AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i293_mixed_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 gcaD 192 UDP-N-acetylglucosamine pyrophosphorylase #2 prs 22 phosphoribosyl pyrophosphate synthetase #3 ctc 84 general stress protein #4 spoVC 106 thermosensitive mutant blocks spore coat formation (stage V sporulation) #5 yacA 103 similar to cell-cycle protein #6 ftsH 97 cell-division protein and general stress protein (class III heat-shock) #7 pabB 166 para-aminobenzoate synthase (subunit A) #8 ybbP 160 alternate gene name: ybbQ; similar to hypothetical proteins #9 yyaF 126 similar to hypothetical proteins Motif number 1 TCCTAAATTCGGAGGTTTATCC 2 9 1 TCGGAGGTTT 0.929797 -14 GACGTAACCGCGGGAGGGTTACGCCTTAAG 4 14 0 CGGGAGGGTT 0.99269 -93 TTTATGAAGACGGGAGTTATGTGACTAAGG 4 76 1 CGGGAGTTAT 0.979294 -31 TATGTGACTAAGGGAGGATTCGCC 4 93 1 AGGGAGGATT 0.946111 -14 CCCGGCGAACCGGGAGTTTTGGCTTTTT 7 9 0 CGGGAGTTTT 0.994811 -158 CCCGGTTCGCCGGGAGTTTTTTTATATTTC 7 25 1 CGGGAGTTTT 0.994811 -142 ********** Masking position 5 Map Score: 8.17661 Number of sites scoring better than the average of aligned sites = 68 Number in coding regions = 49 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 2 ATGTCAGCCCTTTCAGCAGTCCTTGCTTTTTGGTTA 1 15 0 TTTCGTTTGC 0.856946 -178 AATTCTGATTTTTCAAACTTAGTTGCACTCAATAGA 1 77 1 TTTATTTTGC 0.921024 -116 TCCTTATCGTTATGGGTATTGTTTGTAATAGGACAA 3 31 1 TATTTTTTGT 0.939367 -54 CACCATCCTCTTGTCGTTTTAGTTGTCCTATTACAA 3 53 0 TTGTTTTTGT 0.879877 -32 CCCTCCCGCGGTTACGTCTTTTGTGCTAGAATGAGA 4 26 1 GTTTTTGTGC 0.94676 -81 CTGCAGAGCCTATGCTTCTTCTTTGCTTGGAGGGGT 5 21 1 TATTTTTTGC 0.967177 -83 CTGCTTCCGAGATGGTTATTGTTTGTATTGGAATGA 6 19 1 GATTTTTTGT 0.856034 -79 GCCGGGAGTTTTTTTATATTTCGTGCATCAAATATG 7 33 1 TTTTTTGTGC 0.978874 -134 ATTCCTCTATTTTCTTTTTTACTTGTTTTTAATTGT 7 134 0 TTTTTTTTGT 0.974935 -33 CGTTAGCCGCTTTGCTCTTTTTTTGCGGGCTGAGAG 8 15 1 TTTCTTTTGC 0.969521 -146 CATTTCGTATTTTGTGTTTTACGTGTTACGCATATG 8 111 0 TTTTTTGTGT 0.96057 -50 *** * ** **** Masking position 10 Map Score: 8.51019 Number of sites scoring better than the average of aligned sites = 584 Number in coding regions = 473 Number in noncoding regions = 111 Number of orfs with sites within 600 bp upstream = 116 Fraction of orfs with sites within 600 bp upstream = 0.0186315 Motif number 3 AAAAAGCAAGGACTGCTGAAAGGGCTGACATAAG 1 20 1 GCTGGAAGGG 0.87181 -173 TATATTTTTCTATGGATAAAAGGGATATTGGAGG 1 162 1 TTGGAAAGGG 0.941794 -31 TTACGTCTTTTGTGCTAGAATGAGAAGAATTATA 4 37 1 TTGCGAAGAG 0.972128 -70 ATAACTCCCGTCTTCATAAACGGGCTATAATTCT 4 62 0 TTTCAAAGGG 0.909984 -45 ATGCTTCTTCTTTGCTTGGAGGGGTTGAAAGTGT 5 32 1 TTGCGGAGGG 0.988851 -72 TAGTTGTGCTTACTGTGGGAGGAGGTAAGGA 6 77 1 TCTGGGAGAG 0.970248 -21 CGACGAATGTTATTCTTGGAAGAGAAATTCACTT 7 78 1 TTTCGGAGAG 0.980893 -89 TTTGCTCTTTTTTTGCGGGCTGAGAGGGCTGGCA 8 25 1 TTTGGGCGAG 0.940536 -136 TAAATCGAAATGTGGTATAATGGGCTCGCTATGT 8 71 1 TTGGTAAGGG 0.901728 -90 ATGACTGAAATCTTGGAGGACGAGGAA 8 144 1 TTTGGGAGAG 0.986986 -17 * *** *** *** Masking position 12 Map Score: 8.27086 Number of sites scoring better than the average of aligned sites = 466 Number in coding regions = 389 Number in noncoding regions = 77 Number of orfs with sites within 600 bp upstream = 53 Fraction of orfs with sites within 600 bp upstream = 0.00851269 Motif number 4 GCACTCAATAGAAAATTCTTGCACTTCATGAAGTC 1 101 1 GAAATTTACT 0.980754 -92 CTTGAAATCAGAAGATATTTAGGATATATTTTTCT 1 138 1 GAAATTTGAT 0.980754 -55 GTTAGGATATGAATATCTTTAAAATACCTGCTCAT 5 64 1 GAAATTTAAT 0.983992 -40 TAGTACCATAGAAAATCATTCCAATACAAACAATA 6 35 0 GAAATTTAAT 0.983992 -63 TGGTACTATTGAACATAGTTGTGCTTACTGTGGGA 6 62 1 GAAATTTGCT 0.976877 -36 CTTTTCCAGTGAACCTCCTTATAATTGCTCTAGGT 9 54 1 GAACTTTAAT 0.957402 -73 *** ** ** *** Masking position 9 Map Score: 3.92803 Number of sites scoring better than the average of aligned sites = 85 Number in coding regions = 66 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 5 TTAGTTGCACTCAATAGAAAATTCTTGCACT 1 95 1 TCATAGAAAA 0.977655 -98 ATCCCTTTTATCCATAGAAAAATATATCCTA 1 157 0 TCATAGAAAA 0.977655 -36 GTTCAATAGTACCATAGAAAATCATTCCAAT 6 45 0 ACATAGAAAA 0.98275 -53 TTTCTATGGTACTATTGAACATAGTTGTGCT 6 56 1 ACATTGAACA 0.884071 -42 TGATGCACGAAATATAAAAAAACTCCCGGCG 7 32 0 AAATAAAAAA 0.714039 -135 ACATTGCTTTACAATTAAAAACAAGTAAAAA 7 124 1 ACATTAAAAA 0.893328 -43 TTTCATCTCCTCTATATAAAACCGTCATTGT 9 104 0 TCATATAAAA 0.893435 -23 ** ******** Masking position 4 Map Score: 3.56918 Number of sites scoring better than the average of aligned sites = 324 Number in coding regions = 245 Number in noncoding regions = 79 Number of orfs with sites within 600 bp upstream = 87 Fraction of orfs with sites within 600 bp upstream = 0.0139737 Motif number 6 TGCTGAAAGGGCTGACATAAGCCTTTTGCC 1 33 1 GCTGACATAA 0.954455 -160 AAAAAGGACCGCCGGCAAAAGGCTTATGTC 1 46 0 GCCGGCAAAA 0.992295 -147 AGCCCTCTCAGCCCGCAAAAAAAGAGCAAA 8 25 0 GCCCGCAAAA 0.973388 -136 GGCTGAGAGGGCTGGCACATTTCACTTGCT 8 42 1 GCTGGCACAT 0.955097 -119 GAAAAGACAAGCTGACAAAAAAGCATTTTC 9 30 0 GCTGACAAAA 0.981464 -97 ********** Masking position 7 Map Score: 3.24814 Number of sites scoring better than the average of aligned sites = 377 Number in coding regions = 353 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 7 TTTCAGCAGTCCTTGCTTTTTGGTTATTTT 1 11 0 CCTTGCTTTT 0.94953 -182 ATTCAGCACCATCCTCTTGTCGTTTTAG 3 67 0 CCATCCTCTT 0.881449 -18 GAAAAAAGTGAATTTCTCTTCCAAGAATAA 7 87 0 AATTTCTCTT 0.812218 -80 TCACTAACAACATTGCTTTACAATTAAAAA 7 115 1 CATTGCTTTA 0.945734 -52 TTGTATCATTCCTCTATTTTCTTTTT 7 151 0 CATTCCTCTA 0.949531 -16 GCGTTAGCCGCTTTGCTCTTTTTTTGCGGG 8 14 1 CTTTGCTCTT 0.94637 -147 GGCAAGCTGAAAATGCTTTTTTGTCAGCTT 9 22 1 AAATGCTTTT 0.795638 -105 ACCTCCTTATAATTGCTCTAGGTTCAAAAT 9 66 1 AATTGCTCTA 0.94573 -61 ********** Masking position 4 Map Score: 3.50504 Number of sites scoring better than the average of aligned sites = 554 Number in coding regions = 472 Number in noncoding regions = 82 Number of orfs with sites within 600 bp upstream = 76 Fraction of orfs with sites within 600 bp upstream = 0.0122069 Motif number 8 ATGGTGCAAACTGCAGAGCCTATGC 5 6 1 GCAAACTGCA 0.936741 -98 CATCTCGGAAGCAGGCTGCCGA 6 3 0 GCAGGCTGCC 0.992252 -95 CTCTTTTTTTGCGGGCTGAGAGGGCTGGCA 8 29 1 GCGGGCTGAG 0.966951 -132 AAAGGGATTGGCAAGCTGAAAATGCTTTTT 9 13 1 GCAAGCTGAA 0.986179 -114 ACTGGAAAAGACAAGCTGACAAAAAAGCAT 9 34 0 ACAAGCTGAC 0.95491 -93 ********** Masking position 7 Map Score: 1.28837 Number of sites scoring better than the average of aligned sites = 591 Number in coding regions = 564 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 9 TTCAGCAGTCCTTGCTTTTTGGTTATTTT 1 10 0 CTTGCTTTTT 0.907831 -183 GGTTTAAATCCTTATCGTTATGGGTATTGT 3 23 1 CTTATCGTTA 0.876725 -62 GCACCATCCTCTTGTCGTTTTAGTTGTCCT 3 60 0 CTTGTCGTTT 0.981543 -25 TTCTTTTTTACTTGTTTTTAATTGTAAAGC 7 129 0 CTTGTTTTTA 0.938496 -38 TTTTTGTCAGCTTGTCTTTTCCAGTGAACC 9 39 1 CTTGTCTTTT 0.980105 -88 ********** Masking position 3 Map Score: 1.20213 Number of sites scoring better than the average of aligned sites = 372 Number in coding regions = 318 Number in noncoding regions = 54 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 10 AATTAAAAAAGGACCGCCGGCAAAAGGCTT 1 51 0 GGACCGCCGG 0.994146 -142 CAAAACTCCCGGTTCGCCGGGAGTTTTTTT 7 18 1 GGTTCGCCGG 0.997201 -149 ATTATAAGGAGGTTCACTGGAAAAGACAAG 9 49 0 GGTTCACTGG 0.97955 -78 ********** Masking position 5 Map Score: 0.000551327 Number of sites scoring better than the average of aligned sites = 23 Number in coding regions = 20 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 11 ********** No masking Map Score: -3.46502e-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 12 ********** No masking Map Score: -3.46502e-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 13 ********** No masking Map Score: -3.46502e-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