AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i064_Histidine_Biosynthesis_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 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 3 0 TTTATTTTAC 0.958749 -298 CAAAAAAATTGCTTTTTTTAATTTTAAAGTGTATTTTT 1 43 1 GTTTTTTTAA 0.920236 -258 TGTTATTAGATCTTATATTGCCTTAAAAATACACTTTA 1 67 0 TTTTTCTTAA 0.985109 -234 ATAAAATTCATATTGTATATGCTCGCTCAAATGTTATT 1 98 0 TTTTTCTCTC 0.830422 -203 ACAATATGAATTTTATCTGCACTTACCATCATCACCAC 1 120 1 TTTTTCTTCA 0.926836 -181 ACTCGGAAGATATTTTATTATCTTCCAAACATACAATC 1 179 0 TTTTTCTTAA 0.985484 -122 TTTACACTGATTTTTATTACACTCGGAAGATATTTTAT 1 199 0 TTTATCTCAA 0.931981 -102 TTCCGAGGGGTATTTATTGCTTTTACACTGATTTTTAT 1 220 0 TTTATTTTAC 0.95964 -81 AGGGGTTTTCTTTTATCTCAACTTTAAAATAGGAAAAA 1 269 1 TTTTTCTTAA 0.984872 -32 TGTTTATTTTCCTTTGTATCCGTAAAAT 2 75 0 TTTATCTTTA 0.906715 -18 AGCGATTCGAGATTATTTAGTTTTATACTGTTTGTATA 4 34 1 GTTTTTTTAC 0.921602 -78 GGTATGAGGTTTATCATTTGCTTTATACAAACAGTATA 4 57 0 TATATTTTAC 0.716726 -55 TTTTTTATCCTTTTACAATCGGTCGAAT 5 48 0 TTTTTTTTAA 0.973337 -18 * ** * * *** ** Masking position 8 Map Score: 14.0716 Number of sites scoring better than the average of aligned sites = 463 Number in coding regions = 315 Number in noncoding regions = 148 Number of orfs with sites within 600 bp upstream = 123 Fraction of orfs with sites within 600 bp upstream = 0.0197559 Motif number 2 ATTGCCTTAAAAATACACTTTAAAATTAAAAAAAG 1 54 0 AAATCACAAA 0.980945 -247 TTCCAAACATACAATCACGCCTGAAAGATAATCAG 1 160 0 ACAACACGAA 0.95997 -141 GAGTGTAATAAAAATCAGTGTAAAAGCAATAAATA 1 213 1 AAAACAGAAA 0.972103 -88 TAAAAGCAATAAATACCCCTCGGAAGGCAATTTTC 1 233 1 AAATCCCGAA 0.940335 -68 GAGATAAAAGAAAACCCCTCGAAAATTGCCTTCCG 1 253 0 AAAACCCAAA 0.973442 -48 TTGATTATTTAAATGGCGAGTCAAAGCTCGCACTA 2 14 0 AAATGCGAAA 0.782843 -79 TTTGCTTTATACAAACAGTATAAAACTAAATAATC 4 44 0 ACAACAGAAA 0.974195 -68 CATTCATATAACATACACGGAGAAAAAT 4 94 1 ACATCACAAA 0.982386 -18 CGAATTTTGCAAAAATACGACAAAAATTAACCGCT 5 18 0 AAAATACAAA 0.834622 -48 GATCATATAGTCATACAGGATCAAACACA 6 17 1 TCATCAGAAA 0.841576 -19 **** *** *** Masking position 3 Map Score: 7.65246 Number of sites scoring better than the average of aligned sites = 424 Number in coding regions = 350 Number in noncoding regions = 74 Number of orfs with sites within 600 bp upstream = 65 Fraction of orfs with sites within 600 bp upstream = 0.0104401 Motif number 3 TGTATATGCTCGCTCAAATGTTATTAGATCTT 1 91 0 CCTCAAATTT 0.963973 -210 ATTTTTATTACACTCGGAAGATATTTTATTAT 1 196 0 CCTCGGAAAT 0.92176 -105 CAATAAATACCCCTCGGAAGGCAATTTTCGAG 1 239 1 CCTCGGAAGC 0.978669 -62 AAAAGAAAACCCCTCGAAAATTGCCTTCCGAG 1 251 0 CCTCGAAATT 0.985601 -50 AATAATCAATATCTCAAAATGCTGGGTTATCA 2 40 1 ACTCAAAAGC 0.878699 -53 GACACGTAAGCAGTCAAATTTTCATACAACAA 3 35 1 CGTCAAATTT 0.904457 -34 AAACTAAATAATCTCGAATCGCTCTGTGACTT 4 25 0 ACTCGAATGC 0.948802 -87 CTTTTACAATCGGTCGAATTTTGCAAAAATAC 5 35 0 CGTCGAATTT 0.960346 -31 * ******* ** Masking position 8 Map Score: 3.37455 Number of sites scoring better than the average of aligned sites = 161 Number in coding regions = 134 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 4 TAAAATTAAAAAAAGCAATTTTTTTGAAAAA 1 38 0 AAAGCAATTT 0.877736 -263 AAGTGCAGATAAAATTCATATTGTATATGCT 1 113 0 AAATTCATAT 0.952236 -188 AAATCAGTGTAAAAGCAATAAATACCCCTCG 1 224 1 AAAGCAATAA 0.7795 -77 CGCCATTTAAATAATCAATATCTCAAAATGC 2 31 1 AAATCAATAT 0.951463 -62 ATGCTGGGTTATCATCCATTTTACGGATACA 2 58 1 ACATCCATTT 0.919669 -35 GCTTAGATCTATAATTAATATC 3 2 0 AAATTAATAT 0.925779 -67 ACGACACGTAAGCAGTCAAATTTTCATACAA 3 33 1 ACAGTCAAAT 0.77606 -36 TAAACCTCATACCATTCATATAACATACACG 4 82 1 ACATTCATAT 0.951756 -30 * ********* Masking position 4 Map Score: 2.87601 Number of sites scoring better than the average of aligned sites = 285 Number in coding regions = 235 Number in noncoding regions = 50 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 5 CAATTTTTTTGAAAAAAATTGTGTTTTTAG 1 24 0 GAAAAAAATT 0.961289 -277 ATATAAGATCTAATAACATTTGAGCGAGCA 1 87 1 TAATAACATT 0.883008 -214 TTTAAAATAGGAAAAACATT 1 291 1 GAAAAACATT 0.982441 -10 ATTTGCTTTATACAAACAGTATAAAACTAA 4 50 0 TACAAACAGT 0.923523 -62 GCAAAAATACGACAAAAATTAACCGCTCTT 5 15 0 GACAAAAATT 0.964037 -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 6 ATGTAGTGCGAGCTTTGACTCGCCATTT 2 9 1 CGAGCTTTGA 0.986676 -84 GCTTACGTGTCGTGCTTAGATCTATAATTA 3 16 0 CGTGCTTAGA 0.967006 -53 AATCTCGAATCGCTCTGTGACTTAAATAGG 4 18 0 CGCTCTGTGA 0.987113 -94 AAAAATTAACCGCTCTTTCAA 5 2 0 CGCTCTTTCA 0.979884 -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 7 ********** 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 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