AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i254_synecho_ctra_300.orf -o254_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 RCY29546 300 Synechocystis #2 RCY03338 300 Synechocystis #3 RCY11382 300 Synechocystis #4 RCY49571 65 Synechocystis #5 RCY41531 22 Synechocystis #6 RCT00472 300 Chlamydia_trachomatis #7 RCT00473 293 Chlamydia_trachomatis #8 RCT00554 300 Chlamydia_trachomatis #9 RCT00653 300 Chlamydia_trachomatis #10 RCT00657 135 Chlamydia_trachomatis Motif number 1 GTCTTCTTCAAAAAGAGAAGATGAACGATT 1 35 1 AAAAGAGAAG 0.865058 -266 CAAGGGGAGTAAAAAAAAGCATAGGTTCCC 2 60 1 AAAAAAAAGC 0.884244 -241 ATGCTTTTCAAAAAAAAAACTCTCGTGTAA 6 107 0 AAAAAAAAAC 0.914739 -194 CTTGCTTCCTAAAAAAGAAGTTGACTGTCT 6 150 1 AAAAAAGAAG 0.927 -151 ATACACTTTGAGAAGAAAACCTATGAGGAT 7 77 1 AGAAGAAAAC 0.882115 -217 TAAACCATTAAGAAGAAAACCATGTCATCT 7 175 1 AGAAGAAAAC 0.882115 -119 TCATCTGTTAAGAAAAAACGAAGACTTAAG 7 199 1 AGAAAAAACG 0.893797 -95 CATAAGCGTAAAAAAAGACGTCGAAGAGAT 7 238 1 AAAAAAGACG 0.86125 -56 CCAATAATATAGAAAAGAGGTATCTGGAGA 8 151 1 AGAAAAGAGG 0.925881 -150 TACGAATCGTAAAAAAAATGGAATTTTTCT 9 48 0 AAAAAAAATG 0.690715 -253 ACAGCCCTTAAGAAAAAAACTTGTTGGCTA 9 76 0 AGAAAAAAAC 0.9368 -225 CACCTTCTTGAAAAAAAAAGAAAGACAGCC 9 153 0 AAAAAAAAAG 0.925716 -148 GGAGCTCGTGAGAAAAGAGCCTATTATCTC 9 242 0 AGAAAAGAGC 0.914925 -59 ********** Masking position 6 Map Score: 12.6337 Number of sites scoring better than the average of aligned sites = 317 Number in coding regions = 223 Number in noncoding regions = 94 Number of orfs with sites within 600 bp upstream = 97 Fraction of orfs with sites within 600 bp upstream = 0.0155798 Motif number 2 TATGCTTTTTTTTACTCCCCTTGGGGTCAA 2 53 0 TTTACTCCCC 0.91175 -248 AAATTTTATCTTCCTTTCCCATAAGTCTAA 3 62 0 TTCCTTTCCC 0.91175 -239 TTTGCGGGGCTTCATTTCCCCGGTCTTGGT 3 240 1 TTCATTTCCC 0.769177 -61 ACCACTCAGTCATCTTTCCAACGAAACAAC 6 49 1 CATCTTTCCA 0.733638 -252 AAACGATATTTTTCTTCCCCTCCCCTTTCC 6 203 1 TTTCTTCCCC 0.989296 -98 CTCTTGAGGATATATTCCCCTATACCCTAA 6 232 1 TATATTCCCC 0.880904 -69 ACAAGTTTATTCCCAAAAATTGACA 7 6 1 TTTATTCCCA 0.931004 -288 CCATTGTAAACTTCTTCCCATCGCCTGGTG 7 37 1 CTTCTTCCCA 0.971764 -257 CCTCATAGGTTTTCTTCTCAAAGTGTATCG 7 75 0 TTTCTTCTCA 0.750109 -219 CTATACGATTTTTCTTCCCATGGTAGTTGC 8 49 1 TTTCTTCCCA 0.976655 -252 AGGAGCGAGGCTTCCTCCCCTACAAGGGCT 8 265 1 CTTCCTCCCC 0.963438 -36 GGAGAGACATCCTCTTTCCCTAGGCTGTCT 9 131 1 CCTCTTTCCC 0.836452 -170 ********** Masking position 6 Map Score: 11.0151 Number of sites scoring better than the average of aligned sites = 1383 Number in coding regions = 1210 Number in noncoding regions = 173 Number of orfs with sites within 600 bp upstream = 188 Fraction of orfs with sites within 600 bp upstream = 0.030196 Motif number 3 TTCTCTTTTTGAAGAAGACGGAAGTAGGGATAT 1 21 0 GAAGAGGGAA 0.619772 -280 CCTCGCACTCGTGGAAAACGGAACTCTGAAGCA 1 173 0 GTGGAAGGAA 0.954636 -128 CCACGAGTGCGAGGGAGATGGAACTTGGGCTGG 1 192 1 GAGGAGGGAA 0.957836 -109 CCCCAGGGAACAGGCAAAAGTAACCCTTCTAGC 1 238 0 CAGGAAGTAA 0.821487 -63 GGAAATGAGGTTATTTTAAAGACTGCAAG 1 282 0 GAGGTATTAA 0.72458 -19 CGAAGAGGGAATATTAATGGGTAAATG 2 5 1 GAGGAATTAA 0.82183 -296 TAATTGCTTAGAGGATAGGGTAAACATAGACGG 3 32 0 GAGGTAGTAA 0.940504 -269 AGAAGAGGTAATTTCAAGTTACGGGTG 3 284 0 GAGGAATCAA 0.62778 -17 ATATCCTCAAGAGGAAAGGGGAGGGGAAGAAAA 6 212 0 GAGGAAGGAG 0.979299 -89 TATTTTTATGGTTGGTAAAGGAAGCTCTCTCGG 6 267 0 GTTGTAGGAA 0.685141 -34 CGGCTTTCACCAGGCGATGGGAAGAAGTTTACA 7 41 0 CAGGGAGGAA 0.730456 -253 TCCCATGGTAGTTGCTACAGTAATCCTGTTCCG 8 64 1 GTTGTAGTAA 0.435223 -237 ATATAGAAAAGAGGTATCTGGAGAGCTTTCTTA 8 157 1 GAGGATGGAG 0.834279 -144 ATGGACGAATGAGGTTAAAGGAGATGAATAAAG 8 190 0 GAGGTAGGAG 0.964262 -111 GTGGCATCCTGATGAAAGAGGAGGATC 9 284 1 GATGAAGGAG 0.895577 -17 **** ** **** Masking position 12 Map Score: 8.03441 Number of sites scoring better than the average of aligned sites = 1021 Number in coding regions = 894 Number in noncoding regions = 127 Number of orfs with sites within 600 bp upstream = 158 Fraction of orfs with sites within 600 bp upstream = 0.0253774 Motif number 4 GAATATTAATGGGTAAATGGTTCTTAAGTA 2 19 1 GGGTAAATGG 0.932347 -282 TAATTGCTTAGAGGATAGGGTAAACATAGA 3 35 0 GAGGATAGGG 0.985026 -266 AACCAAGACCGGGGAAATGAAGCCCCGCAA 3 241 0 GGGGAAATGA 0.78687 -60 ATATCCTCAAGAGGAAAGGGGAGGGGAAGA 6 215 0 GAGGAAAGGG 0.98059 -86 GGCCAGGTTAGGGTATAGGGGAATATATCC 6 239 0 GGGTATAGGG 0.985026 -62 GAAAACCTATGAGGATCGGGTGCTTGCCCG 7 91 1 GAGGATCGGG 0.952921 -203 TCCTTTCCTTGGGTCTAGGGAGAGACATCC 9 113 1 GGGTCTAGGG 0.952921 -188 ********** Masking position 3 Map Score: 4.91603 Number of sites scoring better than the average of aligned sites = 858 Number in coding regions = 726 Number in noncoding regions = 132 Number of orfs with sites within 600 bp upstream = 132 Fraction of orfs with sites within 600 bp upstream = 0.0212014 Motif number 5 GATCTTGAAAAACCGTAAAAATGGATACAGA 1 70 0 AACGTAAAAA 0.963123 -231 GGCCCCAGGGAACAGGCAAAAGTAACCCTTC 1 242 0 AAAGGCAAAA 0.914842 -59 TAAACAAAATAATAGCAAAAAATACAAGTAT 2 109 1 AAAGCAAAAA 0.843458 -192 TGAATAAAGTAAATGTAAAAAATTTACTCAG 3 99 1 AATGTAAAAA 0.833461 -202 TGAAAAGCATAAGAGTCAGAATCCTTGCTTC 6 127 1 AAAGTCAGAA 0.820899 -174 TTCCTTTACCAACCATAAAAATAATCCTCTA 6 277 1 AACATAAAAA 0.818671 -24 CGCCAAGCATAAGCGTAAAAAAAGACGTCGA 7 231 1 AACGTAAAAA 0.963123 -63 CAAACAAATAAAAAATCAAAAAATCGCTAGA 9 11 0 AAAATCAAAA 0.791637 -290 GTTGGCTACGAATCGTAAAAAAAATGGAATT 9 53 0 AACGTAAAAA 0.963123 -248 TCTGTCTCAAAAAAGGCAAAACAAATCCTGA 9 210 0 AAAGGCAAAA 0.914842 -91 ** ******** Masking position 8 Map Score: 5.27767 Number of sites scoring better than the average of aligned sites = 353 Number in coding regions = 290 Number in noncoding regions = 63 Number of orfs with sites within 600 bp upstream = 73 Fraction of orfs with sites within 600 bp upstream = 0.011725 Motif number 6 CCTTGACATGATCTTGAAAAACCGTAAAAA 1 80 0 ATCTTGAAAA 0.798311 -221 CTCCCTCGCACTCGTGGAAAACGGAACTCT 1 179 0 CTCGTGGAAA 0.898193 -122 AAAAAAAACTCTCGTGTAAATTTATCCCTT 6 96 0 CTCGTGTAAA 0.913018 -205 GAGAGTTTTTTTTTTGAAAAGCATAAGAGT 6 113 1 TTTTTGAAAA 0.633053 -188 CTCCCCTTTCCTCTTGAGGATATATTCCCC 6 222 1 CTCTTGAGGA 0.787989 -79 ATTGGTAAGTCTTTTGAAAAGACTCAGCTA 7 134 0 CTTTTGAAAA 0.909084 -160 AGGGATAAGTCTTTTGTAAACGGAACAGGA 8 87 0 CTTTTGTAAA 0.735465 -214 AGGGCTTCACCTCGTGATAAAC 8 289 1 CTCGTGATAA 0.871249 -12 TTCGAACACCTTCTTGAAAAAAAAAGAAAG 9 159 0 TTCTTGAAAA 0.874342 -142 TGGAGTGGAGCTCGTGAGAAAAGAGCCTAT 9 248 0 CTCGTGAGAA 0.948604 -53 CTCCGCATCTCTCTTGACAACAGAAGCGTA 10 11 0 CTCTTGACAA 0.914706 -125 ********** Masking position 10 Map Score: 6.33425 Number of sites scoring better than the average of aligned sites = 110 Number in coding regions = 83 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 7 CAAGATCATGTCAAGGAATGGTCAACAAAATAC 1 94 1 TCAAGGAGGC 0.952968 -207 TGTTAAGGCCCCAGGGAACAGGCAAAAGTAACC 1 246 0 CCAGGGAAGC 0.959579 -55 AGACTGCAAGCAATGTTAAGGCCCCAGGGAACA 1 259 0 CAATGTAGGC 0.584651 -42 CAATTAGACTTATGGGAAAGGAAGATAAAATTT 3 59 1 TATGGGAGGA 0.650958 -242 ATACCATGACCCTAGTTCTGGCCTCAATTTTGT 3 151 0 CCTAGTCGGC 0.791383 -150 GGGTACGCGTCCTTAGCAGGGACGTACTTTCGA 6 17 1 CCTTAGAGGC 0.869416 -284 GCTCTCTCGGCCAGGTTAGGGTATAGGGGAATA 6 244 0 CCAGGTAGGA 0.750227 -57 CTTCCCATCGCCTGGTGAAAGCCGGCGATACAC 7 50 1 CCTGGTAAGC 0.915183 -244 AGCTAATGCCTATGAGAACGGGCAAGCACCCGA 7 106 0 TATGAGAGGC 0.727693 -188 TTGATTTGTCCATAAGCATGGACGAATGAGGTT 8 207 0 CATAAGAGGC 0.825011 -94 CTCCCTAGACCCAAGGAAAGGACTGTCAAACAG 9 102 0 CCAAGGAGGC 0.982822 -199 TTTCCTTGGGTCTAGGGAGAGACATCCTCTTTC 9 116 1 TCTAGGAAGC 0.902051 -185 AGAAAGACAGCCTAGGGAAAGAGGATGTCTCTC 9 132 0 CCTAGGAAGG 0.734433 -169 GTTTTTGTATTCTGGGGACGGTCTGTAGAATAC 10 82 1 TCTGGGAGGC 0.982717 -54 ****** * ** * Masking position 11 Map Score: 6.03131 Number of sites scoring better than the average of aligned sites = 3041 Number in coding regions = 2837 Number in noncoding regions = 204 Number of orfs with sites within 600 bp upstream = 204 Fraction of orfs with sites within 600 bp upstream = 0.0327658 Motif number 8 TTTATATACTTGTATTTTTTGCTATTATTTTG 2 113 0 TTATTTTTGC 0.746272 -188 GCAAATTGGCTTTATTGTGGGGGCTAGCCGAC 3 213 0 TTATTTGGGG 0.967513 -88 ACAATGGCTGTCAATTTTTGGGAATAAACTTG 7 12 0 TAATTTTGGG 0.950625 -282 AATTTAACTATCTATTTTTATGCCGATCTCTT 7 261 0 TTATTTTATG 0.664932 -33 AATAGATAGTTAAATTGTTTGGGTTCT 7 277 1 TAATTTTTGG 0.866768 -17 GGTAGAAAAGTCTATTTTTAGGGATAAGTCTT 8 104 0 TTATTTTAGG 0.946725 -197 ACCTCTTTTCTATATTATTGGGTACAGTATCC 8 140 0 TTATTTTGGG 0.98134 -161 CTTGAGTTTTTGTATTCTGGGGACGGTCTGTA 10 77 1 TTATTTGGGG 0.967513 -59 * **** ***** Masking position 4 Map Score: 3.01831 Number of sites scoring better than the average of aligned sites = 144 Number in coding regions = 113 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 9 TTGTTGACCATTCCTTGACATGATCTTGAA 1 92 0 TTCCTTGACA 0.830637 -209 AAAATACGAATTTCTTAACATTCATGTAAG 1 120 1 TTTCTTAACA 0.959967 -181 AATTAGAAAATATCTAAACAAAATAATAGC 2 95 1 TATCTAAACA 0.798416 -206 ATTGTCTCTATATCTTAACAAAATTGAGGC 3 134 1 TATCTTAACA 0.897771 -167 AGAGACGGGGTTTTTAGACAGTCAACTTCT 6 165 0 TTTTTAGACA 0.477324 -136 AAAAACCCCGTCTCTAACCAAGAAAACGAT 6 180 1 TCTCTAACCA 0.750438 -121 CCTCATAGGTTTTCTTCTCAAAGTGTATCG 7 75 0 TTTCTTCTCA 0.743164 -219 GTCTTCGTTTTTTCTTAACAGATGACATGG 7 194 0 TTTCTTAACA 0.959967 -100 CTATACGATTTTTCTTCCCATGGTAGTTGC 8 49 1 TTTCTTCCCA 0.887544 -252 ACTCCGCATCTCTCTTGACAACAGAAGCGT 10 12 0 TCTCTTGACA 0.929886 -124 ********** Masking position 5 Map Score: 2.64538 Number of sites scoring better than the average of aligned sites = 168 Number in coding regions = 107 Number in noncoding regions = 61 Number of orfs with sites within 600 bp upstream = 58 Fraction of orfs with sites within 600 bp upstream = 0.00931577 Motif number 10 AGAAGACGGAAGTAGGGATATATTCCTGAA 1 12 0 AGTAGGGATA 0.864543 -289 ACGATCTGCTAGAAGGGTTACTTTTGCCTG 1 231 1 AGAAGGGTTA 0.828953 -70 CGAAGAGGGAATATTAATGGGTA 2 4 1 AGAGGGAATA 0.795089 -297 TTTCTAATTGCGGGGGGAACCTATGCTTTT 2 74 0 CGGGGGGAAC 0.871824 -227 CTTTCCCAACCGAGGGGAAATACCATGACC 3 173 0 CGAGGGGAAA 0.960897 -128 CAAAAAGCTCCGAAGGGATAAATTTACACG 6 84 1 CGAAGGGATA 0.983714 -217 AAAAAGACGTCGAAGAGATCGGCATAAAAA 7 249 1 CGAAGAGATC 0.853237 -45 ACTTTTCTACCGGAGGGATACTGTACCCAA 8 125 1 CGGAGGGATA 0.971593 -176 TTTTTGAGACAGAGGAGATAATAGGCTCTT 9 228 1 AGAGGAGATA 0.886283 -73 ********** Masking position 5 Map Score: 4.04998 Number of sites scoring better than the average of aligned sites = 531 Number in coding regions = 472 Number in noncoding regions = 59 Number of orfs with sites within 600 bp upstream = 75 Fraction of orfs with sites within 600 bp upstream = 0.0120463 Motif number 11 AGCCCAAGTTCCATCTCCCTCGCACTCGTG 1 193 0 CCATCTCCCT 0.974937 -108 TAGTGCGCCGCCATGACCCTTCGATCGCCA 2 281 1 CCATGACCCT 0.992141 -20 AGGGGAAATACCATGACCCTAGTTCTGGCC 3 161 0 CCATGACCCT 0.992141 -140 ********** Masking position 3 Map Score: 0.304426 Number of sites scoring better than the average of aligned sites = 16 Number in coding regions = 15 Number in noncoding regions = 1 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 12 AAAAGTTGAACTAAAGACTAAAATATAGTT 2 232 1 CTAAAGACTA 0.942467 -69 GGTAGCAGGGCTAAAAACTATATTTTAGTC 2 247 0 CTAAAAACTA 0.67998 -54 CTTCCTTTCCCATAAGTCTAATTGCTTAGA 3 53 0 CATAAGTCTA 0.876943 -248 TGAGTCTTTTCAAAAGACTTACCAATTATT 7 138 1 CAAAAGACTT 0.942467 -156 GCTTGGCGATCTTAAGTCTTCGTTTTTTCT 7 209 0 CTTAAGTCTT 0.807805 -85 GTTCCGTTTACAAAAGACTTATCCCTAAAA 8 91 1 CAAAAGACTT 0.942467 -210 CCCTCCGGTAGAAAAGTCTATTTTTAGGGA 8 112 0 GAAAAGTCTA 0.758991 -189 ********** Masking position 5 Map Score: 0.470154 Number of sites scoring better than the average of aligned sites = 108 Number in coding regions = 80 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 13 TTTAGATATTTTCTAATTGCGGGGGGAACC 2 83 0 TTCTAATTGC 0.944164 -218 TTTCCCATAAGTCTAATTGCTTAGAGGATA 3 48 0 GTCTAATTGC 0.934266 -253 TTAAATTTCGTTCTATTTGCCCCGTCAAGC 4 32 1 TTCTATTTGC 0.944164 -34 AAAAAAATATCTCGAATTGCAGTTCAGGAT 9 187 1 CTCGAATTGC 0.969312 -114 CAGGATGCCACTCTATTTGGAGTGGAGCTC 9 265 0 CTCTATTTGG 0.897286 -36 GTGGGCATCTCTTGATTTGCATTATAAGAT 10 40 1 CTTGATTTGC 0.830118 -96 ********** Masking position 5 Map Score: 0.144371 Number of sites scoring better than the average of aligned sites = 143 Number in coding regions = 123 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 14 ********** No masking Map Score: 5.23203e-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: 5.23203e-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