AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i146_synecho_ctra_300.orf -o146_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 RCY53956 141 Synechocystis #2 RCY46666 74 Synechocystis #3 RCY24049 296 Synechocystis #4 RCY51136 225 Synechocystis #5 RCY31840 300 Synechocystis #6 RCY19246 26 Synechocystis #7 RCY21450 40 Synechocystis #8 RCY45007 52 Synechocystis #9 RCY02720 300 Synechocystis #10 RCY12924 270 Synechocystis #11 RCY10301 71 Synechocystis #12 RCY45473 90 Synechocystis #13 RCY39027 118 Synechocystis #14 RCY15481 139 Synechocystis #15 RCY51475 94 Synechocystis #16 RCY40458 110 Synechocystis #17 RCY39045 300 Synechocystis Motif number 1 CAGTAATGGCATGATTGCCCCCT 1 4 0 ATGATTGCCC 0.762548 -138 AGCTTAGCGCAGGTTTGCCGCAAAGGAGAA 1 94 0 AGGTTTGCCG 0.843023 -48 GACGCGGGGGAATTTTGCCCTCTTGTGCCA 2 37 1 AATTTTGCCC 0.984855 -38 CAAAATTTTAAAGCTTGCCTCAGGGACAAA 3 82 0 AAGCTTGCCT 0.685025 -215 CAAGCTTTAAAATTTTGCCCGATCGCCGTA 3 95 1 AATTTTGCCC 0.984855 -202 CAATAAAAACAAGCTTTGCCAGCCTTTATC 3 126 0 AAGCTTTGCC 0.80765 -171 AACCTTGTTAAATTTTTGCCAATTTTCTGG 4 56 0 AATTTTTGCC 0.854306 -170 TTCTGGTTTCAATCTTGGTCATACCCGGTT 5 270 0 AATCTTGGTC 0.624165 -31 TTTCAAAGGAGTTTTTGGCCA 6 16 1 GTTTTTGGCC 0.739174 -11 GTGCCTCCACAATCTTGCCCACAATAACGA 9 162 0 AATCTTGCCC 0.986031 -139 AGGCACACAAATTCTTTCCCGACTAAGGGT 9 186 1 ATTCTTTCCC 0.803522 -115 TCAGAATTGGATTATTGCCCAAACGATTAA 10 122 1 ATTATTGCCC 0.82959 -149 CAAGTCCGGTAAGCTTGACCCAGGTGTAAT 10 248 1 AAGCTTGACC 0.739207 -23 GGTAAACCTCAATTTTTGCCTATTTTTCGC 12 71 0 AATTTTTGCC 0.854306 -20 AGGGGAAACTAGTTTTGGCCAAAAAAAG 13 9 0 AGTTTTGGCC 0.953999 -110 ACGGAGCGTTATTTTTGCCGCGTTTCGCTG 13 41 0 ATTTTTGCCG 0.863452 -78 CAGCTTCTTCAATCTTGCCGGTTAATTGGG 14 34 1 AATCTTGCCG 0.945072 -106 TTTTTGCTTAAGTTTTGCCCAATTAACCGG 14 51 0 AGTTTTGCCC 0.97093 -89 GTTGTGAACCAATTTTGCCCTTCCACTATC 15 53 1 AATTTTGCCC 0.984855 -42 CCCAGCTTCTAACTTTGGCCGACTTAAACC 16 59 1 AACTTTGGCC 0.836616 -52 TCAGCTCAGCAAGCTTGCCGATTATTGTAA 17 109 0 AAGCTTGCCG 0.919028 -192 GTCACTCCAGGGTTTTGGCCTGCCCCCAGG 17 217 1 GGTTTTGGCC 0.78488 -84 ********** Masking position 5 Map Score: 30.8304 Number of sites scoring better than the average of aligned sites = 2105 Number in coding regions = 1856 Number in noncoding regions = 249 Number of orfs with sites within 600 bp upstream = 259 Fraction of orfs with sites within 600 bp upstream = 0.0415997 Motif number 2 TAAAAACAAGCTTTGCCAGCCTTTATCTTACG 3 121 0 CTTGCCGCCT 0.788012 -176 ATCCTAGAAGCCGTTCCGACCCCATACCACCA 3 236 0 CCTTCCACCC 0.987197 -61 CTAGGTTTTTCCTCGCCTAACCTTGTTAAATT 4 72 0 CCCGCCAACC 0.916598 -154 AAATTAACGTCCTTTCCCTTCCCTTTATTCAA 5 19 0 CCTTCCTTCC 0.883164 -282 AAACCACACCCCGCTCCAGCCCATTGGAAGCA 5 76 1 CCCTCCGCCC 0.995971 -225 CTTTGGTGATCCCCGCCGGCCTTTTGGGGGAA 5 140 0 CCCGCCGCCT 0.980811 -161 AGTAATGCCGCCTTGCCTCCCCAATGGCCATG 5 175 1 CCTGCCCCCC 0.996745 -126 TCACCATGACCCCATCCGCCCCAAATTCGACA 10 11 0 CCATCCCCCC 0.979328 -260 GAACCTCGGGCCATTGCCCCCCATGATTTCTT 10 52 0 CCTTGCCCCC 0.963831 -219 ATTGTCCTTGCCTTGCCTGCCCCCCCTATTGT 11 35 1 CCTGCCGCCC 0.996745 -37 GTTTTGGATTCCCCTCCCCTCCATTTTGATGA 17 259 1 CCCTCCCTCC 0.977136 -42 ** **** **** Masking position 7 Map Score: 16.1187 Number of sites scoring better than the average of aligned sites = 558 Number in coding regions = 507 Number in noncoding regions = 51 Number of orfs with sites within 600 bp upstream = 65 Fraction of orfs with sites within 600 bp upstream = 0.0104401 Motif number 3 ATCATGCCATTACTGGGGCCCTTTGCCATGG 1 19 1 TCTGGGGCCC 0.740427 -123 GTATTTTCCTGGTTTTGGGCCATGGCAAAGG 1 38 0 GTTTTGGGCC 0.739712 -104 GTTATCACAGGGGTGGTGGCACAAGAGGGCA 2 52 0 GGTGGTGGCA 0.965377 -23 TGAAAAATTTTTCTGGTGGCATGAAAAAATT 5 46 0 TCTGGTGGCA 0.954824 -255 AAACTTTGAATATTGTAGGCCGGTTTCCCCC 5 116 1 TTTGTAGGCC 0.778169 -185 CCCGCCGGCCTTTTGGGGGAAACCGGCCTAC 5 130 0 TTTGGGGGAA 0.740362 -171 GGCATGGCCATTGGGGAGGCAAGGCGGCATT 5 178 0 TGGGGAGGCA 0.847751 -123 TTCCATTCGTTATTGTGGGCAAGATTGTGGA 9 156 1 TTTGTGGGCA 0.950906 -145 GTGGGCAAGATTGTGGAGGCACACAAATTCT 9 170 1 TGTGGAGGCA 0.94246 -131 GACAAGAAATCATGGGGGGCAATGGCCCGAG 10 49 1 CTGGGGGGCA 0.780842 -222 TGCTTATTAATCGTTTGGGCAATAATCCAAT 10 127 0 TGTTTGGGCA 0.825004 -144 GTGGGCGATCGCCTGGGGGCATTCTGCCAAT 10 218 0 GCTGGGGGCA 0.978189 -53 AAGGACAATGGATTGGTGGCCATTACTAAAC 11 13 0 GTTGGTGGCC 0.949552 -59 GAGAAGACAATAGGGGGGGCAGGCAAGGCAA 11 42 0 TGGGGGGGCA 0.961867 -30 CTTTTTTTGGCCAAAACTAGTT 13 2 1 TTTTTTGGCC 0.572521 -117 TGCCTAGGTAGGTTAGTGGCAGCTTCTTCAA 14 15 1 GTTAGTGGCA 0.582729 -125 AGTCACTCCAGGGTTTTGGCCTGCCCCCAGG 17 216 1 GGTTTTGGCC 0.592417 -85 GCTTCGCTAATCCTGGGGGCAGGCCAAAACC 17 227 0 TCTGGGGGCA 0.980478 -74 * ********* Masking position 8 Map Score: 15.9611 Number of sites scoring better than the average of aligned sites = 3410 Number in coding regions = 3138 Number in noncoding regions = 272 Number of orfs with sites within 600 bp upstream = 285 Fraction of orfs with sites within 600 bp upstream = 0.0457758 Motif number 4 TGGCCCAAAACCAGGAAAATACTAATAAAT 1 47 1 CCAGGAAAAT 0.911562 -95 TGCTGATGGACCAGGTGAACAGAACTAACA 3 206 0 CCAGGTGAAC 0.940503 -91 TAGGAGATTACCAGTAGAATTCGGCT 4 7 0 CCAGTAGAAT 0.876911 -219 TGGCGGATCTCTAGGAGATTACCAGTAGAA 4 18 0 CTAGGAGATT 0.896488 -208 TAGAGATCCGCCAGGCGATCGCCAGAAAAT 4 35 1 CCAGGCGATC 0.89779 -191 CAGGCGATCGCCAGAAAATTGGCAAAAATT 4 46 1 CCAGAAAATT 0.721186 -180 TGGGCTCTATCCATGTGAATAAGTTCTTTG 4 106 0 CCATGTGAAT 0.800523 -120 TTTCATGCCACCAGAAAAATTTTTCAAACC 5 51 1 CCAGAAAAAT 0.69469 -250 AATGGCCATGCCATATGATTTGCTAAAGAG 5 197 1 CCATATGATT 0.501766 -104 ATATTAAGTATCAGGTGATTGCTTGATCTT 8 14 1 TCAGGTGATT 0.7063 -39 TTGATCTTTTCTAGTTGATTTTTTGAT 8 36 1 CTAGTTGATT 0.688945 -17 AGAGCCTAAACCAGGTAAATTTGATTGCGA 9 233 0 CCAGGTAAAT 0.922725 -68 CAGAATGCCCCCAGGCGATCGCCCACAAGT 10 223 1 CCAGGCGATC 0.89779 -48 ATTCATAACTCTAGTTAAATTTCTCTTACC 14 115 1 CTAGTTAAAT 0.383579 -25 CTATCCGTACCTAGGAGATTAACCACT 15 78 1 CTAGGAGATT 0.896488 -17 ********** Masking position 3 Map Score: 9.77957 Number of sites scoring better than the average of aligned sites = 2050 Number in coding regions = 1880 Number in noncoding regions = 170 Number of orfs with sites within 600 bp upstream = 175 Fraction of orfs with sites within 600 bp upstream = 0.0281079 Motif number 5 AGGTACAACCGAGAAATGCTCACGAATAAGCTTAGCGCAGGTT 1 109 0 AGGAACAAAT 0.991136 -33 TCTGACTTCTATAGGGAAAATCTCAAAAAAAATTCTCAAAAGTTTA 4 139 1 AGGAACAAAT 0.991136 -87 GTGTGGTTTTAATGAGAAAATCTCTTTAGCAAATCATATGGCATGG 5 202 0 AGGAACAAAA 0.972479 -99 AATCCTCAAAAAGGAGCAATACAGCAGATAAAAGATGATTGGGAGA 9 260 0 AGGAACAAAT 0.991136 -41 GGATGGGGTCATGGTGAAAGAATGACAAGAAATCATGGGGGGCAAT 10 26 1 AGGAAAAAAT 0.916404 -245 TTGCCGGTTAATTGGGCAAAACTTAAGCAAAAATCTTCCGCCCTAA 14 48 1 AGGAACCAAT 0.963135 -92 AGTTTACTTTAACGGGTAAAGCCAAGGAATAAATCATCAAC 15 6 0 AGGAACAAAA 0.972479 -89 AGATTTGGGATTGGGATAAGCAAATGATTAAAGGTTTAAGTCGGC 16 76 0 AGGTACAAAT 0.972479 -35 ACCGACCCCAAGAGAGCTATACCCTTCAAGAATTCTAATCATAACC 17 24 1 AGGTACAAAT 0.972479 -277 * * * ** * * ** * Masking position 9 Map Score: 10.0643 Number of sites scoring better than the average of aligned sites = 17 Number in coding regions = 13 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 6 TCACGAATAAGCTTAGCGCAGGTTTGCCGCA 1 102 0 GTTAGCGCAG 0.964352 -40 TTCCAGGGGAGATTAGCTCGGGCGTTTTGTC 3 57 1 GTTAGCTCGG 0.965086 -240 AATTTAACAAGGTTAGGCGAGGAAAAACCTA 4 72 1 GTTAGGCGAG 0.811521 -154 TGCCGATAGCAGTTAACCGGGTATGACCAAG 5 256 1 ATTAACCGGG 0.71539 -45 GTTTCAGAAAAGTTAACTGAGTGGATAAATT 7 17 0 ATTAACTGAG 0.784607 -24 CGCGTTCATTGTTGCACGGAGCGTTATTTTT 13 55 0 GTGCACGGAG 0.634339 -64 TCCGTGCAACAATGAACGCGGTATCAATAAC 13 66 1 ATGAACGCGG 0.655593 -53 TTGAAACCTTGGTTAACGAAGTTGCCTATAT 13 97 0 GTTAACGAAG 0.839426 -22 CAATCTTGCCGGTTAATTGGGCAAAACTTAA 14 43 1 GTTAATTGGG 0.689156 -97 AATAAAATTAGGTTAGGGCGGAAGATTTTTG 14 75 0 GTTAGGGCGG 0.915873 -65 TTCCAACAAAGATTAGCTGGGATGTCACTGA 16 16 1 GTTAGCTGGG 0.977588 -95 ATGATTAAAGGTTTAAGTCGGCCAAAGTTAG 16 67 0 GTTAAGTCGG 0.848069 -44 CGGCAAGCTTGCTGAGCTGAGACTCAGTTAA 17 119 1 GTGAGCTGAG 0.928897 -182 GGGTTGAAATGATTAACTGAGTCTCAGCTCA 17 131 0 GTTAACTGAG 0.956309 -170 CTGCCCCCAGGATTAGCGAAGCTGTTTTGGA 17 236 1 GTTAGCGAAG 0.880665 -65 * ********* Masking position 3 Map Score: 8.07647 Number of sites scoring better than the average of aligned sites = 1102 Number in coding regions = 959 Number in noncoding regions = 143 Number of orfs with sites within 600 bp upstream = 171 Fraction of orfs with sites within 600 bp upstream = 0.0274655 Motif number 7 GGGGAATTTTGCCCTCTTGTGCCACCACCC 2 43 1 GCCCTCTTGT 0.959407 -32 GATTAGCTCGGGCGTTTTGTCCCTGAGGCA 3 67 1 GGCGTTTTGT 0.900757 -230 AAATGTCCATAGTCTTTTGTTAAATACGCC 3 155 0 AGTCTTTTGT 0.745074 -142 GATCCCCGCCGGCCTTTTGGGGGAAACCGG 5 135 0 GGCCTTTTGG 0.961752 -166 CGGCATTACTGCTCTTTGGTGATCCCCGCC 5 155 0 GCTCTTTGGT 0.918766 -146 TTCGGTGCCCGCTCTTTTGTAGAATGGAAC 10 80 0 GCTCTTTTGT 0.977055 -191 GAAGGGTATAGCTCTCTTGGGGTCGGTGGT 17 21 0 GCTCTCTTGG 0.959407 -280 GATTAGCGAAGCTGTTTTGGATTCCCCTCC 17 246 1 GCTGTTTTGG 0.936575 -55 ********** Masking position 5 Map Score: 3.93584 Number of sites scoring better than the average of aligned sites = 205 Number in coding regions = 185 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 8 TTTTGAGTAGTTGAAAAGTTTACGGACGCGGGG 2 13 1 TTGAATTTAC 0.746802 -62 TCGCCTAACCTTGTTAAATTTTTGCCAATTTTC 4 59 0 TTGTATTTTT 0.837481 -167 TTGTAAACTTTTGAGAATTTTTTTTGAGATTTT 4 155 0 TTGAATTTTT 0.961273 -71 GGGGTGTGGTTTGAAAAATTTTTCTGGTGGCAT 5 55 0 TTGAATTTTT 0.961273 -246 TGCAATTTATTTGAACTATTTTTGTTGCTTAAA 9 11 1 TTGATTTTTT 0.759259 -290 AGCTAAAGATTTGCTCACTTTTTAAAAGTTGAT 9 96 1 TTGCATTTTT 0.964147 -205 TTGCTCCTTTTTGAGGATTTTTCC 9 287 1 TTGAATTTTC 0.9587 -14 TGGGGGCATTCTGCCAATTTTTCTGATTATAGG 10 203 0 CTGCATTTTC 0.825666 -68 ACCTCAATTTTTGCCTATTTTTCGCTACTCTAG 12 63 0 TTGCATTTTC 0.961758 -28 CGGAAGATTTTTGCTTAAGTTTTGCCCAATTAA 14 55 0 TTGCAGTTTT 0.8351 -85 GTTGATGATTTATTCCTTGGCTTT 15 2 1 TTGAATTATT 0.759259 -93 **** * ***** Masking position 10 Map Score: 6.38175 Number of sites scoring better than the average of aligned sites = 185 Number in coding regions = 140 Number in noncoding regions = 45 Number of orfs with sites within 600 bp upstream = 53 Fraction of orfs with sites within 600 bp upstream = 0.00851269 Motif number 9 TGGTTCCAGGGGAGATTAGCTCGGGCGTTT 3 54 1 GGAGATTAGC 0.926131 -243 TTTATCTTACGGCGATCGGGCAAAATTTTA 3 102 0 GGCGATCGGG 0.850395 -195 CGGATCTCTAGGAGATTACCAGTAGAATTC 4 15 0 GGAGATTACC 0.959521 -211 AGATCCGCCAGGCGATCGCCAGAAAATTGG 4 38 1 GGCGATCGCC 0.499979 -188 AAAGGCCGGCGGGGATCACCAAAGAGCAGT 5 148 1 GGGGATCACC 0.778767 -153 TGGAACCTCGGGCCATTGCCCCCCATGATT 10 56 0 GGCCATTGCC 0.815346 -215 AATGCCCCCAGGCGATCGCCCACAAGTCCG 10 226 1 GGCGATCGCC 0.499979 -45 TCCGTACCTAGGAGATTAACCACT 15 81 1 GGAGATTAAC 0.821545 -14 ********** Masking position 5 Map Score: 7.25588 Number of sites scoring better than the average of aligned sites = 6501 Number in coding regions = 5881 Number in noncoding regions = 620 Number of orfs with sites within 600 bp upstream = 393 Fraction of orfs with sites within 600 bp upstream = 0.0631224 Motif number 10 TTTCCTGGTTTTGGGCCATGGCAAAGGGCCC 1 34 0 TTGGGCCATG 0.561345 -108 TGACATTAGGTTGGGTAAGCGTGTTAGTTCT 3 185 1 TTGGGTAAGG 0.945776 -112 CATGGTGGTATGGGGTCGGAACGGCTTCTAG 3 234 1 TGGGGTCGGA 0.940561 -63 TTGGGGCGGATGGGGTCATGGTGAAAGAATG 10 19 1 TGGGGTCATG 0.969404 -252 CAAACTGTGCTGGGGTAACGGTTA 12 4 0 TGGGGTAACG 0.9435 -87 AGTGGGGTAAGAGAAATTTAACT 14 127 0 TGGGGTAAGG 0.990186 -13 AGTTAGAAGCTGGGCTAAGACAAATTTCAGT 16 42 0 TGGGCTAAGC 0.838364 -69 GATTTGGGATTGGGATAAGCAAATGATTAAA 16 89 0 TGGGATAAGA 0.693478 -22 ATAGCTCTCTTGGGGTCGGTGGTGTCCTCGT 17 13 0 TGGGGTCGGG 0.985752 -288 TCGCTAATCCTGGGGGCAGGCCAAAACCCTG 17 224 0 TGGGGGCAGC 0.930072 -77 ********* * Masking position 1 Map Score: 4.45443 Number of sites scoring better than the average of aligned sites = 930 Number in coding regions = 840 Number in noncoding regions = 90 Number of orfs with sites within 600 bp upstream = 106 Fraction of orfs with sites within 600 bp upstream = 0.0170254 Motif number 11 AGAAAAATTTTTCAAACCACACCCCGCTCCAGC 5 63 1 TTAACCAACC 0.974645 -238 CTCCAGCCCATTGGAAGCAAAACAACAAAACTT 5 89 1 TTAAGCAAAC 0.945345 -212 GATTTTCTCATTAAAACCACACCACATCTCTGC 5 226 1 TTAACCAACC 0.974645 -75 ATGACCAAGATTGAAACCAGAACCGAACCAATG 5 278 1 TTAACCAAAC 0.978888 -23 TTATTTACGGTTTTATTCATAACTCTAGTTAAA 14 101 1 TTATTCAAAC 0.83544 -39 CCTTCAAGAATTCTAATCATAACCATCAAAACT 17 46 1 TTAATCAAAC 0.953658 -255 ** ***** *** Masking position 5 Map Score: 0.433213 Number of sites scoring better than the average of aligned sites = 34 Number in coding regions = 26 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 12 ********** No masking Map Score: -2.03683e-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 13 ********** No masking Map Score: -2.03683e-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 14 ********** No masking Map Score: -2.03683e-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