AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i308_synecho_ctra_300.orf -o308_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 RCY41704 31 Synechocystis #2 RCY18056 198 Synechocystis #3 RCY08755 34 Synechocystis #4 RCY48569 20 Synechocystis #5 RCY29363 49 Synechocystis #6 RCY51306 167 Synechocystis #7 RCY51398 55 Synechocystis #8 RCY29713 300 Synechocystis #9 RCT00361 28 Chlamydia_trachomatis #10 RCT00362 68 Chlamydia_trachomatis #11 RCT00363 300 Chlamydia_trachomatis #12 RCT00547 294 Chlamydia_trachomatis #13 RCT00734 153 Chlamydia_trachomatis Motif number 1 TTATTAAAACAGAATCTTAAAACT 1 3 0 AGACTTAAAA 0.957444 -29 TTAAAAATTATTAAAACAGAATCTTA 1 16 0 AAAATTAAAA 0.953168 -16 ACTCTGATAAAAACAATAAAAACTGACCT 5 31 1 AAAATAAAAA 0.856251 -19 GGCCAAACCCAACGGCTTAAAACCAGTCAAAT 6 91 1 AACCTTAAAA 0.87775 -77 AATTCAGCAAATTAAAATCTGTTTCTC 7 6 1 AGCATTAAAA 0.843098 -50 CCCGCCAGCAAAAAAATTACAATCGTTTATTT 8 11 0 AAAATTACAA 0.903533 -290 AAGTTTGAGTAGATCATTGCAAAGGGGCGTTG 8 67 1 AGAATTGCAA 0.796764 -234 ATACCCAACATGATTCTTAAAAAAAATAAGAA 10 12 0 TGACTTAAAA 0.688895 -57 GCGTCGTAAGAAAAGCTTGAAATAGCGCCTCA 11 93 0 AAACTTGAAA 0.919245 -208 ATAATTCCTAAAAAAATAAAAATAACAAATTA 12 15 1 AAAATAAAAA 0.856251 -280 TATTAAAAGCAAAATATTAAAAACGTTTTTAT 12 94 0 AAAATTAAAA 0.953168 -201 CTCCTGTTAAAAAAAATTGCAAGGCAACGACA 12 174 0 AAAATTGCAA 0.811685 -121 ACTGAATAGTAAAGTCTTAAAATCATAGCGGA 12 265 1 AAACTTAAAA 0.961144 -30 TGCATCTAGAAGAATCTAAAAAGAATTGCTTT 13 25 1 AGACTAAAAA 0.868151 -129 *** ******* Masking position 11 Map Score: 13.6757 Number of sites scoring better than the average of aligned sites = 190 Number in coding regions = 136 Number in noncoding regions = 54 Number of orfs with sites within 600 bp upstream = 62 Fraction of orfs with sites within 600 bp upstream = 0.00995824 Motif number 2 ATTAAACGTTCTCTTCTCTTCAAGAGAAGA 11 179 1 CTCTTCTCTT 0.989028 -122 AAAAAACGCCCTCTTCTCTTGAAGAGAAGA 11 190 0 CTCTTCTCTT 0.989028 -111 CTTTCTATTTCTTTTCTCTTCCCTGTGTGT 11 232 1 CTTTTCTCTT 0.98678 -69 TTTTCCTTGTTTCTTCTCTTAACTCATGAA 11 273 0 TTCTTCTCTT 0.960921 -28 GATTTTAAGACTTTACTATTCAGTGAGAGA 12 259 0 CTTTACTATT 0.808699 -36 TTTCTCACTTTTTTTCTATTTAAAAAAGCA 13 51 0 TTTTTCTATT 0.847439 -103 AAGTCTCTACCTTTTATCTTCCAATAAGGG 13 81 0 CTTTTATCTT 0.906384 -73 ********** Masking position 4 Map Score: 7.96405 Number of sites scoring better than the average of aligned sites = 18 Number in coding regions = 17 Number in noncoding regions = 1 Number of orfs with sites within 600 bp upstream = 1 Fraction of orfs with sites within 600 bp upstream = 0.000160617 Motif number 3 TTAAGCAACTAAAGCGCCTCTATCAACAGC 6 122 1 AAAGCGCCTC 0.980441 -46 GCCTCTATCAACAGCGTCTCCCCGGCGATC 6 137 1 ACAGCGTCTC 0.912362 -31 ATTCCATCCTACAACGCCCCTTTGCAATGA 8 80 0 ACAACGCCCC 0.987699 -221 AATAAGGCCCCTTAATCGTTT 9 18 0 ATAAGGCCCC 0.93464 -11 AGTTAAACACATAACGCCTTGTATAA 11 7 0 ATAACGCCTT 0.943691 -294 AAAGCTTGAAATAGCGCCTCATCAGCATAT 11 84 0 ATAGCGCCTC 0.986687 -217 TTCAATGAAAAAAACGCCCTCTTCTCTTGA 11 198 0 AAAACGCCCT 0.933784 -103 ********** Masking position 3 Map Score: 6.41957 Number of sites scoring better than the average of aligned sites = 146 Number in coding regions = 133 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 4 TGGGGTAAGGCGATCGCCTTAGGTCAAAGG 2 14 0 CGATCGCCTT 0.986029 -185 TAGATGGTATCGATAGGCTTTAGTCCTAAT 6 60 0 CGATAGGCTT 0.96196 -108 ACGGCCAAACCCAACGGCTTAAAACCAGTC 6 89 1 CCAACGGCTT 0.942274 -79 GTCTCCCCGGCGATCGCCTGCTAACG 6 152 1 CGATCGCCTG 0.988402 -16 CTTTTACACTCGATCGCCAGCTTCGCCTGG 8 228 0 CGATCGCCAG 0.973733 -73 ACTCAATGGTCTAACGGCAGGGACTATACC 10 39 0 CTAACGGCAG 0.852609 -30 ACCTCCTGCGCGAAAGGCTTGGACTTCACG 12 214 1 CGAAAGGCTT 0.95103 -81 ********** Masking position 3 Map Score: 6.00706 Number of sites scoring better than the average of aligned sites = 2617 Number in coding regions = 2377 Number in noncoding regions = 240 Number of orfs with sites within 600 bp upstream = 235 Fraction of orfs with sites within 600 bp upstream = 0.0377449 Motif number 5 CTAAGGCGATCGCCTTACCCCAGACTAACT 2 22 1 CGCCTTACCC 0.979022 -177 TACCATCTACGGCCAAACCCAACGGCTTAA 6 81 1 GGCCAAACCC 0.930379 -87 TCAAACTTTGAGCATTACCC 7 46 1 AGCATTACCC 0.96461 -10 AAAAATGGAAAGTCATACCCGCCAGCAAAA 8 30 0 AGTCATACCC 0.933198 -271 AGACTTACCCCGCAATACCCTGTCTGAATG 8 158 0 CGCAATACCC 0.973146 -143 CGATGTTTGGAGACTTACCCCGCAATACCC 8 168 0 AGACTTACCC 0.938865 -133 CTACTCCATAAAAAATACCCAGGCGAAGCT 8 210 1 AAAAATACCC 0.731792 -91 TAACGGCAGGGACTATACCCAACATGATTC 10 28 0 GACTATACCC 0.766231 -41 ********** Masking position 7 Map Score: 4.50902 Number of sites scoring better than the average of aligned sites = 561 Number in coding regions = 513 Number in noncoding regions = 48 Number of orfs with sites within 600 bp upstream = 61 Fraction of orfs with sites within 600 bp upstream = 0.00979762 Motif number 6 GAATTGTTAGAAAACGCAAAATTGTCAGGAA 2 102 0 AAAAGCAAAA 0.910329 -97 AGTTCCTAATACAATGCAAAATGGGGATCTT 2 171 0 ACAAGCAAAA 0.977966 -28 TCTGATAAAAACAATAAAAACTGACCT 5 33 1 ACAAAAAAAC 0.754482 -17 AAGACTCAACTCAACGCAGACCTGCAATAGG 8 255 1 TCAAGCAGAC 0.920986 -46 TCCTACAATAACAAAGCAAACTACAAGTTAA 11 31 0 ACAAGCAAAC 0.985995 -270 GAAAGATTTTTCAATGAAAAAAACGCCCTCT 11 206 0 TCAAGAAAAA 0.91536 -95 AAGAGAAGAAACAAGGAAAACAAATCTA 11 283 1 ACAAGAAAAC 0.964935 -18 TATGTTTTATTAAAAGCAAAATATTAAAAAC 12 102 0 TAAAGCAAAA 0.863541 -193 **** ****** Masking position 4 Map Score: 4.79139 Number of sites scoring better than the average of aligned sites = 282 Number in coding regions = 234 Number in noncoding regions = 48 Number of orfs with sites within 600 bp upstream = 55 Fraction of orfs with sites within 600 bp upstream = 0.00883392 Motif number 7 CGTCAATGCCAGTCTTTTCCTGACAATTTTG 2 86 1 AGTCTTTCCT 0.955944 -113 TTGAGATCAAAATCTTTTCAT 5 1 0 AATCTTTCAT 0.781397 -49 GAATGTCAGCAACCGTCACCTGCCGCCATAG 8 106 1 AACCGTCCCT 0.894377 -195 AAGGCCCCTTAATCGTTTTCTAAAA 9 5 0 AATCGTTTCT 0.939915 -24 TCTTCCTTTGAGTAGTTTCCTACAATAACAA 11 48 0 AGTAGTTCCT 0.900976 -253 TCTGATATTAAACAGTTGCCTAACGGATCAG 11 139 1 AACAGTTCCT 0.873851 -162 TAGCATCATTAAACGTTCTCTTCTCTTCAAG 11 172 1 AAACGTTTCT 0.737073 -129 TTCATTGAAAAATCTTTCTATTTCTTTTCTC 11 219 1 AATCTTTTAT 0.469615 -82 CAGCAGCGTGTGTCGTTGCCTTGCAATTTTT 12 164 1 TGTCGTTCCT 0.936118 -131 TAACAGGAGGTACCGTTACCTCCTGCGCGAA 12 197 1 TACCGTTCCT 0.91774 -98 TGACGGAAGAAGTCTCTACCTTTTATCTTCC 13 89 0 AGTCTCTCCT 0.803392 -65 ******* *** Masking position 11 Map Score: 2.72838 Number of sites scoring better than the average of aligned sites = 894 Number in coding regions = 789 Number in noncoding regions = 105 Number of orfs with sites within 600 bp upstream = 122 Fraction of orfs with sites within 600 bp upstream = 0.0195952 Motif number 8 AAATTGTCAGGAAAAGACTGGCATTGACGC 2 85 0 GAAAAGACTG 0.942877 -114 CCAACAATCTCAAAAGATTGGCTTAACCGA 3 14 0 CAAAAGATTG 0.911011 -21 ATGAAAAGATTTTGATCTCAAC 5 3 1 GAAAAGATTT 0.87434 -47 GACTGAAAATCTTGCCGGTATCCC 8 287 0 GAAAATCTTG 0.967642 -14 AGCGTCGTAAGAAAAGCTTGAAATAGCGCC 11 96 0 GAAAAGCTTG 0.991035 -205 CCTCCTGCGCGAAAGGCTTGGACTTCACGC 12 215 1 GAAAGGCTTG 0.975908 -80 ATCTAATGATGAAATTCTTGACGGAAGAAG 13 108 0 GAAATTCTTG 0.881706 -46 ********** Masking position 4 Map Score: 4.42883 Number of sites scoring better than the average of aligned sites = 328 Number in coding regions = 281 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 45 Fraction of orfs with sites within 600 bp upstream = 0.00722775 Motif number 9 CGTTAGCAGGCGATCGCCGGGG 6 156 0 TTAGCAGGCG 0.992203 -12 ATGCTCAAAGTTTGAAGGGGACAGAGAAAC 7 31 0 TTTGAAGGGG 0.936322 -25 TTGTAATTTTTTTGCTGGCGGGTATGACTT 8 21 1 TTTGCTGGCG 0.964277 -280 GCAATTTTTTTTAACAGGAGGTACCGTTAC 12 186 1 TTAACAGGAG 0.859898 -109 ACAAGCTGAATTAGAAGGCGAGATT 13 139 1 TTAGAAGGCG 0.982603 -15 ********** Masking position 2 Map Score: 1.25362 Number of sites scoring better than the average of aligned sites = 126 Number in coding regions = 116 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 10 GACTGGCATTGACGCAAAAATCACTGATCT 2 70 0 GACGCAAAAA 0.980652 -129 AACAGAGGGATGAAGCTAGT 4 7 0 GAGGGATGAA 0.886854 -14 GTAGATTATGGAGGCAAAAAACAGAAGTTG 6 28 0 GAGGCAAAAA 0.972065 -140 GATGTTAACTTACGCAAAAAGAATTAATTA 12 131 0 TACGCAAAAA 0.906652 -164 TGAAATTCTTGACGGAAGAAGTCTCTACCT 13 99 0 GACGGAAGAA 0.974069 -55 ********** Masking position 6 Map Score: 0.388035 Number of sites scoring better than the average of aligned sites = 80 Number in coding regions = 62 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 11 ********** No masking Map Score: -1.95867e-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: -1.95867e-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: -1.95867e-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