AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i293_synecho_ctra_100.orf -o293_synecho_ctra_100.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 RCY10363 283 Synechocystis #2 RCY45270 150 Synechocystis #3 RCY53977 169 Synechocystis #4 RCY06830 23 Synechocystis #5 RCY08607 154 Synechocystis #6 RCY23989 257 Synechocystis #7 RCY21643 109 Synechocystis #8 RCY09697 66 Synechocystis #9 RCY14174 300 Synechocystis #10 RCY42662 233 Synechocystis #11 RCY39566 239 Synechocystis #12 RCT00090 300 Chlamydia_trachomatis #13 RCT00765 300 Chlamydia_trachomatis #14 RCT00779 300 Chlamydia_trachomatis #15 RCT00803 97 Chlamydia_trachomatis #16 RCT00804 160 Chlamydia_trachomatis Motif number 1 CCGATTTTCACCCCAATCGCCAACCCAGAGAACAACAAT 1 98 0 CCCGCCACCA 0.884691 -186 AGCTCCCAGACATCATTGGCCACTCCAGGGATTTGTCAG 1 156 0 CCGGCCACCG 0.995044 -128 TTGCTGGCTCCAGCGGTGGCAAAGCCTAATGATCCTAAC 3 61 0 CCGGCAACCA 0.992413 -109 GGACGTTCAACCCCTGAGGCAATCCAGTGGGGCGTGATT 6 78 1 CCGGCAACAG 0.981623 -180 CTCAGGATAACTGCTCCGGGAAATTTCAGGTAAATCACG 6 110 0 CCGGGAATTG 0.911999 -148 CCATCGTTGACGGCAAAGGCAGATCTAAACCACGACTGT 6 197 0 CCGGCAGCTA 0.910582 -61 CCTTTGCCGTCAACGATGGGAGAATTCGGCTTGAGCTTG 6 217 1 CCGGGAGTTG 0.802079 -41 TGGCGATCGGGGCAAGCTCAAGCCGAATTCTC 6 236 0 CTGGCAATCG 0.929479 -22 CTGGCGATCGCCGCCTGGGGAATCCCAGAAAAAATTAGA 9 27 1 CCGGGAACCA 0.987571 -274 GAAAATTTTGCCCCGGTGGGCATTTCTCATTTTTGCTAA 9 136 0 CCGGGCATCA 0.950001 -165 CCGCCATTGACAGCCAGGGGAATTCCTCGATAAAACTAT 9 174 1 CCGGGAACCG 0.993902 -127 TCCGGGCACCCGACTAAGGGAAACACCAGTAATCTGCCA 10 190 1 CCGGGAAACG 0.927757 -44 ACCAGCCAGTCACCGTTGGCAAAACCTTAACAAAAAGTT 11 139 0 CCGGCAACCA 0.992413 -101 GAGAGATTTTCGATTGGGGCCATCTAAGGGAACAGAAGG 13 90 1 CTGGCCATAG 0.662632 -211 GGAAAAGAAGCCCTTAAGGCCATTCAAAGGCCTTTTAGC 13 247 1 CTGGCCACAG 0.860091 -54 TCTGCTGAACCCACTAGGGCAGCCCCAAAAACACTA 16 8 0 CCGGCAGCCA 0.980825 -153 * * ***** ** * Masking position 9 Map Score: 21.0694 Number of sites scoring better than the average of aligned sites = 1234 Number in coding regions = 1156 Number in noncoding regions = 78 Number of orfs with sites within 600 bp upstream = 94 Fraction of orfs with sites within 600 bp upstream = 0.015098 Motif number 2 AATATAAACTATTGTTGTTCTCTGGGTTGGCG 1 88 1 ATGTTTTCTC 0.540416 -196 AGTCTAAACCGATTTTCACCCCAATCGCCAAC 1 113 0 GTTTTACCCC 0.882911 -171 CCTACCAAAAACTTCTAACCCCAAGCTCCCAG 1 186 0 ATTCTACCCC 0.828128 -98 GATTATTTCGGGTTCTATCCCCCAGTTTCCTA 3 14 0 GTTCTTCCCC 0.970227 -156 TTTTCAGATGGTTGCTTCCCCCATCCACAGTC 6 171 1 GTGCTCCCCC 0.94964 -87 GATGGGAGACTGTTTTGCCCCCCTAATCATCC 7 70 1 TTTTTCCCCC 0.67303 -40 GGTTCTTCTCTCTGTCAAAGGG 9 289 0 GTTCTCTCTC 0.913276 -12 TCTCTTCCCAGTTTTTGCTCCCCATGTCGAAT 10 65 0 GTTTTCTCCC 0.943151 -169 CCTCCAATAAATTTCTCTTCCCAGTTTTTGCT 10 78 0 ATTCTTTCCC 0.920983 -156 AATCATAGCGGATTCTTTCCTCGCCAATCTCT 10 135 0 GTTCTTCCTC 0.911807 -99 CGCCTTTTCTGTTTTTTCGCCCATAGATGGCC 12 25 1 GTTTTCGCCC 0.740131 -276 ACCGTATATAAATGTTTTTCTCAAGAAAGAAG 12 93 1 ATGTTTTCTC 0.540416 -208 GAAGGTGGCAGATGCTCATCCCATTTATAAAC 12 121 1 GTGCTATCCC 0.914882 -180 CCCAGAGTTGTCTTTTATTCCCCCTTAGGTCT 13 30 1 TTTTTTTCCC 0.717062 -271 TATTATCAAGCCTTCTGTTCCCTTAGATGGCC 13 107 0 CTTCTTTCCC 0.80995 -194 GGCCTTAAGGGCTTCTTTTCCCTCAACCGGAT 13 236 0 GTTCTTTCCC 0.973329 -65 AAAATGCTATTCTCCATTACCTTG 13 287 0 ATGCTTTCTC 0.701722 -14 AACACTTCTTGTTTTTTATCTCTATAATTAGA 16 60 1 GTTTTATCTC 0.728191 -101 * **** ***** Masking position 6 Map Score: 17.2979 Number of sites scoring better than the average of aligned sites = 1257 Number in coding regions = 1086 Number in noncoding regions = 171 Number of orfs with sites within 600 bp upstream = 187 Fraction of orfs with sites within 600 bp upstream = 0.0300353 Motif number 3 GGCATTGTTGCGGAAAATCTGTGGGGGAGA 1 256 0 CGGAAAATCT 0.887248 -28 ATAACTGCTCCGGGAAATTTCAGGTAAATC 6 113 0 CGGGAAATTT 0.795827 -145 TTATCCTGAGAGGAAGAATTGTGTGAGGAA 6 139 1 AGGAAGAATT 0.721989 -119 GAATTGTGTGAGGAAAATTTTCAGATGGTT 6 154 1 AGGAAAATTT 0.934703 -104 TGTTTCCCGTGGGAAAAATTGAAAATTTAG 8 29 1 GGGAAAAATT 0.930493 -38 TAGTAGGAATATTTTTCTGGCGAT 9 5 1 AGGAATATTT 0.923349 -296 CTGTCAATGGCGGAAAATTTTGCCCCGGTG 9 157 0 CGGAAAATTT 0.957815 -144 AGCTGCTTTGGGGAATAACTTGGCCGGCTG 9 256 0 GGGAATAACT 0.796098 -45 TCAACGGCTCGGGAAAAATTCGACATGGGG 10 48 1 GGGAAAAATT 0.930493 -186 AAGCGCTATAAGGAATACTTCGCAAGTTAC 12 65 1 AGGAATACTT 0.761869 -236 CTTTAGAGAACGGAATATTTTTTTTAAAGA 12 168 1 CGGAATATTT 0.950266 -133 GATAAAAATAGGGAATATTTATCTCTGAAA 14 231 1 GGGAATATTT 0.950266 -70 ********** Masking position 5 Map Score: 10.5056 Number of sites scoring better than the average of aligned sites = 625 Number in coding regions = 531 Number in noncoding regions = 94 Number of orfs with sites within 600 bp upstream = 113 Fraction of orfs with sites within 600 bp upstream = 0.0181497 Motif number 4 ACCCCAATCGCCAACCCAGAGAACAACAATA 1 97 0 CAACCCAGAG 0.986883 -187 ACATCATTGGCCACTCCAGGGATTTGTCAGG 1 155 0 CACTCCAGGG 0.852455 -129 CCAAAAACTTCTAACCCCAAGCTCCCAGACA 1 183 0 CAACCCCAAG 0.964622 -101 TGGCTCCTGTCTCCCCCACAGATTTTCCGCA 1 247 1 CCCCCCACAG 0.976319 -37 ATTTCGGGTTCTATCCCCCAGTTTCCTAACC 3 11 0 CATCCCCCAG 0.934743 -159 AGCGGACGTTCAACCCCTGAGGCAATCCAGT 6 75 1 CACCCCTGAG 0.974303 -183 GGTTGCTTCCCCCATCCACAGTCGTGGTTTA 6 180 1 CCATCCACAG 0.782233 -78 ATTACGGCCCCACACCCAAAGTTTTTCTGCT 9 222 0 CCACCCAAAG 0.955375 -79 TGCCCGGAAGCAAACCCAGGGTTTTCGATCC 10 167 0 CAACCCAGGG 0.963067 -67 ACAGAAAAGGCGACCCCCAAGCGTCT 12 6 0 CACCCCCAAG 0.977519 -295 TCGAATCCTTCCACCCCAGAGTTGTCTTTTA 13 16 1 CACCCCAGAG 0.991734 -285 TGCTCTATCCCTAAGAATATCCTTT 14 286 0 CATCCCTAAG 0.84037 -15 * ********* Masking position 6 Map Score: 14.8342 Number of sites scoring better than the average of aligned sites = 504 Number in coding regions = 460 Number in noncoding regions = 44 Number of orfs with sites within 600 bp upstream = 51 Fraction of orfs with sites within 600 bp upstream = 0.00819146 Motif number 5 TTGTTGCGGAAAATCTGTGGGGGAGACAGGAGCC 1 248 0 AAACGGGGGA 0.774589 -36 TTTCCGCAACAATGCCATGGGGCA 1 270 1 AATCAGGGCA 0.971903 -14 ACGCTTCTCAGAAACAATTGGCCACTGTAGCGAA 2 52 0 GAACAGGCCA 0.915792 -99 TGGTAGAATGTATCCCAAGGGCAATGCTAGTTGG 3 107 0 TATCAGGCAA 0.743286 -63 CCCCTGAGGCAATCCAGTGGGGCGTGATTTACCT 6 88 1 AATCGGGGCG 0.800248 -170 CATCGTACCAAAATCAGGTGGGCACCACATCACA 7 40 0 AAACGGGGCA 0.967133 -70 ATTCCTCGATAAAACTATTGGGCACACAGCAGAA 9 195 1 AAACAGGGCA 0.975653 -106 GGGGCCGTAATCTTCAGCCGGCCAAGTTATTCCC 9 242 1 TCTCGGGCCA 0.707045 -59 ATTCAGGGGGAAAACTACCAGCCAGTCACCGTTG 11 160 0 AAACAAGCCA 0.854847 -80 TTATAGCGCTTAAGCAACTGGCCATCTATGGGCG 12 42 0 TAACAGGCCA 0.960225 -259 AAGAAAGCAGAATGCAACAGGCAACTAAAGCTTC 14 14 1 AATCAGGCAA 0.848083 -287 ACCAAACAAAAATTCAAACGGCCATTCACTTTTT 14 123 0 AATCAGGCCA 0.975716 -178 ACTACAATGCTAATCAAACAGGCAGATAATTATT 16 130 0 TAACAAGGCA 0.724493 -31 *** * * ***** Masking position 5 Map Score: 7.41098 Number of sites scoring better than the average of aligned sites = 780 Number in coding regions = 713 Number in noncoding regions = 67 Number of orfs with sites within 600 bp upstream = 74 Fraction of orfs with sites within 600 bp upstream = 0.0118856 Motif number 6 TCGATTCTATCCTACCAAAAACTTCTAACCC 1 197 0 CCTACAAAAA 0.694171 -87 CTATATCGATTCTGAAAATAAATTCTCGGCG 5 23 0 TCTGAAATAA 0.574752 -132 GGGTGGCGCTCCAGAAAAAAAGTGCGCTAGG 5 68 1 CCAGAAAAAA 0.824807 -87 CTTAACTCAACTTAACAATAAAAGGGCTTTA 9 76 0 CTTAAAATAA 0.900724 -225 TTGGCAAAACCTTAACAAAAAGTTTAGAGTT 11 132 0 CTTAAAAAAA 0.951452 -108 CACCTTCTTTCTTGAGAAAAACATTTATATA 12 97 0 CTTGAAAAAA 0.952314 -204 AAAAACGCTCTTTAAAAAAAATATTCCGTTC 12 175 0 TTTAAAAAAA 0.795992 -126 AAAAGAAATTCTAAAGAAAAAGCAAGATTAG 12 215 0 CTAAAAAAAA 0.862863 -86 TTTCTTTTTCCTTAATAATAAAAAGGCTGTG 12 238 1 CTTAAAATAA 0.900724 -63 CTGTGTTAGCCTTAAGAAAAAGCTGTACAAC 12 264 1 CTTAAAAAAA 0.951452 -37 GAACAGAAGGCTTGATAATAATCAGAGGCTG 13 119 1 CTTGAAATAA 0.902394 -182 CTATTTATAACCAAACAAAAATTCAAACGGC 14 135 0 CCAAAAAAAA 0.82207 -166 TTGCAAAGATTTTGATAAAAATAGGGAATAT 14 218 1 TTTGAAAAAA 0.799031 -83 ***** ***** Masking position 7 Map Score: 9.53864 Number of sites scoring better than the average of aligned sites = 149 Number in coding regions = 95 Number in noncoding regions = 54 Number of orfs with sites within 600 bp upstream = 65 Fraction of orfs with sites within 600 bp upstream = 0.0104401 Motif number 7 GAGAACAACAATAGTTTATATTGACTATTT 1 80 0 ATAGTTTATA 0.635639 -204 GTATTTGGGGTTAGGTTATAGTTGTGTATG 11 21 0 TTAGGTTATA 0.849726 -219 AAAGCCCCCCTTTGTTTGTATTTGGGGTTA 11 38 0 TTTGTTTGTA 0.875974 -202 CCCCTTACTCTTTGTTTATAAATGGGATGA 12 136 0 TTTGTTTATA 0.950778 -165 ATTTATTTTTTTTGTTTTTATGACCCCCTA 14 55 0 TTTGTTTTTA 0.826551 -246 TGAATTTTTGTTTGGTTATAAATAGTAAGC 14 141 1 TTTGGTTATA 0.928561 -160 ATTTTATTATTTTGTTTATAAACCTCTAAT 16 86 0 TTTGTTTATA 0.950778 -75 ********** Masking position 10 Map Score: 2.2093 Number of sites scoring better than the average of aligned sites = 35 Number in coding regions = 26 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 8 CAGTTGACCAACAGTTACAAAG 2 3 1 GTTGACCAAC 0.770058 -148 TGTGGCCCAAAATTGCCTTTC 4 2 1 GTGGCCCAAA 0.975062 -22 TGAAAATTTAGTGGACAAAAATAATATAA 8 48 1 GTGGACAAAA 0.925689 -19 TTCCCGAGCCGTTGACCAAAAAACTTTATT 10 33 0 GTTGACCAAA 0.969378 -201 AAAGTTTAGAGTTGCCCAAAGTCTAGAAAA 11 115 0 GTTGCCCAAA 0.97095 -125 GCCAGTCACCGTTGGCAAAACCTTAACAAA 11 144 0 GTTGGCAAAA 0.890199 -96 ********** Masking position 8 Map Score: 3.33314 Number of sites scoring better than the average of aligned sites = 208 Number in coding regions = 188 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 9 CGCCATCTTAACAGTGAGTACACTTCCGAAATAGTC 1 52 1 ACATGTCATC 0.820259 -232 ATAGGGACAAACAATCGATTCTATCCTACCAAAAAC 1 206 0 ACATCTCTTC 0.914837 -78 TGTTTATTATCCACTCCATCCATTGCTAACCGGTGG 2 103 1 CCATCTCATC 0.965452 -48 ACGATTTGTAAAAATCCGCCCAATTTTTAAATTCTG 6 24 0 AAATCCCATT 0.659975 -234 CGGATTTTTACAAATCGTCACAGTTCTAAGGGTAGC 6 42 1 CAATCCCATC 0.943229 -216 TTATCGATTACAATTCTTTGCACTTCCGTATAAATA 11 74 1 CAATCTCATC 0.971418 -166 GCCCCAATCGAAAATCTCTCCTATTCAATAAGAGAT 13 74 0 AAATCTCTTC 0.92869 -227 TATTTTTATCAAAATCTTTGCAATTCGCCTTCTTAA 14 205 0 AAATCTCATC 0.976286 -96 AAAACTCACTACAATGCTAATCAAACA 16 144 0 AAATCTCATC 0.97629 -17 *** ** * ** * * Masking position 5 Map Score: 2.70817 Number of sites scoring better than the average of aligned sites = 109 Number in coding regions = 91 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 10 AGACTGTTTTGCCCCCCTAATCATCCTCAA 7 76 1 GCCCCCCTAA 0.962691 -34 CCAAAGCAGCTCCGCCCTTTGACAGAGAGA 9 275 1 TCCGCCCTTT 0.860661 -26 ATACAGCAAAGCCCCCCTTTGTTTGTATTT 11 45 0 GCCCCCCTTT 0.977747 -195 GTTCTCTAAAGAACCCCTTACTCTTTGTTT 12 149 0 GAACCCCTTA 0.930305 -152 TTGTCTTTTATTCCCCCTTAGGTCTGGTTT 13 37 1 TTCCCCCTTA 0.80228 -264 CGCTATACCAGACGGCCTTAAAATGGCACA 13 193 0 GACGGCCTTA 0.855281 -108 TGAGGGAAAAGAAGCCCTTAAGGCCATTCA 13 243 1 GAAGCCCTTA 0.890996 -58 TTGTTTTTATGACCCCCTATTTGATAGAAG 14 44 0 GACCCCCTAT 0.930165 -257 ********** Masking position 8 Map Score: 2.00379 Number of sites scoring better than the average of aligned sites = 359 Number in coding regions = 293 Number in noncoding regions = 66 Number of orfs with sites within 600 bp upstream = 59 Fraction of orfs with sites within 600 bp upstream = 0.00947639 Motif number 11 CGAAAAAATGCTAAGGATAGAGGCTTTGTAACT 2 23 0 CTAGGAAGGG 0.976526 -128 CGTCACAGTTCTAAGGGTAGCGGACGTTCAACC 6 57 1 CTAGGGAGGG 0.941058 -201 AATTCTTCCTCTCAGGATAACTGCTCCGGGAAA 6 126 0 CTAGGAAATG 0.790102 -132 ACTTGGCCGGCTGAAGATTACGGCCCCACACCC 9 236 0 CTAAGATAGG 0.886227 -65 TTTGCAAAACCTAAAGAGATTGGCGAGGAAAGA 10 121 1 CTAAGAATGG 0.927153 -113 AAATGTTTTTCTCAAGAAAGAAGGTGGCAGATG 12 102 1 CTAAGAAGAG 0.919883 -199 GTAAGGGGTTCTTTAGAGAACGGAATATTTTTT 12 158 1 CTTAGAAAGG 0.886228 -143 AAAAGAAATTCTAAAGAAAAAGCAAGATTAGTG 12 213 0 CTAAGAAAGC 0.935935 -88 CTGTGTTAGCCTTAAGAAAAAGCTGTACAACTT 12 264 1 CTAAGAAAGC 0.935935 -37 GGCCTTTTAGCTCAAGGTAATGGAGAATAGCAT 13 275 1 CTAAGGAAGG 0.959232 -26 CTAAAGAAAGCAGAATGCAACAG 14 1 1 CTAAGAAGAG 0.919883 -300 ** **** ** ** Masking position 2 Map Score: 7.62335 Number of sites scoring better than the average of aligned sites = 138 Number in coding regions = 113 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 12 TTCTCTGGGTTGGCGATTGGGGTGAAAATC 1 105 1 TGGCGATTGG 0.906357 -179 AGAGCTATCCCGGCGTTCCAAACTTCCCTC 3 141 1 CGGCGTTCCA 0.966587 -29 AATAAATTCTCGGCGTTCCGTGGTCAA 5 8 0 CGGCGTTCCG 0.983025 -147 AGATCGTGGGTGGCGCTCCAGAAAAAAAGT 5 61 1 TGGCGCTCCA 0.920131 -94 TGGCGATCGGGGCAAGCTCA 6 248 0 TGGCGATCGG 0.984232 -10 ATTCCCCAGGCGGCGATCGCCAGAAAAATA 9 20 0 CGGCGATCGC 0.97347 -281 ********** Masking position 7 Map Score: 1.41729 Number of sites scoring better than the average of aligned sites = 2543 Number in coding regions = 2344 Number in noncoding regions = 199 Number of orfs with sites within 600 bp upstream = 231 Fraction of orfs with sites within 600 bp upstream = 0.0371025 Motif number 13 CCTGTCTCCCCCACAGATTTTCCGCAACAAT 1 252 1 CCCAGATTTT 0.865844 -32 AATACAATTTTCGCTGATTATTTCGGGTTCT 3 30 0 TCCTGATTAT 0.881213 -140 ATGTGGTGCCCACCTGATTTTGGTACGATGG 7 44 1 CACTGATTTT 0.88669 -66 CTGTTTTGCCCCCCTAATCATCCTCAAAATA 7 79 1 CCCTAATCAT 0.674491 -31 TTATTTTTGTCCACTAAATTTTCAATTTTTC 8 41 0 CCCTAAATTT 0.822393 -26 TAACCAACTCTCTCTAATTTTTTCTGGGATT 9 47 0 TCCTAATTTT 0.822148 -254 GGTAGTTTTCCCCCTGAATTTGCCTTGCCCC 11 175 1 CCCTGAATTT 0.926488 -65 GTACTTGCAGCCTCTGATTATTATCAAGCCT 13 126 0 CCCTGATTAT 0.967688 -175 AACTAACTGATCCTTGATTTTCAGAGATAAA 14 248 0 TCTTGATTTT 0.497836 -53 CTAAAACGTTCAACTGATTTTCTATTACGGA 15 17 0 CACTGATTTT 0.88669 -81 TGTTTATAAACCTCTAATTATAGAGATAAAA 16 73 0 CCCTAATTAT 0.916688 -88 ** ******** Masking position 7 Map Score: 5.85892 Number of sites scoring better than the average of aligned sites = 548 Number in coding regions = 455 Number in noncoding regions = 93 Number of orfs with sites within 600 bp upstream = 101 Fraction of orfs with sites within 600 bp upstream = 0.0162223 Motif number 14 ********** No masking Map Score: 7.04391e-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 15 ********** No masking Map Score: 7.04391e-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