AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i255_heat_shock_mpneu_reg_300.orf -o255_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 Purged sequences: RMP00035 22 Mycoplasma_pneumoniae Input sequences: #1 RMP00031 31 Mycoplasma_pneumoniae #2 RMP00036 300 Mycoplasma_pneumoniae #3 RMP00134 45 Mycoplasma_pneumoniae #4 RMP00137 300 Mycoplasma_pneumoniae #5 RMP00406 300 Mycoplasma_pneumoniae #6 RMP00408 55 Mycoplasma_pneumoniae Motif number 1 ttatcctaattttattttgttagccgc 1 8 0 tttattttgt 0.970458 -24 tgctaatggtttaatttcgaaatcacggat 2 69 0 ttaatttcga 0.958188 -232 acaggaatacttaattttgtcgtgaatgtc 2 147 1 ttaattttgt 0.981376 -154 cgtcaaaatattaattgtgagcttactaat 3 17 1 ttaattgtga 0.914889 -29 cgccagaatattaatttcgttcatcaaaaa 4 281 1 ttaatttcgt 0.967577 -20 cgttttttttttttttttgaaagaaattga 5 88 0 ttttttttga 0.818877 -213 atctcttggcttaattttgtacattttaaa 5 150 0 ttaattttgt 0.981376 -151 aaatttttgctttattttggcactttaaaa 5 254 0 tttattttgg 0.936703 -47 ********** Masking position 5 Map Score: 9.62272 Number of sites scoring better than the average of aligned sites = 94 Number in coding regions = 68 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 2 tttagttatgtgaggtggtttaaccacacccccta 2 112 0 tgatggtttc 0.964304 -189 tgaatgtcgttaaggcggtttcgatagtgggaacg 2 169 1 taacggtttt 0.966803 -132 tgtgttggcgtgaaatggattaaccgtcactactt 2 208 0 tgatggattc 0.757809 -93 ttaattattttaatatggttgagatgaaagaatct 2 265 1 taatggttgt 0.915328 -36 tcaggtaaatgaaggtggttattacccctacatcg 4 125 0 gaatggttac 0.803166 -176 ttaatataattaaatcggtttcgatcaaaaattcg 4 248 1 taacggtttt 0.966803 -53 attcctgttttaatccgcttatcaccaattggt 5 9 0 taacgcttac 0.843612 -292 ttgctttaactaacctgcttttatctaactattta 5 53 0 taatgctttc 0.943669 -248 gccaagagattaagctagttgcaccagtgggcact 5 170 1 taatagttgc 0.880934 -131 cagtgggcactaaagcagtttttcttacttatcaa 5 194 1 taacagtttt 0.865393 -107 tggcactttaaaagctagtttttacctaaaaataa 5 232 0 aaatagtttc 0.686157 -69 taacgcggtttttgctctctaaagg 5 286 0 taacggtttc 0.989046 -15 *** ****** * Masking position 3 Map Score: 7.22935 Number of sites scoring better than the average of aligned sites = 246 Number in coding regions = 222 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 3 aattaaaccattagcaatttaacgaagcttag 2 83 1 ttgcaattta 0.926674 -218 tttgcggattgaattagaatat 4 1 1 ttgcggatta 0.977775 -300 aatttctaggtttgcagattgatcagtatatt 4 28 0 ttgcagatta 0.984935 -273 caattggtgataagcggattaaaacaggaata 5 13 1 tagcggatta 0.901312 -288 ttgctttattttggcactttaaaagctagttt 5 246 0 ttgcacttta 0.980473 -55 aaacaaatcgttagcacttttagcgtttgagt 6 12 0 ttgcacttta 0.980472 -44 tttataatatttagcacataaacat 6 41 1 ttgcacataa 0.931376 -15 ** ******* * Masking position 12 Map Score: 5.52889 Number of sites scoring better than the average of aligned sites = 43 Number in coding regions = 34 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 4 aacattcaaaatcgtagttgcgaa 2 5 1 ttcaaaatcg 0.723502 -296 atggtttaatttcgaaatcacggattttag 2 64 0 ttcgaaatca 0.684152 -237 cacctcacataactaaaacaggaatactta 2 130 1 aactaaaaca 0.778771 -171 cgttcccactatcgaaaccgccttaacgac 2 174 0 atcgaaaccg 0.962327 -127 atttcacgccaacacaaacgcacaacgtta 2 227 1 aacacaaacg 0.766372 -74 agattctttcatctcaaccatattaaaata 2 270 0 atctcaacca 0.914095 -31 ttggacatgcttctaaaacggaccttcata 4 210 0 ttctaaaacg 0.942629 -91 cgaatttttgatcgaaaccgatttaattat 4 253 0 atcgaaaccg 0.962327 -48 caaacttacaatttcaaacgtttttttttt 5 106 0 atttcaaacg 0.776072 -195 attttgtacattttaaaccacgatggcatg 5 137 0 ttttaaacca 0.544896 -164 cactcaaacgctaaaagtgc 6 1 1 cactcaaacg 0.733839 -55 ********** Masking position 6 Map Score: 3.11 Number of sites scoring better than the average of aligned sites = 265 Number in coding regions = 241 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 5 cacaacgttaccgaatatttaattattttaa 2 247 1 cgaatattta 0.953111 -54 tagtttcgtcaaaatattaattgtgagctt 3 10 1 caaatattaa 0.978601 -36 catgtccaagcgaagtattaatataattaaa 4 231 1 caagtattaa 0.95372 -70 aaaaattcgccagaatattaatttcgttcat 4 274 1 cgaatattaa 0.97431 -27 ctgcttttatctaactatttaagtaaatcta 5 43 0 caactattta 0.916966 -258 tgtttatgtgctaaatattataaacaaatcg 6 34 0 caaatattat 0.918593 -22 * ********* Masking position 6 Map Score: 2.76326 Number of sites scoring better than the average of aligned sites = 25 Number in coding regions = 14 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 6 aagcttcgttaaattgctaatggtttaatt 2 83 0 aaattgctaa 0.856904 -218 attctaattcaatccgcaaa 4 1 0 aatccgcaaa 0.943157 -300 tatactgatcaatctgcaaacctagaaatt 4 30 1 aatctgcaaa 0.967008 -271 ttcctgttttaatccgcttatcaccaattg 5 13 0 aatccgctta 0.7945 -288 cgtggtttaaaatgtacaaaattaagccaa 5 145 1 aatgtacaaa 0.811145 -156 actagcttttaaagtgccaaaataaagcaa 5 248 1 aaagtgccaa 0.93367 -53 tcaaacgctaaaagtgctaacgatttgttt 6 14 1 aaagtgctaa 0.968907 -42 atgtttatgtgctaaatattataaa 6 41 0 tatgtgctaa 0.898212 -15 ********** Masking position 2 Map Score: 3.05792 Number of sites scoring better than the average of aligned sites = 129 Number in coding regions = 99 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 7 tcgaaattaaaccattagcaatttaacgaagc 2 79 1 accatgcaat 0.879083 -222 aggtggtttaaccacaccccctaagcttcgtt 2 103 0 accaccccct 0.964922 -198 cactacttagaccgttcccactatcgaaaccg 2 184 0 accgtccact 0.993804 -117 aaatggattaaccgtcactacttagaccgttc 2 199 0 accgtctact 0.977661 -102 cctagaaattaccacctctacttcccagagtt 4 50 1 accacctact 0.960607 -251 tcgtgtggggactattcccactccagctacca 4 163 0 actatccact 0.945144 -138 ttataaacaaatcgttagcacttttagcgttt 6 16 0 atcgtgcact 0.897675 -40 ***** ***** Masking position 1 Map Score: 2.40181 Number of sites scoring better than the average of aligned sites = 97 Number in coding regions = 94 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 8 aacattcaaaatcgtagttgcga 2 1 1 aacacaaatc 0.844429 -300 ggttcaatgtaattcgcaactacgattttgaat 2 14 0 aattcaatac 0.711373 -287 attaattgtgagcttactaatttcactatt 3 26 1 agctctattt 0.795874 -20 tgagtcctccaactcccaaactctgggaagtag 4 67 0 aactcaactc 0.975882 -234 ccctacatcgagttgactatctcgtggactaaa 4 102 0 agttctactc 0.843111 -199 ttcccactccagctaccaagttcaggtaaatga 4 148 0 agctcaattc 0.989624 -153 ggttagttaaagcaatcaatttctttcaaaaaa 5 73 1 agcacaattc 0.972157 -228 tggcatgacaaacttacaatttcaaacgttttt 5 111 0 aactcaattc 0.98364 -190 **** *** *** Masking position 9 Map Score: 1.7348 Number of sites scoring better than the average of aligned sites = 101 Number in coding regions = 79 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 9 ********** No masking Map Score: 1.48036e-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: 1.48036e-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 11 ********** No masking Map Score: 1.48036e-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