AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i164_synecho_ctra_300.orf -o164_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 RCY50395 244 Synechocystis #2 RCY05450 300 Synechocystis #3 RCY38242 51 Synechocystis #4 RCY51764 52 Synechocystis #5 RCY11976 132 Synechocystis #6 RCY02336 194 Synechocystis #7 RCY33232 300 Synechocystis #8 RCY47152 92 Synechocystis #9 RCY08136 202 Synechocystis #10 RCY44540 300 Synechocystis #11 RCY35506 141 Synechocystis #12 RCY39748 135 Synechocystis #13 RCY43947 67 Synechocystis #14 RCT00653 300 Chlamydia_trachomatis Motif number 1 TCCTCAACCCTTCGGCGATCGCCTAGCAAATAAT 1 162 0 TGCGATGCCT 0.632697 -83 CAGAGTGTGACACCGCCAACTCCATCGTCCGAGG 2 13 0 CGCCAATCCA 0.84191 -288 TCAAGGACCACCTACCCTAAGCCAGAAGCGATCA 2 97 1 CCCCTAGCCA 0.968478 -204 GTTTTTTGTTTTTTGCCTAGACCCCCAACAAGGA 2 157 1 TGCCTAACCC 0.73807 -144 GGCAATTTTCTTTGGCGATCGCCAGGGGGATTGC 2 193 0 TGCGATGCCA 0.935062 -108 GTTAGGTTCTCCCAAGGCCATGGCCACAAA 3 7 1 TCCCAAGCCA 0.983719 -45 CACAAAAAATTGGAGCGATCACCATCC 3 35 1 TGCGATACCA 0.785688 -17 GTGGGTCTTGATCCGCCGTTGCCAATG 4 36 1 AGCCGTGCCA 0.738234 -17 GGTGTTAATTTATGGCCTTTGCCAATAAATTTTG 5 57 1 TGCCTTGCCA 0.975821 -76 ATTTTGCTAGAAGTACCATTGCCATCAATTTCTT 5 85 1 AACCATGCCA 0.620892 -48 TTTCTTGATTTTTTCCCTTGACCAAACCCT 5 113 1 TCCCTTACCA 0.934678 -20 AAAGAAGAAGTTTAGCCAAGACCCAATTGTTGCC 6 60 1 TGCCAAACCC 0.796378 -135 TGTGGGCGGAAATTCCCTATGGCAACAATTGGGT 6 80 0 ACCCTAGGCA 0.604041 -115 ATAGGGAATTTCCGCCCACAGCCTCCCCCGTTGT 6 94 1 TCCCACGCCT 0.7147 -101 CCACAATCATCGAGGCGATCGCCATTTGGTAGGG 7 145 0 CGCGATGCCA 0.910414 -156 TTGGGGTGAACCTCCCCTAAACCAAACTCAATAA 7 215 0 CCCCTAACCA 0.886652 -86 TAGGGGAGGTTCACCCCAATGCCACCTTTCTCCG 7 230 1 TCCCAAGCCA 0.983719 -71 TTATCCTTTCAGTTCCCATATCCCCGGCTAATTT 8 50 0 ACCCATTCCC 0.640555 -43 TATCAATTAGTTAACCCTAGTCCATGGCCAAGGG 10 92 1 TCCCTATCCA 0.883322 -209 CTCCTACGGGAAGTCCCTTGGCCATGGACTAGGG 10 106 0 ACCCTTGCCA 0.954242 -195 GAGATTTATTTCGTCCCACTGCCAATCTACCTTG 10 231 1 TCCCACGCCA 0.954423 -70 TGCCAATCTACCTTGCCTTGGGCAGTTCCCTATC 10 250 1 CGCCTTGGCA 0.728988 -51 GCTAGGCAAGTTGGCCGATCGCCAGGCATTATTG 12 48 1 TCCGATGCCA 0.952498 -88 ACTAATCCACTTTGCCCATCTCCAAGGATACTGC 12 110 1 TCCCATTCCA 0.931344 -26 AAGAGGATGTCTCTCCCTAGACCCAAGGAAAGGA 14 113 0 CCCCTAACCC 0.734703 -188 * ***** **** Masking position 6 Map Score: 28.86 Number of sites scoring better than the average of aligned sites = 5281 Number in coding regions = 4868 Number in noncoding regions = 413 Number of orfs with sites within 600 bp upstream = 407 Fraction of orfs with sites within 600 bp upstream = 0.065371 Motif number 2 AAGGTATCGCCATATTTTATCGGCAATGATCAGCCA 1 102 1 CAATTCGGCA 0.987225 -143 GTGATCTTGGCAATTTTCTTTGGCGATCGCCAGGGG 2 199 0 CATTTTGGCA 0.985557 -102 GTGATCGCTCCAATTTTTTGTGGCCATGGCCTTGGG 3 21 0 CATTTTGGCA 0.985557 -31 GTACTTCTAGCAAAATTTATTGGCAAAGGCCATAAA 5 65 0 CAATTTGGCA 0.989467 -68 GGAAAAAATCAAGAAATTGATGGCAATGGTACTTCT 5 93 0 AAAATTGGCA 0.923479 -40 AAGACAATGGCAAAGTTCCATGGCTAATCCCTCATT 6 13 1 CAATTTGGCA 0.989467 -182 AAAAGTTGAGCAAAATTAGCCGGGGATATGGGAACT 8 38 1 CAATTCGGGA 0.943208 -55 TCAATCACCGAAAACTTGAATGGCTAAATCAAACGC 9 36 0 AAATTTGGCA 0.968049 -167 GGATTACCTAAATTAATTGTCGGCTAATTATCAATT 10 64 1 AATATCGGCA 0.878224 -237 CGAATGCAGTGTTCTCCGGGGAATTCAGATAG 10 279 0 CATTTCGGGA 0.923455 -22 CAAATTGTCTCAATAATGCCTGGCGATCGGCCAACT 12 56 0 CATATTGGCA 0.964513 -80 CCCTTAAGAAAAAAACTTGTTGGCTACGAATCGTAA 14 66 0 AAACTTGGCA 0.876222 -235 ** * ** **** * Masking position 2 Map Score: 16.9155 Number of sites scoring better than the average of aligned sites = 246 Number in coding regions = 198 Number in noncoding regions = 48 Number of orfs with sites within 600 bp upstream = 47 Fraction of orfs with sites within 600 bp upstream = 0.00754899 Motif number 3 TCGCCATATTTTATCGGCAATGATCAGCCAAA 1 108 1 TTATCGCAAG 0.96198 -137 CTCCAATTTTTTGTGGCCATGGCCTTGGGAGA 3 18 0 TTGTGGCATG 0.876228 -34 CTAGCAAAATTTATTGGCAAAGGCCATAAATT 5 63 0 TTATTGCAAG 0.951581 -70 AATCAAGAAATTGATGGCAATGGTACTTCTAG 5 91 0 TTGATGCAAG 0.916529 -42 ACTTCTTCTTTTGTCGTCAACGAATGAGGGAT 6 39 0 TTGTCGCAAG 0.988972 -156 CAAGACCCAATTGTTGCCATAGGGAATTTCCG 6 76 1 TTGTTGCATG 0.950886 -119 AGTTTCCATCTTAGCGACAACGGGGGAGGCTG 6 112 0 TTAGCGCAAG 0.855318 -83 CCTAAATTAATTGTCGGCTAATTATCAATTAG 10 70 1 TTGTCGCTAT 0.685321 -231 AGCAACCCGATTGTTGTCAAAGTGCCAAGGTC 10 144 0 TTGTTGCAAG 0.985846 -157 AGAAAAAAACTTGTTGGCTACGAATCGTAAAA 14 64 0 TTGTTGCTAG 0.950889 -237 ****** *** * Masking position 2 Map Score: 9.85365 Number of sites scoring better than the average of aligned sites = 380 Number in coding regions = 345 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 4 ATAATTATTTGCTAGGCGATCGCCGAAGGGT 1 159 1 GCAGGCGATC 0.983812 -86 CAACGGTCTTCCTTGGTAATCAAGGACCACC 2 78 1 CCTGGTAATC 0.8791 -223 TCTGGCTTAGGGTAGGTGGTCCTTGATTACC 2 92 0 GGAGGTGGTC 0.883674 -209 CCCCCAACAAGGACGGCAATCCCCCTGGCGA 2 178 1 GGCGGCAATC 0.9633 -123 ACGGCAATCCCCCTGGCGATCGCCAAAGAAA 2 190 1 CCTGGCGATC 0.970231 -111 GAATCAGCCACCTAGGTGATCTTGGCAATTT 2 219 0 CCAGGTGATC 0.900784 -82 GGATGGTGATCGCTCCAATTT 3 41 0 GGTGGTGATC 0.973805 -11 TAGGACAATTGCTCGACAATCTTTCTAAAAA 7 55 0 GCCGACAATC 0.714702 -246 GCCACAATCATCGAGGCGATCGCCATTTGGT 7 149 0 TCAGGCGATC 0.828743 -152 GAACCGATGCGTGGCAGTCCAGTAAACTG 10 9 1 GCTGGCAGTC 0.943012 -292 AAAGTGCCAAGGTCGGTGCTCCTACGGGAAG 10 127 0 GGCGGTGCTC 0.901619 -174 ACAACAATCGGGTTGCTAATCTATTCTAGAA 10 159 1 GGTGCTAATC 0.774303 -142 TCTCAATAATGCCTGGCGATCGGCCAACTTG 12 54 0 GCTGGCGATC 0.989312 -82 TCTTTCATCAGGATGCCACTCTATTTGGAGT 14 272 0 GGTGCCACTC 0.715507 -29 ** ******** Masking position 10 Map Score: 13.2422 Number of sites scoring better than the average of aligned sites = 3489 Number in coding regions = 3201 Number in noncoding regions = 288 Number of orfs with sites within 600 bp upstream = 288 Fraction of orfs with sites within 600 bp upstream = 0.0462576 Motif number 5 GGATTCTTAGTTTTTTGTTTTTTGCCTAGACC 2 148 1 TTTTTGTTTT 0.959905 -153 TTGTGCTCGGTTCGGTGTTTTTAGGTGTTAAT 5 34 1 TTGGTGTTTT 0.846517 -99 TTGCCATCAATTTCTTGATTTTTTCCCTTGAC 5 103 1 TTCTTGTTTT 0.880476 -30 AGTTAGGGGCTTGGTTGCGTTTGATTTAGCCA 9 20 1 TTGTTGGTTT 0.973834 -183 AACTTACCTGTTGTTTTAGTTTCGCTCCTTGA 10 201 1 TTTTTTGTTT 0.859592 -100 CTGTTTCAGCTTGGTTGCGTTATTTTCCATTC 12 15 1 TTGTTGGTTA 0.902289 -121 GCAAAGTGGATTAGTTTAGTTAGTGCAGTAGC 12 93 0 TTGTTTGTTA 0.670889 -43 ACTCGGTATTTTAGTTGATTTTTTAGTTAGCC 13 22 1 TTGTTGTTTT 0.969814 -46 AGCCTTAGTATTCTTTGATTTTTAAGCC 13 50 1 TTTTTGTTTT 0.959905 -18 TCTAGCGATTTTTTGATTTTTTATTTGTTT 14 9 1 TTTTTGTTTT 0.959905 -292 GATTTTTTATTTGTTTGTGTTGTAGAAAAATT 14 25 1 TTTTTGGTTG 0.852587 -276 TAGGCTGTCTTTCTTTTTTTTTCAAGAAGGTG 14 151 1 TTTTTTTTTT 0.84089 -150 ** **** **** Masking position 6 Map Score: 9.60595 Number of sites scoring better than the average of aligned sites = 254 Number in coding regions = 198 Number in noncoding regions = 56 Number of orfs with sites within 600 bp upstream = 54 Fraction of orfs with sites within 600 bp upstream = 0.00867331 Motif number 6 AAGGACGGCAATCCCCCTGGCGATCGCCAAAGAA 2 186 1 ACCCCGGCAT 0.802804 -115 ATTCTGATCATTATCCAAGGCCTACCAGTTGCCC 2 246 1 TTCCAGGCTA 0.713925 -55 GTTAGGTTCTCCCAAGGCCATGGCCACAAAA 3 8 1 TCCCAGGCAT 0.675931 -44 GTGTTAATTTATGGCCTTTGCCAATAAATTTTGC 5 58 1 AGCCTTGCAA 0.608556 -75 TTTCTTGATTTTTTCCCTTGACCAAACCCT 5 113 1 TTCCCTGACA 0.401306 -20 ACAATGGCAAAGTTCCATGGCTAATCCCTCATTC 6 16 1 ATCCAGGCAA 0.955504 -179 GTTAGGCTTGAACTCCTATGCAAAAGTTAGAGGA 6 170 0 ATCCTTGCAA 0.909228 -25 TCTTTACCTTTTGTCCCCTACCAAATGGCGATCG 7 130 1 TTCCCTACAA 0.735629 -171 AATCGTTTTATTCTCCATGACAAAATCTCCTCAA 7 265 1 TTCCAGACAA 0.710496 -36 TTCAGTTCCCATATCCCCGGCTAATTTTGCTCAA 8 43 0 ATCCCGGCAA 0.978472 -50 AGTGATTTCCTCTGCTCATTTATCCTTT 8 75 0 ATCCTTGCCA 0.729011 -18 CTTCGACTAATCTTCCCTTGCTTACCAATTCTGA 9 78 0 TTCCCTGCTA 0.828694 -125 CTGAAAGGACAACCCCCATGCTAAGCAGGATTAC 10 37 1 ACCCCTGCAA 0.951744 -264 TAGTTAACCCTAGTCCATGGCCAAGGGACTTCCC 10 99 1 TTCCAGGCAA 0.907299 -202 AGATTTATTTCGTCCCACTGCCAATCTACCTTGC 10 232 1 CCCCATGCAA 0.719365 -69 TCCCTATCTGAATTCCCCGGAGAACACTGCATTC 10 276 1 ATCCCGGAAA 0.824017 -25 TTTTCTCACGAGCTCCACTCCAAATAGAGTGGCA 14 256 1 ATCCATCCAA 0.649873 -45 * **** *** ** Masking position 6 Map Score: 9.44322 Number of sites scoring better than the average of aligned sites = 2366 Number in coding regions = 2152 Number in noncoding regions = 214 Number of orfs with sites within 600 bp upstream = 237 Fraction of orfs with sites within 600 bp upstream = 0.0380662 Motif number 7 TGTTTTTTGCCTAGACCCCCAACAAGGACG 2 163 1 CTAGACCCCC 0.959347 -138 AACGGCGGATCAAGACCCACAAATCACGAC 4 26 0 CAAGACCCAC 0.98824 -27 GAAGTTTAGCCAAGACCCAATTGTTGCCAT 6 66 1 CAAGACCCAA 0.985834 -129 CGAAGTTGATCAAGCCACAATCATCGAGGC 7 163 0 CAAGCCACAA 0.85864 -138 AACTCAATAACTATACCCACATCTAATGAC 7 195 0 CTATACCCAC 0.893292 -106 CAAACGCAACCAAGCCCCTAACTGGCGAAG 9 13 0 CAAGCCCCTA 0.920337 -190 ATGTCTCTCCCTAGACCCAAGGAAAGGACT 14 111 0 CTAGACCCAA 0.981633 -190 ********** Masking position 3 Map Score: 5.75206 Number of sites scoring better than the average of aligned sites = 192 Number in coding regions = 166 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 8 AATGATAATTATTTGCTAGGCGATCGCCGA 1 155 1 ATTTGCTAGG 0.919039 -90 AATTGCCAAGATCACCTAGGTGGCTGATTC 2 220 1 ATCACCTAGG 0.803899 -81 GGATAGGGGCAACTGGTAGGCCTTGGATAA 2 256 0 AACTGGTAGG 0.958733 -45 GTTAGGCTTGAACTCCTATGCAAAAGTTAG 6 174 0 AACTCCTATG 0.71794 -21 GGCGATCGCCATTTGGTAGGGGACAAAAGG 7 136 0 ATTTGGTAGG 0.800644 -165 GGGATATGGGAACTGAAAGGATAAATGAGC 8 60 1 AACTGAAAGG 0.871809 -33 CAGTCCAGTAAACTGAAAGGACAACCCCCA 10 25 1 AACTGAAAGG 0.871809 -276 GAAGGGGGGTAACTGCTAGGTTTAAGTTTG 11 19 1 AACTGCTAGG 0.985 -123 TTATTTTCCATTCTGCTAGGCAAGTTGGCC 12 34 1 TTCTGCTAGG 0.902341 -102 CACTTTGCCCATCTCCAAGGATACTGCCC 12 117 1 ATCTCCAAGG 0.929538 -19 ********** Masking position 8 Map Score: 6.12555 Number of sites scoring better than the average of aligned sites = 341 Number in coding regions = 303 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 48 Fraction of orfs with sites within 600 bp upstream = 0.0077096 Motif number 9 GCGAAATTTGGCTGATCATTGCCGATAAAA 1 116 0 GCTGATCATT 0.963883 -129 TTATCCGTTACCTGATCAATGTGCC 1 230 1 CCTGATCAAT 0.949386 -15 GGTGGCTGATTCTGATCATTATCCAAGGCC 2 238 1 TCTGATCATT 0.978148 -63 AGTGATTTCCTCTGCTCATTTATCCTTTCA 8 73 0 TCTGCTCATT 0.954504 -20 GCTTACCAATTCTGATCAATCTCAATCACC 9 63 0 TCTGATCAAT 0.969337 -140 ********** Masking position 6 Map Score: 2.43714 Number of sites scoring better than the average of aligned sites = 49 Number in coding regions = 42 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 10 TGGGATCAATCCCATAGGAAGAGTGTTATCC 1 205 1 CCCAAGGAAG 0.921583 -40 GCGGAAATTCCCTATGGCAACAATTGGGTCT 6 78 0 CCTAGGCAAC 0.927681 -117 GGTCGGTGCTCCTACGGGAAGTCCCTTGGCC 10 117 0 CCTAGGGAAG 0.987219 -184 TAGGGAACTGCCCAAGGCAAGGTAGATTGGC 10 251 0 CCCAGGCAAG 0.987007 -50 TCAGAAATAACTTAATGAAAGATAGCTTGGT 11 114 0 CTTATGAAAG 0.740032 -28 TCTCCCTAGACCCAAGGAAAGGACTGTCAAA 14 105 0 CCCAGGAAAG 0.989205 -196 AGAAAGACAGCCTAGGGAAAGAGGATGTCTC 14 134 0 CCTAGGAAAG 0.989416 -167 AGAGTGGCATCCTGATGAAAGAGGAGGATC 14 281 1 CCTGTGAAAG 0.871318 -20 **** ****** Masking position 9 Map Score: 5.20639 Number of sites scoring better than the average of aligned sites = 314 Number in coding regions = 282 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 11 GCCATATTTTATCGGCAATGATCAGCCAAA 1 110 1 ATCGGCAATG 0.938292 -135 ATTTCGCCCAGTTTGCAATGATAATTATTT 1 139 1 GTTTGCAATG 0.788549 -106 CATTGGCAACGGCGGATCAAG 4 42 0 ATTGGCAACG 0.977118 -11 AGCAAAATTTATTGGCAAAGGCCATAAATT 5 63 0 ATTGGCAAAG 0.972433 -70 TCAAGAAATTGATGGCAATGGTACTTCTAG 5 91 0 GATGGCAATG 0.921709 -42 CAAAGACAATGGCAAAGTTCCATGGCT 6 8 1 AATGGCAAAG 0.897632 -187 TTCTTCTTTTGTCGTCAACGAATGAGGGAT 6 39 0 GTCGTCAACG 0.791512 -156 CAACCCGATTGTTGTCAAAGTGCCAAGGTC 10 144 0 GTTGTCAAAG 0.879683 -157 GGCAAGGTAGATTGGCAGTGGGACGAAATA 10 237 0 ATTGGCAGTG 0.869443 -64 ATCCTTGGAGATGGGCAAAGTGGATTAGTT 12 109 0 ATGGGCAAAG 0.892038 -27 AAAAAAACTTGTTGGCTACGAATCGTAAAA 14 64 0 GTTGGCTACG 0.879255 -237 ********** Masking position 6 Map Score: 9.39163 Number of sites scoring better than the average of aligned sites = 1102 Number in coding regions = 1022 Number in noncoding regions = 80 Number of orfs with sites within 600 bp upstream = 89 Fraction of orfs with sites within 600 bp upstream = 0.0142949 Motif number 12 CCAAACTCCATTTCTCACCTTGCTAGTAGT 2 47 0 TTTCTCACCT 0.681911 -254 ATTCAGTATATTTTGCTACAATTTTATGTT 7 100 1 TTTTGCTACA 0.884332 -201 CGCAATCGTTTTATTCTCCATGACAAAATC 7 262 1 TTATTCTCCA 0.791048 -39 CCCCGGCTAATTTTGCTCAACTTTTGCGGG 8 33 0 TTTTGCTCAA 0.788858 -60 TGGTTGACTCTTTTGCTCCTTGCTACCCTG 9 115 1 TTTTGCTCCT 0.971021 -88 GTTGTTTTAGTTTCGCTCCTTGAGATTTAT 10 210 1 TTTCGCTCCT 0.949936 -91 GTTTGACCTATTTTTCTCCTGAATAATTAA 11 44 1 TTTTTCTCCT 0.954803 -98 AAAAATGGAATTTTTCTACAACACAAACAA 14 35 0 TTTTTCTACA 0.828523 -266 ********** Masking position 2 Map Score: 2.82747 Number of sites scoring better than the average of aligned sites = 561 Number in coding regions = 465 Number in noncoding regions = 96 Number of orfs with sites within 600 bp upstream = 116 Fraction of orfs with sites within 600 bp upstream = 0.0186315 Motif number 13 TGTGACACCGCCAACTCCATCGTCCGAGGG 2 12 0 CCAACTCCAT 0.942385 -289 GACCGTTGCCCAAACTCCATTTCTCACCTT 2 56 0 CAAACTCCAT 0.978134 -245 TCCCCTAAACCAAACTCAATAACTATACCC 7 207 0 CAAACTCAAT 0.966577 -94 CAATTCTGATCAATCTCAATCACCGAAAAC 9 57 0 CAATCTCAAT 0.877068 -146 TTTATTTGAACAAACTAGATAATTATTCCA 9 163 0 CAAACTAGAT 0.873743 -40 TCAGTCAGCAAACTCGGTATTTTAGTTG 13 9 1 CAAACTCGGT 0.942385 -59 ********** Masking position 6 Map Score: 1.93345 Number of sites scoring better than the average of aligned sites = 107 Number in coding regions = 93 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 14 ********** No masking Map Score: -3.65686e-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: -3.65686e-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