AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i257_tpal_bbur_300.orf -o257_tpal_bbur_300.ace -a/home/amcguire/genomes/ORF_tpal.txt -z/home/amcguire/genomes/synecho.fna -g0.40 -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 = 0.4 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 RTP00359 225 AE000520 #2 RTP00361 107 AE000520 #3 RTP00362 118 AE000520 #4 RTP00772 204 AE000520 #5 RBB00112 194 3615 #6 RBB00025 66 3615 Motif number 1 CATTCCTCCGGTAGGAGCGTATGGAGAGGTGCAGGA 1 14 1 GAGGAGAGGG 0.99042 -212 GAGGACTTGCGCATGACAGTGGGGCGAGATCAGTTT 1 48 1 GATGAGGGGG 0.980291 -178 GCCAATAGAGGTGGGCATGCGGTTTGATGCAGGAAG 1 95 1 GGGGCGGTTG 0.929061 -131 GCGGTTTGATGCAGGAAGCGGGGGTGACAGTCGACC 1 113 1 GAGGACGGGG 0.986616 -113 TGTGTGCGGTGACGGCGTGTGCCGGGCCGTGTTTTT 2 82 0 GCGGCGGCGG 0.961131 -26 AGAACAGGAAGGAGCACCGGTAGTAGTTGATGG 3 8 0 GAGCAGTGTG 0.934972 -111 TGCAGCAGGAGAGGGCAAGGGAGGAGAACAGGAAGG 3 32 0 GGGGCGGGGG 0.997062 -87 CGAGTGTAACGGAGCACTGTGCCTTGTGCTAGTCCC 3 81 0 GAGCAGGCTG 0.97512 -38 ACGGGTGAGGAAAGGATCGCGGGTAGGGATAGGACG 4 38 0 AAGGAGGGTG 0.963941 -167 GGGAGATTTCGTAGGCACGGGTGAGGAAAGGATCGC 4 54 0 GAGGCGGGAG 0.986853 -151 GTTTCTGTGTGCGGGGATGTGGGGAGATTTCGTAGG 4 75 0 GGGGGGGGGG 0.994393 -130 TCAAAGGCGAGCAGCACGGTGGGTTTCTGTGTGCGG 4 97 0 GAGCAGGGTT 0.924228 -108 GTCGGTGATCGTAGAAAAGAAGGTAGATGATATCCG 4 135 0 GAGAAGAGTG 0.829303 -70 CGTTTTGAAAGAAGCGGAGGGCGGGGAAATCTGTTG 4 171 0 GAGCGGGGGG 0.993796 -34 * **** * * ** * Masking position 1 Map Score: 21.6829 Number of sites scoring better than the average of aligned sites = 859 Number in coding regions = 248 Number in noncoding regions = 611 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 2 TCCTCCGGTAGGAGCGTATGGAGAGGTGCAGGAG 1 17 1 GGAGATGGGA 0.982342 -209 GACTTGCGCATGACAGTGGGGCGAGATCAGTTTC 1 51 1 TGAGGGGGGA 0.978345 -175 CACCTCTATTGGCACGTTTGGAGGAAACTGATCT 1 74 0 GGCGTTGGGG 0.927931 -152 AATAGAGGTGGGCATGCGGTTTGATGCAGGAAGC 1 98 1 GGCGGGTTGA 0.948425 -128 GTTTGATGCAGGAAGCGGGGGTGACAGTCGACCG 1 116 1 GGACGGGGGA 0.985286 -110 GACCGTCACTGACGTGCAAGGTGAAACGATTATT 1 152 1 GACGAAGGGA 0.813785 -74 ATCTCTTCTCGGATCGGGTATGGGCGCTTTGGGA 2 34 0 GGAGGTATGG 0.74647 -74 AGCAGGAGAGGGCAAGGGAGGAGAACAGGAAGGA 3 31 0 GGCGGAGGGA 0.993649 -88 GGTGAGGAAAGGATCGCGGGTAGGGATAGGACGG 4 37 0 GGAGGGGTGG 0.991126 -168 AGATTTCGTAGGCACGGGTGAGGAAAGGATCGCG 4 53 0 GGCGGTGAGA 0.966238 -152 TCTGTGTGCGGGGATGTGGGGAGATTTCGTAGGC 4 74 0 GGGGGGGGGA 0.994541 -131 GGTGATCGTAGAAAAGAAGGTAGATGATATCCGA 4 134 0 GAAGAGGTGA 0.860713 -71 TGAAAGAAGCGGAGGGCGGGGAAATCTGTTGGTC 4 168 0 GGAGGGGGAA 0.978345 -37 *** * **** ** Masking position 13 Map Score: 16.0798 Number of sites scoring better than the average of aligned sites = 1741 Number in coding regions = 516 Number in noncoding regions = 1225 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 3 TCCTCCGGTAGGAGCGTATGGAGAGGTGCAGG 1 17 1 GGGCGTAGGA 0.99254 -209 CGTATGGAGAGGTGCAGGAGGACTTGCGCATG 1 31 1 GGGCAGGGGA 0.979109 -195 CACCTCTATTGGCACGTTTGGAGGAAACTGAT 1 76 0 GGACGTTGGA 0.986759 -150 ATCGGGTATGGGCGCTTTGGGATATATGGGAA 2 24 0 GGGCTTTGGA 0.949215 -84 AGCAGGAGAGGGCAAGGGAGGAGAACAGGAAG 3 33 0 GGAAGGGGGA 0.977139 -86 TCGCGGGTAGGGATAGGACGGAAGAAGCACAT 4 26 0 GGTAGGAGGA 0.890559 -179 GGTGAGGAAAGGATCGCGGGTAGGGATAGGAC 4 39 0 GGTCGCGGTA 0.886651 -166 TCTGTGTGCGGGGATGTGGGGAGATTTCGTAG 4 76 0 GGATGTGGGA 0.961134 -129 TGAAAGAAGCGGAGGGCGGGGAAATCTGTTGG 4 170 0 GGGGGCGGGA 0.984399 -35 AGTAGGTGCGTTTTGAAAGAAGCGGA 4 189 0 GGGCGTTTGA 0.943365 -16 ** ***** *** Masking position 12 Map Score: 9.40055 Number of sites scoring better than the average of aligned sites = 802 Number in coding regions = 212 Number in noncoding regions = 590 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 4 ACTGATCTCGCCCCACTGTCATGCGCAAGT 1 52 0 CCCCACTGTC 0.910047 -174 TCGACTGTCACCCCCGCTTCCTGCATCAAA 1 117 0 CCCCCGCTTC 0.988279 -109 AAAGCGCCCATACCCGATCCGAGAAGAGAT 2 38 1 TACCCGATCC 0.946994 -70 CCTATCCCTACCCGCGATCCTTTCCTCACC 4 41 1 CCCGCGATCC 0.986053 -164 ATCCTTTCCTCACCCGTGCCTACGAAATCT 4 57 1 CACCCGTGCC 0.977888 -148 TACGAAATCTCCCCACATCCCCGCACACAG 4 77 1 CCCCACATCC 0.978589 -128 AACAGATTTCCCCGCCCTCCGCTTCTTTCA 4 172 1 CCCGCCCTCC 0.987067 -33 AAAAATTTTACCCCTTTCTATAAATAAA 5 177 0 TACCCCTTTC 0.874743 -18 ********** Masking position 3 Map Score: 7.07905 Number of sites scoring better than the average of aligned sites = 2133 Number in coding regions = 609 Number in noncoding regions = 1524 Number of orfs with sites within 600 bp upstream = 46 Fraction of orfs with sites within 600 bp upstream = 0.00738837 Motif number 5 CAGTAAAAATTTTTATTATATAATGTAAATA 5 46 0 TTTTTTATAT 0.965844 -149 ATTTTTACTGGTTTTGTATATTTTGTATTTT 5 67 1 GTTTGTATAT 0.854143 -128 GTTAATCTTATATTGTTATATGTAAATTATT 5 146 1 TATTTTATAT 0.973564 -49 ATATGTAAATTATTTTTATTTATAGAAAGGG 5 163 1 TATTTTATTT 0.884335 -32 GTTGAGTCAATATATTTATATGGTGC 6 6 0 TATATTATAT 0.884335 -61 ACTCTCAGTTTTTTCGTATATTTAATATTAT 6 35 1 TTTTGTATAT 0.950079 -32 GTATATTTAATATTATTATATAAGGAG 6 50 1 TATTTTATAT 0.973563 -17 **** ****** Masking position 8 Map Score: 5.37282 Number of sites scoring better than the average of aligned sites = 32 Number in coding regions = 11 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 6 TGCACCTCTCCATACGCTCCTACCGGAGGAAT 1 15 0 CAACGCCCTA 0.99194 -211 GAGGAAACTGATCTCGCCCCACTGTCATGCGC 1 56 0 ATTCGCCCAC 0.837392 -170 CAGTTTCCTCCAAACGTGCCAATAGAGGTGGG 1 78 1 CAACGTCCAA 0.935664 -148 CATCAAACCGCATGCCCACCTCTATTGGCACG 1 92 0 CAGCCCCCTC 0.928804 -134 CCTCGCGGGGAAGACGCTCCACTTTGAGGTGG 1 203 1 AAACGCCCAC 0.988243 -23 CATATATCCCAAAGCGCCCATACCCGATCCGA 2 28 1 AAGCGCCATA 0.869791 -80 ATCCTTTCCTCACCCGTGCCTACGAAATCTCC 4 57 1 CACCGTCCTA 0.886173 -148 CGTGCCTACGAAATCTCCCCACATCCCCGCAC 4 71 1 AATCTCCCAC 0.782037 -134 CGCTTCTTTCAAAACGCACCTACT 4 191 1 AAACGCCCTA 0.991279 -14 GCATAGAAGTAATACGCTACTATAGCGAATGT 5 103 1 AAACGCACTA 0.908525 -92 ** **** **** Masking position 5 Map Score: 5.73793 Number of sites scoring better than the average of aligned sites = 578 Number in coding regions = 174 Number in noncoding regions = 404 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 7 CGGTGACCGTCACTGACGTGCAAGGTGAAA 1 148 1 CACTGACGTG 0.867225 -78 ACGGCGTGTGCCGGGCCGTGTTTTTGCGTT 2 77 0 CCGGGCCGTG 0.818777 -31 CCTTCTCGCTCAGGGACTAGCACAAGGCAC 3 69 1 CAGGGACTAG 0.901592 -50 TAACGGAGCACTGTGCCTTGTGCTAGTCCC 3 81 0 CTGTGCCTTG 0.953976 -38 CTCCGTTACACTCGGCCGTGTGTCAA 3 103 1 CTCGGCCGTG 0.507048 -16 TTTCTGTGTGCGGGGATGTGGGGAGATTTC 4 80 0 CGGGGATGTG 0.941835 -125 ********** Masking position 5 Map Score: 2.33743 Number of sites scoring better than the average of aligned sites = 611 Number in coding regions = 174 Number in noncoding regions = 437 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 8 ********** No masking Map Score: -1.58208e-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: -1.58208e-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 10 ********** No masking Map Score: -1.58208e-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