AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i015_synecho_ctra_300.orf -o015_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 RCY49691 112 Synechocystis #2 RCY39030 187 Synechocystis #3 RCY05748 42 Synechocystis #4 RCY36146 300 Synechocystis #5 RCT00193 300 Chlamydia_trachomatis #6 RCT00195 29 Chlamydia_trachomatis #7 RCT00196 19 Chlamydia_trachomatis #8 RCT00197 38 Chlamydia_trachomatis #9 RCT00313 295 Chlamydia_trachomatis #10 RCT00316 275 Chlamydia_trachomatis #11 RCT00317 96 Chlamydia_trachomatis Motif number 1 TCAGCAAAACTTCTTTGTGAGAATTCTTAA 1 44 0 TTCTTTGTGA 0.932703 -69 AATTTATTCATCTTTTGTCACAGTTGGCGT 4 29 1 TCTTTTGTCA 0.932703 -272 GTTAATGCTTTTTTTTGTCATAAATCTATA 5 26 1 TTTTTTGTCA 0.960746 -275 GGCCTGCTCGTTTTCTGAGAGTCCTTCCTT 5 163 1 TTTTCTGAGA 0.874325 -138 ATGCCAAAAATCTTCTGTCAACGACTCTAT 5 222 0 TCTTCTGTCA 0.95649 -79 TGTCTTACTTTTTTCTGTGAATTTGCTTAA 9 37 0 TTTTCTGTGA 0.974888 -259 TTCTGTGAGTTTCTTTGTCTGTAAACATGA 9 205 0 TTCTTTGTCT 0.71295 -91 TTGGAAATGGTTTTCTGTGAGTTTCTTTGT 9 217 0 TTTTCTGTGA 0.974888 -79 ********** Masking position 6 Map Score: 7.29016 Number of sites scoring better than the average of aligned sites = 107 Number in coding regions = 73 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 2 TTTGGGCAATTTTTCCCAATAGTCTGCACAGTTTGA 2 21 0 TTTTCCTGTG 0.931333 -167 AATATTCTCATTATCCGCCACGATCGCCGTTTCAGT 2 94 0 TTATCCAGAG 0.929203 -94 GGCGTCACACTTTTCCCCCTGGGGAGCAGATAAGAA 4 54 1 TTTTCCTGGG 0.975669 -247 GGCATAGGGTTTTTGCCGGTGGGGAGTTCCGTATTT 4 184 1 TTTTGCTGGG 0.810196 -117 ATAATCGATTATTTCCTGGTCGTAGCATGCCAAAAA 5 242 0 ATTTCCTGTC 0.866332 -59 CTCTTTAGTTATATCCATTGAGATGG 8 1 0 ATATCCGGAG 0.937381 -38 GTAATACTCGATTTCTTGCAAGGAAGGCTTATTTTT 9 122 0 ATTTCTAGGG 0.730284 -174 ACAGAAAACCATTTCCAACTTGGGCCCACCTTCTCC 9 229 1 ATTTCCTGGC 0.950448 -67 GGGTACCGAGATTTCCTGCATGACCGG 10 2 0 ATTTCCAGAG 0.972096 -274 AAGAGAAAACATTTCCTCATAGATAGCCAAGATAGC 10 116 0 ATTTCCTGAG 0.979658 -160 AAGCATCCTTTTATCCCTGGGGAATCTGT 10 257 1 TTATCCGGAC 0.790162 -19 ATCTTCTAGAATATCCGAAATGAAAGAAGCCTTCAA 11 40 0 ATATCCAGAG 0.947522 -57 ****** * ** * Masking position 4 Map Score: 7.46669 Number of sites scoring better than the average of aligned sites = 818 Number in coding regions = 749 Number in noncoding regions = 69 Number of orfs with sites within 600 bp upstream = 80 Fraction of orfs with sites within 600 bp upstream = 0.0128493 Motif number 3 GTTAAAAGTAGGTTAAGGATTGAGGACAATTTTA 1 13 1 GGTTAAGTGG 0.868305 -100 AACGATGGTAGGCTGGGCTTTGGGCAATTTTTCC 2 41 0 GGCTGGGTGG 0.993202 -147 AATGGGCTGAAATTAGGGGCAGTTAAAT 2 170 0 GGCTGAATGG 0.972583 -18 CTGCTCCCCAGGGGGAAAAGTGTGACGCCAACTG 4 49 0 GGGGGAAGGG 0.840274 -252 ACATCATCCAGGCGGAGTGTGGTGTGAGGAGTGA 4 102 1 GGCGGAGTGG 0.995522 -199 CAATGAAGAGGGCGGAGACGTAAGTTTCCGTTCA 4 133 0 GGCGGAGGAG 0.946457 -168 TCATTGTACAGGTTGGGACGGGGGGCATAGGGTT 4 161 1 GGTTGGGGGG 0.971506 -140 GGTTTTTGCCGGTGGGGAGTTCCGTATTTGTTAA 4 191 1 GGTGGGGTCG 0.940483 -110 TTGCTTTGATGGCTCAGAGTGGAGAAGGTGGGCC 9 251 0 GGCTCAGTGG 0.96755 -45 CATGTCGAACAGCTGAGTTTTCAGCTACAATTAA 10 179 1 AGCTGAGTCG 0.84522 -97 ******* * * * Masking position 2 Map Score: 6.09708 Number of sites scoring better than the average of aligned sites = 797 Number in coding regions = 726 Number in noncoding regions = 71 Number of orfs with sites within 600 bp upstream = 84 Fraction of orfs with sites within 600 bp upstream = 0.0134918 Motif number 4 AATCGAATCAGCAAAACTTCTTTGTGAGAA 1 51 0 GCAAAACTTC 0.931372 -62 CCAAAGCCCAGCCTACCATCGTTGGCCCTG 2 52 1 GCCTACCATC 0.81378 -136 GAAACCGCCCGAACATCATCCAGGCGGAGT 4 90 1 GAACATCATC 0.823012 -211 CTATATGAGTGCAAACCTTCAAGCCTTTCA 5 196 0 GCAAACCTTC 0.981692 -105 GTAGCATGCCAAAAATCTTCTGTCAACGAC 5 227 0 AAAAATCTTC 0.761057 -74 TCGATTATTCACAAATCTTCAGAACTGGAG 5 270 1 ACAAATCTTC 0.918712 -31 TCTTGGATATGCTAATCTTCTTGTCTTACT 9 58 0 GCTAATCTTC 0.921157 -238 TCCAACTTGGGCCCACCTTCTCCACTCTGA 9 242 1 GCCCACCTTC 0.937215 -54 GGTACCCGAAGCAAGTCATCTGGACACCGT 10 31 1 GCAAGTCATC 0.860553 -245 TTAGTGAGTAGAATATCTTCTAGAATATCC 11 60 0 GAATATCTTC 0.856829 -37 ********** Masking position 9 Map Score: 5.06457 Number of sites scoring better than the average of aligned sites = 565 Number in coding regions = 507 Number in noncoding regions = 58 Number of orfs with sites within 600 bp upstream = 70 Fraction of orfs with sites within 600 bp upstream = 0.0112432 Motif number 5 TGGATTTCACTGGAAAATGGATCTAATCACCCCA 4 243 0 TAAATGGTCT 0.726428 -58 AAAAAAAAGCATTAACAAAGAGCTACAGGAT 5 8 0 AAAAAAGGCT 0.92086 -293 TAGCAGAGCAACGACCATGGAGCTCGGAGTCTAA 5 128 0 AACATGGGCT 0.978465 -173 CTCAATGGATATAACTAAAGAGCTTCCCTTCATT 8 15 1 AACAAAGGCT 0.948478 -24 ATAACAAAGGGGCTAAAACCAACT 9 1 1 AACAAGGGCT 0.987463 -295 CCTTCTGTAAAACCAGAAGGCGCTGTATAACGGT 10 56 0 ACAAAGGGCT 0.980339 -220 CCTTCTGGTTTTACAGAAGGCGCTTGAGGACTGT 10 70 1 TCAAAGGGCT 0.948066 -206 CTACAATTAAACCCCGATGGTTCTGTCGCAGTAG 10 203 1 ACCATGGTCT 0.887936 -73 * ** **** *** Masking position 7 Map Score: 2.65061 Number of sites scoring better than the average of aligned sites = 227 Number in coding regions = 206 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 6 CCGTTTCAGTTGCATCGGCTTACAGGGCCA 2 74 0 TGCATCGGCT 0.867995 -114 CCGATGCAACTGAAACGGCGATCGTGGCGG 2 86 1 TGAAACGGCG 0.918096 -102 GCAGATAAGAAGAAACCGCCCGAACATCAT 4 79 1 AGAAACCGCC 0.929487 -222 GCCGTAGCAGAGCAACGACCATGGAGCTCG 5 136 0 AGCAACGACC 0.973441 -165 GTCGTTGCTCTGCTACGGCCTGCTCGTTTT 5 147 1 TGCTACGGCC 0.983176 -154 ATTTTTGGCATGCTACGACCAGGAAATAAT 5 241 1 TGCTACGACC 0.958066 -60 TAGCCAAGATAGCTTCCACGGAATGACAGT 10 99 0 AGCTTCCACG 0.728774 -177 CAAAATATTTAGCAACCGCAATCG 11 5 0 AGCAACCGCA 0.916929 -92 ********** Masking position 6 Map Score: 2.41622 Number of sites scoring better than the average of aligned sites = 830 Number in coding regions = 784 Number in noncoding regions = 46 Number of orfs with sites within 600 bp upstream = 47 Fraction of orfs with sites within 600 bp upstream = 0.00754899 Motif number 7 CAGTTAAAAGTAGGTTAAGGAT 1 1 1 CAGTAAAATA 0.983445 -112 ATTCGATTTGCTTCTACAAATAAAACAGAACT 1 73 1 CTTTACAATA 0.693697 -40 AAATTAGGGGCAGTTAAATATAATAGTTAAGG 2 157 0 CAGTAAATTA 0.924981 -31 TTTTTATCCAGATAAAATTATAGGGAGCC 6 9 1 CAGTAAAATA 0.98345 -21 AGCAAATTCACAGAAAAAAGTAAGACAAGAAG 9 40 1 CAGAAAAATA 0.925023 -256 GAAAATAAATCATATAAAAATAAGCCTTCCTT 9 107 1 CATTAAAATA 0.94189 -189 GCTGAGTTTTCAGCTACAATTAAACCCCGATG 10 190 1 CAGTACAATA 0.975603 -86 *** ***** ** Masking position 6 Map Score: 4.50691 Number of sites scoring better than the average of aligned sites = 38 Number in coding regions = 33 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 8 TTTTGCTGATTCGATTTGCTTCTACAAATA 1 65 1 TCGATTTGCT 0.953062 -48 CACAGTTTGATGGGTTTGCT 2 1 0 TGGGTTTGCT 0.9455 -187 TCCATGGTCGTTGCTCTGCTACGGCCTGCT 5 141 1 TTGCTCTGCT 0.9228 -160 CTTTTTTCTGTGAATTTGCTTAAATAGTTG 9 30 0 TGAATTTGCT 0.767589 -266 ATAAATCTCTTGGATATGCTAATCTTCTTG 9 65 0 TGGATATGCT 0.859926 -231 TTATTTTCTATTGCTTTGATATAAATCTCT 9 85 0 TTGCTTTGAT 0.938214 -211 ATCGAGTATTACGCTTTGATCTATCTTACA 9 146 1 ACGCTTTGAT 0.746038 -150 CGAAAACAAATTGCTTTGATGGCTCAGAGT 9 265 0 TTGCTTTGAT 0.938214 -31 ********** Masking position 5 Map Score: 1.64928 Number of sites scoring better than the average of aligned sites = 644 Number in coding regions = 572 Number in noncoding regions = 72 Number of orfs with sites within 600 bp upstream = 72 Fraction of orfs with sites within 600 bp upstream = 0.0115644 Motif number 9 GGTTTTCCTTGCCGATATAGTT 1 101 0 TTTTCCTTGC 0.841663 -12 CATTCCCTTAATTCCTCCTCAGTAA 3 6 1 CCTTAATTCC 0.885621 -37 TTCTGAGAGTCCTTCCTTCCGTGAAAGGCT 5 175 1 CCTTCCTTCC 0.987453 -126 TAAAAATAAGCCTTCCTTGCAAGAAATCGA 9 121 1 CCTTCCTTGC 0.981828 -175 CGCTTGAGGACTGTCATTCCGTGGAAGCTA 10 90 1 CTGTCATTCC 0.920877 -186 TTGAAGGCTTCTTTCATTTCGGATATTCTA 11 40 1 CTTTCATTTC 0.88903 -57 ********** Masking position 4 Map Score: 0.613642 Number of sites scoring better than the average of aligned sites = 238 Number in coding regions = 188 Number in noncoding regions = 50 Number of orfs with sites within 600 bp upstream = 51 Fraction of orfs with sites within 600 bp upstream = 0.00819146 Motif number 10 ********** No masking Map Score: -3.55028e-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: -3.55028e-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: -3.55028e-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