AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00460_hinf_reg_300.orf -o00460_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 HI0564 153 aspartate--ammonia ligase (asnA) #2 HI0745 225 L-asparaginase II (ansB) #3 HI0885 191 thiol:disulfide interchange protein (dsbD) #4 HI0886 111 H. influenzae predicted coding region HI0886 #5 HI0887 187 phosphoribosylaminoimidazolecarboxamide formyltransferase (purH) #6 HI0888 95 phosphoribosylamine--glycine ligase (purD) #7 HI0889 123 serine hydroxymethyltransferase (serine methylase) (glyA) #8 HI1062 85 (3R)-hydroxymyristol (acyl carrier protein) dehydrase (fabZ) #9 HI1064 56 conserved hypothetical protein Motif number 1 TCCTTTAGATTTTATTTAATTTTTTCACAATG 1 20 1 TTTATTTATT 0.933156 -134 ATTTCAAGTATTTTATTTACTTTCTTTTCTTG 1 70 0 TTTTATTATT 0.892909 -84 AAATAATGATTTTATTTCAAGTATTTTATTTA 1 83 0 TTTATTTAGT 0.886422 -71 CACATAATTTTTTTTGTTGATTGTATAACCTT 2 110 0 TTTTTGTGTT 0.8145 -116 AATAACTTAATTTAGTTAGACTACTTTGGAGA 2 177 1 TTTAGTTGCT 0.740011 -49 TTGGAGAAATTTTTATTCATCTTAGGAGAAAT 2 202 1 TTTTATTACT 0.937066 -24 ATCCTTATACTTATTTTGGCGTATGCTATCAA 3 16 1 TTATTTTGGT 0.607469 -176 CTGATTTTCCTTTTTGTGATCTAAATCATAGT 3 108 1 TTTTTGTACT 0.941276 -84 TTATTTTTTACTTTTGGTAAAAA 4 2 1 TATTTTTATT 0.88059 -110 TGGTAAAAAGTATTTTTCAATTTTAATTATTG 4 25 1 TATTTTTATT 0.88059 -87 CAATTTTAATTATTGTTTAACTACCCGTTAAA 4 42 1 TATTGTTACT 0.754514 -70 ATGACGCCGTTTTAATTCATCTTTAAACAAAA 4 81 1 TTTAATTACT 0.896337 -31 TTTGCCCACATTTATGTGGGCTTTTTTATGCC 5 43 1 TTTATGTGCT 0.819932 -145 TTTAAGAAATTATATTTAATCTTTTCTATATT 5 101 1 TATATTTACT 0.884361 -87 TTCTCATCGCTTATTTTTAACTATTTAATGAA 5 155 1 TTATTTTACT 0.909954 -33 AAAGTACGGCTATTTTTTACCTGCAATTCCCC 6 43 0 TATTTTTACT 0.929425 -53 ATAGCCGTACTTTTTTTAAATTAGGCATACGC 6 62 1 TTTTTTTATT 0.960064 -34 TTATGATGAATTAATTTCATTTAAGTGATGAA 7 20 1 TTAATTTATT 0.766689 -104 GGAATGAAATTTTAATTAAATTTTTATCCATA 7 58 1 TTTAATTATT 0.828822 -66 TGAGTGCGTTTTATTTTTAGCTATAAATATCG 8 18 1 TTATTTTACT 0.909954 -68 ATCCGATAGATTTTATTTGTTTATTTTTTGTA 8 54 1 TTTTATTGTT 0.803103 -32 ATTTGTTTATTTTTTGTAAGGTATCAAC 8 68 1 TTTTTGTAGT 0.833827 -18 ******* * ** Masking position 7 Map Score: 24.3428 Number of sites scoring better than the average of aligned sites = 981 Number in coding regions = 684 Number in noncoding regions = 297 Number of orfs with sites within 600 bp upstream = 225 Fraction of orfs with sites within 600 bp upstream = 0.0361388 Motif number 2 CTTCCTCCTTTAGATTTTATTTAATTTTTT 1 15 1 TAGATTTTAT 0.77633 -139 TAGATTTTATTTAATTTTTTCACAATGAAT 1 25 1 TTAATTTTTT 0.805812 -129 TCAGTAAATAATGATTTTATTTCAAGTATT 1 90 0 ATGATTTTAT 0.909558 -64 GAATTTAAGCATAATTTTTTTGAAAGATAA 2 68 0 ATAATTTTTT 0.900997 -158 TCTCGATCACATAATTTTTTTTGTTGATTG 2 119 0 ATAATTTTTT 0.900997 -107 TACTTTGGAGAAATTTTTATTCATCTTAGG 2 198 1 AAATTTTTAT 0.882877 -28 TCGAGCATCTATATTTTTATACTCAATTCT 3 172 1 ATATTTTTAT 0.908338 -20 TTGTAGTTTCATAATTTTATCCTTATTTTT 5 16 1 ATAATTTTAT 0.949159 -172 AAGATTAAATATAATTTCTTAAAGTGCGGT 5 94 0 ATAATTTCTT 0.864861 -94 TTATGATGAATTAATTTCATTTAAGTGATG 7 20 1 TTAATTTCAT 0.86812 -104 TTTCATTCCTAAATTTTCATCACTTAAATG 7 37 0 AAATTTTCAT 0.833367 -87 AAATTTAATTAAAATTTCATTCCTAAATTT 7 51 0 AAAATTTCAT 0.920908 -73 AATTTTAATTAAATTTTTATCCATAAACAG 7 65 1 AAATTTTTAT 0.882877 -59 TATAATCCGATAGATTTTATTTGTTTATTT 8 50 1 TAGATTTTAT 0.77633 -36 ********** Masking position 5 Map Score: 17.4273 Number of sites scoring better than the average of aligned sites = 635 Number in coding regions = 444 Number in noncoding regions = 191 Number of orfs with sites within 600 bp upstream = 178 Fraction of orfs with sites within 600 bp upstream = 0.0285898 Motif number 3 TGAGCCCTATTTTGACGTACTTAATCAGTAGA 2 18 0 TTACGTACTT 0.869213 -208 GGGCTCAAGTATAACCGCACTTGGGTTATCTT 2 43 1 ATCCGCACTT 0.995896 -183 ATTATGCTTAAATTCCGTACTTGCATAAAGGT 2 83 1 AACCGTACTT 0.964081 -143 CAGGTAAAAAATCACCGCACTTTTTTATTGTT 3 79 0 ATCCGCACTT 0.995896 -113 TTATCGTATTTTTACCGCACTTTAAGAAATTA 5 81 1 TTCCGCACTT 0.993474 -107 TTTATCTAACTATCCCCCTCTTTACAAAAGAG 6 11 1 TACCCCTCTT 0.87834 -85 TTTACCTGCAATTCCCCCTCTTTTGTAAAGAG 6 28 0 ATCCCCTCTT 0.96936 -68 CAGGTAAAAAATAGCCGTACTTTTTTTAAATT 6 52 1 ATCCGTACTT 0.98962 -44 ** ******** Masking position 11 Map Score: 10.7793 Number of sites scoring better than the average of aligned sites = 1321 Number in coding regions = 859 Number in noncoding regions = 462 Number of orfs with sites within 600 bp upstream = 298 Fraction of orfs with sites within 600 bp upstream = 0.0478638 Motif number 4 TGAAAAAATTAAATAAAATCTAAAGGAGGAAG 1 15 0 AAATAAAATA 0.54974 -139 CCAAGAAAAGAAAGTAAATAAAATACTTGAAA 1 69 1 AAAGTAAAAA 0.630543 -85 CCTCGTTAAAAAAGGTTATCAAA 1 141 1 AAAGGTTAAA 0.76608 -13 AATTTTTTTGAAAGATAACCCAAGTGCGGTTA 2 54 0 AAAGATAACA 0.949265 -172 GTACTTGCATAAAGGTTATACAATCAACAAAA 2 99 1 AAAGGTTACA 0.902418 -127 ATTTATAAACAATGGAAAAACAAATTTATGAT 2 148 0 AATGGAAACA 0.890091 -78 TAGATCACAAAAAGGAAAATCAGGTAAAAAAT 3 99 0 AAAGGAAACA 0.977353 -93 ACTTTTTACCAAAAGTAAAAAATAA 4 4 0 AAAAGTAAAA 0.565146 -108 TCTTTAAACAAAAGGAAAGCAA 4 100 1 AAAGGAAAAA 0.938587 -12 TAAATATAGAAAAGATTAAATATAATTTCTTA 5 103 0 AAAGATTATA 0.502296 -85 AAGCGATGAGAATTATAACGCAAACGTTTGCT 5 135 0 AATTATAACA 0.47649 -53 TATTTAATGAAAGGAAAATACA 5 176 1 AAGGAAAACA 0.898721 -12 TTCATCACTTAAATGAAATTAATTCATCATAA 7 20 0 AAATGAAAAA 0.798467 -104 TTATAGCTAAAAATAAAACGCACTCAATATAG 8 12 0 AAATAAAACA 0.887956 -74 GATACCTTACAAAAAATAAACAAATAAAATCT 8 61 0 AAAAAATACA 0.597936 -25 TTTAAGCCAGAAGGAAAAAACA 9 1 0 AAGGAAAACA 0.898721 -56 ******** ** Masking position 8 Map Score: 10.1332 Number of sites scoring better than the average of aligned sites = 1013 Number in coding regions = 790 Number in noncoding regions = 223 Number of orfs with sites within 600 bp upstream = 195 Fraction of orfs with sites within 600 bp upstream = 0.0313203 Motif number 5 TACTTTCTTTTCTTGGTTGAATATCATCTAA 1 54 0 TCTTGTTGAA 0.750768 -100 TTCAAAAAAATTATGCTTAAATTCCGTACTT 2 74 1 TTATGTTAAA 0.844488 -152 TAAATTCCGTACTTGCATAAAGGTTATACAA 2 91 1 ACTTGATAAA 0.659987 -135 AAAAGGAAAATCAGGTAAAAAATCACCGCAC 3 91 0 TCAGGAAAAA 0.892418 -101 ATTTTTTACTTTTGGTAAAAAGTATTTTTCA 4 13 1 TTTGGAAAAA 0.838076 -99 TTGCTTTCCTTTTGTTTAAAGATGAATTAA 4 92 0 TTTTGTTAAA 0.84441 -20 ACGATAAATTTCAGGCATAAAAAAGCCCACA 5 57 0 TCAGGATAAA 0.9737 -131 TGATGAAAATTTAGGAATGAAATTTTAATTA 7 45 1 TTAGGATGAA 0.889095 -79 GTTTAACTGTTTATGGATAAAAATTTAATTA 7 70 0 TTATGATAAA 0.912816 -54 AGTTAAACTATCTGCCATAAATTACATAACA 7 93 1 TCTGCATAAA 0.888354 -31 CGTTTTATTTTTAGCTATAAATATCGTATAA 8 24 1 TTAGCATAAA 0.832534 -62 GTTTTTTCCTTCTGGCTTAAAAAATTGGCTT 9 12 1 TCTGGTTAAA 0.9505 -45 ***** ***** Masking position 10 Map Score: 8.0147 Number of sites scoring better than the average of aligned sites = 485 Number in coding regions = 404 Number in noncoding regions = 81 Number of orfs with sites within 600 bp upstream = 83 Fraction of orfs with sites within 600 bp upstream = 0.0133312 Motif number 6 GGGCTCAAGTATAACCGCACTTGGGTTATC 2 43 1 ATAACCGCAC 0.994863 -183 CAGGTAAAAAATCACCGCACTTTTTTATTG 3 81 0 ATCACCGCAC 0.991274 -111 TTATCGTATTTTTACCGCACTTTAAGAAAT 5 81 1 TTTACCGCAC 0.95884 -107 CAGGTAAAAAATAGCCGTACTTTTTTTAAA 6 52 1 ATAGCCGTAC 0.943557 -44 ATTCTATAAAATAACCGCTCAAGA 9 43 1 ATAACCGCTC 0.983295 -14 ********** Masking position 2 Map Score: 4.81222 Number of sites scoring better than the average of aligned sites = 440 Number in coding regions = 273 Number in noncoding regions = 167 Number of orfs with sites within 600 bp upstream = 129 Fraction of orfs with sites within 600 bp upstream = 0.0207196 Motif number 7 AATAAAATCTAAAGGAGGAAGTTTT 1 6 0 AAAGGAGGAA 0.870882 -148 ATATTCAACCAAGAAAAGAAAGTAAATAAA 1 61 1 AAGAAAAGAA 0.812306 -93 GTTATTTATAAACAATGGAAAAACAAATTT 2 153 0 AACAATGGAA 0.81135 -73 AAATAAGTATAAGGATGGAAA 3 2 0 AAGGATGGAA 0.936881 -190 ATAATGTTGCACAGATAGAATGATAGCTTT 3 46 0 ACAGATAGAA 0.745079 -146 ATTTAGATCACAAAAAGGAAAATCAGGTAA 3 104 0 CAAAAAGGAA 0.916391 -88 TCATCTTTAAACAAAAGGAAAGCAA 4 97 1 ACAAAAGGAA 0.956481 -15 TAACTATTTAATGAAAGGAAAATACA 5 172 1 ATGAAAGGAA 0.844289 -16 ATTTTTTAAGCCAGAAGGAAAAAACA 9 7 0 CCAGAAGGAA 0.932574 -50 ********** Masking position 9 Map Score: 1.88696 Number of sites scoring better than the average of aligned sites = 336 Number in coding regions = 253 Number in noncoding regions = 83 Number of orfs with sites within 600 bp upstream = 70 Fraction of orfs with sites within 600 bp upstream = 0.0112432 Motif number 8 ********** No masking Map Score: -1.52523e-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: -1.52523e-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: -1.52523e-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