AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i014_synecho_ctra_100.orf -o014_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 Purged sequences: RCT00490 17 Chlamydia_trachomatis Input sequences: #1 RCY09935 80 Synechocystis #2 RCY11182 235 Synechocystis #3 RCY06446 94 Synechocystis #4 RCY04603 188 Synechocystis #5 RCY37403 269 Synechocystis #6 RCT00313 295 Chlamydia_trachomatis #7 RCT00480 43 Chlamydia_trachomatis #8 RCT00481 65 Chlamydia_trachomatis #9 RCT00482 20 Chlamydia_trachomatis #10 RCT00483 21 Chlamydia_trachomatis #11 RCT00484 55 Chlamydia_trachomatis #12 RCT00485 22 Chlamydia_trachomatis #13 RCT00488 21 Chlamydia_trachomatis #14 RCT00489 27 Chlamydia_trachomatis #15 RCT00493 16 Chlamydia_trachomatis #16 RCT00495 32 Chlamydia_trachomatis #17 RCT00497 18 Chlamydia_trachomatis #18 RCT00499 23 Chlamydia_trachomatis #19 RCT00502 300 Chlamydia_trachomatis #20 RCT00662 127 Chlamydia_trachomatis Motif number 1 AAAACGCAATTTTTAGCAATAAAAACTATC 2 143 1 TTTTAGCAAT 0.589766 -93 ACGATGAAGGTCACAACAAAATTTGCCAAC 4 155 0 TCACAACAAA 0.705802 -34 TTGAGCGACATCATAGCAAAAACTCTACCC 5 78 1 TCATAGCAAA 0.946339 -192 AAACCAACTATTTAAGCAAATTCACAGAAA 6 26 1 TTTAAGCAAA 0.895139 -270 TTAAGCAAATTCACAGAAAAAAGTAAGACA 6 37 1 TCACAGAAAA 0.87881 -259 GAGATTTATATCAAAGCAATAGAAAATAAA 6 86 1 TCAAAGCAAT 0.915207 -210 TGCACAGGTTATTCAGCAAATCTCATGTTT 6 183 1 ATTCAGCAAA 0.674501 -113 ACAAAGAAACTCACAGAAAACCATTTCCAA 6 217 1 TCACAGAAAA 0.87881 -79 CTCTGAGCCATCAAAGCAATTTGTTTTCGG 6 266 1 TCAAAGCAAT 0.915207 -30 ACGCGGCTCCTTAAAGCAAACAAAGGCGGC 19 161 0 TTAAAGCAAA 0.93036 -140 GATTTCCACGACAAAGAAAACGCGGCTCCT 19 180 0 ACAAAGAAAA 0.599944 -121 CTAATTACACTTTTAGCAAACGGCCATGCC 19 227 0 TTTTAGCAAA 0.817428 -74 TTCTTATAGGCCTAAGCAAAGGAAAACTCA 20 83 0 CCTAAGCAAA 0.801807 -45 ********** Masking position 5 Map Score: 8.99006 Number of sites scoring better than the average of aligned sites = 682 Number in coding regions = 567 Number in noncoding regions = 115 Number of orfs with sites within 600 bp upstream = 125 Fraction of orfs with sites within 600 bp upstream = 0.0200771 Motif number 2 TGGAAAGGAGAAAAATTCTTAAACCCAACCCTTTTC 2 61 1 AATCAAACCC 0.977269 -175 TTAGCAATAAAAACTATCCTCACCCAATCAACTCTT 2 155 1 AATCCACCCA 0.92625 -81 GGTCACAACAAAATTTGCCAACCCCCAGTTTACGTC 4 141 0 AAGCACCCCC 0.981443 -48 ACATCATAGCAAAAACTCTACCCCCAGGCATAGACA 5 85 1 AATCCCCCCA 0.952445 -185 AGAAAGGGAAAAAGATTCCCACCCCCCCTTTGAAAT 5 153 1 AATCACCCCC 0.986716 -117 ATAACAAAGGGGCTAAAACCAACTATTTAAG 6 6 1 AAGCAAACCA 0.950484 -290 TGATGCTAATTTTTCGAAAACACTGACTACCTG 7 8 1 AATCAAACAC 0.881408 -36 AATAATTCACACACCCTTATAACCTA 16 17 0 AATCACACCC 0.985624 -16 TCCCACACCAAAAATCGCAAAAACAAAGCCTGAAAA 19 63 0 AAGCAAACAA 0.76843 -238 TCTTGACGCTAAGAAATCCCACACCAAAAATCGCAA 19 79 0 AATCACACCA 0.977269 -222 ** ** ****** Masking position 2 Map Score: 9.20296 Number of sites scoring better than the average of aligned sites = 295 Number in coding regions = 257 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 42 Fraction of orfs with sites within 600 bp upstream = 0.0067459 Motif number 3 AAATTGTCTCACTACCCCCATGATTTACCT 2 31 1 ACTACCCCCA 0.928421 -205 GAGAAAAATTCTTAAACCCAACCCTTTTCA 2 68 1 CTTAAACCCA 0.865517 -168 TAAAAACTATCCTCACCCAATCAACTCTTC 2 162 1 CCTCACCCAA 0.758872 -74 CAACGAGGAACTAACCCCCAAACTCAACTG 4 89 0 CTAACCCCCA 0.977818 -100 ACAAAATTTGCCAACCCCCAGTTTACGTCG 4 140 0 CCAACCCCCA 0.991066 -49 TAGCAAAAACTCTACCCCCAGGCATAGACA 5 91 1 TCTACCCCCA 0.88032 -179 CCAGGCATAGACAAAACCCAGAGGCCACGG 5 108 1 ACAAAACCCA 0.727821 -162 GAAAAAGATTCCCACCCCCCCTTTGAAATT 5 160 1 CCCACCCCCC 0.908324 -110 AACAAAGGGGCTAAAACCAACTATTTAAGC 6 13 1 CTAAAACCAA 0.752421 -283 TGCTAAATCCCAGGTAGTCAGT 7 32 0 CTAAATCCCA 0.699207 -12 CGAAGTACGACCAACCCTAAATTTTTTTCT 8 31 0 CCAACCCTAA 0.847967 -35 GCTAAGAAATCCCACACCAAAAATCGCAAA 19 78 0 CCCACACCAA 0.88952 -223 TTATCTGATCCTTAACCTAAATTTTCTTAT 20 106 0 CTTAACCTAA 0.500806 -22 ********** Masking position 7 Map Score: 6.92373 Number of sites scoring better than the average of aligned sites = 3409 Number in coding regions = 3064 Number in noncoding regions = 345 Number of orfs with sites within 600 bp upstream = 328 Fraction of orfs with sites within 600 bp upstream = 0.0526823 Motif number 4 CCATGATTTACCTTGGAAAGGAGAAAAATT 2 48 1 CCTTGGAAAG 0.96016 -188 TATCTAATCCCCTTTGAAAAGGGTTGGGTT 2 82 0 CCTTTGAAAA 0.979464 -154 GTAAATACAACCTTTGAAAACTGCCCTTAA 2 115 1 CCTTTGAAAA 0.979464 -121 TCCCACCCCCCCTTTGAAATTCGGGATCTA 5 169 1 CCTTTGAAAT 0.935585 -101 AATAAGCCTTCCTTGCAAGAAATCGAGTAT 6 125 1 CCTTGCAAGA 0.803517 -171 AGTGGAGCTTCCTTGGAAGAAAACTTATAA 19 15 0 CCTTGGAAGA 0.972895 -286 ********** Masking position 4 Map Score: 5.75407 Number of sites scoring better than the average of aligned sites = 166 Number in coding regions = 157 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 5 AATCATGGGGGTAGTGAGACAATTTTTAGACTT 2 23 0 GTTGAGCAAT 0.984213 -213 TGATGTCAGGGTGAAGAGTTGATTGGGTGAGGA 2 171 0 GTAGAGTGAT 0.830555 -65 CTTTATAACTGTAGTGAGGCAATAACC 3 78 1 GTTGAGCAAT 0.984214 -17 CGGGATCTAAGTGTTCAGGCAATAGGATATGAT 5 190 1 GTTCAGCAAT 0.956631 -80 ATCCTTAAATGTACTGAGCTAAAACAGAGAGGG 5 237 1 GTTGAGTAAA 0.962626 -33 CAAATCTCATGTTTACAGACAAAGAAACTCACA 6 199 1 GTACAGCAAA 0.84977 -97 GCAACGGTTATGAGACGAAGTACGACCAA 8 47 0 GTTGAGCGAA 0.961135 -19 GTCAAGTTGTGTGATAAGGTAATTAAAT 19 283 1 GTTAAGTAAT 0.804537 -18 TCTTCATGTGGCACTGAGATAAAGGCTTGAGTT 20 56 1 GCTGAGTAAA 0.857508 -72 ** **** **** Masking position 7 Map Score: 4.70935 Number of sites scoring better than the average of aligned sites = 83 Number in coding regions = 68 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 6 ATTGTCTCACTACCCCCATGATTTACCTTGGAA 2 33 1 TACCCCTGTT 0.780011 -203 GGCAGGAGTTGCCCCGGATGTTTTTGATGGTAT 3 23 1 GCCCCGTGTT 0.968664 -72 CCGAATTAATGCCGCCCTGGCTTTCAATCTAGT 4 49 0 GCCGCCGGTT 0.987717 -140 TGGGGGTTAGTTCCTCGTTGGTTAATGGTGACG 4 99 1 TTCCTCTGTT 0.848426 -90 CCCAGTTTACGTCGTCCGGGGTCGTCACCATTA 4 121 0 GTCGTCGGTC 0.708719 -68 TGTTTACCGTGGCCTCTGGGTTTTGTCTATGCC 5 111 0 GGCCTCGGTT 0.892625 -159 TCCCTTTCTCTCCGTCGCTGTTTACCGTGGCCT 5 129 0 TCCGTCTGTT 0.952011 -141 GTTCGTCTTGCCCTCTCTGTTTTAGCTCAGTA 5 248 0 GCCCTCTGTT 0.988995 -22 TAAATCCCAGGTAGTCAGTGTTTTCGAAAAATT 7 18 0 GTAGTCTGTT 0.645309 -26 TTGCCCATTCGCCGCCTTTGTTTGCTTTAAGGA 19 151 1 GCCGCCTGTT 0.993096 -150 GCTTTAAGGAGCCGCGTTTTCTTTGTCGTGGAA 19 174 1 GCCGCGTTTT 0.68925 -127 TTCACAGACCGCCCCCGGTGCCTAATTACACTT 19 245 0 GCCCCCTGCT 0.961077 -56 ****** ** ** Masking position 12 Map Score: 7.20529 Number of sites scoring better than the average of aligned sites = 1343 Number in coding regions = 1225 Number in noncoding regions = 118 Number of orfs with sites within 600 bp upstream = 143 Fraction of orfs with sites within 600 bp upstream = 0.0229682 Motif number 7 AATTGCGTTTTAAGGGCAGTTTTCAAAGGT 2 124 0 TAAGGGCAGT 0.839161 -112 TCAAAAACATCCGGGGCAACTCCTGCCCTA 3 20 0 CCGGGGCAAC 0.876634 -75 ATGGTATTATCAAGGGCATCTTTTGCAGAC 3 49 1 CAAGGGCATC 0.900364 -46 AGATTGAAAGCCAGGGCGGCATTAATTCGG 4 52 1 CCAGGGCGGC 0.994433 -137 CGCTCAATTACAGGTGCGGTGAACCGGCAG 5 55 0 CAGGTGCGGT 0.834545 -215 CGATTTCTTGCAAGGAAGGCTTATTTTTAT 6 120 0 CAAGGAAGGC 0.830415 -176 TATATTACTTTAAGGGAGGCCCTTCGT 11 39 1 TAAGGGAGGC 0.905431 -17 AAGTTTTCTTCCAAGGAAGCTCCACTAGTA 19 19 1 CCAAGGAAGC 0.714657 -282 TTAAAGCAAACAAAGGCGGCGAATGGGCAA 19 151 0 CAAAGGCGGC 0.974781 -150 CTCCATCCTGCAAGAGCGATTTCCACGACA 19 197 0 CAAGAGCGAT 0.581969 -104 AATTAGGCACCGGGGGCGGTCTGTGAAGCG 19 251 1 CGGGGGCGGT 0.938779 -50 ********** Masking position 6 Map Score: 3.25098 Number of sites scoring better than the average of aligned sites = 3222 Number in coding regions = 3006 Number in noncoding regions = 216 Number of orfs with sites within 600 bp upstream = 221 Fraction of orfs with sites within 600 bp upstream = 0.0354963 Motif number 8 TTAGCATATCCAAGAGATTTATATCAAAGC 6 73 1 CAAGAGATTT 0.985547 -223 TGTCTGTAAACATGAGATTTGCTGAATAAC 6 190 0 CATGAGATTT 0.9643 -106 AAAGAGATATGCAACACGCT 8 1 1 AAAGAGATAT 0.871764 -65 GACATCCACACAAGAGATTTTTCTTGACGC 19 106 0 CAAGAGATTT 0.985547 -195 ********** Masking position 5 Map Score: 1.25267 Number of sites scoring better than the average of aligned sites = 10 Number in coding regions = 9 Number in noncoding regions = 1 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 9 TTTGGGGCTTTCCATTGTCGG 1 1 1 TTTGGGCTTT 0.921362 -80 GTGAGACAATTTTTAGACTTTTTAAACAGAC 2 12 0 TTTAGACTTT 0.969261 -224 AAGGGTTGGGTTTAAGAATTTTTCTCCTTTC 2 63 0 TTTAGAATTT 0.895853 -173 AGGGCATCTTTTGCAGACTTTATAACTGTAG 3 61 1 TTGAGACTTT 0.954992 -34 CGGCAGGTGATTGTAGACGTTAACATTTATG 5 30 0 TTGAGACGTT 0.867177 -240 GCTCAGTACATTTAAGGATTATTAATGACAC 5 225 0 TTTAGGATTA 0.683194 -45 TAGAACGATTTTTCAGGCTTTGTTTTTGCGA 19 54 1 TTTAGGCTTT 0.97441 -247 *** ******* Masking position 2 Map Score: 1.15055 Number of sites scoring better than the average of aligned sites = 113 Number in coding regions = 88 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 10 AACCTTTTCCTCCTAAATGTCAA 1 68 0 CTTTTCCTCC 0.973008 -13 GGGTTTAAGAATTTTTCTCCTTTCCAAGGT 2 57 0 ATTTTTCTCC 0.717348 -179 ATCTTTTTCCCTTTCTCTCCGTCGCTGTTT 5 139 0 CTTTCTCTCC 0.973008 -131 GTTCGTCTTGCCCTCTCTGTTTTAGC 5 254 0 CTTGCCCTCT 0.8112 -16 AACTTGGGCCCACCTTCTCCACTCTGAGCC 6 245 1 CACCTTCTCC 0.835456 -51 AACACTCTCTCCTAAAAATTA 10 10 0 CACTCTCTCC 0.95657 -12 GTTATTCTTCTCTTCCTTCTTTA 18 5 0 CTCTTCCTTC 0.797806 -19 AGCAAACGGCCATGCCCTCCATCCTGCAAG 19 213 0 CATGCCCTCC 0.959975 -88 ********** Masking position 8 Map Score: 1.24071 Number of sites scoring better than the average of aligned sites = 842 Number in coding regions = 716 Number in noncoding regions = 126 Number of orfs with sites within 600 bp upstream = 152 Fraction of orfs with sites within 600 bp upstream = 0.0244137 Motif number 11 ********** No masking Map Score: 4.18042e-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 12 ********** No masking Map Score: 4.18042e-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: 4.18042e-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