AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i180_molybdopterin_biosyntesis_hinf_reg_300.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 TTTTCAAACCATCTCTCATTTTTAGGATATTT 1 16 0 CATCCATTTT 0.851566 -22 ACATAATTTTTTCGCCGCACTTTTGAGCTTCTC 2 26 1 TTCCCACTTT 0.987543 -73 CCTCTGATGCTTGTTCTTATTTATATTAATTAG 2 69 0 TTTCTATTTA 0.906448 -30 GCGGTAAAAACTTACCGCACTTTTGGAGGG 5 8 0 CTCCCACTTT 0.984898 -75 GCGGTAAGTTTTTACCGCATTTTTGATTTATCC 5 23 1 TTCCCATTTT 0.98973 -60 ATTTTTCCTTATTTTTATAAATGAT 5 68 0 TTCCTATTTT 0.977588 -15 AAATTTGCAATTTTTCTCATTTTACCATCCTAT 6 56 0 TTTCCATTTT 0.983662 -82 AATATTACCATTCATCTCACTTTGCTTT 7 6 0 TTTCCACTTT 0.98021 -86 ATTCAATATTTTAACCGCACTTTTATTATATT 7 70 1 TTCCCACTTT 0.987543 -22 TTAGTGATAATTAATCCTATTTATATTAATAAC 8 17 0 TTTCTATTTA 0.906425 -284 CACTAATGAGCTAGTCTTATATTCATTATGTAT 8 44 1 CTTCTATATT 0.721977 -257 ACGGTTTATCCTCTCCGTATTTAGAAAGGTGTA 8 276 1 CTCCTATTTA 0.927315 -25 ** ** ****** Masking position 9 Map Score: 19.3498 Number of sites scoring better than the average of aligned sites = 962 Number in coding regions = 626 Number in noncoding regions = 336 Number of orfs with sites within 600 bp upstream = 241 Fraction of orfs with sites within 600 bp upstream = 0.0387086 Motif number 2 CTTGTTCTTATTTATATTAATTAGCCACAAAAT 2 60 0 TTTTATAATA 0.97636 -39 TTTTGACGTGATTGGATAAATCAAAAATGCGGT 5 36 0 ATTGATAATA 0.794037 -47 TTTTTCCTTATTTTTATAAATGATTTTGACGTG 5 59 0 TTTTATAATA 0.97636 -24 GCCGATTATTTTTTTAGGAAAGACTATT 6 6 0 TTTTAGAAAA 0.835387 -132 AAATTGCAAATTTGAATGAATTAGGCTTTAGAT 6 76 1 TTTAATAATA 0.867205 -62 TAGCTGACAAATTTTATCAAATAAGGATTTTCT 6 115 1 ATTTATAAAA 0.905862 -23 ATTAATCCTATTTATATTAATAACCATAAA 8 8 0 TTTTATAATA 0.973921 -293 TTAAAAATCAATTATATAAAAAAATACATAATG 8 67 0 ATTTATAAAA 0.905862 -234 ATATAATTGATTTTTAAGAATTTAGGAAAATAC 8 83 1 TTTTAAAATT 0.698815 -218 AAAATACTGATTTTCATCAATATTATTGATTGT 8 109 1 TTTCATAATT 0.794014 -192 TGCCACCGTATTTCTATGAAACTTAGGCTAAAC 8 204 0 TTTTATAAAT 0.906767 -97 *** *** *** * Masking position 6 Map Score: 9.28578 Number of sites scoring better than the average of aligned sites = 381 Number in coding regions = 250 Number in noncoding regions = 131 Number of orfs with sites within 600 bp upstream = 112 Fraction of orfs with sites within 600 bp upstream = 0.0179891 Motif number 3 CGTGATTGGATAAATCAAAAATGCGGTAAAAA 5 31 0 TAATCAAAAT 0.672699 -52 CAATCACGTCAAAATCATTTATAAAAATAAGG 5 55 1 AAATCATTAT 0.959306 -28 AGAAAATCCTTATTTGATAAAATT 6 124 0 AAATCCTATT 0.939097 -14 CTTATTTAAAACATTCAATATTTTAACCGCAC 7 58 1 AATTCATATT 0.834691 -34 AATAGGATTAATTATCACTAATGAGCTAGTCT 8 29 1 ATATCATAAT 0.880715 -272 ATTATATAAAAAAATACATAATGAATATAAGA 8 58 0 AAATACTAAT 0.662589 -243 TAAATTCTTAAAAATCAATTATATAAAAAAAT 8 75 0 AAATCATTAT 0.947938 -226 AATATTGATGAAAATCAGTATTTTCCTAAATT 8 101 0 AAATCATATT 0.972842 -200 CTCCATAAACACAATCAATAATATTGATGAAA 8 120 0 AAATCATAAT 0.981201 -181 AGAATGACGAAAAATCAAATTTAACGCATAAC 8 163 1 AAATCAATTT 0.817328 -138 * ***** **** Masking position 5 Map Score: 8.36431 Number of sites scoring better than the average of aligned sites = 237 Number in coding regions = 192 Number in noncoding regions = 45 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 4 TCAAAAGTGCGGCGAAAAAATTATGTGTAT 2 22 0 GGCGAAAAAA 0.960994 -77 TATATTAATTAGCCACAAAATTGAGAAGCT 2 51 0 AGCCACAAAA 0.970024 -48 GCGATTACTCGCCCAAAAAA 3 1 0 GCCCAAAAAA 0.960994 -59 TGGATATTGTACCGAATAACCGAG 4 5 0 ACCGAATAAC 0.890827 -73 TACAATATCCACCCAAAATAAAAGCGACAG 4 24 1 ACCCAAAATA 0.883734 -54 GTTTTAAATAAGCGACAAAAGGAAGCAGAT 7 40 0 AGCGACAAAA 0.960994 -52 TACGGTGGCAAGCCAATAACGCGCTACGTT 8 227 1 AGCCAATAAC 0.933676 -74 ********** Masking position 5 Map Score: 3.39598 Number of sites scoring better than the average of aligned sites = 203 Number in coding regions = 174 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 5 TAATATAAATAAGAACAAGCATCAGAGGCAA 2 74 1 AAGAAAAGCA 0.984696 -25 AGAACTTAAAAAGAAAAAGGGGCGATTACTC 3 21 0 AAGAAAAGGG 0.941743 -39 TATCCACCCAAAATAAAAGCGACAGGAAGTT 4 29 1 AAATAAAGCG 0.880774 -49 CTTGTTGATGAAGAGCAAGCAACTTCCTGTC 4 49 0 AAGAGAAGCA 0.969184 -29 AATCATTTATAAAAATAAGGAAAAAT 5 67 1 AAAAAAAGGA 0.938357 -16 TCTTTCCTAAAAAAATAATCGGCTATTCTAG 6 16 1 AAAAAAATCG 0.931084 -122 AATAAGCGACAAAAGGAAGCAGATGAATATT 7 33 0 AAAAGAAGCA 0.960675 -59 TTCACTCCATAAACACAATCAATAATATTGA 8 125 0 AAACAAATCA 0.813101 -176 TTTTAGAATGACGAAAAATCAAATTTAACGC 8 159 1 ACGAAAATCA 0.831281 -142 ***** ***** Masking position 7 Map Score: 6.32678 Number of sites scoring better than the average of aligned sites = 481 Number in coding regions = 406 Number in noncoding regions = 75 Number of orfs with sites within 600 bp upstream = 70 Fraction of orfs with sites within 600 bp upstream = 0.0112432 Motif number 6 AGCCACAAAATTGAGAAGCTCAAAAGTGCGGC 2 39 0 TTGAAAGCTA 0.9556 -60 TATCCTTTGCTAGAATAGCCGATTATTTTTTT 6 24 0 TAGATAGCCA 0.989975 -114 GCTTTAGATATAGAATAGCTGACAAATTTTAT 6 100 1 TAGATAGCTA 0.990205 -38 TAATGAATATAAGACTAGCTCATTAGTGATAA 8 40 0 AAGATAGCTA 0.968538 -261 AACTCCGAGCTTGTTTAGCCTAAGTTTCATAG 8 192 1 TTGTTAGCCA 0.948828 -109 **** ***** * Masking position 7 Map Score: 0.740927 Number of sites scoring better than the average of aligned sites = 14 Number in coding regions = 7 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 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 CCATCTCTCATTTTTAGGATATTTCAAAT 1 5 0 TTTAGATTTC 0.971599 -33 TTTTCAAACCATCTCTCATTTTTAG 1 23 0 TTTAAATCTC 0.971599 -15 CCCTTTTTCTTTTTAAGTTCTTTTCTCAAGGTAGG 3 31 1 TTTAGTTTTC 0.904849 -29 TTTCCTTATTTTTATAAATGATTTTGACGTGATTG 5 55 0 TTTAAATTTT 0.677737 -28 TTCATTCAAATTTGCAATTTTTCTCATTTTACCAT 6 61 0 TTTAATTCTC 0.904849 -77 GCAGATGAATATTACCATTCATCTCACTTTGCTTT 7 11 0 ATTCAATCTC 0.871315 -81 TCTGCTTCCTTTTGTCGCTTATTTAAAACATTCAA 7 41 1 TTTCGATTTA 0.704831 -51 ATTTTTCGTCATTCTAAAAGATTTCACTCCATAAA 8 143 0 ATTAAATTTC 0.856389 -158 AAAAATCAAATTTAACGCATAACTCCGAGCTTGTT 8 172 1 TTTCGAACTC 0.845335 -129 GGATAAACCGTTTCCAGCGTATCCCTGAATAACGT 8 252 0 TTTAGATCCC 0.919207 -49 *** ** ***** Masking position 3 Map Score: 1.4197 Number of sites scoring better than the average of aligned sites = 354 Number in coding regions = 296 Number in noncoding regions = 58 Number of orfs with sites within 600 bp upstream = 55 Fraction of orfs with sites within 600 bp upstream = 0.00883392 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 Motif number 10 ********** 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 11 ********** 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