AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i227_tpal_bbur_300.orf -o227_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 RTP00410 181 AE000520 #2 RTP00427 300 AE000520 #3 RBB00237 56 3615 #4 RBB00234 23 3615 #5 RBB00232 158 3615 #6 RBB00836 101 3615 #7 RBB00158 51 3615 Motif number 1 ACCCAATCCTGGGCCTTCACCGGCTGAGGAA 1 38 1 GGGCCTTACC 0.786121 -144 GCGACAAAGATCCCCGAACCCATGTCCGTTG 1 146 1 TCCCCGACCC 0.982082 -36 CCCGAACCCATGTCCGTTGCGACGCTACCCT 1 158 1 TGTCCGTGCG 0.962815 -24 GTCTACGTACCGTAAGGTATTA 2 2 1 TCTACGTCCG 0.781687 -299 TATTCATCCTTCTCCTTCACCCTACCCCTTT 2 72 1 TCTCCTTACC 0.974847 -229 CCTTCACCCTACCCCTTTGCGTAAAATATTT 2 85 1 ACCCCTTGCG 0.91176 -216 GGAGAGGTCATACCCGTTCCCATCCCGAACA 2 133 1 TACCCGTCCC 0.948102 -168 GAAGTCAAGCTCTCCTACGCCGATGATACTG 2 166 1 TCTCCTAGCC 0.983957 -135 CGATGATACTGCTCCTTCGCGGGAAAGTAGG 2 186 1 GCTCCTTGCG 0.974288 -115 GTAGCCAGGCTCCCCTTTGCCCATCACTCGC 2 219 1 TCCCCTTGCC 0.992255 -82 GACAAAATATTATCCGAAACCTTAAAGTCCG 2 252 1 TATCCGAACC 0.847603 -49 TCAAACGAATGCGCCGAAGCCACCTGCGGAC 2 278 0 GCGCCGAGCC 0.97208 -23 ******* *** Masking position 5 Map Score: 12.0847 Number of sites scoring better than the average of aligned sites = 3178 Number in coding regions = 978 Number in noncoding regions = 2200 Number of orfs with sites within 600 bp upstream = 59 Fraction of orfs with sites within 600 bp upstream = 0.00947639 Motif number 2 GGGTGCGTTCATTTTTTACGGTGTTTGAGC 1 12 0 ATTTTTTACG 0.966703 -170 ACCAGGCGAAATATTTTACGCAAAGGGGTA 2 94 0 ATATTTTACG 0.929309 -207 ATCCTTTGTTATTTTTTATGCTTTCAATTA 3 37 0 ATTTTTTATG 0.957538 -20 TGTAAGATGTATATTTTTCTTAAGCTTTCA 5 42 0 ATATTTTTCT 0.923861 -117 TATTTTACAAATTTTTTTCTTTCTTGAAAT 5 100 0 ATTTTTTTCT 0.964025 -59 AATTTGTAAAATATTTTTTTTAAAGATAAA 5 117 1 ATATTTTTTT 0.904075 -42 CAAGCTATTAATTTTTTTGTTGTAATTTAA 6 35 0 ATTTTTTTGT 0.883866 -67 ATGGGTGAGTATTATTTTTGCCAAGCTATT 6 56 0 ATTATTTTTG 0.760368 -46 AAAAAATCTAATTTATTATTAAGTACGT 7 9 0 ATTTATTATT 0.745452 -43 AATAAATTAGATTTTTTATTTTTTCAATTT 7 22 1 ATTTTTTATT 0.954158 -30 ********** Masking position 6 Map Score: 10.6972 Number of sites scoring better than the average of aligned sites = 282 Number in coding regions = 80 Number in noncoding regions = 202 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 3 CATAGGGTAGCGTCGCAACGGACATGGGT 1 163 0 AGCTCGCAAC 0.991534 -19 AATATGGTCAAGCCTCACGACTTATTAGTAC 2 42 0 AGCTCACGAC 0.962327 -259 TGACCTCTCCACCATGGCAACCAGGCGAAAT 2 112 0 ACCTGGCAAC 0.981605 -189 GGCGTAGGAGAGCTTGACTTCCGTGTTCGGG 2 156 0 AGCTGACTTC 0.93732 -145 GGCAAAGGGGAGCCTGGCTACTACCTACTTT 2 209 0 AGCTGGCTAC 0.993323 -92 GCCCATCACTCGCTTGACAAAATATTATCCG 2 237 1 CGCTGACAAA 0.918573 -64 AAAAATTAATAGCTTGGCAAAAATAATACTC 6 49 1 AGCTGGCAAA 0.986966 -53 *** ******* Masking position 5 Map Score: 6.7182 Number of sites scoring better than the average of aligned sites = 233 Number in coding regions = 71 Number in noncoding regions = 162 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 4 CCTACCCCTTTGCGTAAAATATTTCGCCTG 2 92 1 TGCGTAAAAT 0.854076 -209 ATGTATATTTTTCTTAAGCTTTCAGTAATA 5 36 0 TTCTTAAGCT 0.779721 -123 ATTTTGAGCATTTGTAAGATGTATATTTTT 5 54 0 TTTGTAAGAT 0.955954 -105 ATTTTTTTCTTTCTTGAAATTTAATAAAAT 5 90 0 TTCTTGAAAT 0.886512 -69 AAGAAAAAAATTTGTAAAATATTTTTTTTA 5 109 1 TTTGTAAAAT 0.956763 -50 AAAATATTTTTTTTAAAGATAAAATGCTTT 5 124 1 TTTTAAAGAT 0.835074 -35 TATTAGGGTATTTTTAAAATATGGGTGAGT 6 76 0 TTTTTAAAAT 0.916452 -26 TTTTTTCAATTTTGAGAAATGT 7 40 1 TTTGAGAAAT 0.823528 -12 ********** Masking position 7 Map Score: 3.02626 Number of sites scoring better than the average of aligned sites = 173 Number in coding regions = 48 Number in noncoding regions = 125 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 5 GCTGGTACTGTAACACCTTTCCATCTTGGG 1 78 1 TAACACCTTT 0.928943 -104 GCCTGGCTACTACCTACTTTCCCGCGAAGG 2 199 0 TACCTACTTT 0.970587 -102 ATTATAAACCTCCTTTTTTCTAA 4 8 0 AACCTCCTTT 0.981069 -16 TTTTCCTCCTTTGATAAAGCAT 5 147 0 TTCCTCCTTT 0.981114 -12 ********** Masking position 8 Map Score: 0.513102 Number of sites scoring better than the average of aligned sites = 71 Number in coding regions = 19 Number in noncoding regions = 52 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 6 TTTCCATCTTGGGAAATAATCGCCGCTTTT 1 95 1 GGGAAATAAT 0.918704 -87 GAAGGAGAAGGATGAATAATATGGTCAAGC 2 60 0 GATGAATAAT 0.904032 -241 TGGCAACCAGGCGAAATATTTTACGCAAAG 2 99 0 GCGAAATATT 0.761468 -202 TTAAGGTTTCGGATAATATTTTGTCAAGCG 2 247 0 GGATAATATT 0.732317 -54 GAAAAAAGGAGGTTTATAAT 4 14 1 GGTTTATAAT 0.796567 -10 GTGTTATATTGATACATATTGTTAT 5 6 0 GATACATATT 0.746874 -153 GCATTTGTAAGATGTATATTTTTCTTAAGC 5 47 0 GATGTATATT 0.809412 -112 AGGTAAATAATAAGCAATAAT 6 2 1 GGTAAATAAT 0.952282 -100 TTAAAATATGGGTGAGTATTATTTTTGCCA 6 63 0 GGTGAGTATT 0.874009 -39 ********** Masking position 7 Map Score: 0.811585 Number of sites scoring better than the average of aligned sites = 951 Number in coding regions = 292 Number in noncoding regions = 659 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 7 ********** No masking Map Score: -1.34049e-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: -1.34049e-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: -1.34049e-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