AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i140_Cytochrome_Biogenesis_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 HI1089 248 heme exporter ATP-binding protein A (ccmA) #2 HI1091 57 heme exporter protein C (ccmC) #3 HI1092 41 heme exporter protein D (ccmD) Motif number 1 ATTTCGTTGAGGTTTTGGTCTATAACCAAAATTGA 1 39 1 GTTTTCTTAA 0.996633 -210 ATCTAAATCAATTTTTTTGCTATTATTTGCTCAAT 1 69 0 ATTTGCTTTA 0.915318 -180 CAAAAAAATTGATTTAGATCATTAAATGTTTTTCC 1 85 1 GTTTTCATAA 0.992294 -164 ATCATTAAATGTTTTTCCTTTTTTAAAAAGTGAAT 1 102 1 GTTTTTTTTA 0.943512 -147 ATTAAATTTTGTTTTAAATCAATAAACCTATCGAT 1 139 1 GTTTTCATAA 0.992248 -110 GTCACTTTCTATTTTCCCTCTGTAATT 1 232 1 ATTTTCTTAA 0.987767 -17 AAAGTGCGGTGGTTTTTCTCTTTAATTTTTAAGGA 2 27 1 GTTTTCTTAA 0.996633 -31 * *** *** *** Masking position 15 Map Score: 10.558 Number of sites scoring better than the average of aligned sites = 92 Number in coding regions = 64 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 2 AATGTATTCCTTCTATTGTTAAAAACA 1 3 1 TGATTTCTTT 0.983601 -246 GATTTCGTTGAGGTTTTGGTCTATAACCAAAATTG 1 38 1 AGTTTTCTTA 0.975467 -211 TTTTTTTGCTATTATTTGCTCAATTTTGGTTATAG 1 58 0 ATATTTCATT 0.726976 -191 GCAAAAAAATTGATTTAGATCATTAAATGTTTTTC 1 84 1 TGTTTTCATA 0.988738 -165 GATCATTAAATGTTTTTCCTTTTTTAAAAAGTGAA 1 101 1 TGTTTTTTTT 0.895932 -148 TTTTAAAAAGTGAATTTATTAAATTTTGTTTTAAA 1 122 1 TGATTTAATT 0.854619 -127 TATTAAATTTTGTTTTAAATCAATAAACCTATCGA 1 138 1 TGTTTTCATA 0.988738 -111 ATCAAATATTAGAATACTGTCACTTTCTATTTTCC 1 214 1 AGATATCATT 0.792568 -35 TGTCACTTTCTATTTTCCCTCTGTAATT 1 231 1 TATTTTCTTA 0.895867 -18 AAAAGTGCGGTGGTTTTTCTCTTTAATTTTTAAGG 2 26 1 TGTTTTCTTA 0.988739 -32 ** *** *** ** Masking position 10 Map Score: 9.88585 Number of sites scoring better than the average of aligned sites = 574 Number in coding regions = 461 Number in noncoding regions = 113 Number of orfs with sites within 600 bp upstream = 83 Fraction of orfs with sites within 600 bp upstream = 0.0133312 Motif number 3 AACCTCAACGAAATCTGTTTTTAACAATAGAAG 1 20 0 AAATTGTTTA 0.937859 -229 GTCTATAACCAAAATTGAGCAAATAATAGCAAA 1 56 1 AAAATGCAAA 0.851581 -193 ATAATAGCAAAAAAATTGATTTAGATCATTAAA 1 78 1 AAAATTTTTA 0.982892 -171 TCCTTTTTTAAAAAGTGAATTTATTAAATTTTG 1 117 1 AAAATGTTTA 0.976444 -132 TGAATTTATTAAATTTTGTTTTAAATCAATAAA 1 132 1 AAATTTTTTA 0.948236 -117 TTGAGTTGCGAAAATTTCATCAAATATTAGAAT 1 196 1 AAAATTTCAA 0.925921 -53 AAAAAATCCTTAAAAATTAAAGA 2 45 0 AAAAATTTAA 0.961063 -13 TATTCCTTATAAAAAATCGCTAAAAACTAACCG 3 15 0 AAAAATCTAA 0.953187 -27 AAAATATTCCTTATAAAAAATCG 3 29 0 AAAAATCTTA 0.961598 -13 **** ** **** Masking position 3 Map Score: 8.27837 Number of sites scoring better than the average of aligned sites = 502 Number in coding regions = 371 Number in noncoding regions = 131 Number of orfs with sites within 600 bp upstream = 132 Fraction of orfs with sites within 600 bp upstream = 0.0212014 Motif number 4 ACGAAATCTGTTTTTAACAATAGAAGGAATA 1 15 0 TTTTAACAAT 0.97034 -234 CTAAATCAATTTTTTTGCTATTATTTGCTCA 1 71 0 TTTTTGCTAT 0.78176 -178 GTTTTTCCTTTTTTAAAAAGTGAATTTATTA 1 112 1 TTTAAAAAGT 0.780904 -137 ATCGATCTACTTCTAAAGAGTTATGTGTTTG 1 168 1 TTTAAAGAGT 0.934043 -81 ACCACCGCACTTTTATACGATGAATAAAA 2 9 0 TTTATACGAT 0.935555 -49 TTCTCTTTAATTTTTAAGGATTTTTT 2 42 1 TTTTAAGGAT 0.967833 -16 GTGCGGTTAGTTTTTAGCGATTTTTTATAAG 3 12 1 TTTTAGCGAT 0.974917 -30 TAGCGATTTTTTATAAGGAATATTTT 3 26 1 TTTAAGGAAT 0.960803 -16 ** ******** Masking position 4 Map Score: 4.79094 Number of sites scoring better than the average of aligned sites = 292 Number in coding regions = 223 Number in noncoding regions = 69 Number of orfs with sites within 600 bp upstream = 76 Fraction of orfs with sites within 600 bp upstream = 0.0122069 Motif number 5 ********** No masking Map Score: -4.09683e-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: -4.09683e-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: -4.09683e-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