AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i138_Transmembrane_Transport_11_aquae_reg_100.orf -o138_aquae_100.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 TTGGCGAGTAAAAGTAAAGCACACCATCCTCAA 1 65 0 AGTAAAGCCA 0.951158 -236 CAAGGCTATAAGCGGGAAGTTAAAAAACTTAAG 1 111 1 AGGGAAGTAA 0.987695 -190 AAAAAACTTAAGAGTAAAGTAAACATAATTGAG 1 132 1 AGTAAAGTAA 0.99153 -169 AGATAAACGTCGAGGAAAATAAAGAACTTGTGA 1 163 1 CGGAAAATAA 0.916563 -138 ATCGTGGAAAAAGGTAAAGTAAAGAAAGCTTTT 1 231 1 AGTAAAGTAA 0.99153 -70 ACAGAATTATAAAGGAAAGAGAAGAGAAA 2 7 0 AGGAAAGAAA 0.967137 -27 AAACATAACGACGGGAAAGTACACCCGAACTGC 4 62 1 AGGAAAGTCA 0.992533 -239 CCACGTATGTATAGTAAAGTACAACCCTGCCAA 4 94 1 AGTAAAGTCA 0.988145 -207 TATGAAAAATACGGGAAAATTAACCCTCTTTGG 4 149 0 AGGAAAATAA 0.981369 -152 TACTACGGGGACGGTGAAATTAAAAGCTTTTCT 4 188 0 AGTGAAATAA 0.934222 -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 0.793842 -180 AACATAATTGAGATAAACGTCGAGGAAAAT 1 153 1 AGATAAACGT 0.787144 -148 GAACTTGTGAAAAAATACGGCGTTCTCGGA 1 186 1 AAAAATACGG 0.951278 -115 TTCCACGATCAAGAAAGCGGGAACTCCGAG 1 210 0 AAGAAAGCGG 0.948941 -91 TTTTGTTCCTAAAAAAGCTTTCTTTACTTT 1 246 0 AAAAAAGCTT 0.969179 -55 GGAATCTATGAAAAATACGGGAAAATTAAC 4 158 0 AAAAATACGG 0.951278 -143 CATAGATTCCAGAAAAGCTTTTAATTTCAC 4 178 1 AGAAAAGCTT 0.93892 -123 TTTTTTAGAAAAAAAAGCGTTTTGGAATTT 4 260 0 AAAAAAGCGT 0.984073 -41 TTTTTTTCTAAAAAAAACTGCAGGAGGTGT 4 275 1 AAAAAAACTG 0.969181 -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 CAATTCCTTCAACTTCCTTCCCTTCCATTC 1 38 0 AACTTCCTTC 0.983713 -263 ACACCATCCTCAATTCCTTCAACTTCCTTC 1 48 0 CAATTCCTTC 0.954653 -253 TAAGTTTTTTAACTTCCCGCTTATAGCCTT 1 112 0 AACTTCCCGC 0.972009 -189 AGTTACTTACCTCCTTTTTTAAGATAC 1 284 0 TACCTCCTTT 0.89284 -17 GACGCAAGGGCACCTCCTGCGGTCTAAAAA 4 233 1 CACCTCCTGC 0.997037 -68 AACTACACACCTCCTGCAGTTTTTTTT 4 284 0 CACCTCCTGC 0.997037 -17 ********** Masking position 5 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 0.927134 -298 TTTAGAGTATCTTAAAAAAGGAGGTAAGTAA 1 278 1 CTTAAAAAGG 0.803496 -23 ACTTACAGAATTATAAAGGAAAGAGAAGAG 2 14 0 ATTATAAGGA 0.835938 -20 CTGTCCCTCAATTACAAAGAGCAGTAAAAGA 4 16 0 ATTACAAGAG 0.982543 -285 ACTCATAAACATAACGACGGGAAAGTACACC 4 56 1 ATAACACGGG 0.941997 -245 AACCCTGCCAATTACGAAAAGCCAGAAATAT 4 116 1 ATTACAAAAG 0.938845 -185 TTTATATCTGATTACTACGGGGACGGTGAAA 4 202 0 ATTACACGGG 0.987378 -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 TTCCTTCAACTTCCTTCCCTTCCATTCTCT 1 35 0 TTCCTTCCCT 0.89044 -266 TGGTGTGCTTTACTTTTACTCGCCAAATTG 1 72 1 TACTTTTACT 0.856555 -229 TACTCTTAAGTTTTTTAACTTCCCGCTTAT 1 118 0 TTTTTTAACT 0.804547 -183 TTATCTCAATTATGTTTACTTTACTCTTAA 1 139 0 TATGTTTACT 0.757344 -162 CACAAGTTCTTTATTTTCCTCGACGTTTAT 1 165 0 TTATTTTCCT 0.868641 -136 GAACGCCGTATTTTTTCACAAGTTCTTTAT 1 181 0 TTTTTTCACA 0.616806 -120 CTAAAAAAGCTTTCTTTACTTTACCTTTTT 1 238 0 TTTCTTTACT 0.963835 -63 ACTCTAAACCTTTTGTTCCTAAAAAAGCTT 1 256 0 TTTTGTTCCT 0.803296 -45 TTTCTCTTCTCTTTCCTTTATAATTCT 2 8 1 TCTCTTTCCT 0.871505 -26 GCAATTCTTTTACTGCTCTTTGTA 4 5 1 TTCTTTTACT 0.963835 -296 AGGGACAGGTTTCTCTCACTCATAAACATA 4 39 1 TTCTCTCACT 0.697855 -262 TGGCAGGGTTGTACTTTACTATACATACGT 4 96 0 GTACTTTACT 0.519393 -205 CGTCTTTATATCTGATTACTACGGGGACGG 4 207 0 TCTGATTACT 0.358636 -94 TCCAAAACGCTTTTTTTTCTAAAAAAAACT 4 264 1 TTTTTTTTCT 0.820094 -37 ********** Masking position 6 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