AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i099_Phosphate_Transport_1_mgen_reg_300.orf -o099_mgen_300.ace -a/home/amcguire/alignace/lib/ORF_mgen.txt -z/skink1/amcguire/genomes/mgen.fna -g0.32 -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 = 0.32 maxlen = 30 weight = 0.8 exclude = 1 Purged sequences: RMG05422 23 Mycoplasma Input sequences: #1 RMG04313 147 Mycoplasma #2 RMG04312 64 Mycoplasma #3 RMG03267 55 Mycoplasma #4 RMG03266 52 Mycoplasma #5 RMG03264 97 Mycoplasma #6 RMG03260 188 Mycoplasma Motif number 1 GCAATTAATAAAAATGCATTTCATTTAAATTAATTGG 1 15 1 AAAATCTTTA 0.942034 -133 CCTGAGTGTCAATTCGAATTCTCTTTAGAAAAGATTT 1 80 1 AATATTTTTA 0.980538 -68 CTCTTTAGAAAAGATTTAATCTGTTTAAAAAGTGCTA 1 100 1 AAAATTTTTA 0.987654 -48 AATCTGTTTAAAAAGTGCTAAAGTTTAGAAATTTCTT 1 117 1 AAACAATTTA 0.855439 -31 TATTTAATGAAATATTGACAATTTTTATTGCTAGTTC 2 14 0 AAAAATTTTA 0.971451 -51 ATATTTCATTAAATACACATTTATTTAATGAGATAAA 2 36 1 AATCTTTTTA 0.950856 -29 AAAACTTATTAAGTGACAGTTTTTTTA 3 1 0 AATATTTTTA 0.980503 -55 GTCACTTAATAAGTTTTATTTAATTTATGGAATATAA 3 21 1 AATATATTTA 0.958012 -35 GATTATCAAAAAGAGATATTTTCTTTAGCATGTACCT 5 42 0 AAAATTTTTA 0.986706 -56 AAATATCGAAAATATCGAGAGAATTTATTAATAAAAA 6 52 1 AAAAAATTTA 0.939104 -137 TATTAATAAAAATAAAAACTATATTTATTATAAGTAA 6 77 1 AAAATTTTTA 0.986706 -112 ** * * * * **** Masking position 2 Map Score: 19.3724 Number of sites scoring better than the average of aligned sites = 163 Number in coding regions = 140 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 2 GCATTTCATTTAAATTAATTGGCTTGTGAAAAAAC 1 30 1 TAAATAATTT 0.764436 -118 GTGAAAAAACTAGACTAAATAATAACCTGAGTGTC 1 55 1 TAGATAATAA 0.767913 -93 AAATCTTTTCTAAAGAGAATTCGAATTGACACTCA 1 82 0 TAAAAGATAA 0.940126 -66 TAGCACTTTTTAAACAGATTAAATCTTTTCTAAAG 1 102 0 TAAAAGATTC 0.940123 -46 TTTAAAGAAATTTCTAAACTTTAGCAC 1 131 0 TAAAAAATAA 0.973868 -17 ATTTATCTCATTAAATAAATGTGTATTTAATGAAA 2 39 0 TTAATAATTA 0.787114 -26 TAAAAAAACTGTCACTTAATAAGTT 3 1 1 TAAAAAATAC 0.981074 -55 TTATATTCCATAAATTAAATAAAACTTATTAAGTG 3 23 0 TAAATAATAC 0.960478 -33 AGGTACATGCTAAAGAAAATATCTCTTTTTGATAA 5 42 1 TAAAAAATTC 0.977993 -56 TCTATACATCTAAACAAATTAACAAAGCCATTTAA 6 14 0 TAAAAAATAA 0.977688 -175 TTTATTTTTATTAATAAATTCTCTCGATATTTTCG 6 58 0 TTAAAAATTC 0.899017 -131 TTACTTATAATAAATATAGTTTTTATTTTTATTAA 6 79 0 TAAAATATTA 0.810997 -110 CGTTGAATTATAACAAAATTAGAAAACGGCTCATT 6 151 0 TAACAAATAA 0.876617 -38 **** *** * ** Masking position 8 Map Score: 14.1686 Number of sites scoring better than the average of aligned sites = 232 Number in coding regions = 201 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 3 ATTTGCAATTAATAAAAATGCATTTC 1 7 1 AATTAATAAA 0.967787 -141 CAAGAACTAGCAATAAAAATTGTCAAT 2 8 1 TAGCAATAAA 0.956954 -57 ATATTCCATAAATTAAATAAAACTTATTAA 3 26 0 AATTAAATAA 0.771449 -30 ATCTAAATATATGCAAAAAACATCG 4 38 1 ATGCAAAAAA 0.684476 -15 CCTTAAAGATTAGCAATTAAAATTTGAAAG 5 14 1 TAGCAATTAA 0.846532 -84 TGTTCTAGATTATCAAAAAGAGATATTTTC 5 56 0 TATCAAAAAG 0.742196 -42 CATCTAAACAAATTAACAAAGCCATTTAAC 6 13 0 AATTAACAAA 0.888638 -176 CGAGAGAATTTATTAATAAAAATAAAAACT 6 67 1 TATTAATAAA 0.946563 -122 TATTTATTATAAGTAATAAGTAAGTAGGAG 6 98 1 AAGTAATAAG 0.939298 -91 CCAAGGTTAGAAGTAATAAATTCTCCTACT 6 120 0 AAGTAATAAA 0.975797 -69 TAATTAATAAACACGTTGAAT 6 178 0 AATTAATAAA 0.967787 -11 ********** Masking position 5 Map Score: 12.5957 Number of sites scoring better than the average of aligned sites = 421 Number in coding regions = 363 Number in noncoding regions = 58 Number of orfs with sites within 600 bp upstream = 42 Fraction of orfs with sites within 600 bp upstream = 0.0067459 Motif number 4 AATGCATTTCATTTAAATTAATTGGCTTGT 1 27 1 ATTTAAATTA 0.90451 -121 TTAAAGAAATTTCTAAACTTTAGCACTTTT 1 127 0 TTCTAAACTT 0.439129 -21 ATATTCCATAAATTAAATAAAACTTATTAA 3 26 0 AATTAAATAA 0.746407 -30 ACCGCATTCTATTTTAATATTA 4 3 0 ATTTTAATAT 0.813981 -50 GCGGTTTTGTATCTAAATATATGCAAAAAA 4 28 1 ATCTAAATAT 0.943786 -25 AAGATTAGCAATTAAAATTTGAAAGGTACA 5 19 1 ATTAAAATTT 0.810976 -79 AAATCTATACATCTAAACAAATTAACAAAG 6 22 0 ATCTAAACAA 0.924705 -167 AGATGTATAGATTTAAATATCGAAAATATC 6 38 1 ATTTAAATAT 0.952927 -151 GAATTTATTAATAAAAATAAAAACTATATT 6 72 1 ATAAAAATAA 0.662875 -117 AACACGTTGAATTATAACAAAATTAGAAAA 6 160 0 ATTATAACAA 0.652186 -29 ********** Masking position 6 Map Score: 3.16436 Number of sites scoring better than the average of aligned sites = 318 Number in coding regions = 267 Number in noncoding regions = 51 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 5 ********** No masking Map Score: 1.67221e-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 6 ********** No masking Map Score: 1.67221e-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 7 ********** No masking Map Score: 1.67221e-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