AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i211_transcription_translation_bsub_reg_100.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 0.962545 -189 CTCATGGCATTTAAGAATAGGAAGAATAATCTA 1 93 0 TTAATAGGAA 0.815476 -127 TTATTACGATTTATTGAAAGGAGATACCC 1 201 1 TTGAAAGGAG 0.981379 -19 ATTGTATTTGCAAAAGAAGTAAATCACTG 2 7 1 TTAAAAGAAG 0.990991 -112 ACTTTCCTAGTGCTTAAAAGAAGGTATTACGCA 3 42 0 TGAAAAGAAG 0.981741 -259 ATCGGCGCTTTTGTTAAAAGGATTGTCTTAATG 3 148 0 TTAAAAGGAT 0.961029 -153 GGTGGAAGTGTTACCGATAGAAGTTCCTTTATG 3 185 1 TTGATAGAAG 0.944417 -116 TTCCTTTATGTTAAAAAAAGAATGTGCTTTGGC 3 208 1 TTAAAAGAAT 0.961774 -93 TGGCGGATGTTGTGCAAAAGCAGCAGATGACAT 3 237 1 TGAAAAGCAG 0.951599 -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 0.989602 -156 TGAAACAGAGGGAAGGATATAAGAAGATTGACAA 1 136 1 GGAGATATAA 0.959148 -84 CGTTTGTAAGGTTATAAAATAAAACGTAATTATT 1 172 1 GTATAAATAA 0.753559 -48 TATTTGCAAAAGAAGTAAATCACTGATATAATTT 2 15 1 AGAGAAATAT 0.962135 -104 CGAAACGCATATGAGAAAATTATATCAGTGATTT 2 31 0 ATAGAAATAA 0.940742 -88 GATTCAGGGCGGAAGGAGATGGATACA 2 102 1 GGAGAGATGT 0.919567 -17 GTCTGTATGCGGTAGAAATTGAAACTTTCCTAGT 3 64 0 GGAGAATTAA 0.93751 -237 GGACAAAAACATGAGAAGATCAATACTTATATCG 3 97 0 ATAGAGATAT 0.890861 -204 GTTGTGCAAAAGCAGCAGATGACATGTTCAGAGT 3 245 1 AGAGAGATAA 0.979372 -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 0.90067 -211 AGGAAGAATAATCTAACCGAGGAAGCAAATAATAA 1 73 0 ATTAGGGAAG 0.945268 -147 TTCCACACGGGATTCAGGGCGGAAGGAGATGGATA 2 92 1 GATAGGGAAG 0.988468 -27 TACTTATATCGTCTGTATGCGGTAGAAATTGAAAC 3 73 0 GTTTGGGTAG 0.967931 -228 TTGTCTTAATGAGTTTTGAAGGAAGCGAGGACAAA 3 124 0 GATTAGGAAG 0.935409 -177 CAAAAGCGCCGATCATGGGTGGAAGTGTTACCGAT 3 168 1 GACTGGGAAG 0.992592 -133 AAAAAAGAATGTGCTTTGGCGGATGTTGTGCAAAA 3 221 1 GTCTGGGATG 0.987074 -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 AAAATACATACAGAACGTCTTTTTGGAAAG 1 39 0 CAGAACGTCT 0.928115 -181 AGAAGATTGACAAAACGTTTGTAAGGTTAT 1 157 1 CAAAACGTTT 0.963694 -63 GAGCATTGTCCGAAACGCATATGAGAAAAT 2 45 0 CGAAACGCAT 0.944055 -74 GTAAAATTCGCAGCACTCTTTATTTTTACC 3 12 0 CAGCACTCTT 0.947998 -289 ATGAGAAGATCAATACTTATATCGTCTGTA 3 91 0 CAATACTTAT 0.796236 -210 TCGCTTCCTTCAAAACTCATTAAGACAATC 3 131 1 CAAAACTCAT 0.963706 -170 AAAAACACCACGCTTTTCATAGTCA 3 286 0 CACCACGCTT 0.953446 -15 ********** Masking position 5 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 AACTAAATCATCCACAATCGT 1 2 1 ACTAAATCAT 0.930396 -218 CCACCTTTCCAAAAAGACGTTCTGTATGTA 1 35 1 AAAAAGACGT 0.926334 -185 AAGGTTATAAAATAAAACGTAATTATTACG 1 179 1 AATAAAACGT 0.975608 -41 ATCTCCTTTCAATAAATCGTAATAATTACG 1 196 0 AATAAATCGT 0.96539 -24 GGAAGCGAGGACAAAAACATGAGAAGATCA 3 109 0 ACAAAAACAT 0.930429 -192 ********** Masking position 5 Map Score: 1.3645 Number of sites scoring better than the average of aligned sites = 161 Number in coding regions = 135 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 7 ********** 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 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