AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i005_synecho_ctra_300.orf -o005_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 RCY08561 119 Synechocystis #2 RCY01957 241 Synechocystis #3 RCY27506 300 Synechocystis #4 RCY30833 46 Synechocystis #5 RCY01603 300 Synechocystis #6 RCY37071 155 Synechocystis Motif number 1 GTTAACCCCCAGAATCCGGAAAGGTTGCCCAACTTTGCTA 1 39 1 AACGGAGCCC 0.916701 -81 AACCTTTTAACCTCGGGGGAACGACGGCACAAAAATCCCC 1 88 0 CCGGGAGCAC 0.982753 -32 TGCAAAGCATTAGCATCGGCAGTAACGCTCT 2 2 0 TCCGGAGCTC 0.943613 -240 CACAATTTGCCGGCCCGGGAAAAGCAGTACTCTGATGATA 2 111 0 CCGGGAGTAC 0.933592 -131 TTCTATTAGGAAGCTTGGTGACAACGGCCCCATTAGTTAG 3 23 0 ACGGTAGCCC 0.854464 -278 TTCTGAAATGCGCCAACGGTGTTTAGCTTTTGCCCTAATT 3 118 0 CCCGGGCTTT 0.548981 -183 GCATTTCAGAATACCACGGACTTTTAGCTAAATACATGGG 3 147 1 ACCGGCGCTA 0.885372 -154 TTTTAGCTAAATACATGGGAACGTTCCTCCCTAGTGTAGC 3 168 1 ACGGGACTCC 0.867037 -133 CCCAGGGATCCATATTGGGGGCGATCGCCAGTTAATGCAA 3 219 0 CAGGGGGCCA 0.902965 -82 CCCAATATGGATCCCTGGGGACTACCGCCTGCCCCATATC 3 240 1 ACGGGAGCCT 0.965247 -61 AATCCAGACCCGTCGGCGGTGCAGAGGTCTTTTACGGATA 5 60 0 CCCGGGGTCT 0.930682 -241 CGGAGTTTACCTCCAGGGGTAGTCTGGCTCGACTGTGATT 5 109 0 CCGGGAGCTC 0.990878 -192 CCCTGGAGGTAAACTCCGGGGCTGGAGCCATAAAGATTAG 5 131 1 ACCGGGGCCA 0.977687 -170 ACTGACACTGTAACAGGGGAAAGTCTCCTCTGTTCACCCT 5 232 0 TCGGGACCTC 0.778492 -69 GGCTCACCACCTGCACCGATGCCAAAAAGTTGTT 5 277 0 CCCTGAGCCA 0.831323 -24 GTGGAACAGACGACAGGGGCGAATCTGCTAATATGTGGTT 6 29 1 CCGGGGGCTA 0.978148 -127 TATGTGGTTGATTCGGCGGCGGCCGGGCAAAGGAGCACAG 6 60 1 ACCGGGGCAA 0.919414 -96 TAACTTTTTCCCACTACGGCCGAATGGTCCTATTCCAGCT 6 123 1 CCCGGCGTCC 0.95666 -33 * * *** * **** Masking position 9 Map Score: 20.6008 Number of sites scoring better than the average of aligned sites = 4119 Number in coding regions = 3884 Number in noncoding regions = 235 Number of orfs with sites within 600 bp upstream = 246 Fraction of orfs with sites within 600 bp upstream = 0.0395117 Motif number 2 ATTGGCTCAACCCAAAAGTACAGTTAACCCC 1 17 1 CCCAAAGTAC 0.937153 -103 TACAGTTAACCCCCAGAATCCGGAAAGGTTG 1 35 1 CCCCAAATCC 0.994968 -85 ACAAAAATCCCCCTAAAATCCTAGCAAAGTT 1 69 0 CCCTAAATCC 0.980302 -51 GGAACGACGGCACAAAAATCCCCCTAAAATC 1 80 0 CACAAAATCC 0.954428 -40 TAGATTGGAGCCCAAATATCATCAGAGTACT 2 95 1 CCCAATATCA 0.868735 -147 CATGTATTTAGCTAAAAGTCCGTGGTATTCT 3 154 0 GCTAAAGTCC 0.819557 -147 GGCGGTAGTCCCCAGGGATCCATATTGGGGG 3 238 0 CCCAGGATCC 0.929963 -63 AGGTTTATTGACCAAAAATCCGGGTCCGAAT 4 12 0 ACCAAAATCC 0.963988 -35 TGTGATTATTGCCCATAATCCAGACCCGTCG 5 85 0 GCCCAAATCC 0.983667 -216 CATACCACGCCCCCACTGTCCGGCAGGGTGA 5 208 1 CCCCATGTCC 0.978016 -93 ***** ***** Masking position 9 Map Score: 9.79449 Number of sites scoring better than the average of aligned sites = 889 Number in coding regions = 780 Number in noncoding regions = 109 Number of orfs with sites within 600 bp upstream = 120 Fraction of orfs with sites within 600 bp upstream = 0.019274 Motif number 3 GGTGGTCATAGTCAAAGGCAGTCAAATTAG 3 94 1 GTCAAAGGCA 0.976544 -207 CCCCATATCTATCTAAGGCAATCTAAGGCA 3 271 1 ATCTAAGGCA 0.995735 -30 ATCTAAGGCAATCTAAGGCAATCTAAGGCA 3 281 1 ATCTAAGGCA 0.995735 -20 ATCTAAGGCAATCTAAGGCA 3 291 1 ATCTAAGGCA 0.995735 -10 TTGGAGTCTTATCCAAGGCTGTGCTCCTTT 6 88 0 ATCCAAGGCT 0.976248 -68 ********** Masking position 5 Map Score: 8.96422 Number of sites scoring better than the average of aligned sites = 33 Number in coding regions = 27 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 4 GGAAGTGCACGGTACACTGAAAAAGAGGGGAATGAATCC 2 47 0 GTACACTGAG 0.995588 -195 TGATATTTGGGCTCCAATCTAGTGGAACGAGGAAGTGCA 2 77 0 GTCCAATGAG 0.987085 -165 TCTTTTCCTCGCTACACTAGGGAGGAACGTTCCCATGTA 3 179 0 GTACACTGAG 0.995588 -122 TGCATCATTCGATACAATCAAGGCGATTGGAGCATT 5 8 0 GTACAATGAG 0.995239 -293 GTCTTTTACGGATACAATTTTAGAGACTGCATCATTCGA 5 35 0 GTACAATGAG 0.995238 -266 ACTTTCCCCTGTTACAGTGTCAGTGACAAAACAACTTTT 5 248 1 GTACAGTGAA 0.949892 -53 * ****** ** * Masking position 8 Map Score: 4.83107 Number of sites scoring better than the average of aligned sites = 12 Number in coding regions = 7 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 5 TCAGTGTACCGTGCACTTCCTCGTTCCACT 2 66 1 GTGCACTTCC 0.836175 -176 AATATCATCAGAGTACTGCTTTTCCCGGGC 2 109 1 GAGTACTGCT 0.836422 -133 GGAATGAATTGTTCACTGCCAACTTTTGTT 2 161 0 GTTCACTGCC 0.954688 -81 GAAGCTTGGTGACAACGGCCCCATTAGTTA 3 24 0 GACAACGGCC 0.93353 -277 CTTTGACTATGACCACCGCAACCCATTTGC 3 81 0 GACCACCGCA 0.958211 -220 GATCCCTGGGGACTACCGCCTGCCCCATAT 3 249 1 GACTACCGCC 0.988118 -52 ATCCGTAAAAGACCTCTGCACCGCCGACGG 5 61 1 GACCTCTGCA 0.748264 -240 GCTCGACTGTGATTATTGCCCATAATCCAG 5 93 0 GATTATTGCC 0.723263 -208 CAGCCCCGGAGTTTACCTCCAGGGGTAGTC 5 125 0 GTTTACCTCC 0.666123 -176 CCGGGCAAAGGAGCACAGCCTTGGATAAGA 6 82 1 GAGCACAGCC 0.95353 -74 AACTTTTTCCCACTACGGCCGAATGGTCCT 6 124 1 CACTACGGCC 0.869595 -32 ********** Masking position 9 Map Score: 4.9525 Number of sites scoring better than the average of aligned sites = 1896 Number in coding regions = 1779 Number in noncoding regions = 117 Number of orfs with sites within 600 bp upstream = 142 Fraction of orfs with sites within 600 bp upstream = 0.0228076 Motif number 6 CAAGCTTCCTAATAGAACTGTCGCGGCAAGTTT 3 46 1 ATAGACTTCG 0.899854 -255 AATGCTCCAATCGCCTTGATTGT 5 1 1 ATGCTCATCG 0.975535 -300 AATTTTAGAGACTGCATCATTCGATACAATCAA 5 26 0 ATGCACATCG 0.993851 -275 TTCATTAAGAAATGTAACAATCGACGTTCTAGA 5 174 1 ATGTACATCG 0.983404 -127 ATTTGACATTAGTGGAACAGACGACAGGGGCGA 6 18 1 ATGGACAACG 0.983074 -138 GGTAGCTGGAATAGGACCATTCGGCCGTAGTGG 6 133 0 AAGGACATCG 0.983074 -23 * **** ** *** Masking position 1 Map Score: 1.92776 Number of sites scoring better than the average of aligned sites = 62 Number in coding regions = 57 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 7 CCCCTAAAATCCTAGCAAAGTTGGGCAACC 1 61 0 CCTAGCAAAG 0.916211 -59 ATTTGCCGGCCCGGGAAAAGCAGTACTCTG 2 117 0 CCGGGAAAAG 0.994788 -125 AAATCAACTCCCTGGAAAAGTGAAATTTTT 2 212 0 CCTGGAAAAG 0.993693 -30 CCTAGTGTAGCGAGGAAAAGACTTGCATTA 3 197 1 CGAGGAAAAG 0.916781 -104 GGTCAATAAACCTGGATATGGGAACGG 4 30 1 CCTGGATATG 0.911974 -17 GACACTGTAACAGGGGAAAGTCTCCTCTGT 5 239 0 CAGGGGAAAG 0.915238 -62 TCGGCGGCGGCCGGGCAAAGGAGCACAGCC 6 72 1 CCGGGCAAAG 0.992242 -84 GGAGCACAGCCTTGGATAAGACTCCAAGGA 6 91 1 CTTGGATAAG 0.897648 -65 ********** Masking position 8 Map Score: 9.15298 Number of sites scoring better than the average of aligned sites = 514 Number in coding regions = 458 Number in noncoding regions = 56 Number of orfs with sites within 600 bp upstream = 66 Fraction of orfs with sites within 600 bp upstream = 0.0106007 Motif number 8 AGCATTAGCATCGGCAGTAACGCTCT 2 7 0 TCGGCAGTAA 0.850706 -235 GAAACTTGCCGCGACAGTTCTATTAGGAAG 3 50 0 GCGACAGTTC 0.884368 -251 TTGGGGGCGATCGCCAGTTAATGCAAGTCT 3 215 0 TCGCCAGTTA 0.964831 -86 TCCAGACCCGTCGGCGGTGCAGAGGTCTTT 5 68 0 TCGGCGGTGC 0.921456 -233 GTAGTCTGGCTCGACTGTGATTATTGCCCA 5 101 0 TCGACTGTGA 0.958498 -200 ATCTAGAACGTCGATTGTTACATTTCTTAA 5 178 0 TCGATTGTTA 0.799948 -123 GGGGAAAGTCTCCTCTGTTCACCCTGCCGG 5 227 0 TCCTCTGTTC 0.917781 -74 GAGGAGACTTTCCCCTGTTACAGTGTCAGT 5 242 1 TCCCCTGTTA 0.930608 -59 TTCGCCCCTGTCGTCTGTTCCACTAATGTC 6 22 0 TCGTCTGTTC 0.973438 -134 ********** Masking position 8 Map Score: 4.08104 Number of sites scoring better than the average of aligned sites = 398 Number in coding regions = 357 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 9 ********** No masking Map Score: 3.35619e-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 10 ********** No masking Map Score: 3.35619e-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: 3.35619e-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