AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/alignace/lib/ORF_bsub.txt -z/skink1/amcguire/genomes/bsub.fna -irhaS_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 ybfI 230 similar to transcriptional regulator (AraC/XylS family) #2 ycxE 122 similar to hypothetical proteins #3 yfiD 154 similar to hypothetical proteins #4 yfiF 93 similar to transcriptional regulator (AraC/XylS family) #5 yulE 25 similar to L-rhamnose isomerase #6 yulB 56 similar to transcriptional regulator (DeoR family) #7 yuxG 137 alternate gene name: yulA; similar to sorbitol-6-phosphate 2-dehydrogenase Motif number 1 CAAACCATTATAACTGAAATATTTGAAAAATA 1 32 1 TAACGAAAAT 0.745518 -199 ATTTTTATTAAAAAAGATAAAATTATTATTGA 1 65 1 AAAAGATAAA 0.964993 -166 TTTAAATTCTTAAACGAAAGCAGACAAATAAC 1 109 1 TAAAGAAACA 0.896894 -122 CTCTATTCCTAAACAGCAACATCATACAAGAA 1 151 1 AAACGCAAAT 0.790617 -80 AAGTACTATAAAACTGTAACAAAAAAAGACCT 3 28 0 AAACGTAAAA 0.949084 -127 ACATTTTACGAAAATGAAATAAAAGTACTATA 3 50 0 AAAAGAAAAA 0.981659 -105 TCATTTTCGTAAAATGTAACAAAATTACTTGA 3 65 1 AAAAGTAAAA 0.945003 -90 TCCTCCTTGATAAATGTTATCACTTACTTAAT 3 129 0 TAAAGTTACA 0.589886 -26 CAAGGCGGACAAAAATAAAAAATCCCCCTGCC 4 35 0 AAAATAAAAA 0.751761 -59 AAAACTGATAAAGGGAGAGAGCC 5 2 1 AAACGATAAG 0.825065 -24 TTTTTAACAAAAAAAGAAAGCAGCAGATATGC 7 26 0 AAAAGAAACA 0.970016 -112 TTTTTTTGTTAAAAAGCAAAAATAAACAAAAA 7 43 1 AAAAGCAAAA 0.948847 -95 AAAATAAACAAAAACGATTCAAAAACAAACAG 7 61 1 AAAAGATTAA 0.716188 -77 ATTCAAAAACAAACAGAAATCATATATAATGA 7 77 1 AAACGAAACA 0.972295 -61 TATATAATGAAAACGGATACAAATAAAAGGGT 7 99 1 AAACGATAAA 0.967641 -39 **** **** ** Masking position 3 Map Score: 18.7836 Number of sites scoring better than the average of aligned sites = 2231 Number in coding regions = 1799 Number in noncoding regions = 432 Number of orfs with sites within 600 bp upstream = 418 Fraction of orfs with sites within 600 bp upstream = 0.0671378 Motif number 2 ACCGTTATTTGTCTGCTTTCGTTTAAGAATTT 1 112 0 GTCGTTTCGT 0.877965 -119 ACAAATAACGGTCTGCTTTCTCTATTCCTAAA 1 132 1 GTCGTTTCTC 0.946035 -99 GCATGATTTTGGGGGATTTCTTGTATGATGTT 1 168 0 GGGGTTTCTT 0.966662 -63 TCCTGAGAGCTGCCGGATTTTCCGGCAGCTCT 2 23 1 TGCGATTTTC 0.917092 -100 CGGATTTTCCGGCAGCTCTTTTTGTGTTCCGG 2 36 1 GGCGTCTTTT 0.960131 -87 CTGTTATTTTGGCTGGAATTGTTGTGATTATT 2 70 0 GGCGAATTGT 0.796317 -53 AAAATGTATTTGCTGTTATTTTGGCTGGAATT 2 82 0 TGCGTATTTT 0.955724 -41 AAAATCCCCCTGCCGTTATTTCGGCAAGGGGA 4 17 0 TGCGTATTTC 0.952801 -77 AATAACGGCAGGGGGATTTTTTATTTTTGTCC 4 29 1 GGGGTTTTTT 0.955765 -65 GCAGCAGATATGCCGCTTTCTCGTTTCA 7 7 0 TGCGTTTCTC 0.98356 -131 GCGGCATATCTGCTGCTTTCTTTTTTTGTTAA 7 23 1 TGCGTTTCTT 0.984609 -115 *** * ****** Masking position 9 Map Score: 12.0932 Number of sites scoring better than the average of aligned sites = 2016 Number in coding regions = 1748 Number in noncoding regions = 268 Number of orfs with sites within 600 bp upstream = 219 Fraction of orfs with sites within 600 bp upstream = 0.0351751 Motif number 3 CTTTGCCCCTCCTATCTGTTCCAAACC 1 8 1 CCTCCTATCT 0.968367 -223 GGGATGCCTCCTGTCGGTGTGGTGGT 1 215 0 CCTCCTGTCG 0.994835 -16 TGTTGGGGAACCTTCTTTCAAAATGTATTT 2 103 0 CCTTCTTTCA 0.843194 -20 CTGCAATCCCCTTGCCGAAATAACGGC 4 8 1 CCCCTTGCCG 0.971996 -86 AATAAAAAATCCCCCTGCCGTTATTTCGGC 4 24 0 CCCCCTGCCG 0.9922 -70 GTAAACGCCTCCTAACAAGTTGGTTCT 4 77 0 CCTCCTAACA 0.950204 -17 ACGGCTCTCTCCCTTTATCAGTTTT 5 6 0 CCCTTTATCA 0.825496 -20 TAACGCCCTTCCTCATATCGTAGTCCGTCT 6 34 0 CCTCATATCG 0.96106 -23 ********** Masking position 6 Map Score: 7.89734 Number of sites scoring better than the average of aligned sites = 317 Number in coding regions = 217 Number in noncoding regions = 100 Number of orfs with sites within 600 bp upstream = 102 Fraction of orfs with sites within 600 bp upstream = 0.0163829 Motif number 4 GGGATGCCTCCTGTCGGTGT 1 221 0 GGGATGCCTC 0.979285 -10 ACGCTCCTGAGAGCTGCCGGATTTTCCGGC 2 19 1 GAGCTGCCGG 0.994358 -104 AACACAAAAAGAGCTGCCGGAAAATCCGGC 2 34 0 GAGCTGCCGG 0.994358 -89 GAAAGCAGCAGATATGCCGCTTTCTCGTTT 7 13 0 GATATGCCGC 0.990616 -125 ATTTGATATTCCTCCATACCCTTT 7 124 0 GATATTCCTC 0.899774 -14 ********** Masking position 5 Map Score: 4.48142 Number of sites scoring better than the average of aligned sites = 278 Number in coding regions = 251 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 5 TATCTTTTTTAATAAAAATTTATTTTTCAA 1 54 0 AATAAAAATT 0.722511 -177 TATTAAAAAAGATAAAATTATTATTGAGGG 1 70 1 GATAAAATTA 0.821062 -161 TATTCGCCGGAACACAAAAAGAGCTGCCGG 2 44 0 AACACAAAAA 0.859538 -79 CAACAATTCCAGCCAAAATAACAGCAAATA 2 78 1 AGCCAAAATA 0.747139 -45 ATAAAACTGTAACAAAAAAAGACCTCTGTG 3 23 0 AACAAAAAAA 0.9464 -132 ACGAAAATGAAATAAAAGTACTATAAAACT 3 45 0 AATAAAAGTA 0.824194 -110 CGTAAAATGTAACAAAATTACTTGACGTAA 3 72 1 AACAAAATTA 0.924939 -83 TAACAAGGCGGACAAAAATAAAAAATCCCC 4 40 0 GACAAAAATA 0.976109 -54 TATATGCTATGATAAAAATATAAGACGGAC 6 12 1 GATAAAAATA 0.9487 -45 TTTGCTTTTTAACAAAAAAAGAAAGCAGCA 7 33 0 AACAAAAAAA 0.9464 -105 TTTGTTAAAAAGCAAAAATAAACAAAAACG 7 47 1 AGCAAAAATA 0.945091 -91 AATGAAAACGGATACAAATAAAAGGGTATG 7 104 1 GATACAAATA 0.865033 -34 ********** Masking position 6 Map Score: 13.4449 Number of sites scoring better than the average of aligned sites = 992 Number in coding regions = 762 Number in noncoding regions = 230 Number of orfs with sites within 600 bp upstream = 240 Fraction of orfs with sites within 600 bp upstream = 0.038548 Motif number 6 ********** No masking Map Score: -6.15168e-14 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: -6.15168e-14 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: -6.15168e-14 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