AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i064_Histidine_Biosynthesis_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 HI0468 300 ATP phosphoribosyltransferase (hisG) #2 HI0469 92 histidinol dehydrogenase (hisD) #3 HI0470 68 histidinol-phosphate aminotransferase (hisC) #4 HI0471 111 imidazoleglycerol-phosphate dehydratase / histidinol-phosphatase (hisB) #5 HI0472 65 amidotransferase (hisH) #6 HI0473 35 phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomerase (hisA) Motif number 1 AAAAATTGTGTTTTTAGTACATTTTTACTA 1 4 0 TTTTATTTTA 0.948673 -297 CAAAAAAATTGCTTTTTTTAATTTTAAAGTGTATTTT 1 43 1 GTTTTTTTTA 0.966737 -258 TGTTATTAGATCTTATATTGCCTTAAAAATACACTTT 1 68 0 TTTATTCTTA 0.981273 -233 ACAATATGAATTTTATCTGCACTTACCATCATCACCA 1 120 1 TTTATTCTTC 0.90799 -181 ACTCGGAAGATATTTTATTATCTTCCAAACATACAAT 1 180 0 TTTTTTCTTA 0.984195 -121 TTTACACTGATTTTTATTACACTCGGAAGATATTTTA 1 200 0 TTTTATCTCA 0.823666 -101 TTCCGAGGGGTATTTATTGCTTTTACACTGATTTTTA 1 221 0 TTTTATTTTA 0.948664 -80 AGGGGTTTTCTTTTATCTCAACTTTAAAATAGGAAAA 1 269 1 TTTATTCTTA 0.981273 -32 TGTTTATTTTCCTTTGTATCCGTAAAAT 2 75 0 GTTATTTTTA 0.960718 -18 AGCGATTCGAGATTATTTAGTTTTATACTGTTTGTAT 4 34 1 GTTATTTTTA 0.960715 -78 TTTTTTATCCTTTTACAATCGGTCGAA 5 49 0 TTTTTTTTTA 0.978904 -17 * **** * *** * Masking position 8 Map Score: 13.4606 Number of sites scoring better than the average of aligned sites = 304 Number in coding regions = 195 Number in noncoding regions = 109 Number of orfs with sites within 600 bp upstream = 98 Fraction of orfs with sites within 600 bp upstream = 0.0157404 Motif number 2 CTTTTTTTAATTTTAAAGTGTATTTTTAAGGCAAT 1 54 1 TTTAGTGATT 0.979803 -247 TCTAATAACATTTGAGCGAGCATATACAATATGAA 1 95 1 TTTCGAGATT 0.944693 -206 CTGATTATCTTTCAGGCGTGATTGTATGTTTGGAA 1 160 1 TTCCGTGTTT 0.964834 -141 TATTTATTGCTTTTACACTGATTTTTATTACACTC 1 213 0 TTTACTGTTT 0.968545 -88 CGGAAGGCAATTTTCGAGGGGTTTTCTTTTATCTC 1 253 1 TTTAGGGTTT 0.94074 -48 GATTATTTAGTTTTATACTGTTTGTATAAAGCAAA 4 44 1 TTTACTGTTT 0.968554 -68 ATTTTTCTCCGTGTATGTTATATGAATG 4 94 0 TTTCGTGATT 0.989617 -18 AGCGGTTAATTTTTGTCGTATTTTTGCAAAATTCG 5 18 1 TTTCGTATTT 0.920077 -48 TGTGTTTGATCCTGTATGACTATATGATC 6 17 0 TTTCCTGATA 0.885626 -19 *** **** ** * Masking position 13 Map Score: 7.31197 Number of sites scoring better than the average of aligned sites = 293 Number in coding regions = 250 Number in noncoding regions = 43 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714 Motif number 3 CACACCTGATTATCTTTCAGGCGTGATTGT 1 155 1 TATCTTTCAG 0.929526 -146 GATATTTTATTATCTTCCAAACATACAATC 1 179 0 TATCTTCCAA 0.985195 -122 GATAATAAAATATCTTCCGAGTGTAATAAA 1 195 1 TATCTTCCGA 0.982196 -106 CCTCGAAAATTGCCTTCCGAGGGGTATTTA 1 242 0 TGCCTTCCGA 0.943577 -59 AATGCTGGGTTATCATCCATTTTACGGATA 2 57 1 TATCATCCAT 0.961376 -36 ATAAACCTCATACCATTCATATAACATACA 4 81 1 TACCATTCAT 0.874571 -31 ********** Masking position 6 Map Score: 2.60821 Number of sites scoring better than the average of aligned sites = 97 Number in coding regions = 88 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 4 GCGAGCATATACAATATGAATTTTATCTGC 1 110 1 ACAATATGAA 0.949374 -191 TCTCAACTTTAAAATAGGAAAAACATT 1 284 1 AAAATAGGAA 0.950031 -17 TTGTTGTATGAAAATTTGACTGCTTACGTG 3 37 0 AAAATTTGAC 0.950158 -32 TTTTCATACAACAATACGAAATATGT 3 53 1 ACAATACGAA 0.97688 -16 GAATTTTGCAAAAATACGACAAAAATTAAC 5 22 0 AAAATACGAC 0.987676 -44 GTATTTTTGCAAAATTCGACCGATTGTAAA 5 35 1 AAAATTCGAC 0.977248 -31 ********** Masking position 5 Map Score: 6.89425 Number of sites scoring better than the average of aligned sites = 75 Number in coding regions = 62 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 5 CTTAAAAATACACTTTAAAATTAAAAAAAG 1 54 0 CACTTTAAAA 0.967709 -247 TAATAAAAATCAGTGTAAAAGCAATAAATA 1 218 1 CAGTGTAAAA 0.973468 -83 CTTTTATCTCAACTTTAAAATAGGAAAAAC 1 278 1 AACTTTAAAA 0.930074 -23 TTTATACAAACAGTATAAAACTAAATAATC 4 44 0 CAGTATAAAA 0.977603 -68 CCGATTGTAAAAGGATAAAAAA 5 54 1 AAGGATAAAA 0.897202 -12 ********** Masking position 6 Map Score: 1.94332 Number of sites scoring better than the average of aligned sites = 61 Number in coding regions = 37 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 6 CTAAAAACACAATTTTTTTCAAAAAAATTG 1 24 1 AATTTTTTTC 0.957507 -277 TGCTCGCTCAAATGTTATTAGATCTTATAT 1 87 0 AATGTTATTA 0.872593 -214 AATGTTTTTCCTATTTTAAA 1 291 0 AATGTTTTTC 0.980684 -10 TTAGTTTTATACTGTTTGTATAAAGCAAAT 4 50 1 ACTGTTTGTA 0.916373 -62 AAGAGCGGTTAATTTTTGTCGTATTTTTGC 5 15 1 AATTTTTGTC 0.960513 -51 ********** Masking position 5 Map Score: 1.31963 Number of sites scoring better than the average of aligned sites = 148 Number in coding regions = 112 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 7 ATGTAGTGCGAGCTTTGACTCGCCATTT 2 9 1 CGAGCTTTGA 0.985421 -84 GCTTACGTGTCGTGCTTAGATCTATAATTA 3 16 0 CGTGCTTAGA 0.963965 -53 AATCTCGAATCGCTCTGTGACTTAAATAGG 4 18 0 CGCTCTGTGA 0.985898 -94 AAAAATTAACCGCTCTTTCAA 5 2 0 CGCTCTTTCA 0.978004 -64 ********** Masking position 6 Map Score: 0.263973 Number of sites scoring better than the average of aligned sites = 91 Number in coding regions = 71 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 8 ********** No masking Map Score: -1.76682e-12 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 9 ********** No masking Map Score: -1.76682e-12 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: -1.76682e-12 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