AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i198_aful_mthe_300.orf -o198_aful_mthe_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 RAG50329 222 Archaeoglobus_fulgidus #2 RAG25938 75 Archaeoglobus_fulgidus #3 RTH00129 300 M.thermo #4 RTH02041 58 M.thermo #5 RTH01062 171 M.thermo #6 RTH01098 51 M.thermo Motif number 1 ATATGAGCAAGATAAGGAAGCTGGCAGAGGAGG 1 131 1 GAAGGAAGCG 0.891153 -92 ATCCTGCGGCGTTCGGGACGCCGTGACCCGAGT 2 18 1 GTGGGACGCG 0.985962 -58 GGGCCGCCGAGATTTGAACTCGGGTCACGGCGT 2 35 0 GATGAACTCG 0.961983 -41 CCTTAAAGCAGATGGGGCCGCCGAGATTTGAAC 2 49 0 GAGGGCCGCG 0.997919 -27 GCCCACAAGGAACAGGGCTGCAGTCAATATATC 3 63 1 AAGGGCTGCG 0.917987 -238 ATCCAAGATAAACAGGCACTCCGATGAGGATGA 3 93 1 AAGGCACTCG 0.910203 -208 ACAGGGCAACAACCTGGACCCTGTGGTCAAGGT 3 164 0 AATGGACCCG 0.933744 -137 GGATAAGATCGAGAGGGCCGGGGGAGAGTGCCT 3 216 1 GAGGGCCGGG 0.988367 -85 AAAAATTGTTGAAGAGAACCCGGCCATTAAGAA 3 258 1 GAAGAACCCG 0.950157 -43 CGGACTTTTCAACTGGAACGGGGATGGTCAGCA 5 60 1 AAGGAACGGG 0.963007 -112 GGATGGTCAGCACCGGAACGCTGGAGACCCGAG 5 81 1 CAGGAACGCG 0.977664 -91 GGACCGCCGAGATTTGAACTCGGGTCTCCAGCG 5 99 0 GATGAACTCG 0.961983 -73 GATTCGATTTGATGGGACCGCCGAGATTTGAAC 5 113 0 GAGGACCGCG 0.996705 -59 ** ******* * Masking position 6 Map Score: 20.3785 Number of sites scoring better than the average of aligned sites = 331 Number in coding regions = 313 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 2 GTTCCTTCCGCGGAAGGCTAAAAACGATTTC 1 28 0 CGGAAGGCAA 0.969778 -195 TAGCCTTCCGCGGAAGGAACATTAAAAATTA 1 39 1 CGGAAGGACA 0.986405 -184 CTGGCAGAGGAGGAAGTCAAATCCAAACCTC 1 151 1 AGGAAGTCAA 0.889863 -72 CACGGCGTCCCGAACGCCGCAGGATCACCAG 2 12 0 CGAACGCCCA 0.889877 -64 CATCCCAGGAAGGCGCAGCAATCTGGA 3 7 1 AGGAAGGCCA 0.994197 -294 GCAATCTGGAAGGACGTTGCAAGGAGACTCG 3 28 1 AGGACGTTCA 0.89558 -273 CAAGGAGACTCGAAAGGCCCACAAGGAACAG 3 47 1 CGAAAGGCCA 0.981257 -254 CACTCCGATGAGGATGAAACAGTTCTCGTGC 3 109 1 AGGATGAACA 0.919278 -192 ACTAAAGAGTAGAATGATTCAGT 4 46 1 AGAATGATCA 0.691552 -13 AATGGCTGGGAGGATGGACCAAGCTACCCTA 5 18 0 AGGATGGACA 0.976599 -154 ******** ** Masking position 4 Map Score: 9.26439 Number of sites scoring better than the average of aligned sites = 294 Number in coding regions = 270 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 3 AAATTAACATGCGGCAAAGATTTAAATTAC 1 64 1 GCGGCAAAGA 0.93189 -159 CGGCGTTCGGGACGCCGTGACCCGAGTTCA 2 24 1 GACGCCGTGA 0.976087 -52 AGCAGATGGGGCCGCCGAGATTTGAACTCG 2 46 0 GCCGCCGAGA 0.997962 -30 ATTTGATGGGACCGCCGAGATTTGAACTCG 5 110 0 ACCGCCGAGA 0.986971 -62 CCATCAAATCGAATCCAAGAACCTCTATTT 5 131 1 GAATCCAAGA 0.872012 -41 ATGCCTCCAAGAAAAACATTAA 5 160 0 GCCTCCAAGA 0.990585 -12 ********** Masking position 10 Map Score: 5.87014 Number of sites scoring better than the average of aligned sites = 159 Number in coding regions = 147 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 4 AGATAAGGAAGCTGGCAGAGGAGGAAGTCA 1 140 1 GCTGGCAGAG 0.911817 -83 AACGCCGCAGGATCACCAGG 2 1 0 GATCACCAGG 0.932942 -75 AAGCAGATGGGGCCGCCGAGATTTGAACTC 2 47 0 GGCCGCCGAG 0.944777 -29 GACTCGAAAGGCCCACAAGGAACAGGGCTG 3 53 1 GCCCACAAGG 0.883281 -248 CGGAAACCTTGACCACAGGGTCCAGGTTGT 3 159 1 GACCACAGGG 0.988928 -142 TGTCTGTGAAAATGACAGGGCAACAACCTG 3 181 0 AATGACAGGG 0.896825 -120 CATTTTCACAGACAGCAAGGGATAAGATCG 3 197 1 GACAGCAAGG 0.888011 -104 ATAAGATCGAGAGGGCCGGGGGAGAGTGCC 3 218 1 GAGGGCCGGG 0.983564 -83 TTATGTTCTTAATGGCCGGGTTCTCTTCAA 3 266 0 AATGGCCGGG 0.972922 -35 GGGACCGTAGGGTAGCTTGGTC 5 3 1 GACCGTAGGG 0.952085 -169 AAACTTCTTCAATGGCTGGGAGGATGGACC 5 29 0 AATGGCTGGG 0.848345 -143 GATTTGATGGGACCGCCGAGATTTGAACTC 5 111 0 GACCGCCGAG 0.987955 -61 ********** Masking position 10 Map Score: 14.3815 Number of sites scoring better than the average of aligned sites = 861 Number in coding regions = 786 Number in noncoding regions = 75 Number of orfs with sites within 600 bp upstream = 55 Fraction of orfs with sites within 600 bp upstream = 0.00883392 Motif number 5 TAGCTTCACCTCATATCGAAATCGTTT 1 7 1 CACCTCATTC 0.961733 -216 TTTAAATCTTTGCCGCATGTTAATTTTTAAT 1 59 0 TGCCGCATTT 0.932718 -164 ATATCAACTACACCTCAGCGTAGTTTTGACC 1 104 0 CACCTCAGGT 0.970944 -119 TGGCGCCTCATTTTTTGCTGACTC 1 209 0 CGCCTCATTT 0.990833 -14 GCGTCCCGAACGCCGCAGGATCACCAGG 2 8 0 CGCCGCAGAT 0.981076 -68 TAAAACACCTCATAATAAACTCTAGA 6 36 0 CACCTCATAT 0.97958 -16 ******** ** Masking position 7 Map Score: 3.03789 Number of sites scoring better than the average of aligned sites = 106 Number in coding regions = 92 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 6 AAGGACCTTTCCAGGCACGAGAACTGTTTCATCCTC 3 118 0 CCGCACGACG 0.987592 -183 AGGTTGTTGCCCTGTCATTTTCACAGACAGCAAGGG 3 182 1 CCGCATTACG 0.996224 -119 GGGGAGAGTGCCTGACACTCGGAAAAATTGTTGAAG 3 236 1 CCGCACTAAA 0.979176 -65 TGAAGAGAACCCGGCCATTAAGAACATAAAGATAAT 3 267 1 CCGCATTAAA 0.982675 -34 GTCCATCCTCCCAGCCATTGAAGAAGTTTCCGGACT 5 30 1 CCGCATTGAG 0.983968 -142 GAAGAAGTTTCCGGACTTTTCAACTGGAACGGGGAT 5 49 1 CCGCTTTACG 0.984873 -123 ** * **** ** * Masking position 6 Map Score: 2.36923 Number of sites scoring better than the average of aligned sites = 37 Number in coding regions = 34 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 7 GCATGTTAATTTTTAATGTTCCTTCCGCGG 1 46 0 TTTTAATGTT 0.91029 -177 TCTGCCAGCTTCCTTATCTTGCTCATATCA 1 129 0 TCCTTATCTT 0.885684 -94 TCGGAGTGCCTGTTTATCTTGGATATATTG 3 87 0 TGTTTATCTT 0.903781 -214 TATTCTATTATCTTTATGTTCTTAATGGCC 3 279 0 TCTTTATGTT 0.973459 -22 ACTTTATATATTTTTATTTTATAAACTAAA 4 22 1 TTTTTATTTT 0.911912 -37 ATCATTCTACTCTTTAGTTTATAAAATAAA 4 34 0 TCTTTAGTTT 0.833577 -25 AGAACCTCTATTTTAATGTTTTTCTTGGAG 5 148 1 TTTTAATGTT 0.91029 -24 ********** Masking position 6 Map Score: 2.16423 Number of sites scoring better than the average of aligned sites = 97 Number in coding regions = 78 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 8 AGTAACGAGGTTTGGATTTGACTTCCTCCT 1 158 0 TTTGGATTTG 0.869682 -65 GCCTGTTTATCTTGGATATATTGACTGCAG 3 80 0 CTTGGATATA 0.897599 -221 TGGAAAGGTCCTTGGAAGCGGAAACCTTGA 3 141 1 CTTGGAAGCG 0.979607 -160 AATAGAGGTTCTTGGATTCGATTTGATGGG 5 130 0 CTTGGATTCG 0.987416 -42 TAATGTTTTTCTTGGAGGCAT 5 161 1 CTTGGAGGCA 0.969324 -11 ********** Masking position 6 Map Score: 0.254486 Number of sites scoring better than the average of aligned sites = 165 Number in coding regions = 156 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 9 ********** No masking Map Score: -3.30951e-14 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 10 ********** No masking Map Score: -3.30951e-14 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 11 ********** No masking Map Score: -3.30951e-14 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