AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00950_bsub_reg_100.orf -o00950_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 yabF 144 similar to hypothetical proteins #2 yclB 89 similar to phenylacrylic acid decarboxylase #3 yefA 255 alternate gene name: yerS; similar to RNA methyltransferase #4 ykrV 94 similar to aspartate aminotransferase #5 aspB 22 aspartate aminotransferase #6 ypmA 142 ypmA #7 trpE 215 anthranilate synthase #8 gerCA 162 heptaprenyl diphosphate synthase component I #9 yqeT 24 similar to ribosomal protein L11 methyltransferase #10 dnaJ 199 heat-shock protein #11 yugG 147 similar to transcriptional regulator (Lrp/AsnC family) #12 ywpB 191 similar to hydroxymyristoyl-(acyl carrier protein) dehydratase #13 prfA 125 peptide chain release factor 1 #14 ywfB 151 alternate gene name: ipa-80d Motif number 1 TTAATACCTAAAAGGTATGATAAGGAGGCGCT 2 16 0 AAAGTATGAA 0.927296 -74 TTAAATGAAAAAAGTAAAGAAAAATTTGGGGT 4 20 0 AAAGAAAGAA 0.920598 -75 AGAATGAGAAGATGGCATGAGAGGATAAAATA 7 171 0 GATGCATGAA 0.942236 -45 TGCGTAAGCGAATGAAAAGATAAAACTCATAC 8 96 1 AATGAAAGAA 0.951607 -67 AATCTGATTCAATGATTAGAAAGTCAAAGTCA 10 66 1 AATGTTAGAA 0.823378 -134 AAAAAAAGTCAAAGCCAAGAGATGCCTGACTT 10 92 0 AAAGCAAGAA 0.977012 -108 TTTTTTGACGAATGCTAAGAAAAAACGAGGAG 11 77 0 AATGTAAGAA 0.973467 -71 AACGTGATATAATGTCATGAGATTTCTTGACA 11 107 1 AATGCATGAA 0.977012 -41 ACACCTTTGCAATGTCAAGAAATCTCATGACA 11 119 0 AATGCAAGAA 0.986317 -29 AGAGCCGTCAAAAGTTATGATATGATAATTAT 12 41 0 AAAGTATGAA 0.927296 -151 AGATGAAGGAGATGTCAAGACA 12 180 1 GATGCAAGAA 0.965115 -12 **** ***** * Masking position 10 Map Score: 14.7844 Number of sites scoring better than the average of aligned sites = 188 Number in coding regions = 153 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714 Motif number 2 ACTTCAAAGGTTTTCAATCACGCTGAAAAGA 3 83 0 TTTTCAATCC 0.978759 -173 TAGGCCAAGTTTTTCTTTCGCTTAAAACTAG 3 223 1 TTTTCTTTCC 0.958093 -33 TTTTTCATCCTCCAGTTTGAAC 6 131 0 TTTTCATCCC 0.969682 -12 TGCTACCCTATTCTCTAACTCAACTCATTCT 7 59 0 TTCTCTAACC 0.684014 -157 TCATGCCATCTTCTCATTCTCCTTGCCATAA 7 183 1 TTCTCATTCC 0.937036 -33 GAGTTTTATCTTTTCATTCGCTTACGCAGGT 8 93 0 TTTTCATTCC 0.974859 -70 CTTTGACTTTTTTTCTTGCCCGGGATAAAAG 10 110 1 TTTTCTTGCC 0.875539 -90 GAATTATGATTTTTCAATTCCTTTTATCCCG 10 130 0 TTTTCAATTC 0.784047 -70 TTTCCTACCTCTTTGCTATTG 12 1 1 TTTCCTACCC 0.808431 -191 ATTAATCTCTTTTTCAACCGCGCTAAAATGT 12 88 0 TTTTCAACCC 0.974364 -104 AGTCAAAAGCATTTCAATCCCAGCTGGAAAA 13 46 0 ATTTCAATCC 0.854115 -80 ********* * Masking position 2 Map Score: 11.1414 Number of sites scoring better than the average of aligned sites = 551 Number in coding regions = 478 Number in noncoding regions = 73 Number of orfs with sites within 600 bp upstream = 75 Fraction of orfs with sites within 600 bp upstream = 0.0120463 Motif number 3 ATACTTATGTATTCAGAGGGTTTTGCGCCC 1 14 1 ATTCAGAGGG 0.950441 -131 ATAACGAAAAAAACAGAGGGCGCAAAACCC 1 31 0 AAACAGAGGG 0.975646 -114 TTTGTCATCTTTTCAGCGTGATTGAAAACC 3 76 1 TTTCAGCGTG 0.874333 -180 TCAAGCCAAGTTTCAGCGTGTAGGCAAACC 3 192 0 TTTCAGCGTG 0.874333 -64 CATTTGCTTTTAACAGCGGGGACAGCCAGC 8 11 0 TAACAGCGGG 0.984506 -152 AAATGCTCGCAAACAGCGGGAGGATACAGC 8 36 1 AAACAGCGGG 0.984506 -127 AATTCCAGTATAGCAGAGGGAGCTTTTCCA 13 23 1 TAGCAGAGGG 0.947497 -103 ACGCACAGGAAAACAGAGGTGAAGACC 13 109 1 AAACAGAGGT 0.817302 -17 ********** Masking position 5 Map Score: 8.14003 Number of sites scoring better than the average of aligned sites = 380 Number in coding regions = 342 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 4 CACTTTGTCTATTATAACGAAAAAAACAGAGGGCGC 1 38 0 ATTTACGAAA 0.853687 -107 TATTTCCTCCAAGACAAAATAAAAACT 1 128 0 ATTCCCCAAA 0.941052 -17 CTATTCTCACCTTCTAAAAAAATCTTGA 4 77 0 ATTTCCCTAA 0.945017 -18 CATTATGTTTATTCTACCCAAAAGAAGTCTTTCTTT 7 115 1 ATTTACCAAA 0.978322 -101 CTATATAACAAATAAACCCAAAAGAAAGACTTCTTT 7 135 0 AATAACCAAA 0.785938 -81 CGCAGGTATCATTATAGCATAAAAAAAAGAATTGGC 8 64 0 ATTTACATAA 0.821815 -99 CATAAATTAGATTGTATCATTTTGAATTATGATTTT 10 148 0 ATTTACATAA 0.821815 -52 TTCAGGGCATAATACAACCATCAAAAAAAGGGAGTG 11 18 0 AATCACCAAA 0.798527 -130 TTGATTCACACCTTTGCAATGTCAAGAAA 11 129 0 ATTACCCTAA 0.872549 -19 ATAATTATAGATTTTACCAATAGCAAAGAGGTAGGA 12 13 0 ATTTACAAAA 0.908781 -179 TAGTATAGTGATTAACCCCAGTCAAAAGCATTTCAA 13 60 0 ATTACCCAAA 0.936662 -66 AATATTGATAATTATTCCCATACAAACAAAAAAACC 14 53 0 ATTTTCCAAA 0.876762 -99 TTTTAAGTAAATTTTATCCAGTGGAAATTGAACTGT 14 103 0 ATTTACCAAA 0.978322 -49 *** ** *** ** Masking position 15 Map Score: 9.31994 Number of sites scoring better than the average of aligned sites = 202 Number in coding regions = 160 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 5 TGGATATATCAGGAGTATGATTGAA 2 75 1 AGGAGTATGA 0.976338 -15 TTTGCGGTGTGGGAGTAGGATGGTGTTTTA 6 29 1 GGGAGTAGGA 0.959553 -114 TGTCCTGAAATGGAGTATGACTAACAATAT 6 99 1 TGGAGTATGA 0.966439 -44 TTGTTCAAACTGGAGGATGAAAAA 6 129 1 TGGAGGATGA 0.913264 -14 CCTTATGGCAAGGAGAATGAGAAGATGGCA 7 186 0 AGGAGAATGA 0.94723 -30 CCTTGCCATAAGGAGTGAGAGCA 7 203 1 AGGAGTGAGA 0.94622 -13 TGAGAAATTCGGGAGAGTGAAGCGAG 10 184 1 GGGAGAGTGA 0.965115 -16 ATCAAAAAAAGGGAGTGACACAGA 11 5 0 GGGAGTGACA 0.820753 -143 ********** Masking position 4 Map Score: 6.62352 Number of sites scoring better than the average of aligned sites = 138 Number in coding regions = 98 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 46 Fraction of orfs with sites within 600 bp upstream = 0.00738837 Motif number 6 TTGGCTTACCAAGCCAAGTT 3 1 0 AAGCCAAGTT 0.991422 -255 TTGGCTTGGTAAGCCAAGCTCAGAATGTTG 3 14 1 AAGCCAAGCT 0.985465 -242 TGGCCTATTCAAGCCAAGTTTCAGCGTGTA 3 200 0 AAGCCAAGTT 0.991422 -56 TGGCTTGAATAGGCCAAGTTTTTCTTTCGC 3 214 1 AGGCCAAGTT 0.981157 -42 AAAAAAGTCAAAGCCAAGAGATGCCTGACT 10 93 0 AAGCCAAGAG 0.953721 -107 ********** Masking position 6 Map Score: 6.4245 Number of sites scoring better than the average of aligned sites = 34 Number in coding regions = 28 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 7 TATAATAGACAAAGTGCATTTTCTGCTTATTAGACGCTCG 1 58 1 AAGGTTTGTT 0.958244 -87 AAGCCGCATAAAGCGGCTTTTGCGGTGTGGGAGTAGGAT 6 10 1 AAGGTTTGTG 0.995157 -133 GTTTTATTTAAAAGCGGATTTCCCGCTCTGTGATACTAGT 6 53 1 AAGGTTTGTG 0.995157 -90 TTAAGAAATAAATGTGAATTTGGGGACAAGGGTGATATTT 8 133 1 AAGGTTTGCG 0.982009 -30 CAGATTATGAAATGTGTTCTTTTCGGTCAGCTCCGGAAGC 10 32 0 AAGGCTTGTG 0.979598 -168 AGTATAGCAGAGGGAGCTTTTCCAGCTGGGATTGAAATGC 13 29 1 AGGGTTTGTG 0.979598 -97 ACTATACTATAATGAGAATGTTACGCACAGGAAAACAGAG 13 87 1 AAGGTGTGAG 0.895883 -39 AACCCTTTAAAAAGGGTTTTTAATTATAGGAATTTAGAAA 14 17 0 AAGGTTTTTG 0.975884 -135 AACCCTTTTTAAAGGGTTTTTTTGTTTGTATGGGAATAAT 14 39 1 AAGGTTTTTA 0.818803 -113 ** * * *** * * * Masking position 11 Map Score: 6.36404 Number of sites scoring better than the average of aligned sites = 93 Number in coding regions = 79 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 8 AATCTATAATTAATACCTAAAAGGTATGATAA 2 25 0 TAATCCTAAA 0.803479 -65 GAATGTTGACAAAATCCTAAAACAGTTTTCGT 3 36 1 AAAACCTAAA 0.976158 -220 AAAAGATGACAAAATCCTAAAACGAAAACTGT 3 57 0 AAAACCTAAA 0.976158 -199 AGCGTGATTGAAAACCTTTGAAGTCTAGGAAG 3 90 1 AAAACTTTAA 0.808763 -166 CACCTTCTAAAAAAATCTTGAAATGATAGTCC 4 66 0 AAAATCTTAA 0.875605 -29 TTGCTATTGGTAAAATCTATAATTATCATATC 12 23 1 TAAATCTAAA 0.809171 -169 CAAAGTTTCTAAATTCCTATAATTAAAAACCC 14 12 1 AAATCCTAAA 0.928254 -140 TACAAACAAAAAAACCCTTTAAAAAGGGTTTT 14 37 0 AAAACCTTAA 0.95551 -115 AAATTTACTTAAAATTTTAAAAGATTGGTTGG 14 125 1 AAAATTTAAA 0.725447 -27 **** **** ** Masking position 8 Map Score: 5.65985 Number of sites scoring better than the average of aligned sites = 249 Number in coding regions = 166 Number in noncoding regions = 83 Number of orfs with sites within 600 bp upstream = 76 Fraction of orfs with sites within 600 bp upstream = 0.0122069 Motif number 9 TATGCCCTGAAATTGTCAATTCTAGCGGAA 11 43 1 AATTGTCAAT 0.972887 -105 AAATGTAACCAACTGTCAATGAGAGCCGTC 12 64 0 AACTGTCAAT 0.982309 -128 GTATGGGAATAATTATCAATATTTTCAAAA 14 66 1 AATTATCAAT 0.900213 -86 GTGGAAATTGAACTGTCAATGTTTTTTGAA 14 89 0 AACTGTCAAT 0.982309 -63 ********** Masking position 6 Map Score: 2.02428 Number of sites scoring better than the average of aligned sites = 26 Number in coding regions = 15 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 10 CGTCTAATAAGCAGAAAATGCACTTTGTCT 1 64 0 GCAGAAAATG 0.816121 -81 ACGCTCGATATAAGAAAAAGTTTCATGAAT 1 91 1 TAAGAAAAAG 0.513362 -54 GCATCGGAGCACAGCGAATGTTGAATTCGT 3 127 1 ACAGCGAATG 0.973875 -129 CACAGGCCTGACAACGAATGCGAAGGTTTG 3 168 1 ACAACGAATG 0.765087 -88 CCTCTAGTTTTAAGCGAAAGAAAAACTTGG 3 227 0 TAAGCGAAAG 0.856367 -29 GAATAGGGTAGCAGAGAATGAGTTTAGTTG 7 77 1 GCAGAGAATG 0.940228 -139 TCCTTATGGCAAGGAGAATGAGAAGATGGC 7 187 0 AAGGAGAATG 0.83447 -29 CCCGCTGTTAAAAGCAAATGCTCGCAAACA 8 21 1 AAAGCAAATG 0.906616 -142 GATACCTGCGTAAGCGAATGAAAAGATAAA 8 90 1 TAAGCGAATG 0.955453 -73 ACTATACTATAATGAGAATGTTACGCACAG 13 87 1 AATGAGAATG 0.772797 -39 ********** Masking position 7 Map Score: 4.22823 Number of sites scoring better than the average of aligned sites = 819 Number in coding regions = 699 Number in noncoding regions = 120 Number of orfs with sites within 600 bp upstream = 99 Fraction of orfs with sites within 600 bp upstream = 0.0159011 Motif number 11 TGTTGAATTCGTGAGCACCGAAGCACAGGC 3 145 1 GTGAGCACCG 0.977243 -111 CGCATTCGTTGTCAGGCCTGTGCTTCGGTG 3 160 0 GTCAGGCCTG 0.967231 -96 TCTTTTTAGTGTCAGCCCCGCTTCCGGAGC 10 13 1 GTCAGCCCCG 0.996828 -187 GTTCTTTTCGGTCAGCTCCGGAAGCGGGGC 10 27 0 GTCAGCTCCG 0.991381 -173 ********** Masking position 4 Map Score: 1.35305 Number of sites scoring better than the average of aligned sites = 51 Number in coding regions = 46 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 12 ACTGTTTTAGGATTTTGTCAACATTCTGAG 3 32 0 GATTTTGTCA 0.909599 -224 TTCGTTTTAGGATTTTGTCATCTTTTCAGC 3 63 1 GATTTTGTCA 0.909599 -193 TTACTTTTTTCATTTAACCATATATGATGA 4 35 1 CATTTAACCA 0.814028 -60 ACGCAGGTATCATTATAGCATAAAAAAAAG 8 71 0 CATTATAGCA 0.776892 -92 ACTTTCTAATCATTGAATCAGATTATGAAA 10 60 0 CATTGAATCA 0.843572 -140 ACATAAATTAGATTGTATCATTTTGAATTA 10 155 0 GATTGTATCA 0.93643 -45 AATCTCATGACATTATATCACGTTTTTTGA 11 101 0 CATTATATCA 0.904972 -47 GATAATTATAGATTTTACCAATAGCAAAGA 12 20 0 GATTTTACCA 0.922819 -172 ********** Masking position 2 Map Score: 1.08563 Number of sites scoring better than the average of aligned sites = 293 Number in coding regions = 227 Number in noncoding regions = 66 Number of orfs with sites within 600 bp upstream = 72 Fraction of orfs with sites within 600 bp upstream = 0.0115644 Motif number 13 ********** No masking Map Score: -6.60562e-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 14 ********** No masking Map Score: -6.60562e-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 15 ********** No masking Map Score: -6.60562e-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