AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i201_excinuclease_abc_mpneu_reg_100.orf -o201_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 RMP00221 157 Mycoplasma_pneumoniae #2 RMP00223 45 Mycoplasma_pneumoniae #3 RMP00624 300 Mycoplasma_pneumoniae Motif number 1 tgttaactaattaattactaataactatcaaagt 1 16 0 ttattcaaaa 0.802886 -142 cttataataaataaaccaaaacaaccaccttaag 1 55 0 ataacaaaaa 0.968149 -103 cagtcaaggggtgaaccccacaaaatcagccccc 1 92 0 gtaaccacaa 0.942237 -66 ttaatacttgttgaattataacaaaataagaaat 1 131 0 ttaataaaaa 0.958997 -27 tagtactaaaatcaataagactaaggg 2 29 1 ataataacaa 0.968149 -17 atgtagactattgaataaaactaaaacaatcgtt 3 67 1 ttaataacaa 0.978013 -234 aatctacacctaaaaccacaataacgattgtttt 3 89 0 taaacaaaaa 0.916957 -212 ttgtccactgaaaaaccaaacgaaatctacacct 3 112 0 aaaacaacaa 0.934832 -189 cgttcgaggaattattaagaataattcctcctac 3 176 1 atattaaaaa 0.816248 -125 aaaccgtgtttttaccacaaccaatcgttagtaa 3 229 1 ttacccacaa 0.925286 -72 attaattcaattgaacgagacaaaccacgtatta 3 262 1 ttaacaacaa 0.987988 -39 ** *** * ** ** Masking position 10 Map Score: 10.1126 Number of sites scoring better than the average of aligned sites = 280 Number in coding regions = 234 Number in noncoding regions = 46 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 2 aattagttaacagcccacttaaggtggttgtt 1 38 1 cagcccacaa 0.996848 -120 cccacaaaatcagcccccaaacttataataaa 1 78 0 cagcccccac 0.973062 -80 tcaaggggtgaaccccacaaaatcagccccca 1 91 0 aaccccacaa 0.938667 -67 aataagaaattagcccagtcaaggggtgaacc 1 109 0 tagcccagaa 0.989816 -49 gtactagggtcatcccagtaacaa 2 3 0 catcccagac 0.915045 -43 tataaatctgtatccaacacaattccctaaaa 3 17 1 tatccaacaa 0.891783 -284 ttttattcaatagtctacataaatgtacctat 3 55 0 tagtctacaa 0.876465 -246 tgggcaatttttgtccactgaaaaaccaaacg 3 124 0 ttgtccacaa 0.952548 -177 tggacaaaaattgcccaccgaaaaattaacac 3 139 1 ttgcccacaa 0.990275 -162 ******** ** Masking position 11 Map Score: 8.93547 Number of sites scoring better than the average of aligned sites = 89 Number in coding regions = 76 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 3 gatagttattagtaattaattagttaacag 1 21 1 agtaattaat 0.914697 -137 ataattcaacaagtattaattc 1 146 1 aagtattaat 0.949685 -12 aaaaagtataaatctgtatccaa 3 4 1 aagtataaat 0.806455 -297 tcgaacgtcaaggtgttaatttttcggtgg 3 153 0 aggtgttaat 0.95827 -148 ttgacgttcgaggaattattaagaataatt 3 172 1 aggaattatt 0.960016 -129 taacagtaggaggaattattcttaataatt 3 185 0 aggaattatt 0.960016 -116 accaatcgttagtaattaattcaattgaac 3 248 1 agtaattaat 0.914697 -53 ********** Masking position 8 Map Score: 9.01605 Number of sites scoring better than the average of aligned sites = 79 Number in coding regions = 67 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 4 accaccttaagtgggctgttaactaattaa 1 36 0 gtgggctgtt 0.99603 -122 ttataagtttgggggctgattttgtggggt 1 82 1 gggggctgat 0.987482 -76 caccccttgactgggctaatttcttatttt 1 113 1 ctgggctaat 0.978752 -45 gtacatttatgtagactattgaataaaact 3 59 1 gtagactatt 0.89513 -242 taatttttcggtgggcaatttttgtccact 3 137 0 gtgggcaatt 0.986044 -164 ********** Masking position 10 Map Score: 3.98601 Number of sites scoring better than the average of aligned sites = 40 Number in coding regions = 35 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 5 taattagttaacagcccacttaaggtggtt 1 37 1 acagcccact 0.991652 -121 ccccacaaaatcagcccccaaacttataat 1 81 0 tcagccccca 0.961572 -77 aaataagaaattagcccagtcaaggggtga 1 112 0 ttagcccagt 0.98676 -46 agtactagggtcatcccagtaacaa 2 6 0 tcatcccagt 0.947925 -40 gtgggcaatttttgtccactgaaaaaccaa 3 127 0 tttgtccact 0.922278 -174 gtggacaaaaattgcccaccgaaaaattaa 3 138 1 attgcccacc 0.948782 -163 ********** Masking position 6 Map Score: 3.01234 Number of sites scoring better than the average of aligned sites = 92 Number in coding regions = 81 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 6 ********** No masking Map Score: 4.00336e-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: 4.00336e-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: 4.00336e-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