AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i164_synecho_ctra_100.orf -o164_synecho_ctra_100.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 RCY50395 244 Synechocystis #2 RCY02336 194 Synechocystis #3 RCY33232 300 Synechocystis #4 RCY47152 92 Synechocystis #5 RCY08136 202 Synechocystis #6 RCY44540 300 Synechocystis #7 RCY35506 141 Synechocystis #8 RCY39748 135 Synechocystis #9 RCY43947 67 Synechocystis #10 RCT00653 300 Chlamydia_trachomatis Motif number 1 TAATTATTTGCTAGGCGATCGCCGAAGGGTTGA 1 160 1 CAGGCGATGC 0.994616 -85 AGCCATGGAACTTTGCCATTGTCTTTG 2 5 0 CTTGCCATGC 0.986101 -190 CCACAATCATCGAGGCGATCGCCATTTGGTAGG 3 146 0 CAGGCGATGC 0.994616 -155 TCCTGCTTAGCATGGGGGTTGTCCTTTCAGTTT 6 34 0 CTGGGGGTGC 0.967588 -267 CGGGAAGTCCCTTGGCCATGGACTAGGGTTAAC 6 101 0 CTGGCCATGC 0.996787 -200 TGCCAATCTACCTTGCCTTGGGCAGTTCCCTAT 6 250 1 CTTGCCTTGC 0.936425 -51 CTCAATAATGCCTGGCGATCGGCCAACTTGCCT 8 51 0 CTGGCGATGC 0.998022 -85 GGGCAGTATCCTTGGAGATGGGCAAAGTGGATT 8 113 0 CTGGAGATGC 0.984953 -23 * ******* * * Masking position 9 Map Score: 12.852 Number of sites scoring better than the average of aligned sites = 1995 Number in coding regions = 1829 Number in noncoding regions = 166 Number of orfs with sites within 600 bp upstream = 173 Fraction of orfs with sites within 600 bp upstream = 0.0277867 Motif number 2 TGTATCTGTGGATTGGTTTCATGAACGGGC 1 58 1 GATTGGTTTC 0.637719 -187 GGCGATCGCCGAAGGGTTGAGGAAGATTAC 1 173 1 GAAGGGTTGA 0.897006 -72 TTGAAACTTAGAAAGGTTAATACTGGTTTT 3 29 1 GAAAGGTTAA 0.703217 -272 CGATTGCGGAGAAAGGTGGCATTGGGGTGA 3 240 0 GAAAGGTGGC 0.952019 -61 CCAGTTAGGGGCTTGGTTGCGTTTGATTTA 5 18 1 GCTTGGTTGC 0.966299 -185 TTAGTCGAAGGAATGGTTGACTCTTTTGCT 5 102 1 GAATGGTTGA 0.928278 -101 TGTAATATAAGCAGGGTAGCAAGGAGCAAA 5 126 0 GCAGGGTAGC 0.905207 -77 ACTGCCCAAGGCAAGGTAGATTGGCAGTGG 6 246 0 GCAAGGTAGA 0.924308 -55 GGGGGTAACTGCTAGGTTTAAGTTTGACCT 7 23 1 GCTAGGTTTA 0.792088 -119 ATGAAAGATAGCTTGGTGAAGAATGAAAAA 7 101 0 GCTTGGTGAA 0.74991 -41 TTCTGTTTCAGCTTGGTTGCGTTATTTTCC 8 13 1 GCTTGGTTGC 0.966299 -123 ATTCTGCTAGGCAAGTTGGCCGATCGCCAG 8 43 1 GCAAGTTGGC 0.765546 -93 TTGGAGATGGGCAAAGTGGATTAGTTTAGT 8 105 0 GCAAAGTGGA 0.70448 -31 ********** Masking position 7 Map Score: 7.83444 Number of sites scoring better than the average of aligned sites = 1160 Number in coding regions = 1071 Number in noncoding regions = 89 Number of orfs with sites within 600 bp upstream = 95 Fraction of orfs with sites within 600 bp upstream = 0.0152586 Motif number 3 ACAAAAGAAGAAGTTTAGCCAAGACCCAATTGTTGCCATAG 2 57 1 AGTAGAAAAT 0.762086 -138 TTGAACTCCTATGCAAAAGTTAGAGGAAAATTAAAAGTAAA 2 156 0 AGAAATAAAT 0.922528 -39 TTCTGAGGGCAACTAAATTTGAAACTTAGAAAGGTT 3 6 1 AGAACAAAAT 0.953575 -295 TAGGGGACAAAAGGTAAAGAAACATAAAATTGTAGCAAAAT 3 109 0 AGAAAAAAAT 0.976012 -192 AGCCGGGGATATGGGAACTGAAAGGATAAATGAGCAGAGGA 4 55 1 AGAACAAAAT 0.953576 -38 TTATCTAGTTTGTTCAAATAAATAGTTAATTTAATGGGATA 5 171 1 TTAAAAAAAT 0.514762 -32 GCCATGGACTAGGGTTAACTAATTGATAATTAGCCGACAAT 6 79 0 AGTAAAAAAT 0.944467 -222 TCAAGGAGCGAAACTAAAACAACAGGTAAGTTGTTTTAATC 6 192 0 AAAAAAAAAT 0.849698 -109 TTAATTATTCAGGAGAAAAATAGGTCAAACTTAAACCTAGC 7 33 0 AGAAATAAAT 0.922527 -109 AAGAATACTAAGGCTAACTAAAAAATCAACTAAAATACCGA 9 24 0 AGAACAAAAT 0.953576 -44 TACAACACAAACAAATAAAAAATCAAAAAATCGCTAGA 10 8 0 AATAAAAAAT 0.702672 -293 GTTGGCTACGAATCGTAAAAAAAATGGAATTTTTCTACAAC 10 43 0 ATTAAAAAAT 0.702672 -258 AAGAAGGTGTTCGAAAAAAATATCTCGAATTGCAGTTCAGG 10 174 1 TGAAATAAAT 0.690837 -127 GTCTCAAAAAAGGCAAAACAAATCCTGAACTGCAATTCGAG 10 197 0 AGAAAAAAAT 0.976012 -104 * * *** ** ** * Masking position 12 Map Score: 10.202 Number of sites scoring better than the average of aligned sites = 260 Number in coding regions = 187 Number in noncoding regions = 73 Number of orfs with sites within 600 bp upstream = 82 Fraction of orfs with sites within 600 bp upstream = 0.0131706 Motif number 4 TTGAGGAAGATTACAATGGGATCAATCCCAT 1 189 1 TTCAATGGGA 0.477699 -56 GATAACACTCTTCCTATGGGATTGATCCCAT 1 204 0 TTCTATGGGA 0.697967 -41 GAATGAGGGATTAGCCATGGAACTTTGCCAT 2 19 0 TTGCCATGGA 0.924738 -176 GACCCAATTGTTGCCATAGGGAATTTCCGCC 2 79 1 TTCCATAGGG 0.580671 -116 TCCTCTAACTTTTGCATAGGAGTTCAAGCCT 2 170 1 TTGCATAGGA 0.919928 -25 CGATCGCCATTTGGTAGGGGACAAAAGGTAA 3 133 0 TTGTAGGGGA 0.939092 -168 TTGAGGAGATTTTGTCATGGAGAATAAAACG 3 268 0 TTGTCATGGA 0.709823 -33 TTGAGCAAAATTAGCCGGGGATATGGGAACT 4 43 1 TTGCCGGGGA 0.984522 -50 AAAGGATAAATGAGCAGAGGAAATCACT 4 75 1 TGGCAGAGGA 0.761196 -18 TCAGAATTGGTAAGCAAGGGAAGATTAGTCG 5 78 1 TAGCAAGGGA 0.764862 -125 GTAATCCTGCTTAGCATGGGGGTTGTCCTTT 6 40 0 TTGCATGGGG 0.945102 -261 GGGAAGTCCCTTGGCCATGGACTAGGGTTAA 6 102 0 TTGCCATGGA 0.924738 -199 GCAAGGTAGATTGGCAGTGGGACGAAATAAA 6 235 0 TTGCAGTGGG 0.936794 -66 GAATGCAGTGTTCTCCGGGGAATTCAGATAG 6 279 0 TTTCCGGGGA 0.820226 -22 TGCCACTCTATTTGGAGTGGAGCTCGTGAGA 10 259 0 TTGGAGTGGA 0.80368 -42 ** ******** Masking position 1 Map Score: 9.69252 Number of sites scoring better than the average of aligned sites = 1896 Number in coding regions = 1714 Number in noncoding regions = 182 Number of orfs with sites within 600 bp upstream = 201 Fraction of orfs with sites within 600 bp upstream = 0.032284 Motif number 5 AACATAAAATTGTAGCAAAATATACTGAAT 3 100 0 TGTAGCAAAA 0.906121 -201 GATTTTGTCATGGAGAATAAAACGATTGCG 3 262 0 TGGAGAATAA 0.92332 -39 CCCGCAAAAGTTGAGCAAAATTAGCCGGGG 4 33 1 TTGAGCAAAA 0.906101 -60 CAGGGTAGCAAGGAGCAAAAGAGTCAACCA 5 115 0 AGGAGCAAAA 0.962594 -88 ATAAATCTCAAGGAGCGAAACTAAAACAAC 6 210 0 AGGAGCGAAA 0.857398 -91 TTAATTATTCAGGAGAAAAATAGGTCAAAC 7 44 0 AGGAGAAAAA 0.952354 -98 CCTAGCAGAATGGAAAATAACGCAACCAAG 8 24 0 TGGAAAATAA 0.70336 -112 TTGTTTGTGTTGTAGAAAAATTCCATTTTT 10 35 1 TGTAGAAAAA 0.882397 -266 GAACACCTTCTTGAAAAAAAAAGAAAGACA 10 156 0 TTGAAAAAAA 0.596367 -145 ********** Masking position 4 Map Score: 4.74345 Number of sites scoring better than the average of aligned sites = 971 Number in coding regions = 822 Number in noncoding regions = 149 Number of orfs with sites within 600 bp upstream = 179 Fraction of orfs with sites within 600 bp upstream = 0.0287504 Motif number 6 TCGCCATATTTTATCGGCAATGATCAGCCA 1 108 1 TTATCGGCAA 0.911235 -137 AGGAAGAGTGTTATCCGTTACCTGATCAAT 1 220 1 TTATCCGTTA 0.736859 -25 ACTTCTTCTTTTGTCGTCAACGAATGAGGG 2 41 0 TTGTCGTCAA 0.915616 -154 GCCTCCCCCGTTGTCGCTAAGATGGAAACT 2 114 1 TTGTCGCTAA 0.774787 -81 TTACTTTTAATTTTCCTCTAACTTTTGCAT 2 157 1 TTTTCCTCTA 0.694865 -38 TCTTTACCTTTTGTCCCCTACCAAATGGCG 3 130 1 TTGTCCCCTA 0.935693 -171 AATGCCACCTTTCTCCGCAATCGTTTTATT 3 247 1 TTCTCCGCAA 0.848017 -54 AACGTTATCCTTTAATCTAAGTCC 4 5 1 TTATCCTTTA 0.587676 -88 CCTAAATTAATTGTCGGCTAATTATCAATT 6 70 1 TTGTCGGCTA 0.975341 -231 AGCAACCCGATTGTTGTCAAAGTGCCAAGG 6 146 0 TTGTTGTCAA 0.730018 -155 AGAAAAAAACTTGTTGGCTACGAATCGTAA 10 66 0 TTGTTGGCTA 0.863696 -235 ********** Masking position 10 Map Score: 4.97511 Number of sites scoring better than the average of aligned sites = 801 Number in coding regions = 707 Number in noncoding regions = 94 Number of orfs with sites within 600 bp upstream = 106 Fraction of orfs with sites within 600 bp upstream = 0.0170254 Motif number 7 AGATTAATATTATCTAAGGATCAAGACTTAC 1 25 0 TATCTAGGAT 0.835561 -220 TAATCTGATGTATCTGTGGATTGGTTTCATG 1 50 1 TATCTGGGAT 0.859869 -195 CCTTCGGCGATCGCCTAGCAAATAATTATCA 1 157 0 TCGCCTGCAA 0.785597 -88 AATGAGGGATTAGCCATGGAACTTTGCCATT 2 18 0 TAGCCAGGAA 0.956448 -177 TGAGCAAAATTAGCCGGGGATATGGGAACTG 4 44 1 TAGCCGGGAT 0.977037 -49 AATGCAGTGTTCTCCGGGGAATTCAGATAGG 6 278 0 TCTCCGGGAA 0.963664 -23 AGTTGGCCGATCGCCAGGCATTATTGAGACA 8 56 1 TCGCCAGCAT 0.951639 -80 ACTTTGCCCATCTCCAAGGATACTGCCC 8 118 1 TCTCCAGGAT 0.972404 -18 ****** **** Masking position 10 Map Score: 3.07442 Number of sites scoring better than the average of aligned sites = 722 Number in coding regions = 638 Number in noncoding regions = 84 Number of orfs with sites within 600 bp upstream = 97 Fraction of orfs with sites within 600 bp upstream = 0.0155798 Motif number 8 GAATTGGTAAGCAAGGGAAGATTAGTCGAA 5 81 1 GCAAGGGAAG 0.90645 -122 AACTATTCTAGCCAGAGTAGAACCTAGATT 7 72 1 GCCAGAGTAG 0.925699 -70 CAACCAAGCTGAAACAGAAGT 8 2 0 GAAACAGAAG 0.879937 -134 ACAGCCTAGGGAAAGAGGATGTCTCTCCCT 10 129 0 GAAAGAGGAT 0.917638 -172 CCTTTTTTGAGACAGAGGAGATAATAGGCT 10 225 1 GACAGAGGAG 0.983527 -76 GCATCCTGATGAAAGAGGAGGATC 10 287 1 GAAAGAGGAG 0.986305 -14 ********** Masking position 4 Map Score: 1.26629 Number of sites scoring better than the average of aligned sites = 142 Number in coding regions = 122 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 9 GGGCGGAAATTCCCTATGGCAACAATTGGG 2 81 0 TCCCTATGGC 0.880203 -114 GGGAATTTCCGCCCACAGCCTCCCCCGTTG 2 97 1 GCCCACAGCC 0.905703 -98 GGGTGAACCTCCCCTAAACCAAACTCAATA 3 216 0 CCCCTAAACC 0.859115 -85 GGGAGGTTCACCCCAATGCCACCTTTCTCC 3 233 1 CCCCAATGCC 0.98161 -68 GAAAGGACAACCCCCATGCTAAGCAGGATT 6 39 1 CCCCCATGCT 0.825748 -262 CTACGGGAAGTCCCTTGGCCATGGACTAGG 6 107 0 TCCCTTGGCC 0.935777 -194 ATTTATTTCGTCCCACTGCCAATCTACCTT 6 234 1 TCCCACTGCC 0.963818 -67 ATAGGGAACTGCCCAAGGCAAGGTAGATTG 6 253 0 GCCCAAGGCA 0.830268 -48 AGGATGTCTCTCCCTAGACCCAAGGAAAGG 10 114 0 TCCCTAGACC 0.948143 -187 ACATCCTCTTTCCCTAGGCTGTCTTTCTTT 10 137 1 TCCCTAGGCT 0.952894 -164 ********** Masking position 4 Map Score: 4.40477 Number of sites scoring better than the average of aligned sites = 2367 Number in coding regions = 2136 Number in noncoding regions = 231 Number of orfs with sites within 600 bp upstream = 249 Fraction of orfs with sites within 600 bp upstream = 0.0399936 Motif number 10 ACTCTTCCTATGGGATTGATCCCATTGTAA 1 199 0 TGGGATTGAT 0.961877 -46 GTATAGTTATTGAGTTTGGTTTAGGGGAGG 3 209 1 TGAGTTTGGT 0.931142 -92 GGGGCTTGGTTGCGTTTGATTTAGCCATTC 5 25 1 TGCGTTTGAT 0.94626 -178 TTTCGGTGATTGAGATTGATCAGAATTGGT 5 59 1 TGAGATTGAT 0.977279 -144 TTTCGCTCCTTGAGATTTATTTCGTCCCAC 6 220 1 TGAGATTTAT 0.891802 -81 ********** Masking position 6 Map Score: 0.522758 Number of sites scoring better than the average of aligned sites = 111 Number in coding regions = 95 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 11 ********** No masking Map Score: -2.46258e-13 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: -2.46258e-13 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: -2.46258e-13 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