AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i307_mixed21_synecho_reg_300.orf -o307_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 RCY48542 119 Synechocystis #2 RCY31870 49 Synechocystis #3 RCY18430 293 Synechocystis #4 RCY40674 143 Synechocystis #5 RCY05882 300 Synechocystis #6 RCY51246 183 Synechocystis #7 RCY38268 228 Synechocystis #8 RCY42426 99 Synechocystis #9 RCY52862 204 Synechocystis Motif number 1 AAAATGCCTAGGGAAAATGGGAAGATTTTCTCG 1 13 1 GGGAAATGAA 0.776027 -107 ATTAATCCCTGGGAGCAAGACACGGTTCGGATG 1 75 0 GGGACAAGAC 0.969752 -45 GGTGGCTGGGGGGAAAGGGCTGCTCGGGGCCCG 3 58 1 GGGAAGGGGC 0.968187 -236 GTATAGTCTTGGGAGATAGTAACCGCAATACAG 3 118 0 GGGAATAGAC 0.926102 -176 CGGGTCATCCGGGGGAAGGCAACAGGTTGGTTT 3 235 1 GGGGAAGGAC 0.993278 -59 ACTTATATGAAGGATATGGTGACCAAAACCTAT 4 50 1 AGGAATGGAC 0.94725 -94 AAAATCTTGGGGAACAGGGGAATGTTAATGAA 5 279 0 GGGACAGGAA 0.978696 -22 ACCAAAAACAAGGATAAGGTAACCCATCCAACT 7 47 0 AGGAAAGGAC 0.975405 -182 AGCCAGTACCGGGGTAGGGAAACAAATTTTTGT 7 120 1 GGGGAGGGAC 0.986346 -109 TATGGGTATTGGGGCCAGGGCACAAAAATTTGT 7 141 0 GGGGCAGGAC 0.99256 -88 TAGGGAGTCAGGGAACAGGGAGCGGAAAAATCG 8 64 0 GGGACAGGGC 0.986324 -36 ATTAACCCAGAGGGTCTGGCTAATTTTTGTCCC 9 142 1 AGGGCTGGAA 0.790694 -63 **** **** ** Masking position 9 Map Score: 18.8034 Number of sites scoring better than the average of aligned sites = 825 Number in coding regions = 733 Number in noncoding regions = 92 Number of orfs with sites within 600 bp upstream = 93 Fraction of orfs with sites within 600 bp upstream = 0.0149374 Motif number 2 GTAGTCAGTGGTGCCAAGATTTACATCCGAA 1 52 1 GTGCCAAATT 0.828533 -68 TATTTTCATTGGGGAGAGATTAATCCCTGGG 1 95 0 GGGGAGAATT 0.972259 -25 CCCTCACCACTGGCAGAGATT 2 39 1 TGGCAGAATT 0.798728 -11 ATTTTTTCAGAGGGAAAAATTCCTCGGCTAA 5 21 0 AGGGAAAATT 0.832817 -280 GCTCCATGGCGGCCAAAAATCTTTAGGACAA 5 75 0 GGCCAAAATC 0.903798 -226 GCGCTAATCTGGGCAAAAATTCGTTGGTTTT 5 158 0 GGGCAAAATT 0.990955 -143 GCCCAGATTAGCGCCAAAATTAAGCGGAGCA 5 175 1 GCGCCAAATT 0.95049 -126 TTTATCTCAGGGGGAATCATTGCTTTAAATC 5 221 1 GGGGAATATT 0.880785 -80 CGAGTTAACTGGGCAAATATCTATGGATTAC 6 87 1 GGGCAAAATC 0.987722 -97 TGGGGCCAGGGCACAAAAATTTGTTTCCCTA 7 134 0 GCACAAAATT 0.840861 -95 GGAACAGGGAGCGGAAAAATCGAATAGAAAA 8 55 0 GCGGAAAATC 0.946512 -45 AGGGGCGAGATCCTAGGGAGTC 8 88 0 GGGGCGAATC 0.928531 -12 AGTTTTTCGGGGACAAAAATTAGCCAGACCC 9 153 0 GGACAAAATT 0.938355 -52 ******* *** Masking position 9 Map Score: 13.1276 Number of sites scoring better than the average of aligned sites = 1653 Number in coding regions = 1426 Number in noncoding regions = 227 Number of orfs with sites within 600 bp upstream = 250 Fraction of orfs with sites within 600 bp upstream = 0.0401542 Motif number 3 TCTTCCCATTTTCCCTAGGCATTTTCC 1 8 0 TTCCCTAGGC 0.974317 -112 CCGTGTCTTGCTCCCAGGGATTAATCTCTC 1 83 1 CTCCCAGGGA 0.825906 -37 GATTAATCTCTCCCCAATGAAAATAAAGT 1 101 1 TCCCCAATGA 0.939223 -19 AGCAGCCCTTTCCCCCCAGCCACCATTTCG 3 52 0 TCCCCCCAGC 0.927638 -242 CGCAATACAGTTCCCAAAGCAAGCAAGCAG 3 98 0 TTCCCAAAGC 0.965834 -196 CGGTTACTATCTCCCAAGACTATACGCCAC 3 126 1 CTCCCAAGAC 0.822041 -168 GCCTATTACCACCCCCATGCCCTAGACGGG 3 209 1 ACCCCCATGC 0.808748 -85 ACCTGTTGCCTTCCCCCGGATGACCCGTCT 3 232 0 TTCCCCCGGA 0.977973 -62 CGAGGAATTTTTCCCTCTGAAAAAATCAAG 5 26 1 TTCCCTCTGA 0.928238 -275 AAAGCAATGATTCCCCCTGAGATAAATATA 5 217 0 TTCCCCCTGA 0.970667 -84 CATTCCCCTGTTCCCCAAGATTTT 5 287 1 TTCCCCAAGA 0.959415 -14 TCAACCAAAGTTCCCAATACGTCCTTCCCA 6 44 1 TTCCCAATAC 0.872098 -140 CAATACGTCCTTCCCAATTCTGCTCAAATC 6 58 1 TTCCCAATTC 0.794524 -126 TGTTCCCTGACTCCCTAGGATCTCGCCCCT 8 80 1 CTCCCTAGGA 0.922683 -20 ********** Masking position 5 Map Score: 13.8424 Number of sites scoring better than the average of aligned sites = 2781 Number in coding regions = 2478 Number in noncoding regions = 303 Number of orfs with sites within 600 bp upstream = 311 Fraction of orfs with sites within 600 bp upstream = 0.0499518 Motif number 4 CCATGCCCTAGACGGGTCATCCGGGGGAAGGCAA 3 223 1 GAGGTCACCG 0.942662 -71 TTGGTTTTCGGAAAGGTGAACCCGTAGCTAGCTT 5 132 0 GAAGTGACCG 0.98179 -169 CTGATGGAAGGAAGATCGACCCAGTGAATGACTA 6 155 1 GAGTCGACCG 0.982173 -29 TGTTTTTGGTGGGGGTTGACCCTGCCATGGTGGG 7 70 1 GGGTTGACCG 0.98949 -159 GGATTGCATTGACATTGGAGCCAGTACCGGGGTA 7 102 1 GAATGGACCG 0.984632 -127 GACAATTATGGGTATTGGGGCCAGGGCACAAAAA 7 146 0 GGATGGGCCG 0.943439 -83 AGCTGGTGACGGGATTTGAACCTGCGACCGACTG 9 46 1 GGATTGACCG 0.98931 -159 CAGAATAGCAGAAGATTAACCCAGAGGGTCTGGC 9 128 1 GAGTTAACCG 0.951417 -77 ** * **** ** * Masking position 11 Map Score: 5.91551 Number of sites scoring better than the average of aligned sites = 204 Number in coding regions = 179 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 5 AATCTCTGCCAGTGGTGAGGGCTTGTTAC 2 31 0 CAGTGGTGAG 0.922607 -19 TCGGCGATCGCCAGGGAAGGCAGGTTTTTT 3 25 0 CCAGGGAAGG 0.839176 -269 GACGGGTCATCCGGGGGAAGGCAACAGGTT 3 233 1 CCGGGGGAAG 0.742261 -61 ATTCGTGTTTCAATGACAAGCATCTTTCCT 4 97 1 CAATGACAAG 0.658867 -47 CGCCATGGAGCAATGATGAGTTAGGTTTGG 5 95 1 CAATGATGAG 0.883975 -206 CCAACTGCCCCAAGGTTAGGAAGAAGGGAG 7 23 0 CAAGGTTAGG 0.853954 -206 CCACCAAAAACAAGGATAAGGTAACCCATC 7 52 0 CAAGGATAAG 0.914735 -177 GTTGACCCTGCCATGGTGGGATTGCATTGA 7 84 1 CCATGGTGGG 0.963419 -145 GGAGCCAGTACCGGGGTAGGGAAACAAATT 7 118 1 CCGGGGTAGG 0.968262 -111 CAGACTCTGACAATTATGGGTATTGGGGCC 7 158 0 CAATTATGGG 0.547043 -71 ACGATGATCAATGATAGGTTAATGAATT 9 9 1 CAATGATAGG 0.953402 -196 TGGTGTAGCTCAGTGGTAGAGCAACTGATT 9 86 0 CAGTGGTAGA 0.696698 -119 ********** Masking position 1 Map Score: 5.74739 Number of sites scoring better than the average of aligned sites = 2546 Number in coding regions = 2285 Number in noncoding regions = 261 Number of orfs with sites within 600 bp upstream = 273 Fraction of orfs with sites within 600 bp upstream = 0.0438484 Motif number 6 AATGTAACAAGCCCTCACCACTGGCAGAGA 2 28 1 GCCCTCACCA 0.977781 -22 CCCTTTCCCCCCAGCCACCATTTCGGCGAT 3 47 0 CCAGCCACCA 0.967049 -247 ATTGTTAGGGGCCGCCGCCAACGGGAACAT 3 169 0 GCCGCCGCCA 0.988434 -125 ATGGCCTATTACCACCCCCATGCCCTAGAC 3 206 1 ACCACCCCCA 0.932911 -88 GGCAGGGTCAACCCCCACCAAAAACAAGGA 7 66 0 ACCCCCACCA 0.988262 -163 AGGTTCAAATCCCGTCACCAGCTTATTTTG 9 39 0 CCCGTCACCA 0.984639 -166 ********** Masking position 10 Map Score: 4.12323 Number of sites scoring better than the average of aligned sites = 1120 Number in coding regions = 1085 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467 Motif number 7 TTTTCTCGACTATTGTAGTCAGTGGTGCCAA 1 38 1 TATTGTATCA 0.961372 -82 GCTTGTTACATTTTGTAATCAAATTGCTC 2 9 0 TTTTGTATCA 0.978919 -41 GTTTCTCTGAATTTGAATTCTATGGACGAAT 4 16 0 ATTTGAATCT 0.766945 -128 TATTGTAGTCATTCACTGGGT 6 173 0 TATTGTATCA 0.961372 -11 CACCAGCTTATTTTGAATTCATTAACCTATC 9 23 0 TTTTGAATCA 0.961372 -182 AGAGCAACTGATTTGTAATCAGTCGGTCGCA 9 68 0 ATTTGTATCA 0.961372 -137 ******* *** Masking position 7 Map Score: 3.28122 Number of sites scoring better than the average of aligned sites = 36 Number in coding regions = 27 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 8 TCGGATGTAAATCTTGGCACCACTGACTAC 1 52 0 ATCTTGGCAC 0.821144 -68 GATGAGTTAGGTTTGGGCAATACAAGCTAG 5 109 1 GTTTGGGCAA 0.891765 -192 TTTGGCGCTAATCTGGGCAAAAATTCGTTG 5 163 0 ATCTGGGCAA 0.981343 -138 AATCTTGGGGAACAGGGGAATGTTAATGAA 5 279 0 AACAGGGGAA 0.885922 -22 AACTTTGGTTGACAGGGCAACAAAGCCAGC 6 26 0 GACAGGGCAA 0.979912 -158 AAATCGAGTTAACTGGGCAAATATCTATGG 6 83 1 AACTGGGCAA 0.981343 -101 GGGTATTGGGGCCAGGGCACAAAAATTTGT 7 141 0 GCCAGGGCAC 0.95063 -88 ********** Masking position 9 Map Score: 3.80472 Number of sites scoring better than the average of aligned sites = 911 Number in coding regions = 814 Number in noncoding regions = 97 Number of orfs with sites within 600 bp upstream = 113 Fraction of orfs with sites within 600 bp upstream = 0.0181497 Motif number 9 CAATAGTCGAGAAAATCTTCCCATTTTCCCTA 1 21 0 GAATCTTCCC 0.842788 -99 GCTCCCAGGGATTAATCTCTCCCCAATGAAAA 1 92 1 ATATCTCTCC 0.792941 -28 TCGTCTAAAAAACCTGCCTTCCCTGGCGATCG 3 19 1 AACGCCTTCC 0.931693 -275 TTTCAATGACAAGCATCTTTCCTTAATTAACA 4 104 1 AACTCTTTCC 0.963151 -40 CTAGCTACGGGTTCACCTTTCCGAAAACCAAC 5 135 1 GTCCCTTTCC 0.875854 -166 AAAGTTCCCAATACGTCCTTCCCAATTCTGCT 6 50 1 ATCTCCTTCC 0.98444 -134 ATATCTATGGATTACTCCTTCCCATTTCTCAT 6 103 1 ATATCCTTCC 0.969882 -81 TCACTGGGTCGATCTTCCTTCCATCAGGGTCA 6 150 0 GACTCCTTCC 0.976937 -34 CCATTATTATTCCTCCCTTCTTCCTAA 7 6 1 ATATCCTCCC 0.940266 -223 ** * ******* Masking position 7 Map Score: 4.76587 Number of sites scoring better than the average of aligned sites = 284 Number in coding regions = 243 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 10 CTTTGGGAACTGTATTGCGGTTACTATCTC 3 109 1 TGTATTGCGG 0.965399 -185 GCAACAGGTTGGTTTAGCGGTTTATTGAGT 3 253 1 GGTTTAGCGG 0.966596 -41 AAAAATTCGTTGGTTTTCGGAAAGGTGAAC 5 145 0 TGGTTTTCGG 0.894158 -156 GACAATTATGGGTATTGGGGCCAGGGCACA 7 150 0 GGTATTGGGG 0.935124 -79 TCGTTAAAAAAGTTTTTCGGGGACAAAAAT 9 164 0 AGTTTTTCGG 0.929091 -41 GGTTTTACTAGGTTTTACGGATCGTTAAAA 9 185 0 GGTTTTACGG 0.967237 -20 ********** Masking position 5 Map Score: 0.638456 Number of sites scoring better than the average of aligned sites = 338 Number in coding regions = 308 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 11 GAAAGATGCTTGTCATTGAAACACGAATAA 4 95 0 TGTCATTGAA 0.926065 -49 GAACTATACCTGTTAATTAAGGAAAGATGC 4 116 0 TGTTAATTAA 0.848431 -28 AACAGGGGAATGTTAATGAACACATGACAT 5 269 0 TGTTAATGAA 0.9669 -32 TTTGTTGCCCTGTCAACCAAAGTTCCCAAT 6 32 1 TGTCAACCAA 0.906568 -152 CTGGCTCCAATGTCAATGCAATCCCACCAT 7 96 0 TGTCAATGCA 0.948886 -133 AGTATCAAATTGTCAATCAAACTAGTCAAA 8 11 0 TGTCAATCAA 0.969263 -89 ATCAATGATAGGTTAATGAATTCAAAATAA 9 17 1 GGTTAATGAA 0.899884 -188 ********** Masking position 5 Map Score: 3.02394 Number of sites scoring better than the average of aligned sites = 119 Number in coding regions = 91 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 12 GAAAATCTTCCCATTTTCCCTAGGCATTTT 1 13 0 CCATTTTCCC 0.833458 -107 ATTTTGTAATCAAATTGCTC 2 1 0 CAAATTGCTC 0.91341 -49 TCATATAAGTCAAGTTTCTCTGAATTTGAA 4 30 0 CAAGTTTCTC 0.889272 -114 TATATTTTGACCCACTGCTCCGCTTAATTT 5 191 0 CCCACTGCTC 0.962404 -110 ATTACTCCTTCCCATTTCTCATCAACAATT 6 113 1 CCCATTTCTC 0.942743 -71 GGTAACCCATCCAACTGCCCCAAGGTTAGG 7 33 0 CCAACTGCCC 0.962404 -196 TGATTACAAATCAGTTGCTCTACCACTGAG 9 78 1 TCAGTTGCTC 0.861483 -127 CTGAGCTACACCAGCATCTCTGATACAGAA 9 103 1 CCAGCATCTC 0.860485 -102 ********** Masking position 8 Map Score: 2.05694 Number of sites scoring better than the average of aligned sites = 952 Number in coding regions = 862 Number in noncoding regions = 90 Number of orfs with sites within 600 bp upstream = 102 Fraction of orfs with sites within 600 bp upstream = 0.0163829 Motif number 13 ********** No masking Map Score: 2.72438e-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 14 ********** No masking Map Score: 2.72438e-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 15 ********** No masking Map Score: 2.72438e-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