AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i010_tpal_bbur_100.orf -o010_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 RTP00796 226 AE000520 #2 RBB00545 300 3615 #3 RBB00736 178 3615 #4 RBB00735 61 3615 Motif number 1 TAAATTGAGCTTTACGTATTATTATTTGCGGTGTG 2 27 0 TTTATTTTTT 0.985362 -274 TTAAAGTTAAATTAGGTTTTGTTGTATTTATATAT 2 61 0 ATTATTTTTT 0.959896 -240 TTTTTTATATAATAAATGTTATTAAGTTGGATATT 2 94 0 AATATTTTTA 0.86036 -207 ATTATATTTTTTCATGTTTTTTTATATAATAAATG 2 111 0 TTCATTTTTT 0.9589 -190 CATGAAAAAATATAATTGATTTTTTTAATCACGCT 2 130 1 TATATATTTT 0.945573 -171 GATTCCCATATTTATGTTTTATTTTAACATTCTTT 2 197 0 TTTATTTTTT 0.985362 -104 TTATATTAATTTTAGATTTTTTTGTTAGACTTTTT 2 247 0 TTTATTTTTT 0.985361 -54 GAAAGATAGTAATAGTTTATATTAATTTTAGATTT 2 263 0 AATATATTTA 0.686962 -38 TTTGCTTAATTTTATATTTTTTTGTCTAGGTTTTT 3 37 1 TTTATTTTTT 0.985361 -142 AACATCATTATACAACTTATTTTATAATTTTAATT 3 80 0 TACATATTTT 0.857615 -99 AAAACCAAATTATAGCTCTTTTTTTAAATTACTCA 3 146 0 TATATTTTTT 0.97996 -33 CATCTATATGTTTATATATTTTTCAAATATCAAGA 4 24 0 TTTATTTTTA 0.959889 -38 **** * ** ** * Masking position 4 Map Score: 18.459 Number of sites scoring better than the average of aligned sites = 115 Number in coding regions = 27 Number in noncoding regions = 88 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 2 TTTTGTTGTATTTATATATAAATTGAGCTTT 2 49 0 TTTATATATA 0.731605 -252 TTTTCATGTTTTTTTATATAATAAATGTTAT 2 107 0 TTTTTATATA 0.901071 -194 TATAATTGATTTTTTTAATCACGCTTATTCT 2 140 1 TTTTTTAATA 0.92171 -161 CTTATTCTATTTATTTAATAAAAGCAGTTTT 2 163 1 TTATTTAATA 0.502782 -138 TTTTAACATTCTTTTTTAAAACTGCTTTTAT 2 180 0 CTTTTTTAAA 0.779767 -121 TATTTATGTTTTATTTTAACATTCTTTTTTA 2 193 0 TTATTTTAAA 0.776259 -108 TTTTGTTAGACTTTTTAATAAGTTTTGTGTA 2 232 0 CTTTTTAATA 0.86287 -69 TAATTTTAGATTTTTTTGTTAGACTTTTTAA 2 245 0 TTTTTTTGTA 0.85911 -56 TTTGTCTAGGTTTTTATCTTAATAATTAAAA 3 57 1 TTTTTATCTA 0.815816 -122 ATTATACAACTTATTTTATAATTTTAATTAT 3 78 0 TTATTTTATA 0.805762 -101 TTGTGGCTAATTTTTAAATTAGCTGCCTTAC 3 114 1 TTTTTAAATA 0.8958 -65 TATAGCTCTTTTTTTAAATTACTCATGTAAG 3 140 0 TTTTTAAATA 0.8958 -39 TGTTTATATATTTTTCAAATATCAAGACCAA 4 20 0 TTTTTCAAAA 0.716509 -42 ********* * Masking position 11 Map Score: 12.4201 Number of sites scoring better than the average of aligned sites = 413 Number in coding regions = 115 Number in noncoding regions = 298 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 3 TTAAATTAGGTTTTGTTGTATTTATATATA 2 60 0 TTTTGTTGTA 0.798196 -241 TTTTTTCATGTTTTTTTATATAATAAATGT 2 110 0 TTTTTTTATA 0.976296 -191 TATAATTGATTTTTTTAATCACGCTTATTC 2 140 1 TTTTTTAATC 0.930482 -161 CTTATTCTATTTATTTAATAAAAGCAGTTT 2 163 1 TTATTTAATA 0.917244 -138 TTTAACATTCTTTTTTAAAACTGCTTTTAT 2 180 0 TTTTTTAAAA 0.879132 -121 TATTTATGTTTTATTTTAACATTCTTTTTT 2 194 0 TTATTTTAAC 0.826384 -107 TTTTGTTAGACTTTTTAATAAGTTTTGTGT 2 233 0 CTTTTTAATA 0.785828 -68 TAATTTTAGATTTTTTTGTTAGACTTTTTA 2 246 0 TTTTTTTGTT 0.784116 -55 TGTTTTTGCTTAATTTTATATTTTTTTGTC 3 33 1 TAATTTTATA 0.7123 -146 TAATTTTATATTTTTTTGTCTAGGTTTTTA 3 43 1 TTTTTTTGTC 0.935194 -136 ATTATACAACTTATTTTATAATTTTAATTA 3 79 0 TTATTTTATA 0.955308 -100 ATTATAGCTCTTTTTTTAAATTACTCATGT 3 143 0 TTTTTTTAAA 0.93599 -36 ********** Masking position 6 Map Score: 10.6815 Number of sites scoring better than the average of aligned sites = 366 Number in coding regions = 105 Number in noncoding regions = 261 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 4 TCTCATGTGGTGTGTGCGTCGCTGACCTTT 1 34 0 TGTGTGCGTC 0.981066 -193 ACACACCACATGAGAGCGGCCAAAGGGCGG 1 49 1 TGAGAGCGGC 0.925711 -178 GGAAGTCCTACCTGTGCGGCAAGCGCAATC 1 116 1 CCTGTGCGGC 0.955132 -111 GCGCTTGCAGTGATTGCGCTTGCCGCACAG 1 127 0 TGATTGCGCT 0.911149 -100 GCAAGCGCATTCTTTGCGTTATGCACCCCA 1 149 1 TCTTTGCGTT 0.933612 -78 ATTTGCGGTGTGTTTGAGGTAGTTGAAG 2 9 0 TGTTTGAGGT 0.940641 -292 TACGTATTATTATTTGCGGTGTGTTTGAGG 2 20 0 TATTTGCGGT 0.949749 -281 TGTATAATGATGTTTGTGGCTAATTTTTAA 3 101 1 TGTTTGTGGC 0.961737 -78 ********** Masking position 6 Map Score: 4.00119 Number of sites scoring better than the average of aligned sites = 596 Number in coding regions = 183 Number in noncoding regions = 413 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 5 AATAATACGTAAAGCTCAATTTATATATAA 2 39 1 AAAGCTCAAT 0.957152 -262 GTTGGATATTAAAGTTAAATTAGGTTTTGT 2 74 0 AAAGTTAAAT 0.893138 -227 GCGTGATTAAAAAAATCAATTATATTTTTT 2 134 0 AAAAATCAAT 0.900355 -167 TGTTAAAATAAAACATAAATATGGGAATCT 2 203 1 AAACATAAAT 0.88736 -98 TCCTCCTTAAAACCAAATTATAGCTCTT 3 161 0 AAAACCAAAT 0.934257 -18 ATCAAGACCAAAAGCCAAAT 4 1 0 AAAGCCAAAT 0.957165 -61 TTGATATTTGAAAAATATATAAACATATAG 4 26 1 AAAAATATAT 0.736004 -36 ********** Masking position 3 Map Score: 2.5841 Number of sites scoring better than the average of aligned sites = 365 Number in coding regions = 109 Number in noncoding regions = 256 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 6 GCCAAAGGGCGGTTTTACCCGCTCCATCCCC 1 67 1 GGTTTTCCCG 0.969035 -160 CAAGGACGATGGATTCGCGTGCCACTACCTG 1 177 0 GGATTCCGTG 0.989039 -50 GGTTTACGTGGTTCTCGCGTGTTATATCAAG 1 204 0 GTTCTCCGTG 0.951648 -23 AGGGTTTACGTGGTTCTCGCGT 1 215 0 GGGTTTCGTG 0.983432 -12 TATGGTTTCTCCTGAAAGATAGTA 2 287 0 GGTTTCCCTG 0.993652 -14 ****** **** Masking position 5 Map Score: 0.745166 Number of sites scoring better than the average of aligned sites = 130 Number in coding regions = 42 Number in noncoding regions = 88 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 7 ********** No masking Map Score: 1.29562e-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 8 ********** No masking Map Score: 1.29562e-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 9 ********** No masking Map Score: 1.29562e-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