AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ctra.txt -z/home/amcguire/genomes/ctra.fna -inarP_ctra_opreg_100.orf -g0.413 -x5 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 = 0.413 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 CT134 300 hypothetical protein #2 CT135 58 hypothetical protein #3 CT483 300 hypothetical protein Motif number 1 TCGACTTAGGAGATTTTCTCTAAGTAGAGTACAATGC 1 24 1 AATTTTTAGG 0.869348 -277 CCAATAAGATAGATCTTGCTTATGCAGCCCAGTCCCG 1 141 0 AATCTTTAGG 0.977371 -160 GGCAGCCAGCATATCCTCTTTAATTGGAATGAAAACC 1 176 0 AATCCTTATG 0.955056 -125 AGGAGAGACCGAAGCTTCGATAGAAAGTAAGGAAATC 1 252 1 GAGCTTTAAG 0.960231 -49 TCGTTCCCCCAAATCTTTTTTAGACTGTTTTA 2 6 0 AATCTTTAAG 0.990141 -53 TAAACAGAGAAGATCCTTCTTAAAAAGGCCTACATCC 3 24 0 AATCCTTAAG 0.992636 -277 AGCTTTAGGAATCGTCTTTGTAAACAGAGAAGATCCT 3 44 0 ACGTCTTAAG 0.774119 -257 ATCTAGGGTGGTTTCTTGTTTATAACGAGAAAGCAAG 3 79 0 GTTCTTTAAG 0.908405 -222 AAACCACCCTAGATCCTTTGTACATCGAACGAAAAGA 3 102 1 AATCCTTAAG 0.992636 -199 TAGTAAAAAAAACTCTTAAATATAAAGAAAGGGGAAT 3 158 0 ACTCTTTAAG 0.977371 -143 TGAAATAAAAGGATCCTCTGTAGATGGGAGTAAAATA 3 272 0 GATCCTTAAG 0.988293 -29 * ***** ** * * Masking position 12 Map Score: 15.427 Number of sites scoring better than the average of aligned sites = 101 Number in coding regions = 101 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 2 TCTACTTAGAGAAAATCTCCTAAGTCGAAGA 1 21 0 GAAAATCTCT 0.88024 -280 CTAGGAACTTAAAAAAATCCTGATAAAAGCT 1 72 0 AAAAAAATCT 0.944306 -229 TCCAATTAAAGAGGATATGCTGGCTGCCCTT 1 185 1 GAGGATATCT 0.921394 -116 GATAGAAAGTAAGGAAATCCTGCGGCGGGAG 1 270 1 AAGGAAATCT 0.973174 -31 CCTTTTTAAGAAGGATCTTCTCTGTTTACAA 3 33 1 AAGGATCTCT 0.976173 -268 CGTTATAAACAAGAAACCACCCTAGATCCTT 3 89 1 AAGAAACCCC 0.916403 -212 CATCGAACGAAAAGAAACTCTATACAAACTT 3 124 1 AAAGAAACCT 0.961953 -177 TTCATTAGTAAAAAAAACTCTTAAATATAAA 3 169 0 AAAAAAACCT 0.940674 -132 TATTCCATAAAAAAAAATACCAAGGTAAAAT 3 235 1 AAAAAAATCC 0.866822 -66 TACCAAGGTAAAATATCTCCTATTTTACTCC 3 252 1 AAATATCTCT 0.825321 -49 CCTGAAATAAAAGGATCCTCTGTAGATGGGA 3 280 0 AAGGATCCCT 0.974559 -21 ******** ** Masking position 5 Map Score: 11.71 Number of sites scoring better than the average of aligned sites = 415 Number in coding regions = 414 Number in noncoding regions = 1 Number of orfs with sites within 600 bp upstream = 1 Fraction of orfs with sites within 600 bp upstream = 0.000160617 Motif number 3 TCTTATTGGTTTTCATTCCAATTAAAGAGG 1 169 1 TTTCATTCCA 0.987668 -132 CCTCTTTTTATTTCGTTCCCCCAAATCTTT 2 25 0 TTTCGTTCCC 0.990513 -34 TAGAGTTTCTTTTCGTTCGATGTACAAAGG 3 116 0 TTTCGTTCGA 0.938367 -185 TATACAAACTTTTTATTCCCCTTTCTTTAT 3 144 1 TTTTATTCCC 0.987669 -157 ATATCTCCTATTTTACTCCCATCTACAGAG 3 264 1 TTTTACTCCC 0.966982 -37 CAGAGGATCCTTTTATTTCAGG 3 289 1 TTTTATTTCA 0.887388 -12 ********** Masking position 7 Map Score: 5.55244 Number of sites scoring better than the average of aligned sites = 71 Number in coding regions = 71 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 4 ACAGTCTTCGACTTAGGAGATTTTCTCTAA 1 17 1 ACTTAGGAGA 0.983344 -284 CATTCCAATTAAAGAGGATATGCTGGCTGC 1 182 1 AAAGAGGATA 0.94458 -119 AGCGATTTCTAATTAGGAGAGACCGAAGCT 1 238 1 AATTAGGAGA 0.986154 -63 GTCTTTGTAAACAGAGAAGATCCTTCTTAA 3 38 0 ACAGAGAAGA 0.933906 -263 TTTTTTTATGGAATAGGAGACTCATTTCTC 3 220 0 GAATAGGAGA 0.979835 -81 GATGGGAGTAAAATAGGAGATATTTTACCT 3 257 0 AAATAGGAGA 0.992531 -44 ********** Masking position 5 Map Score: 7.21626 Number of sites scoring better than the average of aligned sites = 116 Number in coding regions = 116 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 5 TCTGAGTCGCAGCTTTTATCAGGATTTTTT 1 62 1 AGCTTTTATC 0.948816 -239 TTTCTTCGCAAGTTTTTATATTCTAAGAGC 1 103 1 AGTTTTTATA 0.944846 -198 CCGCTTTTTGAGCTCTTAGAATATAAAAAC 1 114 0 AGCTCTTAGA 0.96102 -187 AAAGAGGTAAAGCTTTTAAAG 2 48 1 AGCTTTTAAA 0.972513 -11 GGGAATAAAAAGTTTGTATAGAGTTTCTTT 3 134 0 AGTTTGTATA 0.862332 -167 TAGTAAAAAAAACTCTTAAATATAAAGAAA 3 165 0 AACTCTTAAA 0.819423 -136 ********** Masking position 4 Map Score: 1.78304 Number of sites scoring better than the average of aligned sites = 85 Number in coding regions = 85 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 6 CTGCGACTCAGAAGCATTGTACTCTACTTAGAGAA 1 39 0 GACTGACTCT 0.990087 -262 CGCTATCCACGTATCATAGGTCTCTAAAGGGCAGC 1 207 0 GTCTGTCTCT 0.990087 -94 ACTTTCTATCGAAGCTTCGGTCTCTCCTAATTAGA 1 245 0 GACTGTCTCT 0.996966 -56 TGGAATAGGAGACTCATTTCTCTCTGTAGTCGGAG 3 207 0 GACTTTCTCT 0.99319 -94 ATCTACAGAGGATCCTTTTATTTCAGG 3 284 1 GACTTTTTCA 0.894675 -17 ** * * * ***** Masking position 7 Map Score: 1.3116 Number of sites scoring better than the average of aligned sites = 31 Number in coding regions = 31 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 7 TCCTAAGTCGAAGACTGTCCACCC 1 5 0 AAGACTGTCC 0.984064 -296 AAATCTTTTTTAGACTGTTTTA 2 3 0 TAGACTGTTT 0.912941 -56 TCTGTTTACAAAGACGATTCCTAAAGCTTG 3 53 1 AAGACGATTC 0.975535 -248 GTAGTCGGAGAAGACTATTCATTAGTAAAA 3 187 0 AAGACTATTC 0.985518 -114 ********** Masking position 4 Map Score: 0.505645 Number of sites scoring better than the average of aligned sites = 24 Number in coding regions = 24 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 8 ********** No masking Map Score: -8.92852e-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 9 ********** No masking Map Score: -8.92852e-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 10 ********** No masking Map Score: -8.92852e-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