AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i246_regulatory_cassete1_synecho_reg_300.orf -o246_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 RCY41704 31 Synechocystis #2 RCY18056 198 Synechocystis #3 RCY08755 34 Synechocystis #4 RCY52765 184 Synechocystis #5 RCY48216 97 Synechocystis #6 RCY38762 115 Synechocystis #7 RCY39606 109 Synechocystis #8 RCY28192 204 Synechocystis #9 RCY32608 188 Synechocystis #10 RCY37719 186 Synechocystis #11 RCY15189 19 Synechocystis #12 RCY26294 221 Synechocystis #13 RCY35925 251 Synechocystis #14 RCY00534 35 Synechocystis #15 RCY21204 91 Synechocystis #16 RCY18152 87 Synechocystis Motif number 1 CTAACCTGGTTTTGTCCCACGGCATTTTCGG 4 96 1 TTTGTCCCAG 0.861749 -89 AAAAATTGCCATTGCCTCCGGGAAG 5 5 0 ATTGCCTCCG 0.676955 -93 GCAATTTTTCTTTGCCCCATTGTCTCGCCCC 5 27 1 TTTGCCCCAT 0.852736 -71 AGGGTCAATATGTCCCCCAAGGGCT 7 5 0 TGTCCCCCAG 0.912829 -105 TTATGATGGAATTCCCCCATATCGTAGTGGA 7 68 1 ATTCCCCCAA 0.991645 -42 TACACCTACAAACCCCCCAGGTTGGCCAGAG 9 117 0 AACCCCCCAG 0.923761 -72 GGTTTTTCTTAATCCCTCAAACTTTGGGGGA 10 64 1 AATCCCTCAA 0.841933 -123 GATTAATCAAAATCCCCCAAAGTTTGAGGGA 10 76 0 AATCCCCCAA 0.980245 -111 TTCAGGTGAGATTGTCCCAGAACCTAGCTAT 10 127 0 ATTGTCCCAA 0.9301 -60 GCAAAGAAAGTTTCCCCCATAAGGAAGCCAA 12 145 1 TTTCCCCCAA 0.983902 -77 TAAGGAAGCCAATGCCCCAGAAATAATTGTT 12 164 1 AATGCCCCAA 0.97095 -58 CCGACTGCGTATTCCCCGAAAGCTTATCCGG 13 74 1 ATTCCCCGAA 0.908713 -178 TATCCGGAAATTTCCCCCCTAACTCTACGTC 13 98 1 TTTCCCCCCA 0.94257 -154 AGATAAAGTAATCCCCCCATGGACGTAGAGT 13 119 0 ATCCCCCCAG 0.966649 -133 AACAGTCACAATTGTCCCAGACCGAAAGCAG 13 180 1 ATTGTCCCAA 0.9301 -72 ********* * Masking position 6 Map Score: 19.6636 Number of sites scoring better than the average of aligned sites = 2448 Number in coding regions = 2050 Number in noncoding regions = 398 Number of orfs with sites within 600 bp upstream = 299 Fraction of orfs with sites within 600 bp upstream = 0.0480244 Motif number 2 GGGAAATAAAAAAGGCTGAAGCTAAATTTGGTCAGAGGTC 5 67 0 AGTGAGTTTG 0.828974 -31 AAAAAAGTCAGCCCGGTGAGGAGCAATTGGGAAAACGGCT 8 127 0 GGTGGGTTGG 0.996689 -78 CTTTTAGGATGTTGGATCAGGGCCCGTTGGCAAAAATTCA 9 50 1 GGTCGGTTGG 0.990697 -139 GCTTCCTTGGGGAGGGTGAGGGGCAACTTGAATTTTTGCC 9 78 0 GGTGGGCTTG 0.995655 -111 CCCTCCCCAAGGAAGCTCTGGCCAACCTGGGGGGTTTGTA 9 102 1 GGTCGGCTGG 0.992278 -87 CTCCCTTGGCGTTAGATGCGGTTTGGCTTGA 12 2 0 GGTGGGCTTG 0.995655 -220 TAAAAAAGGAGCCTGTTGGGGCTCCCTTGGCGTTAGATGC 12 23 0 GGTGGGTTGG 0.996689 -199 GCCTCCGGTCAATTGCTGGGGTTGCTGTTGCTACCAAGGC 13 219 0 AGTGGGGTTG 0.951346 -33 * * ** ** **** Masking position 7 Map Score: 7.9436 Number of sites scoring better than the average of aligned sites = 131 Number in coding regions = 117 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 3 GTTTCGGTTAAGCCAATCTTTTGAG 3 5 1 CGGTAAGCCA 0.96765 -30 GGGACAAAACCAGGTTAGCCTTTATAGTTAA 4 83 0 CAGTTAGCCT 0.9712 -102 ACAATGGCCGTGGATAAGCCAAAAGTTTTCG 6 18 0 TGGTAAGCCA 0.708164 -98 AGAAGAATCGGGTAGGACTACATCAAACT 6 97 0 CGGTAGGACT 0.906365 -19 ATTGGGAAAACGGCTTGGGCTGACATTTATT 8 111 0 CGGTTGGGCT 0.974752 -94 ACAAACCCCCCAGGTTGGCCAGAGCTTCCTT 9 110 0 CAGTTGGCCA 0.973654 -79 GCGTTAGATGCGGTTTGGCTTGA 12 3 0 CGGTTGGCTT 0.961511 -219 TACACCGACTCAGTTTGGCAAGAATTATTGA 13 21 0 CAGTTGGCAA 0.805104 -231 GGGAAATTTCCGGATAAGCTTTCGGGGAATA 13 83 0 CGGTAAGCTT 0.913969 -169 ATTACTTGAGCAGATTAGGCTGATCAAATAC 15 53 0 CAGTTAGGCT 0.911847 -39 *** ******* Masking position 5 Map Score: 7.68549 Number of sites scoring better than the average of aligned sites = 678 Number in coding regions = 630 Number in noncoding regions = 48 Number of orfs with sites within 600 bp upstream = 58 Fraction of orfs with sites within 600 bp upstream = 0.00931577 Motif number 4 AGTCTTTTCCTGACAATTTTGCGTTTTCTAAC 2 96 1 TGCATTTTGC 0.983366 -103 TCGAAGAAGATCCCCATTTTGCATTGTATTAG 2 165 1 TCCATTTTGC 0.884466 -34 CTTCAACCATTGGCGTTTTAGCTCGCTCTTGG 4 16 1 TGCTTTTAGC 0.765693 -169 CCGGAGGCAATGGCAATTTTTCTTTGCCCCAT 5 15 1 TGCATTTTTC 0.950923 -83 CTTCTGGATTTGTCCATTTTTTTCAGTCAGGG 7 32 0 TGCATTTTTT 0.827574 -78 GAAATTTTTGTGTCAGTTTTTCAGGACAAGGT 8 39 0 TGCGTTTTTC 0.961458 -166 CTCACCGGGCTGACTTTTTTCCCAGATTTGTT 8 147 1 TGCTTTTTCC 0.900984 -58 AATATAGTCTTGTCTGCTCTGCAAAGGGTTCA 10 20 0 TGCGCTCTGC 0.846185 -167 AAAAACTCCTTGTCAACTTTGCTTTACAAAAA 12 82 1 TGCACTTTGC 0.957789 -140 TAAATAAATGTAACAGTTTTGTAAATTTTTGT 12 107 0 TACGTTTTGT 0.622244 -115 GGGACAATTGTGACTGTTTTCTTGGCAAGTCA 13 166 0 TGCGTTTTCT 0.86963 -86 ** * ******* Masking position 8 Map Score: 5.15864 Number of sites scoring better than the average of aligned sites = 795 Number in coding regions = 699 Number in noncoding regions = 96 Number of orfs with sites within 600 bp upstream = 116 Fraction of orfs with sites within 600 bp upstream = 0.0186315 Motif number 5 GCGAGCTAAAACGCCAATGGTTGAAGGCGA 4 12 0 ACGCCAATGG 0.954688 -173 TAGTCCGAAAATGCCGTGGGACAAAACCAG 4 101 0 ATGCCGTGGG 0.908303 -84 AAAATTGCCATTGCCTCCGGGAAG 5 5 0 TTGCCTCCGG 0.912192 -93 GATTGCTGCCATGACAATGGCCGTGGATAA 6 32 0 ATGACAATGG 0.834157 -84 TCGGATCTTTATGCCTAGGGCCAGCAATGG 6 60 1 ATGCCTAGGG 0.977876 -56 TGACAGGGCTATGACGACGGTATGAAATTT 8 64 0 ATGACGACGG 0.925036 -141 ACTTGAATTTTTGCCAACGGGCCCTGATCC 9 63 0 TTGCCAACGG 0.95982 -126 ACCGCATCTAACGCCAAGGGAGCCCCAACA 12 20 1 ACGCCAAGGG 0.979369 -202 AACGCCTCCGGTCAATTGCTG 13 241 0 ACGCCTCCGG 0.964432 -11 ********** Masking position 5 Map Score: 7.92256 Number of sites scoring better than the average of aligned sites = 808 Number in coding regions = 759 Number in noncoding regions = 49 Number of orfs with sites within 600 bp upstream = 58 Fraction of orfs with sites within 600 bp upstream = 0.00931577 Motif number 6 GGCGATCGCCTTAGGTCAAAGGCAA 2 3 0 TTGGCAAAGC 0.972938 -196 GGCCAGTTAGTCTGGGGTAAGGCGATCGCCTTA 2 23 0 TCGGGTAAGC 0.924758 -176 CGAAAATGCCGTGGGACAAAACCAGGTTAGCCT 4 93 0 GTGGCAAAAC 0.938654 -92 CCACGGCATTTTCGGACTAAGTCCCGGAAATAG 4 112 1 TTGGCTAAGC 0.985779 -73 TTGGAGAAAGGTGGGCCTAATCCAGGCTCAAAC 4 148 0 GTGGCTAATC 0.899667 -37 AATCGGATCTTTATGCCTAGGGCCAGCAATGGT 6 58 1 TTTGCTAGGC 0.756994 -58 GAAGAATCGGGTAGGACTACATCAAACTAACAT 6 92 0 GTGGCTACAC 0.87329 -24 TGTCAGTTTTTCAGGACAAGGTCATTGTTTTAG 8 28 0 TCGGCAAGGC 0.886414 -177 TCCTAAAAGTTTAGGAGAAAAACCCCCGTTTGT 9 26 0 TTGGGAAAAC 0.871093 -163 TGGGGGGTTTGTAGGTGTAAACCGGTTCCCAAT 9 129 1 GTGGGTAAAC 0.93786 -60 GCCAAACTGAGTCGGTGTAAGCCTTGTTAGATT 13 33 1 GTGGGTAAGC 0.976227 -219 TATCCCTGCTTTCGGTCTGGGACAATTGTGACT 13 183 0 TTGGCTGGGC 0.881699 -69 ** ** ***** * Masking position 13 Map Score: 9.79276 Number of sites scoring better than the average of aligned sites = 617 Number in coding regions = 551 Number in noncoding regions = 66 Number of orfs with sites within 600 bp upstream = 72 Fraction of orfs with sites within 600 bp upstream = 0.0115644 Motif number 7 AATGTTTTCTAGAATTGGAGAAAGG 4 170 0 GTTTTAGAAT 0.795841 -15 AATTTTAGTTAAATCTAAAAAAT 9 176 0 ATTTTTTAAA 0.802512 -13 GATCTAAATGGTTTTTCTTAATCCCTCAAACT 10 55 1 GTTTTTTAAT 0.961921 -132 ACTTTGGGGGATTTTGATTAATCTGTCTAGTG 10 84 1 ATTTTTTAAT 0.927674 -103 GTTCACAATAGTTTTTATTGAATTCACATTGC 10 164 1 GTTTTTTGAA 0.868175 -23 AGAAATAATTGTTTTTCTTGATTGCTCGTAGG 12 182 1 GTTTTTTGAT 0.954214 -40 CTCTTCGTTTTCAATAATTCTTGCCAAA 13 7 1 GTTTTATAAT 0.888479 -245 GAGGAATTTTTATGAATAGGAGACTGG 14 6 1 ATTTTTGAAT 0.862588 -30 AATAATGTTGATTTTCGTTGATTTTTGATGGA 16 16 0 ATTTTTTGAT 0.913844 -72 ***** ***** Masking position 5 Map Score: 2.92873 Number of sites scoring better than the average of aligned sites = 261 Number in coding regions = 198 Number in noncoding regions = 63 Number of orfs with sites within 600 bp upstream = 72 Fraction of orfs with sites within 600 bp upstream = 0.0115644 Motif number 8 CCCAGACTAACTGGCCAGGTGTTGTCAATC 2 40 1 CTGGCCAGGT 0.933968 -159 GCAAAAATCACTGATCTGATTGACAACACC 2 57 0 CTGATCTGAT 0.855949 -142 AGCCTGACCTCTGACCAAATTTAGCTTCAG 5 62 1 CTGACCAAAT 0.978579 -36 TCTGTCCTGACCAAATGGT 11 7 1 CTGACCAAAT 0.978579 -13 GCAGATTAGGCTGATCAAATACTAAACAAT 15 45 0 CTGATCAAAT 0.966725 -47 TCAGCCTAATCTGCTCAAGTAATTTAACTA 15 61 1 CTGCTCAAGT 0.915612 -31 ********** Masking position 2 Map Score: 2.13968 Number of sites scoring better than the average of aligned sites = 139 Number in coding regions = 121 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 9 GGCATTGACGCAAAAATCACTGATCTGATT 2 66 0 CAAAAATCAC 0.946586 -133 GCCAACAATCTCAAAAGATTGG 3 23 0 CAACAATCTC 0.805468 -12 AAAACTGACACAAAAATTTCATACCGTCGT 8 51 1 CAAAAATTTC 0.873842 -154 GGCCCGTTGGCAAAAATTCAAGTTGCCCCT 9 70 1 CAAAAATTCA 0.790935 -119 AGTTAAATCTAAAAAATCAAAGTTAAAAAG 9 163 0 AAAAAATCAA 0.67807 -26 CCATTTAGATCAAAAATATAGTCTTGTCTG 10 36 0 CAAAAATATA 0.768719 -151 CTTTGCTTTACAAAAATTTACAAAACTGTT 12 98 1 CAAAAATTTA 0.893587 -124 CTAGCTCCATCAAAAATCAACGAAAATCAA 16 11 1 CAAAAATCAA 0.955526 -77 CAAAAATCAACGAAAATCAACATTATTTGA 16 21 1 CGAAAATCAA 0.833882 -67 ********** Masking position 5 Map Score: 3.01446 Number of sites scoring better than the average of aligned sites = 356 Number in coding regions = 266 Number in noncoding regions = 90 Number of orfs with sites within 600 bp upstream = 104 Fraction of orfs with sites within 600 bp upstream = 0.0167041 Motif number 10 ACATTAATAAATGTCAGCCCAAGCCGTTTT 8 106 1 ATGTCAGCCC 0.947921 -99 TCTGGGAAAAAAGTCAGCCCGGTGAGGAGC 8 143 0 AAGTCAGCCC 0.986627 -62 CACCCTCCCCAAGGAAGCTCTGGCCAACCT 9 100 1 AAGGAAGCTC 0.943264 -89 ATCTAACGCCAAGGGAGCCCCAACAGGCTC 12 25 1 AAGGGAGCCC 0.984384 -197 TTTCCCCCATAAGGAAGCCAATGCCCCAGA 12 155 1 AAGGAAGCCA 0.943264 -67 TATCCAGATAAAGTAATCCCCCCATGGACG 13 125 0 AAGTAATCCC 0.913594 -127 ********** Masking position 6 Map Score: 3.38086 Number of sites scoring better than the average of aligned sites = 182 Number in coding regions = 165 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 11 CGCTCTTGGTATCACGGGTAACAAATTTATGGAA 4 39 1 ACAGGGTACA 0.979636 -146 TATGGAACGGAGCAGGGTTAACTATAAAGGCTAA 4 66 1 ACAGGTTACA 0.973936 -119 CGTGGGACAAAACCAGGTTAGCCTTTATAGTTAA 4 83 0 ACCGGTTGCT 0.905177 -102 CCTACAAACCCCCCAGGTTGGCCAGAGCTTCCTT 9 110 0 CCCGGTTGCA 0.933986 -79 CTCACCTGAAATCCTGGTTCACAATAGTTTTTAT 10 148 1 ACCGGTTACA 0.986562 -39 ATTTTTGTAAAGCAAAGTTGACAAGGAGTTTTTT 12 81 0 ACAAGTTACA 0.852522 -141 CAGGGATAATAGCCTTGGTAGCAACAGCAACCCC 13 208 1 ACCTGGTGCA 0.968228 -44 TCAAATACTAAACAATGGTGACTATTTACACCAT 15 27 0 ACATGGTACA 0.949507 -65 ATTTGACTGCAACCATGGTAACCAAAATACTGAT 16 45 1 ACCTGGTACA 0.973646 -43 * ** **** ** * Masking position 9 Map Score: 7.31235 Number of sites scoring better than the average of aligned sites = 230 Number in coding regions = 204 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 12 ********** No masking Map Score: 3.98858e-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: 3.98858e-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: 3.98858e-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