AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i056_Branched_Chain_Aminoacid_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 HI0682 300 ketol-acid reductoisomerase (ilvC) #2 HI0737 247 acetohydroxy acid synthase II, putative #3 HI0738 71 dihydroxyacid dehydratase (ilvD) #4 HI0986 300 2-isopropylmalate synthase (leuA) #5 HI0987 85 3-isopropylmalate dehydrogenase (beta-IPM dehydrogenase) (leuB) #6 HI0988 175 3-isopropylmalate dehydratase, alpha subunit (leuC) #7 HI0989 23 3-isopropylmalate dehydratase small subunit (leuD) #8 HI1585 266 acetolactate synthase III large subunit (ilvI) Motif number 1 TAAATCGCTGTTCTTTGCTTTGTTTCAATTTTCTT 1 41 0 TTCTTTTTTT 0.935161 -260 GGGGCGTGTTTTCTTTGCCTACTTTCTTTTACACG 1 79 1 TTCTTTATTT 0.722785 -222 AATGTTGCGATTTGTGCAATTATTTTTTTTTGTGA 1 159 0 TTTGTTTTTT 0.968063 -142 TTTGCATATTTTTTTGTTGTGGTTTGATTATAGGA 1 231 0 TTTTTTGTTT 0.946161 -70 TTTTTGTCCTTAATTGTGTAAGGTT 1 286 0 TTTTTTTATT 0.90314 -15 ATATTGAAACTCTTTTCATTTTTTTACATAGGATA 2 15 0 TCTTTTTTTT 0.971117 -233 TTTTTACCGCTCTTTTGGCTTATTTATTGACTGAT 2 64 0 TCTTTTTTTT 0.971117 -184 TTCACCGCACTTTTTTTCGTTTTTTTCTCTCCAAG 2 149 1 TTTTTTTTTT 0.989017 -99 GGTGTTTGTTTCCTGTTGTTTTTATTTTGGG 2 227 0 TGTTTTTTTT 0.946161 -21 TTAGGGTTCGTTTGTATGATTAATTTCTTCGTTAA 3 25 0 TTTGTTTATT 0.758368 -47 GTCAAACTATTTTTTGGCATTTTATATTAAAAATA 4 52 0 TTTTTTTTAT 0.933278 -249 TTTTTATTTATGTTTCGTATTGTTTCTTTATCTCT 4 132 1 TGTTTTTTTT 0.946161 -169 GTGCGGTGCGTTTTTCCTGTATTTTTTAGATAAAA 4 269 0 TTTTTTATTT 0.942128 -32 GTGCGGTTAGTTTTTTTGTATTTTTCCCCTCTTTG 5 33 0 TTTTTATTTT 0.933278 -53 ATTATTTTTCCTATTTTTTACTTCAAAAG 5 67 0 TTTTTTTTTT 0.989017 -19 TTTTCTTTTTCCTCTTTTGAGCC 7 6 0 TCTTTTCTTT 0.780958 -18 AAAATATTATTTTTTATTCAAATTTTTGAATGAGA 8 19 0 TTTTTAATTT 0.716603 -248 AAAAATAATATTTTTACTATTTTATAAAATGCGGC 8 40 1 TTTTTTTTAT 0.933278 -227 AATGCGGCATTTTGTCGCATTTTTTTATTTTTATT 8 67 1 TTTGTTTTTT 0.968063 -200 AAAATTTAGTTTTTTATAAATTTTTCCATCAATAA 8 97 0 TTTTTATTTT 0.933278 -170 TATATTTGGTTTTTTATATTTTTTTAATTGATTTT 8 136 1 TTTTTTTTTT 0.989017 -131 TTTTAATTGATTTTTTTGTTGTTTTAGTGGCTAGA 8 157 1 TTTTTTGTTT 0.946161 -110 TAGACAAATTTTTTTTACTTTGTATTATGTGAAAC 8 188 1 TTTTTTTTAT 0.933278 -79 ATTGACATAATCTGTTCGTTTTTTTAAAAGTGCGG 8 223 1 TCTGTTTTTT 0.918814 -44 ***** ** *** Masking position 5 Map Score: 45.3981 Number of sites scoring better than the average of aligned sites = 658 Number in coding regions = 443 Number in noncoding regions = 215 Number of orfs with sites within 600 bp upstream = 173 Fraction of orfs with sites within 600 bp upstream = 0.0277867 Motif number 2 AATTTTCTTAACGGCAATTTGCTGAACTCG 1 20 0 ACGGCAATTT 0.912775 -281 GTGAATTTTTACCGCTCTTTTGGCTTATTT 2 74 0 ACCGCTCTTT 0.985044 -174 GCCAATTTTCACCGCACTTTTTTTCGTTTT 2 142 1 ACCGCACTTT 0.998074 -106 CAATTTTAAACCCGCACTTTATAAGTTGCG 4 235 1 CCCGCACTTT 0.995533 -66 AGATAAAAAACCCGCAACTTATAAAGTGCG 4 247 0 CCCGCAACTT 0.878875 -54 GGAAAAACGCACCGCACTTTTGGA 4 287 1 ACCGCACTTT 0.998074 -14 AAAAAAACTAACCGCACTTTTGAAGTAAAA 5 51 1 ACCGCACTTT 0.998074 -35 GTGTTTTTCAACCGCACTTTAAATACTTTG 6 111 0 ACCGCACTTT 0.998074 -65 TCGAATTTTAACCGCACTTCCCTTAACGAA 6 142 1 ACCGCACTTC 0.98986 -34 GCGACAAAATGCCGCATTTTATAAAATAGT 8 55 0 GCCGCATTTT 0.922318 -212 CCTTAAATTCACCGCACTTTTAAAAAAACG 8 239 0 ACCGCACTTT 0.998074 -28 ********** Masking position 9 Map Score: 36.0173 Number of sites scoring better than the average of aligned sites = 1257 Number in coding regions = 806 Number in noncoding regions = 451 Number of orfs with sites within 600 bp upstream = 295 Fraction of orfs with sites within 600 bp upstream = 0.0473819 Motif number 3 ATAAGCCAAAAGAGCGGTAAAAATTCACTAA 2 76 1 AGAGCGGTAA 0.991633 -172 AACGAAAAAAAGTGCGGTGAAAATTGGCTTA 2 139 0 AGTGCGGTAA 0.995594 -109 ACAAAATGTGAGAGCAGTAGGTTGAGAGATA 4 160 0 AGAGCAGTGG 0.861461 -141 TCCAAAAGTGCGGTGCGTTTTTCCTGT 4 284 0 AGTGCGGTCG 0.982494 -17 TTTTTAGCAAAGAGGGGAAAAATACAAAAAA 5 26 1 AGAGGGGAAA 0.918366 -60 TTACTTCAAAAGTGCGGTTAGTTTTTTTGTA 5 48 0 AGTGCGGTAG 0.99529 -38 AGGTGCCTGAAGGGCGGAAGGGGGCAATCTC 6 38 1 AGGGCGGAGG 0.971374 -138 CCCAATAAACAGGGGGGACAAAGTATTTAAA 6 93 1 AGGGGGGAAA 0.923921 -83 AAGTATTTAAAGTGCGGTTGAAAAACACATC 6 113 1 AGTGCGGTGA 0.993822 -63 CGTTAAGGGAAGTGCGGTTAAAATTCGATGT 6 139 0 AGTGCGGTAA 0.995594 -37 TTTTTTTAAAAGTGCGGTGAATTTAAGGAGT 8 241 1 AGTGCGGTAA 0.995594 -26 ******** ** Masking position 1 Map Score: 23.7522 Number of sites scoring better than the average of aligned sites = 1492 Number in coding regions = 992 Number in noncoding regions = 500 Number of orfs with sites within 600 bp upstream = 328 Fraction of orfs with sites within 600 bp upstream = 0.0526823 Motif number 4 TATTTTTTTGTTGTGGTTTGATTATAGGATTTT 1 227 0 TTGTGGTTTT 0.813782 -74 ACGAAAAAAAGTGCGGTGAAAATTGGCTTATTT 2 136 0 GTGCGGTGAT 0.992944 -112 CACATTTTGTGTGCGGCTAAGTTGTGGATAAAA 4 181 1 GTGCGGCTTT 0.987155 -120 AACTTATAAAGTGCGGGTTTAAAATTGGGTATT 4 229 0 GTGCGGGTAA 0.964099 -72 ACTTTATAAGTTGCGGGTTTTTTATCTAAAAAA 4 250 1 TTGCGGGTTT 0.960707 -51 TCCAAAAGTGCGGTGCGTTTTTCCTGTATT 4 281 0 GTGCGGTGTT 0.995169 -20 TACTTCAAAAGTGCGGTTAGTTTTTTTGTATTT 5 45 0 GTGCGGTTTT 0.996556 -41 AGTATTTAAAGTGCGGTTGAAAAACACATCGAA 6 114 1 GTGCGGTTAA 0.982123 -62 GTTAAGGGAAGTGCGGTTAAAATTCGATGTGTT 6 136 0 GTGCGGTTAT 0.994966 -40 TTTTTTAAAAGTGCGGTGAATTTAAGGAGTGAA 8 242 1 GTGCGGTGTT 0.995169 -25 ******** ** Masking position 2 Map Score: 19.6371 Number of sites scoring better than the average of aligned sites = 983 Number in coding regions = 646 Number in noncoding regions = 337 Number of orfs with sites within 600 bp upstream = 243 Fraction of orfs with sites within 600 bp upstream = 0.0390299 Motif number 5 AACTGGGGCGTGTTTTCTTTGCCTACTTTC 1 75 1 TGTTTTCTTT 0.526738 -226 TTTGTGCAATTATTTTTTTTTGTGAATTGG 1 154 0 TATTTTTTTT 0.879862 -147 GTTGTGTTTGCATATTTTTTTGTTGTGGTT 1 242 0 CATATTTTTT 0.751132 -59 AAACTCTTTTCATTTTTTTACATAGGATAA 2 14 0 CATTTTTTTA 0.880274 -234 AAAAATTTAGTGAATTTTTACCGCTCTTTT 2 83 0 TGAATTTTTA 0.793845 -165 AAAAATTCACTAAATTTTTTAGGGGAAGAA 2 94 1 TAAATTTTTT 0.577361 -154 CACTTTTTTTCGTTTTTTTCTCTCCAAGCC 2 156 1 CGTTTTTTTC 0.90587 -92 GTTTGTTTCCTGTTGTTTTTATTTTGGGGA 2 225 0 TGTTGTTTTT 0.526738 -23 GGTGTTTGTTTCCTGTTGTTTT 2 236 0 TGTTTGTTTC 0.541872 -12 TGTAAGTAGGTTTATTTTTAATATAAAATG 4 40 1 TTTATTTTTA 0.433152 -261 GTTTGACAGCCAGTTTTTTATTCGTAATAT 4 80 1 CAGTTTTTTA 0.688542 -221 TGTTTCGTATTGTTTCTTTATCTCTCAACC 4 142 1 TGTTTCTTTA 0.63228 -159 TACATCTGACTGTTTTTTTATCCACAACTT 4 199 0 TGTTTTTTTA 0.953796 -102 GCGTTTTTCCTGTATTTTTTAGATAAAAAA 4 267 0 TGTATTTTTT 0.89445 -34 TTAGTTTTTTTGTATTTTTCCCCTCTTTGC 5 32 0 TGTATTTTTC 0.896214 -54 TAAAATTCGATGTGTTTTTCAACCGCACTT 6 122 0 TGTGTTTTTC 0.642965 -54 AATAAAAAATAATATTTTTACTATTTTATA 8 36 1 AATATTTTTA 0.333009 -231 CATTTTGTCGCATTTTTTTATTTTTATTGA 8 74 1 CATTTTTTTA 0.880274 -193 TAGTTTTTTATAAATTTTTCCATCAATAAA 8 96 0 TAAATTTTTC 0.581959 -171 AATGAAAATTTAGTTTTTTATAAATTTTTC 8 106 0 TAGTTTTTTA 0.765371 -161 CATTTATATTTGGTTTTTTATATTTTTTTA 8 132 1 TGGTTTTTTA 0.861246 -135 TGGTTTTTTATATTTTTTTAATTGATTTTT 8 142 1 TATTTTTTTA 0.915605 -125 TTTTTTTAATTGATTTTTTTGTTGTTTTAG 8 154 1 TGATTTTTTT 0.810421 -113 AGTGGCTAGACAAATTTTTTTTACTTTGTA 8 182 1 CAAATTTTTT 0.480751 -85 ATAATCTGTTCGTTTTTTTAAAAGTGCGGT 8 229 1 CGTTTTTTTA 0.933289 -38 ********** Masking position 8 Map Score: 20.8509 Number of sites scoring better than the average of aligned sites = 1114 Number in coding regions = 818 Number in noncoding regions = 296 Number of orfs with sites within 600 bp upstream = 225 Fraction of orfs with sites within 600 bp upstream = 0.0361388 Motif number 6 CGATTTAACTGGGGCGTGTTTTCTTTGCCTA 1 69 1 GGGGGTGTTT 0.774167 -232 AGCCAAAAGAGCGGTAAAAATTCACTAAATT 2 79 1 GCGGAAAAAT 0.817645 -169 GAAAAAAAGTGCGGTGAAAATTGGCTTATTT 2 136 0 GCGGGAAAAT 0.971885 -112 TTTTTATTTTGGGGATAAGTTCAGCATTGTA 2 209 0 GGGGTAAGTT 0.910329 -39 TAAATTTTACTCGGAGAGATTATTT 3 57 1 TCGGGAGATT 0.847088 -15 CATTTTGTGTGCGGCTAAGTTGTGGATAAAA 4 183 1 GCGGTAAGTT 0.952023 -118 TATAAAGTGCGGGTTTAAAATTGGGTATTTA 4 227 0 GGGTTAAAAT 0.563681 -74 TCCAAAAGTGCGGTGCGTTTTTCCTGTATT 4 281 0 GCGGGCGTTT 0.908518 -20 CTTCAAAAGTGCGGTTAGTTTTTTTGTATTT 5 45 0 GCGGTAGTTT 0.965189 -41 AAATAACTAAGGGTGGAGATTGCCCCCTTCC 6 53 0 GGGTGAGATT 0.84587 -123 TAAGGGAAGTGCGGTTAAAATTCGATGTGTT 6 136 0 GCGGTAAAAT 0.947848 -40 TTTTAAAAGTGCGGTGAATTTAAGGAGTGAA 8 244 1 GCGGGAATTT 0.978506 -23 **** ****** Masking position 11 Map Score: 7.72364 Number of sites scoring better than the average of aligned sites = 1002 Number in coding regions = 740 Number in noncoding regions = 262 Number of orfs with sites within 600 bp upstream = 186 Fraction of orfs with sites within 600 bp upstream = 0.0298747 Motif number 7 TTTACTCGTGTAAAAGAAAGTAGGCAAAGAA 1 89 0 TAAAAAAAGT 0.950839 -212 TTTACACGAGTAAAAGAAAGTAGGTCGTTCA 1 106 1 TAAAAAAAGT 0.950839 -195 TGCCAATTCACAAAAAAAAATAATTGCACAA 1 152 1 CAAAAAAAAT 0.849964 -149 GGTTTATTTTTAATATAAAATGCCAAAAAAT 4 48 1 TAATAAAAAT 0.883056 -253 ATACGAAACATAAATAAAAATCCTCTGTGTA 4 121 0 TAAATAAAAT 0.924813 -180 AAAATTTGAATAAAAAATAATATTTTTACTA 8 28 1 TAAAAATAAT 0.792629 -239 AATTTTTCCATCAATAAAAATAAAAAAATGC 8 83 0 TCAATAAAAT 0.719509 -184 AAACCAAATATAAATGAAAATTTAGTTTTTT 8 117 0 TAAATAAAAT 0.924813 -150 AAAAATCAATTAAAAAAATATAAAAAACCAA 8 141 0 TAAAAAATAT 0.792629 -126 ATGTTTCACATAATACAAAGTAAAAAAAATT 8 194 0 TAATAAAAGT 0.843172 -73 ***** ***** Masking position 7 Map Score: 7.03585 Number of sites scoring better than the average of aligned sites = 180 Number in coding regions = 119 Number in noncoding regions = 61 Number of orfs with sites within 600 bp upstream = 53 Fraction of orfs with sites within 600 bp upstream = 0.00851269 Motif number 8 TCAGCAAATTGCCGTTAAGAAAATTGAAAC 1 25 1 GCCGTTAAGA 0.849468 -276 AGCCAAAAGAGCGGTAAAAATTCACTAAAT 2 79 1 GCGGTAAAAA 0.920365 -169 GAAAAAAAGTGCGGTGAAAATTGGCTTATT 2 137 0 GCGGTGAAAA 0.978686 -111 CATTTTGTGTGCGGCTAAGTTGTGGATAAA 4 183 1 GCGGCTAAGT 0.880459 -118 TCCAAAAGTGCGGTGCGTTTTTCCTGTAT 4 282 0 GCGGTGCGTT 0.787962 -19 CTTCAAAAGTGCGGTTAGTTTTTTTGTATT 5 46 0 GCGGTTAGTT 0.93453 -40 TATTTAAAGTGCGGTTGAAAAACACATCGA 6 116 1 GCGGTTGAAA 0.925611 -60 TAAGGGAAGTGCGGTTAAAATTCGATGTGT 6 137 0 GCGGTTAAAA 0.9791 -39 TTTTAAAAGTGCGGTGAATTTAAGGAGTGA 8 244 1 GCGGTGAATT 0.966243 -23 ********** Masking position 2 Map Score: 6.20055 Number of sites scoring better than the average of aligned sites = 751 Number in coding regions = 483 Number in noncoding regions = 268 Number of orfs with sites within 600 bp upstream = 172 Fraction of orfs with sites within 600 bp upstream = 0.0276261 Motif number 9 GCCGTTAAGAAAATTGAAACAAAGCAAAGA 1 35 1 AAATTGAAAC 0.908316 -266 AAAAAATCCTATAATCAAACCACAACAAAA 1 225 1 ATAATCAAAC 0.888867 -76 CAACAAAAAAATATGCAAACACAACATCAT 1 247 1 ATATGCAAAC 0.909102 -54 CCTATGTAAAAAAATGAAAAGAGTTTCAAT 2 18 1 AAAATGAAAA 0.737742 -230 AGATTTCATTATATTGAAACTCTTTTCATT 2 30 0 ATATTGAAAC 0.956292 -218 AAGAACAGGAATATTCAAAATAAGCCAATT 2 119 1 ATATTCAAAA 0.917192 -129 TTGGCATTTTATATTAAAAATAAACCTACT 4 44 0 ATATTAAAAA 0.679743 -257 TTTATTCGTAATATGGAAAACGTTTTACAC 4 96 1 ATATGGAAAA 0.885964 -205 AGGTTGAGAGATAAAGAAACAATACGAAAC 4 143 0 ATAAAGAAAC 0.78387 -158 AAGAGGGGAAAAATACAAAAAAACTAACCG 5 35 1 AAATACAAAA 0.647402 -51 ********** Masking position 7 Map Score: 5.24185 Number of sites scoring better than the average of aligned sites = 272 Number in coding regions = 225 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 46 Fraction of orfs with sites within 600 bp upstream = 0.00738837 Motif number 10 AGAAAACACGCCCCAGTTAAATCGCTGTTC 1 63 0 CCCCAGTTAA 0.947363 -238 CTTTCTTTTACACGAGTAAAAGAAAGTAGG 1 100 1 CACGAGTAAA 0.969657 -201 AAATAATCTCTCCGAGTAAAATTTAGGGTT 3 52 0 TCCGAGTAAA 0.947382 -20 TTTTCCATATTACGAATAAAAAACTGGCTG 4 86 0 TACGAATAAA 0.808462 -215 CAGGCACCTTCCCCCGTAAACGGAGGAAGG 6 17 0 CCCCCGTAAA 0.963866 -159 TTAGAAATATCCCCAATAAACAGGGGGGAC 6 82 1 CCCCAATAAA 0.97673 -94 TAAATTTTTCCATCAATAAAAATAAAAAAA 8 86 0 CATCAATAAA 0.724981 -181 ********** Masking position 9 Map Score: 2.27066 Number of sites scoring better than the average of aligned sites = 154 Number in coding regions = 118 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 11 TACTTGCCTTCCTCCGTTTACGGGGG 6 7 1 CCTTCCTCCG 0.994921 -169 CCTTCAGGCACCTTCCCCCGTAAACGGAGG 6 21 0 CCTTCCCCCG 0.996567 -155 GAGATTGCCCCCTTCCGCCCTTCAGGCACC 6 39 0 CCTTCCGCCC 0.993701 -137 ********** Masking position 4 Map Score: 1.10025 Number of sites scoring better than the average of aligned sites = 11 Number in coding regions = 3 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 12 GTTTGATTATAGGATTTTTTGTTGTTGCGT 1 215 0 AGGATTTTTT 0.912758 -86 TTTTTTACATAGGATAATTT 2 1 0 AGGATAATTT 0.577241 -247 ACCGCTCTTTTGGCTTATTTATTGACTGAT 2 64 0 TGGCTTATTT 0.906695 -184 CGGTGAAAATTGGCTTATTTTGAATATTCC 2 126 0 TGGCTTATTT 0.906695 -122 GCACTTTTTTTCGTTTTTTTCTCTCCAAGC 2 155 1 TCGTTTTTTT 0.864861 -93 TTCGTTTGTATGATTAATTTCTTCGTTAAT 3 24 0 TGATTAATTT 0.20094 -48 AAGTGTAAGTAGGTTTATTTTTAATATAAA 4 37 1 AGGTTTATTT 0.888198 -264 TTTTACACAGAGGATTTTTATTTATGTTTC 4 118 1 AGGATTTTTA 0.681212 -183 GCGTTTTTCCTGTATTTTTTAGATAAAAAA 4 267 0 TGTATTTTTT 0.618549 -34 AAAGTGCGGTTAGTTTTTTTGTATTTTTCC 5 41 0 TAGTTTTTTT 0.701163 -45 CATTTATATTTGGTTTTTTATATTTTTTTA 8 132 1 TGGTTTTTTA 0.845801 -135 ATTTTTTTAATTGATTTTTTTGTTGTTTTA 8 153 1 TTGATTTTTT 0.663806 -114 CATAATCTGTTCGTTTTTTTAAAAGTGCGG 8 228 1 TCGTTTTTTT 0.864861 -39 ********** Masking position 5 Map Score: 4.77958 Number of sites scoring better than the average of aligned sites = 895 Number in coding regions = 710 Number in noncoding regions = 185 Number of orfs with sites within 600 bp upstream = 149 Fraction of orfs with sites within 600 bp upstream = 0.0239319 Motif number 13 ********** No masking Map Score: 2.74513e-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 14 ********** No masking Map Score: 2.74513e-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 15 ********** No masking Map Score: 2.74513e-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