AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i222_tpal_bbur_300.orf -o222_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 RTP01074 300 AE000520 #2 RTP00806 33 AE000520 #3 RTP00346 190 AE000520 #4 RTP00620 147 AE000520 #5 RTP00631 32 AE000520 #6 RTP00632 52 AE000520 #7 RTP00633 162 AE000520 #8 RTP00737 87 AE000520 #9 RBB00769 20 3615 #10 RBB00550 22 3615 #11 RBB00549 89 3615 #12 RBB00245 77 3615 #13 RBB00243 91 3615 #14 RBB00242 19 3615 #15 RBB00051 300 3615 #16 RBB00867 165 3615 Motif number 1 ATCTGCAGACACCTGCTCAGCCGTTGCA 1 6 1 CGACCCTGCC 0.787068 -295 TACGTTGCAGCACGCCCGTGCACTGGAACTTCT 1 39 0 CCGCCGTGCC 0.995535 -262 GTTACAGTGGATGGCCCGTGCCGTGGCAAAGGA 1 135 0 AGGCCGTGCG 0.98188 -166 CATCCACTGTAACGCACGTGCGCGCGGCTGCTG 1 155 1 ACGCCGTGCC 0.995182 -146 GCACGTGCGCGCGGCTGCTGCAGCGCGTAAGAA 1 168 1 GGGCGCTGCG 0.969323 -133 CAGCGCGTAAGAAGCCCGTGCAGCAATAAATAA 1 188 1 GAGCCGTGCG 0.984073 -113 AGAGCAGGGAGTCGCTTCTGCTCCGCAAATAGC 1 228 0 GCGCTCTGCC 0.968066 -73 TGACGAATAGGACGCACGCGCGGGTGTGGTTGT 3 63 1 GCGCCGCGCG 0.995152 -128 GAAAAAGGCAGACGAACGCGCACGCTTTATCAA 3 165 0 GCGACGCGCC 0.942963 -26 TGGAGAACAACACTCGTGCGCTCAAAACTGT 4 9 1 ACACCGTGCC 0.959984 -139 ACATTAGTTCGTTGCTGGTGCACACAAAAGAAG 4 95 1 GTGCGGTGCC 0.962394 -53 CCGCCCTCGAGGCGCGCGTGCAGGAAGTATGGG 7 74 1 GCGCCGTGCG 0.998588 -89 AGGCGCTGCTGCAGCAGCCTCAAG 7 149 0 GCGCGCTGCG 0.989134 -14 CCACGGGGCTGCCGCCCGTGCTCAGGGCATTCA 8 44 1 GCGCCGTGCC 0.998932 -44 * *** ***** * Masking position 11 Map Score: 32.1138 Number of sites scoring better than the average of aligned sites = 73 Number in coding regions = 26 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 2 AATAGCAGACTTTTTATTTATTGCTGCACGGG 1 202 0 TTTTTATATT 0.680231 -99 CAAAAACTTTTTTATTAAGATTTCTTAGCAGT 3 136 0 TTTATTGATT 0.636441 -55 TAATAAAAAAGTTTTTGATAAAGCGTGCGCGT 3 151 1 GTTTTTTAAA 0.709865 -40 CAGCTTTCTCTTTTTTTTGAAAAAGGACGCCG 4 49 1 TTTTTTGAAA 0.963969 -99 TAGAATTTACTTTTTAGTGAATGTATAATAAA 11 17 1 TTTTTAGAAT 0.818044 -73 CACCTCTTTATTTATTCCGATATTTCCATTAT 12 48 0 TTTATTGATA 0.856839 -30 ATCGGTGTGCTTTTTTGTTAAATAAAATATAT 13 24 1 TTTTTTTAAA 0.943626 -68 TATAGTCAAATTTTTAGCGATAAGTTTAAAAA 13 56 1 TTTTTAGATA 0.92104 -36 CTTGCCTGTATTTATTGCTAAATAAGCGGTGA 15 103 0 TTTATTTAAA 0.827928 -198 TCGCACGATTTTTTTAGCGATAAAAAAATAAG 15 205 1 TTTTTAGATA 0.92104 -96 CTTATCTCTATTTTTTTAGAAAATTTTTTTGT 16 36 1 TTTTTTGAAA 0.953711 -130 TTTTAGAAAATTTTTTTGTATATTTTAATTTA 16 49 1 TTTTTTTATA 0.92719 -117 GAGGTGCGTATTTTTACGTAAAAGTGATGAGT 16 97 1 TTTTTATAAA 0.905279 -69 TGAATTTTAATTTTTTAATAAAAAGCGAAAGG 16 130 1 TTTTTTTAAA 0.806199 -36 ****** **** Masking position 10 Map Score: 13.3498 Number of sites scoring better than the average of aligned sites = 293 Number in coding regions = 79 Number in noncoding regions = 214 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 3 TACGTTGCAGCACGCCCGTGCACTGGAACT 1 42 0 CACGCCCGTG 0.54906 -259 GTTACAGTGGATGGCCCGTGCCGTGGCAAA 1 138 0 ATGGCCCGTG 0.820445 -163 CATCCACTGTAACGCACGTGCGCGCGGCTG 1 155 1 AACGCACGTG 0.934543 -146 CAGCGCGTAAGAAGCCCGTGCAGCAATAAA 1 188 1 GAAGCCCGTG 0.971833 -113 TGACGAATAGGACGCACGCGCGGGTGTGGT 3 63 1 GACGCACGCG 0.989764 -128 GAAAAAGGCAGACGAACGCGCACGCTTTAT 3 168 0 GACGAACGCG 0.906296 -23 CGCGCGCCTCGAGGGCGGTGATTTGTGGAC 7 62 0 GAGGGCGGTG 0.85448 -101 CACCGCCCTCGAGGCGCGCGTGCAGGAAGT 7 72 1 GAGGCGCGCG 0.986173 -91 TGCCGCATACGAGGCGCGCATAGCAACGCT 7 121 1 GAGGCGCGCA 0.85031 -42 GGGTTCAGGAGACGGCCGAGTCTTTGAACT 8 15 0 GACGGCCGAG 0.913993 -73 CCACGGGGCTGCCGCCCGTGCTCAGGGCAT 8 44 1 GCCGCCCGTG 0.979622 -44 ********** Masking position 4 Map Score: 11.7891 Number of sites scoring better than the average of aligned sites = 98 Number in coding regions = 32 Number in noncoding regions = 66 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 4 TACGATATAGAAGAGGTGCGGCTTTTTTAT 1 89 0 AAGAGGTGCG 0.982556 -212 AAAGGATATGCAATGGTGTGTGTACGATAT 1 111 0 CAATGGTGTG 0.687968 -190 CGCGCTGCAGCAGCCGCGCGCACGTGCGTT 1 165 0 CAGCCGCGCG 0.839902 -136 TTCCTGTTGCCTGTGATGCGAGACTGCTAA 3 114 1 CTGTGATGCG 0.880749 -77 AGTTTTTGATAAAGCGTGCGCGTTCGTCTG 3 160 1 AAAGCGTGCG 0.84645 -31 TGGAGAACAACACTCGTGCGCTCAAAACTG 4 11 1 CACTCGTGCG 0.904753 -137 ATGTCGTGCGCAGTGATGCGGCGTCCTTTT 4 69 0 CAGTGATGCG 0.961885 -79 CAACGAACTAATGTCGTGCGCAGTGATGCG 4 79 0 ATGTCGTGCG 0.954815 -69 ATACGGAGCGAAGACATGCGGGTAGATA 6 35 1 AAGACATGCG 0.916917 -18 GGTAAGGGTGAAAAGGTGAGGTAAGAGCTC 15 75 1 AAAAGGTGAG 0.763224 -226 ATTGCTAAATAAGCGGTGAGCTCTTACCTC 15 92 0 AAGCGGTGAG 0.902883 -209 ATCGCTAAAAAAATCGTGCGATCTACCCGT 15 196 0 AAATCGTGCG 0.954033 -105 TTATAAATATTTGAGGTGCGTATTTTTACG 16 85 1 TTGAGGTGCG 0.72212 -81 TTTTACGTAAAAGTGATGAGTGTGAATTTT 16 108 1 AAGTGATGAG 0.831382 -58 ********** Masking position 8 Map Score: 10.8935 Number of sites scoring better than the average of aligned sites = 735 Number in coding regions = 207 Number in noncoding regions = 528 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 5 GAAGAGGTGCGGCTTTTTTATGCTCGTCTG 1 80 0 GGCTTTTTTA 0.797118 -221 CTTTATCAAAAACTTTTTTATTAAGATTTC 3 144 0 AACTTTTTTA 0.883269 -47 TCCTAGAATTTACTTTTTAGTGAATGTATA 11 14 1 TACTTTTTAG 0.837142 -76 TAGGAGTATATATTTTTTAG 11 80 1 TATTTTTTAG 0.84607 -10 AGAATCGGTGTGCTTTTTTGTTAAATAAAA 13 21 1 TGCTTTTTTG 0.845212 -71 ATATGGCTTGAGTTTTTTAAACTTATCGCT 13 71 0 AGTTTTTTAA 0.749239 -21 TAGATCGCACGATTTTTTTAGCGATAAAAA 15 201 1 GATTTTTTTA 0.870261 -100 TCATCTCTCTTATTTTTTTATCGCTAAAAA 15 215 0 TATTTTTTTA 0.908828 -86 TTCTTATCTCTATTTTTTTAGAAAATTTTT 16 34 1 TATTTTTTTA 0.908828 -132 TTTTTTAGAAAATTTTTTTGTATATTTTAA 16 47 1 AATTTTTTTG 0.883269 -119 TGTGAATTTTAATTTTTTAATAAAAAGCGA 16 128 1 AATTTTTTAA 0.826704 -38 ********** Masking position 5 Map Score: 6.81461 Number of sites scoring better than the average of aligned sites = 507 Number in coding regions = 148 Number in noncoding regions = 359 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 6 CACCATTGCATATCCTTTGCCACGGCACGGG 1 123 1 TATCCTTGCC 0.967727 -178 GACAATGACCTAGACTTTGACGAATAGGACG 3 46 1 TAGACTTGAC 0.768493 -145 CATGATCGCATTCCTGTTGCCTGTGATGCGA 3 104 1 TTCCTTTGCC 0.97036 -87 AATTCTTCGATTTCCATTGCCTTTTCCTTTC 7 29 0 TTTCCTTGCC 0.979635 -134 GGGGGAGTCTTTGACGTTGCCGCATACGAGG 7 104 1 TTGACTTGCC 0.979461 -59 CCTAATGAGGTTTATCTTGCCTGTATTTATT 15 119 0 TTTATTTGCC 0.950299 -182 GCTTACATACTTGATCTTGCTCCTAATGAGG 15 140 0 TTGATTTGCT 0.770503 -161 AACAATACCTTTTGCCTTTCGCTTTT 16 150 0 TACCTTTGCC 0.953288 -16 ***** ***** Masking position 7 Map Score: 4.2245 Number of sites scoring better than the average of aligned sites = 1022 Number in coding regions = 319 Number in noncoding regions = 703 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 7 GTGTGTACGATATAGAAGAGGTGCGGCTTT 1 94 0 TATAGAAGAG 0.757236 -207 GTGCAGCAATAAATAAAAAGTCTGCTATTT 1 205 1 AAATAAAAAG 0.776004 -96 AAGAAATCTTAATAAAAAAGTTTTTGATAA 3 142 1 AATAAAAAAG 0.776004 -49 TCCTTTTTCAAAAAAAAGAGAAAGCTGCGT 4 46 0 AAAAAAAGAG 0.968008 -102 TGGTGCACACAAAAGAAGAGACATCGTTTA 4 110 1 AAAAGAAGAG 0.944183 -38 ATATTAAATTAAAGGGGAAGAA 10 7 1 AATTAAAGGG 0.582864 -16 ATATCGGAATAAATAAAGAGGTGTATTTGC 12 57 1 AAATAAAGAG 0.940096 -21 GGTAAGGGTGAAAAGGTGAGGTAAGAGCTC 15 75 1 AAAAGGTGAG 0.550997 -226 GCGATAAAAAAATAAGAGAGATGATGGCAT 15 221 1 AATAAGAGAG 0.907657 -80 TTCATTGACCTAAAAGAGAGTTTTAA 15 285 1 TAAAAGAGAG 0.870765 -16 AATTTTCTAAAAAAATAGAGATAAGAAAAC 16 31 0 AAAAATAGAG 0.826688 -135 TTTAATTTTTTAATAAAAAGCGAAAGGCAA 16 135 1 TAATAAAAAG 0.55191 -31 ********** Masking position 2 Map Score: 6.08524 Number of sites scoring better than the average of aligned sites = 395 Number in coding regions = 122 Number in noncoding regions = 273 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 8 TTTATGCTCGTCTGTGTGTGGATACGTTGCAG 1 62 0 TCGTGTTGGA 0.986876 -239 GCGGCTCGGTATCTGCAGGAAGGGCGA 1 284 0 TCGTATTGCA 0.962154 -17 CGCAGCTTTCTCTTTTTTTTGAAAAAGGACGC 4 47 1 TCTTTTTTGA 0.717749 -101 ATGTCTTCGCTCCGTATGTGCACCTCAACGTG 6 20 0 TCGTATTGCA 0.962033 -33 CCTTTTCCTTTCTGTGTATGGAGAAAACGC 7 9 0 TCGTGTTGGA 0.986693 -154 GAATCAGTTTTTTGAAGAGTTTGAA 8 73 0 TCGTTTTTGA 0.942588 -15 ** **** **** Masking position 7 Map Score: 1.30589 Number of sites scoring better than the average of aligned sites = 43 Number in coding regions = 17 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 9 TCCCTTACTCATGAGGAGTC 2 1 1 TCCCTTACTC 0.888336 -33 CGCGTTCGTCTGCCTTTTTCCAG 3 178 1 TGCCTTTTTC 0.97959 -13 AGACATCGTTTACCTTATTCGATGCGCTGT 4 128 1 TACCTTATTC 0.919465 -20 CGATTTCCATTGCCTTTTCCTTTCTGTGTA 7 23 0 TGCCTTTTCC 0.965698 -140 TTTTCACCCTTACCTTTTACGGCGGTAATT 15 59 0 TACCTTTTAC 0.893962 -242 CAATACCTTTTGCCTTTCGCTTTTTATTAA 16 144 0 TGCCTTTCGC 0.958915 -22 ********** Masking position 5 Map Score: 1.10939 Number of sites scoring better than the average of aligned sites = 114 Number in coding regions = 32 Number in noncoding regions = 82 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 10 CACGGGCGTGCTGCAACGTATCCACACACA 1 52 1 CTGCAACGTA 0.883589 -249 TGATGCGAGACTGCTAAGAAATCTTAATAA 3 127 1 CTGCTAAGAA 0.801119 -64 TTGTGTGCACCAGCAACGAACTAATGTCGT 4 92 0 CAGCAACGAA 0.921536 -56 TGCTGGTGCACACAAAAGAAGAGACATCGT 4 107 1 CACAAAAGAA 0.806264 -41 TTGCTTCTGAAAAGAAGGATATTTCG 5 7 1 CTGAAAAGAA 0.968729 -26 TCTCCATACACAGAAAGGAAAAGGCAATGG 7 17 1 CAGAAAGGAA 0.885545 -146 TATACATTCACTAAAAAGTAAATTCTAGGA 11 14 0 CTAAAAAGTA 0.644719 -76 GAAAGTGTCGCAGAAAATTACCGCCGTAAA 15 44 1 CAGAAAATTA 0.722014 -257 AAACAAAAACCTGAAAATAAATTT 16 5 0 CTGAAAATAA 0.859158 -161 ********** Masking position 6 Map Score: 1.42139 Number of sites scoring better than the average of aligned sites = 410 Number in coding regions = 130 Number in noncoding regions = 280 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 11 ATAATTAACATTAATAATTAATTTTATTAT 11 41 0 TTAATAATTA 0.9346 -49 CCTAAATCAATTAATAATTAACATTAATAA 11 54 0 TTAATAATTA 0.9346 -36 ATAGCAAATATTAGTATTTATGCCAATTAC 12 17 0 TTAGTATTTA 0.896734 -61 ATATTTTAATTTAGTAATTATAAATATTTG 16 68 1 TTAGTAATTA 0.958409 -98 ********** Masking position 5 Map Score: 0.35682 Number of sites scoring better than the average of aligned sites = 9 Number in coding regions = 3 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 12 ********** No masking Map Score: 2.78776e-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 13 ********** No masking Map Score: 2.78776e-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 14 ********** No masking Map Score: 2.78776e-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