AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i101_Iron_Transport_hinf_reg_100.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 Motif number 1 TTGCAATTGGTTCTTTACTTGGTGCAGGCA 1 65 1 TTCTTTACTT 0.792437 -236 GGTGCAGGCATTTCTTTGTTAAAAATTCTT 1 85 1 TTTCTTTGTT 0.989166 -216 ATTGTTCCCATTTTTTTATTACTTACTGAT 1 223 1 TTTTTTTATT 0.884286 -78 ATAATGATATTTTCTTACTTAAAATAAGGA 2 42 1 TTTCTTACTT 0.975704 -26 CGCACATCCTTATTTTAAGTAAGAA 2 53 0 ATCCTTATTT 0.77986 -15 AAACGGGCGTTTTCTTTTTTGTTTAAATTC 3 28 1 TTTCTTTTTT 0.977879 -200 TTTTGTTTAAATTCTTAGTTTTTCTGGTTC 3 44 1 ATTCTTAGTT 0.950159 -184 GATCTGATTTTTTCTTAGTTTTCTTTCCCT 3 95 1 TTTCTTAGTT 0.987152 -133 GCATTGCCCCTTTTTTTATTCTTAGGGAAA 3 118 0 TTTTTTTATT 0.884286 -110 CAAATTCCTATTTCTTTTGTTTTCTTTGTT 3 205 1 TTTCTTTTGT 0.892761 -23 TTTCTTTTGTTTTCTTTGTTTTG 3 215 1 TTTCTTTGTT 0.989166 -13 ********** Masking position 5 Map Score: 16.7648 Number of sites scoring better than the average of aligned sites = 347 Number in coding regions = 245 Number in noncoding regions = 102 Number of orfs with sites within 600 bp upstream = 86 Fraction of orfs with sites within 600 bp upstream = 0.013813 Motif number 2 TTGGTTCTTTACTTGGTGCAGGCATTTCTTTGT 1 71 1 ACTGGGCAGC 0.968341 -230 GTAATAAAAAAATGGGAACAATCCCTAGCAACA 1 212 0 AATGGACATC 0.973895 -89 GTGGCAGTTCAATCGGTGCAATCGTGCGAGCCA 1 257 0 AATGGGCATC 0.989625 -44 TTGAACTGCCACTCGGTATTCTGACTTCTGCTT 1 278 1 ACTGGATTTG 0.892018 -23 ACGCCATTTAAACGGGCGTTTTCTTTTTTGTTT 3 19 1 AACGGGTTTC 0.961705 -209 TAAGAATAAAAAAAGGGGCAATGCACCGCCAAA 3 124 1 AAAGGGCATG 0.959143 -104 AATTATTGAAAACAGGGGCTTTGGCGGTGCATT 3 143 0 AACGGGCTTG 0.98464 -85 AAACAAAAGAAATAGGAATTTGGCGAAATTTTA 3 194 0 AATGGATTGG 0.892018 -34 *** ** *** ** Masking position 1 Map Score: 4.03501 Number of sites scoring better than the average of aligned sites = 225 Number in coding regions = 199 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 3 TGCAATCCCAGAAAGCACCAGCACTAAAATA 1 39 0 GAAAGACCAG 0.983582 -262 GTAATTGAGTGAAAGGATCCGCAAGAATTTT 1 106 0 GAAAGATCCG 0.97985 -195 TTTTAAGTAAGAAAATATCATTATACACATA 2 35 0 GAAAAATCAT 0.933019 -33 AAACAAAAAAGAAAACGCCCGTTTAAATGGC 3 21 0 GAAAAGCCCG 0.956343 -207 AAATGAACCAGAAAAACTAAGAATTTAAACA 3 47 0 GAAAACTAAG 0.914616 -181 AGAAAACTAAGAAAAAATCAGATCTTTGGTT 3 88 0 GAAAAATCAG 0.990774 -140 CAAAACAAAGAAAACAAAAGAAATAGGAAT 3 208 0 GAAAAAAAAG 0.899033 -20 ***** ***** Masking position 4 Map Score: 5.07439 Number of sites scoring better than the average of aligned sites = 170 Number in coding regions = 156 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 4 TGTTAAAAATTCTTGCGGATCCTTTCACTC 1 101 1 TCTTGCGGAT 0.94791 -200 TTGAATTAAATCTTGTTGATTAATAGCCGT 1 169 0 TCTTGTTGAT 0.988971 -132 TTGATCCCGATGTTGTTGCTAGGGATTGTT 1 199 1 TGTTGTTGCT 0.937769 -102 TCTTAGTTTTTCTGGTTCATTTTGACTAAA 3 56 1 TCTGGTTCAT 0.964903 -172 AAATCAGATCTTTGGTTGATTTAGTCAAAA 3 75 0 TTTGGTTGAT 0.960575 -153 ********** Masking position 3 Map Score: 0.798233 Number of sites scoring better than the average of aligned sites = 143 Number in coding regions = 129 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 5 TTTCTGGGATTGCAATTGGTTCTTTACTTGG 1 56 1 TGCAATTGTT 0.942313 -245 TGCGGATCCTTTCACTCAATTACCTTCAATC 1 114 1 TTCACTCATT 0.911687 -187 CTCAATTACCTTCAATCACTTTTTGGCTACT 1 128 1 TTCAATCATT 0.965792 -173 CAAGATTTAATTCAATTGATCCCGATGTTGT 1 184 1 TTCAATTGTC 0.968733 -117 GTTCAATCGGTGCAATCGTGCGAGCCAGCGT 1 253 0 TGCAATCGGC 0.954876 -48 AGCCCCTGTTTTCAATAATTCCCGCCCACTT 3 156 1 TTCAATAATC 0.917856 -72 ******** ** Masking position 6 Map Score: 0.0324129 Number of sites scoring better than the average of aligned sites = 182 Number in coding regions = 136 Number in noncoding regions = 46 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 6 ATTGAAGGTAATTGAGTGAAAGGATCCGCAA 1 113 0 ATTGAGGAAA 0.684554 -188 TCAGGCTACCAAGTAGCCAAAAAGTGATTGA 1 139 0 AAGTAGCAAA 0.979921 -162 GCGTATCAGTAAGTAATAAAAAAATGGGAAC 1 226 0 AAGTAAAAAA 0.893543 -75 TCCTTATTTTAAGTAAGAAAATATCATTATA 2 41 0 AAGTAAAAAA 0.893544 -27 AAAACTAAGAATTTAAACAAAAAAGAAAACG 3 35 0 ATTTAACAAA 0.95097 -193 TCTTTGGTTGATTTAGTCAAAATGAACCAGA 3 66 0 ATTTAGCAAA 0.968365 -162 CGTCCGTAAAATTTCGCCAAATTCCTATTTC 3 188 1 ATTTCGCAAA 0.89097 -40 CAAAACAAAGAAAACAAAAGAAATAGGA 3 210 0 AAGAAACAAA 0.864642 -18 ****** **** Masking position 9 Map Score: 3.05726 Number of sites scoring better than the average of aligned sites = 422 Number in coding regions = 346 Number in noncoding regions = 76 Number of orfs with sites within 600 bp upstream = 62 Fraction of orfs with sites within 600 bp upstream = 0.00995824 Motif number 7 ********** No masking Map Score: 1.21035e-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: 1.21035e-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: 1.21035e-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