AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i206_tpal_bbur_100.orf -o206_tpal_bbur_100.ace -a/home/amcguire/genomes/ORF_tpal.txt -z/home/amcguire/genomes/synecho.fna -g0.40 -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 = 0.4 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 RTP00676 38 AE000520 #2 RTP00677 40 AE000520 #3 RBB00127 300 3615 Motif number 1 AGCTTGATAATTAAAATTTTAACAAAAATA 3 45 1 TTAAAATTTT 0.851731 -256 AATTATTTTGATTTATTTTTGTTAAAATTT 3 58 0 ATTTATTTTT 0.658367 -243 AATAAATCAAAATAATTTTTCAAATTGTTT 3 71 1 AATAATTTTT 0.627199 -230 TGCATTTTTATTAAATTCTTAAAACAATTT 3 92 0 TTAAATTCTT 0.965201 -209 AATGCAGATAAAAAATCCTTCCAAAGCTTA 3 116 1 AAAAATCCTT 0.876795 -185 GCTAGTTTTTAAAAATCTCTCGTGTGCTTT 3 156 0 AAAAATCTCT 0.733649 -145 ATGAGTGTCTTTAAATCTGTTATAGTAATC 3 201 0 TTAAATCTGT 0.924354 -100 ATCAATATTAATAAATTTTTGTCTAACTTG 3 236 0 ATAAATTTTT 0.671491 -65 GAATTTAATGTAAAATTTTTCTATCAATAT 3 258 0 TAAAATTTTT 0.70038 -43 AAATTTTACATTAAATTCGTAAGGACAAAA 3 270 1 TTAAATTCGT 0.924343 -31 GAATTTTAATTTTTTGTCCTTACG 3 287 0 TTTAATTTTT 0.94679 -14 ********** Masking position 5 Map Score: 12.1355 Number of sites scoring better than the average of aligned sites = 969 Number in coding regions = 261 Number in noncoding regions = 708 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 2 CCAAAGCTTGATAATTAAAATTTTAACAAA 3 41 1 ATAATTAAAA 0.745404 -260 AATTAAAATTTTAACAAAAATAAATCAAAA 3 53 1 TTAACAAAAA 0.969482 -248 TTAACAAAAATAAATCAAAATAATTTTTCA 3 63 1 TAAATCAAAA 0.884533 -238 TTTTAAGAATTTAATAAAAATGCAGATAAA 3 98 1 TTAATAAAAA 0.969942 -203 AATAAAAATGCAGATAAAAAATCCTTCCAA 3 110 1 CAGATAAAAA 0.935229 -191 GATTTCAAGTTAGACAAAAATTTATTAATA 3 231 1 TAGACAAAAA 0.974815 -70 TTTATTAATATTGATAGAAAAATTTTACAT 3 251 1 TTGATAGAAA 0.931646 -50 TAAATTCGTAAGGACAAAAAATTAAAATTC 3 281 1 AGGACAAAAA 0.908063 -20 ********** Masking position 4 Map Score: 4.82648 Number of sites scoring better than the average of aligned sites = 624 Number in coding regions = 179 Number in noncoding regions = 445 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 3 ATACATATCAAGCTATCCAACTCCAA 3 7 1 ATCAAGCTAT 0.923447 -294 AATTTTAATTATCAAGCTTTGGTAAATTGG 3 33 0 ATCAAGCTTT 0.979948 -268 AAGCTTGATAATTAAAATTTTAACAAAAAT 3 44 1 ATTAAAATTT 0.868229 -257 AATAAATCAAAATAATTTTTCAAATTGTTT 3 71 1 AATAATTTTT 0.848989 -230 TTGCTTGTGAAATAAGCTTTGGAAGGATTT 3 128 0 AATAAGCTTT 0.983275 -173 TATCAATATTAATAAATTTTTGTCTAACTT 3 237 0 AATAAATTTT 0.919709 -64 ********** Masking position 5 Map Score: 2.92493 Number of sites scoring better than the average of aligned sites = 540 Number in coding regions = 160 Number in noncoding regions = 380 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 4 GCTGCGTGCATCCTTCGTGCTCAAGATGA 1 10 0 TCCTTCGTGC 0.992392 -29 GCACACGGTGCTGCGTGCATCCTTCGTG 1 21 0 TGCTGCGTGC 0.992529 -18 AGTGTTGAACTCCAATGTGCAGTAATTACA 2 17 0 TCCAATGTGC 0.979517 -24 TTTAAAAATCTCTCGTGTGCTTTGCTTGTG 3 149 0 TCTCGTGTGC 0.978406 -152 ********** Masking position 8 Map Score: 1.38412 Number of sites scoring better than the average of aligned sites = 63 Number in coding regions = 14 Number in noncoding regions = 49 Number of orfs with sites within 600 bp upstream = 1 Fraction of orfs with sites within 600 bp upstream = 0.000160617 Motif number 5 TAATTATCAAGCTTTGGTAAATTGGAGTTG 3 28 0 GCTTTGGTAA 0.988788 -273 TGTGAAATAAGCTTTGGAAGGATTTTTTAT 3 123 0 GCTTTGGAAG 0.992722 -178 TCTCTCGTGTGCTTTGCTTGTGAAATAAGC 3 141 0 GCTTTGCTTG 0.986689 -160 ********** Masking position 5 Map Score: 0.623185 Number of sites scoring better than the average of aligned sites = 60 Number in coding regions = 14 Number in noncoding regions = 46 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 6 TACGCGTGTAATTACTGCACATT 2 4 1 GCGTGTAATT 0.967339 -37 CAAAGCACACGAGAGATTTTTAAAAACTAG 3 155 1 GAGAGATTTT 0.95469 -146 GTGTTATTTCGCTAGTTTTTAAAAATCTCT 3 166 0 GCTAGTTTTT 0.934812 -135 AGTAATCGCAGAGTGTTATTTCGCTAGTTT 3 178 0 GAGTGTTATT 0.985778 -123 TTGAAATCATGAGTGTCTTTAAATCTGTTA 3 209 0 GAGTGTCTTT 0.983128 -92 ********** Masking position 9 Map Score: 2.3038 Number of sites scoring better than the average of aligned sites = 155 Number in coding regions = 57 Number in noncoding regions = 98 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 7 ********** No masking Map Score: 1.65857e-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 8 ********** No masking Map Score: 1.65857e-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: 1.65857e-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