AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i266_hypothetical11_mpneu_reg_300.orf -o266_mpneu_300.ace -a/home/amcguire/alignace/lib/ORF_mpneu.txt -z/skink1/amcguire/genomes/mpneu.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 RMP00504 194 Mycoplasma_pneumoniae #2 RMP00505 70 Mycoplasma_pneumoniae #3 RMP00506 24 Mycoplasma_pneumoniae #4 RMP00512 146 Mycoplasma_pneumoniae #5 RMP00513 23 Mycoplasma_pneumoniae #6 RMP00517 300 Mycoplasma_pneumoniae Motif number 1 tgaggcgtcgttttggacgacccac 1 180 1 ttttggacga 0.913585 -15 aaagttattttggcaaagaaaaccata 4 130 0 ttttggcaaa 0.933376 -17 aactcgacgattttgccgaaaaatcacaga 6 78 1 ttttgccgaa 0.975856 -223 aatcacagaatattcgcgaatctttcggaa 6 99 1 tattcgcgaa 0.962201 -202 ttcgcgaatctttcggaaaagacacggtaa 6 111 1 tttcggaaaa 0.802366 -190 cattcgggggttttgccggacatcccgagt 6 161 0 ttttgccgga 0.960253 -140 ttgttacaattattggcgaacattcggggg 6 181 0 tattggcgaa 0.989607 -120 ttgttacaattattggacaattttgttaca 6 203 0 tattggacaa 0.917725 -98 aacgtcacaattttggcgaaatttcgaata 6 257 1 ttttggcgaa 0.993442 -44 tcgaaatttttttccgcaaatt 6 289 1 tttccgcaaa 0.886022 -12 ********** Masking position 3 Map Score: 15.0076 Number of sites scoring better than the average of aligned sites = 149 Number in coding regions = 124 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 2 agtctattaatgggaaaaattcccattttacc 1 45 1 tgggaaattc 0.975512 -150 agaagatcgattgtgaatattctttacttaat 1 89 0 ttgtaaattc 0.96211 -106 attctccaacttcttacgatttaacattgtgt 2 38 0 ttctacattt 0.801388 -33 attgtttaattggggacgatttcagtacgaat 4 45 0 tgggacattt 0.952876 -102 ttgataagtttggccaccaattctctatttgc 6 44 0 tggcacaatt 0.870453 -257 tcgacgattttgccgaaaaatcacagaatatt 6 81 1 tgccaaaatc 0.805597 -220 tccgaaagattcgcgaatattctgtgattttt 6 96 0 tcgcaaattc 0.925704 -205 ttacaattattggcgaacattcgggggttttg 6 176 0 tggcaaattc 0.984805 -125 ttggacaattttgttacaattattggcgaaca 6 189 0 ttgtacatta 0.873546 -112 tcggaaaattttgttacaattattggacaatt 6 211 0 ttgtacatta 0.873546 -90 ttcgccaaaattgtgacgtttttactcgatta 6 245 0 ttgtactttt 0.724708 -56 gtcacaattttggcgaaatttcgaatatttcg 6 260 1 tggcaatttc 0.929762 -41 ggaaaaaaatttcgaaatattcgaaatttcgc 6 272 0 ttcgaaattc 0.886253 -29 **** ** **** Masking position 6 Map Score: 9.97905 Number of sites scoring better than the average of aligned sites = 208 Number in coding regions = 187 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 3 cgattgtgaatattctttacttaatcaaatta 1 82 0 tattcttttt 0.95857 -113 tcacaatcgatcttctcctgctgccgttttct 1 105 1 tcttctccct 0.942479 -90 tcaataattctattctccaacttcttacgatt 2 49 0 tattctccct 0.966594 -22 cgcactttaatattgtttaattggggacgatt 4 56 0 tattgttttt 0.792919 -91 atccttggcgtcttctgcgtttattcgcactt 4 81 0 tcttctgctt 0.966594 -66 acggtattctgttttttatgtttttc 6 5 1 tattctgttt 0.981179 -296 tttggccaccaattctctatttgcgacttacg 6 36 0 aattctcttt 0.903308 -265 gattcgcgaatattctgtgatttttcggcaaa 6 89 0 tattctgttt 0.981179 -212 ******** ** Masking position 6 Map Score: 5.36739 Number of sites scoring better than the average of aligned sites = 38 Number in coding regions = 28 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 4 atatacataaatatacataat 4 2 0 atatacataa 0.970228 -145 gatctgaatgatatacataaatatacataa 4 12 0 atatacataa 0.970228 -135 tttggcaaagaaaaccataaaacatatttg 4 119 0 aaaaccataa 0.951449 -28 gcgacttacgaaaaacataaaaaacagaat 6 16 0 aaaaacataa 0.970936 -285 ********** Masking position 7 Map Score: 1.73144 Number of sites scoring better than the average of aligned sites = 10 Number in coding regions = 9 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 5 ccattttaccagtagtaatttgattaagta 1 67 1 agtagtaatt 0.854906 -128 tcagatcggaattcgtactgaaatcgtccc 4 35 1 attcgtactg 0.872488 -112 ttctgcgtttattcgcactttaatattgtt 4 71 0 attcgcactt 0.975527 -76 ttaaccgattagtaattattgcc 5 7 0 attagtaatt 0.912288 -17 gtttttcgtaagtcgcaaatagagaattgg 6 30 1 agtcgcaaat 0.911486 -271 atcacagaatattcgcgaatctttcggaaa 6 100 1 attcgcgaat 0.4921 -201 atttcgaaatattcgaaatttcgccaaaat 6 266 0 attcgaaatt 0.969229 -35 atttcgaatatttcgaaatttttttccgca 6 277 1 tttcgaaatt 0.850507 -24 ********** Masking position 3 Map Score: 2.99786 Number of sites scoring better than the average of aligned sites = 63 Number in coding regions = 54 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 6 tgtcgtgagaaaacggcagcaggagaagat 1 114 0 aaacggcagc 0.958412 -81 tgaatgaataaaacgaatggaacgtgtcgt 1 147 1 aaacgaatgg 0.886052 -48 gacgcctcacaaacgacacgttccattcgt 1 159 0 aaacgacacg 0.992128 -36 gggtcgtccaaaacgacgcctcacaaacga 1 173 0 aaacgacgcc 0.967402 -22 aatctttcggaaaagacacggtaaaaggat 6 117 1 aaaagacacg 0.971738 -184 aagacacggtaaaaggatcgaactcggatt 6 129 1 aaaaggatcg 0.806487 -172 aatcgagtaaaaacgtcacaattttggcga 6 246 1 aaacgtcaca 0.880108 -55 ********** Masking position 3 Map Score: 3.04421 Number of sites scoring better than the average of aligned sites = 72 Number in coding regions = 65 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 7 tctcacgattttttacacaatgttaaatcg 2 24 1 ttttacacaa 0.901987 -47 aaacttatcaattaactcgacgattttgcc 6 65 1 attaactcga 0.935421 -236 cgaactcggattttactcgggatgtccggc 6 147 1 ttttactcgg 0.981899 -154 attgtgacgtttttactcgattacctcgga 6 238 0 ttttactcga 0.989299 -63 ********** Masking position 5 Map Score: 0.241597 Number of sites scoring better than the average of aligned sites = 9 Number in coding regions = 8 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 8 ********** No masking Map Score: 1.26009e-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: 1.26009e-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 10 ********** No masking Map Score: 1.26009e-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