AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i217_bsub_mtub_300.orf -o217_bsub_mtub_300.ace -a/home/amcguire/genomes/ORF_bsub.txt -z/home/amcguire/genomes/bsub.fna -g0.55 -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 = 0.55 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 spoIIIJ 144 alternate gene name: spo0J87 #2 rnpA 151 ribonuclease P (protein component) #3 rpmH 217 ribosomal protein L34 #4 rpmH 300 rpmH Motif number 1 GCATCACCACTGCTTTCTTACAACTTTTAAAAGC 1 8 1 CAGCTCTTCC 0.992439 -137 CAACTTTTAAAAGCGCTTCCTTTCTGGTTGATCAGAA 1 31 1 AAGCTCTTCG 0.976877 -114 TCTTTTATTGCAAAGCATACTTGTATGTATTTTAGCA 1 93 0 CAGCTCTTTG 0.976546 -52 CGTAATGAACCGGGGCATGCTTCCTGGTTCAGATGCA 2 68 1 CGGCTCTTCG 0.989068 -84 GCAACCGCTTCAGGGCATCCTGCCCGCTAAGCTGCTC 4 67 0 CAGCTCTGCC 0.985354 -234 GTCGCAGCCGCATCGCCGACTTTCGGGCGACTGTTCG 4 147 0 CAGCGCTTCG 0.997188 -154 AGGTGGTTTTCGCTGCTGGCCGGCGCGGTCCCTGGAC 4 192 0 CGGCGCCGCG 0.984319 -109 CAGCGAAAACCACCTCCGACTGTCCCGCGGGCCAATC 4 214 1 CATCGCTGCG 0.967808 -87 TCCGGCCACTCACTGCCTTCCAACTCGATTGGCCCGC 4 240 0 CAGCTCCACG 0.981113 -61 ** ** * *** * * Masking position 10 Map Score: 13.3352 Number of sites scoring better than the average of aligned sites = 272 Number in coding regions = 248 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 2 GCATGCCCCGGTTCATTACGCATCACATCTATCTTT 2 52 0 GTCACGCTCC 0.925063 -100 ACAAAGAACCCACCACAACGCAAAAC 4 1 0 CCCACGCAAC 0.985638 -300 CATCCGTACACCCGAGACCGCCACACTCACAAAGAA 4 29 0 CCGACGCACC 0.988077 -272 GCTTCAGGGCATCCTGCCCGCTAAGCTGCTCACCAT 4 62 0 ACCTCGCAAC 0.86338 -239 GTCAAACCTCGCCCACCCGGCAACCGCTTCAGGGCA 4 87 0 GCCAGGCACG 0.989439 -214 GGTTTGACCAGGCGAAGGCGCGTAAGTACCCTCGAA 4 115 1 GCGACGCTAG 0.932373 -186 CCGCATCGCCGACTTTCGGGCGACTGTTCGAGGGTA 4 141 0 GCTTGGCACG 0.816399 -160 ACTAATCCAGGTCGCAGCCGCATCGCCGACTTTCGG 4 158 0 GCGCCGCTCC 0.976322 -143 ACCTCCGACTGTCCCGCGGGCCAATCGAGTTGGAAG 4 225 1 GCCCGGCAAC 0.980564 -76 CTGGCAACATCACCATCCGGCCACTCACTGCCTTCC 4 256 0 CCCAGGCACC 0.990897 -45 * *** *** ** * Masking position 11 Map Score: 6.64977 Number of sites scoring better than the average of aligned sites = 463 Number in coding regions = 425 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 3 AAATTTATTATGAACATGAGATGCATCTGA 2 96 0 TGAACATGAG 0.900793 -56 ATCCACATGCGTGATTTTAGG 3 2 1 TCCACATGCG 0.965856 -216 CCATACCTTTTCAACTTTCGAAACCTTATT 3 82 0 TCAACTTTCG 0.894423 -136 GCTAAGCTGCTCACCATCCGTACACCCGAG 4 49 0 TCACCATCCG 0.987052 -252 GGGCGAGGTTTGACCAGGCGAAGGCGCGTA 4 109 1 TGACCAGGCG 0.982644 -192 TAAGTACCCTCGAACAGTCGCCCGAAAGTC 4 137 1 CGAACAGTCG 0.852904 -164 TCTGGCAACATCACCATCCGGCCACTCACT 4 263 0 TCACCATCCG 0.987052 -38 ********** Masking position 5 Map Score: 3.9624 Number of sites scoring better than the average of aligned sites = 402 Number in coding regions = 360 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 4 AGGAAGCGCTTTTAAAAGTTGTAAGAAAGC 1 22 0 TTTAAAAGTT 0.9742 -123 ATCTTTCAGTTTTAAATGGTGTCTTTTTCT 1 64 0 TTTAAATGGT 0.946675 -81 CATAATAAATTTTAAAAGTTTCTGCCAGCC 2 114 1 TTTAAAAGTT 0.9742 -38 GTTTCGAAAGTTGAAAAGGTATGGTATCCT 3 88 1 TTGAAAAGGT 0.963386 -130 TAAGACTGTCTTTAACAGCTATTCCTCGAG 3 185 1 TTTAACAGCT 0.934629 -33 ********** Masking position 5 Map Score: 2.72054 Number of sites scoring better than the average of aligned sites = 142 Number in coding regions = 122 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 5 CTGGTTGATCAGAAAAAGACACCATTTAAA 1 54 1 AGAAAAAGAC 0.965272 -91 CCCATAACGTGAAAAAAGACCACTGACATT 2 21 0 GAAAAAAGAC 0.986187 -131 TTCACGTTATGGGAAAAGATAGATGTGATG 2 38 1 GGGAAAAGAT 0.942211 -114 TAATTTTACGGAAAAAAGACAAATTCAAAC 3 40 0 GAAAAAAGAC 0.986187 -178 ********** Masking position 5 Map Score: 1.58358 Number of sites scoring better than the average of aligned sites = 163 Number in coding regions = 141 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 6 CAGCCAGTATCGGAGTGAGTCAT 2 139 1 CGGAGTGAGT 0.619801 -13 AGCTATTCCTCGAGGGAGGTGTCATAA 3 201 1 CGAGGGAGGT 0.890021 -17 GTGGCGGTCTCGGGTGTACGGATGGTGAGC 4 41 1 CGGGTGTACG 0.952083 -260 AAGCGGTTGCCGGGTGGGCGAGGTTTGACC 4 94 1 CGGGTGGGCG 0.979185 -207 TTTGACCAGGCGAAGGCGCGTAAGTACCCT 4 117 1 CGAAGGCGCG 0.946812 -184 GGCGACTGTTCGAGGGTACTTACGCGCCTT 4 129 0 CGAGGGTACT 0.963364 -172 GCCCGAAAGTCGGCGATGCGGCTGCGACCT 4 156 1 CGGCGATGCG 0.912036 -145 GCGGGACAGTCGGAGGTGGTTTTCGCTGCT 4 212 0 CGGAGGTGGT 0.953375 -89 CCAGACATAGCGAGGAGACGCCC 4 288 1 CGAGGAGACG 0.934357 -13 ********** Masking position 1 Map Score: 3.44232 Number of sites scoring better than the average of aligned sites = 1002 Number in coding regions = 883 Number in noncoding regions = 119 Number of orfs with sites within 600 bp upstream = 83 Fraction of orfs with sites within 600 bp upstream = 0.0133312 Motif number 7 ********** No masking Map Score: -3.03101e-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: -3.03101e-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 9 ********** No masking Map Score: -3.03101e-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