AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i326_synecho_ctra_300.orf -o326_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 RCY00022 120 Synechocystis #2 RCY52230 73 Synechocystis #3 RCY02381 135 Synechocystis #4 RCY06056 300 Synechocystis #5 RCT00628 300 Chlamydia_trachomatis #6 RCT00819 300 Chlamydia_trachomatis #7 RCT00820 113 Chlamydia_trachomatis #8 RCT00821 94 Chlamydia_trachomatis Motif number 1 TATAATGTGGGGGCCTCTGCTTTAACCGCC 1 28 0 GGGCCTCTGC 0.948291 -93 ATCTTTTCCTGGGTTTCTGGCTTAAACTGA 1 66 1 GGGTTTCTGG 0.945367 -55 ATATGGGGTTAGGGGTCTGGATCAAATTAA 2 50 0 AGGGGTCTGG 0.9767 -24 CGGCACTACCATGGTTTTGGTGTGAAGATT 3 83 1 ATGGTTTTGG 0.725477 -53 CTGTCTCTCTGGGGCTCCGTTGGGGAACAT 4 86 0 GGGGCTCCGT 0.870575 -215 ACGGGCCCCCAGGGCTTTACCCATGGCCGA 4 181 1 AGGGCTTTAC 0.861442 -120 CAGATTTCCTATGGCTCTGGAGGTTTGGGA 5 59 1 ATGGCTCTGG 0.952002 -242 AAGATGATCTAGGTCTTTGTAAGCTTGTCT 6 71 1 AGGTCTTTGT 0.842655 -230 TTAATAAAAGGGTTCTCTGCCTATTCTAGA 7 51 1 GGTTCTCTGC 0.728361 -63 CCATTCAAAAAGGGGTCTAGAATAGGCAGA 7 66 0 AGGGGTCTAG 0.841362 -48 ATGGAAAAATGGGTTTTTGGAGAACATCGA 7 92 1 GGGTTTTTGG 0.902984 -22 ATAGTAAGAGGGGGCTTTGCGGATTTATGG 8 26 1 GGGGCTTTGC 0.985484 -69 AAATACAACAAGGGCTTTGGGACCATAAAT 8 48 0 AGGGCTTTGG 0.98828 -47 ********** Masking position 6 Map Score: 13.3731 Number of sites scoring better than the average of aligned sites = 1864 Number in coding regions = 1698 Number in noncoding regions = 166 Number of orfs with sites within 600 bp upstream = 174 Fraction of orfs with sites within 600 bp upstream = 0.0279473 Motif number 2 CTCTGGGGCTCCGTTGGGGAACATTTTCGG 4 80 0 CCGTTGGGGA 0.987762 -221 AGACAGTCTGCAGGTTGGAACAGAACGTCT 4 110 1 CAGGTTGGAA 0.829401 -191 TTGGAACAGAACGTCTGGGAACCAGGCTCA 4 124 1 ACGTCTGGGA 0.846583 -177 CCCTGGGGGCCCGTTTGGTAGAATGGGCTA 4 165 0 CCGTTTGGTA 0.948862 -136 GCTTGTCTAGCGGTTGGGGGGAGAGGATGG 4 239 1 CGGTTGGGGG 0.961193 -62 ATGGCTCTGGAGGTTTGGGAGTTGCATGTG 5 69 1 AGGTTTGGGA 0.968771 -232 ATTGAAACAGCAGTTCGGGATTCTTACAGA 5 116 1 CAGTTCGGGA 0.972842 -185 CATTTCTTAACGGTTTGGAAGGTTGAATAA 5 218 1 CGGTTTGGAA 0.984021 -83 TTCCATGATACGGTTCGGAAAAGATTTATT 5 243 0 CGGTTCGGAA 0.976436 -58 ********** Masking position 7 Map Score: 9.18876 Number of sites scoring better than the average of aligned sites = 614 Number in coding regions = 570 Number in noncoding regions = 44 Number of orfs with sites within 600 bp upstream = 48 Fraction of orfs with sites within 600 bp upstream = 0.0077096 Motif number 3 GGAAAACCGTTGAAATGGGCG 1 1 1 GGAAAACCTT 0.966964 -120 TGTTGTTCACGGAAAATCATCGTCGGGACTA 3 14 1 GGAAAATCTC 0.972151 -122 GTGTGGGAAAAATTTCCAGTTCATAA 4 6 1 GGAAAAATTC 0.885541 -295 GCTCCGTTGGGGAACATTTTCGGGCTTGATG 4 72 0 GGAACATTTC 0.783692 -229 CTTCGTCTTTTGAAACCCTTCCATGATACGG 5 260 0 TGAAACCCTC 0.9659 -41 AACTCTACAGTGAAAACCCTCCGATCCTTAA 6 23 0 TGAAAACCTC 0.9804 -278 ACTGTAGAGTTGAAAACTGTTTTTGTGTAAG 6 43 1 TGAAAACTTT 0.817258 -258 TCTTAGTATAGGAAACCCTTCAAAAGAAGGC 6 111 0 GGAAACCCTC 0.986387 -190 ******** ** Masking position 4 Map Score: 5.71627 Number of sites scoring better than the average of aligned sites = 485 Number in coding regions = 425 Number in noncoding regions = 60 Number of orfs with sites within 600 bp upstream = 68 Fraction of orfs with sites within 600 bp upstream = 0.0109219 Motif number 4 GGCAATATGGGGTTAGGGGTC 2 63 0 GCAATATGGG 0.979756 -11 GGAGAGGATGGCAAAATGGAACAACATAAT 4 258 1 GCAAAATGGA 0.954428 -43 AGTTGCATGTGCAACATGTGATAAGTTTAT 5 88 1 GCAACATGTG 0.945602 -213 TCACAGGCTAGCAAAATTGGGGCATGATCT 5 143 0 GCAAAATTGG 0.954191 -158 ATTTTTCCATTCAAAAAGGGGTCTAGAATA 7 72 0 TCAAAAAGGG 0.915819 -42 TTTTTGAATGGAAAAATGGGTTTTTGGAGA 7 85 1 GAAAAATGGG 0.954479 -29 ATGTTTAAATACAACAAGGGCTTTGGGACC 8 54 0 ACAACAAGGG 0.900194 -41 ********** Masking position 6 Map Score: 3.97926 Number of sites scoring better than the average of aligned sites = 494 Number in coding regions = 442 Number in noncoding regions = 52 Number of orfs with sites within 600 bp upstream = 60 Fraction of orfs with sites within 600 bp upstream = 0.00963701 Motif number 5 AGCCAGAAACCCAGGAAAAGATCCCTTGGT 1 58 0 CCAGGAAAAG 0.923991 -63 ATTTTTTTCCCCCGGCGATCGCCT 1 107 1 CCCGGCGATC 0.943925 -14 GGCAGAGGTGCCAGGAGAGG 2 1 0 CCAGGAGAGG 0.963152 -73 CGGCCATAGTCCCGACGATGATTTTCCGTG 3 21 0 CCCGACGATG 0.963634 -115 CCCCATCAAGCCCGAAAATGTTCCCCAACG 4 69 1 CCCGAAAATG 0.897579 -232 CGTCTGGGAACCAGGCTCAGTCAAGATTGC 4 135 1 CCAGGCTCAG 0.830541 -166 ATACTAAGAACTCGGAGATGAGTCCAGGAT 6 133 1 CTCGGAGATG 0.932292 -168 GGAGATGAGTCCAGGATCTGTGTATAAGGT 6 146 1 CCAGGATCTG 0.905056 -155 ACACCAAGAGCCCGCAGAAGCTTAGGCAAA 6 239 0 CCCGCAGAAG 0.94392 -62 ********** Masking position 1 Map Score: 4.27865 Number of sites scoring better than the average of aligned sites = 1160 Number in coding regions = 1079 Number in noncoding regions = 81 Number of orfs with sites within 600 bp upstream = 99 Fraction of orfs with sites within 600 bp upstream = 0.0159011 Motif number 6 CATCGTCGGGACTATGGCCGCAACGAACCT 3 31 1 ACTATGGCCG 0.988496 -105 TCACACCAAAACCATGGTAGTGCCGCCGCC 3 78 0 ACCATGGTAG 0.942744 -58 CAGGGCTTTACCCATGGCCGAAAAATCGAG 4 190 1 CCCATGGCCG 0.991696 -111 AAGCTCAAAGCCCATTGCCGTTGCTCGATT 4 213 0 CCCATTGCCG 0.939356 -88 TCCGAACCGTATCATGGAAGGGTTTCAAAA 5 254 1 ATCATGGAAG 0.817906 -47 GTAGTCGAAAAGTATGGCAGAGTTTCTTTA 7 12 1 AGTATGGCAG 0.905115 -102 GCCCCCTCTTACTATGAACGAAAACGCCAG 8 11 0 ACTATGAACG 0.790182 -84 ********** Masking position 4 Map Score: 2.03969 Number of sites scoring better than the average of aligned sites = 1186 Number in coding regions = 1089 Number in noncoding regions = 97 Number of orfs with sites within 600 bp upstream = 108 Fraction of orfs with sites within 600 bp upstream = 0.0173466 Motif number 7 AGAATTCTTATTTTTGCTTAAACAAT 3 120 1 TTTTTGCTAA 0.952497 -16 AAATAAATAGTTTGTTTGTAACAAATCGGAA 5 13 0 TTTGTTTTAA 0.7866 -288 GTTGAATAAATCTTTTCCGAACCGTATCATG 5 239 1 TCTTTTCGAA 0.750095 -62 GTTTCTTTTTTATTAAGGATCGGAGG 6 6 1 TTTTTTATAA 0.840311 -295 TTGAAAACTGTTTTTGTGTAAGATGATCTAG 6 52 1 TTTTTGTTAA 0.906616 -249 GAGTCCAGGATCTGTGTATAAGGTTGGATTC 6 152 1 TCTGTGTTAA 0.796513 -149 AAGTCTTGTGTTTTCTCGTAATTATTTTTGC 6 213 1 TTTTCTCTAA 0.784433 -88 CTCGTAATTATTTTTGCCTAAGCTTCTGCGG 6 227 1 TTTTTGCTAA 0.952491 -74 CTTTAAAAATTCTTTTAATAAAAGGGTTCTC 7 37 1 TCTTTTATAA 0.812755 -77 ******* *** Masking position 3 Map Score: 1.68827 Number of sites scoring better than the average of aligned sites = 263 Number in coding regions = 189 Number in noncoding regions = 74 Number of orfs with sites within 600 bp upstream = 87 Fraction of orfs with sites within 600 bp upstream = 0.0139737 Motif number 8 GCTTAAACTGAGGCTGACCATCATTTTTTT 1 85 1 AGGCTGACCA 0.92919 -36 GGGCTTGATGGGGTTAACAATCCTATGCCG 4 52 0 GGGTTAACAA 0.938778 -249 TTGGTAGAATGGGCTAGCAATCTTGACTGA 4 151 0 GGGCTAGCAA 0.969684 -150 TTGGGGGGAGAGGATGGCAAAATGGAACAA 4 252 1 AGGATGGCAA 0.935895 -49 CGGGCTTCACAGGCTAGCAAAATTGGGGCA 5 149 0 AGGCTAGCAA 0.972499 -152 CCGTTAAGAAATGTTAACAAAACTATCTAA 5 201 0 ATGTTAACAA 0.745574 -100 ********** Masking position 5 Map Score: 0.757853 Number of sites scoring better than the average of aligned sites = 333 Number in coding regions = 276 Number in noncoding regions = 57 Number of orfs with sites within 600 bp upstream = 69 Fraction of orfs with sites within 600 bp upstream = 0.0110826 Motif number 9 GTGGGGGCCTCTGCTTTAACCGCCCATTTC 1 22 0 CTGCTTTAAC 0.976924 -99 CCTGGGTTTCTGGCTTAAACTGAGGCTGAC 1 73 1 TGGCTTAAAC 0.92383 -48 ATTCTTATTTTTGCTTAAACAAT 3 123 1 TTGCTTAAAC 0.964188 -13 CATAGGAAATCTGCTTAAAGGTTTGGCTAA 5 42 0 CTGCTTAAAG 0.976546 -259 AGACGAAGTCCTGTTTTAAGGAGGCTTG 5 283 1 CTGTTTTAAG 0.847765 -18 ********** Masking position 5 Map Score: 0.344128 Number of sites scoring better than the average of aligned sites = 119 Number in coding regions = 100 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 10 TTGGTTATAATGTGGGGGCCTCTGCTTTAA 1 33 0 TGTGGGGGCC 0.988692 -88 ATGATAGGTTCGTTGCGGCCATAGTCCCGA 3 36 0 CGTTGCGGCC 0.988666 -100 TTTTAGTCTTTTTGGCGGCGGCACTACCAT 3 65 1 TTTGGCGGCG 0.9489 -71 TGGGTAAAGCCCTGGGGGCCCGTTTGGTAG 4 174 0 CCTGGGGGCC 0.98679 -127 CGTTGCTCGATTTTTCGGCCATGGGTAAAG 4 195 0 TTTTTCGGCC 0.888495 -106 ACAACAAGGGCTTTGGGACCATAAATCCGC 8 44 0 CTTTGGGACC 0.926087 -51 ********** Masking position 3 Map Score: 1.95077 Number of sites scoring better than the average of aligned sites = 897 Number in coding regions = 853 Number in noncoding regions = 44 Number of orfs with sites within 600 bp upstream = 56 Fraction of orfs with sites within 600 bp upstream = 0.00899454 Motif number 11 TATAACCAAGGGATCTTTTCCTGGGTTTCT 1 54 1 GGATCTTTTC 0.918994 -67 CAATGGGCTTTGAGCTTGTCTAGCGGTTGG 4 226 1 TGAGCTTGTC 0.978296 -75 CCCGGCAGGTGGTTCTTCTCGAAAGTTTAG 5 175 1 GGTTCTTCTC 0.921475 -126 TAGGTCTTTGTAAGCTTGTCTTTTGGATAG 6 80 1 TAAGCTTGTC 0.896238 -221 CTCAGAGTAAGGTGCTTGTCGAGGTCTTT 6 282 1 GGTGCTTGTC 0.986087 -19 ********** Masking position 6 Map Score: 0.155808 Number of sites scoring better than the average of aligned sites = 109 Number in coding regions = 81 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 12 ********** No masking Map Score: 1.86405e-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 AAATAAGAATTCTATTTAACAATCTTCACAC 3 102 0 TCTATTAACA 0.759082 -34 AAACAAACTATTTATTTAGCCAAACCTTTAA 5 27 1 TTTATTAGCC 0.939468 -274 ATGTGATAAGTTTATTGAAACAGCAGTTCGG 5 103 1 TTTATTAAAC 0.950486 -198 TCGGAAAAGATTTATTCAACCTTCCAAACCG 5 228 0 TTTATTAACC 0.949536 -73 GTTTCTTTTTTATTAAGGATCGGAGGGTT 6 9 1 TTTATTAGGA 0.784949 -292 CTCTGAGGACTTTATTCAGAACACCAAGAGC 6 258 0 TTTATTAGAA 0.908947 -43 TATGGCAGAGTTTCTTTAAAAATTCTTTTAA 7 24 1 TTTCTTAAAA 0.738734 -90 AGAGAACCCTTTTATTAAAAGAATTTTTAAA 7 38 0 TTTATTAAAG 0.844996 -76 AAGCCCTTGTTGTATTTAAACATTAATAAAT 8 61 1 TGTATTAAAC 0.836031 -34 ****** **** Masking position 6 Map Score: 1.2484 Number of sites scoring better than the average of aligned sites = 151 Number in coding regions = 118 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 14 ********** No masking Map Score: 1.86405e-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 15 ********** No masking Map Score: 1.86405e-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