AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i101_synecho_ctra_300.orf -o101_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 RCY36839 123 Synechocystis #2 RCY33239 167 Synechocystis #3 RCY02899 51 Synechocystis #4 RCY35187 264 Synechocystis Motif number 1 GGATATATTTTGGCGATCGCCTTTCACTCC 1 73 1 TGGCGATCGC 0.994666 -51 TTCACTCCAAGGGCGATTAACATAGGGAAT 1 95 1 GGGCGATTAA 0.978887 -29 GCCTTGTCCATGGCGATCGCTGTTTATTT 2 10 0 TGGCGATCGC 0.994666 -158 CAATAAAAGGGGGCAACCGGAATAGTTCCC 2 41 0 GGGCAACCGG 0.96911 -127 GAACGGAGTCGGGCAATTAGGTTAATCCCT 2 103 1 GGGCAATTAG 0.931756 -65 GGACGATCGCATAATGCATT 2 158 0 GGACGATCGC 0.970618 -10 ATTGCTGTAGTGGCTATTAATTGTTAAGAA 4 107 0 TGGCTATTAA 0.818904 -158 AGAATCCCCATGGCGACCAAGCATTTAACA 4 154 1 TGGCGACCAA 0.976929 -111 ********** Masking position 6 Map Score: 10.1122 Number of sites scoring better than the average of aligned sites = 8240 Number in coding regions = 7504 Number in noncoding regions = 736 Number of orfs with sites within 600 bp upstream = 509 Fraction of orfs with sites within 600 bp upstream = 0.0817539 Motif number 2 AGTCCCCTTAGAAGAGTTCAGGGGATATATTTTG 1 51 1 GAGGTCAGGG 0.985302 -73 AACAGCGATCGCCATGGACAAGGCAGGGAACTAT 2 16 1 GCAGGCAGGC 0.737428 -152 ACTAAAGTAAAGAACGGAGTCGGGCAATTAGGTT 2 92 1 AAAGGGTGGG 0.966321 -76 AATGCATTGGAGAAAGGGCACGGATCTTTAGGTA 2 132 0 AAAGGCAGGA 0.968801 -36 TTAGCCTGGAATGGCCTTGGGTTGTCTTTGG 3 31 0 GAAGGCTGGG 0.995836 -21 AAAACAAGTAAATGAGGTCATGGGG 4 2 0 ATGGGCAGGG 0.983017 -263 AGGACTGGGGGACAGGGAAATGGGTTTTAATGCC 4 195 0 GCAGGAAGGG 0.981629 -70 AGAGATTATTGTAGAGGACTGGGGGACAGGGAAA 4 209 0 GAGGGCTGGG 0.997329 -56 * ** ** ** *** Masking position 6 Map Score: 9.049 Number of sites scoring better than the average of aligned sites = 1129 Number in coding regions = 1022 Number in noncoding regions = 107 Number of orfs with sites within 600 bp upstream = 115 Fraction of orfs with sites within 600 bp upstream = 0.0184709 Motif number 3 ATCGCCTTTCACTCCAAGGGCGATTAACAT 1 88 1 ACTCCAAGGG 0.947363 -36 TTCCCTGCCTTGTCCATGGCGATCGCTGTT 2 16 0 TGTCCATGGC 0.963753 -152 CCGTGCCCTTTCTCCAATGCATTATGCGAT 2 143 1 TCTCCAATGC 0.970807 -25 CTCCAAAGACAACCCAAGGCCATTCCAGGC 3 29 1 AACCCAAGGC 0.984925 -23 AAAGGAAGAATCCCCATGGCGACCAAGCAT 4 148 1 TCCCCATGGC 0.994853 -117 TCGGCATTAAAACCCATTTCCCTGTCCCCC 4 193 1 AACCCATTTC 0.788762 -72 CATTTCCCTGTCCCCCAGTCCTCTACAATA 4 207 1 TCCCCCAGTC 0.954819 -58 ********** Masking position 5 Map Score: 5.16122 Number of sites scoring better than the average of aligned sites = 2557 Number in coding regions = 2287 Number in noncoding regions = 270 Number of orfs with sites within 600 bp upstream = 275 Fraction of orfs with sites within 600 bp upstream = 0.0441696 Motif number 4 GCTTACCCTGACAGTCCCCTTAGAAGAGTT 1 39 1 ACAGTCCCCT 0.996538 -85 GGCAACCGGAATAGTTCCCTGCCTTGTCCA 2 30 0 ATAGTTCCCT 0.982898 -138 TTAATGCCGAATAGTCCTCTGTTAAATGCT 4 173 0 ATAGTCCTCT 0.981988 -92 GCATTAAAACCCATTTCCCTGTCCCCCAGT 4 196 1 CCATTTCCCT 0.964127 -69 TCCCTGTCCCCCAGTCCTCTACAATAATCT 4 211 1 CCAGTCCTCT 0.992864 -54 ********** Masking position 5 Map Score: 6.40281 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 = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 5 GCCTTTTGGACAATAAACAGTATTGAAGTT 1 11 0 CAATAAACAG 0.982933 -113 AAATAAACAGCGATCGCCAT 2 1 1 AAATAAACAG 0.894536 -167 GAAAGATTATCAATAAAAGGGGGCAACCGG 2 51 0 CAATAAAAGG 0.937028 -117 TATCTAAAAACAAGTAAATGAGGTCATGGG 4 12 0 CAAGTAAATG 0.815755 -253 TTATTCTTAACAATTAATAGCCACTACAGC 4 104 1 CAATTAATAG 0.830559 -161 GCAATATTTGCAGGAAAAAGGAAGAATCCC 4 132 1 CAGGAAAAAG 0.910799 -133 GGCGACCAAGCATTTAACAGAGGACTATTC 4 165 1 CATTTAACAG 0.835172 -100 ********** Masking position 6 Map Score: 3.08337 Number of sites scoring better than the average of aligned sites = 461 Number in coding regions = 403 Number in noncoding regions = 58 Number of orfs with sites within 600 bp upstream = 65 Fraction of orfs with sites within 600 bp upstream = 0.0104401 Motif number 6 AATTTCTTACTATTCCTAATTATTCTTAAC 4 85 1 TATTCCTAAT 0.96036 -180 TATTCCTAATTATTCTTAACAATTAATAGC 4 95 1 TATTCTTAAC 0.96036 -170 CAATAATCTCTAATCTTATTAGTAGTTAAT 4 232 1 TAATCTTATT 0.942351 -33 TATTAGTAGTTAATCTTAATAACTATG 4 248 1 TAATCTTAAT 0.976361 -17 ********** Masking position 4 Map Score: 0.787985 Number of sites scoring better than the average of aligned sites = 28 Number in coding regions = 21 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 7 ********** No masking Map Score: 6.06393e-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 8 ********** No masking Map Score: 6.06393e-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 9 ********** No masking Map Score: 6.06393e-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