AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i222_Ribosomal_Operon___Transcription_synecho_reg_100.orf -o222_synecho_100.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 RCY30362 266 Synechocystis #2 RCY37275 283 Synechocystis #3 RCY38704 140 Synechocystis #4 RCY05947 54 Synechocystis #5 RCY42648 300 Synechocystis #6 RCY26670 202 Synechocystis Motif number 1 ATTAGACAAATTTGGCAAGGCAG 1 4 0 TTTGGCAAGG 0.761099 -263 CGTTAAATATCTTTACGATCGCCATTGGCT 1 67 1 CTTTACGATC 0.408819 -200 CTTCCCATGGCTAGCCAATGGCGATCGTAA 1 79 0 CTAGCCAATG 0.760201 -188 TGTATTTTAGCTTCCCATGGCTAGCCAATG 1 89 0 CTTCCCATGG 0.803549 -178 TTTACTCGCTCTCCCCTAGGGTACTCTGGC 1 150 0 CTCCCCTAGG 0.803364 -117 ATTCGTTAAATTTTCCGAGGGTTGATGGGA 2 67 1 TTTTCCGAGG 0.958409 -217 ATAGAGTGGCCTTCCCCATCCCATCAACCC 2 85 0 CTTCCCCATC 0.898478 -199 GCTGAAGGCATTACCCCAGGCCACTCCGGG 2 192 0 TTACCCCAGG 0.918936 -92 TTTTGCTCACTTTTCCGCTGGGTGCCATGG 3 29 1 TTTTCCGCTG 0.785389 -112 CCCATCCCAACTTTCCATGGCACCCAGCGG 3 43 0 CTTTCCATGG 0.832933 -98 CTAGCGGGATTTTCCCCATCCCAACTTTCC 3 57 0 TTTCCCCATC 0.809156 -84 CTCCAAAACACTTTCCCAGGTAAAGCTGAA 3 95 1 CTTTCCCAGG 0.989466 -46 GCTGTTGTTTTTTGGCTAGGTCTGAAGATT 5 37 0 TTTGGCTAGG 0.791079 -264 AGAGCGCCTGCTTTGCAAGCAGGATGTCAG 5 122 0 CTTTGCAAGC 0.733938 -179 GATTTTTCCGCTTTCCTATGGCTTATCAGG 5 246 1 CTTTCCTATG 0.946958 -55 CTTTTTACCATTTTACCCGGCTCAATTGT 5 282 1 TTTTACCCGG 0.69031 -19 GTTACCGATTCTACCCCAGCAGAGAGCGCA 6 23 0 CTACCCCAGC 0.870989 -180 AACGGGCGATTTTTCCTAGGTTTAGCCGAT 6 50 1 TTTTCCTAGG 0.955095 -153 TTTCCTAGGTTTAGCCGATGTTGGCCTTGA 6 61 1 TTAGCCGATG 0.66163 -142 CGATGTTGGCCTTGACCATGGCCGAGGAAA 6 76 1 CTTGACCATG 0.765176 -127 GATAATTGGTCTTTCCTCGGCCATGGTCAA 6 87 0 CTTTCCTCGG 0.946045 -116 GAAAGACCAATTATCCCCTGTTGATCAACC 6 102 1 TTATCCCCTG 0.686945 -101 TAAACAAGGCCTTTGCTAGGGCGGAATTAC 6 166 1 CTTTGCTAGG 0.919896 -37 ********** Masking position 2 Map Score: 22.2669 Number of sites scoring better than the average of aligned sites = 5980 Number in coding regions = 5295 Number in noncoding regions = 685 Number of orfs with sites within 600 bp upstream = 600 Fraction of orfs with sites within 600 bp upstream = 0.0963701 Motif number 2 TAGACAAATTTGGCAAGGCAG 1 2 0 TGGCAAGGCA 0.862463 -265 TTTAACGCAATGGTGTGGGGCCATAGAATG 1 44 0 TGGTGTGGGG 0.920304 -223 ACTCTGGCTTTGGGAAAGGGTAAATGGGGT 1 128 0 TGGGAAAGGG 0.979454 -139 GAGTACCCTAGGGGAGAGCGAGTAAATTGC 1 154 1 GGGGAGAGCG 0.934086 -113 CGAGGGTTGATGGGATGGGGAAGGCCACTC 2 82 1 TGGGATGGGG 0.994116 -202 TGACCCGGAGTGGCCTGGGGTAATGCCTTC 2 189 1 TGGCCTGGGG 0.970926 -95 TTGCTTAGTTTGCGATGGCGTCAGCGGCAT 2 232 0 TGCGATGGCG 0.966674 -52 CATGGAAAGTTGGGATGGGGAAAATCCCGC 3 54 1 TGGGATGGGG 0.994116 -87 CAGCTTTACCTGGGAAAGTGTTTTGGAGTT 3 93 0 TGGGAAAGTG 0.860789 -48 TTAGCTCAGTTGGTAGAGCGCCTGCTTTGC 5 136 0 TGGTAGAGCG 0.964257 -165 GCCTTGACCATGGCCGAGGAAAGACCAATT 6 84 1 TGGCCGAGGA 0.730023 -119 ACAAGGCCTTTGCTAGGGCGGAATTACGAG 6 169 1 TGCTAGGGCG 0.918349 -34 ********** Masking position 8 Map Score: 13.7357 Number of sites scoring better than the average of aligned sites = 2110 Number in coding regions = 1919 Number in noncoding regions = 191 Number of orfs with sites within 600 bp upstream = 215 Fraction of orfs with sites within 600 bp upstream = 0.0345326 Motif number 3 GCCATGGGAAGCTAAAATACAGGCCGGATA 1 98 1 GCTAAAATAC 0.924163 -169 CTTTGGGAAAGGGTAAATGGGGTTATCCGG 1 121 0 GGGTAAATGG 0.842457 -146 AAATTGCAGGCCGAAAATCCGAGAGAATCG 1 177 1 CCGAAAATCC 0.864177 -90 CGAGAGAATCGGTAAAATGGCAAAGTCAGC 1 196 1 GGTAAAATGG 0.975897 -71 GGGTTTACAAGCGAAAATGCTGACTTTGCC 1 214 0 GCGAAAATGC 0.969815 -53 CACTAACTAGCCTAAAATAGAGTGGCCTTC 2 101 0 CCTAAAATAG 0.750246 -183 GGAAAAGTGAGCAAAAATAGCGCTAACTAC 3 15 0 GCAAAAATAG 0.925137 -126 AGTTGGGATGGGGAAAATCCCGCTAGGGTT 3 61 1 GGGAAAATCC 0.977602 -80 AACTTCTATGGCTATAATAGCTGAGGTTTG 5 203 0 GCTATAATAG 0.640376 -98 ATAGGAAAGCGGAAAAATCCTTGCTTGTTG 5 235 0 GGAAAAATCC 0.956844 -66 AATTGAGCCGGGTAAAATGGTAAAAAGTTG 5 279 0 GGTAAAATGG 0.975897 -22 CCAGCAGAGAGCGCAAATCCTTTGTTA 6 8 0 GCGCAAATCC 0.848254 -195 TCTCTGCTGGGGTAGAATCGGTAACGGGCG 6 28 1 GGTAGAATCG 0.87569 -175 GCTAAACCTAGGAAAAATCGCCCGTTACCG 6 46 0 GGAAAAATCG 0.970561 -157 GGAAAAATGGGTCTCTCGTA 6 193 0 GGAAAAATGG 0.965091 -10 ********** Masking position 6 Map Score: 20.5172 Number of sites scoring better than the average of aligned sites = 1011 Number in coding regions = 855 Number in noncoding regions = 156 Number of orfs with sites within 600 bp upstream = 182 Fraction of orfs with sites within 600 bp upstream = 0.0292323 Motif number 4 ATTGCCTTCATTCTATGGCCCCACACCATT 1 36 1 TTCTATGGCC 0.98474 -231 TATTTTAGCTTCCCATGGCTAGCCAATGGC 1 87 0 TCCCATGGCT 0.987064 -180 TCCCCTAGGGTACTCTGGCTTTGGGAAAGG 1 139 0 TACTCTGGCT 0.945635 -128 CATCCCAACTTTCCATGGCACCCAGCGGAA 3 41 0 TTCCATGGCA 0.905536 -100 TGTTGTGAACTTCTATGGCTATAATAGCTG 5 210 0 TTCTATGGCT 0.987712 -91 TTTTCCGCTTTCCTATGGCTTATCAGGTAA 5 249 1 TCCTATGGCT 0.9886 -52 TGTTGGCCTTGACCATGGCCGAGGAAAGAC 6 79 1 GACCATGGCC 0.893876 -124 ********** Masking position 6 Map Score: 9.57614 Number of sites scoring better than the average of aligned sites = 232 Number in coding regions = 204 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 5 AAGCCAGAGTACCCTAGGGGAGAGCGAGTA 1 148 1 ACCCTAGGGG 0.647759 -119 CATCCCATCAACCCTCGGAAAATTTAACGA 2 69 0 ACCCTCGGAA 0.947237 -215 CTTTCCATGGCACCCAGCGGAAAAGTGAGC 3 33 0 CACCCAGCGG 0.877981 -108 TGGAGTTAGAACCCTAGCGGGATTTTCCCC 3 70 0 ACCCTAGCGG 0.966146 -71 ACTGAGCTAAACCCCCGTGAACTGGTGCAT 5 156 1 ACCCCCGTGA 0.876043 -145 TACCGATTCTACCCCAGCAGAGAGCGCAAA 6 21 0 ACCCCAGCAG 0.984841 -182 ACATCGGCTAAACCTAGGAAAAATCGCCCG 6 52 0 AACCTAGGAA 0.879237 -151 TCGTAATTCCGCCCTAGCAAAGGCCTTGTT 6 168 0 GCCCTAGCAA 0.927895 -35 ********** Masking position 4 Map Score: 5.80569 Number of sites scoring better than the average of aligned sites = 1091 Number in coding regions = 1019 Number in noncoding regions = 72 Number of orfs with sites within 600 bp upstream = 91 Fraction of orfs with sites within 600 bp upstream = 0.0146161 Motif number 6 GGTAAAATGGCAAAGTCAGCATTTTCGCTT 1 206 1 CAAAGTCAGC 0.782601 -61 CTTGTAAACCCAACATTACCTACAAACTTC 1 233 1 CAACATTACC 0.919614 -34 AAACTTCAACAAAAAACACCT 1 256 1 AAAAAACACC 0.88979 -11 CGAAAGTTGTAAACATGACCCGGAGTGGCC 2 174 1 AAACATGACC 0.950513 -110 GAAAAGTGAGCAAAAATAGCGCTAACTACT 3 14 0 CAAAAATAGC 0.675091 -127 CCTAGCCAAAAAACAACAGCCAGGAATATC 5 47 1 AAACAACAGC 0.948519 -254 CTTTGGTAACAAACCTCAGCTATTATAGCC 5 194 1 AAACCTCAGC 0.930732 -107 TAAACCTAGGAAAAATCGCCCGTTACCGAT 6 44 0 AAAAATCGCC 0.895576 -159 TGGTCAAGGCCAACATCGGCTAAACCTAGG 6 64 0 CAACATCGGC 0.963324 -139 CCCTGTTGATCAACCTGACCAGCGCTAATC 6 117 1 CAACCTGACC 0.91724 -86 CCATCCCCATAAACAAGGCCTTTGCTAGGG 6 157 1 AAACAAGGCC 0.876435 -46 ********** Masking position 3 Map Score: 7.22543 Number of sites scoring better than the average of aligned sites = 1059 Number in coding regions = 984 Number in noncoding regions = 75 Number of orfs with sites within 600 bp upstream = 84 Fraction of orfs with sites within 600 bp upstream = 0.0134918 Motif number 7 GGGTAAATGGGGTTATCCGGCCTGTATTTT 1 111 0 GGTTATCCGG 0.982386 -156 CACACCATCTGGTGAACCGGA 2 2 0 GGTGAACCGG 0.97883 -282 ATACAGCATAGGTTAATAGGTTAGTCTTAC 2 34 0 GGTTAATAGG 0.945827 -250 ATTTTCCGAGGGTTGATGGGATGGGGAAGG 2 76 1 GGTTGATGGG 0.894631 -208 CTTTCCTATGGCTTATCAGGTAACAACTTT 5 256 1 GCTTATCAGG 0.963373 -45 ACTGATTAGCGCTGGTCAGGTTGATCAACA 6 120 0 GCTGGTCAGG 0.947013 -83 ********** Masking position 3 Map Score: 1.34985 Number of sites scoring better than the average of aligned sites = 276 Number in coding regions = 242 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 45 Fraction of orfs with sites within 600 bp upstream = 0.00722775 Motif number 8 AATGGGGTTATCCGGCCTGTATTTTAGCTT 1 106 0 TCCGGCCTGT 0.9889 -161 CTCTCGGATTTTCGGCCTGCAATTTACTCG 1 172 0 TTCGGCCTGC 0.985298 -95 TTTCAGATATTCCTGGCTGTTGTTTTTTGG 5 52 0 TCCTGGCTGT 0.976855 -249 ACCGCTGACATCCTGCTTGCAAAGCAGGCG 5 118 1 TCCTGCTTGC 0.977788 -183 ********** Masking position 8 Map Score: 0.70698 Number of sites scoring better than the average of aligned sites = 79 Number in coding regions = 69 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 9 ********** No masking Map Score: -1.93735e-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: -1.93735e-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: -1.93735e-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