AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i211_transcription_translation_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 ytiA 219 similar to hypothetical proteins #2 rpmE 118 ribosomal protein L31 #3 rho 300 transcriptional terminator Rho Motif number 1 TAAACCACCTTTCCAAAAAGACGTTCTGTATGT 1 31 1 TTAAAAGACG 0.958046 -189 CTCATGGCATTTAAGAATAGGAAGAATAATCTA 1 93 0 TTAATAGGAA 0.797033 -127 TTATTACGATTTATTGAAAGGAGATACCC 1 201 1 TTGAAAGGAG 0.979093 -19 ATTGTATTTGCAAAAGAAGTAAATCACTG 2 7 1 TTAAAAGAAG 0.989873 -112 ACTTTCCTAGTGCTTAAAAGAAGGTATTACGCA 3 42 0 TGAAAAGAAG 0.979498 -259 ATCGGCGCTTTTGTTAAAAGGATTGTCTTAATG 3 148 0 TTAAAAGGAT 0.956356 -153 GGTGGAAGTGTTACCGATAGAAGTTCCTTTATG 3 185 1 TTGATAGAAG 0.937879 -116 TTCCTTTATGTTAAAAAAAGAATGTGCTTTGGC 3 208 1 TTAAAAGAAT 0.957185 -93 TGGCGGATGTTGTGCAAAAGCAGCAGATGACAT 3 237 1 TGAAAAGCAG 0.945857 -64 ** ******** Masking position 7 Map Score: 8.78065 Number of sites scoring better than the average of aligned sites = 468 Number in coding regions = 353 Number in noncoding regions = 115 Number of orfs with sites within 600 bp upstream = 141 Fraction of orfs with sites within 600 bp upstream = 0.022647 Motif number 2 ATCTAACCGAGGAAGCAAATAATAAACCCAAAAT 1 64 0 GGAGAAATAA 0.989499 -156 TGAAACAGAGGGAAGGATATAAGAAGATTGACAA 1 136 1 GGAGATATAA 0.958757 -84 CGTTTGTAAGGTTATAAAATAAAACGTAATTATT 1 172 1 GTATAAATAA 0.751712 -48 TATTTGCAAAAGAAGTAAATCACTGATATAATTT 2 15 1 AGAGAAATAT 0.961771 -104 CGAAACGCATATGAGAAAATTATATCAGTGATTT 2 31 0 ATAGAAATAA 0.940187 -88 GATTCAGGGCGGAAGGAGATGGATACA 2 102 1 GGAGAGATGT 0.918831 -17 GTCTGTATGCGGTAGAAATTGAAACTTTCCTAGT 3 64 0 GGAGAATTAA 0.936926 -237 GGACAAAAACATGAGAAGATCAATACTTATATCG 3 97 0 ATAGAGATAT 0.889892 -204 GTTGTGCAAAAGCAGCAGATGACATGTTCAGAGT 3 245 1 AGAGAGATAA 0.979171 -56 ** ** **** * * Masking position 7 Map Score: 6.166 Number of sites scoring better than the average of aligned sites = 604 Number in coding regions = 521 Number in noncoding regions = 83 Number of orfs with sites within 600 bp upstream = 96 Fraction of orfs with sites within 600 bp upstream = 0.0154192 Motif number 3 GAAAGGTGGTTTACGATTGTGGATGATTTAGTT 1 9 0 TTCAGGGATG 0.912412 -211 AGGAAGAATAATCTAACCGAGGAAGCAAATAATAA 1 73 0 ATTAGGGAAG 0.952027 -147 TTCCACACGGGATTCAGGGCGGAAGGAGATGGATA 2 92 1 GATAGGGAAG 0.989948 -27 TACTTATATCGTCTGTATGCGGTAGAAATTGAAAC 3 73 0 GTTTGGGTAG 0.971975 -228 TTGTCTTAATGAGTTTTGAAGGAAGCGAGGACAAA 3 124 0 GATTAGGAAG 0.943315 -177 CAAAAGCGCCGATCATGGGTGGAAGTGTTACCGAT 3 168 1 GACTGGGAAG 0.993534 -133 AAAAAAGAATGTGCTTTGGCGGATGTTGTGCAAAA 3 221 1 GTCTGGGATG 0.988732 -80 ** * * * ***** Masking position 11 Map Score: 2.48949 Number of sites scoring better than the average of aligned sites = 286 Number in coding regions = 250 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 4 CTTTCCAAAAAGACGTTCTGTATGTATTTT 1 39 1 AGACGTTCTG 0.931352 -181 ATAACCTTACAAACGTTTTGTCAATCTTCT 1 157 0 AAACGTTTTG 0.965387 -63 ATTTTCTCATATGCGTTTCGGACAATGCTC 2 45 1 ATGCGTTTCG 0.946616 -74 GGTAAAAATAAAGAGTGCTGCGAATTTTAC 3 12 1 AAGAGTGCTG 0.950383 -289 TACAGACGATATAAGTATTGATCTTCTCAT 3 91 1 ATAAGTATTG 0.80416 -210 GATTGTCTTAATGAGTTTTGAAGGAAGCGA 3 131 0 ATGAGTTTTG 0.9654 -170 TGACTATGAAAAGCGTGGTGTTTTT 3 286 1 AAGCGTGGTG 0.955597 -15 ********** Masking position 1 Map Score: 2.18216 Number of sites scoring better than the average of aligned sites = 552 Number in coding regions = 506 Number in noncoding regions = 46 Number of orfs with sites within 600 bp upstream = 49 Fraction of orfs with sites within 600 bp upstream = 0.00787022 Motif number 5 TTGGAAAGGTGGTTTACGATTGTGGATGAT 1 17 0 GGTTTACGAT 0.995032 -203 ATGTATTTTGGGTTTATTATTTGCTTCCTC 1 60 1 GGTTTATTAT 0.964187 -160 AATGCCATGAGGTTTACGATGTGAAACAGA 1 115 1 GGTTTACGAT 0.995032 -105 ********** Masking position 6 Map Score: 2.12128 Number of sites scoring better than the average of aligned sites = 11 Number in coding regions = 9 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 6 GGTTATAAAATAAAACGTAATTATTACGATT 1 181 1 TAAACGTAAT 0.947244 -39 CTCCTTTCAATAAATCGTAATAATTACGTTT 1 193 0 TAAACGTAAT 0.947244 -27 TTTCGGACAATGCTCCGAAATAATAACTCTG 2 60 1 TGCTCGAAAT 0.977614 -59 AAATAAAGAGTGCTGCGAATTTTACTGCGTA 3 17 1 TGCTCGAATT 0.929941 -284 CTGCGAATTTTACTGCGTAATACCTTCTTTT 3 29 1 TACTCGTAAT 0.983042 -272 **** ****** Masking position 9 Map Score: 0.935889 Number of sites scoring better than the average of aligned sites = 71 Number in coding regions = 62 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 7 CCAAAATACATACAGAACGTCTTTTTGGAA 1 41 0 TACAGAACGT 0.954416 -179 TAAGAAGATTGACAAAACGTTTGTAAGGTT 1 155 1 GACAAAACGT 0.981448 -65 AAGGTTATAAAATAAAACGTAATTATTACG 1 179 1 AATAAAACGT 0.976014 -41 ATCTCCTTTCAATAAATCGTAATAATTACG 1 196 0 AATAAATCGT 0.941534 -24 ********** Masking position 6 Map Score: 0.172937 Number of sites scoring better than the average of aligned sites = 102 Number in coding regions = 65 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 8 ********** No masking Map Score: -9.63906e-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: -9.63906e-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 10 ********** No masking Map Score: -9.63906e-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