AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i111_Amino_Acid_Transport_2_hinf_reg_300.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 HI1549 146 ABC transporter, ATP-binding protein #2 HI1556 59 2-hydroxyacid dehydrogenase #3 HI1560 22 H. influenzae predicted coding region HI1560 #4 HI1561 106 peptide chain release factor 1 (prfA) #5 HI1562 252 H. influenzae predicted coding region HI1562 #6 HI1563 32 conserved hypothetical protein #7 HI1564 32 H. influenzae predicted coding region HI1564 #8 HI1564.1 284 H. influenzae predicted coding region HI1564.1 Motif number 1 AGATAACACCATCAAAAACTTGCACGAGTCTATCACACT 1 87 0 AAAAACGAGT 0.90941 -60 ATTTCATCAAAAGTGCGGTTAATTTTGACCGCAC 2 6 1 AAAAATGATT 0.968569 -54 CGCACTTTGTATATAAAAAAGGAGCAATTA 2 40 1 ATAAAAGATT 0.955665 -20 TAAGTCACCGAAAATAAAATCGGCGTATTCTAGCCGATT 4 75 0 AATAAAGATT 0.909416 -32 GGGCTTAAGACTGAAAAAAGTGAGCAATTTTGATCACTT 5 18 0 CAAAAAGATT 0.961773 -235 GGTGTGAAATGATTAAAAATTGAACTATTTAATTAGGAG 5 66 0 GTAAAAGATT 0.862197 -187 CTTTACAGAGAGTACAACAAAGCATAATTGGCAACTAGG 5 128 1 AACAAAGATT 0.981202 -125 TCAAAAACACACTAAAACAAGGCGACAATATGCTTGCTA 5 169 0 AAAAAAGAAT 0.95885 -84 CCTGATCTTCAAGAAAAAATTGAAGCAATTAAAGAAGAA 5 221 1 AAAAAAGAAT 0.958858 -32 GGTATCGACTCCTAAAAAACCGCAAGATTATA 6 4 0 CAAAAAGATT 0.961773 -29 AGCACGTTTAATCTAAAATTGGTCATATTTAGTCCTATA 8 43 1 ATAAATGATT 0.884512 -242 TTAGTCCTATAAAAAAAATAATAATAATTCTCAAACATA 8 71 1 AAAAATTATT 0.754582 -214 GTATTTTCTCACAACAATAAAGATTGATTTTTGATAAAA 8 124 1 AACAAAGATT 0.98127 -161 AAAATCAAGAAATAAAAACTATTCTTATTATTTTCTGTA 8 160 1 AAAAACTATT 0.819116 -125 CGCATTATAGGAAACAAGCAGGTTTAAATACAGAAAATA 8 188 0 GACAACGAAT 0.750108 -97 AGCCCACCAAAAAACAATCGAGAGATATT 8 266 1 AACAACGATT 0.974665 -19 * **** * * *** Masking position 7 Map Score: 18.555 Number of sites scoring better than the average of aligned sites = 688 Number in coding regions = 519 Number in noncoding regions = 169 Number of orfs with sites within 600 bp upstream = 160 Fraction of orfs with sites within 600 bp upstream = 0.0256987 Motif number 2 ACACTTTTCCTTGAGCTTAAATTTCAATAC 1 62 0 TTGAGCTTAA 0.792008 -85 TGCCGCTAAAGTGCGGTTAAAACGAGTAAA 1 125 1 GTGCGGTTAA 0.993064 -22 TTCATCAAAAGTGCGGTTAATTTTGACCGC 2 13 1 GTGCGGTTAA 0.993064 -47 TATATACAAAGTGCGGTCAAAATTAACCGC 2 25 0 GTGCGGTCAA 0.984562 -35 GAGGGAATTGGAGGGCTTAAGACTGAAAAA 5 39 0 GAGGGCTTAA 0.960419 -214 TTGTTTTTTGGTGGGCTAAAGCCCACCCTA 8 253 0 GTGGGCTAAA 0.967459 -32 ********** Masking position 7 Map Score: 6.56314 Number of sites scoring better than the average of aligned sites = 562 Number in coding regions = 333 Number in noncoding regions = 229 Number of orfs with sites within 600 bp upstream = 168 Fraction of orfs with sites within 600 bp upstream = 0.0269836 Motif number 3 AACGTTATCTTGAAAAACATTTTCC 1 6 1 TATCTTGAAA 0.797471 -141 TGAAAAACATTTTCCTGAAACAGGATTTGA 1 21 1 TTTCCTGAAA 0.713815 -126 ATTTCATCAAAAGTGCGGTTA 2 2 1 TTTCATCAAA 0.723627 -58 GCTTCAATTTTTTCTTGAAGATCAGGCTGT 5 217 0 TTTCTTGAAG 0.942897 -36 TCTTCTTTAATTGCTTCAATTTTTTCTTGA 5 229 0 TTGCTTCAAT 0.846478 -24 AGTAGTTACTTGAAAATCTTCAAAT 7 18 0 TTACTTGAAA 0.915583 -15 AGAAAATACCTTTCTTCATATAATATGTTT 8 103 0 TTTCTTCATA 0.9358 -182 ATAGTTTTTATTTCTTGATTTTTATCAAAA 8 152 0 TTTCTTGATT 0.911189 -133 ********** Masking position 8 Map Score: 4.26021 Number of sites scoring better than the average of aligned sites = 238 Number in coding regions = 194 Number in noncoding regions = 44 Number of orfs with sites within 600 bp upstream = 55 Fraction of orfs with sites within 600 bp upstream = 0.00883392 Motif number 4 TTTTTACTCGTTTTAACCGCACTT 1 133 0 TACTCGTTTT 0.916729 -14 ACACCCAGTATACTGGGTGTGAAATGATTA 5 90 0 TACTGGGTGT 0.985669 -163 ACACCCAGTATACTGGGTGTTGTACTCTCT 5 100 1 TACTGGGTGT 0.985669 -153 CTGGGTGTTGTACTCTCTTTACAGAGAGTA 5 112 1 TACTCTCTTT 0.950241 -141 TGCTTTGTTGTACTCTCTGTAAAGAGAGTA 5 122 0 TACTCTCTGT 0.967772 -131 CGCCTTGTTTTAGTGTGTTTTTGATTTGCC 5 184 1 TAGTGTGTTT 0.864463 -69 ********** Masking position 4 Map Score: 3.33279 Number of sites scoring better than the average of aligned sites = 62 Number in coding regions = 47 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 5 CTAGTTGCCAATTATGCTTTGTTGTACTCT 5 136 0 ATTATGCTTT 0.881915 -117 ACAAGGCGACAATATGCTTGCTAATCCTAG 5 162 0 AATATGCTTG 0.98902 -91 TGCCTATTCCGTTATGCTTGGGCTAACGGC 8 13 0 GTTATGCTTG 0.946387 -272 TTTTAGATTAAACGTGCTTGCCTATTCCGT 8 31 0 AACGTGCTTG 0.97113 -254 TTCTTCATATAATATGTTTGAGAATTATTA 8 92 0 AATATGTTTG 0.933042 -193 TCTGTATTTAAACCTGCTTGTTTCCTATAA 8 193 1 AACCTGCTTG 0.971132 -92 ********** Masking position 5 Map Score: 3.49448 Number of sites scoring better than the average of aligned sites = 147 Number in coding regions = 131 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 6 AGTGCGGTTAAAACGAGTAAAAA 1 134 1 AAACGAGTAA 0.898573 -13 TGTATATAAAAAAGGAGCAATTA 2 47 1 AAAGGAGCAA 0.97116 -13 TGGCAGAAAGTGATCAAAATTGCTCAC 5 8 1 AAGTGATCAA 0.923843 -245 AGACTGAAAAAAGTGAGCAATTTTGATCAC 5 20 0 AAGTGAGCAA 0.964705 -233 ACTGGGTGTGAAATGATTAAAAATTGAACT 5 79 0 AAATGATTAA 0.897209 -174 ATAGGACTAAATATGACCAATTTTAGATTA 8 51 0 ATATGACCAA 0.923843 -234 TATTTTTTTTATAGGACTAAATATGACCAA 8 61 0 ATAGGACTAA 0.829615 -224 ********** Masking position 6 Map Score: 2.70202 Number of sites scoring better than the average of aligned sites = 180 Number in coding regions = 160 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 7 TTAGGAGGGAATTGGAGGGCTTAAGACTGA 5 43 0 ATTGGAGGGC 0.984944 -210 AACTATTTAATTAGGAGGGAATTGGAGGGC 5 53 0 TTAGGAGGGA 0.95934 -200 TTAGTAGTTGTAGGGTGGGCTTTAGCCCAC 8 243 1 TAGGGTGGGC 0.982139 -42 TCGATTGTTTTTTGGTGGGCTAAAGCCCAC 8 257 0 TTTGGTGGGC 0.993987 -28 ********** Masking position 5 Map Score: 0.692914 Number of sites scoring better than the average of aligned sites = 52 Number in coding regions = 33 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 8 TAAATTTCAATACACCTAAAGTATTCAAAT 1 45 0 TACACCTAAA 0.955732 -102 AGGGAAAATTGACAGCGAAAAGGAAATTAA 4 43 0 GACAGCGAAA 0.980207 -64 TTGTAAGTCACCGAAAATAAAATCGG 4 91 0 GTCACCGAAA 0.981324 -16 GGTATCGACTCCTAAAAAACCGCAAG 6 17 0 GACTCCTAAA 0.971407 -16 ********** Masking position 8 Map Score: 0.0776032 Number of sites scoring better than the average of aligned sites = 27 Number in coding regions = 23 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 9 ********** No masking Map Score: 1.3951e-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: 1.3951e-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: 1.3951e-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