AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i129_Transmembrane_Transport_3_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 HI1692 173 molybdenum ABC transporter, permease protein (modB) #2 HI1693 137 molybdenum ABC transporter, periplasmic-binding protein (modA) Motif number 1 GAGGTAAGATGCTCTATAATAACAAAAGGGC 1 48 0 GCTCTATATA 0.899653 -126 TTAAAGAGAGGCTATTTAGATAAGGATTCAT 1 113 1 GCTATTTAAT 0.932909 -61 AAGCCTAAGCGTTATATATTTTACTAAATAA 2 40 1 GTTATATATT 0.987525 -98 CAAAAGAAAAATTATTTAGTAAAATATATAA 2 51 0 ATTATTTATA 0.887346 -87 TTTTTCTTTTGCTATATGATTGTTATTTATT 2 71 1 GCTATATGTT 0.953723 -67 CTATATGATTGTTATTTATTTCAATATATAA 2 82 1 GTTATTTATT 0.987525 -56 TATTTACTTGATTATATATTGAAATAAATAA 2 93 0 ATTATATATG 0.868774 -45 ACGATTAAACGTTATTTACTTGATTATATAT 2 105 0 GTTATTTATT 0.987525 -33 ******** ** Masking position 5 Map Score: 8.44576 Number of sites scoring better than the average of aligned sites = 189 Number in coding regions = 147 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 2 TTTGCTGTTCCTAAGTAATCCTAAG 2 6 1 TGTTCCTAAG 0.982132 -132 TGTTCCTAAGTAATCCTAAGTGGTAAGCCT 2 16 1 TAATCCTAAG 0.995794 -122 TCCTAAGTGGTAAGCCTAAGCGTTATATAT 2 29 1 TAAGCCTAAG 0.992851 -109 AAATAACGTTTAATCGTAGGAGATGATTT 2 119 1 TAATCGTAGG 0.981064 -19 ********** Masking position 7 Map Score: 3.82552 Number of sites scoring better than the average of aligned sites = 21 Number in coding regions = 18 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 3 ATATTTCTGCCCTTTTGTTATTATAGAGCA 1 40 1 CCTTTTGTTA 0.968388 -134 GATAAGGATTCATTTTGCTTACCCAATTTT 1 131 1 CATTTTGCTT 0.978266 -43 CAATTTTTTTCATTTTTCAATCTGACGCCA 1 154 1 CATTTTTCAA 0.918889 -20 AAGCGTTATATATTTTACTAAATAATTTTT 2 46 1 TATTTTACTA 0.942855 -92 AAATAATTTTTCTTTTGCTATATGATTGTT 2 65 1 TCTTTTGCTA 0.986101 -73 ********** Masking position 5 Map Score: 2.34846 Number of sites scoring better than the average of aligned sites = 405 Number in coding regions = 357 Number in noncoding regions = 48 Number of orfs with sites within 600 bp upstream = 53 Fraction of orfs with sites within 600 bp upstream = 0.00851269 Motif number 4 AATAGTCATGAAGGGCGGATATTTCTGCCCT 1 22 1 AAGGGCGGTA 0.99654 -152 ATAATAACAAAAGGGCAGAAATATCCGCCCT 1 33 0 AAGGGCAGAA 0.986392 -141 TCCCACATTGATGAGAGGTAAGATGCTCTAT 1 62 0 ATGAGAGGAA 0.979439 -112 AAGGGATTTAAAGAGAGGCTATTTAGATAAG 1 106 1 AAGAGAGGTA 0.991759 -68 ******** ** Masking position 1 Map Score: 2.0242 Number of sites scoring better than the average of aligned sites = 74 Number in coding regions = 51 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 5 ********** No masking Map Score: 2.58227e-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 6 ********** No masking Map Score: 2.58227e-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 7 ********** No masking Map Score: 2.58227e-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