AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i241_synecho_ctra_100.orf -o241_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 RCY10628 106 Synechocystis #2 RCY33025 54 Synechocystis #3 RCY40193 300 Synechocystis #4 RCY28673 246 Synechocystis #5 RCT00247 300 Chlamydia_trachomatis Motif number 1 GCCCATTTTACCCACCATCCAGCCGAGGTTA 1 25 1 CCCACCTCCA 0.984858 -82 TCCGCCCAAACCTATCAGACCCTTACCAGCC 1 85 1 CCTATCGACC 0.946492 -22 CTATCAGACCCTTACCAGCCA 1 96 1 CTTACCGCCA 0.900365 -11 ACAAGCACTCTCTCTCTGCCCACTAAAAACT 2 14 1 TCTCTCGCCC 0.975049 -41 AATTTAATTCCCTATCTTCCCATTCCGTATT 3 251 1 CCTATCTCCC 0.980417 -50 CCAGTTTTAGCCCCCCGGCCAAGACTTTCTC 4 15 1 CCCCCCGCCA 0.995671 -232 TTCTCTATTGCCTCCCAGACAACAACAACAG 4 41 1 CCTCCCGACA 0.96943 -206 GGGGAGTGATTCCATCTTACCTTTGTCCTAG 4 82 0 TCCATCTACC 0.79612 -165 GATGGAATCACTCCCCGTCCTAGGCGTATTT 4 97 1 CTCCCCTCCT 0.858517 -150 TGCCGCTGTTTCCCCGCTCCCAATATAGAAT 4 159 1 TCCCCGTCCC 0.90178 -88 ATTCTCCCCCCCCCCCCTCCCATCAAACAGA 5 83 0 CCCCCCTCCC 0.99745 -218 CACGCCCTCTCCGCCCAAGGAATTTC 5 285 0 CCTCTCGCCC 0.994383 -16 ****** **** Masking position 10 Map Score: 19.3397 Number of sites scoring better than the average of aligned sites = 3034 Number in coding regions = 2707 Number in noncoding regions = 327 Number of orfs with sites within 600 bp upstream = 293 Fraction of orfs with sites within 600 bp upstream = 0.0470607 Motif number 2 CAAGCCCATTTTACCCACCATCCAGCCGAGGT 1 22 1 TACCCACCTC 0.812748 -85 AAGACAAGCACTCTCTCTCTGCCCACTAAAAA 2 11 1 CCTCTCTCGC 0.904366 -44 CGACCGCTGATAGCCTCTCTTCTTTTTGTGTC 3 159 0 TGCCTCTCTC 0.983762 -142 ATAAATTTAATTCCCTATCTTCCCATTCCGTA 3 248 1 TCCCTATCTC 0.882835 -53 ACTCCAGTTTTAGCCCCCCGGCCAAGACTTTC 4 12 1 TGCCCCCCGC 0.992836 -235 ACTTTCTCTATTGCCTCCCAGACAACAACAAC 4 38 1 TGCCTCCCGA 0.950819 -209 TAAGATGGAATCACTCCCCGTCCTAGGCGTAT 4 94 1 TACTCCCCTC 0.812748 -153 GGTTATGCCGCTGTTTCCCCGCTCCCAATATA 4 154 1 CGTTTCCCGC 0.830845 -93 GTATCAAAAGTTGCCTCCCTTTTAATAAG 5 8 0 TGCCTCCCTT 0.935092 -293 TCTCCCCCCCCCCCCTCCCATCAAACAGAAGT 5 80 0 CCCCTCCCTC 0.992032 -221 CACGCCCTCTCCGCCCAAGGAATT 5 287 0 CCCCTCTCGC 0.98397 -14 * ******* ** Masking position 9 Map Score: 10.249 Number of sites scoring better than the average of aligned sites = 1501 Number in coding regions = 1340 Number in noncoding regions = 161 Number of orfs with sites within 600 bp upstream = 195 Fraction of orfs with sites within 600 bp upstream = 0.0313203 Motif number 3 TCAGCCCCAGTTTATCTTGTTTTTCTATTAACCTCGGCTG 1 44 0 TTTTTTTTAA 0.958774 -63 CACGACGAAGTTTATGAATTTTTTCAACGATTTCATCCTT 3 75 0 TTTTTTTTAA 0.958773 -226 TCGTCGTGCTTACTCTAAGTCTTTTAACCACGATTTACAG 3 107 1 TACTCTTTAA 0.920136 -194 TAGGGGTTTCTTCGTGTTTTTTTTCAGGATGGACATTAGG 3 204 0 TTTTTTTTGT 0.814523 -97 ATTATTTCCTTTAGTCCTTTCTTTGTATCAGT 3 279 1 TTTTCTTTAA 0.935758 -22 CTCCCCGTCCTAGGCGTATTTTTTATGGTAAAGACTGCCA 4 107 1 TACTTTTTGA 0.961081 -140 CAACTATACTTAAGTGTTGTTTTTTCGGCAGAGTAAAATA 5 41 1 TATTTTTTGA 0.948457 -260 TAAAAATTTCTTCTTCCTATCTTTTGGAGATAGACCCTCT 5 113 1 TTTTCTTTGA 0.951331 -188 AGACCCTCTTTACACAAACTTTTTTTGAAAAAGAAACAGA 5 144 1 TACTTTTTGA 0.961079 -157 AAGAAACAGATTAACAACCTTTTTATACAGATAAAAGTTT 5 174 1 TTCTTTTTAG 0.866822 -127 CAGATAAAAGTTTGCTTTCTTTTTTAAAAAAATCTTTGCT 5 201 1 TTCTTTTTAA 0.968954 -100 ** * ***** * * Masking position 10 Map Score: 7.46937 Number of sites scoring better than the average of aligned sites = 382 Number in coding regions = 292 Number in noncoding regions = 90 Number of orfs with sites within 600 bp upstream = 87 Fraction of orfs with sites within 600 bp upstream = 0.0139737 Motif number 4 TCAACCCAAGCCCATTTTACCCACCATCCAG 1 16 1 CCCATTTACC 0.895038 -91 GCGGACTCAGCCCCAGTTTATCTTGTTTTTC 1 59 0 CCCCATTTAT 0.729041 -48 TAAAAACTAACCCAATTTTCTAAGGCCT 2 37 1 CCCAATTTCT 0.953064 -18 CCTATGTAATCCCTAATGTCCATCCTGAAAA 3 193 1 CCCTATGTCC 0.977763 -108 AAATTTAATTCCCTATCTTCCCATTCCGTAT 3 250 1 CCCTACTTCC 0.912901 -51 GGCGGTTATGCCGCTGTTTCCCCGCTCCCAA 4 151 1 CCGCTTTTCC 0.949389 -96 CTGTCCCTGTCCGATCTGTCCAATGATTCTA 4 184 0 CCGATTGTCC 0.964694 -63 GTAAACCCGCCCGAACTGTCCCTGTCCGATC 4 199 0 CCGAATGTCC 0.981164 -48 ACTTTTGATACCCAACTATACTTAAGTGTTG 5 29 1 CCCAATATAC 0.833596 -272 ***** ***** Masking position 2 Map Score: 5.18153 Number of sites scoring better than the average of aligned sites = 1521 Number in coding regions = 1327 Number in noncoding regions = 194 Number of orfs with sites within 600 bp upstream = 198 Fraction of orfs with sites within 600 bp upstream = 0.0318021 Motif number 5 GGGCAGAGAGAGAGTGCTTGTCTT 2 4 0 AGAGTGTTGT 0.91342 -51 TCATCCTTAAACATGGCTAGTCTCCTAAAAG 3 52 0 ACATGGTAGT 0.894116 -249 GTGTCTTCGTACATTGCCTGTAAATCGTGGT 3 133 0 ACATTGCTGT 0.89584 -168 CACAAAAAGAAGAGAGGCTATCAGCGGTCGC 3 161 1 AGAGAGCTAT 0.813188 -140 CATAACCGCCACATTGGCAGTCTTTACCATA 4 130 0 ACATTGCAGT 0.951532 -117 GACAGATCGGACAGGGACAGTTCGGGCGGGT 4 195 1 ACAGGGCAGT 0.932376 -52 GTTTGTGTAAAGAGGGTCTATCTCCAAAAGA 5 132 0 AGAGGGCTAT 0.944531 -169 ****** **** Masking position 3 Map Score: 1.72282 Number of sites scoring better than the average of aligned sites = 298 Number in coding regions = 272 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 6 TCTTCTTTTTGTGTCTTCGTACATTGCCTG 3 144 0 GTGTCTTCGT 0.962572 -157 CGCTGATAGCCTCTCTTCTTTTTGTGTCTT 3 157 0 CTCTCTTCTT 0.95515 -144 TGAAGTAGGGGTTTCTTCGTGTTTTTTTTC 3 219 0 GTTTCTTCGT 0.985982 -82 TCCTTTAGTCCTTTCTTTGTATCAGT 3 285 1 CTTTCTTTGT 0.971473 -16 GAGAATAAAAATTTCTTCTTCCTATCTTTT 5 108 1 ATTTCTTCTT 0.936141 -193 TTGTTAATCTGTTTCTTTTTCAAAAAAAGT 5 161 0 GTTTCTTTTT 0.965754 -140 TAAAAGTTTGCTTTCTTTTTTAAAAAAATC 5 205 1 CTTTCTTTTT 0.965754 -96 ********** Masking position 6 Map Score: 7.9516 Number of sites scoring better than the average of aligned sites = 77 Number in coding regions = 63 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 7 TGATAGGTTTGGGCGGACTCAGCCCCAGTTTA 1 70 0 GGGCGACCAG 0.995463 -37 AAAGTTCATAGGGCGTAAACAGTATCGGTAAT 3 24 0 GGGCGAACAG 0.990321 -277 AAACTTCGTCGTGCTTACTCTAAGTCTTTTAA 3 102 1 GTGCTACCTA 0.928144 -199 GATTACATAGGTGCGACCGCTGATAGCCTCTC 3 172 0 GTGCGCCCTG 0.983993 -129 CTTGGCCGGGGGGCTAAAACTGGAGTT 4 6 0 GGGCTAACTG 0.985457 -241 ***** ** *** Masking position 4 Map Score: 0.458872 Number of sites scoring better than the average of aligned sites = 138 Number in coding regions = 127 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 8 ********** No masking Map Score: -2.59896e-14 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 9 ********** No masking Map Score: -2.59896e-14 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 10 ********** No masking Map Score: -2.59896e-14 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