AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i206_tpal_bbur_300.orf -o206_tpal_bbur_300.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 TATTTTTGTTAAAATTTTAATTATCAAGCT 3 45 0 AAAATTTTAA 0.865257 -256 AAATTTTAACAAAAATAAATCAAAATAATT 3 58 1 AAAAATAAAT 0.683029 -243 AAACAATTTGAAAAATTATTTTGATTTATT 3 71 0 AAAAATTATT 0.621907 -230 AAATTGTTTTAAGAATTTAATAAAAATGCA 3 92 1 AAGAATTTAA 0.968601 -209 TAAGCTTTGGAAGGATTTTTTATCTGCATT 3 116 0 AAGGATTTTT 0.883921 -185 AAAGCACACGAGAGATTTTTAAAAACTAGC 3 156 1 AGAGATTTTT 0.748561 -145 GATTACTATAACAGATTTAAAGACACTCAT 3 201 1 ACAGATTTAA 0.931838 -100 CAAGTTAGACAAAAATTTATTAATATTGAT 3 236 1 AAAAATTTAT 0.660591 -65 ATATTGATAGAAAAATTTTACATTAAATTC 3 258 1 AAAAATTTTA 0.689679 -43 TTTTGTCCTTACGAATTTAATGTAAAATTT 3 270 0 ACGAATTTAA 0.931826 -31 CGTAAGGACAAAAAATTAAAATTC 3 287 1 AAAAATTAAA 0.951997 -14 ********** Masking position 1 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 CCAAAGCTTGATAATTAAAATTTTAACAAAA 3 41 1 ATAATAAAAT 0.90202 -260 TTAACAAAAATAAATCAAAATAATTTTTCAA 3 63 1 TAAATAAAAT 0.96832 -238 TCTTAAAACAATTTGAAAAATTATTTTGATT 3 75 0 ATTTGAAAAT 0.672888 -226 TTTTAAGAATTTAATAAAAATGCAGATAAAA 3 98 1 TTAATAAAAT 0.977186 -203 ATTTCGCTAGTTTTTAAAAATCTCTCGTGTG 3 160 0 TTTTTAAAAT 0.729374 -141 TAGACAAAAATTTATTAATATTGATAGAAAA 3 241 1 TTTATAATAT 0.824799 -60 CTTACGAATTTAATGTAAAATTTTTCTATCA 3 262 0 TAATGAAAAT 0.915346 -39 GTAAGGACAAAAAATTAAAATTC 3 288 1 AAAATAAAAT 0.94749 -13 ***** ***** Masking position 7 Map Score: 7.32697 Number of sites scoring better than the average of aligned sites = 432 Number in coding regions = 124 Number in noncoding regions = 308 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 3 ATGTGCAGTAATTACACGCGTA 2 3 0 ATTACACGCG 0.95808 -38 ATACATATCAAGCTATCCAACTCC 3 5 1 ATATCAAGCT 0.989734 -296 AAAATTTTAATTATCAAGCTTTGGTAAATT 3 35 0 TTATCAAGCT 0.967028 -266 AACTAGCGAAATAACACTCTGCGATTACTA 3 179 1 ATAACACTCT 0.933023 -122 GACACTCATGATTTCAAGTTAGACAAAAAT 3 222 1 ATTTCAAGTT 0.92808 -79 ********** Masking position 6 Map Score: 1.5785 Number of sites scoring better than the average of aligned sites = 104 Number in coding regions = 26 Number in noncoding regions = 78 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 4 TTTATTTTTGTTAAAATTTTAATTATCAAG 3 47 0 TTAAAATTTT 0.905624 -254 AATAAATCAAAATAATTTTTCAAATTGTTT 3 71 1 AATAATTTTT 0.757148 -230 CTGCATTTTTATTAAATTCTTAAAACAATT 3 93 0 ATTAAATTCT 0.960383 -208 AAATGCAGATAAAAAATCCTTCCAAAGCTT 3 115 1 AAAAAATCCT 0.764793 -186 CATGAGTGTCTTTAAATCTGTTATAGTAAT 3 202 0 TTTAAATCTG 0.814092 -99 TATCAATATTAATAAATTTTTGTCTAACTT 3 237 0 AATAAATTTT 0.935745 -64 CGAATTTAATGTAAAATTTTTCTATCAATA 3 259 0 GTAAAATTTT 0.849233 -42 AAAATTTTACATTAAATTCGTAAGGACAAA 3 269 1 ATTAAATTCG 0.922204 -32 GAATTTTAATTTTTTGTCCTTACG 3 287 0 TTTAATTTTT 0.852567 -14 ********** Masking position 5 Map Score: 6.2575 Number of sites scoring better than the average of aligned sites = 1070 Number in coding regions = 311 Number in noncoding regions = 759 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 5 TCATCTTGAGCACGAAGGATGCACGCAGC 1 10 1 GCACGAAGGA 0.99215 -29 CACGAAGGATGCACGCAGCACCGTGTGC 1 21 1 GCACGCAGCA 0.992291 -18 TGTAATTACTGCACATTGGAGTTCAACACT 2 17 1 GCACATTGGA 0.978873 -24 CACAAGCAAAGCACACGAGAGATTTTTAAA 3 149 1 GCACACGAGA 0.977819 -152 ********** Masking position 3 Map Score: 1.38412 Number of sites scoring better than the average of aligned sites = 67 Number in coding regions = 16 Number in noncoding regions = 51 Number of orfs with sites within 600 bp upstream = 1 Fraction of orfs with sites within 600 bp upstream = 0.000160617 Motif number 6 ********** 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 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