AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i134_Transmembrane_Transport_8_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 HI0097 272 iron(III) ABC transporter, periplasmic-binding protein (hitA) #2 HI0098 216 iron(III) ABC transporter, permease protein (hitB) Motif number 1 CTTGCTACCCTTGCGGCACACTTGCTTTTTC 1 191 1 TTGGGCACAC 0.990365 -82 TTTTTTCAAATACACGCACGCAATATTTGGA 2 11 0 TACCGCACGC 0.996501 -206 TTTGAAAAAATTCACGCACGCGTTTACAATT 2 32 1 TTCCGCACGC 0.999134 -185 AACTTTTCAGTTCACGCACGCAAGCGGTTAA 2 74 0 TTCCGCACGC 0.999134 -143 CAGACCGCCATTCTGGCTCACTTTACTTATC 2 136 1 TTCGGCTCAC 0.98033 -81 TTCTGTCGCACGCAAAATGACAT 2 204 0 CTGCGCACGC 0.995477 -13 *** ******* Masking position 6 Map Score: 13.8319 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 2 AAATTGATATTTAGATGAAAAACAAAACGGT 1 42 0 TTAGTGAAAA 0.976644 -231 CTAATTTTATTTAAATGCAAATAGTTCTCAA 1 76 0 TTAATGCAAA 0.976644 -197 CAATTCAGGCTGAACTGAATAATTTGCACTC 1 121 1 TGAATGAATA 0.923896 -152 GCTCCTTATGTTGAGTGCAAATTATTCAGTT 1 133 0 TTGATGCAAA 0.938652 -140 ATGTTTAAATTGCATTGAAAAGCTCCTTATG 1 154 0 TGCATGAAAA 0.978534 -119 AGCAAAACTATTAGCAGAAAAAGCAAGTGTG 1 207 0 TTAGAGAAAA 0.89209 -66 CTTGCGTGCGTGAACTGAAAAGTTCACATTC 2 81 1 TGAATGAAAA 0.98545 -136 AATGGCGGTCTGCGAGGCAAAGTTAAATCCT 2 117 0 TGCGGGCAAA 0.930915 -100 **** ****** Masking position 9 Map Score: 7.28485 Number of sites scoring better than the average of aligned sites = 324 Number in coding regions = 262 Number in noncoding regions = 62 Number of orfs with sites within 600 bp upstream = 46 Fraction of orfs with sites within 600 bp upstream = 0.00738837 Motif number 3 GTTTAATGTACCGTTTTGTTTTTCATCTAA 1 33 1 CCGTTTTGTT 0.981306 -240 ATTCTATGCCTAATTTTATTTAAATGCAAA 1 86 0 TAATTTTATT 0.757023 -187 ATTGAAAAGCTCCTTATGTTGAGTGCAAAT 1 142 0 TCCTTATGTT 0.926788 -131 TTTCTGCTAATAGTTTTGCTGATATTACCG 1 218 1 TAGTTTTGCT 0.962143 -55 CGCAAGCGGTTAATTTTGTTAGAGAATTGT 2 57 0 TAATTTTGTT 0.960032 -160 AATCGGGCTTCCGTTATGTTTGCCGTTTCT 2 172 1 CCGTTATGTT 0.958045 -45 TTTCTGTATGTCATTTTGCGTGCGACAGAA 2 197 1 TCATTTTGCG 0.911283 -20 ********** Masking position 5 Map Score: 3.30883 Number of sites scoring better than the average of aligned sites = 404 Number in coding regions = 347 Number in noncoding regions = 57 Number of orfs with sites within 600 bp upstream = 46 Fraction of orfs with sites within 600 bp upstream = 0.00738837 Motif number 4 TTTTGTTTTTCATCTAAATATCAATTTAAA 1 46 1 CATCTAAATA 0.959048 -227 AATAGTTCTCAATTTAAATTGATATTTAGA 1 58 0 AATTTAAATT 0.495397 -215 GAACTATTTGCATTTAAATAAAATTAGGCA 1 80 1 CATTTAAATA 0.831077 -193 TTTTCAATGCAATTTAAACATTTCAAACTT 1 164 1 AATTTAAACA 0.861339 -109 CTGCGAGGCAAAGTTAAATCCTTTTAGGAA 2 109 0 AAGTTAAATC 0.867914 -108 CTTTACTTATCATCTTAATCGGGCTTCCGT 2 156 1 CATCTTAATC 0.891618 -61 ********** Masking position 5 Map Score: 1.41683 Number of sites scoring better than the average of aligned sites = 297 Number in coding regions = 250 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 5 TGGTCAGCACAAAGAAGCCGCTACGGCT 1 255 1 AAAGAAGCCG 0.946719 -18 GAAAAAATTCACGCACGCGTTTACAATTCT 2 35 1 ACGCACGCGT 0.813477 -182 CAGTTCACGCACGCAAGCGGTTAATTTTGT 2 68 0 ACGCAAGCGG 0.98273 -149 GGCAAACATAACGGAAGCCCGATTAAGATG 2 166 0 ACGGAAGCCC 0.987306 -51 AAAATGACATACAGAAACGGCAAACATAAC 2 184 0 ACAGAAACGG 0.962799 -33 ********** Masking position 5 Map Score: 1.43112 Number of sites scoring better than the average of aligned sites = 133 Number in coding regions = 116 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 6 ATCAATTTAAATTGAGAACTATTTGCATTT 1 65 1 ATTGAGAACT 0.959782 -208 TGTGCTGACCATTATAAACGGTAATATCAG 1 236 0 ATTATAAACG 0.938148 -37 TTGTTAGAGAATTGTAAACGCGTGCGTGAA 2 42 0 ATTGTAAACG 0.98364 -175 TCCTTTTAGGAATGTGAACTTTTCAGTTCA 2 91 0 AATGTGAACT 0.959727 -126 ********** Masking position 7 Map Score: 0.246648 Number of sites scoring better than the average of aligned sites = 34 Number in coding regions = 29 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 7 ********** No masking Map Score: 4.64285e-13 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: 4.64285e-13 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: 4.64285e-13 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