AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00940_bsub_reg_100.orf -o00940_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 ybbD 27 alternate gene name: yzbA; similar to beta-hexosaminidase #2 ybbE 84 similar to beta-lactamase #3 ybbF 25 similar to sucrose phosphotransferase enzyme II #4 ybbI 170 similar to hypothetical proteins #5 yckE 153 similar to beta-glucosidase #6 yclB 89 similar to phenylacrylic acid decarboxylase #7 bcsA 73 naringenin-chalcone synthase #8 xpt 300 xanthine phosphoribosyltransferase #9 cypA 300 cytochrome P450-like enzyme #10 bioI 68 cytochrome P450-like enzyme #11 bioW 251 6-carboxyhexanoate-CoA ligase #12 bglP 300 phosphotransferase system (PTS) beta-glucoside-specific enzyme IIABC component Motif number 1 GATTTTAAGCATCCAATGGGAATTGGGTGCTTTT 5 1 1 GTTTTGTATT 0.927194 -153 CCTTATCATACCTTTTAGGTATTAATTATAGATTTAATAGATAT 6 23 1 CTTTTGTATT 0.982314 -67 CGCGGCGGAGTTTTTTTTGCATATAAAAAAGATTGTTGCGGCAC 7 17 1 TTTTTGTATT 0.979569 -57 TTTAATTTTGTTTTTTTAGATATCATTCGTATTTCAAGGGGATT 8 22 0 TTTTTGAATT 0.950244 -279 CGGGAATTTTTATTTTCAGCCTATGCAAGAGATTAGAATCTTGA 8 69 1 TTTTTGTGTT 0.938065 -232 ACGTGTACGGTTTTTTGTGATATCAGCATTGCTTGCTCTTTATT 8 222 1 TTTTTGAATT 0.950244 -79 TGTCTACCTCCGTTATGAGAATAAAAAAAGCATTGCCCGCTCAA 8 265 0 CTTATGTATT 0.91899 -36 CTATGCCGGCTCTTTTAAGGATTTGGAAAATTTTTTAGCCCCAT 9 63 0 TTTTTGTGTT 0.938073 -238 CGAAAAAGACCGTTTTGTGTGAAAACGGTCTTTTTGTTTCCTTT 11 25 1 CTTTTGAATT 0.956754 -227 TCAACGCTTTCATTTTTGGTGTTGACTATCGTTTCTAGAACAAA 12 27 0 CTTTTGTATT 0.982314 -274 TGACGGGTCGTTTTATTTGTTTGTAGGTATACTTTAGCACTAGA 12 82 0 TTTATGTATT 0.907347 -219 TTTTTTATTCTCTTTTAGGAGGTGATGCAGCATTTGATACAAAA 12 205 1 TTTTTGGATT 0.953739 -96 TGTATACCTCCTTTTTATGGGGGGACTGCTGGATGAAAGGTGGC 12 266 0 CTTTTGGAAT 0.717633 -35 * **** * * * ** Masking position 6 Map Score: 12.4027 Number of sites scoring better than the average of aligned sites = 317 Number in coding regions = 243 Number in noncoding regions = 74 Number of orfs with sites within 600 bp upstream = 81 Fraction of orfs with sites within 600 bp upstream = 0.01301 Motif number 2 TCAGTTCGATTAAATTGTTTCTGTTTTAGGGATAGT 2 26 1 TATTTCTTTT 0.634747 -59 CCCCTTTCTGTGCTTCTATCCCGTTTACTATCCCTA 2 52 0 TTTCTCCTTT 0.949008 -33 AGCGGCCCGATTCTTCGCCGTCCTTTA 4 2 0 TTTCCTCTTT 0.972369 -169 GGAGAACAGTTGATCCTTCATCATTTCTTATAGTCT 4 39 1 TTCCCTCTTT 0.932254 -132 TCTGTTATGATATTTCAACTATGTTTTTAAATTTTT 4 93 0 TTTCCATTTT 0.707091 -78 GGGAATTGGGTGCTTTTGCGTTATTTACAGGTAGGC 5 28 1 TTTTCTTTTT 0.90371 -126 ATATCAGCATTGCTTGCTCTTTATTTGAGCGGGCAA 8 241 1 TTTGCTTTTT 0.713695 -60 ATTTGGAAAATTTTTTAGCCCCATTTTGATTAATGT 9 51 0 TTTTCCCTTT 0.954303 -250 CGGTATGATGTCGATTGTTTTTATTTTTGAACAGAA 10 30 1 TATTTTTTTT 0.615678 -39 CAAAACGGTCTTTTTCGATTTCTTTTTACAG 11 6 0 TTTCTTCTTT 0.944922 -246 GTGAAAACGGTCTTTTTGTTTCCTTTTAACCAACTG 11 43 1 TTTTTTCTTT 0.90371 -209 TTAGAATATATTATTCTCTCCTGTTTCTGTCAATAG 11 99 0 TTTCTCTTTT 0.900727 -153 TCTTCTTGCATCATTTCTCGCCCTTTCACTGATAAC 11 195 0 TTTTCCCTTT 0.954303 -57 AGTCTCCTCCTGCACCTGCACCATTTAGGTTTTGCC 12 146 0 TACCCCCTTT 0.839398 -155 TCATTTAGGTTTTTTTATTCTCTTTTAGGAGGTGAT 12 195 1 TTTTTTCTTT 0.90371 -106 GTGGCCGCCTTTCACCAGCTTTTTTTGTATCAAATG 12 235 0 TACCCTTTTT 0.701392 -66 * *** * ** *** Masking position 14 Map Score: 11.2369 Number of sites scoring better than the average of aligned sites = 1728 Number in coding regions = 1391 Number in noncoding regions = 337 Number of orfs with sites within 600 bp upstream = 356 Fraction of orfs with sites within 600 bp upstream = 0.0571796 Motif number 3 TAAAACCCCTCCCCTTCAAGATGCC 3 8 0 AAACCTCCCA 0.979536 -18 AAATAACGCAAAAGCACCCAATTCCCATTGGATGCTT 5 17 0 AAACCCATCA 0.908471 -137 AGCTCAGCTAATATTGCCTACCTGTAAATAACGCAAA 5 42 0 ATACCTCTAA 0.727451 -112 AAGAAAGCGCCTCCTTATCATACCTTTTAG 6 4 1 AAACCTCTCA 0.985343 -86 ATATGCAAAAAAAACTCCGCCGCGGCGGAG 7 4 0 AAACCGCCCG 0.951486 -70 CTGAAAATAAAAATTCCCGAACTTTAATTTTGTTTTT 8 51 0 AAACCGATAA 0.924324 -250 CAAATCCTTAAAAGAGCCGGCATAGAAGTATTAGGAG 9 82 1 AAACCGCTAA 0.973868 -219 GATAAGGGCCAAAATGCCGTCCCCGCATTTTGAAATA 9 183 0 AAACCGCCCA 0.989478 -118 AAAGGAAACAAAAAGACCGTTTTCACACAAAACGGTC 11 32 0 AAACCGTTCA 0.94485 -220 AAAGAGAATAAAAAAACCTAAATGACACAGATTGCGA 12 183 0 AAACCTATCA 0.956584 -118 *** *** * * ** Masking position 3 Map Score: 6.32548 Number of sites scoring better than the average of aligned sites = 323 Number in coding regions = 266 Number in noncoding regions = 57 Number of orfs with sites within 600 bp upstream = 51 Fraction of orfs with sites within 600 bp upstream = 0.00819146 Motif number 4 AGAAACTTCCTCCTATCGTCTAATCAT 1 11 0 TCCTCCTATC 0.911214 -17 AGGCTAGCCCCTTTCTGTGCTTCTA 2 70 0 TGCCCCTTTC 0.874243 -15 CAGTTGATCCTTCATCATTTCTTATAGTCTT 4 45 1 TCATCATTTC 0.908971 -126 AATATTGAGATATATCATTTTAAAACAGGGG 4 142 1 TTATCATTTT 0.741731 -29 GAGGATGCCCCCTGTTTTAAAATGAT 4 155 0 TCCCCCTGTT 0.699825 -16 GAGACAGTCATTAATCATTTTGCTGCCTAAA 9 144 0 TAATCATTTT 0.414706 -157 GATTAATGACTGTCTCATATCTTTTATTTCA 9 159 1 TTCTCATATC 0.694264 -142 CTGATCTCAATGGATCATTTTACAAATCGTC 9 227 1 TGATCATTTT 0.737884 -74 GTGATTTTCTCCTTTCTGTTCAAAAA 10 53 0 TTCTCCTTTC 0.963529 -16 ACGGTCTTTTTGTTTCCTTTTAACCAACTGC 11 49 1 TTTTCCTTTT 0.58624 -203 CTGCCATAAATCGATCCTTTCTTCTATTGAC 11 76 1 TGATCCTTTC 0.924404 -176 AATATATTATTCTCTCCTGTTTCTGTCAATA 11 100 0 TTCTCCTGTT 0.820338 -152 AGTTTCTTCTTGCATCATTTCTCGCCCTTTC 11 204 0 TCATCATTTC 0.908971 -48 ATTTAGGTTTTGCCTGCTTTCGCAGTAACAA 12 129 0 TCCTGCTTTC 0.808208 -172 GTGTATACCTCCTTTTTATGGGGGGA 12 285 0 TCCTCCTTTT 0.964898 -16 * ********* Masking position 8 Map Score: 9.44097 Number of sites scoring better than the average of aligned sites = 1235 Number in coding regions = 802 Number in noncoding regions = 433 Number of orfs with sites within 600 bp upstream = 460 Fraction of orfs with sites within 600 bp upstream = 0.0738837 Motif number 5 TGTGATATCAGCATTGCTTGCTCTTTATTTG 8 237 1 GCTTGCTTGC 0.90746 -64 AATAAAAAAAGCATTGCCCGCTCAAATAAAG 8 259 0 GCTTGCCCGC 0.990991 -42 TTTGATTAATGTTATCCCCCCTGCTGCTATA 9 32 0 GTATCCCCCC 0.930133 -269 GGGCCAAAATGCCGTCCCCGCATTTTGAAAT 9 184 0 GCGTCCCCGC 0.981551 -117 CACCATTTAGGTTTTGCCTGCTTTCGCAGTA 12 133 0 GTTTGCCTGC 0.956018 -168 CTTTCATCCAGCAGTCCCCCCATAAAAAGGA 12 271 1 GCGTCCCCCC 0.986118 -30 ** ******** Masking position 5 Map Score: 2.0231 Number of sites scoring better than the average of aligned sites = 180 Number in coding regions = 166 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 6 GCTTCTCAGTTCGATTAAATTGTTTCTGTT 2 21 1 TCGATTAAAT 0.933248 -64 ATGAAAAATATCTATTAAATCTATAATTAA 6 44 0 TCTATTAAAT 0.861208 -46 TATGAGTGTTCCTATTATATTGTAATAAAT 8 117 0 CCTATTATAT 0.925914 -184 CCATATCCACGCGATTATATGAGTGTTCCT 8 134 0 GCGATTATAT 0.938655 -167 TTAAACTTGATCGATTATATAGCAGCAGGG 9 15 1 TCGATTATAT 0.96308 -286 AAATTGTTAACCAATTATATTCAAAGGTTA 11 139 0 CCAATTATAT 0.876353 -113 ********** Masking position 5 Map Score: 1.83986 Number of sites scoring better than the average of aligned sites = 75 Number in coding regions = 69 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 7 ATTTTTGAAATTTTATTTCACTTAAGACTAT 4 68 0 TTTTATTTCC 0.784796 -103 ATGAAACGCGTTTCATATCAACTCGATGTTA 5 89 0 TTTCATATCA 0.907626 -65 AATAGATATTTTTCATATGGATATATCAGGA 6 58 1 TTTCATATGA 0.857938 -32 CAACAATCTTTTTTATATGCAAAAAAAACTC 7 24 0 TTTTATATGA 0.933534 -50 CTTTTATATCGAATCCCCTTGA 8 2 1 TTTTATATCA 0.958073 -299 GTTCGGGAATTTTTATTTTCAGCCTATGCAA 8 66 1 TTTTATTTTA 0.809808 -235 GTCTCATATCTTTTATTTCAAAATGCGGGGA 9 170 1 TTTTATTTCA 0.939788 -131 ATCGTCCTGATTTTATATTTAAAGATTATCA 9 252 1 TTTTATATTA 0.861757 -49 TGACGGGTCGTTTTATTTGTTTGTAGGTATA 12 95 0 TTTTATTTGT 0.601963 -206 CACCAGCTTTTTTTGTATCAAATGCTGCATC 12 228 0 TTTTGTATCA 0.826555 -73 ********* * Masking position 6 Map Score: 5.46617 Number of sites scoring better than the average of aligned sites = 289 Number in coding regions = 216 Number in noncoding regions = 73 Number of orfs with sites within 600 bp upstream = 79 Fraction of orfs with sites within 600 bp upstream = 0.0126887 Motif number 8 CCTGTCTACCTCCGTTATGAGAA 8 288 0 GTCTACCTCC 0.993 -13 TCATTCGACCTCCATCTTTGAAA 9 288 0 TTCGACCTCC 0.954486 -13 TAGTGCTAAAGTATACCTACAAACAAATAA 12 84 1 GTATACCTAC 0.956623 -217 GTGTATACCTCCTTTTTATGGG 12 289 0 GTATACCTCC 0.989087 -12 ********** Masking position 5 Map Score: 0.912275 Number of sites scoring better than the average of aligned sites = 10 Number in coding regions = 6 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 9 ACGCGTTTCATAGCCTATGATAGGTTTATC 5 109 1 TAGCCTATGA 0.922782 -45 TTTTTATTTTCAGCCTATGCAAGAGATTAG 8 75 1 CAGCCTATGC 0.883648 -226 AAGATTATCATAACCTTTCAAAGATGGAGG 9 273 1 TAACCTTTCA 0.910122 -28 TTCTAATTGTTAACCTTTGAATATAATTGG 11 129 1 TAACCTTTGA 0.93007 -123 GGAGGTGATGCAGCATTTGATACAAAAAAA 12 222 1 CAGCATTTGA 0.880372 -79 TGAAAGGTGGCCGCCTTTCACCAGCTTTTT 12 247 0 CCGCCTTTCA 0.966741 -54 TGAAAGGCGGCCACCTTTCATCCAGCAGTC 12 257 1 CCACCTTTCA 0.933658 -44 ********** Masking position 6 Map Score: 0.678293 Number of sites scoring better than the average of aligned sites = 531 Number in coding regions = 485 Number in noncoding regions = 46 Number of orfs with sites within 600 bp upstream = 47 Fraction of orfs with sites within 600 bp upstream = 0.00754899 Motif number 10 ********** No masking Map Score: 2.56749e-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 11 ********** No masking Map Score: 2.56749e-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: 2.56749e-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