AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00460_hinf_reg_100.orf -o00460_hinf_100.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 HI0564 153 aspartate--ammonia ligase (asnA) #2 HI0745 225 L-asparaginase II (ansB) #3 HI0889 123 serine hydroxymethyltransferase (serine methylase) (glyA) #4 HI1062 85 (3R)-hydroxymyristol (acyl carrier protein) dehydrase (fabZ) #5 HI1064 56 conserved hypothetical protein Motif number 1 CTTCCTCCTTTAGATTTTATTTAATTTTTTC 1 15 1 TAGATTTATT 0.947005 -139 AGTATTTTATTTACTTTCTTTTCTTGGTTGA 1 65 0 TTACTTTTTT 0.871244 -89 TCAGTAAATAATGATTTTATTTCAAGTATTT 1 89 0 ATGATTTATT 0.947005 -65 TTTGATAACCTTTTTTAACGAGGAGT 1 138 0 TAACCTTTTT 0.712353 -16 GAATTTAAGCATAATTTTTTTGAAAGATAAC 2 67 0 ATAATTTTTT 0.957652 -159 TCTCGATCACATAATTTTTTTTGTTGATTGT 2 118 0 ATAATTTTTT 0.957652 -108 ATCGAGATCATAAATTTGTTTTTCCATTGTT 2 142 1 TAAATTTTTT 0.957658 -84 TTGTTTATAAATAACTTAATTTAGTTAGACT 2 168 1 ATAACTTATT 0.917919 -58 TACTTTGGAGAAATTTTTATTCATCTTAGGA 2 198 1 AAATTTTATT 0.838971 -28 TTATGATGAATTAATTTCATTTAAGTGATGA 3 20 1 TTAATTTATT 0.96831 -104 AAATTTAATTAAAATTTCATTCCTAAATTTT 3 50 0 AAAATTTATT 0.976194 -74 TTTATGGATAAAAATTTAATTAAAATTTCAT 3 61 0 AAAATTTATT 0.976193 -63 TATAATCCGATAGATTTTATTTGTTTATTTT 4 50 1 TAGATTTATT 0.947005 -36 ******* *** Masking position 6 Map Score: 19.085 Number of sites scoring better than the average of aligned sites = 573 Number in coding regions = 427 Number in noncoding regions = 146 Number of orfs with sites within 600 bp upstream = 137 Fraction of orfs with sites within 600 bp upstream = 0.0220045 Motif number 2 TTTATTTAATTTTTTCACAATGAATTAGATGAT 1 30 1 TTTTTCATGA 0.939481 -124 TAAAATCATTATTTACTGAATAATACTCAAAAA 1 101 1 ATTTACATAA 0.852079 -53 TTGATAACCTTTTTTAACGAGGAGTAATATTTT 1 130 0 TTTTTAAGGA 0.933454 -24 AGCATAATTTTTTTGAAAGATAACCCAAGTGCG 2 58 0 TTTTGAATAA 0.92871 -168 GCAAGTACGGAATTTAAGCATAATTTTTTTGAA 2 74 0 AATTTAATAA 0.863599 -152 GTTTTTCCATTGTTTATAAATAACTTAATTTAG 2 159 1 TGTTTAATAA 0.911017 -67 AATTAATTTCATTTAAGTGATGAAAATTTAGGA 3 28 1 ATTTAAATGA 0.925245 -96 AAGTGATGAAAATTTAGGAATGAAATTTTAATT 3 42 1 AATTTAATGA 0.838935 -82 TTTAATTAAATTTTTATCCATAAACAGTTAAAC 3 68 1 TTTTTAATAA 0.979757 -56 GTGCGTTTTATTTTTAGCTATAAATATCGTATA 4 21 1 TTTTTAATAA 0.979364 -65 TAAGCCAATTTTTTAAGCCAGAAGGAAAAAACA 5 11 0 TTTTAAAGAA 0.909232 -46 TGAGCGGTTATTTTATAGAATAAGCCAATTTTT 5 31 0 TTTTATATAA 0.792091 -26 ****** **** Masking position 10 Map Score: 9.04857 Number of sites scoring better than the average of aligned sites = 532 Number in coding regions = 363 Number in noncoding regions = 169 Number of orfs with sites within 600 bp upstream = 148 Fraction of orfs with sites within 600 bp upstream = 0.0237713 Motif number 3 TTCATTGTGAAAAAATTAAATAAAATCTAAA 1 23 0 AAAATTAAAT 0.843292 -131 AAAAGAAAGTAAATAAAATACTTGAAATAAA 1 74 1 AATAAAATAC 0.575368 -80 TTCAGTAAATAATGATTTTATTTCAAGTATT 1 90 0 AAGATTTTAT 0.476015 -64 AATAATACTCAAAAATATTACTCCTCGTTAA 1 119 1 AAAATATTAC 0.811979 -35 TATCTTTCAAAAAAATTATGCTTAAATTCCG 2 69 1 AAAATTATGC 0.710802 -157 GTACTTGCATAAAGGTTATACAATCAACAAA 2 99 1 AAGGTTATAC 0.866162 -127 TTATACAATCAACAAAAAAAATTATGTGATC 2 114 1 AAAAAAAAAA 0.540276 -112 ATTTATAAACAATGGAAAAACAAATTTATGA 2 149 0 AAGGAAAAAC 0.848172 -77 GTTTATGGATAAAAATTTAATTAAAATTTCA 3 62 0 AAAATTTAAT 0.63322 -62 TTTATCCATAAACAGTTAAACTATCTGCCAT 3 80 1 AAAGTTAAAC 0.924876 -44 ATTTATAGCTAAAAATAAAACGCACTCAATA 4 15 0 AAAATAAAAC 0.954651 -71 GATACCTTACAAAAAATAAACAAATAAAATC 4 62 0 AAAAATAAAC 0.939696 -24 TTTAAGCCAGAAGGAAAAAACA 5 2 0 AAGAAAAAAC 0.917123 -55 ** ******** Masking position 2 Map Score: 5.30139 Number of sites scoring better than the average of aligned sites = 1441 Number in coding regions = 1109 Number in noncoding regions = 332 Number of orfs with sites within 600 bp upstream = 251 Fraction of orfs with sites within 600 bp upstream = 0.0403148 Motif number 4 CTTAATCAGTAGAGAAAACA 2 1 0 AGAGAAAACA 0.971083 -225 AGACTACTTTGGAGAAATTTTTATTCATCT 2 194 1 GGAGAAATTT 0.942406 -32 ATTCATCTTAGGAGAAATCT 2 216 1 GGAGAAATCT 0.988275 -10 TTACATAACAGGAGAACACA 3 114 1 GGAGAACACA 0.987452 -10 TAAGCCAGAAGGAAAAAACA 5 1 0 GGAAAAAACA 0.971098 -56 ********** Masking position 5 Map Score: 3.31923 Number of sites scoring better than the average of aligned sites = 65 Number in coding regions = 51 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 5 TTGTGAAAAAATTAAATAAAATCTAAAGGA 1 20 0 ATTAAATAAA 0.472237 -134 TTGGTTGAATATCATCTAATTCATTGTGAA 1 43 0 ATCATCTAAT 0.828364 -111 TTTTTTGTTGATTGTATAACCTTTATGCAA 2 103 0 ATTGTATAAC 0.868765 -123 TATGATCTCGATCACATAATTTTTTTTGTT 2 124 0 ATCACATAAT 0.914252 -102 TTGTTTATAAATAACTTAATTTAGTTAGAC 2 168 1 ATAACTTAAT 0.788725 -58 TTTCTCCAAAGTAGTCTAACTAAATTAAGT 2 181 0 GTAGTCTAAC 0.522887 -45 CTAAATTTTCATCACTTAAATGAAATTAAT 3 29 0 ATCACTTAAA 0.762508 -95 TTTATGGCAGATAGTTTAACTGTTTATGGA 3 84 0 ATAGTTTAAC 0.843325 -40 TCTGCCATAAATTACATAACAGGAGAACAC 3 103 1 ATTACATAAC 0.882128 -21 AGCTATAAATATCGTATAATCCGATAGATT 4 36 1 ATCGTATAAT 0.88959 -50 GGCTTATTCTATAAAATAACCGCTCAAGA 5 38 1 ATAAAATAAC 0.817648 -19 ********** Masking position 8 Map Score: 2.56287 Number of sites scoring better than the average of aligned sites = 547 Number in coding regions = 419 Number in noncoding regions = 128 Number of orfs with sites within 600 bp upstream = 92 Fraction of orfs with sites within 600 bp upstream = 0.0147767 Motif number 6 ********** No masking Map Score: 1.82142e-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 7 ********** No masking Map Score: 1.82142e-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: 1.82142e-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