AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i211_synecho_ctra_300.orf -o211_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 RCY30174 31 Synechocystis #2 RCY42399 64 Synechocystis #3 RCY23794 104 Synechocystis #4 RCY53156 108 Synechocystis #5 RCY31741 108 Synechocystis #6 RCY09512 82 Synechocystis #7 RCY38222 137 Synechocystis #8 RCY33689 119 Synechocystis #9 RCY05922 107 Synechocystis #10 RCY14231 101 Synechocystis #11 RCY17023 68 Synechocystis #12 RCY34894 39 Synechocystis #13 RCY03648 59 Synechocystis #14 RCY03870 91 Synechocystis #15 RCY00359 106 Synechocystis #16 RCY25341 23 Synechocystis #17 RCY37057 40 Synechocystis #18 RCY34487 29 Synechocystis #19 RCY46798 32 Synechocystis #20 RCY53151 73 Synechocystis #21 RCY50421 39 Synechocystis #22 RCY31267 300 Synechocystis #23 RCT00022 75 Chlamydia_trachomatis #24 RCT00470 138 Chlamydia_trachomatis #25 RCT00471 300 Chlamydia_trachomatis Motif number 1 TAAAAAATTAACAACAGGGGGTTACTCTAAGG 3 42 0 AACAGGGGGT 0.983574 -63 TTACACGGAGATATAAGGGAGGTCGCGTCA 4 89 1 AAAAGGGAGG 0.9749 -20 TAAACAGGACAGGGATGGGGGGAAGA 5 5 0 AGATGGGGGG 0.942704 -104 TCTGCCCGTAAAAATAGGGGCGA 9 2 0 AATAGGGGCG 0.900802 -106 CTACATAGGCACAAAAGGGGGATGACCGCAAT 22 48 0 AAAAGGGGGA 0.988608 -253 ATCTCACATAACAGAAGGGAGAGCATACCCGA 23 18 0 AAAAGGGAGA 0.960764 -58 AAACGGTACTAAAACAGGGGGATTATAAAAAG 24 73 0 AACAGGGGGA 0.991129 -66 GACCCGACTAAAACAAGGGAGTCTTTCGTGGT 25 167 0 AAAAGGGAGT 0.929199 -134 AGTCGGGTCTAGAGCAGGGGCGGAAGTCATAC 25 190 1 AACAGGGGCG 0.979334 -111 CCTTTCTTGAAAGTCTGGGGGATTGTCCCTGG 25 221 1 AGCTGGGGGA 0.930336 -80 * * ******** Masking position 1 Map Score: 10.4826 Number of sites scoring better than the average of aligned sites = 322 Number in coding regions = 263 Number in noncoding regions = 59 Number of orfs with sites within 600 bp upstream = 59 Fraction of orfs with sites within 600 bp upstream = 0.00947639 Motif number 2 CGTGTAAATAGCTTGACCGACGCTATCTCAG 4 65 0 GCTTGACGAC 0.967866 -44 AATATAGGTTGCTCCATTGGCCAACCTATGC 8 30 0 GCTCCATGGC 0.972231 -90 TTACAAAGCTGCTTCCTTGACCGTCTTTTTT 9 77 1 GCTTCCTGAC 0.979203 -31 GTCTAGCATTGCTTGCGGGGCAAAGGTGATA 15 15 0 GCTTGCGGGC 0.934919 -92 ATCAAGCTTTGCTTGAGAGACCACCTTCGGC 22 103 0 GCTTGAGGAC 0.977651 -198 CTCAAGCAAAGCTTGATTGAAACGCTCCATC 22 117 1 GCTTGATGAA 0.796369 -184 TGATTGAAACGCTCCATCGACGTAACTGAAT 22 130 1 GCTCCATGAC 0.986234 -171 TTGGTCAACAGCTTCATAGCCAGTGAATAAC 22 163 0 GCTTCATGCC 0.946131 -138 AAGCAGAAAGGCTCCCCGGACATAAAGCGAC 22 212 0 GCTCCCCGAC 0.971623 -89 GACGATAACGGCCCCAGGGACAATCCCCCAG 25 235 0 GCCCCAGGAC 0.930846 -66 ******* *** Masking position 2 Map Score: 10.2294 Number of sites scoring better than the average of aligned sites = 307 Number in coding regions = 282 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 3 CGTTATTAAGCGGGGGTATTTTTGAAAACT 2 45 1 CGGGGGTATT 0.87435 -20 AAATTAACAACAGGGGGTTACTCTAAGGCA 3 40 0 CAGGGGGTTA 0.739622 -65 TTCCCCTCAGTGGGGAGAGTTAATTTAATA 7 49 1 TGGGGAGAGT 0.888629 -89 CCTATTTTTACGGGCAGAGTTGCATCAATC 9 16 1 CGGGCAGAGT 0.882702 -92 TCCCCATAGCCTGGGAGAGAGCGATAATAG 10 30 1 CTGGGAGAGA 0.890977 -72 AGTCGCGGCTCAGGGTGATTGGTCAGCAAT 14 14 1 CAGGGTGATT 0.93306 -78 GATGATGATTCAGGTGGATTGATGGAGACT 14 45 0 CAGGTGGATT 0.939671 -47 TATTCCTGCTGGTAGATTCTCCTAAGGG 14 74 0 CTGGTAGATT 0.858924 -18 GCCCTAGCGGTAGGGAGAGTTAGTCCTACA 22 75 0 TAGGGAGAGT 0.890595 -226 GGTACTAAAACAGGGGGATTATAAAAAGAA 24 71 0 CAGGGGGATT 0.989023 -68 TCTTGAAAGTCTGGGGGATTGTCCCTGGGG 25 225 1 CTGGGGGATT 0.982507 -76 ********** Masking position 4 Map Score: 7.97509 Number of sites scoring better than the average of aligned sites = 1223 Number in coding regions = 1068 Number in noncoding regions = 155 Number of orfs with sites within 600 bp upstream = 152 Fraction of orfs with sites within 600 bp upstream = 0.0244137 Motif number 4 AGGCAAAAAAGAATGTCCCTAGCGGG 5 93 1 GATGCCCTAG 0.961947 -16 TATTTGTTGTGATTGACGATGGCGCTTTTTTC 8 57 1 GATGCGATGG 0.986704 -63 GCTGAAGGCCCCAAGCCTTTACTAA 11 4 1 GAGGCCCAAG 0.916234 -65 TCAGAGAGTAGATGGACGAAGGGAACTCGAGC 15 59 0 GAGGCGAAGG 0.969797 -48 AGGCGTTAATGAATGGCGATAGCGT 17 4 0 GATGCGATAG 0.960508 -37 CGATAATTACGAATACCCATGGGTTTAGATAA 20 48 0 GATACCATGG 0.854513 -26 TCCCTACCGCTAGGGCCGAAGGTGGTCTCTCA 22 89 1 TAGGCGAAGG 0.863441 -212 GACCAAAGGTTATTGCCGCTGGTCGTCGCTTT 22 188 1 TATGCGCTGG 0.94953 -113 AAGTCTGGGGGATTGTCCCTGGGGCCGTTATC 25 231 1 GATGCCCTGG 0.987201 -70 ** ** ****** Masking position 2 Map Score: 7.5971 Number of sites scoring better than the average of aligned sites = 468 Number in coding regions = 430 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 5 TTAATTTTTTACCTTTGCCACCGTCAAATTA 7 15 0 ACTTTGCCAC 0.959954 -123 GCTCGTCTTGACATTTTGCCC 8 1 0 ACTTTTGCCC 0.964747 -119 TGGCTATCACCTTTGCCCCGCAAGCAATG 15 9 1 ACTTTGCCCC 0.993588 -98 TTGAGAGACCACCTTCGGCCCTAGCGGTAGG 22 91 0 ACTTCGGCCC 0.985325 -210 TTCAGGGGATACTTTTTCCCCATATACAGGT 25 65 1 ACTTTTCCCC 0.981259 -236 GAAAGGTATGACTTCCGCCCCTGCTCTAGAC 25 196 0 ACTCCGCCCC 0.979154 -105 ** ******** Masking position 4 Map Score: 5.76305 Number of sites scoring better than the average of aligned sites = 187 Number in coding regions = 168 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 6 TTTTTGCTAACAGCTTTTTTGAGCAAATCG 4 22 1 CAGCTTTTTT 0.964214 -87 ATTGACGATGGCGCTTTTTTCGATACTTTA 8 68 1 GCGCTTTTTT 0.910529 -52 ATACTTTATTCCGCTTTATTTTTAGGAGGT 8 90 1 CCGCTTTATT 0.965954 -30 GTCAAGGAAGCAGCTTTGTAAGCTTTCCCT 9 68 0 CAGCTTTGTA 0.836846 -40 TCCGATTTTTTTAGGAAAACG 16 2 1 CCGATTTTTT 0.855311 -22 GCCCAGCTTTGTTCCTAAAATAC 22 288 0 CAGCTTTGTT 0.970182 -13 TGTTTTAGTACCGTTTTGTTGCTAATGCTA 24 89 1 CCGTTTTGTT 0.877128 -50 TTATTCTTTTTAGCTTTTTTTGTAGGTGTT 25 119 1 TAGCTTTTTT 0.777523 -182 GGTGTTAACTACGCTTTATTAAAGACCACG 25 143 1 ACGCTTTATT 0.78633 -158 ********** Masking position 5 Map Score: 5.41961 Number of sites scoring better than the average of aligned sites = 215 Number in coding regions = 182 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 7 CTGTTGTTAATTTTTTAGGAGTTCAGTTAC 3 57 1 TTTTTTAGGA 0.97802 -48 ATTCCGCTTTATTTTTAGGAGGTCATTAAC 8 97 1 ATTTTTAGGA 0.916511 -23 TCCGATTTTTTTAGGAAAACGCC 16 7 1 TTTTTTAGGA 0.97802 -17 ATTTACACTTTTATTTAGGTAGAGGGTTAC 22 247 1 TTATTTAGGT 0.854728 -54 TGTCTATCGGTATTTTAGGAACAAAGCTGG 22 279 1 TATTTTAGGA 0.916511 -22 TTTTAGCTTTTTTTGTAGGTGTTAACTACG 25 126 1 TTTTGTAGGT 0.897122 -175 ********** Masking position 6 Map Score: 2.96612 Number of sites scoring better than the average of aligned sites = 26 Number in coding regions = 16 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 8 TAGAGGGGTACGGGTAAATCCAAAT 1 17 0 GGGTACGGGT 0.89291 -15 TCCTCTGACTGAGATAGCGTCGGTCAAGCT 4 57 1 GAGATAGCGT 0.907498 -52 AGATATAAGGGAGGTCGCGTCA 4 97 1 GAGGTCGCGT 0.84358 -12 ATAAATTTATGGAGTAGGGTTTAAGACAGA 6 38 0 GGAGTAGGGT 0.863022 -45 TCCCCACTGAGGGGAAGCATTAATTTTTTA 7 35 0 GGGGAAGCAT 0.929053 -103 ACTGCGGTTAGGGAAAGCTTACAAAGCTGC 9 59 1 GGGAAAGCTT 0.765666 -49 CCCAGGCTATGGGGAAGGATTTTGGTTACC 10 15 0 GGGGAAGGAT 0.904329 -87 CGAGCACATCGGGTTAGGGTCTAGCATTGC 15 34 0 GGGTTAGGGT 0.966204 -73 TTAATGAATGGCGATAGCGT 17 1 0 GCGATAGCGT 0.851953 -40 TTTAGGTAGAGGGTTACCGTGTCTATCGGT 22 260 1 GGGTTACCGT 0.80813 -41 CATAACAGAAGGGAGAGCATACCCGAACAT 23 14 0 GGGAGAGCAT 0.751164 -62 AAGCTAAAAAGAATAAGGGTATAAATTTAG 25 105 0 GAATAAGGGT 0.452953 -196 ********** Masking position 10 Map Score: 3.87608 Number of sites scoring better than the average of aligned sites = 1163 Number in coding regions = 1041 Number in noncoding regions = 122 Number of orfs with sites within 600 bp upstream = 134 Fraction of orfs with sites within 600 bp upstream = 0.0215226 Motif number 9 CAAATCGTAATTTCCTCTGACTGAGATAGCGT 4 45 1 TTTCCTCTAT 0.869077 -64 TCTTCCCCCCATCCCTGTCCTGT 5 2 1 CTTCCCCCAC 0.972039 -107 GTTGATTTTCCTCTAAATAAGTTCAATA 6 65 0 TTTCCTCTAT 0.869077 -18 AAAATTAATGCTTCCCCTCAGTGGGGAGAGTT 7 38 1 CTTCCCCTAT 0.978739 -100 GCTTTGTAAGCTTTCCCTAACCGCAGTGTTTA 9 54 0 CTTTCCCTAC 0.91392 -54 AACCAAAATCCTTCCCCATAGCCTGGGAGAGA 10 18 1 CTTCCCCAAC 0.976393 -84 GGGGAAAAAGTATCCCCTGAACTTCGAAAAGG 25 54 0 TATCCCCTAC 0.914834 -247 GGGGATACTTTTTCCCCATATACAGGTCAGAA 25 69 1 TTTCCCCAAA 0.833244 -232 ******** * * Masking position 10 Map Score: 2.04124 Number of sites scoring better than the average of aligned sites = 528 Number in coding regions = 461 Number in noncoding regions = 67 Number of orfs with sites within 600 bp upstream = 75 Fraction of orfs with sites within 600 bp upstream = 0.0120463 Motif number 10 TCCCTGTCCTGTTTATTGAAGCTTTCAAGCAATCA 5 22 1 GTTATTATTT 0.979498 -87 AGTGGGGAGAGTTAATTTAATATTTGCCATGACAC 7 57 1 GTTATTATTT 0.979489 -81 GCGATAATAGGTTAATTCATTGTTTTGCTTCATCC 10 50 1 GTTATTATTT 0.979498 -52 TTAGATAACAGTTAATTCAGTATTCAGTGGTGGTC 20 21 0 GTTATTATTC 0.955586 -53 CTTTCTGCTTGTTTATTTACACTTTTATTTAGGTA 22 233 1 GTTATTATTT 0.979498 -68 *** *** * *** Masking position 7 Map Score: 1.17337 Number of sites scoring better than the average of aligned sites = 39 Number in coding regions = 30 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 11 CCCCCTGTTGTTAATTTTTTAGGAGTTCAGTTAC 3 53 1 TTAATTTAGA 0.658202 -52 TTTTTAGGAGTTCAGTTACCATGCGACACAGATG 3 68 1 TTCATTCAGC 0.930888 -37 ATATTAAAAATTAAGTTCACAGGAGATGGAATTT 11 40 0 TTAATTAAGA 0.658195 -29 ACCAAACCCATTAACATCCAAGGAAATTACT 12 19 1 TTAAATCAGA 0.930637 -21 AGTTCAGTTCCAACGAATAAAAACAA 19 17 0 TTCATTCAGA 0.969064 -16 CTGATCAGACTTAAAAGCCTAAGCATTCAGTATC 22 12 0 TTAAAGCAGC 0.804214 -289 GAATAACTAATTCAGTTACGTCGATGGAGCGTTT 22 136 0 TTCATTCTGA 0.896988 -165 GAATTAGTTATTCACTGGCTATGAAGCTGTTGAC 22 157 1 TTCATGCAGA 0.957088 -144 ATGTGAGATTTTCACATACTAAGATAGTGATTTT 23 41 1 TTCAATCAGA 0.95535 -35 TAAATAAAAATTAAAAGACCTGGAATACTATACT 24 33 0 TTAAAGCTGA 0.726424 -106 **** ** * * ** Masking position 4 Map Score: 2.2737 Number of sites scoring better than the average of aligned sites = 166 Number in coding regions = 150 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 12 TGATTACTGCTGCTTGCCTTAGAGTAACCC 3 26 1 TGCTTGCCTT 0.8682 -79 GTTGATTTTCCTCTAAATAAGT 6 71 0 TGATTTTCCT 0.859475 -12 AAAAAATTAATGCTTCCCCTCAGTGGGGAG 7 36 1 TGCTTCCCCT 0.979757 -102 GCCTGATTTTCTTTGGCAACACT 7 125 0 TGATTTTCTT 0.663607 -13 GGCCAACCTATGCTCGTCTTGACATTTTGC 8 13 0 TGCTCGTCTT 0.697046 -107 CAGCTTTGTAAGCTTTCCCTAACCGCAGTG 9 58 0 AGCTTTCCCT 0.871797 -50 GTAACCAAAATCCTTCCCCATAGCCTGGGA 10 16 1 TCCTTCCCCA 0.74147 -86 AAGTGAAAATTCCATCTCCTGTGAACTTAA 11 34 1 TCCATCTCCT 0.641821 -35 TCCTGCTGGTAGATTCTCCTAAGGGATGAT 14 69 0 AGATTCTCCT 0.686059 -23 GGAATTGCGGTCATCCCCCTTTTGTGCCTA 22 45 1 TCATCCCCCT 0.817013 -256 TGTTCGGGTATGCTCTCCCTTCTGTTATGT 23 15 1 TGCTCTCCCT 0.944343 -61 ATACTCCAGGTCCTTTTCTTCTCAAGA 24 8 0 TCCTTTTCTT 0.757812 -131 ********** Masking position 8 Map Score: 2.70308 Number of sites scoring better than the average of aligned sites = 1462 Number in coding regions = 1270 Number in noncoding regions = 192 Number of orfs with sites within 600 bp upstream = 201 Fraction of orfs with sites within 600 bp upstream = 0.032284 Motif number 13 CAGTTAAATTTTTTGCTAACAGCTTTTTTG 4 13 1 TTTTGCTAAC 0.747431 -96 AGGTTGCTCCATTGGCCAACCTATGCTCGT 8 26 0 ATTGGCCAAC 0.908523 -94 GGGGAAGGATTTTGGTTACCATTG 10 5 0 TTTGGTTACC 0.912266 -97 TGTTAATGGGTTTGGTTAACGTTG 12 5 0 TTTGGTTAAC 0.965989 -35 GCTCAGGGTGATTGGTCAGCAATAAGTCTC 14 21 1 ATTGGTCAGC 0.906001 -71 ATTAACGCCTATTCGTTAACACACT 17 26 1 ATTCGTTAAC 0.833543 -15 GGCAATAACCTTTGGTCAACAGCTTCATAG 22 175 0 TTTGGTCAAC 0.97058 -126 ********** Masking position 8 Map Score: 1.29952 Number of sites scoring better than the average of aligned sites = 427 Number in coding regions = 376 Number in noncoding regions = 51 Number of orfs with sites within 600 bp upstream = 58 Fraction of orfs with sites within 600 bp upstream = 0.00931577 Motif number 14 TTTTACCTTTGCCACCGTCAAATTAATAA 7 10 0 GCCACCGTCA 0.983413 -128 CGAAAAAAGCGCCATCGTCAATCACAACAA 8 60 0 GCCATCGTCA 0.990203 -60 ACGCTATCGCCATTCATTAACG 17 3 1 GCTATCGCCA 0.974574 -38 CCCTGGGGCCGTTATCGTCACCATGATCTA 25 247 1 GTTATCGTCA 0.942682 -54 ********** Masking position 4 Map Score: 0.500036 Number of sites scoring better than the average of aligned sites = 82 Number in coding regions = 74 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 15 AGCAGCAGTAATCAAACCCATTGAGCTTG 3 10 0 ATCAAACCCA 0.957467 -95 CAACGTTAACCAAACCCATTAACATCCA 12 9 1 ACCAAACCCA 0.988943 -31 CTACTCTCTGACCAAGCCCAGAGACCCTGT 15 80 1 ACCAAGCCCA 0.981295 -27 TTAACTGTTATCTAAACCCATGGGTATTCG 20 41 1 TCTAAACCCA 0.899084 -33 ********** Masking position 5 Map Score: 0.221161 Number of sites scoring better than the average of aligned sites = 104 Number in coding regions = 96 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432