AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i134_Transmembrane_Transport_8_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 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 TCCTATTATTTCTTCAATGCTTTTTTCAATT 1 81 1 TTTCAATGCT 0.905504 -220 TTCAATGCTTTTTTCAATTCAAGTAATTCAC 1 93 1 TTTCAATTCA 0.934515 -208 CGACGTAACTGTTTCAATTCGCTTTCCATTT 1 123 1 GTTCAATTCG 0.89727 -178 GGTTTCTGCTTGTTGAGAGCGCATCATCACT 1 179 1 TTTGAGAGCG 0.94726 -122 GAGTGCAAATTATTCAGTTCAGCCTGAATTG 2 121 0 TTTCAGTTCA 0.974901 -152 AAGCTCCTTATGTTGAGTGCAAATTATTCAG 2 135 0 TTTGAGTGCA 0.988844 -138 CATAAGGAGCTTTTCAATGCAATTTAAACAT 2 154 1 TTTCAATGCA 0.974901 -119 TCCAAATATTGCGTGCGTGTATTTGAA 3 7 1 TTTGCGTGCG 0.988831 -210 AAAATTAACCGCTTGCGTGCGTGAACTGAAA 3 70 1 GTTGCGTGCG 0.971412 -147 GAATGTGAACTTTTCAGTTCACGCACGCAAG 3 81 0 TTTCAGTTCA 0.974901 -136 CTGTATGTCATTTTGCGTGCGACAGAA 3 200 1 TTTGCGTGCG 0.988831 -17 * ********* Masking position 4 Map Score: 18.1101 Number of sites scoring better than the average of aligned sites = 223 Number in coding regions = 202 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 2 GAAAAAGCAAGTGTGCCGCAAGGGTAGCAAG 2 191 0 GTGTGCCCAA 0.984849 -82 TCCAAATATTGCGTGCGTGTATTTGAAAAAA 3 11 1 GCGTGCGGTA 0.994356 -206 AATTGTAAACGCGTGCGTGAATTTTTTCAAA 3 32 0 GCGTGCGGAA 0.998602 -185 TTAACCGCTTGCGTGCGTGAACTGAAAAGTT 3 74 1 GCGTGCGGAA 0.998602 -143 GATAAGTAAAGTGAGCCAGAATGGCGGTCTG 3 136 0 GTGAGCCGAA 0.968755 -81 ATGTCATTTTGCGTGCGACAGAA 3 204 1 GCGTGCGCAG 0.99272 -13 ******* *** Masking position 6 Map Score: 10.8953 Number of sites scoring better than the average of aligned sites = 25 Number in coding regions = 22 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 3 TATTCCGCCTTATTTATTTGATCTGACATTTTAATAGTTAT 1 26 0 TTTTTTAATT 0.869158 -275 GGAATAATTGTTCCGCCTTTTCCTATTATTTCTTCAATGCT 1 61 1 TCCTTTTATT 0.960804 -240 TCGCTTTCCATTTCAGCTTGTTTATACAGTTTTTTGTCGGT 1 141 1 TCCTTAAATT 0.944774 -160 GAGCGCATCATCACTACTTCTTGTCACAATTGCAAAACTTC 1 195 1 TCCTTTAATT 0.981863 -106 GCAGAATTGACCGCACTTTGTGTTGAAACTTAATCTCTCAA 1 237 1 CCTTTTAATT 0.940676 -64 TGCAAATAGTTCTCAATTTAAATTGATATTTAGATGAAAAA 2 51 0 TCTTTTAATT 0.987019 -222 GCCTGAATTGTGGCTATTCTATGCCTAATTTTATTTAAATG 2 90 0 TCTTCCTATT 0.866859 -183 TGCGGCACACTTGCTTTTTCTGCTAATAGTTTTGCTGATAT 2 202 1 TCTTTTAATT 0.987019 -71 ACGCACGCGTTTACAATTCTCTAACAAAATTAACCGCTTGC 3 45 1 TCTTCAAATT 0.944774 -172 CCGTTATGTTTGCCGTTTCTGTATGTCATTTTGCGTGCGAC 3 182 1 TCTTCTTATT 0.960804 -35 * * *** * * * ** Masking position 8 Map Score: 6.20678 Number of sites scoring better than the average of aligned sites = 152 Number in coding regions = 109 Number in noncoding regions = 43 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714 Motif number 4 AGGCGGAATAATTGTTCCGCCTTTTCCTAT 1 57 1 ATTGTTCCGC 0.911106 -244 AACAAGCTGAAATGGAAAGCGAATTGAAAC 1 133 0 AATGGAAAGC 0.939049 -168 ACTTCCGCAGAATTGACCGCACTTTGTGTT 1 231 1 AATTGACCGC 0.979171 -70 GTATCTGGATAATAAACCGCTTGAGAGATT 1 268 0 AATAAACCGC 0.944303 -33 TGGTTCGTTTAATGTACCGTTTTGTTTTTC 2 27 1 AATGTACCGT 0.895061 -246 TTTAAATTGCATTGAAAAGCTCCTTATGTT 2 152 0 ATTGAAAAGC 0.781982 -121 TACCGTTTATAATGGTCAGCACAAAGAAGC 2 243 1 AATGGTCAGC 0.961019 -30 TCTCTAACAAAATTAACCGCTTGCGTGCGT 3 62 1 AATTAACCGC 0.967633 -155 ********** Masking position 1 Map Score: 5.65194 Number of sites scoring better than the average of aligned sites = 624 Number in coding regions = 452 Number in noncoding regions = 172 Number of orfs with sites within 600 bp upstream = 128 Fraction of orfs with sites within 600 bp upstream = 0.0205589 Motif number 5 TTATAGATAAAAATGATAACTATTA 1 6 1 GATAAAAATG 0.906602 -295 AAATGATAACTATTAAAATGTCAGATCAAA 1 21 1 TATTAAAATG 0.963454 -280 TTTAAATTGATATTTAGATGAAAAACAAAA 2 46 0 TATTTAGATG 0.952386 -227 TGCCTAATTTTATTTAAATGCAAATAGTTC 2 80 0 TATTTAAATG 0.894791 -193 ACGGAAGCCCGATTAAGATGATAAGTAAAG 3 156 0 GATTAAGATG 0.971635 -61 ********** Masking position 6 Map Score: 3.3673 Number of sites scoring better than the average of aligned sites = 92 Number in coding regions = 81 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 6 TGCTTTTTTCAATTCAAGTAATTCACGACGTAAC 1 98 1 ATTAAGATTC 0.967541 -203 ATGGAAAGCGAATTGAAACAGTTACGTCGTGAAT 1 118 0 ATTAAAATTA 0.926284 -183 TTCTTGTCACAATTGCAAAACTTCCGCAGAATTG 1 212 1 ATTCAAATTC 0.967541 -89 ATTTTATTTAAATGCAAATAGTTCTCAATTTAAA 2 70 0 ATGAAAATTC 0.984891 -203 CCTTATGTTGAGTGCAAATTATTCAGTTCAGCCT 2 127 0 ATGAAATTTC 0.931193 -146 TTTTCAATGCAATTTAAACATTTCAAACTTGCTA 2 164 1 ATTAAAATTC 0.989783 -109 GCGTGCGTGTATTTGAAAAAATTCACGCACGCGT 3 21 1 ATTAAAATTC 0.989783 -196 * ** *** * *** Masking position 7 Map Score: 6.52761 Number of sites scoring better than the average of aligned sites = 47 Number in coding regions = 30 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 7 AGAAGTAGTGATGATGCGCTCTCAACAAGC 1 186 0 ATGATGCGCT 0.944087 -115 TATCTGGATAATAAACCGCTTGAGAGATTA 1 267 0 ATAAACCGCT 0.986654 -34 TGCACTCAACATAAGGAGCTTTTCAATGCA 2 145 1 ATAAGGAGCT 0.937675 -128 GTCAGCACAAAGAAGCCGCTACGGCT 2 257 1 AGAAGCCGCT 0.980501 -16 CTCTAACAAAATTAACCGCTTGCGTGCGTG 3 63 1 ATTAACCGCT 0.966954 -154 ********** Masking position 4 Map Score: 1.14112 Number of sites scoring better than the average of aligned sites = 102 Number in coding regions = 87 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 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 Motif number 10 ********** 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