AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i101_Iron_Transport_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 HI1272 300 ABC transporter, ATP-binding protein #2 HI1472 67 iron chelatin ABC transporter, periplasmic-binding protein, putative #3 HI1475 227 H. influenzae predicted coding region HI1475 #4 HI1476 227 transcriptional regulatory protein Motif number 1 AATTTGGCGAAATTTTACGGACGTAAGTGG 3 181 0 AATTTTACGG 0.93466 -47 GCAACATGCAACTATTACGGATAATATACA 4 43 0 ACTATTACGG 0.998121 -185 GCCAAATGAAACTATTACGGTGTATTTTAT 4 77 0 ACTATTACGG 0.998121 -151 CTATTGTTTTACTATTTCGAATAAAAACAA 4 118 1 ACTATTTCGA 0.967828 -110 CTTAATTAGTTCTATTACGGGTAATAATTT 4 151 1 TCTATTACGG 0.991013 -77 AATAATTACAACTATTACGGGATTAAAAAC 4 182 0 ACTATTACGG 0.998121 -46 TAATTATTCAACTATTACGACTAAAGAGGT 4 204 1 ACTATTACGA 0.993146 -24 ********** Masking position 5 Map Score: 19.1112 Number of sites scoring better than the average of aligned sites = 15 Number in coding regions = 9 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 2 AAGAATTTTTAACAAAGAAATGCCTGCACC 1 85 0 AACAAAGAAA 0.990118 -216 ATCAGTAAGTAATAAAAAAATGGGAACAAT 1 223 0 AATAAAAAAA 0.885217 -78 TCCTTATTTTAAGTAAGAAAATATCATTAT 2 42 0 AAGTAAGAAA 0.94009 -26 GAATTTAAACAAAAAAGAAAACGCCCGTTT 3 28 0 AAAAAAGAAA 0.964705 -200 GAACCAGAAAAACTAAGAATTTAAACAAAA 3 44 0 AACTAAGAAT 0.905924 -184 AGGGAAAGAAAACTAAGAAAAAATCAGATC 3 95 0 AACTAAGAAA 0.985598 -133 TTTCCCTAAGAATAAAAAAAGGGGCAATGC 3 118 1 AATAAAAAAA 0.885217 -110 AACAAAGAAAACAAAAGAAATAGGAATTTG 3 205 0 ACAAAAGAAA 0.85075 -23 CAAAACAAAGAAAACAAAAGAAA 3 215 0 AACAAAGAAA 0.990118 -13 TGCATGTTGCAACTATAAAATACACCGTAA 4 63 1 AACTATAAAA 0.730973 -165 ********** Masking position 5 Map Score: 13.7544 Number of sites scoring better than the average of aligned sites = 400 Number in coding regions = 292 Number in noncoding regions = 108 Number of orfs with sites within 600 bp upstream = 92 Fraction of orfs with sites within 600 bp upstream = 0.0147767 Motif number 3 TAGTCGTACACAAGATCCTATTTTAGTGCTGGT 1 21 1 CAAGACCTTT 0.954056 -280 TGCACCAAGTAAAGAACCAATTGCAATCCCAGA 1 58 0 AAAGACCTTG 0.953662 -243 GTTGCTAGGGATTGTTCCCATTTTTTTATTACT 1 213 1 ATTGTCCTTT 0.912835 -88 GGCTCGCACGATTGCACCGATTGAACTGCCACT 1 258 1 ATTGCCCTTG 0.942878 -43 AACAAAAAAGAAAACGCCCGTTTAAATGGCGTT 3 18 0 AAAACCCTTT 0.970073 -210 TAAATCAACCAAAGATCTGATTTTTTCTTAGTT 3 82 1 AAAGACTTTT 0.808101 -146 TTGGCGGTGCATTGCCCCTTTTTTTATTCTTAG 3 123 0 ATTGCCCTTT 0.974608 -105 ATGCACCGCCAAAGCCCCTGTTTTCAATAATTC 3 144 1 AAAGCCCTTT 0.991518 -84 AAAATTTCGCCAAATTCCTATTTCTTTTGTTTT 3 195 1 CAAATCCTTT 0.804059 -33 TTAATACACCTTTTTTGCTGTACCT 4 3 1 AATACCCTTT 0.959232 -225 ***** ** *** Masking position 11 Map Score: 9.23695 Number of sites scoring better than the average of aligned sites = 333 Number in coding regions = 284 Number in noncoding regions = 49 Number of orfs with sites within 600 bp upstream = 49 Fraction of orfs with sites within 600 bp upstream = 0.00787022 Motif number 4 TATTTTAGTGCTGGTGCTTTCTGGGATTGC 1 39 1 CTGGTGCTTT 0.952989 -262 GGGATTGCAATTGGTTCTTTACTTGGTGCA 1 61 1 TTGGTTCTTT 0.860227 -240 GGCAGTTCAATCGGTGCAATCGTGCGAGCC 1 258 0 TCGGTGCAAT 0.901788 -43 CTTAGTTTTTCTGGTTCATTTTGACTAAAT 3 57 1 CTGGTTCATT 0.954595 -171 AATCAGATCTTTGGTTGATTTAGTCAAAAT 3 74 0 TTGGTTGATT 0.817036 -154 AGGGGCTTTGGCGGTGCATTGCCCCTTTTT 3 133 0 GCGGTGCATT 0.984345 -95 TACAGCAAAAAAGGTGTATTAA 4 3 0 AAGGTGTATT 0.799971 -225 TGTACCTTATGTGGTGTATATTATCCGTAA 4 29 1 GTGGTGTATA 0.798098 -199 TGAAACTATTACGGTGTATTTTATAGTTGC 4 71 0 ACGGTGTATT 0.940791 -157 ********** Masking position 5 Map Score: 3.72523 Number of sites scoring better than the average of aligned sites = 714 Number in coding regions = 647 Number in noncoding regions = 67 Number of orfs with sites within 600 bp upstream = 53 Fraction of orfs with sites within 600 bp upstream = 0.00851269 Motif number 5 TAATCAACAAGATTTAATTCAATTGATCCCGA 1 177 1 GATTTATCAA 0.947257 -124 GAAAAACTAAGAATTTAAACAAAAAAGAAAAC 3 36 0 GAATTTACAA 0.787226 -192 ATCTTTGGTTGATTTAGTCAAAATGAACCAGA 3 66 0 GATTTATAAA 0.918449 -162 CTTTCCCTAAGAATAAAAAAAGGGGCAATGCA 3 117 1 GAATAAAAAG 0.774704 -111 AAGTGGGCGGGAATTATTGAAAACAGGGGCTT 3 155 0 GAATTATAAA 0.942819 -73 TAAAACAATAGATTAAAATATAGCCAAATGAA 4 97 0 GATTAAAATA 0.757879 -131 GTTTTTATTCGAAATAGTAAAACAATAGATTA 4 114 0 GAAATATAAA 0.698801 -114 TTACTATTTCGAATAAAAACAATGACTTAATT 4 126 1 GAATAAACAA 0.963362 -102 ACTATTACGGGATTAAAAACTAAATTATTACC 4 170 0 GATTAAACTA 0.833108 -58 CGTAATAGTTGAATAATTACAACTATTACGGG 4 191 0 GAATAATCAA 0.963362 -37 ****** * *** Masking position 2 Map Score: 3.68429 Number of sites scoring better than the average of aligned sites = 584 Number in coding regions = 492 Number in noncoding regions = 92 Number of orfs with sites within 600 bp upstream = 78 Fraction of orfs with sites within 600 bp upstream = 0.0125281 Motif number 6 CCAGAAAGCACCAGCACTAAAATAGGATCT 1 33 0 CCAGCACTAA 0.95988 -268 CAAAGAAATGCCTGCACCAAGTAAAGAACC 1 73 0 CCTGCACCAA 0.973695 -228 CTTGCGGATCCTTTCACTCAATTACCTTCA 1 112 1 CTTTCACTCA 0.962096 -189 CACTCAATTACCTTCAATCACTTTTTGGCT 1 126 1 CCTTCAATCA 0.936873 -175 GGAACAATCCCTAGCAACAACATCGGGATC 1 201 0 CTAGCAACAA 0.865872 -100 TCTTAGTTTTCTTTCCCTAAGAATAAAAAA 3 107 1 CTTTCCCTAA 0.920673 -121 AAAGCCCCTGTTTTCAATAATTCCCGCCCA 3 154 1 TTTTCAATAA 0.703119 -74 ********** Masking position 10 Map Score: 0.506663 Number of sites scoring better than the average of aligned sites = 441 Number in coding regions = 401 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 7 CAGGCTACCAAGTAGCCAAAAAGTGATTGA 1 139 0 AGTAGCCAAA 0.958369 -162 CTTTGGTTGATTTAGTCAAAATGAACCAGA 3 66 0 TTTAGTCAAA 0.934889 -162 GTCCGTAAAATTTCGCCAAATTCCTATTTC 3 189 1 TTTCGCCAAA 0.792448 -39 TAGATTAAAATATAGCCAAATGAAACTATT 4 91 0 TATAGCCAAA 0.955539 -137 ********** Masking position 3 Map Score: 0.154879 Number of sites scoring better than the average of aligned sites = 118 Number in coding regions = 100 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 8 ********** No masking Map Score: -1.65313e-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: -1.65313e-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: -1.65313e-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