AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i223_Pseudouridylate_Synthase_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 HI1194 300 glycine cleavage system transcriptional activator (gcvA) #2 HI1196 35 succinyl-CoA synthetase, beta subunit (sucC) #3 HI1198 120 conserved hypothetical protein #4 HI1199 47 conserved hypothetical protein Motif number 1 TGAGTGGCGTTTTTTTCATCCCGATTTTA 1 10 0 TTTTTTCATC 0.776128 -291 TATGATGTTGTGTTTGCATATAGTTCGGGA 1 119 0 TGTTTGCATA 0.929548 -182 TCATTAAGTATGGTTGTATTGTAAGGAAAA 1 188 1 TGGTTGTATT 0.807918 -113 ACAAGTGACGTTTTTTTATTTGAGGTATTA 1 230 1 TTTTTTTATT 0.851515 -71 ATTTCAAATTAGTTTTTCTAATACCTCAAA 1 248 0 AGTTTTTCTA 0.813714 -53 GTGAACTGTTTTCATAACCAAAAAGG 2 7 1 TGTTTTCATA 0.971733 -29 CCGCACTTTAGTTTTCTAAAGCGTAGAT 3 9 1 TAGTTTTCTA 0.831212 -112 AAGCGTAGATTGGCTTTCTACGCCTTTATT 3 29 1 TGGCTTTCTA 0.892052 -92 TCTACGCCTTTATTTTTATATGCTCGCCAT 3 45 1 TATTTTTATA 0.854205 -76 GTGTTTCTTCCTTAAAAAATGTG 3 108 0 TTTCTTCCTT 0.798538 -13 TGTTTTCCTTGAATAATGGA 4 38 0 TGTTTTCCTT 0.969242 -10 ********** Masking position 5 Map Score: 6.6148 Number of sites scoring better than the average of aligned sites = 997 Number in coding regions = 748 Number in noncoding regions = 249 Number of orfs with sites within 600 bp upstream = 230 Fraction of orfs with sites within 600 bp upstream = 0.0369419 Motif number 2 TGGTAATTCCTTACTAGTTAATGAGTTTCAGAC 1 154 0 TTATTTAATG 0.919162 -147 TTACAATACAACCATACTTAATGATTGGTAATT 1 179 0 ACCTTTAATG 0.960889 -122 TTATAAAATTTTCGTCTATAATGGACAAGATTT 1 278 0 TTCTATAATG 0.984322 -23 AATTTTGTGCTCACTTTATAATGGCGAGCATAT 3 62 0 TCATATAATG 0.984322 -59 GTGTTTCTTCCTTAAAAAATGTGCGCTGATT 3 100 0 TCCTAAAATG 0.97865 -21 TGTTTTCCTTGAATAATGGAAAGGTCGC 4 30 0 TCCTATAATG 0.994647 -18 *** * ****** Masking position 5 Map Score: 5.24956 Number of sites scoring better than the average of aligned sites = 97 Number in coding regions = 80 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 3 GGGATGAAAAAAACGCCACTCAATGAGAGC 1 18 1 AAACGCCACT 0.996085 -283 CGATTTGGTTAAACGCTGCTCTCATTGAGT 1 35 0 AAACGCTGCT 0.990448 -266 TCAAATAAAAAAACGTCACTTGTCCTTTCC 1 223 0 AAACGTCACT 0.994235 -78 TGAATAATGGAAAGGTCGCTTTCACAAGCG 4 19 0 AAAGGTCGCT 0.989925 -29 ********** Masking position 3 Map Score: 4.76157 Number of sites scoring better than the average of aligned sites = 15 Number in coding regions = 10 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 4 AAACGCTGCTCTCATTGAGTGGCGTTTTTT 1 25 0 CTCATTGAGT 0.988949 -276 CAATTTGTTACTCATTTACTTCCTGTATAT 1 73 0 CTCATTTACT 0.983708 -228 AAGTCTGAAACTCATTAACTAGTAAGGAAT 1 152 1 CTCATTAACT 0.990695 -149 GGAATTACCAATCATTAAGTATGGTTGTAT 1 177 1 ATCATTAAGT 0.964026 -124 ********** Masking position 5 Map Score: 3.57652 Number of sites scoring better than the average of aligned sites = 18 Number in coding regions = 14 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 5 ACTCATTTACTTCCTGTATATTATTAAACC 1 64 0 TTCCTGTATA 0.924222 -237 AATAAATCTTGTCCATTATAGACGAAAATT 1 275 1 GTCCATTATA 0.970244 -26 TGGCTTTCTACGCCTTTATTTTTATATGCT 3 39 1 CGCCTTTATT 0.969278 -82 TTTATATGCTCGCCATTATAAAGTGAGCAC 3 59 1 CGCCATTATA 0.984797 -62 AAAGCGACCTTTCCATTATTCAAGGAAAAC 4 27 1 TTCCATTATT 0.96438 -21 ********** Masking position 7 Map Score: 2.03199 Number of sites scoring better than the average of aligned sites = 55 Number in coding regions = 42 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 6 GTTCGGGAAACCGAACTTGAGTAACAATTT 1 97 0 CCGAACTTGA 0.990393 -204 GTTCGGTTTCCCGAACTATATGCAAACACA 1 111 1 CCGAACTATA 0.985838 -190 CCGCACTTTAGTTTTCTAAA 3 1 1 CCGCACTTTA 0.996338 -120 GCAATTTTGTGCTCACTTTATAATGGCGAG 3 67 0 GCTCACTTTA 0.962331 -54 ********** Masking position 5 Map Score: 2.56719 Number of sites scoring better than the average of aligned sites = 390 Number in coding regions = 269 Number in noncoding regions = 121 Number of orfs with sites within 600 bp upstream = 91 Fraction of orfs with sites within 600 bp upstream = 0.0146161 Motif number 7 CTTGTCCTTTCCTACCCTTTTCCTTACAAT 1 205 0 CCTACCCTTT 0.986651 -96 AGAAAGCCAATCTACGCTTTAGAAAACTAA 3 18 0 TCTACGCTTT 0.993858 -103 AGATTGGCTTTCTACGCCTTTATTTTTATA 3 35 1 TCTACGCCTT 0.992701 -86 ********** Masking position 4 Map Score: 1.36985 Number of sites scoring better than the average of aligned sites = 23 Number in coding regions = 20 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 8 GAGTAACAATTTGTTACTCATTTACTTCCT 1 79 0 TTGTTACTCA 0.991361 -222 GAGTAACAAATTGTTACTCAAGTTCGGTTT 1 90 1 TTGTTACTCA 0.991361 -211 ATACTTAAGTCTGAAACTCATTAACTAGTA 1 146 1 CTGAAACTCA 0.968869 -155 ********** Masking position 6 Map Score: 0.976371 Number of sites scoring better than the average of aligned sites = 10 Number in coding regions = 8 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 9 ********** No masking Map Score: 8.19556e-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: 8.19556e-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: 8.19556e-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