AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i117_synecho_ctra_300.orf -o117_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 RCY01680 178 Synechocystis #2 RCY30308 130 Synechocystis #3 RCY29023 276 Synechocystis #4 RCY02288 123 Synechocystis #5 RCY29002 265 Synechocystis #6 RCY23921 112 Synechocystis #7 RCY13644 166 Synechocystis #8 RCY28985 201 Synechocystis #9 RCT00187 300 Chlamydia_trachomatis #10 RCT00189 215 Chlamydia_trachomatis #11 RCT00457 300 Chlamydia_trachomatis #12 RCT00659 160 Chlamydia_trachomatis Motif number 1 AGATCAGGCCAACGGCAGGGGGCAAGGGGG 1 151 0 AACGGCAGGG 0.979749 -28 AAAAACGGCGATCGCCAGGGAAAAAAATCC 2 26 1 ATCGCCAGGG 0.993511 -105 TGAAAACGTCAGGGCAAGGCAACA 2 117 0 AACGTCAGGG 0.929572 -14 ACCTCTAGCAATCGGAGGGTGATATTGACT 3 82 0 ATCGGAGGGT 0.852022 -195 ACCAGGGGCGATCGCCGTGGTGGGGGCAGG 3 217 1 ATCGCCGTGG 0.964695 -60 ACCTTGCCCGATCGCCAAGGAAGCCATAAA 5 64 0 ATCGCCAAGG 0.930444 -202 TTACCCAAGGAGCGGAGGGGTTTGCGCTGT 5 136 0 AGCGGAGGGG 0.955204 -130 TTTAACTACTACCGGAGGGGTGGAAGGTCT 5 184 0 ACCGGAGGGG 0.975127 -82 GATTCACACCGGAATGGGATTTCTTTG 5 249 0 ACCGGAATGG 0.839203 -17 GCAGATGCCGATCGCCAGGGAGCAATGGGT 7 67 0 ATCGCCAGGG 0.993511 -100 TACTTTGGTTATCGTCGGGGCAGGTTTATG 9 130 1 ATCGTCGGGG 0.979748 -171 CAAGGCGTTAATCGCAAGAGATATGCAGAA 9 213 0 ATCGCAAGAG 0.832573 -88 ********** Masking position 1 Map Score: 17.2009 Number of sites scoring better than the average of aligned sites = 1121 Number in coding regions = 1045 Number in noncoding regions = 76 Number of orfs with sites within 600 bp upstream = 84 Fraction of orfs with sites within 600 bp upstream = 0.0134918 Motif number 2 ATCAGGCCAACGGCAGGGGGCAAGGGGGAC 1 149 0 CGGCAGGGGG 0.852202 -30 CCAACTTCGACCGGATAGGTAATTTTGCTG 2 60 0 CCGGATAGGT 0.942294 -71 CAGGTTAAGGCCGGATCGGTAGGCTTTATG 3 38 0 CCGGATCGGT 0.962477 -239 GCCGTGGTGGGGGCAGGGGTTTTGTTAAGA 3 230 1 GGGCAGGGGT 0.955049 -47 GGGGAGCGCTATTTGAAGTT 3 267 0 GGGGAGCGCT 0.774845 -10 GCATCTTGAGCCGGATGTGACTAGAATCGG 4 59 1 CCGGATGTGA 0.791564 -65 GACTAGAATCGGGAATAGGTTTATATTCAT 4 77 1 GGGAATAGGT 0.68816 -47 TACCCAAGGAGCGGAGGGGTTTGCGCTGTG 5 135 0 GCGGAGGGGT 0.992088 -131 TTAACTACTACCGGAGGGGTGGAAGGTCTG 5 183 0 CCGGAGGGGT 0.99318 -83 GATTCACACCGGAATGGGATTTCTTTGAT 5 247 0 CGGAATGGGA 0.824922 -19 AGAAAAGTTACCGGAGCTGAACCGGAATGA 6 14 1 CCGGAGCTGA 0.80917 -99 TCTTTAAAATGCGGAGAGGTCTTGTCTAGA 10 46 1 GCGGAGAGGT 0.972511 -170 GCGAAGGGGAAGAAGGTGGA 11 1 1 GCGAAGGGGA 0.94155 -300 ********** Masking position 5 Map Score: 12.2911 Number of sites scoring better than the average of aligned sites = 1094 Number in coding regions = 989 Number in noncoding regions = 105 Number of orfs with sites within 600 bp upstream = 117 Fraction of orfs with sites within 600 bp upstream = 0.0187922 Motif number 3 ACGCACCAAGGCAATTAAGCACAAAAAGGGGAATTTTTT 1 89 0 GAATAAAAGG 0.910583 -90 TTACGGGAACTTTCGTCAAATAGGCTACATAAAG 3 6 1 GAATTAAAGG 0.951538 -271 TTCTAAAGGACTAATAAACTCTAAAAAGAAAGCCGCCAC 3 126 0 CAAAAAAAGA 0.863444 -151 AGATCAAAGGCCAAAACTTTGCAAACAGACTCTAATCAG 6 47 1 CAAATAAAGA 0.924192 -66 ATATTGACTAGGAAAAATCCCCAGATAGGATCTAACCAG 7 117 1 GAAATAAAGG 0.982215 -50 AAAAAAGAGGGAAACATTTTGGAAGGAGAGGATCGTATC 9 261 0 GAAATAGAGA 0.872049 -40 AGCGAACACTTAAAAAAGAGGGAAACATTTT 9 280 0 CAAATAAAGG 0.982215 -21 TGATTAGATCGCAATACAATATACAAAGGAATCTACTAT 10 132 1 GAAAAAAAGG 0.966265 -84 AGAAATATTTCAAAAAATATTTAGGAAGGAGCTGGTATA 11 118 0 CAAATAGAGG 0.968627 -183 GAAAACGCACCAAAAAGTCTCAAGACAGGTCTAGAATAC 11 251 0 CAAATAAAGG 0.982215 -50 GCATTTTTCTCAAAGACAATTAAAAAAGGCTTAT 12 6 0 CAAAAAAAGG 0.966265 -155 ATTCTAGATTGCAAATATATATATGAAGGAGGTATATTT 12 50 0 GAATTAGAGG 0.916505 -111 * ** * * * * *** Masking position 13 Map Score: 12.8304 Number of sites scoring better than the average of aligned sites = 100 Number in coding regions = 80 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 4 ACAAAAAGGGGAATTTTTTCTGTAACTGAC 1 78 0 GAATTTTTTC 0.946967 -101 TGCTGGCCTGGATTTTTTTCCCTGGCGATC 2 35 0 GATTTTTTTC 0.876756 -96 GAAGTTTTTAGAATCTTAACAAAACCCCTG 3 243 0 GAATCTTAAC 0.734026 -34 CCAATTACCGGAATTTTCTCATGGGTGCGC 5 13 0 GAATTTTCTC 0.966081 -253 GGTTGAAAGTGAATTTTTCCCTGGGCAGTC 8 71 0 GAATTTTTCC 0.86721 -131 TTGCAAAGGAGAATTTTCACAAAACTTCTT 8 107 0 GAATTTTCAC 0.966082 -95 AATTCCGATAGATTTTTCAATGGTACGACG 8 140 1 GATTTTTCAA 0.737549 -62 TTTAAAGAGAGAATCTTTTCTACGCACGGA 10 24 0 GAATCTTTTC 0.91793 -192 AAAGAGAGTTGAATTTTCAACTCTCTTTTT 11 70 1 GAATTTTCAA 0.875858 -231 CTGGTATAGAGAATCTTTTAAGAAAAAAAA 11 96 0 GAATCTTTTA 0.734816 -205 TTTTTTCTAAGATTTTTCACGCTCGAGGTC 12 113 1 GATTTTTCAC 0.918996 -48 ********** Masking position 2 Map Score: 9.07964 Number of sites scoring better than the average of aligned sites = 407 Number in coding regions = 340 Number in noncoding regions = 67 Number of orfs with sites within 600 bp upstream = 77 Fraction of orfs with sites within 600 bp upstream = 0.0123675 Motif number 5 CAGTGGGACGCACCAAGGCAATTAAGCACA 1 105 0 CACCAAGGCA 0.971168 -74 AAACGGCGATCGCCAGGGAAAAAAATCCAG 2 28 1 CGCCAGGGAA 0.993894 -103 TGAAAACGTCAGGGCAAGGCAACACA 2 115 0 CGTCAGGGCA 0.976416 -16 AAAAGAAAGCCGCCACTGAAGCAATGGGCG 3 112 0 CGCCACTGAA 0.89469 -165 CCCCTGCCCCCACCACGGCGATCGCCCCTG 3 219 0 CACCACGGCG 0.90398 -58 CTTGCCCGATCGCCAAGGAAGCCATAAATT 5 62 0 CGCCAAGGAA 0.987588 -204 AGATGCCGATCGCCAGGGAGCAATGGGTCC 7 65 0 CGCCAGGGAG 0.982519 -102 TCGGCATCTGCACCAAGAAAAGGCTTAGGC 7 86 1 CACCAAGAAA 0.720646 -81 CTTTGGTTATCGTCGGGGCAGGTTTATGCG 9 132 1 CGTCGGGGCA 0.903887 -169 ********** Masking position 4 Map Score: 8.75122 Number of sites scoring better than the average of aligned sites = 1327 Number in coding regions = 1260 Number in noncoding regions = 67 Number of orfs with sites within 600 bp upstream = 79 Fraction of orfs with sites within 600 bp upstream = 0.0126887 Motif number 6 ATCTATGCCCATGTCCCCCTTGCCCCCTGC 1 137 1 ATGTCCCCCT 0.917189 -42 TGGCCTGGATTTTTTTCCCTGGCGATCGCC 2 32 0 TTTTTTCCCT 0.9409 -99 CTGATTAATTTTTGCCCCCAACTTCGACCG 2 77 0 TTTGCCCCCA 0.859771 -54 CTTAGCAAAAATTGTCCCCAAAATTGGCAT 4 33 1 ATTGTCCCCA 0.91119 -91 ATTTCGCTAGATTGTCCCCTGATTAGAGTC 6 74 0 ATTGTCCCCT 0.966508 -39 CCGAGGACCCATTGCTCCCTGGCGATCGGC 7 61 1 ATTGCTCCCT 0.93684 -106 CTCAACCGCCTTTTCTCTCTATCACACCCT 8 36 1 TTTTCTCTCT 0.743011 -166 TTGAAAGTGAATTTTTCCCTGGGCAGTCAG 8 69 0 ATTTTTCCCT 0.956364 -133 TCCTTCCAAAATGTTTCCCTCTTTTTTAAG 9 273 1 ATGTTTCCCT 0.893749 -28 CGTCTCCACCTTCTTCCCCTTCGC 11 5 0 TTCTTCCCCT 0.841625 -296 AAAGAAAAGCTTTTTCCTCTTACAAACAAG 11 174 0 TTTTTCCTCT 0.849059 -127 TTTTGGGAGCATTTTTCTCAAAGACAATTA 12 23 0 ATTTTTCTCA 0.63237 -138 ********** Masking position 2 Map Score: 8.84877 Number of sites scoring better than the average of aligned sites = 1750 Number in coding regions = 1479 Number in noncoding regions = 271 Number of orfs with sites within 600 bp upstream = 291 Fraction of orfs with sites within 600 bp upstream = 0.0467395 Motif number 7 CAGCTTAAACTTTTGTGATAGGCTATGCGAG 1 48 0 TTTTGTATAG 0.687978 -131 GGGGCAGGGGTTTTGTTAAGATTCTAAAAAC 3 239 1 TTTTGTAAGA 0.86324 -38 TGGGGACAATTTTTGCTAAGGCTACAATGAA 4 22 0 TTTTGCAAGG 0.954166 -102 ATTACCGGAATTTTCTCATGGGTGCGCTA 5 9 0 TTTTCTATGG 0.81932 -257 CCGGTCGGAGTTTACCCAAGGAGCGGAGGGG 5 146 0 TTTACCAAGG 0.770746 -120 GGTCAAGAAGTTTTGTGAAAATTCTCCTTTG 8 103 1 TTTTGTAAAA 0.686397 -99 ATCGGAATTCCTTTGCAAAGGAGAATTTTCA 8 118 0 CTTTGCAAGG 0.89034 -84 TTCCGATAGATTTTTCAATGGTACGACGCTT 8 142 1 TTTTTCATGG 0.589485 -60 GGTACGACGCTTTTCCAAAGATTTTCTCGGA 8 161 1 TTTTCCAAGA 0.909957 -41 CATAAAAGGCCTTTGCCAAGAGTGATAATTT 10 83 0 CTTTGCAAGA 0.795281 -133 TTCTATAGTTTTTTCTAAAAGAGAGTTGAAT 11 53 1 TTTTCTAAAG 0.855799 -248 CTCTCTTTTTTTTTCTTAAAAGATTCTCTAT 11 90 1 TTTTCTAAAA 0.752542 -211 AGATGATCGACTTACTGAAAGAAATATTTCA 11 145 0 CTTACTAAAG 0.28451 -156 AAAGCTTTTCTTTTGCTATAATTCGCTAGTT 11 191 1 TTTTGCATAA 0.634098 -110 TTGGGAGCATTTTTCTCAAAGACAATTAAAA 12 20 0 TTTTCTAAAG 0.827946 -141 ATTTTTTGTTTTTTTCTAAGATTTTTCACGC 12 104 1 TTTTTCAAGA 0.666573 -57 ****** **** Masking position 8 Map Score: 9.78783 Number of sites scoring better than the average of aligned sites = 1148 Number in coding regions = 966 Number in noncoding regions = 182 Number of orfs with sites within 600 bp upstream = 198 Fraction of orfs with sites within 600 bp upstream = 0.0318021 Motif number 8 AACCGATCTAAGCTTAATTTTTCAGGGGAT 1 15 0 AGCTTAATTT 0.620555 -164 CCCCTTTTTGTGCTTAATTGCCTTGGTGCG 1 97 1 TGCTTAATTG 0.829583 -82 AATAAAGCACTGATTAATTTTTGCCCCCAA 2 86 0 TGATTAATTT 0.45615 -45 AATTAATCAGTGCTTTATTGTGTTGCCTTG 2 97 1 TGCTTTATTG 0.903714 -34 CGGATCGGTAGGCTTTATGTAGCCTATTTG 3 27 0 GGCTTTATGT 0.899207 -250 GGGTGATATTGACTTTATGTCTTATCTTCA 3 66 0 GACTTTATGT 0.530244 -211 CTTCAGTGGCGGCTTTCTTTTTAGAGTTTA 3 121 1 GGCTTTCTTT 0.966415 -156 TTCAATTTATGGCTTCCTTGGCGATCGGGC 5 59 1 GGCTTCCTTG 0.831558 -207 CACCGGAATGGGATTTCTTTGATCCTAACA 5 240 0 GGATTTCTTT 0.784516 -26 GGATAATCAAGGCTTAATTTCGCTAGATTG 6 90 0 GGCTTAATTT 0.936085 -23 AAAAGGCTTAGGCTATATTGACTAGGAAAA 7 103 1 GGCTATATTG 0.688144 -64 TGCAGCAAGCTACTTTCTTTCTCTGGGAGT 9 100 1 TACTTTCTTT 0.62235 -201 TTGTTTAATTTGCTTTCTTTATGGGTAGTA 10 196 1 TGCTTTCTTT 0.928698 -20 ********** Masking position 4 Map Score: 4.83011 Number of sites scoring better than the average of aligned sites = 813 Number in coding regions = 676 Number in noncoding regions = 137 Number of orfs with sites within 600 bp upstream = 135 Fraction of orfs with sites within 600 bp upstream = 0.0216833 Motif number 9 TTTGCCCCCAACTTCGACCGGATAGGTAAT 2 67 0 ACTTCGACCG 0.985489 -64 TTCATTGCCAACCTTGCCCGATCGCCAAGG 5 74 0 ACCTTGCCCG 0.923097 -192 CCTTGGGTAAACTCCGACCGGGGATCACAG 5 156 1 ACTCCGACCG 0.982549 -110 TTGGTCTTTAACCTAGTCCGAGAAAATCTT 8 178 0 ACCTAGTCCG 0.934559 -24 AGATGTTTTTACTCCGTGCGTAGAAAAGAT 10 12 1 ACTCCGTGCG 0.953569 -204 TTTGAAGGGGACCTCGAGCGTGAAAAATCT 12 122 0 ACCTCGAGCG 0.982321 -39 ********** Masking position 1 Map Score: 2.17646 Number of sites scoring better than the average of aligned sites = 64 Number in coding regions = 62 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 10 GGTAATTTTGCTGGCCTGGATTTTTTTCCC 2 43 0 CTGGCCTGGA 0.873642 -88 ATTCCGGTAATTGGTCAAGATTAAGACCCC 5 29 1 TTGGTCAAGA 0.836958 -237 TTTACTAGAGCCGGTCAGGACAGTTTAACT 5 207 0 CCGGTCAGGA 0.969169 -59 ACTTTCAACCCCGGTCAAGAAGTTTTGTGA 8 91 1 CCGGTCAAGA 0.982305 -111 CGTAATCACACCTGTTAAGATTAGAGCTCC 9 56 0 CCTGTTAAGA 0.622205 -245 GCGGAGAGGTCTTGTCTAGAGAGTGTTAAA 10 56 1 CTTGTCTAGA 0.913152 -160 TAGGAAGGAGCTGGTATAGAGAATCTTTTA 11 106 0 CTGGTATAGA 0.856377 -195 AGTCTCAAGACAGGTCTAGAATACTCTTAT 11 245 0 CAGGTCTAGA 0.933209 -56 ********** Masking position 10 Map Score: 2.58279 Number of sites scoring better than the average of aligned sites = 213 Number in coding regions = 181 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 42 Fraction of orfs with sites within 600 bp upstream = 0.0067459 Motif number 11 GCGAGATAAACCGATCTAAGCTTAATTTTT 1 23 0 CCGATCTAAG 0.832869 -156 AATTACCTATCCGGTCGAAGTTGGGGGCAA 2 66 1 CCGGTCGAAG 0.980036 -65 GCCTACCGATCCGGCCTTAACCTGAAGATA 3 44 1 CCGGCCTTAA 0.756408 -233 CTAGTCACATCCGGCTCAAGATGCCAATTT 4 53 0 CCGGCTCAAG 0.958843 -71 AAACCTATTCCCGATTCTAGTCACATCCGG 4 69 0 CCGATTCTAG 0.876219 -55 TCTGTGATCCCCGGTCGGAGTTTACCCAAG 5 157 0 CCGGTCGGAG 0.966437 -109 TTCCACCCCTCCGGTAGTAGTTAAACTGTC 5 189 1 CCGGTAGTAG 0.92452 -77 ACTGTCCTGACCGGCTCTAGTAAAAGTTGT 5 213 1 CCGGCTCTAG 0.968087 -53 ********** Masking position 9 Map Score: 3.08409 Number of sites scoring better than the average of aligned sites = 390 Number in coding regions = 357 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 12 ********** No masking Map Score: 2.17669e-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: 2.17669e-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: 2.17669e-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