AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i009_Nucleotide_Biosynthes_mpneu_reg_100.orf -o009_mpneu_100.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 RMP00517 300 Mycoplasma_pneumoniae Motif number 1 accaattctctatttgcgacttacgaaaaa 1 31 0 tatttgcgac 0.959517 -270 aactcgacgattttgccgaaaaatcacaga 1 78 1 ttttgccgaa 0.996859 -223 aatcacagaatattcgcgaatctttcggaa 1 99 1 tattcgcgaa 0.975726 -202 tttaccgtgtcttttccgaaagattcgcga 1 112 0 cttttccgaa 0.982445 -189 cattcgggggttttgccggacatcccgagt 1 161 0 ttttgccgga 0.988853 -140 ttgttacaattattggcgaacattcggggg 1 181 0 tattggcgaa 0.992983 -120 ttgtaacaaaattttccgaggtaatcgagt 1 224 1 attttccgag 0.909336 -77 aacgtcacaattttggcgaaatttcgaata 1 257 1 ttttggcgaa 0.996263 -44 tttcgaaatttttttccgcaaatt 1 287 1 tttttccgca 0.982446 -14 ********** Masking position 4 Map Score: 18.895 Number of sites scoring better than the average of aligned sites = 65 Number in coding regions = 62 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 2 acggtattctgttttttatgtttttcg 1 6 1 attctgtttt 0.984145 -295 ttatcaattaactcgacgattttgccgaaaaa 1 69 1 actcgaattt 0.964973 -232 attcgcgaatattctgtgatttttcggcaaaa 1 88 0 attctgattt 0.974807 -213 cgatccttttaccgtgtcttttccgaaagatt 1 117 0 accgtgtttt 0.803509 -184 aaaggatcgaactcggattttactcgggatgt 1 140 1 actcggttta 0.942283 -161 attggcgaacattcgggggttttgccggacat 1 168 0 attcgggttt 0.989886 -133 tgttacaattattggacaattttgttacaatt 1 200 0 attggaattt 0.944955 -101 tttcgccaaaattgtgacgtttttactcgatt 1 246 0 attgtggttt 0.948801 -55 atttcgaaatattcgaaatttcgccaaaattg 1 264 0 attcgatttc 0.935496 -37 atttcgaatatttcgaaatttttttccgcaaa 1 277 1 tttcgatttt 0.897269 -24 ****** **** Masking position 10 Map Score: 10.1446 Number of sites scoring better than the average of aligned sites = 164 Number in coding regions = 142 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 3 gcaaaatcgtcgagttaattgataagtttgg 1 63 0 cgagtaattg 0.922013 -238 tgtgatttttcggcaaaatcgtcgagttaat 1 75 0 cggcaaatcg 0.936844 -226 cgaaaaatcacagaatattcgcgaatctttc 1 94 1 cagatattcg 0.924671 -207 gtgtcttttccgaaagattcgcgaatattct 1 105 0 cgaagattcg 0.748045 -196 ggattttactcgggatgtccggcaaaacccc 1 154 1 cgggtgtccg 0.939172 -147 ggcaaaacccccgaatgttcgccaataattg 1 174 1 ccgatgttcg 0.957707 -127 caaaattttccgaggtaatcgagtaaaaacg 1 230 1 cgagtaatcg 0.985097 -71 aaaaaaatttcgaaatattcgaaatttcgcc 1 271 0 cgaatattcg 0.599565 -30 **** ****** Masking position 1 Map Score: 9.29871 Number of sites scoring better than the average of aligned sites = 78 Number in coding regions = 67 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 4 gttcgccaataattgtaacaaaattgtcca 1 190 1 aattgtaaca 0.994521 -111 attgtccaataattgtaacaaaattttccg 1 212 1 aattgtaaca 0.994521 -89 atttcgccaaaattgtgacgtttttactcg 1 249 0 aattgtgacg 0.992357 -52 ********** Masking position 8 Map Score: 3.60101 Number of sites scoring better than the average of aligned sites = 3 Number in coding regions = 1 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 5 gcaaatagagaattggtggccaaacttatc 1 44 1 aattggtggc 0.929782 -257 tttttcggcaaaatcgtcgagttaattgat 1 71 0 aaatcgtcga 0.95705 -230 gtcttttccgaaagattcgcgaatattctg 1 104 0 aaagattcgc 0.973846 -197 agacacggtaaaaggatcgaactcggattt 1 130 1 aaaggatcga 0.936453 -171 caaaacccccgaatgttcgccaataattgt 1 176 1 gaatgttcgc 0.963993 -125 attttgttacaattattggacaattttgtt 1 206 0 aattattgga 0.893745 -95 aaaaatttcgaaatattcgaaatttcgcca 1 270 0 aaatattcga 0.978642 -31 ********** Masking position 2 Map Score: 4.87047 Number of sites scoring better than the average of aligned sites = 86 Number in coding regions = 75 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 6 ********** No masking Map Score: 7.91135e-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: 7.91135e-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: 7.91135e-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