AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i216_synecho_ctra_100.orf -o216_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 RCY44131 300 Synechocystis #2 RCY51226 208 Synechocystis #3 RCY12795 137 Synechocystis #4 RCY04561 102 Synechocystis #5 RCY30742 53 Synechocystis #6 RCY03877 300 Synechocystis #7 RCY26596 300 Synechocystis #8 RCT00023 187 Chlamydia_trachomatis #9 RCT00025 59 Chlamydia_trachomatis #10 RCT00028 25 Chlamydia_trachomatis #11 RCT00029 63 Chlamydia_trachomatis #12 RCT00628 300 Chlamydia_trachomatis #13 RCT00629 98 Chlamydia_trachomatis Motif number 1 CTGACTGTAACCCCTGTCCCCCAAAGGTCCCTG 1 60 1 CCCCTCCCCA 0.973039 -241 CCCCAAAGGTCCCTGTTCACCCCCAATCGGGCA 1 78 1 CCCTTCCCCC 0.98809 -223 TTTTTTGCCACCCCAGCTGCCCGATTGGGGGTG 1 95 0 CCCCCTCCCG 0.921454 -206 GGTCAACCTACCCTCTGGCCCAGTGAACTATTC 1 158 0 CCCTGGCCAG 0.849053 -143 GGCCACCTTGCCCCTGTCCACACCACTGGGACC 1 247 1 CCCCTCACAC 0.949139 -54 GGAAATATGGCCCAGATCGCCAGTTAGGAACTG 2 19 0 CCCATCCCAG 0.991617 -190 CCCTTTCTCTCCCTTTTCCCCCGGGGGAGTGAT 2 114 1 CCCTTCCCCG 0.994534 -95 GGTTTAGATACCCACCTCAACAATCCAGTAATG 6 127 0 CCCATCACAA 0.853379 -174 GCGGACCCAGGCCTCTCCTCCCCAATGGCGATC 6 172 0 GCCTCCCCCC 0.918909 -129 GCCAGGGCAACCCTTTGCTACAGTTGAATTGGT 6 240 1 CCCTGCACAG 0.952181 -61 CTAAATTTATCCCCGGCCTACCGGATTTCTATC 7 34 0 CCCCCCACCG 0.984013 -267 GTCAAGGATTCCGAACTCTCCCCCGGGCACAAA 7 136 0 CCGATCCCCC 0.892098 -165 GCCGCAGATAGCCATGGCACCAGGGCTTTCCCA 7 174 0 GCCAGCCCAG 0.924818 -127 TTTTCAGGGGCCCAGCTCAATCGCCGCAGATAG 7 196 0 CCCATCATCG 0.796235 -105 ACATGCAACTCCCAAACCTCCAGAGCCATAGGA 12 65 0 CCCACCCCAG 0.989828 -236 **** ** **** Masking position 2 Map Score: 17.1961 Number of sites scoring better than the average of aligned sites = 2616 Number in coding regions = 2340 Number in noncoding regions = 276 Number of orfs with sites within 600 bp upstream = 228 Fraction of orfs with sites within 600 bp upstream = 0.0366206 Motif number 2 GGCCATATTTCCCCGATAAAGCAGCGCAATT 2 40 1 CCCCGATAAG 0.863766 -169 AATCAATTTGCCCCACTAATTTTTCAGCTTT 5 25 0 CCCCACTAAT 0.948347 -29 GGATTTCTATCCCTAAAAATTGAATGTTTTC 7 14 0 CCCTAAAAAT 0.98337 -287 GTCAGCCACTCCCCACTAAATTTATCCCCGG 7 51 0 CCCCACTAAT 0.948347 -250 TGAGCTGGGCCCCTGAAAATTTACGACCCTA 7 210 1 CCCTGAAAAT 0.9768 -91 AAATTTACGACCCTAAAAATTCTGGCCCCAA 7 226 1 CCCTAAAAAT 0.98337 -75 AAAATTCTGGCCCCAAAAAATAGGTTAGAAT 7 241 1 CCCCAAAAAT 0.989507 -60 CTAGACTTTACTCTGAAAAGTCAGATTCAAA 8 87 0 CTCTGAAAAT 0.786252 -101 GTCTAGTGTTCCCCAAAAATTGATTGCCAAT 8 112 1 CCCCAAAAAT 0.989507 -76 TGTATTTCACCTAAAAATTCTTTTT 10 7 0 ACCTAAAAAT 0.837828 -19 ********* * Masking position 8 Map Score: 12.9919 Number of sites scoring better than the average of aligned sites = 376 Number in coding regions = 312 Number in noncoding regions = 64 Number of orfs with sites within 600 bp upstream = 65 Fraction of orfs with sites within 600 bp upstream = 0.0104401 Motif number 3 CTGTCCCCTGGGAGTTTCCCTGGG 1 1 1 CTGCCCGGGG 0.996431 -300 GGGGGTGAACAGGGACCTTTGGGGGACAGGGGTT 1 68 0 AGGACCTGGG 0.779484 -233 GCCACCCCAGCTGCCCGATTGGGGGTGAACAGGG 1 88 0 CTGCCGTGGG 0.960746 -213 CTAGGGTCAACCTACCCTCTGGCCCAGTGAACTA 1 161 0 CCTCCCTGGC 0.947034 -140 AGAGGGTAGGTTGACCCTAGAGAGGAAAATATTC 1 175 1 TTGCCCGAGG 0.862147 -126 CATCCCAAAGCGGTCCCAGTGGTGTGGACAGGGG 1 257 0 CGGCCCTGGG 0.995154 -44 TTTCTCTCCCTTTTCCCCCGGGGGAGTGATACGT 2 117 1 TTTCCCGGGG 0.983374 -92 CCAGGCCTCTCCTCCCCAATGGCGATCGCCGTGT 6 165 0 CCTCCCTGGG 0.993503 -136 GGTCCCATCCCCTAACCATGGGCGGACCCAGGCC 6 192 0 CCTACCGGGG 0.969375 -109 TGAGTCAGTTTGTGCCCGGGGGAGAGTTCGGAAT 7 128 1 TGTCCCGGGG 0.982984 -173 GGCACCAGGGCTTTCCCAATGGGGTCAAGGATTC 7 158 0 CTTCCCTGGG 0.993638 -143 *** *** *** * Masking position 6 Map Score: 15.0628 Number of sites scoring better than the average of aligned sites = 845 Number in coding regions = 758 Number in noncoding regions = 87 Number of orfs with sites within 600 bp upstream = 100 Fraction of orfs with sites within 600 bp upstream = 0.0160617 Motif number 4 TAGTTGTGACCGTTTTTTGCCACCCCAGCTG 1 109 0 CGTTTTTTGC 0.898969 -192 ACCACTGGGACCGCTTTGGGATGGCCTTTTG 1 268 1 CCGCTTTGGA 0.930979 -33 AGAGAAAGGGCGGTTTTTGCAACTAAGCTTT 2 93 0 CGGTTTTTGA 0.959077 -116 CGGCTTTTCAATTATGATCCA 3 1 1 CGGCTTTTCA 0.973581 -137 ACTGATTTACCCTCTTTTGCAAAAGTTGCTT 3 90 0 CCTCTTTTGA 0.978185 -48 AATAAACCGTCGTCTTTTGGATCAAACTCAA 4 71 1 CGTCTTTTGA 0.982314 -32 TGTAATTTACCCTTTTTTCAACCAGAGTTTT 6 53 1 CCTTTTTTCA 0.883363 -248 GGTGTTCGCCCCGCTTTTCTCTAGATAACAG 8 26 0 CCGCTTTTCC 0.93566 -162 AACAGGACTTCGTCTTTTGAAACCCTTCCAT 12 267 0 CGTCTTTTGA 0.982314 -34 ********* * Masking position 6 Map Score: 8.78353 Number of sites scoring better than the average of aligned sites = 154 Number in coding regions = 135 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 5 CTAGGGTCAACCTACCCTCTGGCCCAGTGA 1 165 0 CCTACCCTCT 0.689457 -136 AACTGAATATTTTCCTCTCTAGGGTCAACC 1 183 0 TTTCCTCTCT 0.760987 -118 AAATATTCAGTTTACCCAATGTCCAACATT 1 201 1 TTTACCCAAT 0.765962 -100 GTAGGCCACCTTGCCCCTGTCCACACCACT 1 244 1 TTGCCCCTGT 0.824159 -57 CTGGGCCATATTTCCCCGATAAAGCAGCGC 2 37 1 TTTCCCCGAT 0.911474 -172 AAAGTTGCTTTTTTCCCACTTGCCTTGCTG 3 70 0 TTTTCCCACT 0.888219 -68 TCATAACTGATTTACCCTCTTTTGCAAAAG 3 96 0 TTTACCCTCT 0.855184 -42 TTCAATCAATTTGCCCCACTAATTTTTCAG 5 29 0 TTGCCCCACT 0.974307 -25 CCAGGCCTCTCCTCCCCAATGGCGATCGCC 6 169 0 CCTCCCCAAT 0.860732 -132 GTCGTCAGCCACTCCCCACTAAATTTATCC 7 55 0 ACTCCCCACT 0.952194 -246 AACGCGAAATTTTTCCCAGTCTATTTTTAT 7 276 1 TTTTCCCAGT 0.654405 -25 AGCGGGGTGTTCGCCCCGCTTTTCTCTAGA 8 32 0 TCGCCCCGCT 0.962638 -156 AGCGGGGCGAACACCCCGCTTTTTTTGTTT 8 42 1 ACACCCCGCT 0.613164 -146 TCTAATATTTTCTCCTCACTTTTTACCGCA 9 34 1 TCTCCTCACT 0.86944 -26 CTTACAGATCATGCCCCAATTTTGCTAGCC 12 138 1 ATGCCCCAAT 0.777754 -163 ********** Masking position 10 Map Score: 10.7136 Number of sites scoring better than the average of aligned sites = 1813 Number in coding regions = 1553 Number in noncoding regions = 260 Number of orfs with sites within 600 bp upstream = 280 Fraction of orfs with sites within 600 bp upstream = 0.0449727 Motif number 6 TGGGTAAACTGAATATTTTCCTCTCTAGGGT 1 188 0 GAATTTTTCC 0.984834 -113 AAATATATTCCTCAAAAGGCC 1 290 0 AAATTATTCC 0.932108 -11 GTTGTAAAACGAAATTTTTCCATAACTTTAA 2 149 1 GAAATTTTCC 0.96537 -60 CCTAAAAATTGAATGTTTTCCTC 7 3 0 GAATTTTTCC 0.984887 -298 ACTCCCCACTAAATTTATCCCCGGCCTACCG 7 44 0 AAATTATCCC 0.808597 -257 TGATAAACGCGAAATTTTTCCCAGTCTATTT 7 271 1 GAAATTTTCC 0.96537 -30 AAGGTTGAATAAATCTTTTCCGAACCGTATC 12 236 1 AAATTTTTCC 0.969288 -65 **** ****** Masking position 3 Map Score: 7.23123 Number of sites scoring better than the average of aligned sites = 208 Number in coding regions = 174 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 7 TGCAAAAACCGCCCTTTCTCTCCCTTTTCC 2 103 1 GCCCTTTCTC 0.979155 -106 CTTGACTTTACTGAAAAGCTGAA 5 4 1 GACTTTACTG 0.961146 -50 ATCCAGTAATGACCTTGCTGATCACTCGAA 6 108 0 GACCTTGCTG 0.96771 -193 TTTGAACAGAACTTTCTGTTATCTAGAG 8 9 1 GAACTTTCTG 0.868891 -179 GGGAACACTAGACTTTACTCTGAAAAGTCA 8 95 0 GACTTTACTC 0.949556 -93 GACTTCTTCTGCCTTTACTCTAGTATCTCT 8 164 0 GCCTTTACTC 0.957883 -24 GCGGCATTAAGCCCTTTCTGCTGTTCTCAA 11 24 1 GCCCTTTCTG 0.984051 -40 ********** Masking position 5 Map Score: 5.88281 Number of sites scoring better than the average of aligned sites = 121 Number in coding regions = 104 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 8 ACAGGGACCTTTGGGGGACAGGGGTTACAGT 1 63 0 TTGGGGACAG 0.942435 -238 TGCCCGATTGGGGGTGAACAGGGACCTTTGG 1 80 0 GGGGGAACAG 0.995581 -221 CAGGGGCAAGGTGGCCTACAGAAAAATGTTG 1 232 0 GTGGCTACAG 0.91328 -69 CGGTCCCAGTGGTGTGGACAGGGGCAAGGTG 1 250 0 GGTGGGACAG 0.969849 -51 CTGCATTCTAGCGGCCAACAGTCCGGGCGCA 3 38 1 GCGGCAACAG 0.958233 -100 CCAACAGTCCGGGCGCAACAGCAAGGCAAGT 3 52 1 GGGCCAACAG 0.928366 -86 GATCGCCATTGGGGAGGAGAGGCCTGGGTCC 6 172 1 GGGGGGAGAG 0.96015 -129 AGAGAAAAGCGGGGCGAACACCCCGCTTTTT 8 35 1 GGGGGAACAC 0.983486 -153 CAATCAATTTTTGGGGAACACTAGACTTTAC 8 107 0 TTGGGAACAC 0.841429 -81 ATCTCTTGACGTTGAGAACAGCAGAAAGGGC 11 34 0 GTTGGAACAG 0.952035 -30 **** ****** Masking position 8 Map Score: 9.11532 Number of sites scoring better than the average of aligned sites = 482 Number in coding regions = 419 Number in noncoding regions = 63 Number of orfs with sites within 600 bp upstream = 58 Fraction of orfs with sites within 600 bp upstream = 0.00931577 Motif number 9 GTAAACTGAATATTTTCCTCTCTAGGGTCA 1 186 0 TATTTTCCTC 0.975749 -115 AAATATATTCCTCAAAAGGCCAT 1 288 0 TATATTCCTC 0.924409 -13 AAAAATTGAATGTTTTCCTC 7 1 0 TGTTTTCCTC 0.977495 -300 ACAGTCGGGATGTTTTCTTCTATGATTGAT 7 89 0 TGTTTTCTTC 0.950683 -212 AATTATCTAATATTTTCTCCTCACTTTTTA 9 29 1 TATTTTCTCC 0.889434 -31 ********** Masking position 5 Map Score: 1.56989 Number of sites scoring better than the average of aligned sites = 65 Number in coding regions = 57 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 10 CCACTGGGACCGCTTTGGGATGGCCTTTTG 1 269 1 CGCTTTGGGA 0.896638 -32 CCCAGATCGCCAGTTAGGAACTGCTAGGAA 2 12 0 CAGTTAGGAA 0.892153 -197 CTTTTAACGGCGGGACGGAACTTTAACTAT 6 278 0 CGGGACGGAA 0.840173 -23 GCCCGGGGGAGAGTTCGGAATCCTTGACCC 7 141 1 GAGTTCGGAA 0.892464 -160 ATGGCTCTGGAGGTTTGGGAGTTGCATGTG 12 69 1 AGGTTTGGGA 0.871769 -232 ATTGAAACAGCAGTTCGGGATTCTTACAGA 12 116 1 CAGTTCGGGA 0.976913 -185 CATTTCTTAACGGTTTGGAAGGTTGAATAA 12 218 1 CGGTTTGGAA 0.981642 -83 TTCCATGATACGGTTCGGAAAAGATTTATT 12 243 0 CGGTTCGGAA 0.991027 -58 ********** Masking position 10 Map Score: 5.134 Number of sites scoring better than the average of aligned sites = 284 Number in coding regions = 257 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 11 CAGTTCCTAACTGGCGATCTGGGCCATATT 2 19 1 CTGGCGATCT 0.578913 -190 CCTTTTCCCCCGGGGGAGTGATACGTTGTA 2 125 1 CGGGGGAGTG 0.977813 -84 TTACCGTGATCCGGGGATCGTTAGCCGATA 4 24 1 CCGGGGATCG 0.986053 -79 ACCAAATTACACGGCGATCGCCATTGGGGA 6 157 1 ACGGCGATCG 0.84932 -144 ATCGCCATTGGGGAGGAGAGGCCTGGGTCC 6 173 1 GGGAGGAGAG 0.726444 -128 ATCCGGTAGGCCGGGGATAAATTTAGTGGG 7 41 1 CCGGGGATAA 0.833913 -260 GATAAATTTAGTGGGGAGTGGCTGACGACA 7 56 1 GTGGGGAGTG 0.923209 -245 AGTTTGTGCCCGGGGGAGAGTTCGGAATCC 7 134 1 CGGGGGAGAG 0.977813 -167 ATGGCTATCTGCGGCGATTGAGCTGGGCCC 7 192 1 GCGGCGATTG 0.934392 -109 ********** Masking position 7 Map Score: 2.02527 Number of sites scoring better than the average of aligned sites = 2363 Number in coding regions = 2196 Number in noncoding regions = 167 Number of orfs with sites within 600 bp upstream = 193 Fraction of orfs with sites within 600 bp upstream = 0.030999 Motif number 12 ********** No masking Map Score: 5.77204e-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 GATCAATAACTAAGGGGTGGGGGTTAAAAATC 2 187 1 TAAGGTGGGG 0.921196 -22 CGGATCACGGTAACAGGTTGCGAATC 4 5 0 TAAGGTTGCG 0.930752 -98 ACCCTTAGTTTAAATGGTCGGTTAATTATTAT 6 22 0 TAAGGTCGGT 0.820446 -279 TTGTTGTCCATTATTGGTTTCTCTCCTTCGAG 6 82 1 TTAGGTTTCT 0.841616 -219 AGCAAGGTCATTACTGGATTGTTGAGGTGGGT 6 119 1 TTAGGATTGT 0.846115 -182 CCGCCCATGGTTAGGGGATGGGACCGATCAGA 6 201 1 TTAGGATGGG 0.957102 -100 GGAAATCTGCTTAAAGGTTTGGCTAAATAAAT 12 36 0 TTAGGTTTGG 0.974634 -265 TTAACATTTCTTAACGGTTTGGAAGGTTGAAT 12 214 1 TTAGGTTTGG 0.974634 -87 *** ******* Masking position 3 Map Score: 0.699194 Number of sites scoring better than the average of aligned sites = 345 Number in coding regions = 308 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 14 ********** No masking Map Score: 5.77204e-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: 5.77204e-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