AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00920_hinf_reg_300.orf -o00920_hinf_300.ace -a/home/amcguire/genomes/ORF_hinf.txt -z/home/amcguire/genomes/hinf.fna -g0.38 -x5 -e 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 = 1 Input sequences: #1 HI0086 300 cystathionine gamma-synthase (metB) #2 HI0122 274 cystathionine beta-lyase (metC) #3 HI0604 300 adenylate cyclase (cyaA) #4 HI0605 73 glycerol-3-phosphate dehydrogenase (NAD+) (gpsA) #5 HI1102 152 cysteine synthetase, putative (cysZ) #6 HI1103 98 cysteine synthetase (cysK) #7 HI1263 103 homoserine acetyltransferase (met2) Motif number 1 TAAACGGTTAGACAATTTTTTTAAATCTGT 1 151 0 GACAATTTTT 0.900772 -150 TTTGAACAAAATGAACTTTTTTTAAACGGT 1 173 0 ATGAACTTTT 0.777194 -128 TGATGGAAAAATGAAATTTTATGTAATTTT 1 217 1 ATGAAATTTT 0.905121 -84 ATGAAATTTTATGTAATTTTCTAATTTCTA 1 227 1 ATGTAATTTT 0.736284 -74 TTCTACTTTTATCACTTTTTCCTTTGTGCC 1 252 1 ATCACTTTTT 0.953182 -49 CTAAAGTGCGGTCAATTTTTCT 2 3 0 GTCAATTTTT 0.962884 -272 GCGACCTTAGGTGGCTTTTTTTATCATCAG 2 60 0 GTGGCTTTTT 0.90477 -215 GCCACCTAAGGTCGCTTTTTATAAATAATT 2 75 1 GTCGCTTTTT 0.914243 -200 CTTTAATTTTATCAATTATTTATAAAAAGC 2 88 0 ATCAATTATT 0.774737 -187 CTTACTCAATATCACTTATTAAGGAAT 3 8 0 ATCACTTATT 0.754417 -293 AACAATCAAAATGACTTTTTTACCTAAGAG 3 162 0 ATGACTTTTT 0.947765 -139 TGTGATTTATGTCACATTTTTTTGCATTTA 3 225 1 GTCACATTTT 0.9158 -76 TAAATTGTTCGCCAATTTTTGTTGTTCTGG 3 269 1 GCCAATTTTT 0.803607 -32 CCACACTTTGAAGTATTTTTTCACCTACTG 5 75 0 AAGTATTTTT 0.675503 -78 ACTTCAAAGTGTGGAATTTTAAAGGAAAAG 5 91 1 GTGGAATTTT 0.833202 -62 TAGATCAAATAACTATTTTTTTAATCAAAA 6 25 1 AACTATTTTT 0.700225 -74 TTAGCTTGTCAAGAAATTTTAGCCGTCTAA 7 33 0 AAGAAATTTT 0.769522 -71 ********** Masking position 7 Map Score: 13.4191 Number of sites scoring better than the average of aligned sites = 831 Number in coding regions = 651 Number in noncoding regions = 180 Number of orfs with sites within 600 bp upstream = 171 Fraction of orfs with sites within 600 bp upstream = 0.0274655 Motif number 2 AGAAAAATTGACCGCACTTTAGCTAAAGA 2 10 1 GACCGCACTT 0.994027 -265 CATTGCCTAATACCGCAGATGAAGTAAAAT 2 188 1 TACCGCAGAT 0.953884 -87 GGTACTATCCTACCACTCTTAGGTAAAAAA 3 147 1 TACCACTCTT 0.933407 -154 TCCTTTAAAATTCCACACTTTGAAGTATTT 5 87 0 TTCCACACTT 0.933407 -66 GCTTAAAACAGACCGCACTTTTCCTTTAAA 5 108 0 GACCGCACTT 0.994027 -45 TTATTTATAGTACCGCACTTTTGATTAAAA 6 43 0 TACCGCACTT 0.995971 -56 ACGGCTAAATTATCGCACATCA 7 3 0 TATCGCACAT 0.933179 -101 ********** Masking position 10 Map Score: 9.67691 Number of sites scoring better than the average of aligned sites = 1636 Number in coding regions = 1120 Number in noncoding regions = 516 Number of orfs with sites within 600 bp upstream = 328 Fraction of orfs with sites within 600 bp upstream = 0.0526823 Motif number 3 TGTTCAAATAAATCACAGAAAATGATGGAAAAATG 1 195 1 AAACGAAAAA 0.571999 -106 GAAAAAGTGATAAAAGTAGAAATTAGAAAATTACA 1 238 0 TAAGAGAAAA 0.887688 -63 CGCTTTTTATAAATAATTGATAAAATTAAAGCTCG 2 87 1 AAAATGATAA 0.587868 -188 CAATGGAAAAAATAAAGAGAAAACAACAAATAATT 2 158 0 AAAAAGAAAA 0.917561 -117 CAGGTGCGGATAGGAATTGAAACCATAGTTATTTT 2 218 1 TAAATGAAAA 0.925982 -57 ATATTTTTCTTATCAACGCAAAGTATTATAAAATA 3 39 0 TAAAGCAAAA 0.914233 -262 AGCTATCCACTAATAATAGAAAATATAGATTTTTA 3 76 1 TAAAAGAAAA 0.905726 -225 ACTTAGGGAGTATAAATGCAAAAAAATGTGACATA 3 232 0 TAAAGCAAAA 0.914233 -69 GTAACCTATCAACCACAGGAAAATA 4 1 0 AAACGGAAAA 0.944325 -73 ATTTATCTAGTAAAAGAGGAAATAAGTATAGATAT 4 42 0 TAAGGGAAAA 0.965531 -32 TACCATATTTCAGTAGGTGAAAAAATACTTCAAAG 5 65 1 CAAGTGAAAA 0.760003 -88 GCATATTTTTATTGAAAGGAAAGAAAA 5 136 1 ATAAGGAAAA 0.795184 -17 CTACAGTTATAAATAGATCAAATAACTATTTTTTT 6 12 1 AAAGTCAAAA 0.788691 -87 AACGAAGTCCAACGAAAGGAAAATATT 6 82 1 AAAAGGAAAA 0.975276 -17 ** ** ***** * Masking position 10 Map Score: 8.37472 Number of sites scoring better than the average of aligned sites = 480 Number in coding regions = 369 Number in noncoding regions = 111 Number of orfs with sites within 600 bp upstream = 95 Fraction of orfs with sites within 600 bp upstream = 0.0152586 Motif number 4 ACATAAAATTTCATTTTTCCATCATTTTCTGTGA 1 207 0 TCATTTTCAA 0.689606 -94 TGGTTTATTCTAAATTATCTCTGATGATAAAAAA 2 40 1 TAATTATCCA 0.96315 -235 TTATTTAAATTAACTTATAGGGCAAAAATAACTA 2 243 0 TAATTATAGA 0.473461 -32 AGAAAAATATCAAGCTATCCACTAATAATAGAAA 3 64 1 CAACTATCAA 0.937785 -237 TATAAAAATCTATATTTTCTATTATTAGTGGATA 3 79 0 TATTTTTCAA 0.725522 -222 ACTATAAATTTTACCTATCAACAATCAAAATGAC 3 177 0 TTACTATCAA 0.70389 -124 ACATAAATCACAATTTTTCGAAAAATACTATAAA 3 203 0 CAATTTTCAA 0.90479 -98 AATTGGCGAACAATTTACCACTTAGGGAGTATAA 3 252 0 CAATTACCCA 0.751707 -49 TATCTTTCGGTAACCTATCAACCACAGGAAAATA 4 11 0 TAACTATCAA 0.953533 -63 ATCTACAATTTATCTAGTAAAAGAGGAAA 4 55 0 CAATTATCAA 0.953547 -19 CACTTTGAAGTATTTTTTCACCTACTGAAATATG 5 68 0 TATTTTTCCA 0.711962 -85 TCTAAACGGCTAAATTATCGCACATCA 7 4 0 TAATTATCCA 0.963152 -100 GAATGGCGTTTAAACTATCAGTAAGTCGATTAGC 7 58 0 TAACTATCGA 0.90918 -46 *** ***** * * Masking position 14 Map Score: 4.64091 Number of sites scoring better than the average of aligned sites = 318 Number in coding regions = 278 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 5 CTTTAGCTAAAGATGGTTTATTCTAAATTA 2 27 1 AGATGGTTTA 0.922254 -248 TTATCATCAGAGATAATTTAGAATAAACCA 2 40 0 AGATAATTTA 0.888314 -235 TTGCCCTATAAGTTAATTTAAATAAGGAAA 2 252 1 AGTTAATTTA 0.715375 -23 TTTTGATTGTTGATAGGTAAAATTTATAGT 3 181 1 TGATAGGTAA 0.804263 -120 TTCCTGTGGTTGATAGGTTACCGAAAGATA 4 15 1 TGATAGGTTA 0.963052 -59 ACTTCGTTAATGTTGGTTTATTTATAGTAC 6 60 0 TGTTGGTTTA 0.829963 -39 TGATGTGCGATAATTTAGCCGTTTAGA 7 8 1 CGATAATTTA 0.895681 -96 ATCGACTTACTGATAGTTTAAACGCCATTC 7 62 1 TGATAGTTTA 0.969325 -42 CTGATTATTACGATAGGTTTTCA 7 91 1 CGATAGGTTT 0.773059 -13 ********** Masking position 4 Map Score: 3.84386 Number of sites scoring better than the average of aligned sites = 121 Number in coding regions = 101 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 6 AAAGGAAAAAGTGATAAAAGTAGAAATTAGA 1 246 0 GTGTAAAAGT 0.821323 -55 TTTACGTGTTAAAAAACGTTTAGCAT 1 285 0 GTGTAAAAAA 0.908929 -16 ATTATCTCTGATGATAAAAAAAGCCACCTAA 2 53 1 ATGTAAAAAA 0.737949 -222 ATTAACTTATAGGGCAAAAATAACTATGGTT 2 238 0 AGGCAAAAAT 0.534847 -37 TCAACGCAAAGTATTATAAAATACCTTACTC 3 31 0 GTATATAAAA 0.861795 -270 TTTTCGAAAAATACTATAAATTTTACCTATC 3 192 0 ATATATAAAT 0.795318 -109 GCAAAAAAATGTGACATAAATCACAATTTTT 3 219 0 GTGCATAAAT 0.932775 -82 TACCACTTAGGGAGTATAAATGCAAAAAAAT 3 240 0 GGATATAAAT 0.85552 -61 TTCGGCGAGAGTGCTATAAATGGTGCTAATG 5 33 1 GTGTATAAAT 0.969942 -120 CAAAAGTGCGGTACTATAAATAAACCAACAT 6 50 1 GTATATAAAT 0.932301 -49 *** ******* Masking position 6 Map Score: 3.95713 Number of sites scoring better than the average of aligned sites = 255 Number in coding regions = 211 Number in noncoding regions = 44 Number of orfs with sites within 600 bp upstream = 42 Fraction of orfs with sites within 600 bp upstream = 0.0067459 Motif number 7 CGAGCCTCGTTTCCCGCTCCAATTCGTGGC 1 16 0 TTCCCGCTCC 0.904961 -285 AACTGAGCTATTCCCGCATTCGCTGTTATT 1 84 1 TTCCCGCATT 0.898386 -217 AGAAAAATTGACCGCACTTTAGCTAAAG 2 9 1 TGACCGCACT 0.981092 -266 TTTCAATTCCTATCCGCACCTGATTTTACT 2 210 0 TATCCGCACC 0.900047 -65 TTCCTTTAAAATTCCACACTTTGAAGTATT 5 88 0 ATTCCACACT 0.753892 -65 TGCTTAAAACAGACCGCACTTTTCCTTTAA 5 109 0 AGACCGCACT 0.962858 -44 TTTATTTATAGTACCGCACTTTTGATTAAA 6 44 0 GTACCGCACT 0.965981 -55 ********** Masking position 5 Map Score: 1.17805 Number of sites scoring better than the average of aligned sites = 1559 Number in coding regions = 1063 Number in noncoding regions = 496 Number of orfs with sites within 600 bp upstream = 319 Fraction of orfs with sites within 600 bp upstream = 0.0512367 Motif number 8 ********** No masking Map Score: 2.24775e-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 CATCTGCGGTATTAGGCAATGGAAAAAATA 2 179 0 ATTAGGCAAT 0.892351 -96 AATATCACTTATTAAGGAAT 3 1 0 ATTAAGGAAT 0.957684 -300 AGTGATATTGAGTAAGGTATTTTATAATAC 3 22 1 AGTAAGGTAT 0.949534 -279 TAAGAAAAATATCAAGCTATCCACTAATAA 3 62 1 ATCAAGCTAT 0.892456 -239 TATCGGCAGAATTAAGCTATTTACGCAATA 3 111 1 ATTAAGCTAT 0.957792 -190 AACTATCGCGCGTAAGGAATAAAA 5 5 0 CGTAAGGAAT 0.873094 -148 ********** Masking position 4 Map Score: 0.195735 Number of sites scoring better than the average of aligned sites = 67 Number in coding regions = 53 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 10 ********** No masking Map Score: 2.24775e-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 11 ********** No masking Map Score: 2.24775e-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 12 ********** No masking Map Score: 2.24775e-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