AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i122_Arsenical_Resistance_Pump_bsub_reg_300.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 TTCATTCTCAATTAAAACTTTGATATAGATGTGAACGGGA 2 21 0 ATAATTGTAT 0.942082 -141 CCCTTGAAATATGATATACTTTGTATTGATATTCATTCTC 2 52 0 ATAATTTTAT 0.98678 -110 GTTTTTGCCTATTATAGAGTTTTCAGCAATTGACCACAAG 2 116 0 ATAATTTGAT 0.944281 -46 CCCCGTCATTATATAAACTTTTATTTATATAAACAATCCC 3 111 0 ATTATTTTAT 0.968551 -190 TTTGGCGTGTATATAACGATTTGCTTATATATTGATTTGG 3 256 1 ATTATTTTAT 0.858331 -45 TAGGTATTATATCAAATTTTTTTGATTAATATATAAGAGG 5 21 1 ATAATTTTAT 0.982777 -40 AGAAAAAAACATTAAATAATTTTTGTGAATATGTAGAATC 6 57 0 ATAATTTTAT 0.987235 -244 GAGGTTTTCCATTTTTATTATTTCCTCCATCGCTACTTTG 6 140 0 ATTTATTTAT 0.701007 -161 ATGCAAGCAAATAAATCAATTTATTTTGATTAATTGTAAA 6 208 0 ATATTTTTAT 0.776287 -93 GCCTTCTTTAATCAATTTTTTTTGATGTATTTATTATACT 6 264 0 ATATTTTTAT 0.973332 -37 ** * * *** * ** Masking position 11 Map Score: 11.5725 Number of sites scoring better than the average of aligned sites = 176 Number in coding regions = 124 Number in noncoding regions = 52 Number of orfs with sites within 600 bp upstream = 61 Fraction of orfs with sites within 600 bp upstream = 0.00979762 Motif number 2 CTGCTTGTTTGACGGAGGAGGGGAAAGGATCGTTTC 1 18 0 GGGAGGGGAA 0.849993 -82 CTGGTATCATAAGAAAGGCAGCTTAACATGAGCGGA 1 65 1 AAAAGGAGAA 0.819765 -35 GCAGCTTAACATGAGCGGAGGTTTTATT 1 82 1 AAGCGGGGTA 0.992644 -18 AAGTTTATATAATGACGGGGGCGCTAAGGAAACGCG 3 131 1 AGACGGGGTA 0.981671 -170 CATATGGAAACGTAAAGGGGAATGTATAATCATTTG 3 224 1 CAAAGGGATA 0.883443 -77 TAAAAAAGGTGAGGATAAAGTA 4 2 1 AAAAGGGATA 0.970096 -21 TGATTAATATATAAGAGGGGGAATTAAA 5 43 1 AAGAGGGGTA 0.992036 -18 TTGCTACTACAGCAACGGAGATCATAAACGCTAATT 6 107 0 AAACGGGATA 0.972335 -194 GTAGTAGCAAAGTAGCGATGGAGGAAATAATAAAAA 6 133 1 AAGCGAGGAA 0.913522 -168 AAAAAAATTGATTAAAGAAGGCGATATGA 6 282 1 AAAAGAGGTA 0.952097 -19 * ***** ** ** Masking position 16 Map Score: 6.00935 Number of sites scoring better than the average of aligned sites = 562 Number in coding regions = 409 Number in noncoding regions = 153 Number of orfs with sites within 600 bp upstream = 169 Fraction of orfs with sites within 600 bp upstream = 0.0271442 Motif number 3 CGTCCTGCCTCCCGTTCACATCTATATCAAAGTTTTA 2 12 1 CCCTATATAT 0.978969 -150 TAAACAAAGGCCCTTGAAATATGATATACTTTGTATT 2 65 0 CCCTTAATAT 0.793782 -97 ATTTCAAGGGCCTTTGTTTATTCATTTCTTCTACCTT 2 82 1 CCTTATATTT 0.949915 -80 ATAAACAATCCCTTCTGGTATAAATATTAGACTATTT 3 86 0 CCTCATATAT 0.986118 -215 TTCCTTAGCGCCCCCGTCATTATATAAACTTTTATTT 3 125 0 CCCCTTATAA 0.938118 -176 TATACATTCCCCTTTACGTTTCCATATGTAGCGCTCC 3 215 0 CCTTTTATAT 0.949915 -86 ATGAGCTCCTCCTTCCCAAATCAATATATAAGCAAAT 3 274 0 CCTCATATAT 0.986118 -27 TTTAATTCCCCCTCTTATATATTAATCAAAAAAA 5 37 0 CCCCATATTA 0.938118 -24 TCATATCGCCTTCTTTAATCAATTTTTTTTGATGT 6 276 0 CCTCATATTT 0.973865 -25 *** * ** **** Masking position 14 Map Score: 6.722 Number of sites scoring better than the average of aligned sites = 166 Number in coding regions = 122 Number in noncoding regions = 44 Number of orfs with sites within 600 bp upstream = 46 Fraction of orfs with sites within 600 bp upstream = 0.00738837 Motif number 4 AACAAGCAGTGCCTTTTTTTCTGGTATCAT 1 45 1 GCCTTTTTTT 0.98759 -55 ATGTTAAGCTGCCTTTCTTATGATACCAGA 1 64 0 GCCTTTCTTA 0.972862 -36 TATTTCAAGGGCCTTTGTTTATTCATTTCT 2 81 1 GCCTTTGTTT 0.972862 -81 CTAAAGAGACCTGTTTTTTAATATCCAG 3 9 1 ACCTGTTTTT 0.907682 -292 CTTTATCCTCACCTTTTTTA 4 1 0 ACCTTTTTTA 0.964145 -22 TCATATCGCCTTCTTTAATCAATTTTT 6 284 0 GCCTTCTTTA 0.966775 -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 5 CACTGCTTGTTTGACGGAGGAGGGGAAAGGA 1 25 0 TTGAGGAGGA 0.96095 -75 AGATGTGAACGGGAGGCAGGACGG 2 4 0 GGGAGCAGGA 0.995859 -158 AACGCGGGGAGCGACTCAGGTTTTCGTTTCA 3 161 1 GCGATCAGGT 0.93336 -140 ATATTGATTTGGGAAGGAGGAGCTCAT 3 284 1 GGGAGGAGGA 0.997153 -17 TAGCAAAGTAGCGATGGAGGAAATAATAAAA 6 137 1 GCGAGGAGGA 0.997153 -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 6 TGCCTTTTTTTCTGGTATCATAAGAAAGGC 1 54 1 TCTGGTATCA 0.986585 -46 CAGATGATTGTCTAGTTTCAGCTTGGGCTC 3 36 1 TCTAGTTTCA 0.970019 -265 AACAATCCCTTCTGGTATAAATATTAGACT 3 90 0 TCTGGTATAA 0.952522 -211 CGACTCAGGTTTTCGTTTCAAAGTTTTGAT 3 172 1 TTTCGTTTCA 0.881225 -129 ATCAAAAAAATTTGATATAATACCTAAAAA 5 17 0 TTTGATATAA 0.598844 -44 AACGCTAATTTCTAATTTCAAGAAAAAAAC 6 87 0 TCTAATTTCA 0.898149 -214 AAAACCTCTATCTGGTTACACAAGCTTTTA 6 172 1 TCTGGTTACA 0.952103 -129 ********** Masking position 10 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 7 CCCTCTTATATATTAATCAAAAAAATTTGA 5 32 0 TATTAATCAA 0.769412 -29 TAGAATCGATAATAATTCGAGATAATACGT 6 34 0 AATAATTCGA 0.831802 -267 CTACTTTGCTACTACAGCAACGGAGATCAT 6 118 0 ACTACAGCAA 0.837334 -183 CGGGTTTTACAATTAATCAAAATAAATTGA 6 203 1 AATTAATCAA 0.941426 -98 AATGCAAGCAAATAAATCAATTTATTTTGA 6 219 0 AATAAATCAA 0.973646 -82 TGATTTTTAAAATAATGCAAGCAAATAAAT 6 232 0 AATAATGCAA 0.915364 -69 GAGTATAATAAATACATCAAAAAAAATTGA 6 263 1 AATACATCAA 0.961332 -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 8 AAGGGCCTTTGTTTATTCATTTCTTCTACCTT 2 87 1 GTTATCATTT 0.924487 -75 CACCCAATTGGTTTTTGCCTATTATAGAGTTT 2 134 0 GTTTTCCTAT 0.952114 -28 AAAGAGACCTGTTTTTTAATATCCAGATGATT 3 13 1 GTTTTAATAT 0.946301 -288 AATTATTATCGATTCTACATATTCACAAAAAT 6 47 1 GTTCTCATAT 0.959393 -254 ACCAGATAGAGGTTTTCCATTTTTATTATTTC 6 156 0 GTTTTCATTT 0.980247 -145 GCTTTTAGCGGGTTTTACAATTAATCAAAATA 6 195 1 GTTTTCAATT 0.955695 -106 TTATACTCATGATTTTTAAAATAATGCAAGCA 6 239 0 GTTTTAAAAT 0.884392 -62 * **** ***** Masking position 6 Map Score: 3.37395 Number of sites scoring better than the average of aligned sites = 467 Number in coding regions = 392 Number in noncoding regions = 75 Number of orfs with sites within 600 bp upstream = 75 Fraction of orfs with sites within 600 bp upstream = 0.0120463 Motif number 9 AAACGATCCTTTCCCCTCCTCCGTCAAACA 1 19 1 TTCCCCTCCT 0.982118 -81 AATAAAACCTCCGCTCATGTTAAGCTGC 1 82 0 CTCCGCTCAT 0.976641 -18 TTCCTTAGCGCCCCCGTCATTATATAAACT 3 132 0 CCCCCGTCAT 0.978324 -169 ACCTGAGTCGCTCCCCGCGTTTCCTTAGCG 3 152 0 CTCCCCGCGT 0.982352 -149 TTTAATTCCCCCTCTTATATATTAAT 5 45 0 TCCCCCTCTT 0.975612 -16 ********** Masking position 10 Map Score: 0.361575 Number of sites scoring better than the average of aligned sites = 138 Number in coding regions = 86 Number in noncoding regions = 52 Number of orfs with sites within 600 bp upstream = 63 Fraction of orfs with sites within 600 bp upstream = 0.0101189 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 Motif number 11 ********** 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 12 ********** 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