AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i222_Ribosomal_Operon___Transcription_synecho_reg_300.orf -o222_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 RCY30362 266 Synechocystis #2 RCY37275 283 Synechocystis #3 RCY38704 140 Synechocystis #4 RCY05947 54 Synechocystis #5 RCY42648 300 Synechocystis #6 RCY26670 202 Synechocystis #7 RCY31923 135 Synechocystis #8 RCY04429 240 Synechocystis #9 RCY45916 300 Synechocystis Motif number 1 CATTGGCTAGCCATGGGAAGCTAAAATACA 1 89 1 CCATGGGAAG 0.969884 -178 GGTACTCTGGCTTTGGGAAAGGGTAAATGG 1 131 0 CTTTGGGAAA 0.798938 -136 GCCAGAGTACCCTAGGGGAGAGCGAGTAAA 1 150 1 CCTAGGGGAG 0.925231 -117 TCCCATCAACCCTCGGAAAATTTAACGAAT 2 67 0 CCTCGGAAAA 0.739142 -217 GGGTTGATGGGATGGGGAAGGCCACTCTAT 2 85 1 GATGGGGAAG 0.915522 -199 CCCGGAGTGGCCTGGGGTAATGCCTTCAGC 2 192 1 CCTGGGGTAA 0.971261 -92 TCCATGGCACCCAGCGGAAAAGTGAGCAAA 3 30 0 CCAGCGGAAA 0.758861 -111 CCGCTGGGTGCCATGGAAAGTTGGGATGGG 3 43 1 CCATGGAAAG 0.888226 -98 GGAAAGTTGGGATGGGGAAAATCCCGCTAG 3 57 1 GATGGGGAAA 0.844159 -84 TTCAGCTTTACCTGGGAAAGTGTTTTGGAG 3 95 0 CCTGGGAAAG 0.977667 -46 CCTGATAAGCCATAGGAAAGCGGAAAAATC 5 246 0 CATAGGAAAG 0.73759 -55 TGCGCTCTCTGCTGGGGTAGAATCGGTAAC 6 23 1 GCTGGGGTAG 0.93421 -180 ATCGGCTAAACCTAGGAAAAATCGCCCGTT 6 50 0 CCTAGGAAAA 0.82849 -153 GGGATTCTTACTTTGGGTAGAAACCCTTGC 8 84 1 CTTTGGGTAG 0.75164 -157 AGCGATAATTCAAGGGGAAAATTATGACTC 8 168 0 CAAGGGGAAA 0.929684 -73 TCAGCCTTGGGTAGTTAAAATTTT 8 227 0 CCTTGGGTAG 0.959908 -14 CCTACTCAAACAAGGGGGAGATTTAACTGC 9 52 1 CAAGGGGGAG 0.893128 -249 TCACTGTAGACCAGGGGCAATGGTCAATAG 9 139 0 CCAGGGGCAA 0.886415 -162 ********** Masking position 9 Map Score: 20.5124 Number of sites scoring better than the average of aligned sites = 3865 Number in coding regions = 3445 Number in noncoding regions = 420 Number of orfs with sites within 600 bp upstream = 409 Fraction of orfs with sites within 600 bp upstream = 0.0656923 Motif number 2 GCAATGGTGTGGGGCCATAGAATGAAGGCAA 1 37 0 GGGCCATAGA 0.90397 -230 TATCTTTACGATCGCCATTGGCTAGCCATGG 1 74 1 ATGCCATTGG 0.802433 -193 TCGCCATTGGCTAGCCATGGGAAGCTAAAAT 1 85 1 CTGCCATGGG 0.901867 -182 TCCGAGGGTTGATGGGATGGGGAAGGCCACT 2 80 1 GAGGGATGGG 0.931353 -204 CATGACCCGGAGTGGCCTGGGGTAATGCCTT 2 187 1 AGGGCCTGGG 0.827437 -97 TTTTCCGCTGGGTGCCATGGAAAGTTGGGAT 3 39 1 GGGCCATGGA 0.985455 -102 GCCATGGAAAGTTGGGATGGGGAAAATCCCG 3 52 1 GTGGGATGGG 0.977238 -89 CTCAGCTATTATAGCCATAGAAGTTCACAAC 5 208 1 ATGCCATAGA 0.638504 -93 TTTAGCCGATGTTGGCCTTGACCATGGCCGA 6 70 1 GTGGCCTTGA 0.624184 -133 GGCCTTGTTTATGGGGATGGATCAAATACTG 6 146 0 ATGGGATGGA 0.873983 -57 ACTGATTGGAGTAGTGATGGA 7 1 0 GTGTGATGGA 0.879492 -135 GTCAGTTTGCGAGGTGATGGGAGCGATAATT 8 188 0 GAGTGATGGG 0.787284 -53 GGATTTTAGTGGGGCGATTGAGCGGGATGAT 9 22 0 GGGCGATTGA 0.920713 -279 CTGTAGACCAGGGGCAATGGTCAATAGAAGT 9 135 0 GGGCAATGGT 0.705085 -166 CACAGGGGAGGGAGCAATGGGTTCATAAACA 9 276 0 GGGCAATGGG 0.955376 -25 ** ******** Masking position 8 Map Score: 9.06794 Number of sites scoring better than the average of aligned sites = 3254 Number in coding regions = 2987 Number in noncoding regions = 267 Number of orfs with sites within 600 bp upstream = 276 Fraction of orfs with sites within 600 bp upstream = 0.0443302 Motif number 3 TTTGGGAAAGGGTAAATGGGGTTATCCGGC 1 120 0 GGTAAATGGG 0.957192 -147 CGAGAGAATCGGTAAAATGGCAAAGTCAGC 1 196 1 GGTAAAATGG 0.978607 -71 ATACAGCATAGGTTAATAGGTTAGTCTTAC 2 34 0 GGTTAATAGG 0.787774 -250 ATTTTCCGAGGGTTGATGGGATGGGGAAGG 2 76 1 GGTTGATGGG 0.813205 -208 TGGGTGCCATGGAAAGTTGGGATGGGGAAA 3 47 1 GGAAAGTTGG 0.866953 -94 AATTGAGCCGGGTAAAATGGTAAAAAGTTG 5 279 0 GGTAAAATGG 0.978607 -22 TCTCTGCTGGGGTAGAATCGGTAACGGGCG 6 28 1 GGTAGAATCG 0.840244 -175 GCTAAACCTAGGAAAAATCGCCCGTTACCG 6 46 0 GGAAAAATCG 0.893104 -157 GATCAACAGGGGATAATTGGTCTTTCCTCG 6 98 0 GGATAATTGG 0.933985 -105 GGAAAAATGGGTCTCTCGTA 6 193 0 GGAAAAATGG 0.968988 -10 ********** Masking position 2 Map Score: 10.8624 Number of sites scoring better than the average of aligned sites = 623 Number in coding regions = 531 Number in noncoding regions = 92 Number of orfs with sites within 600 bp upstream = 110 Fraction of orfs with sites within 600 bp upstream = 0.0176678 Motif number 4 AAAATACAGGCCGGATAACCCCATTTACCC 1 111 1 CCGGATAACC 0.964992 -156 TTTCCCAAAGCCAGAGTACCCTAGGGGAGA 1 141 1 CCAGAGTACC 0.873863 -126 TCCGGTTCACCAGATGGTGTG 2 2 1 CCGGTTCACC 0.872333 -282 TAAACATGACCCGGAGTGGCCTGGGGTAAT 2 183 1 CCGGAGTGGC 0.87619 -101 AAAGTTGTTACCTGATAAGCCATAGGAAAG 5 256 0 CCTGATAAGC 0.977248 -45 TGTTGATCAACCTGACCAGCGCTAATCAGT 6 120 1 CCTGACCAGC 0.954231 -83 TGGATCAAATACTGATTAGCGCTGGTCAGG 6 130 0 ACTGATTAGC 0.812255 -73 GGTACAACTACCAGATCAGCAATTAGGCAT 7 109 1 CCAGATCAGC 0.9727 -27 TCGAGGCTTCCCTGATAAGCTTTTCGGGGA 8 58 1 CCTGATAAGC 0.977248 -183 ********** Masking position 2 Map Score: 6.24482 Number of sites scoring better than the average of aligned sites = 272 Number in coding regions = 240 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467 Motif number 5 CTGCCTTGCCAAATTTGTCTAA 1 1 1 CGCCTGCCAA 0.934492 -266 CTTGTAAACCCAACATTACCTACAAACTTCAA 1 233 1 CACATACCTA 0.912201 -34 GGTGTGATGTAAGACTAACCTATTAACCTATG 2 26 1 AGACTACCTA 0.771215 -258 AAGTTTCCCACTAACTAGCCTAAAATAGAGTG 2 107 0 CAACTGCCTA 0.970725 -177 GACGCCATCGCAAACTAAGCAAGCATTAATAC 2 240 1 CAACTAGCAA 0.924144 -44 CGCAATCTTCAGACCTAGCCAAAAAACAACAG 5 34 1 AACCTGCCAA 0.902068 -267 AGGCGCTCTACCAACTGAGCTAAACCCCCGTG 5 143 1 CAACTAGCTA 0.953839 -158 CTTTGGTAACAAACCTCAGCTATTATAGCCAT 5 194 1 AACCTAGCTA 0.906847 -107 TGGTCAAGGCCAACATCGGCTAAACCTAGGAA 6 62 0 CACATGGCTA 0.849901 -141 CCCTGTTGATCAACCTGACCAGCGCTAATCAG 6 117 1 CACCTACCAG 0.882187 -86 CATCACCTCGCAAACTGACCTAGTAAGAAAAT 8 200 1 CAACTACCTA 0.972571 -41 * **** ***** Masking position 6 Map Score: 6.88697 Number of sites scoring better than the average of aligned sites = 516 Number in coding regions = 440 Number in noncoding regions = 76 Number of orfs with sites within 600 bp upstream = 95 Fraction of orfs with sites within 600 bp upstream = 0.0152586 Motif number 6 TACTCGCTCTCCCCTAGGGTACTCTGGCTTTG 1 146 0 CCCCTAGTAC 0.970749 -121 GCTCACTTTTCCGCTGGGTGCCATGGAAAGTT 3 33 1 CCGCTGGGCC 0.98588 -108 GGGGAAAATCCCGCTAGGGTTCTAACTCCAAA 3 70 1 CCGCTAGTTC 0.972979 -71 CGGTTCGAGTCCGCTAATCTCCATACTTTTTC 5 90 0 CCGCTAATCC 0.989128 -211 CGGACTCGAACCGCTGACATCCTGCTTGCAAA 5 109 1 CCGCTGATCC 0.99098 -192 CTCAATCGCCCCACTAAAATCCCTACTCAAAC 9 31 1 CCACTAATCC 0.945753 -270 TTGACCATTGCCCCTGGTCTACAGTGAAAATA 9 142 1 CCCCTGGTAC 0.975655 -159 ******* *** Masking position 5 Map Score: 5.13641 Number of sites scoring better than the average of aligned sites = 137 Number in coding regions = 124 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 7 GGCCTGCAATTTACTCGCTCTCCCCTAGGG 1 159 0 TTACTCGCTC 0.863565 -108 AGCGCTATTTTTGCTCACTTTTCCGCTGGG 3 21 1 TTGCTCACTT 0.848699 -120 GGTCTGAAGATTGCGCCCTAGATATACTAG 5 19 0 TTGCGCCCTA 0.982927 -282 CTGGTGCATGTTACGCCCTTTGGTAACAAA 5 177 1 TTACGCCCTT 0.953334 -124 AACAAAGGATTTGCGCTCTCTGCTGGGGTA 6 12 1 TTGCGCTCTC 0.963071 -191 TCTCTCGTAATTCCGCCCTAGCAAAGGCCT 6 172 0 TTCCGCCCTA 0.944946 -31 TATGAACCCATTGCTCCCTCCCCTGTGGCC 9 280 1 TTGCTCCCTC 0.985064 -21 ********** Masking position 2 Map Score: 4.43652 Number of sites scoring better than the average of aligned sites = 145 Number in coding regions = 119 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 8 AAAATGGCAAAGTCAGCATTTTCGCTTGTA 1 209 1 AGTCAGCATT 0.88078 -58 TCGCAAACTAAGCAAGCATTAATACAAATC 2 247 1 AGCAAGCATT 0.975757 -37 AAAAAACAACAGCCAGGAATATCTGAAAAC 5 54 1 AGCCAGGAAT 0.897628 -247 CTGCTTGCAAAGCAGGCGCTCTACCAACTG 5 130 1 AGCAGGCGCT 0.869477 -171 GTTCACAACAAGCAAGGATTTTTCCGCTTT 5 230 1 AGCAAGGATT 0.981432 -71 TCATAATTCTAGCAAGGGTTTCTACCCAAA 8 95 0 AGCAAGGGTT 0.972644 -146 CCCTTGTTTGAGTAGGGATTTTAGTGGGGC 9 38 0 AGTAGGGATT 0.906578 -263 ********** Masking position 1 Map Score: 2.11283 Number of sites scoring better than the average of aligned sites = 154 Number in coding regions = 124 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 9 AATACAGGCCGGATAACCCCATTTACCCTTT 1 113 1 GGATAACCCA 0.963047 -154 CAATAGATGCCGCTGACGCCATCGCAAACTA 2 226 1 CGCTGAGCCA 0.794145 -58 GGCTACTCCTAGTATATCTAG 5 1 1 GGCTACCCTA 0.852821 -300 GGCCAACATCGGCTAAACCTAGGAAAAATCG 6 56 0 GGCTAACCTA 0.965259 -147 CCTCGGCCATGGTCAAGGCCAACATCGGCTA 6 72 0 GGTCAAGCCA 0.734365 -131 AAAAGCTCTGGGCCAAGGCAATTTGGTATTA 7 65 1 GGCCAAGCAA 0.90172 -71 AATGAATTTAGGATAAATCTAAATCTGGATT 8 19 0 GGATAATCTA 0.879407 -222 GTGATGGGAGCGATAATTCAAGGGGAAAATT 8 175 0 CGATAATCAA 0.599606 -66 CGATTGAGCGGGATGATCCTATCTTTAA 9 8 0 GGATGACCTA 0.90272 -293 TCTCTAAGCAGGATAAGGCAAAAGCTCCCCA 9 229 0 GGATAAGCAA 0.943098 -72 ****** **** Masking position 11 Map Score: 0.745843 Number of sites scoring better than the average of aligned sites = 947 Number in coding regions = 853 Number in noncoding regions = 94 Number of orfs with sites within 600 bp upstream = 101 Fraction of orfs with sites within 600 bp upstream = 0.0162223 Motif number 10 ********** No masking Map Score: 2.80908e-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 GCCATGGGAAGCTAAAATACAGGCCGGATAA 1 98 1 GCAAAATACA 0.953383 -169 AACTAAGCAAGCATTAATACAAATCAGTAGA 2 252 1 GCTTAATACA 0.953382 -32 GCATGTAATTGCCTTAATTCATCTGAAAATT 4 18 1 GCTTAATTCA 0.953383 -37 TTCAGACCTAGCCAAAAAACAACAGCCAGGA 5 41 1 GCAAAAAACA 0.834588 -260 TTTAGATTTATCCTAAATTCATTTTTTGTCC 8 27 1 TCTAAATTCA 0.759841 -214 GGTGATGGGAGCGATAATTCAAGGGGAAAAT 8 176 0 GCATAATTCA 0.953383 -65 ** ******** Masking position 6 Map Score: 0.0171472 Number of sites scoring better than the average of aligned sites = 86 Number in coding regions = 72 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 12 ********** No masking Map Score: 2.80908e-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: 2.80908e-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: 2.80908e-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