC 3 135 1 ATGGTAAAAA 0.883751 -166 CACTCCTGCGGAGGCAAAATCGAATTTGCC 5 179 0 GAGGCAAAAT 0.813813 -25 AATCAAAAATGCGGTAAAAACTTACCGCAC 10 21 0 GCGGTAAAAA 0.90792 -62 TTATAAAAATAAGGAAAAAT 10 73 1 AAGGAAAAAT 0.863101 -10 GGATAATAGGATGGTAAAATGAGAAAAATT 11 51 1 ATGGTAAAAT 0.935446 -87 AGTGAGATGAATGGTAATATTCATCTGCTT 12 18 1 ATGGTAATAT 0.695546 -74 TAATAAAAGTGCGGTTAAAATATTGAATGT 12 68 0 GCGGTTAAAA 0.608513 -24 ********** Masking position 7 Map Score: 1.32668 Number of sites scoring better than the average of aligned sites = 588 Number in coding regions = 506 Number in noncoding regions = 82 Number of orfs with sites within 600 bp upstream = 107 Fraction of orfs with sites within 600 bp upstream = 0.017186 Motif number 13 TACTTGATAACTTCTGCGTAGCATACATGAG 1 92 1 CTTCTGCGAG 0.855622 -187 AGACGGTTATCGCCAGGCGAGACTGTTTCGG 1 168 0 CGCCAGGCAG 0.843865 -111 CACGACGCAACGTCAGCGCAACCGCCGACAA 1 198 0 CGTCAGCGAA 0.852063 -81 GTCGTGATATCATCAGGGCAGACCGGTTACA 1 223 1 CATCAGGGAG 0.978825 -56 TGATATACATCATCAGGGAGGCATAGCGTGC 3 30 0 CATCAGGGGG 0.968843 -271 CTAGCCTCTGCACCTGGGTCAACTGATACGG 3 195 1 CACCTGGGCA 0.954694 -106 TAAAGATTGCCACCAGGGCGAAGGAAGAAAT 3 249 1 CACCAGGGGA 0.954914 -52 GACTGTATGCCACCTCGGGCGTAGCGCTGGG 5 125 0 CACCTCGGCG 0.851754 -79 GAAAACACTCCTGCGGAGGCAAAATCGA 5 186 0 CTCCTGCGAG 0.885545 -18 TAAGAACAAGCATCAGAGGCAATCCA 7 83 1 CATCAGAGCA 0.714958 -16 ******** ** Masking position 4 Map Score: 1.73099 Number of sites scoring better than the average of aligned sites = 2754 Number in coding regions = 2559 Number in noncoding regions = 195 Number of orfs with sites within 600 bp upstream = 167 Fraction of orfs with sites within 600 bp upstream = 0.026823 Motif number 14 ********** No masking Map Score: 5.89994e-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 15 ********** No masking Map Score: 5.89994e-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