AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00740_bsub_reg_100.orf -o00740_bsub_100.ace -a/home/amcguire/genomes/ORF_bsub.txt -z/home/amcguire/genomes/bsub.fna -g0.44 -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 = 0.44 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 ylxS 300 alternate gene name: ymxA; similar to hypothetical proteins #2 nusA 34 nusA #3 truB 81 tRNA pseudouridine 55 synthase #4 ribH 32 riboflavin synthase (beta subunit) #5 ypuE 258 ypuE Motif number 1 GAGCGGGTTTCCCCACTCTTTGCCTCGGTA 1 150 0 CCCCACTCTT 0.952562 -151 GTGGGGAAACCCGCTCTTTTGTATTGAACA 1 164 1 CCGCTCTTTT 0.942592 -137 TTTTTAGCCCCTGCTCTTTTGAAGCAGGGT 1 227 1 CTGCTCTTTT 0.92729 -74 GTTCTTCCTCCTTGTGCTGTCGA 1 288 0 CTTCCTCCTT 0.946757 -13 TTAACGGTCTCCCCCCTTAAAACATTTG 2 17 0 CTCCCCCCTT 0.975157 -18 ATACGCCTATCCTCTCTTTTT 3 2 0 CCTCTCTTTT 0.97109 -80 TATCGTCTGTCCTCTTTCTTCGTTTATAAG 3 31 1 CCTCTTTCTT 0.945477 -51 TTGCCTTTCACTCCTTCTTTTGAGTTTTTT 3 62 0 CTCCTTCTTT 0.905572 -20 ATGATTCCCATCCTTTTTTGTGATATTT 4 15 0 CATCCTTTTT 0.812273 -18 AAAACATCACCTTTCGGATCGAAG 5 5 1 CATCACCTTT 0.931763 -254 AAAAACAAAACATCACCCTTCGATCCGAAA 5 22 0 CATCACCCTT 0.956246 -237 CCTTCTCCCATCCAGACTTTC 5 248 0 CTTCTCCCAT 0.885605 -11 ********** Masking position 10 Map Score: 14.8652 Number of sites scoring better than the average of aligned sites = 1718 Number in coding regions = 1192 Number in noncoding regions = 526 Number of orfs with sites within 600 bp upstream = 529 Fraction of orfs with sites within 600 bp upstream = 0.0849663 Motif number 2 CGAGGCAAAGAGTGGGGAAACCCGCTCTTT 1 153 1 AGTGGGGAAA 0.984802 -148 TCAAAAGAGCAGGGGCTAAAAAGTAAACGA 1 219 0 AGGGGCTAAA 0.939414 -82 TTTTATGCAGAGTGACGAGACGAATATGAG 1 257 1 AGTGACGAGA 0.805674 -44 CGACAGCACAAGGAGGAAGAAC 1 289 1 AGGAGGAAGA 0.933682 -12 AAATGTTTTAAGGGGGGAGACCGTTAA 2 18 1 AGGGGGGAGA 0.996412 -17 ACTCAAAAGAAGGAGTGAAAGGCAA 3 67 1 AGGAGTGAAA 0.944846 -15 ATCACAAAAAAGGATGGGAATCAT 4 19 1 AGGATGGGAA 0.889178 -14 TCTTCGGGGCAGGGTGGAAATCCCGACCGG 5 134 1 AGGGTGGAAA 0.987226 -125 ********** Masking position 1 Map Score: 7.74938 Number of sites scoring better than the average of aligned sites = 485 Number in coding regions = 291 Number in noncoding regions = 194 Number of orfs with sites within 600 bp upstream = 179 Fraction of orfs with sites within 600 bp upstream = 0.0287504 Motif number 3 GCAAATGGATATACGCTTACCTTCATACCTA 1 73 0 ATACGCTACC 0.961969 -228 CAATAAAACTATACCATAACCATATTTTTAT 1 105 0 ATACCATACC 0.98575 -196 TTGGAAATGCTAACGATTACCGAGGCAAAGA 1 133 1 TAACGATACC 0.969551 -168 GCTAAAAAGTAAACGATGAACATGTCGAGAC 1 204 0 AAACGATAAC 0.952307 -97 AAAACATCACCTTTCGGATCG 5 1 1 AAAACATACC 0.977585 -258 TGAGAAAAACAAAACATCACCCTTCGATCCG 5 25 0 AAAACATACC 0.977585 -234 ******* *** Masking position 7 Map Score: 4.84338 Number of sites scoring better than the average of aligned sites = 117 Number in coding regions = 104 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 4 CAAAAGAGCGGGTTTCCCCACTCTTTGCCTC 1 154 0 GTTTCCCCAC 0.98806 -147 GTTCTTCCTCCTTGTGCTGTC 1 290 0 GTCTTCCTCC 0.975413 -11 TTAACGGTCTCCCCCCTTAAAACATT 2 19 0 GTCTCCCCCC 0.99786 -16 ATGATTCCCATCCTTTTTTGTGA 4 20 0 GTTCCCATCC 0.97458 -13 CGCCGGTCGGGATTTCCACCCTGCCCCGAAG 5 135 0 GTTTCCACCC 0.994809 -124 * ********* Masking position 3 Map Score: 3.98277 Number of sites scoring better than the average of aligned sites = 73 Number in coding regions = 56 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 5 CGCTTATGTATGCATAGAAGC 1 1 0 TGCATAAAGC 0.988911 -300 CTTCTATGCATACATAAGCGCAAAAAGTGCC 1 12 1 TACATAGCGC 0.975262 -289 TTATTGCAAATGGATATACGCTTACCTTCAT 1 78 0 TGGATAACGC 0.914439 -223 TCCTGTTCAATACAAAAGAGCGGGTTTCCCC 1 166 0 TACAAAGAGC 0.937902 -135 AAAACCCTGCTTCAAAAGAGCAGGGGCTAAA 1 229 0 TTCAAAGAGC 0.937902 -72 CTCGTCACTCTGCATAAAAACCCTGCTTCAA 1 245 0 TGCATAAAAC 0.966916 -56 TTGAGTTTTTTTCTTATAAACGAAGAAAGAG 3 42 0 TTCTTAAAAC 0.715865 -40 AAAGCACATTTGCTTTAGAGCCCGTGACCCG 5 171 1 TGCTTTGAGC 0.897203 -88 GTGACCCGTGTGCATAAGCACGCGGTGGATT 5 194 1 TGCATAGCAC 0.979323 -65 ****** **** Masking position 1 Map Score: 7.41993 Number of sites scoring better than the average of aligned sites = 641 Number in coding regions = 586 Number in noncoding regions = 55 Number of orfs with sites within 600 bp upstream = 50 Fraction of orfs with sites within 600 bp upstream = 0.00803084 Motif number 6 GCTTCTATGCATACATAAGC 1 1 1 GCTTCTATGC 0.956139 -300 GGCACTTTTTGCGCTTATGTATGCATAGAA 1 13 0 GCGCTTATGT 0.976088 -288 ATGAAGGTAAGCGTATATCCATTTGCAATA 1 78 1 GCGTATATCC 0.92235 -223 GGGGAAACCCGCTCTTTTGTATTGAACAGG 1 166 1 GCTCTTTTGT 0.878815 -135 TTGAAGCAGGGTTTTTATGCAGAGTGACGA 1 245 1 GTTTTTATGC 0.885358 -56 CAGACGATATACGCCTATCCTCTCTTTTT 3 10 0 ACGCCTATCC 0.854204 -72 CGGTAGTAAAGCACATTTGCTTTAGAGCCC 5 164 1 GCACATTTGC 0.843702 -95 AATCCACCGCGTGCTTATGCACACGGGTCA 5 195 0 GTGCTTATGC 0.976127 -64 ********** Masking position 6 Map Score: 2.57198 Number of sites scoring better than the average of aligned sites = 1518 Number in coding regions = 1406 Number in noncoding regions = 112 Number of orfs with sites within 600 bp upstream = 93 Fraction of orfs with sites within 600 bp upstream = 0.0149374 Motif number 7 ********** No masking Map Score: 2.93755e-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: 2.93755e-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: 2.93755e-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