AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i035_Sugars_Metabolism_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 HI1024 49 hexulose-6-phosphate synthase, putative #2 HI1027 58 L-xylulose kinase (lyx) #3 HI1028 30 conserved hypothetical protein #4 HI1030 71 conserved hypothetical transmembrane protein #5 HI1031 175 conserved hypothetical protein Motif number 1 TCAATAGGCTGGATTTTACATAATAAAAATC 2 9 1 CTGTTTTAAT 0.989712 -50 TTTTTATGGGCTGGATTTTTATTATGTAAAATC 2 22 0 CTGTTTTTTT 0.948168 -37 ATATTCTCCTTAGTTTTTTATGGGCTGGATT 2 38 0 CTTTTTTTAT 0.989296 -21 CACAAATGTGATTCGTTTTATATTATGGCGTTT 4 30 0 ATTTTTTAAT 0.982977 -42 AATAATTTTACTGATTTTGTGATCTAGATCCTA 5 41 0 CTGTTTGTAT 0.938932 -135 AATCAGTAAAATTATTTTAACATATTGATTTAT 5 58 1 ATTTTTAAAT 0.900022 -118 AAATAAATAAATTATTTATAAATCAATATGTTA 5 75 0 ATTTTATAAT 0.89717 -101 TAAATAATTTATTTATTTTACATTTATTGACTG 5 90 1 ATTTTTTAAT 0.973028 -86 ATTGACTGAGCTTTCTTATTTTTGTAAATTATG 5 115 1 CTTTTATTTT 0.877176 -61 TTTTTCCTCTCTTAATTTTATATAGTAAAATTA 5 153 0 CTTTTTTAAT 0.992652 -23 *** ***** ** Masking position 7 Map Score: 15.1063 Number of sites scoring better than the average of aligned sites = 275 Number in coding regions = 185 Number in noncoding regions = 90 Number of orfs with sites within 600 bp upstream = 64 Fraction of orfs with sites within 600 bp upstream = 0.0102795 Motif number 2 CTTCCTCATATTATTTAAGGAAAAACG 1 33 1 TTATTAGAAA 0.785469 -17 TGGGCTGGATTTTTATTATGTAAAATCCAGCCT 2 16 0 TTTTTAGTAA 0.498277 -43 AAAAGTCTCCTTGTGTTAAGAAAGTCTGTT 3 8 0 TTGTTAGAAA 0.907345 -23 TTCACAATATGAAATATTATCACA 5 2 1 TCACAAGAAA 0.967703 -174 ATATGAAATATTATCACAAGAAAATAGGATCTA 5 17 1 TTATAAGAAA 0.979576 -159 GAAAGCTCAGTCAATAAATGTAAAATAAATAAA 5 97 0 TCAAAAGTAA 0.919559 -79 TTTTTGTAAATTATGAAACGTAATTTTACTATA 5 133 1 TTATAAGTAA 0.927493 -43 AAACGTAATTTTACTATATAAAATTAAGAGAGG 5 148 1 TTACAAAAAA 0.763575 -28 CTATATAAAATTAAGAGAGGAAAAA 5 161 1 TTAAAAGAAA 0.975621 -15 **** * * **** Masking position 8 Map Score: 9.96781 Number of sites scoring better than the average of aligned sites = 412 Number in coding regions = 299 Number in noncoding regions = 113 Number of orfs with sites within 600 bp upstream = 106 Fraction of orfs with sites within 600 bp upstream = 0.0170254 Motif number 3 ATGAGGAAGGCAGTATAATTCTGTCTTTAA 1 12 0 CAGTATAATT 0.973087 -38 CAGCAATATGTTTCCAGTAA 4 1 1 CAGCAATATG 0.954751 -71 AATATGTTTCCAGTAAAACGCCATAATATA 4 15 1 CAGTAAAACG 0.985473 -57 ATCACAAAATCAGTAAAATTATTTTAACAT 5 51 1 CAGTAAAATT 0.992785 -125 TAATTTTATATAGTAAAATTACGTTTCATA 5 144 0 TAGTAAAATT 0.964733 -32 ********** Masking position 5 Map Score: 4.9757 Number of sites scoring better than the average of aligned sites = 161 Number in coding regions = 132 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 4 TCAATAGGCTGGATTTTACATAAT 2 5 1 TAGGCTGGAT 0.992734 -54 TAGTTTTTTATGGGCTGGATTTTTATTATG 2 29 0 TGGGCTGGAT 0.997324 -30 ACTGATTTTGTGATCTAGATCCTATTTTCT 5 35 0 TGATCTAGAT 0.948357 -141 ********** Masking position 9 Map Score: 0.696509 Number of sites scoring better than the average of aligned sites = 40 Number in coding regions = 28 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 5 ACTGCCTTCCTCATATTATTTAAGGAAAAA 1 28 1 TCATATTATT 0.965219 -22 CAGTAAAACGCCATAATATAAAACGAATCA 4 25 1 CCATAATATA 0.910295 -47 TATTTTCTTGTGATAATATTTCATATTGTG 5 13 0 TGATAATATT 0.922317 -163 GACTGAGCTTTCTTATTTTTGTAAATTATG 5 118 1 TCTTATTTTT 0.937002 -58 AAATTACGTTTCATAATTTACAAAAATAAG 5 129 0 TCATAATTTA 0.965218 -47 TTTTTCCTCTCTTAATTTTATATAGTAAA 5 157 0 TCTTAATTTT 0.965221 -19 ********** Masking position 5 Map Score: 4.74351 Number of sites scoring better than the average of aligned sites = 210 Number in coding regions = 170 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 6 ********** No masking Map Score: 5.63761e-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: 5.63761e-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: 5.63761e-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