AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i222_Ribosomal_Operon_+_Transcription_bsub_reg_300.orf -aORF_bsub.txt -zbsub.fna -g0.435 -x5 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 = 0.435 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 pheS 300 phenylalanyl-tRNA synthetase (alpha subunit) #2 rplT 31 ribosomal protein L20 #3 infC 171 initiation factor IF-3 #4 thrZ 300 threonyl-tRNA synthetase Motif number 1 CGCGCAGTGTACGCGGTCCCGGCGACAACT 1 110 0 ACGCGGTCCC 0.991294 -191 CGAGTTGTGGCCGCGGTACCACCCTTATTT 1 204 0 CCGCGGTACC 0.973248 -97 CCGCGGCCACAACTCGTCCCTTGTACAAGG 1 218 1 AACTCGTCCC 0.987462 -83 AAATAAAAAAAACCCGTCCCTTGTACAAGG 1 236 0 AACCCGTCCC 0.99389 -65 TGTGATTAACCCGTGGTTCCACCCAAGTTC 4 214 0 CCGTGGTTCC 0.946279 -87 GTTAATCACACACTCGTCCCTATCTGCGGG 4 234 1 CACTCGTCCC 0.99389 -67 TAAAAAAACACACCCGTCCCGCAGATAGGG 4 251 0 CACCCGTCCC 0.997032 -50 ********** Masking position 7 Map Score: 12.8024 Number of sites scoring better than the average of aligned sites = 115 Number in coding regions = 105 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 2 CACCTCTTGAGTTGTCGCCGGGACCGCGTACA 1 101 1 GTTGTGCGGG 0.99002 -200 ACCTTTACGCGCAGTGTACGCGGTCCCGGCGA 1 115 0 GCAGTTCGCG 0.987716 -186 ACAGACTGATGCTGTCGTCAGCTTCATTGACA 1 169 0 GCTGTGCAGC 0.738878 -132 CAAGGGACGAGTTGTGGCCGCGGTACCACCCT 1 209 0 GTTGTGCGCG 0.985338 -92 ACACATGCATGTAGTTGGCAGGTTGACCGTAC 3 29 1 GTAGTGCAGG 0.986263 -143 ACAGATGTTCGTAGTGTGGGTGTTTTATAATG 3 73 1 GTAGTTGGTG 0.817283 -99 CATTTTGAATGCATTTTGCAGGCAAACAAAAA 3 112 0 GCATTTCAGG 0.886502 -60 CCGCCTTGGAGCAGCATTGGGGAACTGAAGTA 4 126 1 GCAGCTGGGG 0.946697 -175 GTGCTGTAACGCAGCATAGACGGCATTGGTTA 4 156 0 GCAGCTGACG 0.836874 -145 CAAATACTATGTTGTCGGCTCGGTGCTGTAAC 4 178 0 GTTGTGCTCG 0.897015 -123 CGACAACATAGTATTTGTCGGGAACTTGGGTG 4 193 1 GTATTGCGGG 0.962884 -108 ***** * **** Masking position 1 Map Score: 9.79707 Number of sites scoring better than the average of aligned sites = 990 Number in coding regions = 910 Number in noncoding regions = 80 Number of orfs with sites within 600 bp upstream = 66 Fraction of orfs with sites within 600 bp upstream = 0.0106007 Motif number 3 TACAAGGGACGGGTTTTTTTTATTTTCCAA 1 241 1 GGGTTTTTTT 0.940936 -60 AGACATATGACGGTTTGTTTACATAAAAGG 1 271 1 CGGTTTGTTT 0.98107 -30 TGTTCGTAGTGTGGGTGTTTTATAATGCCC 3 78 1 GTGGGTGTTT 0.974221 -94 AATGCCCACACTTTTTGTTTGCCTGCAAAA 3 101 1 CTTTTTGTTT 0.764971 -71 GGGTGTGTTTTTTTATTTGA 4 1 1 GGGTGTGTTT 0.996073 -300 ATAGGGACGAGTGTGTGATTAACCCGTGGT 4 227 0 GTGTGTGATT 0.962262 -74 TCTGCGGGACGGGTGTGTTTTTTTATATAC 4 256 1 GGGTGTGTTT 0.996073 -45 ********** Masking position 6 Map Score: 9.01858 Number of sites scoring better than the average of aligned sites = 183 Number in coding regions = 146 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 4 ATCAACTGCTTTCCAGGGAGAAAATGCCGC 1 33 1 TTCCAGGGAG 0.969692 -268 TTAAAAATGCTCTCAGTCAGCGGCATTTTC 1 52 0 TCTCAGTCAG 0.910977 -249 GTGAAGCCAATTTCCGGCTGCGTTAAAAAT 1 74 0 TTTCCGGCTG 0.947821 -227 ACCACCCTTATTTCAGACAGACTGATGCTG 1 187 0 TTTCAGACAG 0.988228 -114 TGAATGCATTTTGCAGGCAAACAAAAAGTG 3 109 0 TTGCAGGCAA 0.771489 -63 TAGTTACGGTTTTCAGAGAGGGAAGGAAAG 4 64 1 TTTCAGAGAG 0.97255 -237 TCCACCCAAGTTCCCGACAAATACTATGTT 4 197 0 TTCCCGACAA 0.837304 -104 ********** Masking position 1 Map Score: 3.57922 Number of sites scoring better than the average of aligned sites = 821 Number in coding regions = 757 Number in noncoding regions = 64 Number of orfs with sites within 600 bp upstream = 61 Fraction of orfs with sites within 600 bp upstream = 0.00979762 Motif number 5 CGACAACTCAAGAGGTGAAGCCAATTTCCGG 1 87 0 AGGGTGAAGC 0.995523 -214 CACTGCGCGTAAAGGTGAACCGGAATCTGAT 1 131 1 AAGGTGAACC 0.940807 -170 TGTGTCAATCAGGTGAGAAGCGG 3 3 0 AGTGAGAAGC 0.987881 -169 ATTCAAAATGAGTTGTGAATCAATTCGAAGA 3 134 1 AGTGTGAATC 0.981059 -38 GATATTCCTAAGCTGGGAAGCTCTCACCTTT 4 90 0 AGTGGGAAGC 0.991791 -211 ** ******** Masking position 8 Map Score: 3.48673 Number of sites scoring better than the average of aligned sites = 110 Number in coding regions = 96 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 6 CAGTCAGCGGCATTTTCTCCCTGGAAAGCAGT 1 37 0 CATTTCTCCT 0.990647 -264 GAGGTGAAGCCAATTTCCGGCTGCGTTAAAAA 1 75 0 CAATTCCGCT 0.904039 -226 TGAATTTCCCTCCTAATTGTTCCT 2 18 0 AATTTCCCCT 0.962638 -14 TCATTCATGTCCTTTTCTTCGCATGTATTCAA 4 32 0 CCTTTCTCGC 0.943475 -269 GAAGCTCTCACCTTTCCTTCCCTCTCTGAAAA 4 73 0 CCTTTCTCCC 0.986449 -228 TTAGGAATATCATTTACCGCCTTGGAGCAGCA 4 110 1 CATTTCCCCT 0.994031 -191 ***** ** *** Masking position 5 Map Score: 1.6681 Number of sites scoring better than the average of aligned sites = 269 Number in coding regions = 233 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467 Motif number 7 AAAATGCTCTCAGTCAGCGGCATTTTCTCCC 1 48 0 CAGTCACGGC 0.870266 -253 GAGGTGAAGCCAATTTCCGGCTGCGTTAAAA 1 76 0 CAATTTCGGC 0.760166 -225 ACCTCTTGAGTTGTCGCCGGGACCGCGTACA 1 102 1 TTGTCGCGGG 0.982729 -199 CCTTTACGCGCAGTGTACGCGGTCCCGGCGA 1 115 0 CAGTGTCGCG 0.931344 -186 CAGACTGATGCTGTCGTCAGCTTCATTGACA 1 169 0 CTGTCGCAGC 0.915318 -132 AAGGGACGAGTTGTGGCCGCGGTACCACCCT 1 209 0 TTGTGGCGCG 0.923897 -92 GTCCCTTGTACAAGGGACGGGTTTTTTTTAT 1 233 1 CAAGGGCGGG 0.837457 -68 CACATGCATGTAGTTGGCAGGTTGACCGTAC 3 30 1 TAGTTGCAGG 0.908055 -142 ATTTTGAATGCATTTTGCAGGCAAACAAAAA 3 112 0 CATTTTCAGG 0.612176 -60 AAATACTATGTTGTCGGCTCGGTGCTGTAAC 4 178 0 TTGTCGCTCG 0.659439 -123 GACAACATAGTATTTGTCGGGAACTTGGGTG 4 194 1 TATTTGCGGG 0.887018 -107 ACACTCGTCCCTATCTGCGGGACGGGTGTGT 4 243 1 CTATCTCGGG 0.928732 -58 ****** **** Masking position 8 Map Score: 3.43589 Number of sites scoring better than the average of aligned sites = 2336 Number in coding regions = 2143 Number in noncoding regions = 193 Number of orfs with sites within 600 bp upstream = 137 Fraction of orfs with sites within 600 bp upstream = 0.0220045 Motif number 8 GGCCGCGGTACCACCCTTATTTCAGACAGAC 1 195 0 CCACCCTATT 0.959224 -106 TGAATTTCCCTCCTAATTGTTCCTTATC 2 14 0 CCCTCCTATT 0.9932 -18 CCGCTTCTCACCTGATTGACACATGCA 3 7 1 CTCACCTATT 0.981667 -165 CGAATTGATTCACAACTCATTTTGAATGCAT 3 130 0 CACAACTATT 0.947626 -42 TTTAGAACACTCCTTATTCATTGTTGTA 4 283 0 CACTCCTATT 0.98952 -18 ******* *** Masking position 7 Map Score: 1.98823 Number of sites scoring better than the average of aligned sites = 78 Number in coding regions = 51 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 9 ********** No masking Map Score: -1.24812e-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: -1.24812e-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: -1.24812e-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