AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i096_Nitrogen_Transport_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) Motif number 1 TCAAACCATCTCTCATTTTTAGGATATTTC 1 15 0 TCTCATTTTT 0.991355 -23 AATTTTTTCGCCGCACTTTTGAGCTTCTCA 2 30 1 CCGCACTTTT 0.994875 -69 CTTTTGAGCTTCTCAATTTTGTGGCTAATT 2 45 1 TCTCAATTTT 0.965859 -54 TGATGCTTGTTCTTATTTATATTAATTAGC 2 68 0 TCTTATTTAT 0.905678 -31 CAACTTCCTGTCGCTTTTATTTTGGGTGGA 4 31 0 TCGCTTTTAT 0.922678 -47 TAAAAACTTACCGCACTTTTGGAGGG 5 7 0 CCGCACTTTT 0.994875 -76 TAAGTTTTTACCGCATTTTTGATTTATCCA 5 27 1 CCGCATTTTT 0.996546 -56 ATTTTTCCTTATTTTTATAAATGATT 5 67 0 CCTTATTTTT 0.976527 -16 ********** Masking position 7 Map Score: 16.7528 Number of sites scoring better than the average of aligned sites = 1024 Number in coding regions = 669 Number in noncoding regions = 355 Number of orfs with sites within 600 bp upstream = 266 Fraction of orfs with sites within 600 bp upstream = 0.0427241 Motif number 2 ATTTGAAATATCCTAAAAATGAGAGATG 1 8 1 ATTCCTAAAA 0.808681 -30 GATCCGATAAAATACACATAAT 2 2 1 ATCGATAAAA 0.932784 -97 CACAAAATTGAGAAGCTCAAAAGTGCGGCGA 2 37 0 AGAGCTCAAA 0.920366 -62 ATTTATATTAATTAGCCACAAAATTGAGAAG 2 53 0 ATAGCCACAA 0.941452 -46 AGGGGCGATTACTCGCCCAAAAAA 3 4 0 ACCGCCCAAA 0.949312 -56 CTCGGTTATTCGGTACAATATCCACCCA 4 8 1 ATCGGTACAA 0.968831 -70 TCGGTACAATATCCACCCAAAATAAAAGCGA 4 20 1 ATCACCCAAA 0.899512 -58 TAAATCAAAAATGCGGTAAAAACTTACCGCA 5 22 0 ATCGGTAAAA 0.986356 -61 GATTTATCCAATCACGTCAAAATCATTTATA 5 47 1 ATACGTCAAA 0.924034 -36 ATTTATAAAAATAAGGAAAAAT 5 71 1 ATAGGAAAAA 0.884426 -12 ** ******** Masking position 10 Map Score: 7.08025 Number of sites scoring better than the average of aligned sites = 947 Number in coding regions = 818 Number in noncoding regions = 129 Number of orfs with sites within 600 bp upstream = 127 Fraction of orfs with sites within 600 bp upstream = 0.0203983 Motif number 3 TGCCTCTGATGCTTGTTCTTATTTATATTA 2 74 0 GCTTGTTCTT 0.989705 -25 AGTAATCGCCCCTTTTTCTTTTTAAGTTCT 3 22 1 CCTTTTTCTT 0.9877 -38 ACTTCCTGTCGCTTTTATTTTGGGTGGATA 4 29 0 GCTTTTATTT 0.849243 -49 ACAGGAAGTTGCTTGCTCTTCATCAACAAG 4 50 1 GCTTGCTCTT 0.967299 -28 AATACCCCCTTGTTGATGAAGAGCAAG 4 61 0 CCTTGTTGAT 0.974167 -17 GTTTTTACCGCATTTTTGATTTATCCAATC 5 30 1 CATTTTTGAT 0.756735 -53 ATTTTTCCTTATTTTTATAAATGATT 5 67 0 CCTTATTTTT 0.933797 -16 ********** Masking position 4 Map Score: 5.44428 Number of sites scoring better than the average of aligned sites = 727 Number in coding regions = 619 Number in noncoding regions = 108 Number of orfs with sites within 600 bp upstream = 96 Fraction of orfs with sites within 600 bp upstream = 0.0154192 Motif number 4 TTGGGCGAGTAATCGCCCCTTTTTCTTTTT 3 15 1 AATCGCCCCT 0.983112 -45 AAATCCTACCTTGAGAAAAGA 3 49 0 AATCCTACCT 0.970891 -11 TTCGGTACAATATCCACCCAAAATAAAAGC 4 19 1 TATCCACCCA 0.984743 -59 AATACCCCCTTGTTGATGAA 4 68 0 AATACCCCCT 0.975173 -10 ATTTTTGATTTATCCAATCACGTCAAAATC 5 41 1 TATCCAATCA 0.845897 -42 ********** Masking position 3 Map Score: 1.42612 Number of sites scoring better than the average of aligned sites = 156 Number in coding regions = 125 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 5 ********** No masking Map Score: -5.58897e-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 6 ********** No masking Map Score: -5.58897e-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 7 ********** No masking Map Score: -5.58897e-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