AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i101_mgen_mpneu_300.orf -o101_mgen_mpneu_300.ace -a/home/amcguire/genomes/ORF_mgen.txt -z/home/amcguire/genomes/mgen.fna -g0.36 -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 = 0.36 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 RMP00426 250 Mycoplasma_pneumoniae #2 RMP00427 300 Mycoplasma_pneumoniae Motif number 1 aaattttcttgaaaaatttac 1 1 0 gaaaatttac 0.926414 -250 taggaaaaataaagtttaaacaaaattttct 1 23 0 aaatttaaac 0.941503 -228 tttatttaaagaacaaataacactttttaag 1 59 1 gaaaaataac 0.871399 -192 cgctttagtgaaatttttaacaacgaaaaaa 1 90 0 aaattttaac 0.959288 -161 aattaaaacgaaactttttaccagacattag 1 124 0 aaatttttac 0.951988 -127 atttttcgaaaaaattaaaacgaaacttttt 1 136 0 aaattaaaac 0.86506 -115 tttacgacttaaaagatatacgttttttgct 1 167 0 aaagatatac 0.81042 -84 taaaaaactcgaattatttacgacttaaaag 1 183 0 gaatatttac 0.96697 -68 acgacgaaaagaataaaaaactcgaattatt 1 196 0 gaaaaaaaac 0.822049 -55 tttcgtcgttaaagtattaacttaattcaaa 1 218 1 aaatattaac 0.965518 -33 aagccccgccgaaatttctactcctacatcg 2 55 0 gaatttctac 0.887379 -246 *** ******* Masking position 3 Map Score: 10.0758 Number of sites scoring better than the average of aligned sites = 133 Number in coding regions = 117 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 2 ttcagaagaacccaccttaatctacttcaaggactaac 2 12 0 ccccaatccc 0.986397 -289 ccgaaatttctactcctacatcgaccgcttcagaagaa 2 40 0 tccccatccc 0.997696 -261 agtttgtgggtgcaccggaagccccgccgaaatttcta 2 66 0 tcccaagccc 0.996976 -235 caaacttgccttctaattcaaccgcaacgggatgcaat 2 98 1 tcaacaaccc 0.95263 -203 gtcctttcagtcccaaggctgctagttccaaggttacc 2 138 1 tcaactgcgc 0.835144 -163 ctccagaaaattccaccacatctccctcgggaatggta 2 172 0 tcaccatccc 0.994127 -129 cattccccagtgcccaacaagctgctcctccagaaaat 2 199 0 tccaaagccc 0.9923 -102 atgtgcgggttacgccccaatcgggcccacttacccca 2 234 1 tcccaatcgc 0.989751 -67 * * ** **** * * Masking position 12 Map Score: 8.05612 Number of sites scoring better than the average of aligned sites = 34 Number in coding regions = 23 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 3 gaactagcagccttgggactgaaaggacgaa 2 135 0 cctgggactg 0.998564 -166 ggaatggtaaccttggaactagcagccttgg 2 150 0 cctggaacta 0.977999 -151 accacatctccctcgggaatggtaaccttgg 2 165 0 cctgggaatg 0.997788 -136 cttgttgggcactggggaatgtgcgggttac 2 216 1 actgggaatg 0.991317 -85 *** ******* Masking position 8 Map Score: 4.32634 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 4 ttatttttcctaagttctttatttaaagaa 1 42 1 taagttcttt 0.879546 -209 aaaagtgttatttgttctttaaataaagaa 1 56 0 tttgttcttt 0.846877 -195 tttaagttttttcgttgttaaaaatttcac 1 84 1 ttcgttgtta 0.96456 -167 ggtaaaaagtttcgttttaattttttcgaa 1 133 1 ttcgttttaa 0.79242 -118 ttaaaagatatacgttttttgctatttttc 1 160 0 tacgtttttt 0.863705 -91 gtatatcttttaagtcgtaaataattcgag 1 177 1 taagtcgtaa 0.69386 -74 ttttattcttttcgtcgttaaagtattaac 1 209 1 ttcgtcgtta 0.972252 -42 agttagtccttgaagtagatta 2 3 1 ttagtccttg 0.890037 -298 cgggatgcaattcgtcctttcagtcccaag 2 125 1 ttcgtccttt 0.978731 -176 ********** Masking position 5 Map Score: 5.97833 Number of sites scoring better than the average of aligned sites = 79 Number in coding regions = 70 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 5 gaagtagattaaggtgggttcttctgaagcg 2 22 1 aaggtgggtc 0.992029 -279 agaaggcaagtttgtgggtgcaccggaagcc 2 81 0 tttgtgggtc 0.978205 -220 gaggagcagcttgttgggcactggggaatgt 2 207 1 ttgttgggcc 0.988431 -94 ctcgttggggtaagtgggcccgattggggcg 2 246 0 taagtgggcc 0.979778 -55 tcaccaaacaaggttgggtacgtggaacagg 2 278 0 aggttgggtc 0.978914 -23 ********* * Masking position 5 Map Score: 1.56493 Number of sites scoring better than the average of aligned sites = 6 Number in coding regions = 6 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 catcgaccgcttcagaagaacccaccttaatct 2 27 0 ttcgagaccc 0.994349 -274 tcggcggggcttccggtgcacccacaaacttgc 2 74 1 ttcgggaccc 0.99857 -227 tggtggaattttctggaggagcagcttgttggg 2 192 1 ttcgggagca 0.989611 -109 gtgggcccgattggggcgtaacccgcacattcc 2 231 0 ttggggaacc 0.989649 -70 *** ** * **** Masking position 10 Map Score: 0.00720796 Number of sites scoring better than the average of aligned sites = 1 Number in coding regions = 1 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: 1.48747e-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 8 ********** No masking Map Score: 1.48747e-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: 1.48747e-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