AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i112_Amino_Acid_Transport_3_aful_reg_300.orf -o112_aful_300.ace -a/home/amcguire/alignace/lib/ORF_aful.txt -z/skink1/amcguire/genomes/aful.fna -g0.49 -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 = 0.49 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 RAG29671 300 Archaeoglobus_fulgidus #2 RAG49483 266 Archaeoglobus_fulgidus Motif number 1 AAATGGGATTGAAAGCGAGACATT 1 4 1 TGGGATTGAA 0.994203 -297 CCCATTTTGGTCTGATTTCAACCCGTCAGGA 1 55 0 TCTGATTTAA 0.982457 -246 CAGACCAAAATGGGATTGAAAGGCAGACGAC 1 72 1 TGGGATTGAA 0.994203 -229 CCCATTTTGGTCTGATTTCAACTGTTCCTTG 1 123 0 TCTGATTTAA 0.982457 -178 CAGACCAAAATGGGATTGAAAGTAAGAACAT 1 140 1 TGGGATTGAA 0.994203 -161 CCCATTTTGGTCTGATTTCAACTTGGGAGCT 1 196 0 TCTGATTTAA 0.982457 -105 CAGACCAAAATGGGATTGAAAGGCAATGGCG 1 213 1 TGGGATTGAA 0.994203 -88 CCCACTTTAGTCTGATTTCAAAAAACGCCGG 2 66 0 TCTGATTTAA 0.982457 -201 AGAGCTTTAGGCGGTTTTAAACTCTCGTCGG 2 146 0 GCGGTTTTAA 0.959502 -121 TTGGGCGTTTGGGGATTTTTAAACGGTTAAA 2 214 0 GGGGATTTTA 0.952073 -53 TTCTCGATGGGCGGTTTGGTATTTAAGGTTT 2 243 0 GCGGTTTGTA 0.887501 -24 ******** ** Masking position 11 Map Score: 27.1149 Number of sites scoring better than the average of aligned sites = 185 Number in coding regions = 82 Number in noncoding regions = 103 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 2 TCTCGCTTTCAATCCCATTT 1 1 0 AATCCCATTT 0.9892 -300 ATCCCATTTTGGTCTGATTTCAACCCGTCA 1 58 0 GGTCTGATTT 0.990025 -243 TCTGCCTTTCAATCCCATTTTGGTCTGATT 1 69 0 AATCCCATTT 0.9892 -232 ATCCCATTTTGGTCTGATTTCAACTGTTCC 1 126 0 GGTCTGATTT 0.990025 -175 TCTTACTTTCAATCCCATTTTGGTCTGATT 1 137 0 AATCCCATTT 0.9892 -164 ATCCCATTTTGGTCTGATTTCAACTTGGGA 1 199 0 GGTCTGATTT 0.990025 -102 ATTGCCTTTCAATCCCATTTTGGTCTGATT 1 210 0 AATCCCATTT 0.9892 -91 ATCCCACTTTAGTCTGATTTCAAAAAACGC 2 69 0 AGTCTGATTT 0.989202 -198 AAATTTACGTAATCCCACTTTAGTCTGATT 2 80 0 AATCCCACTT 0.955365 -187 AACTCTCGTCGGTCTGAGTTTTGTTTCCTT 2 128 0 GGTCTGAGTT 0.958661 -139 ********** Masking position 7 Map Score: 26.311 Number of sites scoring better than the average of aligned sites = 253 Number in coding regions = 67 Number in noncoding regions = 186 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 3 TTCAATCCCATTTTGGTCTGATTTCAACCC 1 62 0 TTTTGGTCTG 0.992545 -239 TTCAATCCCATTTTGGTCTGATTTCAACTG 1 130 0 TTTTGGTCTG 0.992545 -171 TTCAATCCCATTTTGGTCTGATTTCAACTT 1 203 0 TTTTGGTCTG 0.992545 -98 TACTTTTCCTCTTTTTTCTGAACACC 2 7 0 CTTTTTTCTG 0.874924 -260 GCGATAATCGTTTTTGCCGGCGTTTTTTGA 2 50 1 TTTTTGCCGG 0.902129 -217 CGTAATCCCACTTTAGTCTGATTTCAAAAA 2 73 0 CTTTAGTCTG 0.986179 -194 TTTAAACTCTCGTCGGTCTGAGTTTTGTTT 2 132 0 CGTCGGTCTG 0.967608 -135 TGGAGAAGAGCTTTAGGCGGTTTTAAACTC 2 153 0 CTTTAGGCGG 0.970869 -114 TGGTTCTCGATGGGCGGTTTGGTATTT 2 250 0 CGATGGGCGG 0.903976 -17 ********** Masking position 8 Map Score: 13.163 Number of sites scoring better than the average of aligned sites = 251 Number in coding regions = 153 Number in noncoding regions = 98 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 4 CATGCCCAATAAATTGTGTTAATGTCTCGC 1 25 0 AAATTGTGTT 0.962095 -276 ACATCTCATAAACTTGTGTTGGACTCGGTA 1 167 1 AACTTGTGTT 0.893561 -134 AAAAATTAGAAAATCTTTTTCCTCTTGCCA 1 266 0 AAATCTTTTT 0.912048 -35 AAAGATTTTCTAATTTTTTTATGAATGTAG 1 278 1 TAATTTTTTT 0.91488 -23 ATTATCGCAGCAATTGTTTTTTACTTTTCC 2 28 0 CAATTGTTTT 0.948706 -239 ATTGCTGCGATAATCGTTTTTGCCGGCGTT 2 44 1 TAATCGTTTT 0.927732 -223 GGGATTACGTAAATTTATTTGTGGAAAGTG 2 94 1 AAATTTATTT 0.788927 -173 ********** Masking position 2 Map Score: 3.94766 Number of sites scoring better than the average of aligned sites = 124 Number in coding regions = 82 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 55 Fraction of orfs with sites within 600 bp upstream = 0.00883392 Motif number 5 GGGTTGAAATCAGACCAAAATGGGATTGAA 1 62 1 CAGACCAAAA 0.981772 -239 CAGTTGAAATCAGACCAAAATGGGATTGAA 1 130 1 CAGACCAAAA 0.981772 -171 GGTAGCTCCCAAGTTGAAATCAGACCAAAA 1 193 1 AAGTTGAAAT 0.430266 -108 AAGTTGAAATCAGACCAAAATGGGATTGAA 1 203 1 CAGACCAAAA 0.981772 -98 CAAGCGTGGCAAGAGGAAAAAGATTTTCTA 1 260 1 AAGAGGAAAA 0.983217 -41 GTTCAGAAAAAAGAGGAAAAGTAAAAAACA 2 14 1 AAGAGGAAAA 0.983217 -253 GGAAAGTGTGACAAGGAAACAAAACTCAGA 2 116 1 ACAAGGAAAC 0.460898 -151 ********** Masking position 7 Map Score: 3.25179 Number of sites scoring better than the average of aligned sites = 414 Number in coding regions = 292 Number in noncoding regions = 122 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 6 ACCCGTCAGGACATGCCCAATAAATTGTGT 1 36 0 ACATGCCCAA 0.954204 -265 TGTTCCTTGACAACGCCCCAGTAGTGTACG 1 102 0 CAACGCCCCA 0.991553 -199 TCCAGCAAATCCACCACCAAATTTATTCAT 2 179 1 CCACCACCAA 0.953013 -88 AAAAATCCCCAAACGCCCAAACCTTAAATA 2 225 1 AAACGCCCAA 0.99017 -42 CTTAAATACCAAACCGCCCATCGAGAACCA 2 247 1 AAACCGCCCA 0.965334 -20 ********** Masking position 3 Map Score: 1.94427 Number of sites scoring better than the average of aligned sites = 65 Number in coding regions = 55 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 7 ********** No masking Map Score: 1.55852e-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: 1.55852e-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 9 ********** No masking Map Score: 1.55852e-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