AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -imodE_ecoli_hinf_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 HI1047 253 anaerobic dimethyl sulfoxide reductase, chain A (dmsA) #7 HI1675 91 molybdenum cofactor biosynthesis protein C (moaC) #8 HI1676 300 molybdenum cofactor biosynthesis protein A (moaA) #9 HI1692 173 molybdenum ABC transporter, permease protein (modB) #10 HI1693 137 molybdenum ABC transporter, periplasmic-binding protein (modA) Motif number 1 GATATTTTTTCTTATCTACCTCACAAAGGTTAGCAA 2 71 1 CTTATTATAA 0.917376 -96 TTAATGTAACGTTATGTAGGCGACAATATAACGACT 2 131 0 GTTATTACAA 0.935025 -36 CGATCATGACGCTATATACATGATTACATAGCGAAA 3 103 1 GCTATTATAA 0.985176 -198 ATAGCAGTTCGCTATATAGGCTTGTATACATCGAAT 5 124 0 GCTATTACTA 0.837678 -177 ATAGCGAACTGCTATAGAAATAATTACACAATACGG 5 145 1 GCTATGATAA 0.95839 -156 TAACAAATTGACTATGGATTTAAAAATCCGTTAGCA 6 73 0 ACTATGATAA 0.799263 -181 GATAATTAATCCTATTTATATTAATAACCATAAA 8 9 0 CCTATTATAA 0.946726 -292 TCTTATATTCATTATGTATTTTTTTATATAATTGAT 8 58 1 ATTATTATTA 0.616603 -243 TTAAAGAGAGGCTATTTAGATAAGGATTCATTTTGC 9 113 1 GCTATTATAA 0.985176 -61 AAGCCTAAGCGTTATATATTTTACTAAATAATTTTT 10 40 1 GTTATTATAA 0.976483 -98 CTATATGATTGTTATTTATTTCAATATATAATCAAG 10 82 1 GTTATTATAA 0.976483 -56 ACGATTAAACGTTATTTACTTGATTATATATTGAAA 10 100 0 GTTATTATAA 0.976483 -38 ***** ** * * * Masking position 8 Map Score: 11.8008 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 GGCATTTTCTTTTTCTCAACTTCCTGCTTTT 2 34 1 TTTTTCAACT 0.763647 -133 TGCCGATATTTTTTCTTATCTACCTCACAAA 2 67 1 TTTTTTATCT 0.872974 -100 TCCCAGCAGTTATTGCTAACCTTTGTGAGGT 2 88 0 TATTCTAACC 0.626165 -79 AAAACCGCCATTTTCCCTTATTCTGTAGCGA 3 65 1 TTTTCCTTAT 0.541198 -236 TAAATGAGATTTTTACCATCCACACTTTCGC 3 133 0 TTTTCCATCC 0.871335 -168 CTGCGGGCGCTTTTTTTGTCTCCCTTTGATA 5 15 1 TTTTTTGTCT 0.482521 -286 TCGCTGTCGTTTTTACCAAACCACGGCGACT 5 266 0 TTTTCCAAAC 0.726818 -35 TAAGTTTAACTATTATTAACTAGAGGATCTT 6 14 0 TATTTTAACT 0.529872 -240 GTTTTAGTTATTTTTCAATCTGACTGTGGGG 6 223 1 TTTTCAATCT 0.86457 -31 TTAACCGCACTTTTATTATATT 7 80 1 TTTTTTATAT 0.792046 -12 TCATTATGTATTTTTTTATATAATTGATTTT 8 66 1 TTTTTTATAT 0.792047 -235 AAAATCAGTATTTTCCTAAATTCTTAAAAAT 8 92 0 TTTTCTAAAT 0.886538 -209 TAAGGATTCATTTTGCTTACCCAATTTTTTT 9 133 1 TTTTCTTACC 0.538945 -41 ATTTTTTTCATTTTTCAATCTGACGCCA 9 156 1 TTTTCAATCT 0.86457 -18 GCGTTATATATTTTACTAAATAATTTTTCTT 10 48 1 TTTTCTAAAT 0.88649 -90 ATAATTTTTCTTTTGCTATATGATTGTTATT 10 67 1 TTTTCTATAT 0.916807 -71 GATTGTTATTTATTTCAATATATAATCAAGT 10 88 1 TATTCAATAT 0.450059 -50 **** ****** Masking position 4 Map Score: 8.12433 Number of sites scoring better than the average of aligned sites = 705 Number in coding regions = 540 Number in noncoding regions = 165 Number of orfs with sites within 600 bp upstream = 192 Fraction of orfs with sites within 600 bp upstream = 0.0308384 Motif number 3 AGAAAAGCACTCCCCTTTTGTGCGGTCAGC 1 63 0 TCCCCTTTTG 0.986993 -66 CTGATCTCTCCTTTTGACGTT 4 6 0 TCTCCTTTTG 0.979698 -16 GCTTTTTTTGTCTCCCTTTGATACCGAACA 5 23 1 TCTCCCTTTG 0.986993 -278 TTACCATTCATCTCACTTTGCTTT 7 5 0 TCTCACTTTG 0.962462 -87 CGGATATTTCTGCCCTTTTGTTATTATAGA 9 37 1 TGCCCTTTTG 0.945646 -137 TATGGGAATATCCCACATTGATGAGAGGTA 9 73 0 TCCCACATTG 0.908644 -101 ********** Masking position 8 Map Score: 5.68613 Number of sites scoring better than the average of aligned sites = 86 Number in coding regions = 65 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 4 CAATATAACGACTAACTCGGAATTTTCCCAGCAGTT 2 108 0 ATAACCGAAT 0.953624 -59 TAAAAATCTCATTTACACGCTAGTATCGGCATAACC 3 149 1 ATTACCGTAT 0.985783 -152 ATTACTCCTCACTTACACGTAATACTACTTTCGAGT 5 56 1 ATTACCGAAT 0.959373 -245 CTATAGAAATAATTACACAATACGGTTTGTTACTGG 5 156 1 ATTACCATAT 0.871765 -145 TATTAGATAAACTAACACGCCACTATGCTAACGGAT 6 48 1 ATAACCGCAT 0.94541 -206 AAAGATTATAATTAACTCGTTTTAGTTATTTTTCAA 6 205 1 ATAACCGTTT 0.928346 -49 ACAAGCTCGGAGTTATGCGTTAAATTTGATTTTTCG 8 170 0 ATTATCGTAT 0.866434 -131 GTGGCAAGCCAATAACGCGCTACGTTATTCAGGGAT 8 231 1 ATAACCGTAT 0.982542 -70 ATTAAACGTTATTTACTTGATTATATATTGAAATAA 10 97 0 ATTACTGTTT 0.682309 -41 * **** ** ** * Masking position 5 Map Score: 4.14447 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 5 CGCTATATACATGATTACATAGCGAAAGTG 3 112 1 ATGATTACAT 0.751099 -189 CGTGTAAGTGAGGAGTAATTATTGTTCGGT 5 45 0 AGGAGTAATT 0.941063 -256 ATACCTATTAATGATTAATTGATTTGGCTC 6 158 1 ATGATTAATT 0.936531 -96 TAATATAAATAGGATTAATTATCACTAATG 8 22 1 AGGATTAATT 0.977613 -279 TATTTAGATAAGGATTCATTTTGCTTACCC 9 125 1 AGGATTCATT 0.941063 -49 CTTACCACTTAGGATTACTTAGGAACAGCA 10 13 0 AGGATTACTT 0.97312 -125 ********** Masking position 6 Map Score: 2.37666 Number of sites scoring better than the average of aligned sites = 27 Number in coding regions = 18 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 6 TTATTGTGACGGAAAACGAACGCCACGCAA 1 32 1 GGAAAACGAA 0.91401 -97 AATATCGGCAGGAAAAGCAGGAAGTTGAGA 2 47 0 GGAAAAGCAG 0.875005 -120 TACTTTCGAGTGAAAATCTACCTATCTCTT 5 81 1 TGAAAATCTA 0.713697 -220 TCGAATAATTTGAAAATCAAAGAGATAGGT 5 100 0 TGAAAATCAA 0.951501 -201 TGAGCCATTATGAAAACGAAAATCCCTGAT 5 215 1 TGAAAACGAA 0.848221 -86 CCTAAATTCTTAAAAATCAATTATATAAAA 8 79 0 TAAAAATCAA 0.846993 -222 ATAATATTGATGAAAATCAGTATTTTCCTA 8 105 0 TGAAAATCAG 0.882763 -196 TTAGAATGACGAAAAATCAAATTTAACGCA 8 161 1 GAAAAATCAA 0.913259 -140 AATTGGGTAAGCAAAATGAATCCTTATCTA 9 129 0 GCAAAATGAA 0.782562 -45 GCGTCAGATTGAAAAATGAAAAAAATTGGG 9 152 0 GAAAAATGAA 0.859858 -22 GGATTACTTAGGAACAGCAAA 10 2 0 GGAACAGCAA 0.774515 -136 ********** Masking position 6 Map Score: 5.17473 Number of sites scoring better than the average of aligned sites = 797 Number in coding regions = 690 Number in noncoding regions = 107 Number of orfs with sites within 600 bp upstream = 128 Fraction of orfs with sites within 600 bp upstream = 0.0205589 Motif number 7 GAGACTATTCTAACCGCTAAGCACAGAAAAGCA 1 84 0 TAACCCTACA 0.98159 -45 TGGTAACCCCTTAATGTAACGTTATG 2 151 0 TAACCCTATG 0.900304 -16 TCTACCTCTAAAGGACGATGCACG 3 2 1 CTACCCTAGG 0.93496 -299 AGTATCGGCATAACCACTAAACACTCTAGCCTC 3 170 1 TAACCCTACA 0.98159 -131 ATAGGATTAATTATCACTAATGAGCTAGTCTTA 8 30 1 TTATCCTAGA 0.90003 -271 ATAGAGCATCTTACCTCTCATCAATGTGGGATA 9 62 1 TTACCCTACA 0.985801 -112 ACGCTTAGGCTTACCACTTAGGATTACTTAGGA 10 19 0 TTACCCTAGA 0.985801 -119 ***** ** * ** Masking position 10 Map Score: 2.24838 Number of sites scoring better than the average of aligned sites = 76 Number in coding regions = 67 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 8 CAAAAGTCTTATTGTGACGGAAAACGAACGC 1 24 1 ATTTGACGGA 0.922883 -105 ACGCCACGCAAAGCTGACCGCACAAAAGGGG 1 51 1 AAGTGACCGC 0.88188 -78 TCATGAGACTATTCTAACCGCTAAGCACAGA 1 90 0 ATTTAACCGC 0.950491 -39 TGTAGGCGACAATATAACGACTAACTCGGAA 2 122 0 AATTAACGAC 0.796836 -45 CTTTACGAGCATTGTCACGGCCAAAGCACCG 3 223 0 ATTTCACGGC 0.931607 -78 ACACGCCACTATGCTAACGGATTTTTAAATC 6 62 1 ATGTAACGGA 0.856487 -192 AACATTCAATATTTTAACCGCACTTTTATTA 7 67 1 ATTTAACCGC 0.950491 -25 CGAAAAATCAAATTTAACGCATAACTCCGAG 8 170 1 AATTAACGCA 0.778081 -131 TTCATTTTTCAATCTGACGCCA 9 162 1 AATTGACGCC 0.912937 -12 *** ******* Masking position 5 Map Score: 1.92705 Number of sites scoring better than the average of aligned sites = 438 Number in coding regions = 377 Number in noncoding regions = 61 Number of orfs with sites within 600 bp upstream = 80 Fraction of orfs with sites within 600 bp upstream = 0.0128493 Motif number 9 TAGAATAGTCTCATGACTATATCTGGAGTT 1 105 1 TCATGACTAT 0.964768 -24 TTCCTGCTTTTCCTGCCGATATTTTTTCTT 2 54 1 TCCTGCCGAT 0.967743 -113 AATAGCACGATCATGACGCTATATACATGA 3 96 1 TCATGACGCT 0.965271 -205 TGTTTAGTGGTTATGCCGATACTAGCGTGT 3 163 0 TTATGCCGAT 0.927323 -138 TATCCGCCCTTCATGACTATTAAGATTCTA 9 13 0 TCATGACTAT 0.964768 -161 ********** Masking position 4 Map Score: 0.845746 Number of sites scoring better than the average of aligned sites = 212 Number in coding regions = 196 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 10 TTCCCTGAATGCCCGCTTAG 2 1 1 TTCCCTGAAT 0.883168 -166 CACGCTATGCCTCCCTGATGATGTATATCA 3 31 1 CTCCCTGATG 0.978527 -270 AACCGCCATTTTCCCTTATTCTGTAGCGAA 3 67 1 TTCCCTTATT 0.825282 -234 TTTCTTCCTTCGCCCTGGTGGCAATCTTTA 3 249 0 CGCCCTGGTG 0.961896 -52 GAAAACGAAAATCCCTGATGCGGTATTGGC 5 226 1 ATCCCTGATG 0.966654 -75 TGAGGTGAGTCGCCGTGGTTTGGTAAAAAC 5 259 1 CGCCGTGGTT 0.810353 -42 TTTCCAGCGTATCCCTGAATAACGTAGCGC 8 247 0 ATCCCTGAAT 0.915269 -54 CTCTCTTTAAATCCCTTGTTTATGGGAATA 9 93 0 ATCCCTTGTT 0.868999 -81 ********** Masking position 6 Map Score: 2.53225 Number of sites scoring better than the average of aligned sites = 544 Number in coding regions = 469 Number in noncoding regions = 75 Number of orfs with sites within 600 bp upstream = 90 Fraction of orfs with sites within 600 bp upstream = 0.0144555 Motif number 11 AATAAGGGAAAATGGCGGTTTTACTTTGAT 3 57 0 AATGGCGGTT 0.938621 -244 TACATAGCGAAAGTGTGGATGGTAAAAATC 3 127 1 AAGTGTGGAT 0.907254 -174 AATATAATAAAAGTGCGGTTAAAATATTGA 7 72 0 AAGTGCGGTT 0.971223 -20 AATAGTCATGAAGGGCGGATATTTCTGCCC 9 22 1 AAGGGCGGAT 0.99136 -152 ATAATAACAAAAGGGCAGAAATATCCGCCC 9 34 0 AAGGGCAGAA 0.870111 -140 ********** Masking position 2 Map Score: 0.384746 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 12 ********** No masking Map Score: 5.23913e-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: 5.23913e-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 ********** No masking Map Score: 5.23913e-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