AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i122_Arsenical_Resistance_Pump_bsub_reg_100.orf -aORF_bsub.txt -zbsub.fna -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 ycgR 99 ycgR #2 ycgS 161 similar to aromatic hydrocarbon catabolism #3 ydeT 300 similar to transcriptional regulator (ArsR family) #4 yqcL 22 similar to hypothetical proteins #5 yqcK 60 similar to hypothetical proteins #6 yqcJ 300 similar to transcriptional regulator (ArsR family) Motif number 1 TCCCGTTCACATCTATATCAAAGTTTTAATTGAGAATGAA 2 21 1 ATACAATTAT 0.942679 -141 GAGAATGAATATCAATACAAAGTATATCATATTTCAAGGG 2 52 1 ATAAAAATAT 0.972821 -110 CTTGTGGTCAATTGCTGAAAACTCTATAATAGGCAAAAAC 2 116 1 ATCAAAATAT 0.891742 -46 GGGATTGTTTATATAAATAAAAGTTTATATAATGACGGGG 3 111 1 ATAAAATAAT 0.969941 -190 CCAAATCAATATATAAGCAAATCGTTATATACACGCCAAA 3 256 0 ATAAAATAAT 0.853538 -45 CCTCTTATATATTAATCAAAAAAATTTGATATAATACCTA 5 21 0 ATAAAATTAT 0.97681 -40 GATTCTACATATTCACAAAAATTATTTAATGTTTTTTTCT 6 57 1 ATAAAATTAT 0.973665 -244 CAAAGTAGCGATGGAGGAAATAATAAAAATGGAAAACCTC 6 140 1 ATAAATAAAT 0.715219 -161 GGGTTTTACAATTAATCAAAATAAATTGATTTATTTGCTT 6 204 1 ATAAAATTAT 0.779252 -97 AGTATAATAAATACATCAAAAAAAATTGATTAAAGAAGGC 6 264 1 ATAAAATTAT 0.988151 -37 ** * *** ** ** Masking position 10 Map Score: 11.5725 Number of sites scoring better than the average of aligned sites = 206 Number in coding regions = 146 Number in noncoding regions = 60 Number of orfs with sites within 600 bp upstream = 65 Fraction of orfs with sites within 600 bp upstream = 0.0104401 Motif number 2 AAGGGCCTTTGTTTATTCATTTCTTCTACCT 2 87 1 GTTATTCATT 0.914561 -75 AGAAGGGATTGTTTATATAAATAAAAGTTTA 3 107 1 GTTATATAAA 0.834427 -194 ATAAATAAAAGTTTATATAATGACGGGGGCG 3 123 1 GTTATATAAT 0.940996 -178 CACGCCAAATGATTATACATTCCCCTTTACG 3 234 0 GTTATACATT 0.983534 -67 ATAACGATTTGCTTATATATTGATTTGGGAA 3 268 1 GTTATATATT 0.968155 -33 TAATTCCCCCTCTTATATATTAATCAAAAAA 5 38 0 TTTATATATT 0.748774 -23 AATTATTATCGATTCTACATATTCACAAAAA 6 47 1 GTTCTACATA 0.853113 -254 ACCAGATAGAGGTTTTCCATTTTTATTATTT 6 157 0 GTTTTCCATT 0.853114 -144 GCTTTTAGCGGGTTTTACAATTAATCAAAAT 6 195 1 GTTTTACAAT 0.919811 -106 * ********* Masking position 6 Map Score: 5.55722 Number of sites scoring better than the average of aligned sites = 248 Number in coding regions = 197 Number in noncoding regions = 51 Number of orfs with sites within 600 bp upstream = 54 Fraction of orfs with sites within 600 bp upstream = 0.00867331 Motif number 3 AACAAGCAGTGCCTTTTTTTCTGGTATCAT 1 45 1 GCCTTTTTTT 0.988102 -55 ATGTTAAGCTGCCTTTCTTATGATACCAGA 1 64 0 GCCTTTCTTA 0.973966 -36 TATTTCAAGGGCCTTTGTTTATTCATTTCT 2 81 1 GCCTTTGTTT 0.973966 -81 CTAAAGAGACCTGTTTTTTAATATCCAG 3 9 1 ACCTGTTTTT 0.911196 -292 CTTTATCCTCACCTTTTTTA 4 1 0 ACCTTTTTTA 0.965591 -22 TCATATCGCCTTCTTTAATCAATTTTT 6 284 0 GCCTTCTTTA 0.968119 -17 ********** Masking position 4 Map Score: 5.40033 Number of sites scoring better than the average of aligned sites = 607 Number in coding regions = 515 Number in noncoding regions = 92 Number of orfs with sites within 600 bp upstream = 87 Fraction of orfs with sites within 600 bp upstream = 0.0139737 Motif number 4 CACTGCTTGTTTGACGGAGGAGGGGAAAGGA 1 25 0 TTGAGGAGGA 0.95814 -75 AGATGTGAACGGGAGGCAGGACGG 2 4 0 GGGAGCAGGA 0.995549 -158 AACGCGGGGAGCGACTCAGGTTTTCGTTTCA 3 161 1 GCGATCAGGT 0.928712 -140 ATATTGATTTGGGAAGGAGGAGCTCAT 3 284 1 GGGAGGAGGA 0.99694 -17 TAGCAAAGTAGCGATGGAGGAAATAATAAAA 6 137 1 GCGAGGAGGA 0.99694 -164 **** ****** Masking position 4 Map Score: 3.98578 Number of sites scoring better than the average of aligned sites = 87 Number in coding regions = 62 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 5 GCCTTTCTTATGATACCAGAAAAAAAGGCA 1 54 0 TGATACCAGA 0.985224 -46 GAGCCCAAGCTGAAACTAGACAATCATCTG 3 36 0 TGAAACTAGA 0.967034 -265 AGTCTAATATTTATACCAGAAGGGATTGTT 3 90 1 TTATACCAGA 0.947889 -211 ATCAAAACTTTGAAACGAAAACCTGAGTCG 3 172 0 TGAAACGAAA 0.870579 -129 TTTTTAGGTATTATATCAAATTTTTTTGAT 5 17 1 TTATATCAAA 0.575097 -44 GTTTTTTTCTTGAAATTAGAAATTAGCGTT 6 87 1 TGAAATTAGA 0.888846 -214 TAAAAGCTTGTGTAACCAGATAGAGGTTTT 6 172 0 TGTAACCAGA 0.947432 -129 ********** Masking position 5 Map Score: 3.56949 Number of sites scoring better than the average of aligned sites = 531 Number in coding regions = 467 Number in noncoding regions = 64 Number of orfs with sites within 600 bp upstream = 64 Fraction of orfs with sites within 600 bp upstream = 0.0102795 Motif number 6 CCCTCTTATATATTAATCAAAAAAATTTGA 5 32 0 TATTAATCAA 0.763879 -29 TAGAATCGATAATAATTCGAGATAATACGT 6 34 0 AATAATTCGA 0.827431 -267 CTACTTTGCTACTACAGCAACGGAGATCAT 6 118 0 ACTACAGCAA 0.833078 -183 CGGGTTTTACAATTAATCAAAATAAATTGA 6 203 1 AATTAATCAA 0.939697 -98 AATGCAAGCAAATAAATCAATTTATTTTGA 6 219 0 AATAAATCAA 0.972841 -82 TGATTTTTAAAATAATGCAAGCAAATAAAT 6 232 0 AATAATGCAA 0.912937 -69 GAGTATAATAAATACATCAAAAAAAATTGA 6 263 1 AATACATCAA 0.960166 -38 ********** Masking position 10 Map Score: 2.16602 Number of sites scoring better than the average of aligned sites = 215 Number in coding regions = 181 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 7 TGTTTGACGGAGGAGGGGAAAGGATCGTTTCA 1 17 0 AGAGGGGAAG 0.994298 -83 GCAGCTTAACATGAGCGGAGGTTTTATT 1 82 1 AGAGCGGAGT 0.955041 -18 AGTTTATATAATGACGGGGGCGCTAAGGAAAC 3 132 1 AGACGGGGGG 0.981174 -169 CGCTAAGGAAACGCGGGGAGCGACTCAGGTTT 3 152 1 AGCGGGGAGG 0.990124 -149 TATGGAAACGTAAAGGGGAATGTATAATCATT 3 226 1 TAAGGGGAAG 0.869367 -75 ATTAATATATAAGAGGGGGAATTAAA 5 45 1 AGAGGGGGAT 0.979939 -16 * ******** * Masking position 7 Map Score: 1.04898 Number of sites scoring better than the average of aligned sites = 192 Number in coding regions = 117 Number in noncoding regions = 75 Number of orfs with sites within 600 bp upstream = 72 Fraction of orfs with sites within 600 bp upstream = 0.0115644 Motif number 8 ********** No masking Map Score: -9.92328e-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 9 ********** No masking Map Score: -9.92328e-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 10 ********** No masking Map Score: -9.92328e-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