AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i063_synecho_ctra_300.orf -o063_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 RCY16794 188 Synechocystis #2 RCY17332 228 Synechocystis #3 RCY32570 127 Synechocystis #4 RCY06192 207 Synechocystis #5 RCY19916 97 Synechocystis #6 RCY47027 173 Synechocystis #7 RCY44761 150 Synechocystis #8 RCY52233 205 Synechocystis #9 RCY20619 187 Synechocystis #10 RCY32067 88 Synechocystis #11 RCY21220 22 Synechocystis #12 RCY46107 44 Synechocystis #13 RCY43084 300 Synechocystis #14 RCT00269 19 Chlamydia_trachomatis #15 RCT00270 194 Chlamydia_trachomatis #16 RCT00272 264 Chlamydia_trachomatis Motif number 1 TTTTGCTTCAGACTGTTTTGGCACAGTTCAATCTTTATTCTG 1 130 0 GCGTTGGAAT 0.78208 -59 TTGACCGGGCGCTGGGGAGGGTTTTGGCTAAAATTTTCCCTT 2 17 1 GTGGGGGAAA 0.973316 -212 TTAACTCCTGGGCGGGGCTACGACCGCAGAAAAAAGGCCCAA 4 132 0 GCGGGCGAAA 0.981839 -76 CGGGACACAGGTCAGTGAGAGGAACGGTTAACTCCTGGGCGG 4 159 0 GCGTGGGAAC 0.964302 -49 AAGGATGAACGCCTGGACTGGATCTGTCAAAAAATGTTACAG 6 126 0 GCGGAGGAAA 0.993077 -48 AATGGCGGAGTAGGGAAAGGATGAACGCCTGGACT 6 149 0 GCGAGGGGAA 0.971984 -25 CCAATCCATTGCCTGGGGCCGACACGTTCACACTCTTATAGT 8 107 0 GCGGGGGACA 0.988671 -99 GAATAGCACTGACGGTTTCTGGGGAGTCGGAAGACATGTTAA 9 100 0 GCGTTGGGAA 0.907312 -88 AAAAAGCCTTGGCAGGACAGGTTCAGTTTAAAAGCTTATGGG 9 153 0 GCGGAGGAAA 0.993077 -35 GGAAAAAGCCGCCCGAATTTGTTTGGTAAAAACTTTGCCGCC 13 24 1 GCGAAGGAAA 0.965806 -277 CACTGCCAGGGACGGGGATAGGGGGGACTAAATCACCACTAA 13 103 0 GCGGGGGAAA 0.998037 -198 ACTGTGACAAGACTGGGCAAGCCTAGTCAAAAATAGCGAGGA 13 193 0 GCGGGGGAAA 0.998037 -108 * * *** * * *** Masking position 16 Map Score: 17.7794 Number of sites scoring better than the average of aligned sites = 303 Number in coding regions = 277 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 2 GGGAAAAATGCCAGAAGCAT 1 1 1 GGGAAAAATG 0.778991 -188 GACGATCGCCAGGAAAAGGGATTAAATTTT 1 79 1 AGGAAAAGGG 0.82375 -110 GCCCGACTCCCGGAAAAATTTAATCCCTTT 1 93 0 CGGAAAAATT 0.502741 -96 ACCGGGCGCTGGGGAGGGTTTTGGCTAAAA 2 20 1 GGGGAGGGTT 0.431699 -209 TGTCTTCACAAGGGAAAATTTTAGCCAAAA 2 38 0 AGGGAAAATT 0.802822 -191 TCGTTGTAGAAGGGAAGGTGTTTGAGTCAT 3 45 1 AGGGAAGGTG 0.817422 -83 CTAGCAAAAAAGGAAAGATGACTCAAACAC 3 62 0 AGGAAAGATG 0.742027 -66 AGGGAAAGAGCCAGATTTACC 3 117 0 GGGAAAGAGC 0.914737 -11 TGCTGGACCTGCGGAAAAGCAGCTAAACAA 4 18 0 GCGGAAAAGC 0.82191 -190 CGAGTTTTATGGGGATGGGGCCGCCTTGGC 6 38 1 GGGGATGGGG 0.698657 -136 ATGGCGGAGTAGGGAAAGGATGAACGCCTG 6 153 0 AGGGAAAGGA 0.7022 -21 TGCTTTTTTTAGGAAAAATCTATTATGCAG 7 105 1 AGGAAAAATC 0.856162 -46 GGGAAATAGCACGGAATAGCACTGACGGTT 9 125 0 ACGGAATAGC 0.394333 -63 AAAGCTTATGGGGAAATAGCACGGAATAGC 9 135 0 GGGAAATAGC 0.649692 -53 CGGAAAAAGCCTTGGCAGGA 9 178 0 CGGAAAAAGC 0.892452 -10 GAAAAGTAGAGGGAATAAGCTCAATGGTGC 10 32 0 GGGAATAAGC 0.755046 -57 ACGGAAGATCAGGGAAAAGTAGAGGGAATA 10 45 0 AGGGAAAAGT 0.899214 -44 CAGTGCAACTACGGAAGATCAGGGAAAAGT 10 55 0 ACGGAAGATC 0.632181 -34 AGATGAAATGCGGAAAAAGCCGCCCGAATT 13 13 1 CGGAAAAAGC 0.892452 -288 ATGGCAAATTCGGGATAATGAGCCGGGTTA 13 73 1 CGGGATAATG 0.573937 -228 TGCCAGGGACGGGGATAGGGGGGACTAAAT 13 112 0 GGGGATAGGG 0.738894 -189 AATTATGGGCAGGGAAAAGCCTATTCGACC 13 264 0 AGGGAAAAGC 0.970946 -37 TCTAATAGGGAGGGAGGATCTGTACAGATC 15 15 1 AGGGAGGATC 0.823477 -180 CAAAGACCGAAGGGAGGATCTGTACAGATC 15 31 0 AGGGAGGATC 0.823477 -164 CTTTTCGTAAAGGGAAAGGAATTGGGAGAT 16 75 1 AGGGAAAGGA 0.7022 -190 GTGAAATAAACGGGAGAAGTTGTTCTCTGT 16 208 1 CGGGAGAAGT 0.679417 -57 ********** Masking position 5 Map Score: 19.6491 Number of sites scoring better than the average of aligned sites = 5037 Number in coding regions = 4411 Number in noncoding regions = 626 Number of orfs with sites within 600 bp upstream = 586 Fraction of orfs with sites within 600 bp upstream = 0.0941214 Motif number 3 TAATCCCTTTTCCTGGCGATCGTCGTTGGCAT 1 71 0 TCCGGCGTCG 0.983796 -118 GGTCAGTTGACCGGGCGCTGGGGAGGGTTTT 2 10 1 ACCGGCGTGG 0.950111 -219 CAATTATTTTCCTTGGCGATCGCCGTGGCGGT 4 76 0 CCTGGCGTCG 0.993265 -132 ATTGTCTTTTTCTCGGCGTTCCTGCTCCTTGG 4 104 1 TCTGGCGTCC 0.979669 -104 ACGGTTAACTCCTGGGCGGGGCTACGACCGCA 4 146 0 CCTGGCGGGC 0.972478 -62 CCTTTCGGCGATCGGTTCGGGACA 4 194 0 TTTGGCGTCG 0.802508 -14 GATGGGGCCGCCTTGGCAATGCTGACCCCTAG 6 51 1 CCTGGCATGC 0.973179 -123 ACAGATCCAGTCCAGGCGTTCATCCTTTCCCT 6 141 1 TCCGGCGTCA 0.871468 -33 ACGTGTCGGCCCCAGGCAATGGATTGGAACCA 8 122 1 CCCGGCATGG 0.978101 -84 ACTGACGGTTTCTGGGGAGTCGGAAGACATGT 9 103 0 TCTGGGATCG 0.739851 -85 CGGAAAAAGCCTTGGCAGGACAGGTTCAGTT 9 167 0 CCTGGCAGAC 0.819989 -21 CTATCCCCGTCCCTGGCAGTGTCAACGCTGAC 13 124 1 CCCGGCATGT 0.836137 -177 CGAGGAAAGCCCTAGGCGTTAGCTTCAATTCT 13 167 0 CCTGGCGTAG 0.966709 -134 CTGTGACAAGACTGGGCAAGCCTAGTCAAAAA 13 202 0 ACTGGCAGCC 0.81999 -99 *** **** *** Masking position 6 Map Score: 14.9004 Number of sites scoring better than the average of aligned sites = 3215 Number in coding regions = 2978 Number in noncoding regions = 237 Number of orfs with sites within 600 bp upstream = 239 Fraction of orfs with sites within 600 bp upstream = 0.0383874 Motif number 4 TTTTAGCCAAAACCCTCCCCAGCGCCCGGTCAA 2 17 0 AACCCTCCGC 0.97198 -212 TTTCGGAGAGAAGCCTGCTAAGCGTAACCATAA 2 168 0 AAGCCTGCGC 0.993434 -61 GTCTATCAGCAAGCCTGCCTAGCAAAAAAGGAA 3 77 0 AAGCCTGCGC 0.993434 -51 GCTGCAATCAAAACCGCCACGGCGATCGCCAAG 4 64 1 AAACCGCCGC 0.981726 -144 ATAGGTACGGAAACCTGCACTTCCGAGAACTAA 8 62 1 AAACCTGCTC 0.961695 -144 AAAAAACCAAAAACCTGCTTTGCCAGCCTAAAT 9 18 0 AAACCTGCGC 0.995572 -170 GACTCCCCAGAAACCGTCAGTGCTATTCCGTGC 9 114 1 AAACCGTCGC 0.951681 -74 AAAAACCTGAATGGCAAGGTGGAAT 16 3 1 AAACCTGAGC 0.961696 -262 ******** ** Masking position 2 Map Score: 10.4361 Number of sites scoring better than the average of aligned sites = 103 Number in coding regions = 97 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 5 TTGGCCATCAAATTCTGGCGGCAGGTGCTATG 2 78 1 AACTGGCGGC 0.992151 -151 GGCTTGCTGATAGACTGGGGGAGGTAAATCTG 3 95 1 TACTGGGGGA 0.96686 -33 AGTTTACCAAAAATATGGCGGAGGCAGGGGTT 5 46 0 AAATGGCGGA 0.947994 -52 CCTAGCCCCCAATACTGGGGGAATCAGATTCG 7 42 1 AACTGGGGGA 0.987608 -109 AATCCTCCTTTAACCAGGGGGATTTTTTGTGC 7 76 1 TACAGGGGGA 0.92696 -75 AGGTTTCCGTACCTATGGGGGCATCTAGCCGT 8 46 0 ACATGGGGGC 0.884786 -160 TTACCAAACAAATTCGGGCGGCTTTTTCCGCA 13 21 0 AACGGGCGGC 0.978823 -280 ATTTGCCATCAAACCAGGCGGCAAAGTTTTTA 13 50 0 AACAGGCGGC 0.98214 -251 ** ******** Masking position 7 Map Score: 6.94867 Number of sites scoring better than the average of aligned sites = 417 Number in coding regions = 353 Number in noncoding regions = 64 Number of orfs with sites within 600 bp upstream = 63 Fraction of orfs with sites within 600 bp upstream = 0.0101189 Motif number 6 GGCCCTAAGGCAGAATAAAGATTGAACTGT 1 120 1 CAGAATAAAG 0.816816 -69 GCTCCAAAACCAGAGAAAAGAAAGAGAGTG 2 203 0 CAGAGAAAAG 0.773575 -26 GCTACGACCGCAGAAAAAAGGCCCAAGGAG 4 128 0 CAGAAAAAAG 0.952156 -80 CTAAAAAAAGCACAAAAAATCCCCCTGGTT 7 87 0 CACAAAAAAT 0.634867 -64 TAGATTTTTCCTAAAAAAAGCACAAAAAAT 7 97 0 CTAAAAAAAG 0.946023 -54 CTAATAATTCCAAAAAAAACCAAAAACCTG 9 34 0 CAAAAAAAAC 0.851845 -154 AATTATTAGTCACAAAAAAGCTGTCGTATA 9 55 1 CACAAAAAAG 0.952156 -133 ATCCTTTTAAGAAAAAAAAGGAAAACTACT 15 152 0 GAAAAAAAAG 0.738059 -43 AAGGATTGTTCTCAAAAAAGAAGGGTCTC 15 176 1 CTCAAAAAAG 0.935302 -19 AAAAAGTCTGCTATAAAAAGTGCTTTAATC 16 102 0 CTATAAAAAG 0.669959 -163 TTCTAAAAATTTAAAAAAAGTCTGCTATAA 16 116 0 TTAAAAAAAG 0.580001 -149 TATAACCATTCTAAATAAACAGACAGAGAA 16 230 0 CTAAATAAAC 0.483412 -35 ********** Masking position 7 Map Score: 5.26448 Number of sites scoring better than the average of aligned sites = 439 Number in coding regions = 350 Number in noncoding regions = 89 Number of orfs with sites within 600 bp upstream = 90 Fraction of orfs with sites within 600 bp upstream = 0.0144555 Motif number 7 AGAGCCAGATTTACCTCCCCCAGTCTATCA 3 102 0 TTACCTCCCC 0.978138 -26 AGAGGAACGGTTAACTCCTGGGCGGGGCTA 4 154 0 TTAACTCCTG 0.928906 -54 TGCGTGGCGTTAACTCCCCTTTTGACCAA 8 10 1 TTAACTCCCC 0.990032 -196 AATTTTAATTAACTCCCGTTAACAAGTA 8 188 0 TTAACTCCCG 0.985546 -18 TTAGTGGTGATTTAGTCCCCCCTATCCCCG 13 103 1 TTTAGTCCCC 0.895546 -198 ********** Masking position 6 Map Score: 1.65938 Number of sites scoring better than the average of aligned sites = 79 Number in coding regions = 64 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 8 GCCCGACTCCCGGAAAAATTTAATCCCTTTTC 1 91 0 CGAAAATTTA 0.747725 -98 TGTCTTCACAAGGGAAAATTTTAGCCAAAACC 2 36 0 AGAAAATTTT 0.701692 -193 TCCGCAGGTCCAGCAATATTTTGAAATTGAAG 4 33 1 CGAATATTTT 0.954678 -175 ACCCCTGCCTCCGCCATATTTTTGGTAAACTA 5 47 1 CGCATATTTT 0.814571 -51 ATGGGAAACGTTTTAAGAATATTT 6 3 1 GGAACGTTTT 0.850697 -171 TAGAGCCAATCTGTAACATTTTTTGACAGATC 6 116 1 CGAACATTTT 0.977531 -58 TCAAACCAGGCGGCAAAGTTTTTACCAAACAA 13 42 0 CGAAAGTTTT 0.90057 -259 CCTATTCGACCTGTAACATTTTGCTTAATTGA 13 243 0 CGAACATTTT 0.977531 -58 GAATGGCAAGGTGGAATATTTTTCAAGCATAT 16 19 1 GGAATATTTT 0.865156 -246 GTTTATTTCACGGAAACATATTACATCAGAAC 16 187 0 CGAACATATT 0.859582 -78 * * ******** Masking position 6 Map Score: 4.65134 Number of sites scoring better than the average of aligned sites = 249 Number in coding regions = 214 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 9 AGATTGAACTGTGCCAAAACAGTCTGAAGCAA 1 138 1 GTGCAAACAG 0.960166 -51 GCAAGCCTGCCTAGCAAAAAAGGAAAGATGAC 3 70 0 CTACAAAAAG 0.468157 -58 TTTTGGTAAACTAACAACGCTGTTGCCTTTAG 5 66 1 CTACAAGCTG 0.956013 -32 TGGGGCCGCCTTGGCAATGCTGACCCCTAGGC 6 53 1 TTGCAAGCTG 0.936307 -121 GGCTAGGGGACTTTCAATACAGGTTTTAAAAC 7 17 0 CTTCAAACAG 0.835776 -134 GCGATTTAGGCTGGCAAAGCAGGTTTTTGGTT 9 15 1 CTGCAAGCAG 0.987137 -173 TGAACCTGTCCTGCCAAGGCTTTTTCCG 9 170 1 CTGCAAGCTT 0.902965 -18 GTCCCTGGCAGTGTCAACGCTGACATATTGTC 13 132 1 GTGCAAGCTG 0.983166 -169 GGTGGGCACTGTGACAAGACTGGGCAAGCCTA 13 210 0 GTGCAAACTG 0.967453 -91 *** *** **** Masking position 6 Map Score: 5.60596 Number of sites scoring better than the average of aligned sites = 390 Number in coding regions = 352 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 46 Fraction of orfs with sites within 600 bp upstream = 0.00738837 Motif number 10 CAAAACCCTCCCCAGCGCCCGGTCAACTGA 2 13 0 CCCAGCGCCC 0.605369 -216 CAATTATTTTCCTTGGCGATCGCCGTGGCG 4 78 0 CCTTGGCGAT 0.738624 -130 CGTTCCTGCTCCTTGGGCCTTTTTTCTGCG 4 120 1 CCTTGGGCCT 0.951584 -88 CAGGGGTTGTTCCTGGGTCCACAAAGGACT 5 24 0 TCCTGGGTCC 0.734545 -74 CAGGAACAACCCCTGCCTCCGCCATATTTT 5 39 1 CCCTGCCTCC 0.959717 -59 GATGGGGCCGCCTTGGCAATGCTGACCCCT 6 51 1 CCTTGGCAAT 0.655962 -123 CAATGCTGACCCCTAGGCCTACCAAAATTT 6 67 1 CCCTAGGCCT 0.865088 -107 ATTGAAAGTCCCCTAGCCCCCAATACTGGG 7 31 1 CCCTAGCCCC 0.882749 -120 CCTTGCCTCTCCATTGCCAT 11 1 1 CCTTGCCTCT 0.944342 -22 CAGATAAACTTTGGCTCTGGAATCTGTA 12 27 0 CTTTGGCTCT 0.646493 -18 CCTAGGGCTTTCCTCGCTATTTTTGACTAG 13 183 1 TCCTCGCTAT 0.475989 -118 ATAGGCTTTTCCCTGCCCATAATTGTACTA 13 270 1 CCCTGCCCAT 0.936467 -31 TACAGATCCTCCCTCCCTATTAGAAGAG 15 9 0 CCCTCCCTAT 0.81539 -186 ACAGATCCTCCCTTCGGTCTTTGTCCATGA 15 38 1 CCTTCGGTCT 0.854851 -157 ********** Masking position 4 Map Score: 3.57068 Number of sites scoring better than the average of aligned sites = 4471 Number in coding regions = 4050 Number in noncoding regions = 421 Number of orfs with sites within 600 bp upstream = 414 Fraction of orfs with sites within 600 bp upstream = 0.0664953 Motif number 11 CAAAAAAGCTGTCGTATAGTATGGTATTAG 9 67 1 GTCGTATAGT 0.910553 -121 AATGTTACAGGTCGAATAGGCTTTTCCCTG 13 255 1 GTCGAATAGG 0.972427 -46 CTCTTCTAATAGGGAGGGAGGAT 15 4 1 TTCTAATAGG 0.776275 -191 TCTTTCTCTCTTCGTAAAGGAATTCTGTAG 15 121 1 TTCGTAAAGG 0.957317 -74 TATCATAAATGTCGTATATGCTTGAAAAAT 16 36 0 GTCGTATATG 0.910553 -229 GATGCAACTTTTCGTAAAGGGAAAGGAATT 16 68 1 TTCGTAAAGG 0.957317 -197 ********** Masking position 6 Map Score: 0.695222 Number of sites scoring better than the average of aligned sites = 47 Number in coding regions = 44 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 12 TTCTGCCTTAGGGCCCGACTCCCGGAAAAA 1 105 0 GGGCCCGACT 0.986641 -84 TTATGGGGATGGGGCCGCCTTGGCAATGCT 6 44 1 GGGGCCGCCT 0.991451 -130 TCCATTGCCTGGGGCCGACACGTTCACACT 8 115 0 GGGGCCGACA 0.99498 -91 GACACAACGATGGGCCGAAAAGCCATGGTT 8 149 0 TGGGCCGAAA 0.926319 -57 ********** Masking position 5 Map Score: 0.320911 Number of sites scoring better than the average of aligned sites = 100 Number in coding regions = 98 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 13 TCAATCTTTATTCTGCCTTAGGGCCCGACTC 1 114 0 TTCTGCTTAG 0.898532 -75 TGATAATCTCTTTTGCTTCAGACTGTTTTGG 1 151 0 TTTTGCTCAG 0.940586 -38 GTTTTTGCCTAATTACCTGAATT 3 3 1 TTTTGCTAAT 0.957165 -125 AGCAAGTCCTTTCTGCATAATAGATTTTTCC 7 116 0 TTCTGCTAAT 0.948793 -35 ACCTGTAACATTTTGCTTAATTGACGGTGGG 13 236 0 TTTTGCTAAT 0.957172 -65 TCATGGTACTTGTTGCGTAAGATTATTATCA 15 73 0 TGTTGCTAAG 0.927797 -122 ****** **** Masking position 4 Map Score: 0.152445 Number of sites scoring better than the average of aligned sites = 77 Number in coding regions = 59 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 14 GTGAGATTAAGGATCGGTAGACGCACTTGT 2 118 1 GGATCGGTAG 0.956323 -111 AAAGAGAGTGGGTTTCGGAGAGAAGCCTGC 2 183 0 GGTTTCGGAG 0.834641 -46 TCTTTTCTCTGGTTTTGGAGCTAATTT 2 212 1 GGTTTTGGAG 0.895886 -17 TTCGGCGATCGGTTCGGGACACAGGTCAGT 4 185 0 GGTTCGGGAC 0.96574 -23 CCCAGGCAATGGATTGGAACCATGGCTTTT 8 132 1 GGATTGGAAC 0.84528 -74 TTTGGCTCTGGAATCTGTACTTAGCATTGT 12 16 0 GAATCTGTAC 0.708011 -29 ACCGAAGGGAGGATCTGTACAGATCCTCCC 15 26 0 GGATCTGTAC 0.913802 -169 AAAGGGAAAGGAATTGGGAGATTAAAGCAC 16 83 1 GAATTGGGAG 0.86704 -182 ********** Masking position 9 Map Score: 0.409883 Number of sites scoring better than the average of aligned sites = 386 Number in coding regions = 358 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 15 ********** No masking Map Score: 6.21968e-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