AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i180_molybdopterin_biosyntesis_hinf_reg_100.orf -a/home/amcguire/alignace/lib/ORF_hinf.txt -z/skink1/amcguire/genomes/hinf.fna -g0.38 -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 = 0.38 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 HI0329 37 conserved hypothetical protein #2 HI0330 98 opacity associated protein (oapA) #3 HI0331 59 opacity associated protein (oapB) #4 HI0334 77 GTP pyrophosphokinase (relA) #5 HI0336 82 molybdopeterin biosynthesis protein (mog) #6 HI1448 137 molybdopterin biosynthesis protein (moeA) #7 HI1675 91 molybdenum cofactor biosynthesis protein C (moaC) #8 HI1676 300 molybdenum cofactor biosynthesis protein A (moaA) Motif number 1 TCAAACCATCTCTCATTTTTAGGATATTTC 1 15 0 TCTCATTTTT 0.973294 -23 AATTTTTTCGCCGCACTTTTGAGCTTCTCA 2 30 1 CCGCACTTTT 0.990442 -69 CTTTTGAGCTTCTCAATTTTGTGGCTAATT 2 45 1 TCTCAATTTT 0.851748 -54 TGATGCTTGTTCTTATTTATATTAATTAGC 2 68 0 TCTTATTTAT 0.788339 -31 CAACTTCCTGTCGCTTTTATTTTGGGTGGA 4 31 0 TCGCTTTTAT 0.71938 -47 TAAAAACTTACCGCACTTTTGGAGGG 5 7 0 CCGCACTTTT 0.990442 -76 TAAGTTTTTACCGCATTTTTGATTTATCCA 5 27 1 CCGCATTTTT 0.992124 -56 ATTTTTCCTTATTTTTATAAATGATT 5 67 0 CCTTATTTTT 0.951163 -16 TTGCAATTTTTCTCATTTTACCATCCTATT 6 55 0 TCTCATTTTA 0.822404 -83 TTACCATTCATCTCACTTTGCTTT 7 5 0 TCTCACTTTG 0.912211 -87 AATATTTTAACCGCACTTTTATTATATT 7 74 1 CCGCACTTTT 0.990442 -18 TGGCTTGCCACCGTATTTCTATGAAACTTA 8 212 0 CCGTATTTCT 0.883057 -89 TTTATCCTCTCCGTATTTAGAAAGGTGTAA 8 280 1 CCGTATTTAG 0.8169 -21 ********** Masking position 7 Map Score: 19.511 Number of sites scoring better than the average of aligned sites = 2006 Number in coding regions = 1405 Number in noncoding regions = 601 Number of orfs with sites within 600 bp upstream = 383 Fraction of orfs with sites within 600 bp upstream = 0.0615162 Motif number 2 CCTTATTTTTATAAATGATTTTGACGTGATTG 5 55 0 ATAATGATTT 0.963631 -28 AATTTTATCAAATAAGGATTTTCT 6 124 1 AATAGGATTT 0.936943 -14 GTGCGGTTAAAATATTGAATGTTTTAAATAAG 7 58 0 AATATGAATT 0.95266 -34 AGACTAGCTCATTAGTGATAATTAATCCTATT 8 29 0 ATTATGATAT 0.89058 -272 TAAAAAAATACATAATGAATATAAGACTAGCT 8 52 0 CATATGAATT 0.82473 -249 ATTTTTTTATATAATTGATTTTTAAGAATTTA 8 75 1 ATAATGATTT 0.940831 -226 AATTTAGGAAAATACTGATTTTCATCAATATT 8 101 1 AATATGATTT 0.984418 -200 TTTCATCAATATTATTGATTGTGTTTATGGAG 8 120 1 ATTATGATTT 0.980803 -181 GTTATGCGTTAAATTTGATTTTTCGTCATTCT 8 163 0 AAATTGATTT 0.833786 -138 **** ***** * Masking position 8 Map Score: 8.25123 Number of sites scoring better than the average of aligned sites = 183 Number in coding regions = 154 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 3 GATCCGATAAAATACACATAATT 2 2 1 ATGATAAAAT 0.973243 -97 CTCGGTTATTCGGTACAATATCCACCCAA 4 8 1 ATGGTACAAT 0.921828 -70 TAAATCAAAAATGCGGTAAAAACTTACCGCAC 5 21 0 ATGGTAAAAA 0.812198 -62 TTTTGACGTGATTGGATAAATCAAAAATGCGG 5 37 0 ATGATAAATC 0.832736 -46 ATTTATAAAAATAAGGAAAAAT 5 71 1 ATGGAAAAAT 0.961126 -12 GGATGGTAAAATGAGAAAAATTGCAAATTTGA 6 59 1 ATGAAAAATT 0.950506 -79 GAAAATCCTTATTTGATAAAATTTGTCAGCTA 6 115 0 ATGATAAAAT 0.953991 -23 TTTGTCGCTTATTTAAAACATTCAATATTTTA 7 51 1 ATAAAACATT 0.506064 -41 ATTAATATAAATAGGATTAATTATCACTAATG 8 20 1 ATGATTAATT 0.753801 -281 AAAATCAATTATATAAAAAAATACATAATGAA 8 65 0 ATAAAAAAAT 0.802561 -236 ATCTTTTAGAATGACGAAAAATCAAATTTAAC 8 156 1 ATCGAAAAAT 0.761991 -145 GCTCGGAGTTATGCGTTAAATTTGATTTTTCG 8 170 0 ATGTTAAATT 0.825717 -131 ** ******** Masking position 10 Map Score: 7.12663 Number of sites scoring better than the average of aligned sites = 533 Number in coding regions = 424 Number in noncoding regions = 109 Number of orfs with sites within 600 bp upstream = 108 Fraction of orfs with sites within 600 bp upstream = 0.0173466 Motif number 4 ATTTGAAATATCCTAAAAATGAGAG 1 6 1 AAATATCCTA 0.821297 -32 ATATTGTACCGAATAACCGAG 4 2 0 GAATAACCGA 0.990263 -76 TCCTTTGCTAGAATAGCCGATTATTTTTTT 6 24 0 GAATAGCCGA 0.990974 -114 TTTAGATATAGAATAGCTGACAAATTTTAT 6 102 1 GAATAGCTGA 0.954625 -36 TGAATGTTTTAAATAAGCGACAAAAGGAAG 7 45 0 AAATAAGCGA 0.887385 -47 GCGTATCCCTGAATAACGTAGCGCGTTATT 8 241 0 GAATAACGTA 0.907067 -60 ********** Masking position 5 Map Score: 3.04691 Number of sites scoring better than the average of aligned sites = 124 Number in coding regions = 109 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 5 AAATCCTACCTTGAGAAAAGAACTTAAAAA 3 40 0 TTGAGAAAAG 0.957585 -20 TACCCCCTTGTTGATGAAGAGCAAGCAACT 4 56 0 TTGATGAAGA 0.905235 -22 GTCAAAATCATTTATAAAAATAAGGAAAAA 5 62 1 TTTATAAAAA 0.851469 -21 CGATTATTTTTTTAGGAAAGACTATT 6 7 0 TTTAGGAAAG 0.938887 -131 GGATGGTAAAATGAGAAAAATTGCAAATTT 6 59 1 ATGAGAAAAA 0.883835 -79 AAATCCTTATTTGATAAAATTTGTCAGCTA 6 115 0 TTGATAAAAT 0.743045 -23 TTTTTAAGAATTTAGGAAAATACTGATTTT 8 93 1 TTTAGGAAAA 0.948916 -208 ATCAATAATATTGATGAAAATCAGTATTTT 8 109 0 TTGATGAAAA 0.956857 -192 ATCTTTTAGAATGACGAAAAATCAAATTTA 8 156 1 ATGACGAAAA 0.735574 -145 CCTCTCCGTATTTAGAAAGGTGTAAA 8 285 1 TTTAGAAAGG 0.805552 -16 ********** Masking position 4 Map Score: 8.32003 Number of sites scoring better than the average of aligned sites = 645 Number in coding regions = 518 Number in noncoding regions = 127 Number of orfs with sites within 600 bp upstream = 114 Fraction of orfs with sites within 600 bp upstream = 0.0183103 Motif number 6 ACATAATTTTTTCGCCGCACTTTTGAGCTT 2 26 1 TTCGCCGCAC 0.985197 -73 GCGGTAAAAACTTACCGCACTTTTGGAGGG 5 11 0 CTTACCGCAC 0.984039 -72 GCGGTAAGTTTTTACCGCATTTTTGATTTA 5 23 1 TTTACCGCAT 0.982751 -60 AATATTACCATTCATCTCACTTTGCTTT 7 9 0 TTCATCTCAC 0.84365 -83 ATTCAATATTTTAACCGCACTTTTATTATA 7 70 1 TTAACCGCAC 0.985236 -22 AAAAATCAAATTTAACGCATAACTCCGAGC 8 172 1 TTTAACGCAT 0.916092 -129 ********** Masking position 2 Map Score: 4.53534 Number of sites scoring better than the average of aligned sites = 1042 Number in coding regions = 684 Number in noncoding regions = 358 Number of orfs with sites within 600 bp upstream = 247 Fraction of orfs with sites within 600 bp upstream = 0.0396723 Motif number 7 ********** No masking Map Score: 8.97716e-13 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 8 ********** No masking Map Score: 8.97716e-13 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 9 ********** No masking Map Score: 8.97716e-13 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