AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i061_synecho_ctra_100.orf -o061_synecho_ctra_100.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 RCY43942 278 Synechocystis #2 RCY36761 300 Synechocystis #3 RCY02311 300 Synechocystis Motif number 1 CGGGGCTTGGCCATGGCCCCACCAGGGATTT 1 93 1 CATGGCCCCA 0.961839 -186 CTTTTTGTTACAAACTTCCCCTCTGCCATTG 1 141 0 CAACTTCCCC 0.960347 -138 TTATTTACGGCGATCGCCCCCACCACAAGAG 1 246 1 CATCGCCCCC 0.998368 -33 CCAGCGTTGAACAATTCCCCC 2 1 0 AAATTCCCCC 0.857126 -300 TTAAGGAAACCTACCTCCCCCCCGTAATGAC 2 113 1 CACCTCCCCC 0.998044 -188 AACAGCTCTCACCTCGCCCCCCAAGTCCAAG 2 230 1 ACTCGCCCCC 0.983098 -71 AATAAAACCTACCCCACAGGCATCA 2 286 0 AACCTACCCC 0.925319 -15 TTAATTTCGTCTCCCTCCCCAAATTTGGCGA 3 79 1 CCCCTCCCCA 0.967917 -222 CCAAATTTGGCGATCGCCCCCATGAAGCGGT 3 97 1 CATCGCCCCC 0.998368 -204 GTAAAATTAACCACCGCCCCCAGGCTGAGGG 3 161 1 CACCGCCCCC 0.998971 -140 TGGGAGACCCCAAAGGGCCCCTCAGCCTGGG 3 179 0 CAAGGGCCCC 0.948068 -122 * ********* Masking position 8 Map Score: 23.4657 Number of sites scoring better than the average of aligned sites = 1127 Number in coding regions = 1031 Number in noncoding regions = 96 Number of orfs with sites within 600 bp upstream = 112 Fraction of orfs with sites within 600 bp upstream = 0.0179891 Motif number 2 TTCAGACGGTCAAAGGTCGAAGTATTTTTA 1 33 0 CAAAGGTCGA 0.770184 -246 CCTGGTGGGGCCATGGCCAAGCCCCGAACA 1 89 0 CCATGGCCAA 0.915064 -190 GGGATGTAAGCCTAGTTTAAAGCAGTTCCC 1 216 0 CCTAGTTTAA 0.905788 -63 ACCTCGCCCCCCAAGTCCAAGGTCTTTACG 2 240 1 CCAAGTCCAA 0.961677 -61 TCACCGAAAACCCAGATTAACCATTTTT 3 9 0 CCCAGATTAA 0.895543 -292 AGCAAAATCGCTCAGGTTAATTTCGTCTCC 3 63 1 CTCAGGTTAA 0.866305 -238 CGAACCACTGCCTAGGCTAACTGGTAAAAT 3 138 1 CCTAGGCTAA 0.979071 -163 AACCACCGCCCCCAGGCTGAGGGGCCCTTT 3 169 1 CCCAGGCTGA 0.98685 -132 TCTGTTGCCACCAATTCTAACCAACCATTC 3 263 1 CCAATTCTAA 0.754851 -38 TAACCAAGGTTGACCAAGGAATG 3 288 0 CCAAGGTTGA 0.97958 -13 ********** Masking position 10 Map Score: 8.53858 Number of sites scoring better than the average of aligned sites = 2030 Number in coding regions = 1801 Number in noncoding regions = 229 Number of orfs with sites within 600 bp upstream = 250 Fraction of orfs with sites within 600 bp upstream = 0.0401542 Motif number 3 ATTGGTACAAGTTACCAACAAAAATCCCTG 1 115 0 GTTACCAACA 0.981426 -164 GTTGCTTTTTGTTACAAACTTCCCCTCTGC 1 146 0 GTTACAAACT 0.962383 -133 GTTTAAAGCAGTTCCCAACCAATGGAGGGT 1 202 0 GTTCCCAACC 0.979291 -77 TCACCCCCTCGTTCCAAACTTTTGTACGGT 2 187 1 GTTCCAAACT 0.954975 -114 CTTTTGTACGGTTACCAGTCCTATGAACAG 2 205 1 GTTACCAGTC 0.884952 -96 GTGAAGAATAGTTACAAGCAAAATCGCTCA 3 47 1 GTTACAAGCA 0.968647 -254 TCCAATATCCGTTGCTAGCTCCTATGACAA 3 228 1 GTTGCTAGCT 0.910209 -73 AAACTCCTCTGTTGCCACCAATTCTAACCA 3 256 1 GTTGCCACCA 0.95177 -45 ********** Masking position 7 Map Score: 6.84413 Number of sites scoring better than the average of aligned sites = 460 Number in coding regions = 418 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 4 CCCTTATTTACGGCGATCGCCCCCACCACA 1 243 1 CGGCGATCGC 0.992043 -36 ATTCAAAAACCGGGGAATGCCCTGCCACGA 2 151 1 CGGGGAATGC 0.942533 -150 TTGGGGGGCGAGGTGAGAGCTGTTCATAGG 2 224 0 AGGTGAGAGC 0.913817 -77 TCTGGGTTTTCGGTGAGCGATAATGTGAAG 3 23 1 CGGTGAGCGA 0.983702 -278 TCGCCAAATTTGGGGAGGGAGACGAAATTA 3 80 0 TGGGGAGGGA 0.92169 -221 TCCCCAAATTTGGCGATCGCCCCCATGAAG 3 94 1 TGGCGATCGC 0.982248 -207 AAGCGGTTAAAGGCGAACGAACCACTGCCT 3 121 1 AGGCGAACGA 0.964016 -180 ********** Masking position 6 Map Score: 4.422 Number of sites scoring better than the average of aligned sites = 6338 Number in coding regions = 5765 Number in noncoding regions = 573 Number of orfs with sites within 600 bp upstream = 358 Fraction of orfs with sites within 600 bp upstream = 0.0575008 Motif number 5 TGCCATTGGTACAAGTTACCAACAAAAATC 1 119 0 ACAAGTTACC 0.946424 -160 AAATCTCAATAAAAGTTACCCTCCATTGGT 1 185 1 AAAAGTTACC 0.979721 -94 CCCCCACCACAAGAGGTAACTACGAGC 1 262 1 AAGAGGTAAC 0.93727 -17 ACCACAACAAAATAGTTAAATTTGTTACCT 2 37 1 AATAGTTAAA 0.878719 -264 CTTTGTCGAGAAAAGGTAACAAATTTAACT 2 50 0 AAAAGGTAAC 0.962224 -251 TAATGTGAAGAATAGTTACAAGCAAAATCG 3 43 1 AATAGTTACA 0.919307 -258 ********** Masking position 4 Map Score: 2.55329 Number of sites scoring better than the average of aligned sites = 177 Number in coding regions = 138 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 42 Fraction of orfs with sites within 600 bp upstream = 0.0067459 Motif number 6 TAACTATTTTGTTGTGGTTAGTTCCAGCGT 2 25 0 GTTGTGGTTA 0.964096 -276 TTTTTGAATTGTAGCGGTCATTACGGGGGG 2 130 0 GTAGCGGTCA 0.970568 -171 TCGCCCCCATGAAGCGGTTAAAGGCGAACG 3 110 1 GAAGCGGTTA 0.975595 -191 GTTAGCCTAGGCAGTGGTTCGTTCGCCTTT 3 129 0 GCAGTGGTTC 0.979222 -172 CAGCCTGGGGGCGGTGGTTAATTTTACCAG 3 158 0 GCGGTGGTTA 0.984015 -143 ********** Masking position 8 Map Score: 1.95143 Number of sites scoring better than the average of aligned sites = 177 Number in coding regions = 169 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 7 GGTAACTTGTACCAATGGCAGAGGGGAAGTTT 1 129 1 ACCAATGGGA 0.98267 -150 GCAGTTCCCAACCAATGGAGGGTAACTTTTAT 1 193 0 ACCAATGGGG 0.991533 -86 AGCGGTCATTACGGGGGGGAGGTAGGTTTCCT 2 116 0 ACGGGGGGGG 0.9794 -185 AAAGTTTGGAACGAGGGGGTGAAGACCTTCGT 2 177 0 ACGAGGGGGA 0.984364 -124 GGGCCCCTCAGCCTGGGGGCGGTGGTTAATTT 3 164 0 GCCTGGGGGG 0.92839 -137 ACATCTGGACAGCAATGGGAGACCCCAAAGGG 3 193 0 AGCAATGGGA 0.959883 -108 AGGTTGACCAAGGAATGGTTGGTTAGAATTGG 3 273 0 AGGAATGGGG 0.974109 -28 ******** ** Masking position 7 Map Score: 3.74032 Number of sites scoring better than the average of aligned sites = 653 Number in coding regions = 606 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 59 Fraction of orfs with sites within 600 bp upstream = 0.00947639 Motif number 8 GGAACTGCTTTAAACTAGGCTTACATCCCT 1 217 1 TAAACTAGGC 0.966581 -62 AAAAATGGTTAATCTGGGTTTTCGGTGAG 3 10 1 TAATCTGGGT 0.932694 -291 GAGACGAAATTAACCTGAGCGATTTTGCTT 3 62 0 TAACCTGAGC 0.95963 -239 TTTTACCAGTTAGCCTAGGCAGTGGTTCGT 3 137 0 TAGCCTAGGC 0.981049 -164 TAACCAAGGTTGACCAAGGA 3 291 0 TAACCAAGGT 0.939401 -10 ********** Masking position 2 Map Score: 0.3887 Number of sites scoring better than the average of aligned sites = 465 Number in coding regions = 420 Number in noncoding regions = 45 Number of orfs with sites within 600 bp upstream = 57 Fraction of orfs with sites within 600 bp upstream = 0.00915516 Motif number 9 CGTCTGAATGCCCCATATTCCAAAATATCA 1 55 1 CCCCATATTC 0.911118 -224 TAACAAAAAGCAACATGGCCAGCAAATCTC 1 162 1 CAACATGGCC 0.95708 -117 AATGCCCTGCCACGAAGGTCTTCACCCCCT 2 166 1 CACGAAGGTC 0.907298 -135 TCACCTCGCCCCCCAAGTCCAAGGTCTTTA 2 238 1 CCCCAAGTCC 0.982414 -63 ACCCCACAGGCATCATGTTCATTTTGCGGA 2 271 0 CATCATGTTC 0.91274 -30 CCATTGCTGTCCAGATGTCCTTCCAATATC 3 207 1 CCAGATGTCC 0.960292 -94 ********** Masking position 5 Map Score: 0.136953 Number of sites scoring better than the average of aligned sites = 1217 Number in coding regions = 1145 Number in noncoding regions = 72 Number of orfs with sites within 600 bp upstream = 80 Fraction of orfs with sites within 600 bp upstream = 0.0128493 Motif number 10 ********** No masking Map Score: 6.77448e-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: 6.77448e-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: 6.77448e-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