AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i134_Transmembrane_Transport_8_ecoli_hinf_reg_300.orf -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -g0.46 -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 = 0.46 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 HI0096 300 H. influenzae predicted coding region HI0096 #2 HI0097 272 iron(III) ABC transporter, periplasmic-binding protein (hitA) #3 HI0098 216 iron(III) ABC transporter, permease protein (hitB) Motif number 1 AATTGAAAAAAGCATTGAAGAAATAATAGGA 1 81 0 AGCATTGAAA 0.900673 -220 GTGAATTACTTGAATTGAAAAAAGCATTGAA 1 93 0 TGAATTGAAA 0.931054 -208 AAATGGAAAGCGAATTGAAACAGTTACGTCG 1 123 0 CGAATTGAAC 0.892068 -178 AGTGATGATGCGCTCTCAACAAGCAGAAACC 1 179 0 CGCTCTCAAA 0.944433 -122 CAATTCAGGCTGAACTGAATAATTTGCACTC 2 121 1 TGAACTGAAA 0.973514 -152 CTGAATAATTTGCACTCAACATAAGGAGCTT 2 135 1 TGCACTCAAA 0.988218 -138 ATGTTTAAATTGCATTGAAAAGCTCCTTATG 2 154 0 TGCATTGAAA 0.973514 -119 TTCAAATACACGCACGCAATATTTGGA 3 7 0 CGCACGCAAA 0.988205 -210 TTTCAGTTCACGCACGCAAGCGGTTAATTTT 3 70 0 CGCACGCAAC 0.969838 -147 CTTGCGTGCGTGAACTGAAAAGTTCACATTC 3 81 1 TGAACTGAAA 0.973514 -136 TTCTGTCGCACGCAAAATGACATACAG 3 200 0 CGCACGCAAA 0.988205 -17 ********* * Masking position 8 Map Score: 18.1101 Number of sites scoring better than the average of aligned sites = 507 Number in coding regions = 470 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 46 Fraction of orfs with sites within 600 bp upstream = 0.00738837 Motif number 2 GAAAAAGCAAGTGTGCCGCAAGGGTAGCAAG 2 191 0 GTGTGCCCAA 0.984122 -82 TCCAAATATTGCGTGCGTGTATTTGAAAAAA 3 11 1 GCGTGCGGTA 0.994075 -206 AATTGTAAACGCGTGCGTGAATTTTTTCAAA 3 32 0 GCGTGCGGAA 0.998532 -185 TTAACCGCTTGCGTGCGTGAACTGAAAAGTT 3 74 1 GCGTGCGGAA 0.998532 -143 GATAAGTAAAGTGAGCCAGAATGGCGGTCTG 3 136 0 GTGAGCCGAA 0.967251 -81 ATGTCATTTTGCGTGCGACAGAA 3 204 1 GCGTGCGCAG 0.992358 -13 ******* *** Masking position 6 Map Score: 10.8953 Number of sites scoring better than the average of aligned sites = 196 Number in coding regions = 195 Number in noncoding regions = 1 Number of orfs with sites within 600 bp upstream = 1 Fraction of orfs with sites within 600 bp upstream = 0.000160617 Motif number 3 CAGTTTTTTGTCGGTTTCTGCTTGTTGAGA 1 167 1 TCGGTTTCTG 0.979003 -134 AACACAAAGTGCGGTCAATTCTGCGGAAGT 1 231 0 GCGGTCAATT 0.930629 -70 AATCTCTCAAGCGGTTTATTATCCAGATAC 1 268 1 GCGGTTTATT 0.987809 -33 TGTGTATGGTTCGTTTAATGTACCGTTTTG 2 21 1 TCGTTTAATG 0.807363 -252 CGGCACACTTGCTTTTTCTGCTAATAGTTT 2 204 1 GCTTTTTCTG 0.858112 -69 AGCCGTAGCGGCTTCTTTGTGCTGACC 2 256 0 GCGGCTTCTT 0.971539 -17 ACGCACGCAAGCGGTTAATTTTGTTAGAGA 3 62 0 GCGGTTAATT 0.980585 -155 CGTTATGTTTGCCGTTTCTGTATGTCATTT 3 183 1 GCCGTTTCTG 0.975118 -34 ********** Masking position 9 Map Score: 6.07745 Number of sites scoring better than the average of aligned sites = 1613 Number in coding regions = 1491 Number in noncoding regions = 122 Number of orfs with sites within 600 bp upstream = 128 Fraction of orfs with sites within 600 bp upstream = 0.0205589 Motif number 4 TTATAGATAAAAATGATAACTATTAAAAT 1 7 1 ATAAAATGAA 0.950926 -294 AATGATAACTATTAAAATGTCAGATCAAATAAA 1 22 1 ATTAAATGAG 0.902595 -279 TCGTGAATTACTTGAATTGAAAAAAGCATTGAA 1 93 0 CTTAATTGAA 0.839457 -208 TTAAATTGATATTTAGATGAAAAACAAAACGGT 2 42 0 ATTAGATGAA 0.949468 -231 TAAATATCAATTTAAATTGAGAACTATTTGCAT 2 60 1 TTTAATTGAA 0.926415 -213 GCCTAATTTTATTTAAATGCAAATAGTTCTCAA 2 76 0 ATTAAATGAA 0.978693 -197 AAATGTTTAAATTGCATTGAAAAGCTCCTTATG 2 154 0 ATTCATTGAA 0.688501 -119 GGGTAGCAAGTTTGAAATGTTTAAATTGCATTG 2 168 0 TTTAAATGTA 0.809882 -105 GTGCTGACCATTATAAACGGTAATATCAGCAAA 2 232 0 TTAAAACGAA 0.710944 -41 TTAAATCCTTTTAGGAATGTGAACTTTTCAGTT 3 93 0 TTAGAATGAA 0.735028 -124 CGGAAGCCCGATTAAGATGATAAGTAAAGTGAG 3 152 0 ATTAGATGAA 0.949621 -65 *** ***** ** Masking position 2 Map Score: 5.94411 Number of sites scoring better than the average of aligned sites = 246 Number in coding regions = 168 Number in noncoding regions = 78 Number of orfs with sites within 600 bp upstream = 90 Fraction of orfs with sites within 600 bp upstream = 0.0144555 Motif number 5 GATCAAATAAATAAGGCGGAATAATTGTTCC 1 44 1 AAAGGCGGAA 0.987826 -257 AAATAATAGGAAAAGGCGGAACAATTATTCC 1 61 0 AAAGGCGGAA 0.987832 -240 AAACTGTATAAACAAGCTGAAATGGAAAGCG 1 142 0 ACAAGCTGAA 0.97512 -159 AGAAACCGACAAAAAACTGTATAAACAAGCT 1 155 0 AAAAACTGTA 0.851636 -146 ATGCGCTCTCAACAAGCAGAAACCGACAAAA 1 172 0 ACAAGCAGAA 0.939604 -129 TAGATGAAAAACAAAACGGTACATTAAACGA 2 31 0 AAAAACGGTA 0.922213 -242 ATAGCCACAATTCAGGCTGAACTGAATAATT 2 114 1 TCAGGCTGAA 0.730319 -159 GAAACGGCAAACATAACGGAAGCCCGATTAA 3 170 0 AATAACGGAA 0.853018 -47 * ********* Masking position 11 Map Score: 5.79287 Number of sites scoring better than the average of aligned sites = 916 Number in coding regions = 833 Number in noncoding regions = 83 Number of orfs with sites within 600 bp upstream = 99 Fraction of orfs with sites within 600 bp upstream = 0.0159011 Motif number 6 GATCAAATAAATAAGGCGGAATAATTGTTC 1 44 1 ATAAGGCGGA 0.975441 -257 AAATAATAGGAAAAGGCGGAACAATTATTC 1 62 0 AAAAGGCGGA 0.982733 -239 AAACTGTATAAACAAGCTGAAATGGAAAGC 1 143 0 AACAAGCTGA 0.97354 -158 ATGCGCTCTCAACAAGCAGAAACCGACAAA 1 173 0 AACAAGCAGA 0.954266 -128 ATAGCCACAATTCAGGCTGAACTGAATAAT 2 114 1 TTCAGGCTGA 0.946192 -159 ********** Masking position 4 Map Score: 2.55293 Number of sites scoring better than the average of aligned sites = 464 Number in coding regions = 422 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714 Motif number 7 ********** No masking Map Score: -1.16286e-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: -1.16286e-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: -1.16286e-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