AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/alignace/lib/ORF_hinf.txt -z/skink1/amcguire/genomes/hinf.fna -imalT_hinf_opreg_300.orf -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 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) #4 HI1354 300 glutaminyl-tRNA synthetase (glnS) #5 HI1355 65 conserved hypothetical protein #6 HI1356 61 4-alpha-glucanotransferase (malQ) Motif number 1 CGCCTTATTTATTTGATCTGACATTTTAATAGTTATC 1 25 0 ATTTATGATT 0.897683 -276 TTCAATGCTTTTTTCAATTCAAGTAATTCACGACGTA 1 93 1 TTTTATCATT 0.973965 -208 TTCAATTCGCTTTCCATTTCAGCTTGTTTATACAGTT 1 135 1 TTTCATCATT 0.845134 -166 GGTTTCTGCTTGTTGAGAGCGCATCATCACTACTTCT 1 179 1 TGTTAGCGTT 0.829596 -122 ACTTCCGCAGAATTGACCGCACTTTGTGTTGAAACTT 1 231 1 AATTAGCATT 0.874666 -70 ATAGTTCTCAATTTAAATTGATATTTAGATGAAAAAC 2 50 0 ATTTATGATA 0.622126 -223 GCCTAATTTTATTTAAATGCAAATAGTTCTCAATTTA 2 72 0 ATTTAGCATT 0.983674 -201 AAGCTCCTTATGTTGAGTGCAAATTATTCAGTTCAGC 2 129 0 TGTTAGCATT 0.970908 -144 CATAAGGAGCTTTTCAATGCAATTTAAACATTTCAAA 2 154 1 TTTTAGCATA 0.951977 -119 CGATACCGCTTTTTAATGTGATGTAGTGGAGGGAGGC 4 15 0 TTTTATGATT 0.938957 -286 GCCAGCTCCCATTTGATAGGAAATTTTGCTGTTTTTG 4 65 0 ATTTAGGATT 0.961202 -236 TCGTGGCGGTTTTTTATGGCAAGTTTTTACAATCTTT 4 171 1 TTTTAGCATT 0.990623 -130 ATCACGTTTGTTTTGACCGCACTTGGTTGATTAAAA 5 10 0 TTTTAGCATT 0.990623 -56 ACAAACGTGATTTTGACCGCACTTTTTATTTGTATCA 5 36 1 TTTTAGCATT 0.990623 -30 **** * *** * * Masking position 6 Map Score: 17.8916 Number of sites scoring better than the average of aligned sites = 652 Number in coding regions = 454 Number in noncoding regions = 198 Number of orfs with sites within 600 bp upstream = 155 Fraction of orfs with sites within 600 bp upstream = 0.0248956 Motif number 2 GTCAATTCTGCGGAAGTTTTGCAATTGTGA 1 218 0 CGGAAGTTTT 0.80376 -83 CAGAATTGACCGCACTTTGTGTTGAAACTT 1 238 1 CGCACTTTGT 0.983648 -63 AACTTAATCTCTCAAGCGGTTTATTATCCA 1 263 1 CTCAAGCGGT 0.759404 -38 TATCCAGATACGAAATTTGTTGGT 1 287 1 CGAAATTTGT 0.796608 -14 AATACACGCACGCAATATTTGGA 3 4 0 CGCAATATTT 0.808572 -213 AAAAAATTCACGCACGCGTTTACAATTCTC 3 36 1 CGCACGCGTT 0.965828 -181 AGTTCACGCACGCAAGCGGTTAATTTTGTT 3 67 0 CGCAAGCGGT 0.975644 -150 AAAAACTTACCGCACTTTGTGCATTTATAC 4 126 1 CGCACTTTGT 0.983648 -175 GGTTTTTTATGGCAAGTTTTTACAATCTTT 4 178 1 GGCAAGTTTT 0.786954 -123 TTGTTTTGACCGCACTTGGTTGATTAAAA 5 10 0 CGCACTTGGT 0.98252 -56 TGATTTTGACCGCACTTTTTATTTGTATCA 5 43 1 CGCACTTTTT 0.969352 -23 ********** Masking position 4 Map Score: 12.7174 Number of sites scoring better than the average of aligned sites = 724 Number in coding regions = 554 Number in noncoding regions = 170 Number of orfs with sites within 600 bp upstream = 128 Fraction of orfs with sites within 600 bp upstream = 0.0205589 Motif number 3 TTGTTCCGCCTTTTCCTATTATTTCTTCAATG 1 68 1 TTTTCTATTT 0.883955 -233 CTTCAATGCTTTTTTCAATTCAAGTAATTCAC 1 92 1 TTTTCAATTA 0.902474 -209 TTCAGCTTGTTTATACAGTTTTTTGTCGGTTT 1 152 1 TTATCAGTTT 0.959715 -149 TCTGCGGAAGTTTTGCAATTGTGACAAGAAGT 1 210 0 TTTTCAATTT 0.963001 -91 AAGCGGTTTATTATCCAGATACGAAATTTGTT 1 276 1 TTATCAGATC 0.792452 -25 TGAGTGCAAATTATTCAGTTCAGCCTGAATTG 2 121 0 TTATCAGTTA 0.894402 -152 CTGCTAATAGTTTTGCTGATATTACCGTTTAT 2 221 1 TTTTCTGATT 0.83634 -52 GTGCGTGAATTTTTTCAAATACACGCACGCAA 3 19 0 TTTTCAAATC 0.806797 -198 TCACGCACGCGTTTACAATTCTCTAACAAAAT 3 43 1 GTTTCAATTT 0.817123 -174 GGAATGTGAACTTTTCAGTTCACGCACGCAAG 3 81 0 CTTTCAGTTA 0.824304 -136 TGATAGGAAATTTTGCTGTTTTTGCCTGCATT 4 57 0 TTTTCTGTTT 0.924381 -244 TATGGCAAGTTTTTACAATCTTTTATTTAAAT 4 185 1 TTTTCAATCT 0.791526 -116 TTCGGCTATTCTATACAAATCTAAGGGAAAAT 4 254 0 CTATCAAATT 0.662231 -47 CTAACAAGAGTTATACAGTTGTGAT 6 47 1 TTATCAGTTT 0.959715 -15 **** ***** * Masking position 4 Map Score: 11.0831 Number of sites scoring better than the average of aligned sites = 556 Number in coding regions = 452 Number in noncoding regions = 104 Number of orfs with sites within 600 bp upstream = 84 Fraction of orfs with sites within 600 bp upstream = 0.0134918 Motif number 4 TCTCAACAAGCAGAAACCGACAAAAAACTG 1 167 0 CAGAAACCGA 0.927972 -134 ACTTCCGCAGAATTGACCGCACTTTGTGTT 1 231 1 AATTGACCGC 0.784902 -70 GTATCTGGATAATAAACCGCTTGAGAGATT 1 268 0 AATAAACCGC 0.980168 -33 AAACTATTAGCAGAAAAAGCAAGTGTGCCG 2 204 0 CAGAAAAAGC 0.746627 -69 GGTCAGCACAAAGAAGCCGCTACGGCT 2 256 1 AAGAAGCCGC 0.959758 -17 TCTCTAACAAAATTAACCGCTTGCGTGCGT 3 62 1 AATTAACCGC 0.939824 -155 AAATGACATACAGAAACGGCAAACATAACG 3 183 0 CAGAAACGGC 0.961926 -34 TGAATGCAGGCAAAAACAGCAAAATTTCCT 4 55 1 CAAAAACAGC 0.910368 -246 AACTTGCCATAAAAAACCGCCACGAAATTA 4 166 0 AAAAAACCGC 0.971824 -135 ********** Masking position 2 Map Score: 7.63142 Number of sites scoring better than the average of aligned sites = 347 Number in coding regions = 269 Number in noncoding regions = 78 Number of orfs with sites within 600 bp upstream = 65 Fraction of orfs with sites within 600 bp upstream = 0.0104401 Motif number 5 ATCAAATAAATAAGGCGGAATAATTGTTCC 1 45 1 TAAGGCGGAA 0.909069 -256 AATAATAGGAAAAGGCGGAACAATTATTCC 1 61 0 AAAGGCGGAA 0.964676 -240 AACTGTATAAACAAGCTGAAATGGAAAGCG 1 142 0 ACAAGCTGAA 0.93883 -159 GAAACCGACAAAAAACTGTATAAACAAGCT 1 155 0 AAAAACTGTA 0.801224 -146 TGCGCTCTCAACAAGCAGAAACCGACAAAA 1 172 0 ACAAGCAGAA 0.823479 -129 AGATGAAAAACAAAACGGTACATTAAACGA 2 31 0 CAAAACGGTA 0.886245 -242 TAGCCACAATTCAGGCTGAACTGAATAATT 2 115 1 TCAGGCTGAA 0.778718 -158 GCTGACCATTATAAACGGTAATATCAGCAA 2 233 0 ATAAACGGTA 0.775672 -40 AAACGGCAAACATAACGGAAGCCCGATTAA 3 170 0 CATAACGGAA 0.626718 -47 CATCACATTAAAAAGCGGTATCGCCGTGAA 4 29 1 AAAAGCGGTA 0.962556 -272 GGGATTATAGCTAAGCTGAAAGTGATGACA 6 18 0 CTAAGCTGAA 0.848886 -44 ********** Masking position 10 Map Score: 5.89812 Number of sites scoring better than the average of aligned sites = 694 Number in coding regions = 603 Number in noncoding regions = 91 Number of orfs with sites within 600 bp upstream = 54 Fraction of orfs with sites within 600 bp upstream = 0.00867331 Motif number 6 TCAATTCAAGTAATTCACGACGTAACTGTT 1 106 1 TAATTCACGA 0.902517 -195 AGAATAGCCACAATTCAGGCTGAACTGAAT 2 111 1 CAATTCAGGC 0.973977 -162 GAATTTTTTCAAATACACGCACGCAATATT 3 15 0 AAATACACGC 0.962818 -202 GTATTTGAAAAAATTCACGCACGCGTTTAC 3 29 1 AAATTCACGC 0.988399 -188 GTGAACTTTTCAGTTCACGCACGCAAGCGG 3 78 0 CAGTTCACGC 0.983433 -139 ********** Masking position 4 Map Score: 2.36799 Number of sites scoring better than the average of aligned sites = 84 Number in coding regions = 77 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 7 ATTTTAATAGTTATCATTTTTATCTATAA 1 7 0 TTCATTTTAT 0.947375 -294 TTTATTTGATCTGACATTTTAATAGTTATCATT 1 22 0 CTCATTTAAT 0.961011 -279 ACCAACAAATTTCGTATCTGGATAATAAACCGC 1 278 0 TTTATCTGAT 0.761059 -23 ACCGTTTTGTTTTTCATCTAAATATCAATTTAA 2 42 1 TTCATCTAAT 0.942882 -231 TTGAGAACTATTTGCATTTAAATAAAATTAGGC 2 76 1 TTCATTTAAT 0.963444 -197 CTCACTTTACTTATCATCTTAATCGGGCTTCCG 3 152 1 TTCATCTAAT 0.942882 -65 TTTTTACAATCTTTTATTTAAATCTAGTATTTC 4 194 1 CTTATTTAAT 0.939232 -107 TTATTTAAATCTAGTATTTCTATGGCAAGAACA 4 207 1 CTTATTTTAT 0.913475 -94 TTTATTTTCCCTTAGATTTGTATAGAATAGCCG 4 251 1 CTGATTTTAT 0.794249 -50 GCCGAATATTTTTTTATTTTAACGAGAGAAA 4 280 1 TTTATTTAAC 0.756834 -21 TTGACCGCACTTTTTATTTGTATCAACT 5 48 1 TTTATTTTAT 0.918625 -18 ** ***** *** Masking position 6 Map Score: 8.00931 Number of sites scoring better than the average of aligned sites = 203 Number in coding regions = 158 Number in noncoding regions = 45 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 8 TGAAACTTAATCTCTCAAGCGGTTTATTAT 1 260 1 TCTCTCAAGC 0.930254 -41 TTTTTCAAATACACGCACGCAATATTTGGA 3 11 0 ACACGCACGC 0.993707 -206 TTGAAAAAATTCACGCACGCGTTTACAATT 3 33 1 TCACGCACGC 0.99807 -184 ACTTTTCAGTTCACGCACGCAAGCGGTTAA 3 74 0 TCACGCACGC 0.99807 -143 TTCTGTCGCACGCAAAATGACAT 3 204 0 TGTCGCACGC 0.9904 -13 ********** Masking position 7 Map Score: 8.75246 Number of sites scoring better than the average of aligned sites = 14 Number in coding regions = 11 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 1 Fraction of orfs with sites within 600 bp upstream = 0.000160617 Motif number 9 ********** No masking Map Score: -3.47212e-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: -3.47212e-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: -3.47212e-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