AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i138_Transmembrane_Transport_11_aquae_reg_300.orf -o138_aquae_300.ace -a/home/amcguire/genomes/ORF_aquae.txt -z/home/amcguire/genomes/aquae.fna -g0.44 -x5 -e 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 = 0.44 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 RAA01426 300 Aquifex_aeolicus #2 RAA01427 33 Aquifex_aeolicus #3 RAA01432 57 Aquifex_aeolicus #4 RAA00823 300 Aquifex_aeolicus Motif number 1 TTGAGGATGGTGTGCTTTACTTTTACTCGCCAA 1 65 1 TGGCTTTACT 0.945366 -236 CTTAAGTTTTTTAACTTCCCGCTTATAGCCTTG 1 111 0 TTACTTCCCT 0.986173 -190 CTCAATTATGTTTACTTTACTCTTAAGTTTTTT 1 132 0 TTACTTTACT 0.990478 -169 TCACAAGTTCTTTATTTTCCTCGACGTTTATCT 1 163 0 TTATTTTCCG 0.907068 -138 AAAAGCTTTCTTTACTTTACCTTTTTCCACGAT 1 231 0 TTACTTTACT 0.990478 -70 TTTCTCTTCTCTTTCCTTTATAATTCTGT 2 7 1 TTTCTTTCCT 0.963166 -27 GCAGTTCGGGTGTACTTTCCCGTCGTTATGTTT 4 62 0 TGACTTTCCT 0.991604 -239 TTGGCAGGGTTGTACTTTACTATACATACGTGG 4 94 0 TGACTTTACT 0.986677 -207 CCAAAGAGGGTTAATTTTCCCGTATTTTTCATA 4 149 1 TTATTTTCCT 0.979081 -152 AGAAAAGCTTTTAATTTCACCGTCCCCGTAGTA 4 188 1 TTATTTCACT 0.926576 -113 ** ******* * Masking position 7 Map Score: 17.0905 Number of sites scoring better than the average of aligned sites = 196 Number in coding regions = 180 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 2 AGCGGGAAGTTAAAAAACTTAAGAGTAAAG 1 121 1 TAAAAAACTT 0.802701 -180 AACATAATTGAGATAAACGTCGAGGAAAAT 1 153 1 AGATAAACGT 0.796217 -148 GAACTTGTGAAAAAATACGGCGTTCTCGGA 1 186 1 AAAAATACGG 0.953766 -115 TTCCACGATCAAGAAAGCGGGAACTCCGAG 1 210 0 AAGAAAGCGG 0.951542 -91 TTTTGTTCCTAAAAAAGCTTTCTTTACTTT 1 246 0 AAAAAAGCTT 0.97078 -55 GGAATCTATGAAAAATACGGGAAAATTAAC 4 158 0 AAAAATACGG 0.953766 -143 CATAGATTCCAGAAAAGCTTTTAATTTCAC 4 178 1 AGAAAAGCTT 0.942 -123 TTTTTTAGAAAAAAAAGCGTTTTGGAATTT 4 260 0 AAAAAAGCGT 0.984913 -41 TTTTTTTCTAAAAAAAACTGCAGGAGGTGT 4 275 1 AAAAAAACTG 0.970783 -26 ********** Masking position 5 Map Score: 9.83875 Number of sites scoring better than the average of aligned sites = 268 Number in coding regions = 248 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 3 GAATGGAAGGGAAGGAAGTTGAAGGAATTG 1 38 1 GAAGGAAGTT 0.984765 -263 GAAGGAAGTTGAAGGAATTGAGGATGGTGT 1 48 1 GAAGGAATTG 0.957503 -253 AAGGCTATAAGCGGGAAGTTAAAAAACTTA 1 112 1 GCGGGAAGTT 0.973798 -189 GTATCTTAAAAAAGGAGGTAAGTAACT 1 284 1 AAAGGAGGTA 0.899165 -17 TTTTTAGACCGCAGGAGGTGCCCTTGCGTC 4 233 0 GCAGGAGGTG 0.997231 -68 AAAAAAAACTGCAGGAGGTGTGTAGTT 4 284 1 GCAGGAGGTG 0.997231 -17 ********** Masking position 6 Map Score: 7.82335 Number of sites scoring better than the average of aligned sites = 190 Number in coding regions = 162 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 4 GACTTATCAAGAGACTCCTCGAA 1 3 1 CTTATAAGAG 0.917648 -298 TTTAGAGTATCTTAAAAAAGGAGGTAAGTAA 1 278 1 CTTAAAAAGG 0.78148 -23 ACTTACAGAATTATAAAGGAAAGAGAAGAG 2 14 0 ATTATAAGGA 0.816725 -20 CTGTCCCTCAATTACAAAGAGCAGTAAAAGA 4 16 0 ATTACAAGAG 0.98009 -285 ACTCATAAACATAACGACGGGAAAGTACACC 4 56 1 ATAACACGGG 0.934228 -245 AACCCTGCCAATTACGAAAAGCCAGAAATAT 4 116 1 ATTACAAAAG 0.930687 -185 TTTATATCTGATTACTACGGGGACGGTGAAA 4 202 0 ATTACACGGG 0.985594 -99 ***** ***** Masking position 7 Map Score: 1.36097 Number of sites scoring better than the average of aligned sites = 301 Number in coding regions = 287 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 5 AGAGAATGGAAGGGAAGGAAGTTGAAGGAA 1 35 1 AGGGAAGGAA 0.89044 -266 CAATTTGGCGAGTAAAAGTAAAGCACACCA 1 72 0 AGTAAAAGTA 0.856555 -229 ATAAGCGGGAAGTTAAAAAACTTAAGAGTA 1 118 1 AGTTAAAAAA 0.804547 -183 TTAAGAGTAAAGTAAACATAATTGAGATAA 1 139 1 AGTAAACATA 0.757344 -162 ATAAACGTCGAGGAAAATAAAGAACTTGTG 1 165 1 AGGAAAATAA 0.868641 -136 ATAAAGAACTTGTGAAAAAATACGGCGTTC 1 181 1 TGTGAAAAAA 0.616806 -120 AAAAAGGTAAAGTAAAGAAAGCTTTTTTAG 1 238 1 AGTAAAGAAA 0.963835 -63 AAGCTTTTTTAGGAACAAAAGGTTTAGAGT 1 256 1 AGGAACAAAA 0.803296 -45 AGAATTATAAAGGAAAGAGAAGAGAAA 2 8 0 AGGAAAGAGA 0.871505 -26 TACAAAGAGCAGTAAAAGAATTGC 4 5 0 AGTAAAAGAA 0.963835 -296 TATGTTTATGAGTGAGAGAAACCTGTCCCT 4 39 0 AGTGAGAGAA 0.697855 -262 ACGTATGTATAGTAAAGTACAACCCTGCCA 4 96 1 AGTAAAGTAC 0.519393 -205 CCGTCCCCGTAGTAATCAGATATAAAGACG 4 207 1 AGTAATCAGA 0.358636 -94 AGTTTTTTTTAGAAAAAAAAGCGTTTTGGA 4 264 0 AGAAAAAAAA 0.820094 -37 ********** Masking position 5 Map Score: 5.7738 Number of sites scoring better than the average of aligned sites = 1509 Number in coding regions = 1399 Number in noncoding regions = 110 Number of orfs with sites within 600 bp upstream = 91 Fraction of orfs with sites within 600 bp upstream = 0.0146161 Motif number 6 ********** No masking Map Score: -1.4826e-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 7 ********** No masking Map Score: -1.4826e-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: -1.4826e-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