AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i128_Transmembrane_Transport_2_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 HI0620 300 28 kDa outer membrane protein (hlpA) #2 HI0621 175 ABC transporter, ATP-binding protein Motif number 1 CAACTAAAGTGACTAGCGTAAGAGTAACGCCAT 1 60 0 GACTACTAAA 0.961864 -241 TGCCATTGCAGAATAACCAACTAAAGTGACTAG 1 77 0 GAATACAACA 0.975818 -224 AACTACGGGCGTATATCGCAATATGCCTTATGT 1 149 1 GTATACCAAA 0.948241 -152 TAATCATAACGAATAGCACAATAATAATGGTTG 1 193 0 GAATACCAAA 0.99031 -108 TATTCGTTATGATTAGCCAAAAACTCGGCGATA 1 211 1 GATTACAAAA 0.974012 -90 CTCGGCGATACACTGGCTAAAAAAGTGGATCAT 1 234 1 CACTGCAAAA 0.905724 -67 TAGACATCTAGAATACCAAAACAGATTTAAAAA 2 132 1 GAATACAAAA 0.993461 -44 GATTTAAAAACAATAAATAAAAAGGGCTTAT 2 155 1 CAATAAAAAA 0.857194 -21 ***** * *** * Masking position 10 Map Score: 5.60583 Number of sites scoring better than the average of aligned sites = 131 Number in coding regions = 100 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 2 TGTTCGTAAATTCTATTTGTCAGAAGCTCTAC 1 16 1 TTCTTTGTCA 0.982905 -285 AGCACAATAATAATGGTTGCCACCCAAGTTAC 1 180 0 TAATTTGCCA 0.954655 -121 CTCTTACCTTTTATACATGTCAAATTGACAAA 2 12 1 TTATATGTCA 0.973797 -164 ATTAAATAGATAATTTTTGTCAATTTGACATG 2 27 0 TAATTTGTCA 0.973778 -149 TAGTTATGACTTATATTTGCTAATTGCTTGGA 2 58 0 TTATTTGCTA 0.957383 -118 ATATGTCAGATTATCTTTTTTAGACAGATTAG 2 87 0 TTATTTTTTA 0.900772 -89 TGTTTTGGTATTCTAGATGTCTAGATTGCTAT 2 123 0 TTCTATGTCT 0.790482 -53 CCCTTTTTATTTATTGTTTTTAAATCTGTTTT 2 149 0 TTATTTTTTA 0.900789 -27 **** ****** Masking position 8 Map Score: 5.67137 Number of sites scoring better than the average of aligned sites = 217 Number in coding regions = 167 Number in noncoding regions = 50 Number of orfs with sites within 600 bp upstream = 47 Fraction of orfs with sites within 600 bp upstream = 0.00754899 Motif number 3 CAGAAGCTCTACCTACGCTAATTAATGGCGTTACT 1 36 1 ACAGCTATAA 0.994186 -265 CGTAGTTGATAGCGAGGCTACCTAAACCACCGCCC 1 121 0 ACAGCTATAA 0.994186 -180 AATGGTTGCCACCCAAGTTACATAAGGCATATTGC 1 166 0 ACAGTTATAA 0.979014 -135 ACTCGGCGATACACTGGCTAAAAAAGTGGATCATC 1 233 1 AATGCTAAAA 0.881486 -68 AAAAAAGTGGATCATCGTTAATTAAACGCAACTCT 1 252 1 ACTGTTATAA 0.972846 -49 AAATTGACAAAAATTATCTATTTAATCCAAGCAAT 2 33 1 AATTCTATAA 0.907178 -143 TATAAGTCATAACTAATCTGTCTAAAAAAGATAAT 2 75 1 ACATCTGTAA 0.934871 -101 * * * **** *** Masking position 14 Map Score: 4.03317 Number of sites scoring better than the average of aligned sites = 197 Number in coding regions = 165 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 4 CTAATTAATGGCGTTACTCTTACGCTAGTC 1 53 1 GCGTTACTCT 0.979903 -248 AAGGCATATTGCGATATACGCCCGTAGTTG 1 148 0 GCGATATACG 0.988498 -153 CATTATTATTGTGCTATTCGTTATGATTAG 1 197 1 GTGCTATTCG 0.947886 -104 CAAAAACTCGGCGATACACTGGCTAAAAAA 1 228 1 GCGATACACT 0.988502 -73 ********** Masking position 5 Map Score: 0.349886 Number of sites scoring better than the average of aligned sites = 59 Number in coding regions = 52 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 5 TTTTGGCTAATCATAACGAATAGCACAATA 1 203 0 TCATAACGAA 0.982765 -98 TAAACGCAACTCTTAACTTAAACAGGAAGG 1 274 1 TCTTAACTTA 0.956179 -27 CAAATATAAGTCATAACTAATCTGTCTAAA 2 71 1 TCATAACTAA 0.98545 -105 ********** Masking position 5 Map Score: 0.206286 Number of sites scoring better than the average of aligned sites = 17 Number in coding regions = 15 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 6 AGCGTAGGTAGAGCTTCTGACAAATAGAATT 1 24 0 GAGTTCTGAC 0.982642 -277 AATTAATGGCGTTACTCTTACGCTAGTCACT 1 55 1 GTTCTCTTAC 0.912203 -246 ACTTTAGTTGGTTATTCTGCAATGGCAGGAA 1 83 1 GTTTTCTGCA 0.943216 -218 CCGCCCCCTTGTGTTCCTGCCATTGCAGAAT 1 96 0 GTGTCCTGCC 0.98663 -205 AGGATTTCCTTCCTGTTTAAGTT 1 288 0 GATTCCTTCC 0.967823 -13 GTCTAAAAAAGATAATCTGACATATTGACAT 2 94 1 GATATCTGAC 0.954029 -82 *** ******* Masking position 8 Map Score: 1.01817 Number of sites scoring better than the average of aligned sites = 181 Number in coding regions = 159 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 7 ********** No masking Map Score: -1.68098e-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: -1.68098e-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: -1.68098e-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