AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i061_synecho_ctra_300.orf -o061_synecho_ctra_300.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 0.963719 -186 CTTTTTGTTACAAACTTCCCCTCTGCCATTG 1 141 0 CAACTTCCCC 0.962298 -138 TTATTTACGGCGATCGCCCCCACCACAAGAG 1 246 1 CATCGCCCCC 0.998452 -33 CCAGCGTTGAACAATTCCCCC 2 1 0 AAATTCCCCC 0.863432 -300 TTAAGGAAACCTACCTCCCCCCCGTAATGAC 2 113 1 CACCTCCCCC 0.998144 -188 AACAGCTCTCACCTCGCCCCCCAAGTCCAAG 2 230 1 ACTCGCCCCC 0.983948 -71 AATAAAACCTACCCCACAGGCATCA 2 286 0 AACCTACCCC 0.928866 -15 TTAATTTCGTCTCCCTCCCCAAATTTGGCGA 3 79 1 CCCCTCCCCA 0.969507 -222 CCAAATTTGGCGATCGCCCCCATGAAGCGGT 3 97 1 CATCGCCCCC 0.998452 -204 GTAAAATTAACCACCGCCCCCAGGCTGAGGG 3 161 1 CACCGCCCCC 0.999023 -140 TGGGAGACCCCAAAGGGCCCCTCAGCCTGGG 3 179 0 CAAGGGCCCC 0.950591 -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 0.785366 -246 CCTGGTGGGGCCATGGCCAAGCCCCGAACA 1 89 0 CCATGGCCAA 0.921648 -190 GGGATGTAAGCCTAGTTTAAAGCAGTTCCC 1 216 0 CCTAGTTTAA 0.913023 -63 ACCTCGCCCCCCAAGTCCAAGGTCTTTACG 2 240 1 CCAAGTCCAA 0.964787 -61 TCACCGAAAACCCAGATTAACCATTTTT 3 9 0 CCCAGATTAA 0.903481 -292 AGCAAAATCGCTCAGGTTAATTTCGTCTCC 3 63 1 CTCAGGTTAA 0.876158 -238 CGAACCACTGCCTAGGCTAACTGGTAAAAT 3 138 1 CCTAGGCTAA 0.980798 -163 AACCACCGCCCCCAGGCTGAGGGGCCCTTT 3 169 1 CCCAGGCTGA 0.987943 -132 TCTGTTGCCACCAATTCTAACCAACCATTC 3 263 1 CCAATTCTAA 0.770744 -38 TAACCAAGGTTGACCAAGGAATG 3 288 0 CCAAGGTTGA 0.981263 -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 0.979556 -164 GTTGCTTTTTGTTACAAACTTCCCCTCTGC 1 146 0 GTTACAAACT 0.958676 -133 GTTTAAAGCAGTTCCCAACCAATGGAGGGT 1 202 0 GTTCCCAACC 0.977211 -77 TCACCCCCTCGTTCCAAACTTTTGTACGGT 2 187 1 GTTCCAAACT 0.950575 -114 CTTTTGTACGGTTACCAGTCCTATGAACAG 2 205 1 GTTACCAGTC 0.874607 -96 GTGAAGAATAGTTACAAGCAAAATCGCTCA 3 47 1 GTTACAAGCA 0.965535 -254 TCCAATATCCGTTGCTAGCTCCTATGACAA 3 228 1 GTTGCTAGCT 0.901883 -73 AAACTCCTCTGTTGCCACCAATTCTAACCA 3 256 1 GTTGCCACCA 0.947074 -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 0.992154 -36 ATTCAAAAACCGGGGAATGCCCTGCCACGA 2 151 1 CGGGGAATGC 0.9433 -150 TTGGGGGGCGAGGTGAGAGCTGTTCATAGG 2 224 0 AGGTGAGAGC 0.914932 -77 TCTGGGTTTTCGGTGAGCGATAATGTGAAG 3 23 1 CGGTGAGCGA 0.983929 -278 TCGCCAAATTTGGGGAGGGAGACGAAATTA 3 80 0 TGGGGAGGGA 0.922712 -221 TCCCCAAATTTGGCGATCGCCCCCATGAAG 3 94 1 TGGCGATCGC 0.982495 -207 AAGCGGTTAAAGGCGAACGAACCACTGCCT 3 121 1 AGGCGAACGA 0.964506 -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 0.94401 -160 AAATCTCAATAAAAGTTACCCTCCATTGGT 1 185 1 AAAAGTTACC 0.978773 -94 CCCCCACCACAAGAGGTAACTACGAGC 1 262 1 AAGAGGTAAC 0.934471 -17 ACCACAACAAAATAGTTAAATTTGTTACCT 2 37 1 AATAGTTAAA 0.87366 -264 CTTTGTCGAGAAAAGGTAACAAATTTAACT 2 50 0 AAAAGGTAAC 0.960492 -251 TAATGTGAAGAATAGTTACAAGCAAAATCG 3 43 1 AATAGTTACA 0.91578 -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 ACGCTGGAACTAACCACAACAAAATAGTTA 2 25 1 TAACCACAAC 0.968059 -276 CCCCCCGTAATGACCGCTACAATTCAAAAA 2 130 1 TGACCGCTAC 0.973833 -171 CGTTCGCCTTTAACCGCTTCATGGGGGCGA 3 110 0 TAACCGCTTC 0.978103 -191 AAAGGCGAACGAACCACTGCCTAGGCTAAC 3 129 1 GAACCACTGC 0.981532 -172 CTGGTAAAATTAACCACCGCCCCCAGGCTG 3 158 1 TAACCACCGC 0.985812 -143 ********** Masking position 3 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 AAACTTCCCCTCTGCCATTGGTACAAGTTACC 1 129 0 TCCCATTGGT 0.987843 -150 ATAAAAGTTACCCTCCATTGGTTGGGAACTGC 1 193 1 CCCCATTGGT 0.992234 -86 AGGAAACCTACCTCCCCCCCGTAATGACCGCT 2 116 1 CCCCCCCCGT 0.969798 -185 ACGAAGGTCTTCACCCCCTCGTTCCAAACTTT 2 177 1 TCCCCCTCGT 0.98241 -124 CCCTTTGGGGTCTCCCATTGCTGTCCAGATGT 3 193 1 TCCCATTGCT 0.976997 -108 CCAATTCTAACCAACCATTCCTTGGTCAACCT 3 273 1 CCCCATTCCT 0.985247 -28 ** ******** Masking position 12 Map Score: 3.63317 Number of sites scoring better than the average of aligned sites = 165 Number in coding regions = 153 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 8 GGAACTGCTTTAAACTAGGCTTACATCCCT 1 217 1 TAAACTAGGC 0.97179 -62 AAAAATGGTTAATCTGGGTTTTCGGTGAG 3 10 1 TAATCTGGGT 0.942873 -291 GAGACGAAATTAACCTGAGCGATTTTGCTT 3 62 0 TAACCTGAGC 0.965885 -239 TTTTACCAGTTAGCCTAGGCAGTGGTTCGT 3 137 0 TAGCCTAGGC 0.98404 -164 TAACCAAGGTTGACCAAGGA 3 291 0 TAACCAAGGT 0.948621 -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 ********** 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 10 TGATATTTTGGAATATGGGGCATTCAGACG 1 55 0 GAATATGGGG 0.911404 -224 GAGATTTGCTGGCCATGTTGCTTTTTGTTA 1 162 0 GGCCATGTTG 0.9572 -117 AGGGGGTGAAGACCTTCGTGGCAGGGCATT 2 166 0 GACCTTCGTG 0.907595 -135 TAAAGACCTTGGACTTGGGGGGCGAGGTGA 2 238 0 GGACTTGGGG 0.982475 -63 TCCGCAAAATGAACATGATGCCTGTGGGGT 2 271 1 GAACATGATG 0.913013 -30 GATATTGGAAGGACATCTGGACAGCAATGG 3 207 0 GGACATCTGG 0.960426 -94 ********** Masking position 6 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 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 Motif number 13 ********** 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