AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i223_Pseudouridylate_Synthase_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 ypuL 91 similar to hypothetical proteins #2 dacB 122 D-alanyl-D-alanine carboxypeptidase (penicillin-binding protein 5*) #3 ypuI 54 similar to hypothetical proteins from B. subtilis #4 ypuG 280 similar to hypothetical proteins Motif number 1 TGCCAAATCTAAAAAAAACGCCGTTT 1 6 0 AAAAAAACGC 0.891537 -86 TAGGAATTTGAAAAAGCTTGTTTGTTAAGGT 1 37 1 AAAAAGCTGT 0.944139 -55 TTAAGGTTGAAAAAAGTAAGATAATACTTGA 1 61 1 AAAAAGTAGA 0.834637 -31 ACTCTCCCTGAAAAAGGGAGAGTAAACG 2 8 0 AAAAAGGAGA 0.882085 -115 AGCAAACATAAAAAAACTCTCCCTGAAAAAG 2 23 0 AAAAAACCTC 0.956416 -100 TATGATGATGAAAAAGCGCGATTCATTAAAC 3 13 0 AAAAAGCCGA 0.992801 -42 AGATATAAGGAAGAAGCTATC 3 44 1 AAGAAGCATC 0.947142 -11 GATAAAAGGAAAAAAGAACGCCCGGCCTCTA 4 53 1 AAAAAGACGC 0.981602 -228 TTTCCTTTCTAAGAAGCACTAGAGGCCGGGC 4 72 0 AAGAAGCCTA 0.965312 -209 GAAGCGGGAGAAAAAGCCTTTGCTTCTGGTT 4 102 0 AAAAAGCTTT 0.898861 -179 ATAAGCCACCAAAAAGCTCTCGTCCAATACT 4 203 0 AAAAAGCCTC 0.993023 -78 ******* *** Masking position 5 Map Score: 13.8799 Number of sites scoring better than the average of aligned sites = 1776 Number in coding regions = 1424 Number in noncoding regions = 352 Number of orfs with sites within 600 bp upstream = 255 Fraction of orfs with sites within 600 bp upstream = 0.0409573 Motif number 2 AAGTAAGATAATACTTGAGGTGAAAGAC 1 74 1 ATACTTGAGG 0.758733 -18 CATAACTGATGGACATGCGCATAAACTTGT 2 75 1 GGACATGCGC 0.935272 -48 ACCACCACAAGGACGTGAGCAAAC 2 109 1 GGACGTGAGC 0.957969 -14 CATCATCATAAGATATAAGGAAGAAGCTAT 3 34 1 AGATATAAGG 0.750976 -21 CACTAAAAGCACATTAAAGGAGGAAGCACC 4 11 0 ACATTAAAGG 0.689617 -270 ACCATAGAAGGGATAAAAGGAAAAAAGAAC 4 42 1 GGATAAAAGG 0.91186 -239 TTTCTAAGAAGCACTAGAGGCCGGGCGTTC 4 68 0 GCACTAGAGG 0.981705 -213 TGCTCGGAGCGCAGAAGCGGGAGAAAAAGC 4 116 0 GCAGAAGCGG 0.881868 -165 AATATTCAAAACACAAGAGGTGTTTGCTCG 4 140 0 ACACAAGAGG 0.974678 -141 AAATAGTATTGGACGAGAGCTTTTTGGTGG 4 199 1 GGACGAGAGC 0.970906 -82 ********** Masking position 3 Map Score: 6.43024 Number of sites scoring better than the average of aligned sites = 1339 Number in coding regions = 1131 Number in noncoding regions = 208 Number of orfs with sites within 600 bp upstream = 149 Fraction of orfs with sites within 600 bp upstream = 0.0239319 Motif number 3 GAAAAAGCTTGTTTGTTAAGGTTGAAAAAA 1 46 1 GTTTGTTAAG 0.914467 -46 CGTTTACTCTCCCTTTTTCAG 2 2 1 GTTTACTCTC 0.893968 -121 GTTTGTACAAGTTTATGCGCATGTCCATCA 2 81 0 GTTTATGCGC 0.895887 -42 CCTTGTGGTGGTTTGTACAAGTTTATGCGC 2 91 0 GTTTGTACAA 0.917415 -32 GTTTGCTCACGTCCTTGTGG 2 113 0 GTTTGCTCAC 0.977975 -10 CACAAGAGGTGTTTGCTCGGAGCGCAGAAG 4 129 0 GTTTGCTCGG 0.988312 -152 TTTTGAAGGAGTTTGTACAGAATATTCAAA 4 160 0 GTTTGTACAG 0.976298 -121 ********** Masking position 4 Map Score: 4.86958 Number of sites scoring better than the average of aligned sites = 547 Number in coding regions = 497 Number in noncoding regions = 50 Number of orfs with sites within 600 bp upstream = 54 Fraction of orfs with sites within 600 bp upstream = 0.00867331 Motif number 4 TAAGGTTGAAAAAAGTAAGATAATACTTGA 1 62 1 AAAAGTAAGA 0.963427 -30 CTCTCCCTGAAAAAGGGAGAGTAAACG 2 8 0 AAAAGGGAGA 0.984193 -115 ATCATAAGATATAAGGAAGAAGCTATC 3 38 1 ATAAGGAAGA 0.976749 -17 AAAAGCACATTAAAGGAGGAAGCACC 4 7 0 TAAAGGAGGA 0.94981 -274 TAGAAGGGATAAAAGGAAAAAAGAACGCCC 4 46 1 AAAAGGAAAA 0.982917 -235 GTGCTTCTTAGAAAGGAAAACCAGAAGCAA 4 84 1 GAAAGGAAAA 0.962852 -197 ********** Masking position 4 Map Score: 7.00305 Number of sites scoring better than the average of aligned sites = 584 Number in coding regions = 442 Number in noncoding regions = 142 Number of orfs with sites within 600 bp upstream = 172 Fraction of orfs with sites within 600 bp upstream = 0.0276261 Motif number 5 CTTACTTTTTTCAACCTTAACAAACAAGCTT 1 50 0 TCAACCTAAC 0.880738 -42 GTCTTTCACCTCAAGTATTATCTTA 1 77 0 TTCACCTAAG 0.906541 -15 AATATAATTGTTATTCATAACTGATGGACAT 2 60 1 TTATTCAAAC 0.867809 -63 ACTTGTACAAACCACCACAAGGACGTGAGCA 2 99 1 ACCACCAAAG 0.969694 -24 GCGCTTTTTCATCATCATAAGATATAAGGAA 3 25 1 ATCATCAAAG 0.943516 -30 CTTAGAAAGGAAAACCAGAAGCAAAGGCTTT 4 90 1 AAAACCAAAG 0.835453 -191 TTTGTACAGAATATTCAAAACACAAGAGGTG 4 148 0 ATATTCAAAC 0.867809 -133 CTGTACAAACTCCTTCAAAACAGGATATGAA 4 170 1 TCCTTCAAAC 0.926333 -111 ******* *** Masking position 9 Map Score: 1.31255 Number of sites scoring better than the average of aligned sites = 874 Number in coding regions = 771 Number in noncoding regions = 103 Number of orfs with sites within 600 bp upstream = 91 Fraction of orfs with sites within 600 bp upstream = 0.0146161 Motif number 6 ********** No masking Map Score: -4.80737e-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 7 ********** No masking Map Score: -4.80737e-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: -4.80737e-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