AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i182_riboflafin_biosynthesis_synecho_reg_300.orf -o182_synecho_300.ace -a/home/amcguire/alignace/lib/ORF_synecho.txt -z/skink1/amcguire/genomes/synecho.fna -g0.48 -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 = 0.48 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 RCY15119 104 Synechocystis #2 RCY05413 300 Synechocystis #3 RCY49636 271 Synechocystis #4 RCY36009 224 Synechocystis #5 RCY14921 295 Synechocystis #6 RCY19765 134 Synechocystis #7 RCY00557 221 Synechocystis #8 RCY19918 108 Synechocystis Motif number 1 TTCGAGTCTCTCGCTGCCCATCCTAAAACCTAG 2 16 1 TCGTGCCCCC 0.949508 -285 CTTAGGTCAACTCGTCTCCTTCGGGGTGAGTCC 2 65 1 CTCTCTCCCG 0.951217 -236 GGGTGGGAAATTTTTCCCCGGTCAATGAAACCA 2 108 0 TTTTCCCCTC 0.72837 -193 ATTGAGCAAGACTGTCCCCGGCTGAAATCCTCG 2 258 0 ACTTCCCCCT 0.689312 -43 CCTGGTTCCGCTGGCCCCCATCC 3 1 0 CTGCCCCCCC 0.968178 -271 TTTAGAGAAATTCATCCCCTACGACGAAGAAAC 3 82 1 TTCTCCCCCG 0.991075 -190 GTTGCAACAGTCGATCTTCTGCGACCACCGTTG 3 161 1 TCGTCTTCCG 0.718372 -111 CCGTTGTCAATTTTCCTCCAGCTTCTTAAGTTT 3 188 1 TTTCCTCCCT 0.899069 -84 ACCTTGAACGTTTCTGTCCCCCGTATCCCGTCC 3 240 1 TTTTGTCCCG 0.897153 -32 ATGGGTACTGTTCTTGTCCGTCGAAGAGATGAT 4 11 0 TTCTGTCCCG 0.923383 -214 GAGCTGCAACTCTCCCTCCAGCCATGGCATTGG 4 155 1 TCTCCTCCCC 0.927827 -70 AGCCATGGCATTGGCCCCCAACTGGCACAATTG 4 174 1 TTGCCCCCCT 0.971001 -51 CTATGACATCTTCCTCCTCTTCCAAGAAAAGCC 5 226 1 TTCTCCTCCC 0.873622 -70 AAAAGCCGTGCCGTTGCCCTACGAAATTATTTT 5 252 1 CCGTGCCCCG 0.922399 -44 ACGAAATTATTTTTCCCCCTTCGGCAATAAATT 5 272 1 TTTCCCCCCG 0.983868 -24 TAATTCCCCCCTCACCCCCATCGCTAT 6 5 0 CTCCCCCCCG 0.975761 -130 TGTCTCCAGTTTGCTCCCCTACTCTGACCCTAT 7 84 1 TTGTCCCCCT 0.977841 -138 ATTTCTCTTCTTTCTCTCCAACTACTGCTTACC 7 176 1 TTTTCTCCCT 0.921503 -46 AGATTCCATTTCCCTACCCTGCCATGATCTCAG 8 75 1 TCCTACCCCC 0.782775 -34 *** ***** ** Masking position 9 Map Score: 22.7394 Number of sites scoring better than the average of aligned sites = 3747 Number in coding regions = 3410 Number in noncoding regions = 337 Number of orfs with sites within 600 bp upstream = 361 Fraction of orfs with sites within 600 bp upstream = 0.0579827 Motif number 2 GGGAAATTACCGGGATAGGGCGATCGCCTC 1 13 0 CGGGATAGGG 0.992173 -92 CTGGGCTGTGGGGGATAGCCCCGAAAAACT 1 49 1 GGGGATAGCC 0.936488 -56 TTCCCTAGATCGGGTTAGCGGTAGATCAGA 1 78 0 CGGGTTAGCG 0.983934 -27 AGCACATAGCCGGATTACCCAGAGGCGATC 2 153 0 CGGATTACCC 0.955084 -148 GTAAATCGGACGGGATACGGGGGACAGAAA 3 250 0 CGGGATACGG 0.989821 -22 CGGTCAACCCCGGAAAACGGTCAATACCTT 4 48 0 CGGAAAACGG 0.938935 -177 TTTTTCAGGTCGGGTTACGCTTAGATAAAG 5 38 0 CGGGTTACGC 0.986809 -258 ATAGCGATGGGGGTGAGGGGGGAATTAGC 6 10 1 GGGGTGAGGG 0.856149 -125 CGAGTTGTTGCGGAAAAGGCGCTAGTGTCT 6 99 0 CGGAAAAGGC 0.939632 -36 CACCCAAGGACGAAATAGGGTCAGAGTAGG 7 101 0 CGAAATAGGG 0.840314 -121 TTTTTAGCAACGGATTACCCAGCAATTCCC 8 29 0 CGGATTACCC 0.955084 -80 ********** Masking position 7 Map Score: 14.5813 Number of sites scoring better than the average of aligned sites = 550 Number in coding regions = 509 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 49 Fraction of orfs with sites within 600 bp upstream = 0.00787022 Motif number 3 CGGGATAGGGCGATCGCCTCCC 1 1 0 CGATGCCTCC 0.959491 -104 GGTAATTTCCCCATGGCCTGGGCTGTGGGGGA 1 32 1 CCATGCCTGG 0.600482 -73 TACCCAGAGGCGATCGCCTAGCTCTGTGGGTG 2 136 0 CGATGCCTGC 0.973089 -165 CATCATAGGACTATAGCCATGGCAGAATAAGT 3 42 1 CTATGCCAGG 0.675388 -230 GACGAAGAAACCAAAGCCTTCCCAGAAAAGCT 3 104 1 CCAAGCCTCC 0.963882 -168 ATTAAGCATACCTTTGCCTTCGGTCAACCCCG 4 66 0 CCTTGCCTCG 0.757156 -159 CAGTTGGGGGCCAATGCCATGGCTGGAGGGAG 4 166 0 CCAAGCCAGG 0.556247 -59 CCGATGGTCACCATTGGCTAGGGAATAGTTTA 5 168 1 CCATGGCTGG 0.961871 -128 TATCAATGGTCCATGGACAGAGCTAATTCCCC 6 29 0 CCATGACAAG 0.767268 -106 TTACCATTGACCAATGCCAGACACTAGCGCCT 6 81 1 CCAAGCCAAC 0.914364 -54 **** **** ** Masking position 8 Map Score: 9.81425 Number of sites scoring better than the average of aligned sites = 2445 Number in coding regions = 2254 Number in noncoding regions = 191 Number of orfs with sites within 600 bp upstream = 204 Fraction of orfs with sites within 600 bp upstream = 0.0327658 Motif number 4 TGAACCGGTTCTGCTTAGGTCAACTCGTCTC 2 52 1 CGCTTAGGTC 0.845234 -249 TCGTCTCCTTCGGGGTGAGTCCTTAATTACC 2 76 1 CGGGTGAGTC 0.895657 -225 GGAAAATTGACAACGGTGGTCGCAGAAGATC 3 173 0 CACGGTGGTC 0.898217 -99 TGACCGTTTTCCGGGGTTGACCGAAGGCAAA 4 55 1 CGGGGTTGAC 0.840574 -170 GAGTTGCAGCTCGGGGTGGTCAAGGTTAGGG 4 136 0 TGGGGTGGTC 0.990958 -89 ATTAATCTTCTAAGGTTTGTCCCATT 4 209 1 TAGGTTTGTC 0.835899 -16 TCATACGAATCTGGGTAGGTCTTGCTATGAC 5 202 1 CGGGTAGGTC 0.980274 -94 CGCTAGTGTCTGGCATTGGTCAATGGTAAAG 6 79 0 TGCATTGGTC 0.835981 -56 TTTGCAATTGTTGGTGTTGTCTCCAGTTTGC 7 67 1 TGGTGTTGTC 0.897169 -155 TATTTCGTCCTTGGGTGGGTCAGGAGATCCC 7 114 1 TGGGTGGGTC 0.982841 -108 ATGGGTTTGGTCTGAGATCATG 8 97 0 TGGTTTGGTC 0.970643 -12 * ********* Masking position 11 Map Score: 6.6878 Number of sites scoring better than the average of aligned sites = 909 Number in coding regions = 820 Number in noncoding regions = 89 Number of orfs with sites within 600 bp upstream = 105 Fraction of orfs with sites within 600 bp upstream = 0.0168648 Motif number 5 GGTGTAGTTCCCTAGATCGGGTT 1 92 0 TGAGTTCCCT 0.957809 -13 GGGTGAGTCCTTAATTACCCTGGTTTCATTG 2 88 1 TTATTACCCT 0.844032 -213 AATCCGGCTATGTGCTTCCCTCAGGGCACAT 2 167 1 TGGCTTCCCT 0.955017 -134 CATGGCAGAATAAGTTTCCCTTTTTTAGAGA 3 59 1 TAGTTTCCCT 0.950683 -213 TCGTAGGGGATGAATTTCTCTAAAAAAGGGA 3 75 0 TGATTTCTCT 0.877376 -197 ACCACCGTTGTCAATTTTCCTCCAGCTTCTT 3 184 1 TCATTTTCCT 0.715283 -88 GAAACGAGTCTAGAGTTCCCTTGGCATTATC 4 106 0 TAAGTTCCCT 0.909711 -119 GAACTCTAGACTCGTTTCCCTAACCTTGACC 4 119 1 CTGTTTCCCT 0.871355 -106 TTGTCTCCAGTTTGCTCCCCTACTCTGACCC 7 83 1 TTGCTCCCCT 0.785704 -139 GGGTTAGTAGTTGATTTCTCTTCTTTCTCTC 7 163 1 TTATTTCTCT 0.855596 -59 TTGACTAGATTCCATTTCCCTACCCTGCCAT 8 69 1 TCATTTCCCT 0.96959 -40 ** ******** Masking position 6 Map Score: 5.29434 Number of sites scoring better than the average of aligned sites = 574 Number in coding regions = 479 Number in noncoding regions = 95 Number of orfs with sites within 600 bp upstream = 112 Fraction of orfs with sites within 600 bp upstream = 0.0179891 Motif number 6 AGGCGATCGCCCTATCCCGGTAATTTCCCCAT 1 14 1 CTATCCGGTA 0.912349 -91 TACCGCTAACCCGATCTAGGGAACTACACC 1 85 1 CGATCTGGGA 0.948709 -20 AGAACCGGTTCATATCTAGGTTTTAGGATGGG 2 32 0 CTATCTGGTT 0.875357 -269 CCTCAGGGCACATATTTTGGTAGCTTACTTAG 2 185 1 CTATTTGGTA 0.955156 -116 ATTTTGGTAGCTTACTTAGGGAAAGATTCAAC 2 198 1 CTACTTGGGA 0.87571 -103 ATAAGTTTCCCTTTTTTAGAGAAATTCATCCC 3 68 1 CTTTTTGAGA 0.668448 -204 TATTTTAAAGCTTTTCTGGGAAGGCTTTGGTT 3 112 0 CTTTCTGGAA 0.94811 -160 TTACATCATACGAATCTGGGTAGGTCTTGCTA 5 197 1 CAATCTGGTA 0.887236 -99 AACGGCACGGCTTTTCTTGGAAGAGGAGGAAG 5 235 0 CTTTCTGGAA 0.94811 -61 ATTATGGTGGCATTTTTCGGGATCTCCTGACC 7 131 0 CTTTTTGGGA 0.958466 -91 * ***** **** Masking position 1 Map Score: 4.87765 Number of sites scoring better than the average of aligned sites = 308 Number in coding regions = 251 Number in noncoding regions = 57 Number of orfs with sites within 600 bp upstream = 64 Fraction of orfs with sites within 600 bp upstream = 0.0102795 Motif number 7 CGGTAGATCAGAGTTTTTCGGGGCTATCCC 1 60 0 GAGTTTTTCG 0.923109 -45 GAGAGTTCGAGTCTCTCGCTGCCCATCC 2 9 1 GAGTCTCTCG 0.86079 -292 TGTGGGTGGGAAATTTTTCCCCGGTCAATG 2 114 0 AAATTTTTCC 0.778962 -187 TATTATCGTTGAATCTTTCCCTAAGTAAGC 2 207 0 GAATCTTTCC 0.845208 -94 TTTAGAGTTTCTCCTTATAAATTG 2 287 0 GAGTTTCTCC 0.9732 -14 CGTAGGGGATGAATTTCTCTAAAAAAGGGA 3 75 0 GAATTTCTCT 0.680718 -197 TAACAAAGCTAAATTGTTGCAACAGTCGAT 3 146 1 AAATTGTTGC 0.734277 -126 GCTGGAGGGAGAGTTGCAGCTCGGGGTGGT 4 147 0 GAGTTGCAGC 0.783452 -78 AAATAGGGCCGAGTTGTTGCGGAAAAGGCG 6 108 0 GAGTTGTTGC 0.954991 -27 GCTTACCATAAAGTTTTTGCTGTTTTCACC 7 202 1 AAGTTTTTGC 0.848941 -20 TCACAGTCGGGAATTGCTGGGTAATCCGTT 8 21 1 GAATTGCTGG 0.869145 -88 ********** Masking position 2 Map Score: 4.05892 Number of sites scoring better than the average of aligned sites = 963 Number in coding regions = 851 Number in noncoding regions = 112 Number of orfs with sites within 600 bp upstream = 123 Fraction of orfs with sites within 600 bp upstream = 0.0197559 Motif number 8 CACAGCCCAGGCCATGGGGAAATTACCGGGA 1 28 0 GCCTGGGGAA 0.941457 -77 CATGGCCTGGGCTGTGGGGGATAGCCCCGAA 1 43 1 GCTTGGGGGA 0.980584 -62 ATCGCCTAGCTCTGTGGGTGGGAAATTTTTC 2 125 0 TCTTGGGTGG 0.93248 -176 TAGGCGATCGCCTCTGGGTAATCCGGCTATG 2 148 1 CCTTGGGTAA 0.501462 -153 CAAAATATGTGCCCTGAGGGAAGCACATAGC 2 173 0 GCCTGAGGGA 0.892253 -128 TAGGACTATAGCCATGGCAGAATAAGTTTCC 3 47 1 GCCTGGCAGA 0.8396 -225 TTGACCGTTTTCCGGGGTTGACCGAAGGCAA 4 54 1 TCCGGGTTGA 0.627303 -171 GAGAGTTGCAGCTCGGGGTGGTCAAGGTTAG 4 138 0 GCTGGGGTGG 0.975114 -87 GGGGGCCAATGCCATGGCTGGAGGGAGAGTT 4 162 0 GCCTGGCTGG 0.971294 -63 CTATTCCCTAGCCAATGGTGACCATCGGTGA 5 165 0 GCCATGGTGA 0.754998 -131 CAATTTATTGCCGAAGGGGGAAAAATAATT 5 276 0 GCCAAGGGGG 0.720923 -20 ATAGCGATGGGGGTGAGGGGGGAATT 6 6 1 GATGGGGTGA 0.716935 -129 CCCTATTTCGTCCTTGGGTGGGTCAGGAGAT 7 111 1 TCCTGGGTGG 0.972031 -111 *** ******* Masking position 7 Map Score: 6.40792 Number of sites scoring better than the average of aligned sites = 3986 Number in coding regions = 3625 Number in noncoding regions = 361 Number of orfs with sites within 600 bp upstream = 355 Fraction of orfs with sites within 600 bp upstream = 0.057019 Motif number 9 ********** No masking Map Score: 2.62433e-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: 2.62433e-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 11 ********** No masking Map Score: 2.62433e-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