AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i320_synecho_ctra_300.orf -o320_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 Purged sequences: RCT00490 17 Chlamydia_trachomatis Input sequences: #1 RCY53439 283 Synechocystis #2 RCY05376 78 Synechocystis #3 RCY50998 180 Synechocystis #4 RCY24801 300 Synechocystis #5 RCY46934 166 Synechocystis #6 RCT00475 159 Chlamydia_trachomatis #7 RCT00476 19 Chlamydia_trachomatis #8 RCT00477 107 Chlamydia_trachomatis #9 RCT00478 286 Chlamydia_trachomatis #10 RCT00480 43 Chlamydia_trachomatis #11 RCT00481 65 Chlamydia_trachomatis #12 RCT00482 20 Chlamydia_trachomatis #13 RCT00483 21 Chlamydia_trachomatis #14 RCT00484 55 Chlamydia_trachomatis #15 RCT00485 22 Chlamydia_trachomatis #16 RCT00488 21 Chlamydia_trachomatis #17 RCT00489 27 Chlamydia_trachomatis #18 RCT00493 16 Chlamydia_trachomatis #19 RCT00495 32 Chlamydia_trachomatis #20 RCT00497 18 Chlamydia_trachomatis #21 RCT00499 23 Chlamydia_trachomatis #22 RCT00502 300 Chlamydia_trachomatis #23 RCT00517 300 Chlamydia_trachomatis Motif number 1 TTCGGTGGCGATCGGGCCTAGAACCTGGCCAAAGTG 1 126 0 ACGGCCTCCT 0.819791 -158 GCCCATTGGGATCCCCCCTGGGCCATGAGCCCAGAA 1 174 1 ACCCCCTCAT 0.957819 -110 ATTCCCCAAACAATCCGCCAAATCCT 1 268 1 CACCGCCCCT 0.961633 -16 ACGCTTACTTCTCACCCCTAACTCCTGCTGTTCAAC 3 79 1 CCCCCCTCCT 0.997857 -102 TAAGCGGGCTCGAACCGCTGACCCCTTGCATGCCAT 4 20 1 CACCGCTCCT 0.983134 -281 AATAATTCACACACCCTTATAACCTATCTGCA 19 8 0 CCCCCTTCCT 0.976008 -25 TAGCAAACGGCCATGCCCTCCATCCTGCAAGAGCGA 22 208 0 CAGCCCTCCT 0.972323 -93 CGCTTCACAGACCGCCCCCGGTGCCTAATTACACTT 22 245 0 ACCCCCCCCT 0.982606 -56 ACGCCGCATCCTCACCCCTACTCCCTCTCTTTACAC 23 84 0 CCCCCCTCCT 0.997857 -217 ACACACCTTACTCTCCGCTTATCCATCCACAATACG 23 117 0 CCCCGCTCAT 0.972762 -184 * * ***** *** Masking position 16 Map Score: 13.0086 Number of sites scoring better than the average of aligned sites = 371 Number in coding regions = 338 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 2 GGGAAAACTTTTGCTAAAAATCTAGGACAAACG 1 32 1 TTGCTAAACT 0.983498 -252 CTAGCTATCATTGCTAAAACACT 2 66 1 TTGCTAAACT 0.983498 -13 CAACACTAAATTGCTAAACACCAAACCTTAG 3 9 0 TTGCTAAACA 0.863804 -172 TATAGCTCAGTTGGTAGAGCACTTGCATGGCAT 4 49 0 TTGGTAGACT 0.967345 -252 AAGGATAATTTTGGTAAAAAGCTTGACAATGGG 4 120 0 TTGGTAAACT 0.975812 -181 TTCAACACAATTGTAAGAAAACTATAACTTAGC 6 51 0 TTGTAAGACT 0.780643 -109 GTAAAGCCTTTTGGGAGATTCCTGATTTCGTTA 8 13 1 TTGGGAGACT 0.919155 -95 AATGGATTGTATGTTAAAGTTCTAAAAAAAAGC 9 21 0 ATGTTAAACT 0.675182 -266 GATGCTAATTTTTCGAAAACACTGACTACCTGG 10 12 1 TTTCGAAACT 0.743202 -32 AATTGCTAAACCACTA 18 2 0 TTGCTAAACT 0.983498 -15 TGGAGCTTCCTTGGAAGAAAACTTATAACGCT 22 10 0 TTGGAAGACT 0.880242 -291 GCATGGCCGTTTGCTAAAAGTGTAATTAGGCAC 22 228 1 TTGCTAAAGT 0.853332 -73 TGATCTCACCTTTTTAAAGTTCTTTTTTTGCGC 23 241 0 TTTTTAAACT 0.711931 -60 ******** ** Masking position 6 Map Score: 11.0659 Number of sites scoring better than the average of aligned sites = 258 Number in coding regions = 215 Number in noncoding regions = 43 Number of orfs with sites within 600 bp upstream = 50 Fraction of orfs with sites within 600 bp upstream = 0.00803084 Motif number 3 TATATTTAAGTTTTGAGTTCTCTTCTCCTAATCATTTTCCTAGCTA 2 27 1 TTATCTCTAT 0.927699 -52 ACCAAAATTATCCTTGATCTTCTTTTCCCCTAGGGTTCTGGAACAG 4 138 1 TTGTCTCCTT 0.879565 -163 CTTACAATTGTGTTGAAAATCAGCCTCATTTCGTTTCTATGGAAGA 6 67 1 TTACATCTTT 0.811259 -93 ATTCCTGATTTCGTTAGTAACCCTTTCCTTTATTGTGTAAAATTTG 8 30 1 TTACCTCTTT 0.983581 -78 GCCTTTCTTAACACTCGCGTCTTGTCATTTTCTATATTTG 8 78 0 TTATCTCTTT 0.981029 -30 ATACAATCCATTGTAGCTTTTCCAGTCGTGCGTGCTAGAACTTCTT 9 42 1 TTGTCTCTCT 0.898705 -245 TGGCGAGGACTCTTTAGGGTCCTCGTCGTTTTTGCTCAGATGGTGG 9 97 1 TTACCTCTTT 0.983581 -190 AATTTAGGGTTGGTCGTACTTCGTCTCATAACCGTTGC 11 38 1 TTGTCTCTAT 0.913462 -28 TCGTTACCGTCCTAATCTTTTAATTTG 17 2 0 TTACCTCTTT 0.983581 -26 TGTAGTAATGTCGTCAATACTCCTTTCATTTAGCTTAATAGCTTTT 23 19 1 TTATCTCTTT 0.981029 -282 TTTTCAGGACTACTCGAAAACCTGCTCCTTTTCTCTCTATTATTTC 23 162 0 TTGCCTCTTT 0.980112 -139 TTTCGAGTAGTCCTGAAAACTCTTTTGGTGTAACATGGTGGTCTCG 23 189 1 TTATCTGTTT 0.846141 -112 * * * ** ** * * * Masking position 16 Map Score: 10.5632 Number of sites scoring better than the average of aligned sites = 25 Number in coding regions = 22 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 4 TGGTTTTCGGTGGCGATCGGGCCTAGAACC 1 137 0 TGGCGATCGG 0.986808 -147 AGGATTTGGCGGATTGTTTGGGGAAT 1 268 0 TGGCGGATTG 0.811985 -16 AAGCGTTAAATGGGAGTCGGAGCGGGTTCA 3 55 0 TGGGAGTCGG 0.928436 -126 AAAACCACCCTGGCGATCGCTGTTCCAGAA 4 173 0 TGGCGATCGC 0.897286 -128 CCCCTATCGATGGGGGCTGGTTACCATTCA 4 203 1 TGGGGGCTGG 0.924737 -98 TTACATGGTTTGGGCATCGGGATTATGAAT 4 228 0 TGGGCATCGG 0.976988 -73 CATTGCTCCCTGGCGATCGGCATCTGCACC 5 88 0 TGGCGATCGG 0.986808 -79 TAAAATCCCTTGGGCTTTGGCCCGTGCAAG 9 163 1 TGGGCTTTGG 0.846316 -124 AGGCGGCGAATGGGCAATGGTATATGACCT 22 138 0 TGGGCAATGG 0.861206 -163 ATGGAGGGCATGGCCGTTTGCTAAAAGTGT 22 221 1 TGGCCGTTTG 0.913167 -80 TAGGCACCGGGGGCGGTCTGTGAAGCGTTG 22 254 1 GGGCGGTCTG 0.847671 -47 ********** Masking position 3 Map Score: 8.61815 Number of sites scoring better than the average of aligned sites = 2263 Number in coding regions = 2090 Number in noncoding regions = 173 Number of orfs with sites within 600 bp upstream = 181 Fraction of orfs with sites within 600 bp upstream = 0.0290716 Motif number 5 CTACCGATAAGATGGGAGGGTTGTTCATTCCCC 1 242 1 GATGGAGGGG 0.762439 -42 TTTAGCAATTTAGTGTTGAGTGGCTAATTGCTG 3 24 1 TAGTGTGAGG 0.847553 -157 CAGCAGGAGTTAGGGGTGAGAAGTAAGCGTTAA 3 76 0 TAGGGTGAGG 0.982672 -105 CATGGCATGCAAGGGGTCAGCGGTTCGAGCCCG 4 24 0 AAGGGTCAGG 0.714387 -277 GACTCGGGGCTATAGCTCAGTTGGTAGAGCACT 4 59 0 TATAGTCAGG 0.889192 -242 ATTTCGTTTCTATGGAAGAGATGACTCGCTTGT 6 94 1 TATGGAGAGG 0.970744 -66 TTGTGCGTGCTATGGCACAGGAGAAAGAGAGGC 6 123 1 TATGGACAGG 0.920113 -37 GAACTTCTTGTAAAGCTGTGGCGAGGACTCTTT 9 79 1 TAAAGTGTGG 0.507455 -208 CTTTTTGATTTATAGATGAGGAGAGCTATTTAA 9 247 1 TATAGTGAGG 0.958537 -40 TTATAGCTAAGGAGTTTGGG 12 2 1 TATAGTAAGG 0.836154 -19 AGGGTAAAGTAGAGTCGAACT 16 5 1 TAAAGAGAGG 0.876463 -17 TAAAGAAGGAAGAGAAGAATAAC 21 5 1 GAAGGAGAGG 0.908779 -19 AGAGAGGGAGTAGGGGTGAGGATGCGGCGTATT 23 90 1 TAGGGTGAGT 0.762405 -211 GCGTATTGTGGATGGATAAGCGGAGAGTAAGGT 23 116 1 GATGGTAAGG 0.877541 -185 AGAAATAATAGAGAGAAAAGGAGCAGGTTTTCG 23 161 1 GAGAGAAAGG 0.726534 -140 ***** **** * Masking position 2 Map Score: 9.15199 Number of sites scoring better than the average of aligned sites = 437 Number in coding regions = 364 Number in noncoding regions = 73 Number of orfs with sites within 600 bp upstream = 76 Fraction of orfs with sites within 600 bp upstream = 0.0122069 Motif number 6 AGAATTGGCCAATTTTTCTGGGCTCATGGCC 1 194 0 AATTTTCTGG 0.801906 -90 ACCTCCTTTTGCTTTTTCTGTTAAAAAAACT 4 276 0 GCTTTTCTGT 0.96943 -25 TATAGCCTAAGCCTTTTCTTGGTGCAGATGC 5 68 1 GCTTTTCTTG 0.963754 -99 ACTTAGCTCAGCATTTTCAGAAATACCTGCG 6 27 0 GCTTTTCAGA 0.910611 -133 ATCCATTGTAGCTTTTCCAGTCGTGCGTGCT 9 47 1 GCTTTCCAGT 0.857427 -240 AACCTAGAACGATTTTTCAGGCTTTGTTTTT 22 50 1 GATTTTCAGG 0.971028 -251 CCACACAAGAGATTTTTCTTGACGCTAAGAA 22 100 0 GATTTTCTTG 0.931192 -201 TTAAGGAGCCGCGTTTTCTTTGTCGTGGAAA 22 177 1 GCTTTTCTTT 0.912229 -124 TACACCAAAAGAGTTTTCAGGACTACTCGAA 23 190 0 GATTTTCAGG 0.971028 -111 ** ******** Masking position 6 Map Score: 5.26394 Number of sites scoring better than the average of aligned sites = 372 Number in coding regions = 327 Number in noncoding regions = 45 Number of orfs with sites within 600 bp upstream = 58 Fraction of orfs with sites within 600 bp upstream = 0.00931577 Motif number 7 GGGCTCATGGCCCAGGGGGGATCCCAATGG 1 176 0 CCCAGGGGGG 0.963519 -108 TGTCTCCCCCAGATGGGTTGTCCGTAG 3 164 0 CCCAGATGGG 0.780494 -17 GGGGCTATAGCTCAGTTGGTAGAGCACTTG 4 57 0 CTCAGTTGGT 0.916724 -244 AGGAAAAATCCCCAGATAGGATCTAACCAG 5 32 0 CCCAGATAGG 0.966779 -135 GTCGTTTTTGCTCAGATGGTGGAATGGTAG 9 121 1 CTCAGATGGT 0.965098 -166 TGCTAAATCCCAGGTAGTCAGTGTTTTC 10 26 0 CCCAGGTAGT 0.967561 -18 ********** Masking position 4 Map Score: 4.37367 Number of sites scoring better than the average of aligned sites = 359 Number in coding regions = 337 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 8 GCAGGAGTTAGGGGTGAGAAGTAAGCGTTA 3 77 0 GGGGTGAGAA 0.971032 -104 AGGTTATAAGGGTGTGTGAATTATT 19 18 1 GGTGTGTGAA 0.989355 -15 TGCGATTTTTGGTGTGGGATTTCTTAGCGT 22 80 1 GGTGTGGGAT 0.947956 -221 CACCGGGGGCGGTCTGTGAAGCGTTGTCAA 22 258 1 GGTCTGTGAA 0.947001 -43 GCGTTGTCAAGTTGTGTGATAAGGTAATTA 22 278 1 GTTGTGTGAT 0.839862 -23 AGAGGGAGTAGGGGTGAGGATGCGGCGTAT 23 92 1 GGGGTGAGGA 0.911617 -209 CGGAGAGTAAGGTGTGTCAAATAAAAGAAA 23 136 1 GGTGTGTCAA 0.947001 -165 ********** Masking position 5 Map Score: 3.04369 Number of sites scoring better than the average of aligned sites = 97 Number in coding regions = 81 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 9 CAGAAAAATTGGCCAATTCTTCTTCCGGGT 1 205 1 GGCCAATTCT 0.934119 -79 ATCGGTAGTGGGCCAACCCGGAAGAAGAAT 1 220 0 GGCCAACCCG 0.967472 -64 TTTGGGGAATGAACAACCCTCCCATCTTAT 1 248 0 GAACAACCCT 0.934595 -36 TTCATTCCCCAAACAATCCGCCAAATCCT 1 265 1 AAACAATCCG 0.560958 -19 TTAAATATAAAGACAATTCTCGAAT 2 6 0 AGACAATTCT 0.774881 -73 GGCGACCTACGGACAACCCATCTGGGGGAG 3 158 1 GGACAACCCA 0.913149 -23 GACGAAGTACGACCAACCCTAAATTTTTTT 11 33 0 GACCAACCCT 0.910508 -33 TGGACAATTGTAGTAATGTCG 23 2 1 GGACAATTGT 0.720566 -299 AGAGTTTTCAGGACTACTCGAAAACCTGCT 23 182 0 GGACTACTCG 0.879244 -119 GTGTATAACCGGACTATTCTCACGAAAAAT 23 280 0 GGACTATTCT 0.846951 -21 ********** Masking position 6 Map Score: 2.91797 Number of sites scoring better than the average of aligned sites = 851 Number in coding regions = 783 Number in noncoding regions = 68 Number of orfs with sites within 600 bp upstream = 76 Fraction of orfs with sites within 600 bp upstream = 0.0122069 Motif number 10 ATTTAAGTTTTGAGTTCTCTTCTCCTAATC 2 30 1 TGAGTTCTCT 0.797904 -49 CTTTTCCCCTAGGGTTCTGGAACAGCGATC 4 159 1 AGGGTTCTGG 0.952281 -142 CAGGGAGCAATGGGTCCTCGGAATCCGCTA 5 106 1 TGGGTCCTCG 0.990972 -61 AGGACCCTAAAGAGTCCTCGCCACAGCTTT 9 90 0 AGAGTCCTCG 0.981684 -197 AGGACTCTTTAGGGTCCTCGTCGTTTTTGC 9 102 1 AGGGTCCTCG 0.99347 -185 ********** Masking position 5 Map Score: 2.0175 Number of sites scoring better than the average of aligned sites = 8 Number in coding regions = 7 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 11 TGTCCGTAGGTCGCCGCAATAATGAGTACGCAT 3 140 0 TCCGCAAAAT 0.829173 -41 GGCACCACTTTCAGCACAATAGAATACTGTGAC 4 89 0 TCCACAAAGA 0.946667 -212 AGGCTGATTTTCAACACAATTGTAAGAAAACTA 6 60 0 TCCACAATGT 0.690808 -100 TTGTGCAAATTTTACACAATAAAGGAAAGGGTT 8 48 0 TTCACAAAAA 0.95835 -60 TTGTGTAAAATTTGCACAAATATAGAAAATGAC 8 62 1 TTCACAATAT 0.743351 -46 ACCTGCGACATCCACACAAGAGATTTTTCTTGA 22 109 0 TCCACAAAGA 0.946668 -192 GCAAGAGCGATTTCCACGACAAAGAAAACGCGG 22 185 0 TTCACGAAAA 0.908207 -116 ACTCCCTCTCTTTACACAGCAAACGTATTGTCT 23 68 0 TTCACAGAAA 0.827449 -233 GGTCTCGTTCTTTGCGCAAAAAAAGAACTTTAA 23 228 1 TTCGCAAAAA 0.908207 -73 AACCGGACTATTCTCACGAAAAATGTTTCGTGA 23 271 0 TTCACGAAAA 0.908209 -30 ** ***** *** Masking position 1 Map Score: 2.13745 Number of sites scoring better than the average of aligned sites = 84 Number in coding regions = 66 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 12 AAAATTTTCGTTTGTCCTAGATTTTTAGCA 1 43 0 TTTGTCCTAG 0.889939 -241 GAATTGGCCAATTTTTCTGGGCTCATGGCC 1 194 0 ATTTTTCTGG 0.859367 -90 TCTCCTAATCATTTTCCTAGCTATCATTGC 2 50 1 ATTTTCCTAG 0.952789 -29 TATCTGGGGATTTTTCCTAGTCAATATAGC 5 44 1 TTTTTCCTAG 0.963341 -123 AGTTCATTGCTTTTTTTTAGAACTTTAACA 9 13 1 TTTTTTTTAG 0.7384 -274 AACCCTAAATTTTTTTCTAGCGTGTTGCAT 11 19 0 TTTTTTCTAG 0.956065 -47 CACACAAGAGATTTTTCTTGACGCTAAGAA 22 100 0 ATTTTTCTTG 0.8048 -201 ********** Masking position 5 Map Score: 2.34881 Number of sites scoring better than the average of aligned sites = 207 Number in coding regions = 168 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 13 AAGCGTTGCTGGGAATAACCTGGTTTGCCAAA 1 81 0 GGGATAACCG 0.974857 -203 AAATGGAGCTAAGCGGGCTCGAACCG 4 5 1 GGACTAAGCG 0.974643 -296 TCCCCAGATAGGATCTAACCAGCAGTTCTTAA 5 22 0 GGACTAACCG 0.986584 -145 TTGTTTGACAGGAACTGAGCCGAACT 5 151 1 GGACTGAGCG 0.969573 -16 ATGGGCAATGGTATATGACCTGCGACATCCAC 22 127 0 GTAATGACCG 0.929084 -174 TGTGTATAACCGGACTATTCTCA 23 288 0 GTGATAACCG 0.929084 -13 *** ****** * Masking position 6 Map Score: 0.440767 Number of sites scoring better than the average of aligned sites = 145 Number in coding regions = 130 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 14 ACCACTTTCAGCACAATAGAATACTGTGAC 4 89 0 GCACAATAGA 0.829852 -212 GCCATAGCACGCACAAGCGAGTCATCTCTT 6 109 0 GCACAAGCGA 0.989711 -51 GCGTGCTATGGCACAGGAGAAAGAGAGGCA 6 127 1 GCACAGGAGA 0.955141 -33 AGAAGTTCTAGCACGCACGACTGGAAAAGC 9 57 0 GCACGCACGA 0.848119 -230 CACCATCTGAGCAAAAACGACGAGGACCCT 9 112 0 GCAAAAACGA 0.81247 -175 ACGGGCCAAAGCCCAAGGGATTTTAAGTCC 9 158 0 GCCCAAGGGA 0.837476 -129 ACTCGAACTTGCACGGGCCAAAGCCCAAGG 9 170 0 GCACGGGCCA 0.867169 -117 TGCGACATCCACACAAGAGATTTTTCTTGA 22 109 0 ACACAAGAGA 0.786608 -192 CCTCCATCCTGCAAGAGCGATTTCCACGAC 22 198 0 GCAAGAGCGA 0.939846 -103 ********** Masking position 10 Map Score: 1.31744 Number of sites scoring better than the average of aligned sites = 215 Number in coding regions = 195 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 15 ********** No masking Map Score: 4.32964e-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