AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i231_protease_clp_synecho_reg_300.orf -o231_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 RCY26220 201 Synechocystis #2 RCY36788 79 Synechocystis #3 RCY02011 299 Synechocystis #4 RCY53113 300 Synechocystis Motif number 1 ACGCCGTTGCCCAATGGAGTGATCTAGTTAG 1 50 1 CCATGGAGTG 0.955439 -152 TATTTATAGACCACTGGCGATCGGCATGGTA 1 113 0 CCATGGCGAT 0.983741 -89 ATTACCCAAGCCAGTGCCGAGGAACGAAATT 1 143 0 CCATGCCGAG 0.971204 -59 GCCCAAATTACCCTTGGGGTGTCAGAGGCAT 3 18 1 CCCTGGGGTG 0.985446 -282 CCCTCCCTGTCCTAGGGCGTTAGTCCCCCAA 3 118 1 CCTGGGCGTT 0.984974 -182 TTTACTTGAGCCTTGGGGGACTAACGCCCTA 3 130 0 CCTGGGGGAC 0.921335 -170 CGGGGGGTCCCCCAGGCCGGTTTGAGAGAAT 4 27 0 CCCGGCCGGT 0.979939 -274 CCTGGGGGACCCCCCGGCGGGAAAAGATTCT 4 42 1 CCCCGGCGGG 0.697493 -259 GCCATTTTTTCCTAGGGCGAGAATCTTTTCC 4 61 0 CCTGGGCGAG 0.995021 -240 TCGGGGAAGACCTGTGGCGGTCAACCCAATT 4 112 0 CCTTGGCGGT 0.992047 -189 ACTAAGTTCACCCCTGGAGGGCTGGGAAGGA 4 239 0 CCCTGGAGGG 0.974519 -62 *** ******* Masking position 2 Map Score: 18.8809 Number of sites scoring better than the average of aligned sites = 1698 Number in coding regions = 1548 Number in noncoding regions = 150 Number of orfs with sites within 600 bp upstream = 170 Fraction of orfs with sites within 600 bp upstream = 0.0273049 Motif number 2 TCCCCTGGCTCCCAATCCCTAGA 2 2 1 CCCCTGCCCC 0.993919 -78 TGGCTCCCAATCCCTAGAAGCGGAGAATATGG 2 16 1 TCCCTAAGCG 0.851476 -64 GCCCGGTATGCCTCTGACACCCCAAGGGTAAT 3 24 0 CCTCTGCCCC 0.975895 -276 CAGATTAACCTCCTGCCCTCCCTGTCCTAGGG 3 103 1 TCCTGCCCCC 0.96813 -197 TTTTCCCCACTCCTTGGACGCCGGCTTGATCC 3 230 1 TCCTTGAGCC 0.982878 -70 GCCGGCTTGATCCCTGTCCGCCTTTTTCTTAA 3 249 1 TCCCTGCGCC 0.993222 -51 TTAGTCCCATTCTCTCAAACCGGCCTGGGGGA 4 19 1 TCTCTCACCG 0.916534 -282 AGGGCGAGAATCTTTTCCCGCCGGGGGGTCCC 4 47 0 TCTTTTCGCC 0.838261 -254 GGAAATGTTTCCCTTCTAGCCCCGCAACGCAA 4 147 0 CCCTTCACCC 0.987547 -154 GGTCTGTGGGCCCTTCTACCCGTGTTATGCTA 4 196 0 CCCTTCACCG 0.968644 -105 ATTTCTGCAGTCCTTCCCAGCCCTCCAGGGGT 4 229 1 TCCTTCCGCC 0.992657 -72 ****** * *** Masking position 2 Map Score: 14.8655 Number of sites scoring better than the average of aligned sites = 1708 Number in coding regions = 1480 Number in noncoding regions = 228 Number of orfs with sites within 600 bp upstream = 224 Fraction of orfs with sites within 600 bp upstream = 0.0359782 Motif number 3 ATTCCGTAGCATTTCCAGAATATTTCCAGA 1 172 1 ATTTCCAGAA 0.83018 -30 TTTCCAGAATATTTCCAGAAAATTACCAT 1 183 1 ATTTCCAGAA 0.83018 -19 TACCGTAGTATTCTCCCTAGATTGTGCCAT 2 44 0 TTCTCCCTAG 0.827349 -36 GAAAAGTTTTTTTTCCCCACTCCTTGGACG 3 220 1 TTTTCCCCAC 0.910769 -80 TTTTTCTTAATTTTCCCTACCTTTCCCCGT 3 271 1 TTTTCCCTAC 0.965415 -29 TTTCCCTACCTTTCCCCGTACCTAACCC 3 282 1 TTTCCCCGTA 0.831501 -18 GGCGAGAATCTTTTCCCGCCGGGGGGTCCC 4 47 0 TTTTCCCGCC 0.980258 -254 CGGGTGCCATTTTTTCCTAGGGCGAGAATC 4 67 0 TTTTTCCTAG 0.666991 -234 CGCCACAGGTCTTCCCCGAGCCATTGCGTT 4 124 1 CTTCCCCGAG 0.955257 -177 GAAGGGAAACATTTCCCTCGGTCTAAGTGA 4 163 1 ATTTCCCTCG 0.922002 -138 TTCTGCAGTCCTTCCCAGCCCTCCAGGGGT 4 231 1 CTTCCCAGCC 0.86559 -70 ACCATCGAGATTTCCCATCA 4 291 1 TTTCCCATCA 0.813681 -10 ********** Masking position 2 Map Score: 7.32064 Number of sites scoring better than the average of aligned sites = 3304 Number in coding regions = 2931 Number in noncoding regions = 373 Number of orfs with sites within 600 bp upstream = 375 Fraction of orfs with sites within 600 bp upstream = 0.0602313 Motif number 4 TCCCCTGGCTCCCAATCCCTAGA 2 4 1 CCTGGCTCCC 0.940733 -76 CCCGTTGGCCCAAATTACCC 3 1 1 CCCGTTGGCC 0.95314 -299 CAGAGGCATACCGGGCCTCCGCAAACTAGA 3 40 1 CCGGGCCTCC 0.950165 -260 CGCCCTAGGACAGGGAGGGCAGGAGGTTAA 3 107 0 CAGGGAGGGC 0.929303 -193 AAGATGAGACCATGTCGGCAACAAAGTTGA 3 168 1 CATGTCGGCA 0.84936 -132 TTCCCCACTCCTTGGACGCCGGCTTGATCC 3 232 1 CTTGGACGCC 0.900374 -68 CGGCTTGATCCCTGTCCGCCTTTTTCTTAA 3 251 1 CCTGTCCGCC 0.983166 -49 CTCAAACCGGCCTGGGGGACCCCCCGGCGG 4 32 1 CCTGGGGGAC 0.931556 -269 TGGGGGACCCCCCGGCGGGAAAAGATTCTC 4 44 1 CCCGGCGGGA 0.970274 -257 ATAATATAAGCCGGGTGCCATTTTTTCCTA 4 78 0 CCGGGTGCCA 0.887924 -223 TAAGTTCACCCCTGGAGGGCTGGGAAGGAC 4 238 0 CCTGGAGGGC 0.989267 -63 ********** Masking position 1 Map Score: 7.28287 Number of sites scoring better than the average of aligned sites = 3674 Number in coding regions = 3456 Number in noncoding regions = 218 Number of orfs with sites within 600 bp upstream = 202 Fraction of orfs with sites within 600 bp upstream = 0.0324446 Motif number 5 TCCCCTGGCTCCCAATCCCT 2 1 1 TCCCCTGGCT 0.92325 -79 ATTAACCTCCTGCCCTCCCTGTCCTAGGGC 3 106 1 TGCCCTCCCT 0.978638 -194 TTTCTTAATTTTCCCTACCTTTCCCCGTAC 3 273 1 TTCCCTACCT 0.966284 -27 CGAGAATCTTTTCCCGCCGGGGGGTCCCCC 4 45 0 TTCCCGCCGG 0.958458 -256 CGGGAAAAGATTCTCGCCCTAGGAAAAAAT 4 59 1 TTCTCGCCCT 0.979788 -242 CCACAGGTCTTCCCCGAGCCATTGCGTTGC 4 126 1 TCCCCGAGCC 0.940719 -175 AATGTTTCCCTTCTAGCCCCGCAACGCAAT 4 146 0 TTCTAGCCCC 0.843881 -155 AGGGAAACATTTCCCTCGGTCTAAGTGAAC 4 165 1 TTCCCTCGGT 0.951612 -136 CTGCAGTCCTTCCCAGCCCTCCAGGGGTGA 4 233 1 TCCCAGCCCT 0.979387 -68 ********** Masking position 1 Map Score: 6.3969 Number of sites scoring better than the average of aligned sites = 1965 Number in coding regions = 1792 Number in noncoding regions = 173 Number of orfs with sites within 600 bp upstream = 194 Fraction of orfs with sites within 600 bp upstream = 0.0311597 Motif number 6 AATGCACTGACTAAATTGACAGGAAATAAG 1 19 0 CTAAATTGAC 0.961868 -183 TCCGGAATAGGTAAATTGACAGGGCAGATT 3 79 1 GTAAATTGAC 0.814836 -221 CTCATCTTACCTAGATTTACTTGAGCCTTG 3 146 0 CTAGATTTAC 0.931454 -154 TTACTTTGCTTTAGGTTAACTCAACTTTGT 3 188 0 TTAGGTTAAC 0.907325 -112 TTATGATCAATTGGGTTGACCGCCACAGGT 4 104 1 TTGGGTTGAC 0.922884 -197 CCGTGTTATGCTAGGTTCACTTAGACCGAG 4 179 0 CTAGGTTCAC 0.987477 -122 GCAGTGGGCACTAAGTTCACCCCTGGAGGG 4 249 0 CTAAGTTCAC 0.973886 -52 ********** Masking position 9 Map Score: 3.96377 Number of sites scoring better than the average of aligned sites = 249 Number in coding regions = 216 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 7 TCCCCTGGCTCCCAATCCCTAGAAG 2 5 1 CTGGCCCCAA 0.993889 -75 CGGTATGCCTCTGACACCCCAAGGGTAATTT 3 22 0 CTGACCCCCA 0.992362 -278 CCTTGGGGGACTAACGCCCTAGGACAGGGAG 3 120 0 CTAACCCCTA 0.954139 -180 AGGGATCAAGCCGGCGTCCAAGGAGTGGGGA 3 233 0 CCGGCTCCAA 0.956287 -67 TGTTTCCCTTCTAGCCCCGCAACGCAATGGC 4 143 0 CTAGCCCGCA 0.982484 -158 GCAGTCCTTCCCAGCCCTCCAGGGGTGAACT 4 235 1 CCAGCCTCCA 0.969111 -66 ***** ***** Masking position 11 Map Score: 3.03141 Number of sites scoring better than the average of aligned sites = 560 Number in coding regions = 476 Number in noncoding regions = 84 Number of orfs with sites within 600 bp upstream = 81 Fraction of orfs with sites within 600 bp upstream = 0.01301 Motif number 8 AGATGTAACTTATTTCCTGTCAATTTA 1 7 1 AACTTATTCC 0.876111 -195 TCAGTGCATTAACGCCGTTGCCCAATGGAGT 1 39 1 AACGCCGTGC 0.973364 -163 GTCTATAAATAATTTCGTTCCTCGGCACTGG 1 133 1 AATTTCGTCC 0.962596 -69 TGGCTTGGGTAATTCCGTAGCATTTCCAGAA 1 161 1 AATTCCGTGC 0.961868 -41 AGGTTAACTCAACTTTGTTGCCGACATGGTC 3 175 0 AACTTTGTGC 0.943088 -125 TCATTGATTTAGTCCCATTCTCTCAA 4 6 1 GATTTAGTCC 0.849858 -295 CTAGCCCCGCAACGCAATGGCTCGGGGAAGA 4 133 0 AACGCAATGC 0.796959 -168 TCCAGGGGTGAACTTAGTGCCCACTGCCCCC 4 252 1 AACTTAGTCC 0.981988 -49 ******** ** Masking position 2 Map Score: 2.4266 Number of sites scoring better than the average of aligned sites = 439 Number in coding regions = 391 Number in noncoding regions = 48 Number of orfs with sites within 600 bp upstream = 45 Fraction of orfs with sites within 600 bp upstream = 0.00722775 Motif number 9 CATTAACCAACTGCATTGATTCTAACTAGA 1 72 0 CTGCATTGAT 0.964733 -130 CCGTAGTATTCTCCCTAGATTGTGCCATAT 2 42 0 CTCCCTAGAT 0.913912 -38 TCCTTGGACGCCGGCTTGATCCCTGTCCGC 3 240 1 CCGGCTTGAT 0.973097 -60 TGATCCCTGTCCGCCTTTTTCTTAATTTTC 3 256 1 CCGCCTTTTT 0.913493 -44 TGGCGGTCAACCCAATTGATCATAATATAA 4 99 0 CCCAATTGAT 0.938935 -202 TGCCCACTGCCCCCATTGTTTCACCATCGA 4 269 1 CCCCATTGTT 0.977478 -32 ********** Masking position 6 Map Score: 0.597094 Number of sites scoring better than the average of aligned sites = 751 Number in coding regions = 669 Number in noncoding regions = 82 Number of orfs with sites within 600 bp upstream = 87 Fraction of orfs with sites within 600 bp upstream = 0.0139737 Motif number 10 ********** No masking Map Score: -1.12023e-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: -1.12023e-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 12 ********** No masking Map Score: -1.12023e-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