AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i068_synecho_ctra_300.orf -o068_synecho_ctra_300.ace -a/home/amcguire/genomes/ORF_synecho.txt -z/home/amcguire/genomes/synecho.fna -g0.46 -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 = 0.46 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 RCY08909 235 Synechocystis #2 RCY30587 76 Synechocystis #3 RCY04328 85 Synechocystis #4 RCY51876 36 Synechocystis #5 RCY53629 161 Synechocystis #6 RCY42873 96 Synechocystis #7 RCY48238 125 Synechocystis #8 RCY06379 275 Synechocystis #9 RCY15935 102 Synechocystis #10 RCY30833 46 Synechocystis #11 RCY01603 300 Synechocystis Motif number 1 ACTTTAACCCATTGGGTGAAGGGAAGTTAG 1 65 1 ATTGGGTGAA 0.627564 -171 CCAGACTGTGACTGGGGTTTTCCAACCTAA 1 91 0 ACTGGGGTTT 0.872737 -145 CAGCCTTCTCAATGGGGATTCATCATTGGT 1 137 0 AATGGGGATT 0.722432 -99 CATTGAGAAGGCTGGGGAAAAGGGTAGCGA 1 153 1 GCTGGGGAAA 0.98771 -83 ACAGCAGAGAACTGGGGGTAAATCTTTAGT 1 209 0 ACTGGGGGTA 0.988058 -27 ACTGGGGAATTTAACAGGCA 2 67 0 ACTGGGGAAT 0.974533 -10 TGGTGGCTGTGTTGGGGATTTTGTTCTCCA 5 93 1 GTTGGGGATT 0.860317 -69 ACGGCTTGAACCTGGGGGAATGGCT 7 6 0 CCTGGGGGAA 0.98191 -120 ACAGCAAAGCGCAGGGGAAAGTATTTAAAA 7 42 0 GCAGGGGAAA 0.962689 -84 GCCTAGCAAAGCTGGGGGTTCACATTTTGG 8 250 1 GCTGGGGGTT 0.986102 -26 CCAGACTACCCCTGGAGGTAAACTCCGGGG 11 122 1 CCTGGAGGTA 0.755263 -179 CCACTGTCCGGCAGGGTGAACAGAGGAGAC 11 220 1 GCAGGGTGAA 0.839359 -81 TGACACTGTAACAGGGGAAAGTCTCCTCTG 11 240 0 ACAGGGGAAA 0.95056 -61 ********** Masking position 5 Map Score: 16.735 Number of sites scoring better than the average of aligned sites = 2890 Number in coding regions = 2583 Number in noncoding regions = 307 Number of orfs with sites within 600 bp upstream = 309 Fraction of orfs with sites within 600 bp upstream = 0.0496306 Motif number 2 GCGGCTCACAAAATAGTAGACTAG 3 3 1 GGCCACAAAT 0.976595 -83 CCCCAACACAGCCACCAACAATAGACCCAGGT 5 78 0 GCCCCAACAT 0.916622 -84 AGAAATAGCTGGAGAACAAAATCCCCAACACA 5 100 0 GGAAACAAAT 0.614246 -62 ACCATGCCTCCTAAATTGCGTATTAAA 5 145 0 GCCCCTAAAT 0.946099 -17 AGGGCTAGCCGCCACACAATATCATGGTTTTA 6 14 1 GCCCACAATT 0.951975 -83 TGGCAATTTTTCCTCCCAAAATAGATGACAAT 6 71 1 TCCCCCAAAT 0.946099 -26 TTTGCTGTTTGCCCCCCAAAGTTGCCCTGTCC 7 64 1 GCCCCCAAAT 0.995047 -62 GCAAGAAGGTGGCTCCCACTCTCTTTGGATTA 8 60 1 GGCCCCACTT 0.976757 -216 AGCTTTGCTAGGCTACCAAATTTTCAGACCAG 8 231 0 GGCACCAAAT 0.976595 -45 TGCACACCAAAATGTGAACCCCC 8 263 0 GCAACCAAAT 0.884618 -13 GATCATACCACGCCCCCACTGTCCGGCAGGGT 11 205 1 CGCCCCACTT 0.844759 -96 *** ****** * Masking position 8 Map Score: 9.96585 Number of sites scoring better than the average of aligned sites = 1290 Number in coding regions = 1108 Number in noncoding regions = 182 Number of orfs with sites within 600 bp upstream = 136 Fraction of orfs with sites within 600 bp upstream = 0.0218439 Motif number 3 GGTGGATTGGGACTAACGAT 1 1 1 GGTGGATTGG 0.975489 -235 TCCACCGGTTGGCGGTTTGGGTTTGAATTT 5 28 0 GGCGGTTTGG 0.94022 -134 ACCGCCAACCGGTGGAATTGAACCGCACTT 5 42 1 GGTGGAATTG 0.91823 -120 GTCTATTGTTGGTGGCTGTGTTGGGGATTT 5 84 1 GGTGGCTGTG 0.813699 -78 ACGCAATTTAGGAGGCATGGT 5 151 1 GGAGGCATGG 0.944644 -11 ATGGTTTTAAGGTGGGCTTGGCCCACTTTT 6 37 1 GGTGGGCTTG 0.961593 -60 GCTTGAACCTGGGGGAATGGCT 7 3 0 GGGGGAATGG 0.957513 -123 AAAAAGTTGCGGCAGGCTGGTTGTTGTTTA 8 28 1 GGCAGGCTGG 0.925631 -248 CTGAAAATTTGGTAGCCTAGCAAAGCTGGG 8 236 1 GGTAGCCTAG 0.824437 -40 TACCTCCAGGGGTAGTCTGGCTCGACTGTG 11 112 0 GGTAGTCTGG 0.934252 -189 GCCGGACAGTGGGGGCGTGGTATGATCTAG 11 202 0 GGGGGCGTGG 0.964668 -99 ********** Masking position 5 Map Score: 9.62165 Number of sites scoring better than the average of aligned sites = 1651 Number in coding regions = 1554 Number in noncoding regions = 97 Number of orfs with sites within 600 bp upstream = 98 Fraction of orfs with sites within 600 bp upstream = 0.0157404 Motif number 4 GCGGCTCACAAAATAGTAGACTAGACTCTACTT 3 11 1 AAATAGGACA 0.969294 -75 TTGTTTTGAAAAATTGAAGGAGAACACAAA 3 66 1 AAATTGGGAA 0.971144 -20 TTAGTTAAAGAAATAGCTGGAGAACAAAATCCC 5 107 0 AAATAGGGAA 0.987239 -55 ATTGCCATAAAAAAAGTGGGCCAAGCCCACCTT 6 45 0 AAAAAGGGCA 0.950968 -52 TTTCCTCCCAAAATAGATGACAATGGCA 6 79 1 AAATAGGACA 0.969294 -18 ATTGCTTGCAAAATTGCTGGATATGCTATTCGA 9 26 0 AAATTGGGAA 0.971144 -77 TCCCAATGGTAAATAGCAGTAAATGTCAGTTTA 9 70 0 AAATAGGTAA 0.936806 -33 ****** *** * Masking position 3 Map Score: 5.01197 Number of sites scoring better than the average of aligned sites = 136 Number in coding regions = 123 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 5 TGGAAAACCCCAGTCACAGTCTGGACAAAAC 1 97 1 CAGTCACGTC 0.95505 -139 TTGCATTTGTCAGTCAATGTTGTTTTGAAAA 3 47 1 CAGTCAAGTT 0.940454 -39 CAGGTTCAAGCCGTAAATATTTTTAAATACT 7 22 1 CCGTAAAATT 0.739894 -104 AGTATCTGCATCGTCAACGTCTAACCC 7 109 1 TCGTCAAGTC 0.951753 -17 CTCAAAAAATCCTTAAAAGTCTAGACGCAAA 8 152 1 CCTTAAAGTC 0.925577 -124 ACGGGATTAACCGTCAGCGTCATTCAGTGGA 8 197 0 CCGTCAGGTC 0.981935 -79 TGGTAAATAGCAGTAAATGTCAGTTTATTTA 9 66 0 CAGTAAAGTC 0.977545 -37 AAAATTGTATCCGTAAAAGACCTCTGCACCG 11 53 1 CCGTAAAGAC 0.952286 -248 ******* *** Masking position 6 Map Score: 3.97616 Number of sites scoring better than the average of aligned sites = 399 Number in coding regions = 363 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 45 Fraction of orfs with sites within 600 bp upstream = 0.00722775 Motif number 6 TGGACAGAAATTCAAACCCAAACCGCCAAC 5 21 1 TTCAAACCCA 0.88038 -141 CTACCAAATTTTCAGACCAGTTTACGGGAT 8 221 0 TTCAGACCAG 0.974624 -55 GATTCGGACCCGGATTTTTGGT 10 3 1 TTCGGACCCG 0.989046 -44 TTGCCCATAATCCAGACCCGTCGGCGGTGC 11 78 0 TCCAGACCCG 0.995399 -223 TCTTTATGGCTCCAGCCCCGGAGTTTACCT 11 137 0 TCCAGCCCCG 0.989844 -164 ********** Masking position 1 Map Score: 3.68883 Number of sites scoring better than the average of aligned sites = 84 Number in coding regions = 70 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 7 CCTTGCTGTACTCGTTGATTATTCCTGTTC 2 33 1 CTCGTTGATT 0.962134 -44 AGACTAGACTCTACTTGCTTTGCATTTGTC 3 28 1 CTACTTGCTT 0.960487 -58 TGGGAGCCACCTTCTTGCTTTAAACAACAA 8 48 0 CTTCTTGCTT 0.960487 -228 GAGCTAAAAACTCCTTGATTTCTGTATGTC 8 125 0 CTCCTTGATT 0.988946 -151 ATGCTCCAATCGCCTTGATTGTATCGAATG 11 12 1 CGCCTTGATT 0.975788 -289 ********** Masking position 5 Map Score: 3.10641 Number of sites scoring better than the average of aligned sites = 32 Number in coding regions = 22 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 8 GTTAGACGTTGACGATGCAGATACTTTAGTT 7 103 0 GCGATGCAGA 0.971014 -23 ATTTCTGTATGTCGAGGCACAGCTTCAACAA 8 107 0 GCGAGGCACA 0.934142 -169 TGACCAAAAATCCGGGTCCGAATC 10 4 0 TCGGGTCCGA 0.856213 -43 CAGACCCGTCGGCGGTGCAGAGGTCTTTTAC 11 65 0 GCGGTGCAGA 0.988466 -236 CTGCACCGCCGACGGGTCTGGATTATGGGCA 11 76 1 GCGGGTCTGG 0.962268 -225 AATAATCACAGTCGAGCCAGACTACCCCTGG 11 106 1 GCGAGCCAGA 0.951573 -195 GGAGGTAAACTCCGGGGCTGGAGCCATAAAG 11 135 1 TCGGGGCTGG 0.962265 -166 ACTTTTTGGCATCGGTGCAGGTGGTGAGCC 11 281 1 ACGGTGCAGG 0.928547 -20 * ********* Masking position 4 Map Score: 3.01044 Number of sites scoring better than the average of aligned sites = 755 Number in coding regions = 730 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 9 AGTGTGAGAAGTCTGAAAAAAGTTCCATAATTT 1 35 0 GTTAAAAAGT 0.95844 -201 GGGGAAAAGGGTAGCGAAGATGTCATAATTTTT 1 166 1 GTGAAGATGT 0.844286 -70 TTTAGTAATCTTTGTTAAAAATTATGACATCTT 1 182 0 TTGAAAAATT 0.731788 -54 AGTCAATGTTGTTTTGAAAAATTGAAGGAGAAC 3 58 1 GTTAAAAATT 0.819531 -28 CCTAAATTGCGTATTAAAAAAGTTTAGTTAAAG 5 130 0 GTTAAAAAGT 0.95844 -32 GCGTAAGGATTTAGAGAAAAAGTTGCGGCAGGC 8 12 1 TTGAAAAAGT 0.932686 -264 TAAAAGTCTAGACGCAAAGTAGTCTTTTTGTTT 8 165 1 GAGAAGTAGT 0.739869 -111 TATGCTATTCGAAGATAAAAAGTATTT 9 5 0 GAGAAAAAGT 0.973622 -98 CACCTGCACCGATGCCAAAAAGTTGTTTTGTCA 11 271 0 GAGAAAAAGT 0.973622 -30 ** * ******* Masking position 7 Map Score: 3.12997 Number of sites scoring better than the average of aligned sites = 431 Number in coding regions = 350 Number in noncoding regions = 81 Number of orfs with sites within 600 bp upstream = 94 Fraction of orfs with sites within 600 bp upstream = 0.015098 Motif number 10 ********** No masking Map Score: -7.01005e-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: -7.01005e-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: -7.01005e-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