AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/alignace/lib/ORF_bsub.txt -z/skink1/amcguire/genomes/bsub.fna -ityrR_bsub_opreg_300.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 ydgF 171 similar to amino acid ABC transporter (permease) #2 dinB 168 nuclease inhibitor #3 gabP 300 gamma-aminobutyrate (GABA) permease #4 yqiR 152 similar to transcriptional regulator (sigma-L-dependent) #5 aapA 300 amino acid permease #6 ytnA 135 similar to proline permease #7 asnB 149 asparagine synthetase #8 metK 300 S-adenosylmethionine synthetase #9 gerAA 300 gerAA #10 yvbW 300 similar to amino acid permease #11 rocR 240 transcriptional regulator (NtrC/NifA family) Motif number 1 CAATAAACAATTTTCAATGGAGGAACACATAAA 1 149 1 TTTGGGAAAA 0.812465 -23 GGGTAAACTATAATGAGGAGGGGAAGATA 2 1 0 TAAAGGAAAA 0.944328 -168 ACATTGAACATAAAGTTTAGCGGGGTAAACTATAATGAG 2 23 0 TAAAGGGGAA 0.692104 -146 TGTTGACATATATAGTTTAGAGGAATAAACTAATTGACA 2 59 0 TATAGGAAAA 0.96614 -110 GCGGAGCAAATAAATTGGATGAGAGAAAAAGTGTTCCTT 3 17 0 TAAAAGAGAA 0.622729 -284 TCATTTCCTTTATTGTCCAGCGGAAAAAATATTTTGTCA 4 34 1 TATAGGAAAA 0.873774 -119 GGAAAAAATATTTTGTCAAGAGAAGAAAACGTGGTAACA 4 55 1 TTTAGAAGAA 0.522507 -98 GGTTGTGCAAATTATTGCAACGGAATAAATAGGTGTGCA 4 97 1 ATTAGGAAAA 0.599796 -56 TCGGATATTATAACATTTAAAAGAATAGATACTTTTATT 5 231 0 TAAAAGAAAA 0.582824 -70 TTTACTCATCTTTTTATTACTGGAGGAAAATAAAA 5 276 1 TTTAGGAGAA 0.959926 -25 ATAATGATATTTTTTTCTAGGGGAGAAGAAGC 6 114 1 TTTAGGAGAA 0.960128 -22 CCTTGAGCGATAAGAGTGAAAGGCACAAAGACCAAACCC 8 128 1 TAAAGGCAAA 0.655482 -173 TGATGTCTCTTATACATCAAAGGAGTACGGCAGGACAAA 9 84 0 TATAGGAGAG 0.781598 -217 GTGGCACAGGTAAGGCTAGCTGGAAAACAAGAAGAAATT 9 155 0 TAAGGGAAAA 0.777848 -146 AGTAAGTTTTTTTATGAAAGCGGAGGATACGAAGTGGCA 9 188 0 TTTAGGAGAA 0.961162 -113 CAGTATATCATTTTTTTAACAGGAAAAGATAACCTCTAC 9 245 1 TTTAGGAAAA 0.954514 -56 CCGGGAGTGGTAAGACGGAACGGAATAGATTGAATATTC 10 99 1 TAAAGGAAAA 0.944328 -202 AGAACTTGCATTTATATAAAGGGAAAGCAGGATAACATG 11 41 0 TTTAGGAAGA 0.812466 -200 GCTTCTATTTTATAAAAAAACGGAGAGGATATGCAAAAG 11 178 0 TATAGGAGGA 0.874475 -63 *** * **** * * Masking position 1 Map Score: 16.9225 Number of sites scoring better than the average of aligned sites = 404 Number in coding regions = 299 Number in noncoding regions = 105 Number of orfs with sites within 600 bp upstream = 119 Fraction of orfs with sites within 600 bp upstream = 0.0191134 Motif number 2 TCATCAATCCTTTTTTAGTAAAAAAGATAGAAATTTT 1 76 1 TTAGAAAAAA 0.92243 -96 TTGACATATATAGTTTAGAGGAATAAACTAATTGACA 2 59 0 TTAGGAATAA 0.934418 -110 TGTCGAAAATTCGTGTAAGAAAATATACCAGCTTATT 3 201 0 TTAAAAATAA 0.865652 -100 ATTTCCTTTATTGTCCAGCGGAAAAAATATTTTGTCA 4 36 1 TTAGGAAAAA 0.942877 -117 AAAAAATATTTTGTCAAGAGAAGAAAACGTGGTAACA 4 57 1 TTAGGAGAAA 0.89285 -96 TTGTGCAAATTATTGCAACGGAATAAATAGGTGTGCA 4 99 1 TTAAGAATAA 0.899011 -54 ATCTTTTTATTACTGGAGGAAAATAAAA 5 283 1 TTAGAAATAA 0.911605 -18 AATGATATTTTTTTCTAGGGGAGAAGAAGC 6 116 1 TTAGGAGAAA 0.891831 -20 GGTTTCACAGTTATGTAAAAAAATAAACATGAATACA 7 56 0 TTAAAAATAA 0.865652 -94 CTCCATGAAATACTCTAACACAGTATATCATTTTTTT 9 225 1 TTAAAAGTAA 0.764858 -76 GTATATCATTTTTTTAACAGGAAAAGATAACCTCTAC 9 247 1 TTACGAAAAA 0.759076 -54 CTCCTTCTCGTTTTCAAAAACAAAAAAGCCCGCCGTC 10 262 0 TTAAAAAAAA 0.881855 -39 CAGGATAACATGTTGAAACAGAAAACAAGGGGGAATT 11 16 0 TTAAAAAAAA 0.881859 -225 * * ** * **** * Masking position 7 Map Score: 9.97479 Number of sites scoring better than the average of aligned sites = 292 Number in coding regions = 203 Number in noncoding regions = 89 Number of orfs with sites within 600 bp upstream = 97 Fraction of orfs with sites within 600 bp upstream = 0.0155798 Motif number 3 GGAAAAAATGTTTCGTTTTTTATTCGCTGTGTGAT 3 125 0 TTCTTTTTTC 0.954177 -176 GAAAACCCCTTTATCTTTTCATTTCCTTTATTGTC 4 16 1 TTTTTTATTC 0.746315 -137 AACCCTATGTTACCACGTTTTCTTCTCTTGACAAA 4 66 0 TACCTTTTTC 0.804677 -87 TCCAAATGACTTTCCTGTTTTACTCTGCTATTCAG 5 127 1 TTCTTTTCTC 0.960194 -174 AGCCTTGTTGTTATCCTTTTATTTCTCCATCATCA 6 39 1 TTTCTTATTC 0.845425 -97 GTTAAGCGGCTTTCCCTTTTTTATCGTTGTATTCA 7 29 1 TTCCTTTATC 0.874017 -121 GGTTTCTCTGTTATTTATTATGTTCAACTGAGTGA 8 54 1 TTTTTTTTTC 0.892179 -247 GGTTTGGTCTTTGTGCCTTTCACTCTTATCGCTCA 8 131 0 TTTCTTCCTC 0.787973 -170 AGCTGTTCAATTTCTTCTTGTTTTCCAGCTAGCCT 9 147 1 TTCTTTTTTC 0.954177 -154 TTCTGATCACTTTCTTTTACTGCTCCCAATCTATG 10 14 0 TTCTTATCTC 0.719649 -287 CGCAGCCTGATTCTTCTTTGAACTCGCCCGGGAGT 10 72 1 TTTCTTACTC 0.86368 -229 ATTTGAATTCCCCCTTGTTTTCTGTTTCAACA 11 8 1 TTCCTTTTTC 0.974819 -233 CAGAATGTTTTTGCACCTTGTCCTCGAAAATTGTA 11 108 0 TTCCTTTCTC 0.978187 -133 ** * * ** * *** Masking position 8 Map Score: 9.05808 Number of sites scoring better than the average of aligned sites = 555 Number in coding regions = 451 Number in noncoding regions = 104 Number of orfs with sites within 600 bp upstream = 114 Fraction of orfs with sites within 600 bp upstream = 0.0183103 Motif number 4 TTTACTAAAAAAGGATTGATGAAAAGAATTT 1 67 0 AAGGATTGTG 0.966516 -105 CACTCTACATAAGAACTCATGTTCGTGTATA 2 113 1 AAGAACTCTG 0.791474 -56 AGAATGCGAGAAGCACTGGTGTCCTTGGGTT 3 70 0 AAGCACTGTG 0.926647 -231 GACTACTCGAAAGCCTTGTTGTCTG 6 5 0 AAGCCTTGTG 0.965866 -131 GAGTAGTCGAAAGCCTTGTTGTTATCCTTTT 6 28 1 AAGCCTTGTG 0.965866 -108 CCTCCTGCACAAGGCCTCCCGAAAGACCTTG 8 271 0 AAGGCCTCCG 0.940469 -30 CAAATATTCAAAGGATTCCCGCGTATATCTT 9 44 0 AAGGATTCCG 0.932934 -257 TGGCACAGGTAAGGCTAGCTGGAAAACAAGA 9 162 0 AAGGCTAGTG 0.878897 -139 CGGTCAGCCGAAGGCTCGTCGTCTCTTTATC 10 214 1 AAGGCTCGCG 0.884508 -87 GTGCCAAATCAAGAATTCGTGTGTTTTCTAC 11 80 1 AAGAATTCTG 0.842043 -161 ******** ** Masking position 2 Map Score: 5.40434 Number of sites scoring better than the average of aligned sites = 339 Number in coding regions = 299 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 5 TCCATTTAGGGAGCCGCTTTT 1 2 0 GAGCCGCTTT 0.944123 -170 TCCCTAAATGGAGCCGCTTTTTTCGGGAAA 1 20 1 GAGCCGCTTT 0.944123 -152 GTTAAAATTCCCCCTTTCGTGTGTATA 2 152 0 TTCCCCCTTT 0.94545 -17 AAGTTACCTCCTTTTAAAATGCAA 3 287 0 TACCTCCTTT 0.848259 -14 CTTCAGAAAACCCCTTTATCTTTTCAT 4 8 1 AAACCCCTTT 0.892968 -145 CCCGATACCCCTTTGTATGAAAAA 4 139 0 ATACCCCTTT 0.893009 -14 TTTTATAGCCGCTTACTGGTTAAGC 7 6 1 TAGCCGCTTA 0.776367 -144 AAAAAAGGGAAAGCCGCTTAACCAGTAAGC 7 21 0 AAGCCGCTTA 0.810475 -129 TTGTCCTGCCGTACTCCTTTGATGTATAAG 9 85 1 GTACTCCTTT 0.725182 -216 TTCATGAAGAATCCTGCTTTTGACCTGTAA 10 163 0 ATCCTGCTTT 0.873213 -138 ATTTGAATTCCCCCTTGTTTTCTGTTT 11 8 1 TTCCCCCTTG 0.783291 -233 TCAACATGTTATCCTGCTTTCCCTTTATAT 11 37 1 ATCCTGCTTT 0.873213 -204 ********** Masking position 8 Map Score: 5.81371 Number of sites scoring better than the average of aligned sites = 972 Number in coding regions = 795 Number in noncoding regions = 177 Number of orfs with sites within 600 bp upstream = 186 Fraction of orfs with sites within 600 bp upstream = 0.0298747 Motif number 6 TTTTTCTAGGGGAGAAGAAGC 6 125 1 GGAGAAGAAG 0.975458 -11 ACTGTACATTGTATAAGAGGGAGCGAGTTC 8 228 1 GTATAAGAGG 0.8482 -73 TGAAAGCGGAGGATACGAAGTGGCACAGGT 9 183 0 GGATACGAAG 0.938379 -118 CTAAGGTTTTGGATAAGAGGTGACCTCA 9 283 1 GGATAAGAGG 0.960675 -18 TAATAGATAAAGAGACGACGAGCCTTCGGC 10 220 0 AGAGACGACG 0.84508 -81 AGATTAGGTAGGAGACGGCGGGCTTTTTTG 10 249 1 GGAGACGGCG 0.959701 -52 TTTTTGAAAACGAGAAGGAGAGGTAGAAGA 10 279 1 CGAGAAGGAG 0.812271 -22 AGAAGGAGAGGTAGAAGAGG 10 291 1 GTAGAAGAGG 0.934618 -10 ********** Masking position 5 Map Score: 2.62943 Number of sites scoring better than the average of aligned sites = 414 Number in coding regions = 361 Number in noncoding regions = 53 Number of orfs with sites within 600 bp upstream = 48 Fraction of orfs with sites within 600 bp upstream = 0.0077096 Motif number 7 TGGGATTTTTGGCGGAGCAAATAAATTGGA 3 37 0 GGCGGAGCAA 0.957042 -264 GGTAACATAGGGTTGTGCAAATTATTGCAA 4 87 1 GGTTGTGCAA 0.899986 -66 CGGAATAAATAGGTGTGCAAATTTTTTCAT 4 117 1 AGGTGTGCAA 0.917361 -36 GAGGCCGGCAGGGGGATCAAATCGATAGGA 5 37 0 GGGGGATCAA 0.946716 -264 CAATCATAGTGGGTATGCAATTATACAAAT 5 66 1 GGGTATGCAA 0.871814 -235 GTCTATAAATAGGGGTTCAATGATGACAAT 7 109 1 AGGGGTTCAA 0.880088 -41 CATTGTATAAGAGGGAGCGAGTTCCGTATC 8 234 1 GAGGGAGCGA 0.823962 -67 CCTTGTGCAGGAGGAAGCAAATC 8 288 1 GAGGAAGCAA 0.652993 -13 TGATCTAATGAGCTGTTCAATTTCTTCTTG 9 137 1 AGCTGTTCAA 0.52565 -164 AGAGCTGCGGGGTGGTGCGACGCAGCCTGA 10 52 1 GGTGGTGCGA 0.900662 -249 ********** Masking position 10 Map Score: 2.84062 Number of sites scoring better than the average of aligned sites = 510 Number in coding regions = 414 Number in noncoding regions = 96 Number of orfs with sites within 600 bp upstream = 107 Fraction of orfs with sites within 600 bp upstream = 0.017186 Motif number 8 GTCCAAATCACATTAAAATTCTTTTCATCA 1 52 1 CATTAAAATT 0.943865 -120 ATTATTATAACACTAAAATTTCTATCTTTT 1 97 0 CACTAAAATT 0.862385 -75 TTATAATAATCATTAAAAATAGATTGCTGA 1 117 1 CATTAAAAAT 0.780631 -55 GAGTGCTCGAAAATAAAATTTGTTGACATA 2 88 0 AAATAAAATT 0.777059 -81 TTGCCTCCATAATTAAAATTGTCATCATTG 7 126 0 AATTAAAATT 0.911543 -24 TAAATATGCCAATTAACATTCTCTAATATA 8 198 1 AATTAACATT 0.812846 -103 GTATATCTTGAATTAAAATTAAAATCTGCC 9 23 0 AATTAAAATT 0.911543 -278 ********** Masking position 5 Map Score: 2.25183 Number of sites scoring better than the average of aligned sites = 62 Number in coding regions = 48 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 9 AAAACGAAACATTTTTTCCACACATTCGCT 3 141 1 ATTTTTTCCA 0.85474 -160 AAACCCCTTTATCTTTTCATTTCCTTTATT 4 18 1 ATCTTTTCAT 0.824861 -135 TTGACAAAATATTTTTTCCGCTGGACAATA 4 44 0 ATTTTTTCCG 0.929863 -109 TTGCACACCTATTTATTCCGTTGCAATAAT 4 107 0 ATTTATTCCG 0.766875 -46 AGGTGTGCAAATTTTTTCATACAAAGGGGT 4 127 1 ATTTTTTCAT 0.712333 -26 ATATAATGATATTTTTTTCTAGGGGAGAAG 6 112 1 ATTTTTTTCT 0.558785 -24 CAAAGACCAAACCCTTTCCTCGATGGAAAA 8 153 1 ACCCTTTCCT 0.782883 -148 AAATAAAAAAACCTTTTCCATCGAGGAAAG 8 166 0 ACCTTTTCCA 0.875149 -135 AGTAGAGGTTATCTTTTCCTGTTAAAAAAA 9 255 0 ATCTTTTCCT 0.968325 -46 GGAATATTCAATCTATTCCGTTCCGTCTTA 10 109 0 ATCTATTCCG 0.862195 -192 ATGTTTTTGCACCTTGTCCTCGAAAATTGT 11 109 0 ACCTTGTCCT 0.782883 -132 ********** Masking position 1 Map Score: 4.08593 Number of sites scoring better than the average of aligned sites = 733 Number in coding regions = 623 Number in noncoding regions = 110 Number of orfs with sites within 600 bp upstream = 134 Fraction of orfs with sites within 600 bp upstream = 0.0215226 Motif number 10 AAAAGCGGCTCCCTAAATGGAGCC 1 5 1 GCGGCTCCCT 0.994442 -167 CCCGAAAAAAGCGGCTCCATTTAGGGAGCC 1 17 0 GCGGCTCCAT 0.987531 -155 TACATGTCTTGTGGCTCTATTTTTCACTCG 5 171 0 GTGGCTCTAT 0.933856 -130 TACTGGTTAAGCGGCTTTCCCTTTTTTATC 7 24 1 GCGGCTTTCC 0.934862 -126 GCACCACCCCGCAGCTCTCTGTTCTGATCA 10 40 0 GCAGCTCTCT 0.969566 -261 ********** Masking position 6 Map Score: 0.98512 Number of sites scoring better than the average of aligned sites = 123 Number in coding regions = 105 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 11 CCTCATTATAGTTTACCCCGCTAAACTTTATGT 2 22 1 GTTTACCGTA 0.968796 -147 TGACAGGCTAGTTTTAATCGGTAACGATTTGTA 5 89 0 GTTTTATGTA 0.778098 -212 GACTTTCCTGTTTTACTCTGCTATTCAGGTAGA 5 134 1 TTTTACCGTA 0.776135 -167 GATGAGTAAAGTTTTATCGGATATTATAACATT 5 253 0 GTTTTACGTA 0.969136 -48 GCCGCTTACTGGTTAAGCGGCTTTCCCTTTTTT 7 18 1 GGTTAACGTT 0.774683 -132 AATAGTATTTGGTTTCACAGTTATGTAAAAAAA 7 70 0 GGTTTCCGTA 0.979927 -80 CCCAGCAACCGGTTTCTCTGTTATTTATTATGT 8 44 1 GGTTTCCGTA 0.979927 -257 TATTCCCTATGTTTTAACGGCTAACCTTCGTTA 10 133 1 GTTTTACGTA 0.969136 -168 ****** * * ** Masking position 4 Map Score: 2.79562 Number of sites scoring better than the average of aligned sites = 116 Number in coding regions = 97 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 12 ATCATTTTTCTGAATATTCCGTACGGATTG 6 84 0 TGAATATTCC 0.723788 -52 GCGAGTTCAAAGAAGAATCAGGCTGCGTCG 10 69 0 AGAAGAATCA 0.843192 -232 CGGAATAGATTGAATATTCCCTATGTTTTA 10 119 1 TGAATATTCC 0.723788 -182 TGATTCTTCATGAAGAATCCTGCTTTTGAC 10 169 0 TGAAGAATCC 0.974584 -132 GGATTCTTCATGAAGAATCAACAAGAGTGG 10 179 1 TGAAGAATCA 0.930011 -122 ********** Masking position 6 Map Score: 0.168142 Number of sites scoring better than the average of aligned sites = 98 Number in coding regions = 91 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 13 ********** No masking Map Score: 7.48502e-13 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: 7.48502e-13 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: 7.48502e-13 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