AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i021_Succinyl-CoA_Synthetase_synecho_reg_300.orf -o021_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 RCY10148 16 Synechocystis #2 RCY23515 146 Synechocystis #3 RCY19118 39 Synechocystis #4 RCY26516 95 Synechocystis #5 RCY51144 104 Synechocystis #6 RCY06801 171 Synechocystis #7 RCY33546 300 Synechocystis Motif number 1 CGCAACTACAACTTTTATCCTCCGGAGGCA 3 16 1 ACTTTTATCC 0.850007 -24 TTTCCGAATAGCCTCTCTCCAAATGATATA 4 59 1 GCCTCTCTCC 0.987742 -37 GTGGCTTGATGCCCTACTCCGCAGCTATCG 5 62 0 GCCCTACTCC 0.994717 -43 ATATGCCCCCACCTTAATCCTGGGTTATTT 6 82 1 ACCTTAATCC 0.964348 -90 TTAAGTTATTGCTCCACTCCCTCCAGTTGA 6 112 1 GCTCCACTCC 0.971881 -60 TAAAGTTGCTCCCCTACTCCCAAAAACTTG 7 70 1 CCCCTACTCC 0.985963 -231 GATAATTCTGACCTTTCTCCATTATTTTCC 7 254 0 ACCTTTCTCC 0.987039 -47 ********** Masking position 8 Map Score: 8.9232 Number of sites scoring better than the average of aligned sites = 513 Number in coding regions = 438 Number in noncoding regions = 75 Number of orfs with sites within 600 bp upstream = 80 Fraction of orfs with sites within 600 bp upstream = 0.0128493 Motif number 2 CTATCAGTAGCGATCGCCGTTGATCCCCG 2 3 0 CACCGTGCCC 0.997013 -144 GGGTAGACCCCCATCACCAAAGCCCCCAATAATGAGG 2 42 1 CACCAAGCCC 0.996921 -105 TTTTTCCGGTCTATCTCTGCAGGCCTCCACCTTCCCC 2 119 1 CACCGAGCTC 0.995227 -28 GTATCGTCAACCAGAGCAAAATGTCCC 5 1 0 CAACAATCCC 0.932275 -104 TACAGTGAAGCTTGGACTGGTTGACCCCGATAGCTGC 5 35 1 CTGCGTTCCC 0.924405 -70 GGCTTGATGCCCTACTCCGCAGCTATCGGGGTCAACC 5 53 0 CTCCGAGATC 0.865942 -52 GACTCCAAGGGCAATAGTACTGAAATCGAAAT 6 6 1 CAGCAAGCTG 0.845096 -166 CCTAGCAGCACCACCACAATATGCCCCCACCTTAATC 6 64 1 CACCAATCCC 0.990665 -108 AGGCGATCGCCAAACTCAGTTGTGCCCTCAAGTGAGC 7 152 0 CACCGTGCCC 0.997013 -149 * * * * * ** *** Masking position 7 Map Score: 8.92194 Number of sites scoring better than the average of aligned sites = 680 Number in coding regions = 640 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 47 Fraction of orfs with sites within 600 bp upstream = 0.00754899 Motif number 3 AGCGATCGCCGTTGATCCCCG 2 2 0 GTTGATCCCC 0.959951 -145 TGATAGGGGGGTAGACCCCCATCACCAAAG 2 34 1 GTAGACCCCC 0.965044 -113 CCCCATCACCAAAGCCCCCAATAATGAGGG 2 50 1 AAAGCCCCCA 0.897018 -97 GCTTGGACTGGTTGACCCCGATAGCTGCGG 5 44 1 GTTGACCCCG 0.959455 -61 ACTGTGGCTTGATGCCCTACTCCGCAGCTA 5 65 0 GATGCCCTAC 0.789644 -40 GTTTTCCTTTAATAATCCCCCC 5 93 1 AATAATCCCC 0.849312 -12 ACCACCACAATATGCCCCCACCTTAATCCT 6 73 1 TATGCCCCCA 0.80557 -99 ATAACTTAAAAATAACCCAGGATTAAGGTG 6 91 0 AATAACCCAG 0.640531 -81 TTTTTAAGTTATTGCTCCACTCCCTCCAGT 6 109 1 ATTGCTCCAC 0.900441 -63 AGAAAATCTAGAAACCCCAG 7 1 0 GAAACCCCAG 0.795221 -300 TCTTCTTAAAGTTGCTCCCCTACTCCCAAA 7 64 1 GTTGCTCCCC 0.98158 -237 TGCCGCCCAGAAAACTCCCCTAACAAAAAA 7 196 1 AAAACTCCCC 0.865918 -105 ********** Masking position 7 Map Score: 9.39052 Number of sites scoring better than the average of aligned sites = 5217 Number in coding regions = 4641 Number in noncoding regions = 576 Number of orfs with sites within 600 bp upstream = 452 Fraction of orfs with sites within 600 bp upstream = 0.0725988 Motif number 4 CTTGCTGAGTCCTGGTTTTTCCGGTCTATCTCT 2 104 1 CCTTTTTCCG 0.994833 -43 TAAAAATAGACTTCAATTTTCCGAATAGCCTCT 4 42 1 CTTTTTTCCG 0.989387 -54 GGGCATCAAGCCACAGTTTTCCTTTAATAATCC 5 78 1 CCATTTTCCT 0.985788 -27 CCTAATGTTTTTTGGTTTTTCCTAGCAGCACCA 6 44 1 TTTTTTTCCT 0.95467 -128 CTGGGGTTTCTAGATTTTCTTTAAATCTTAT 7 9 1 TCTTTTTCTT 0.849443 -292 TCTTATTTTCCTTAAATTTTCCGTAATCTCTTC 7 36 1 CTTTTTTCCG 0.98937 -265 TGACCTTTCTCCATTATTTTCCTACCTCATGTC 7 243 0 CCATTTTCCT 0.985788 -58 *** ******* Masking position 7 Map Score: 7.97246 Number of sites scoring better than the average of aligned sites = 274 Number in coding regions = 230 Number in noncoding regions = 44 Number of orfs with sites within 600 bp upstream = 52 Fraction of orfs with sites within 600 bp upstream = 0.00835207 Motif number 5 CTACTGATAGGGGGGTAGACCCCCATCACC 2 30 1 GGGGGTAGAC 0.976621 -117 CCCCAATAATGAGGGAAGATGGTATGACTG 2 65 1 GAGGGAAGAT 0.844735 -82 TGTGCCTCCGGAGGATAAAAGTTGTAGTTG 3 18 0 GAGGATAAAA 0.663315 -22 TTTATCCTCCGGAGGCACACC 3 29 1 GGAGGCACAC 0.919015 -11 GGATTAAGGTGGGGGCATATTGTGGTGGTG 6 72 0 GGGGGCATAT 0.945625 -100 CCCTCCAGTTGATGGCAAAATTGCTTGCCG 6 130 1 GATGGCAAAA 0.888312 -42 CATACTAGGCGGCGGTAAAAAGGACTTGAA 7 101 0 GGCGGTAAAA 0.943377 -200 CTGCTCACTTGAGGGCACAACTGAGTTTGG 7 150 1 GAGGGCACAA 0.982299 -151 GAGTTTTCTGGGCGGCAGAATATCAGGCGA 7 183 0 GGCGGCAGAA 0.985298 -118 ********** Masking position 7 Map Score: 5.2483 Number of sites scoring better than the average of aligned sites = 1879 Number in coding regions = 1665 Number in noncoding regions = 214 Number of orfs with sites within 600 bp upstream = 222 Fraction of orfs with sites within 600 bp upstream = 0.0356569 Motif number 6 AGGACTCAGCAAGGTTTAGTTCCAGTCATAC 2 86 0 AAGGTTTAGT 0.91486 -61 CGGAGGATAAAAGTTGTAGTTGCGAAACC 3 9 0 AAGTTGTAGT 0.964566 -31 AACAGGAAGTAAGTTTTAGAGA 4 2 0 AAGTTTTAGG 0.975402 -94 GAAATCCCTAATGTTTTTTGGTTTTTCCTAG 6 38 1 ATGTTTTTTG 0.734065 -134 GGTTATTTTTAAGTTATTGCTCCACTCCCTC 6 104 1 AAGTTATTGT 0.908932 -68 GACTTGAATCAAGTTTTTGGGAGTAGGGGAG 7 78 0 AAGTTTTTGG 0.975402 -223 GCTCACCATGATTTTTTTGTTAGGGGAGTTT 7 207 0 ATTTTTTTGT 0.737955 -94 TTAAAAAATGATGTTGTAGATAATTCTGACC 7 271 0 ATGTTGTAGT 0.94435 -30 ********* * Masking position 1 Map Score: 2.87006 Number of sites scoring better than the average of aligned sites = 572 Number in coding regions = 469 Number in noncoding regions = 103 Number of orfs with sites within 600 bp upstream = 122 Fraction of orfs with sites within 600 bp upstream = 0.0195952 Motif number 7 TTAGTCAGAATTAACAGGAAGTAAGTTTTA 4 15 0 TTAACAGGAA 0.849529 -81 GGGGGGATTATTAAAGGAAAACTGTGGCTT 5 85 0 TTAAAGGAAA 0.962834 -20 GAAAATAAGATTTAAAGAAAATCTAGAAAC 7 16 0 TTTAAAGAAA 0.942893 -285 TTACGGAAAATTTAAGGAAAATAAGATTTA 7 32 0 TTTAAGGAAA 0.969056 -269 TTAAGAAGAGATTACGGAAAATTTAAGGAA 7 43 0 ATTACGGAAA 0.920204 -258 ********** Masking position 4 Map Score: 0.868416 Number of sites scoring better than the average of aligned sites = 167 Number in coding regions = 140 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 8 CGGGGATCAACGGCGATCGCTA 2 3 1 GGGATCAACG 0.953375 -144 TATCTCTGCAGGCCTCCACCTTCCCCT 2 130 1 GGCCTCCACC 0.966203 -17 CGCAGCTATCGGGGTCAACCAGTCCAAGCT 5 43 0 GGGGTCAACC 0.960965 -62 TGCGGAGTAGGGCATCAAGCCACAGTTTTC 5 69 1 GGCATCAAGC 0.969278 -36 ACCACAATATGCCCCCACCTTAATCCTGGG 6 76 1 GCCCCCACCT 0.817511 -96 AAGCAATTTTGCCATCAACTGGAGGGAGTG 6 126 0 GCCATCAACT 0.978444 -46 TTGGGAGTAGGGGAGCAACTTTAAGAAGAG 7 63 0 GGGAGCAACT 0.933168 -238 ACTCAGTTGTGCCCTCAAGTGAGCAGCAGT 7 146 0 GCCCTCAAGT 0.950964 -155 ********** Masking position 6 Map Score: 3.39176 Number of sites scoring better than the average of aligned sites = 811 Number in coding regions = 740 Number in noncoding regions = 71 Number of orfs with sites within 600 bp upstream = 83 Fraction of orfs with sites within 600 bp upstream = 0.0133312 Motif number 9 TCTCTAAAACTTACTTCCTGTTAATTCT 4 7 1 AAATACTTCC 0.905832 -89 TTCTGACTAAAAATAGACTTCAATTTTCCGAA 4 35 1 AAAGACTTCA 0.991106 -61 GGCGGCGGTAAAAAGGACTTGAATCAAGTTTT 7 92 0 AAAGACTTGA 0.987079 -209 CCTAGTATGGAATTTGACTTCATTACTGCTGC 7 122 1 AATGACTTCA 0.971322 -179 CATGGTGAGCAAAGAGACATGAGGTAGGAAAA 7 228 1 AAAGACATGA 0.958767 -73 *** ******* Masking position 7 Map Score: 0.286235 Number of sites scoring better than the average of aligned sites = 48 Number in coding regions = 36 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 10 ********** No masking Map Score: 1.87173e-13 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: 1.87173e-13 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 12 ********** No masking Map Score: 1.87173e-13 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