AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/alignace/lib/ORF_bsub.txt -z/skink1/amcguire/genomes/bsub.fna -igalR_bsub_opreg_100.orf -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 ydjK 300 similar to sugar transporter #2 yfiG 174 similar to metabolite transport protein #3 yhjM 103 similar to transcriptional regulator (LacI family) #4 yisR 123 alternate gene name: yuxC, yucF; similar to transcriptional regulator (AraC/XylS family) #5 yjmC 104 similar to malate dehydrogenase #6 yjmE 24 similar to D-mannonate hydrolase #7 yjmG 47 similar to hexuronate transporter #8 yjmH 87 similar to transcriptional regulator (LacI family) #9 ccpA 274 transcriptional regulator (Lacl family) #10 yufN 300 similar to ABC transporter (lipoprotein) #11 yufO 75 similar to ABC transporter (ATP-binding protein) #12 araE 137 permease #13 ywtG 300 similar to metabolite transport protein #14 rbsR 300 transcriptional regulator (LacI family) #15 galK 80 galactokinase #16 ywcC 300 alternate gene name: ipa-33d #17 galE 114 UDP-glucose 4-epimerase #18 yxcC 238 similar to metabolite transport protein Motif number 1 CATAACCTCGTTCATTTGGTATTTATTAGTCACTTA 1 68 0 TTTTTTTTAT 0.894984 -233 CAGAAAATAGTTGTTCATGTTTTTATCCAATAACCT 1 189 0 TTTCTTTTAT 0.945787 -112 ACTGTTTCCCCCAGTCTTTTTCAAAATGCGT 1 280 0 TTCCTTTTTT 0.61866 -21 GACAACGAGATTTCTCGCGTCTTTATCATATGAAGA 2 36 0 TTTCTTTTAT 0.945787 -139 AATCTAAAAATTTATTACAAATTTATCCTAGTTTCT 3 35 1 TTTTATTTAT 0.632843 -69 GAAGTATCGTTTCTATCCCTTTTTATTATAAGGAAA 4 62 0 TTATTTTTAT 0.700915 -62 CAAACACATTTTATTTACAAATTATTTTAAATATTC 5 25 0 TTTTATTATT 0.342508 -80 AAGTGCCTCCTTCCTTTTCAGTTTTTTGGGCACTCT 5 77 0 TTTTATTTTT 0.614519 -28 TTTTTTATGCTTTCTCGTTTATTTAGTTATAAAAAC 9 42 1 TTTCTTTTAG 0.879134 -233 TCTCATGAAATTATACACGTTTTTATAGATGATGAA 9 90 0 TTACTTTTAT 0.8275 -185 TTTTTCATTATTCATCAAATTTAATTACTTCTCATG 9 119 0 TTTCTTAATT 0.438909 -156 TTATCCCTTGTTTTTCTTTTATTTTGAAATAAAGGA 11 39 1 TTTCTTTTTG 0.870586 -37 AAATGTAATTTTCGTTAAATTTTAATATAAGTACGT 12 58 1 TTTTTTTAAT 0.73579 -80 TTTTCGATAAATATTCCTATATTTATAAGTTCTTGT 13 55 1 ATTCTTTTAT 0.48456 -246 TTCCAATCATTTACTTGTATTTTTTTCAATGTCGCC 13 160 0 TTTTTTTTTT 0.887413 -141 TTTCCGGCCATTAAACCTTTTTATTTTTCTGATCAT 13 201 0 TTACTTATTT 0.396964 -100 TGAAGATTTCTTGAACAAATATTAAGTTTTATTAAA 14 111 0 TTACTTTAAG 0.395256 -190 AATTTAAGGTTTTCACTCTTTTTTTGACAAAGTCTT 14 159 0 TTACTTTTTG 0.649108 -142 AAACCTTAAATTTTTCAATTATATATACAATTTACA 14 183 1 TTTCTTATAT 0.721316 -118 ACAATTAGATTTCTTTTGATATTTTTATTGCTAACT 14 216 1 TTTTTTTTTT 0.887413 -85 ATTGGTTATATTAGTCATTTTTTTAGGGAATAGGTA 16 91 0 TTTCTTTTAG 0.879134 -210 CAGTCAGTATTTAATTGTTTATTATTATAAATAAGG 16 130 0 TTTTTTTATT 0.72033 -171 TTATTAATAGTTTTTTCATATTTTTTAGC 17 4 0 TTTTATTTTT 0.614519 -111 TTTAAGAAGTTTAATCGTTTATTAATAGTTTTTTCA 17 22 0 TTTCTTTAAT 0.850763 -93 ATCTATTAACTTTGTTACATATTTTTAGATACTTCA 18 184 1 TTTTTTTTTT 0.887413 -55 ** ** * ***** Masking position 12 Map Score: 14.6899 Number of sites scoring better than the average of aligned sites = 1832 Number in coding regions = 1409 Number in noncoding regions = 423 Number of orfs with sites within 600 bp upstream = 429 Fraction of orfs with sites within 600 bp upstream = 0.0689046 Motif number 2 TCAATCCCTATGGAAGCGATTTCATTTCTCGTT 1 130 0 TGAGCGTTTC 0.984032 -171 TACCCCTTGTTGTAACCGCTTTCTAAAAAGATT 2 76 0 TTACCGTTTC 0.987469 -99 GTTGTTGACATGTTACCGATTTCAGAAACTAGG 3 61 0 TTACCGTTTC 0.987469 -43 CGTGTCTAACCCCTTTCGTAAATAAAA 4 5 1 TTACCCTTTC 0.949439 -119 TAAAATGTGTTTGTAGGGGTTTCGCTTGGAGAG 5 48 1 TGAGGGTTTC 0.960005 -57 TCAGTTTCTGTTGCACCGCTTTCG 7 2 0 TGACCGTTTC 0.990632 -46 CAGAAAACGATGTCACGGTTTTCCGCCCGGAAC 10 53 1 TTACGGTTTC 0.968447 -248 AATAGAACTGTCTCAGCGCATTCCATTTGTTAT 10 152 1 TTAGCGATTC 0.853689 -149 TCCTTGTTTATGTAACCGTTTACATAGATAGAT 14 269 0 TTACCGTTAC 0.951342 -32 GGTCATTTTTTAGGAGGGTTTACATC 17 99 1 TGAGGGTTAC 0.856231 -16 GTTAATAGATTAGTACCCATTTCCTATCTCATT 18 161 0 TGACCCTTTC 0.961832 -78 * * **** **** Masking position 5 Map Score: 14.7426 Number of sites scoring better than the average of aligned sites = 165 Number in coding regions = 144 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 3 CTCATAACCTTCCCTTCTTCTTAGCATGTC 1 161 0 TCCCTTCTTC 0.981597 -140 CCAGGGCTGCTGCCTTCCTCACATTTCGTA 1 234 0 TGCCTTCCTC 0.967357 -67 AGCCAATGCATCCCTCCTTCAGCAATACCC 2 104 0 TCCCTCCTTC 0.948681 -71 GGCTTTCTTCCCCTTCTTTCAAGAATGGC 2 156 0 CCCCTTCTTT 0.964809 -19 ATTTTCCCTTCCTTAAAAAAGTTG 3 90 0 TCCCTTCCTT 0.981597 -14 CGTGTCTAACCCCTTTCGTAAATAAAATC 4 10 1 CCCCTTTCGT 0.72444 -114 GCAAGTGCCTCCTTCCTTTTCAGTT 5 90 0 TGCCTCCTTC 0.865172 -15 CTAATTCCCTTCCTTATCATACCGG 8 73 0 TCCCTTCCTT 0.981597 -15 CCGCCCGGAACGCCTTCCGCATCCTTCTCT 10 75 1 CGCCTTCCGC 0.89417 -226 CGAGCCCTTATCCCTTGTTTTTCTTTTATT 11 32 1 TCCCTTGTTT 0.828833 -44 AAAGATGACTCCCTTTCTCCATCAGCTGC 13 282 0 TCCCTTTCTC 0.936542 -19 ATTTTTTATTCCCCTTATTTCTTCATAGAA 15 38 0 CCCCTTATTT 0.728829 -43 ********** Masking position 5 Map Score: 11.6283 Number of sites scoring better than the average of aligned sites = 461 Number in coding regions = 337 Number in noncoding regions = 124 Number of orfs with sites within 600 bp upstream = 139 Fraction of orfs with sites within 600 bp upstream = 0.0223257 Motif number 4 CATTGTTCTTTTAACGAGAAATGAAATCGC 1 118 1 TTAACGAGAA 0.890908 -183 TATAACTAAATAAACGAGAAAGCATAAAAA 9 43 0 TAAACGAGAA 0.906681 -232 AATTTGATGAATAATGAAAAATAATGTACA 9 134 1 ATAATGAAAA 0.768234 -141 ATATCTTGAATAAACGAAAAATCGGATTGG 10 279 1 TAAACGAAAA 0.961997 -22 TATTTCAAAATAAAAGAAAAACAAGGGATA 11 40 0 TAAAAGAAAA 0.796602 -36 ATATTAAAATTTAACGAAAATTACATTTAA 12 56 0 TTAACGAAAA 0.955039 -82 ATTGAAGGTTTAAATGAAAACGCTTTACTC 12 97 1 TAAATGAAAA 0.940741 -41 ATAGGAATATTTATCGAAAAATGTCTTTCG 13 45 0 TTATCGAAAA 0.836901 -256 ATTGTATATATAATTGAAAAATTTAAGGTT 14 184 0 TAATTGAAAA 0.797526 -117 GGATAGTATGTAAATGAAAATAAATCATTT 16 165 1 TAAATGAAAA 0.940741 -136 TAAACACTATATAATGAAAACAGGTCATTT 17 77 1 ATAATGAAAA 0.768234 -38 ********** Masking position 7 Map Score: 9.63006 Number of sites scoring better than the average of aligned sites = 309 Number in coding regions = 259 Number in noncoding regions = 50 Number of orfs with sites within 600 bp upstream = 59 Fraction of orfs with sites within 600 bp upstream = 0.00947639 Motif number 5 CAGGCTTCAGAAAATAGTTGTTCATGTTTTTATC 1 198 0 AAAAGTTGCA 0.785374 -103 TCCCTTCCTTAAAAAAGTTGTTGACATGTTACCG 3 76 0 AAAAGTTGGA 0.862624 -28 TTATTATAAGGAAATGGAGGTACACTTTAAAACG 4 42 0 GAAGGAGGCA 0.967679 -82 AATCCGACTTAAAAAGGAGGATGATTCAA 4 105 1 AAAGGAGGGA 0.98424 -19 TCTGGAAATATAGTGGGAGAGGCGGTATGT 8 7 1 AAAAGTGGGA 0.909505 -81 AGGCGGGGAAGAGAAGGATGCGGAAGGCGTTCCG 10 80 0 GAAGGATGGA 0.969788 -221 GAATCGCAGGGATAAGGAGGTCGAGCCCTTATCC 11 11 1 GAAGGAGGGA 0.980907 -65 TTAATGGCCGGAAAAAGAGGCTAAAAGATTTCTA 13 223 1 GAAAGAGGAA 0.721984 -78 AGTCTTCACAAATATGGATGAAGATTTCTTGAAC 14 131 0 AAAGGATGGA 0.975012 -170 CGGTTACATAAACAAGGAGGAGCTGTT 14 284 1 AAAGGAGGCT 0.80826 -17 AAACTTCTTAAAAATGGATGTGGACCGGTTCTAA 17 46 1 AAAGGATGGA 0.975012 -69 CTTTATAGCCAAAAGAGATGATCACAGATCCGCT 18 99 0 AAAAGATGCA 0.911445 -140 ** * ***** ** Masking position 4 Map Score: 10.8706 Number of sites scoring better than the average of aligned sites = 347 Number in coding regions = 271 Number in noncoding regions = 76 Number of orfs with sites within 600 bp upstream = 72 Fraction of orfs with sites within 600 bp upstream = 0.0115644 Motif number 6 AAATTTATCCTAGTTTCTGAAATCGGTAACAT 3 53 1 TAGTTCGAAA 0.760609 -51 AACGTTGATTTTATTTACGAAAGGGGTTAGAC 4 14 0 TTATTAGAAA 0.736434 -110 CACGTTTTTATAGATGATGAAAACGTATACTT 9 79 0 TAGATAGAAA 0.851544 -196 GTTTATGCTATAGATAAGGATAAGTGTATCCA 9 233 1 TAGATAGATA 0.748427 -42 TTGGTTAGTTGATCCCGAAAAACTAAGTCA 10 9 1 TTGATCGAAA 0.812555 -292 TTCTAAGAAATTGTTCAGGACAGCCCATCACA 10 204 1 TTGTTAGACA 0.911849 -97 GATTTTTCGTTTATTCAAGATATAACCCCCCA 10 270 0 TTATTAGATA 0.591699 -31 TTATAAGTTCTTGTTTTTGAAAATTGATAACG 13 77 1 TTGTTTGAAA 0.735901 -224 TTTTTGAAAATTGATAACGATAATGTACTGAA 13 90 1 TTGATAGATA 0.876794 -211 AACTTAATATTTGTTCAAGAAATCTTCATCCA 14 119 1 TTGTTAGAAA 0.960091 -182 TAACTTCGGATTGTTCATGATAATCTATCTAT 14 247 1 TTGTTAGATA 0.925801 -54 CAGCTCCTCCTTGTTTATGTAACCGTTTACAT 14 277 0 TTGTTAGTAA 0.703067 -24 GGAGTAAGGTTTGATTAAGACATTT 18 4 0 TTGATAGACA 0.855069 -235 CAGATCCGCTGAGTTTAGGAAAAACGAAATAA 18 77 0 GAGTTAGAAA 0.594655 -162 ***** * **** Masking position 12 Map Score: 7.50583 Number of sites scoring better than the average of aligned sites = 488 Number in coding regions = 414 Number in noncoding regions = 74 Number of orfs with sites within 600 bp upstream = 90 Fraction of orfs with sites within 600 bp upstream = 0.0144555 Motif number 7 TTGTAACCGCTTTCTAAAAAGATTATAAGACAA 2 67 0 TTTCAAAGAT 0.943862 -108 ATACTTGGTTTTTATAACTAAATAAACGAGAAA 9 52 0 TTTAAAAAAT 0.700551 -223 CTTCCCCGCCTTTCGAAGGAAATACTCACACCA 10 103 1 TTTCAAAAAT 0.967417 -198 CGCTCCTTTATTTCAAAATAAAAGAAAAACAAG 11 45 0 TTTCAAAAAA 0.790465 -31 GAAAGACATTTTTCGATAAATATTCCTATATTT 13 46 1 TTTCATATAT 0.664313 -255 GATCATAAGTTTTCCAATCATTTACTTGTATTT 13 174 0 TTTCAAATTT 0.664313 -127 GGCTAAAAGATTTCTAAAAAAATCCCACAGACA 13 241 1 TTTCAAAAAT 0.967417 -60 GCAATAAAAATATCAAAAGAAATCTAATTGTAA 14 214 0 TATCAAAAAT 0.880483 -87 GTTTCCGTTTTTTCAAAACAAATGTTTCAAATG 18 132 1 TTTCAAAAAT 0.967417 -107 AAAACAAATGTTTCAAATGAGATAGGAAATGGG 18 146 1 TTTCAAAGAT 0.943862 -93 GCCAATGAAGTATCTAAAAATATGTAACAAAGT 18 192 0 TATCAAATAT 0.794427 -47 **** ** **** Masking position 6 Map Score: 6.62312 Number of sites scoring better than the average of aligned sites = 159 Number in coding regions = 111 Number in noncoding regions = 48 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467 Motif number 8 CAGATATAACAAAAATGTCACTATAACATC 1 22 1 AAAAATGTCA 0.929906 -279 TTATGCACAAAGAAATGACCATTGTTCTTT 1 99 1 AGAAATGACC 0.945808 -202 TCTTTTAACGAGAAATGAAATCGCTTCCAT 1 124 1 AGAAATGAAA 0.602904 -177 GATGTCCTGAAATGACAAAACAATGTC 2 8 1 TGAAATGACA 0.825779 -167 GAAATGACAAAACAATGTCTTCATATGATA 2 19 1 AACAATGTCT 0.70694 -156 CTTTATGTAGAGAAATGTCATAATGTCCGA 9 202 0 AGAAATGTCA 0.938192 -73 ATATTTATCGAAAAATGTCTTTCGAGTAGT 13 39 0 AAAAATGTCT 0.874328 -262 CTCCATCAGCTGCAATGACATTGTCTGTGG 13 265 0 TGCAATGACA 0.621656 -36 AGTTAGCAATAAAAATATCAAAAGAAATCT 14 222 0 AAAAATATCA 0.487719 -79 TATTCCCTAAAAAAATGACTAATATAACCA 16 95 1 AAAAATGACT 0.905499 -206 TTAGCCTATTAAAAATGACCCCTGGGAAAC 16 193 1 AAAAATGACC 0.937761 -108 AACCCTCCTAAAAAATGACCTGTTTTCATT 17 89 0 AAAAATGACC 0.937761 -26 ********** Masking position 5 Map Score: 6.99929 Number of sites scoring better than the average of aligned sites = 451 Number in coding regions = 388 Number in noncoding regions = 63 Number of orfs with sites within 600 bp upstream = 73 Fraction of orfs with sites within 600 bp upstream = 0.011725 Motif number 9 CATGAACAACTATTTTCTGAAGCCTGCTTA 1 206 1 TATTTTCTGA 0.710265 -95 TATGTTGGTTCAGTTTCTGTTGCACCGCTT 7 14 0 CAGTTTCTGT 0.727956 -34 AAAACCACTCCTTTTACTGGATACACTTAT 9 252 0 CTTTTACTGG 0.758333 -23 ACCGTGACATCGTTTTCTGAAGTAAGACTT 10 42 0 CGTTTTCTGA 0.884981 -259 GAATCGATAAAATTTTCTGATAATAACAAA 10 177 0 AATTTTCTGA 0.860997 -124 TTTGAACCAAATTTTTCTGGGGGGTTATAT 10 253 1 ATTTTTCTGG 0.87031 -48 ATCTTGTTTGCATTTTCTGTCA 12 3 0 CATTTTCTGT 0.939713 -135 AAACCTTTTTATTTTTCTGATCATAAGTTT 13 195 0 ATTTTTCTGA 0.839033 -106 CTTTTAGCCTCTTTTTCCGGCCATTAAACC 13 220 0 CTTTTTCCGG 0.823033 -81 GCTGCAATGACATTGTCTGTGGGATTTTTT 13 257 0 CATTGTCTGT 0.727956 -44 CATAATTAAACATTTTCTGGGATGATAGTC 14 31 1 CATTTTCTGG 0.969874 -270 GGTTTTCACTCTTTTTTTGACAAAGTCTTC 14 158 0 CTTTTTTTGA 0.601573 -143 ********** Masking position 4 Map Score: 4.15087 Number of sites scoring better than the average of aligned sites = 564 Number in coding regions = 492 Number in noncoding regions = 72 Number of orfs with sites within 600 bp upstream = 88 Fraction of orfs with sites within 600 bp upstream = 0.0141343 Motif number 10 TGGATAAAAACATGAACAACTATTTTCTGAA 1 196 1 CATGAACAAT 0.913195 -105 GGCAGCAGCCCTGGAATAAGTTTTTGACATA 1 250 1 CTGGAATAAT 0.769408 -51 TCTATTCTTCCCTGAATAAGCGTGGTGTGAG 10 127 0 CCTGAATAAC 0.936288 -174 GATGGGCTGTCCTGAACAATTTCTTAGAATC 10 202 0 CCTGAACAAT 0.959519 -99 GGGGTTATATCTTGAATAAACGAAAAATCGG 10 273 1 CTTGAATAAC 0.903345 -28 ATGAAGATTTCTTGAACAAATATTAAGTTTT 14 117 0 CTTGAACAAT 0.937789 -184 GATAGATTATCATGAACAATCCGAAGTTAGC 14 245 0 CATGAACAAC 0.94346 -56 TTATCTTACACCGGATCAATCTTTAGCGGTA 16 252 0 CCGGATCAAC 0.792329 -49 ********* * Masking position 5 Map Score: 2.0869 Number of sites scoring better than the average of aligned sites = 252 Number in coding regions = 233 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 11 TAAAAAAAGGCCGCACGGCGGCCTTTTGGA 9 19 0 CCGCACGGCG 0.985688 -256 TCACGGTTTTCCGCCCGGAACGCCTTCCGC 10 65 1 CCGCCCGGAA 0.987819 -236 GTAATCATTACCGCCAGGAGAAAAAT 16 285 1 CCGCCAGGAG 0.987809 -16 AAAACCTTACCCGCGCGGAGTAAGGTTTGA 18 22 0 CCGCGCGGAG 0.992807 -217 ********** Masking position 4 Map Score: 1.22346 Number of sites scoring better than the average of aligned sites = 40 Number in coding regions = 38 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 12 CCTTCCCTTCTTCTTAGCATGTCAATCCCT 1 154 0 TTCTTAGCAT 0.92761 -147 AAATCTCGTTGTCTTATAATCTTTTTAGAA 2 59 1 GTCTTATAAT 0.717202 -116 TACCTCCATTTCCTTATAATAAAAAGGGAT 4 54 1 TCCTTATAAT 0.823548 -70 CTAATTCCCTTCCTTATCATACCGGCTGCG 8 68 0 TCCTTATCAT 0.880995 -20 CGATAAAATTTTCTGATAATAACAAATGGA 10 173 0 TTCTGATAAT 0.889853 -128 CCTGAACAATTTCTTAGAATCGATAAAATT 10 193 0 TTCTTAGAAT 0.889853 -108 CTTTTTATTTTTCTGATCATAAGTTTTCCA 13 191 0 TTCTGATCAT 0.92761 -110 TTAATGGTTTCTCTGAGCATAAAGTTATTT 18 53 1 CTCTGAGCAT 0.794438 -186 ********** Masking position 6 Map Score: 0.712623 Number of sites scoring better than the average of aligned sites = 223 Number in coding regions = 179 Number in noncoding regions = 44 Number of orfs with sites within 600 bp upstream = 57 Fraction of orfs with sites within 600 bp upstream = 0.00915516 Motif number 13 ********** No masking Map Score: 4.18753e-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: 4.18753e-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: 4.18753e-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