AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i122_bsub_mtub_300.orf -o122_bsub_mtub_300.ace -a/home/amcguire/genomes/ORF_bsub.txt -z/home/amcguire/genomes/bsub.fna -g0.55 -x5 -e 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 = 0.55 maxlen = 30 weight = 0.8 exclude = 1 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) #7 Rv2641 101 hypothetical protein Rv2641 #8 Rv2642 135 hypothetical protein Rv2642 Motif number 1 CTCAATTAAAACTTTGATATAGATGTGAACG 2 24 0 ATTTGATATA 0.980738 -138 AGGCCCTTGAAATATGATATACTTTGTATTG 2 64 0 ATATGATATA 0.854192 -98 CATTATATAAACTTTTATTTATATAAACAAT 3 114 0 ATTTTATTTA 0.812788 -187 ATTTGCTTATATATTGATTTGGGAAGGAGGA 3 274 1 AATTGATTTG 0.786918 -27 TAATCAAAAAAATTTGATATAATACCTAAAA 5 18 0 ATTTGATATA 0.980715 -43 ATATCAAATTTTTTTGATTAATATATAAGAG 5 29 1 TTTTGATTAA 0.884271 -32 AAATCAATTTATTTTGATTAATTGTAAAACC 6 205 0 ATTTGATTAA 0.955577 -96 TAATCAAAATAAATTGATTTATTTGCTTGCA 6 216 1 AATTGATTTA 0.95557 -85 TAATCAATTTTTTTTGATGTATTTATTATAC 6 265 0 TTTTGATGTA 0.868746 -36 ACATCAAAAAAAATTGATTAAAGAAGGCGAT 6 276 1 AATTGATTAA 0.884362 -25 GTGCAACATCTCTTTGATATATGTCAAGGTA 7 28 0 TTTTGATATA 0.947624 -74 GTTCGGCGCCATTTTGATATAAGTCAAACAA 7 64 1 ATTTGATATA 0.980731 -38 * ********* Masking position 7 Map Score: 14.1624 Number of sites scoring better than the average of aligned sites = 329 Number in coding regions = 263 Number in noncoding regions = 66 Number of orfs with sites within 600 bp upstream = 75 Fraction of orfs with sites within 600 bp upstream = 0.0120463 Motif number 2 AAACCTGAGTCGCTCCCCGCGTTTCCTTAGC 3 153 0 CGCTCCCGCG 0.995015 -148 AGGCCCACCCTGCCAGATACCTTG 7 4 1 CCCACCTGCC 0.974414 -98 AAAGAGATGTTGCACACTGGGTTCGGCGCCA 7 44 1 TGCACCTGGG 0.941211 -58 GGCTTGGAGACGCACCCCGGGGTCAGGCCTA 8 14 0 CGCACCCGGG 0.993773 -122 GGGGTGCGTCTCCAAGCCGCGGAGCCCACCC 8 27 1 TCCAACCGCG 0.97386 -109 AGCCGCGGAGCCCACCCCGGGCCACTCAATG 8 41 1 CCCACCCGGG 0.994835 -95 CTCAATGCCCCCTAACCCGCGTAGCGCCGTT 8 65 1 CCTAACCGCG 0.973872 -71 CGCGTAGCGCCGTTCACCGCGTGGCCGCTTG 8 82 1 CGTTCCCGCG 0.978057 -54 GAATCAGGTCCGCAAGCGGCCACGCGGTGAA 8 94 0 CGCAACGGCC 0.932114 -42 ***** ***** Masking position 7 Map Score: 13.5508 Number of sites scoring better than the average of aligned sites = 193 Number in coding regions = 176 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 3 GCTTAACATGAGCGGAGGTTTTATT 1 85 1 AGCGGGGTAT 0.961836 -15 TTTATATAATGACGGGGGCGCTAAGGAAACGCGG 3 134 1 GACGGGGTAA 0.987816 -167 ATGGAAACGTAAAGGGGAATGTATAATCATTTGG 3 227 1 AAAGGGATAT 0.945175 -74 ATTGATTTGGGAAGGAGGAGCTCAT 3 286 1 GAAGGGGTCA 0.950801 -15 TAAAAAAGGTGAGGATAAAGTA 4 5 1 AAAGGGATAA 0.970471 -18 TTAATATATAAGAGGGGGAATTAAA 5 46 1 AGAGGGGTAA 0.980007 -15 CTACTACAGCAACGGAGATCATAAACGCTAATTT 6 106 0 AACGGGATAA 0.969892 -195 GCAAAGTAGCGATGGAGGAAATAATAAAAATGGA 6 139 1 GATGGGGTAA 0.953284 -162 AAAATTGATTAAAGAAGGCGATATGA 6 285 1 AAAGAGGTAT 0.83758 -16 ***** ** *** Masking position 12 Map Score: 6.32552 Number of sites scoring better than the average of aligned sites = 261 Number in coding regions = 178 Number in noncoding regions = 83 Number of orfs with sites within 600 bp upstream = 85 Fraction of orfs with sites within 600 bp upstream = 0.0136524 Motif number 4 CTGTTTCACCCAATTGGTTTTTGCCTATTAT 2 141 0 CAATTGTTTT 0.901153 -21 CTGAAATAGTCTAATATTTATACCAGAAGGG 3 83 1 CTAATTTTAT 0.746288 -218 ATATACACGCCAAATGATTATACATTCCCCT 3 239 0 CAAATATTAT 0.964861 -62 AATATATAAGCAAATCGTTATATACACGCCA 3 258 0 CAAATGTTAT 0.952634 -43 TCCTCCTTCCCAAATCAATATATAAGCAAAT 3 274 0 CAAATAATAT 0.807116 -27 GGTATTATATCAAATTTTTTTGATTAATATA 5 23 1 CAAATTTTTT 0.94862 -38 CGTATTATCTCGAATTATTATCGATTCTACA 6 35 1 CGAATATTAT 0.874792 -266 AAAAAAACATTAAATAATTTTTGTGAATATG 6 64 0 TAAATATTTT 0.710566 -237 GCAAATAAATCAATTTATTTTGATTAATTGT 6 211 0 CAATTATTTT 0.928887 -90 CTTCTTTAATCAATTTTTTTTGATGTATTTA 6 271 0 CAATTTTTTT 0.894131 -30 ***** ***** Masking position 5 Map Score: 6.27713 Number of sites scoring better than the average of aligned sites = 427 Number in coding regions = 360 Number in noncoding regions = 67 Number of orfs with sites within 600 bp upstream = 77 Fraction of orfs with sites within 600 bp upstream = 0.0123675 Motif number 5 TCCTTTCCCCTCCTCCGTCAAACAAGCAGTG 1 25 1 TCCTCCTCAA 0.949046 -75 CCGTCCTGCCTCCCGTTCACATCT 2 4 1 TCCTGCTCCC 0.993393 -158 TGAAACGAAAACCTGAGTCGCTCCCCGCGTT 3 161 0 ACCTGATCGC 0.975407 -140 ATGAGCTCCTCCTTCCCAAATCAATAT 3 284 0 TCCTCCTCCC 0.993393 -17 TTTTATTATTTCCTCCATCGCTACTTTGCTA 6 137 0 TCCTCCTCGC 0.995455 -164 CCGCTTGCGGACCTGATTCGATATTTGTCAA 8 106 1 ACCTGATCGA 0.930564 -30 ****** **** Masking position 4 Map Score: 4.98448 Number of sites scoring better than the average of aligned sites = 141 Number in coding regions = 113 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 6 ATGATACCAGAAAAAAAGGCACTGCTTGTT 1 45 0 AAAAAAAGGC 0.983899 -55 TCTGGTATCATAAGAAAGGCAGCTTAACAT 1 64 1 TAAGAAAGGC 0.964947 -36 AGAAATGAATAAACAAAGGCCCTTGAAATA 2 81 0 AAACAAAGGC 0.964947 -81 CTGGATATTAAAAAACAGGTCTCTTTAG 3 9 0 AAAAACAGGT 0.883041 -292 TAAAAAAGGTGAGGATAAAG 4 1 1 TAAAAAAGGT 0.953807 -22 AAAAATTGATTAAAGAAGGCGATATGA 6 284 1 TAAAGAAGGC 0.957162 -17 ********** Masking position 7 Map Score: 4.07144 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 7 TGCCTTTTTTTCTGGTATCATAAGAAAGGC 1 54 1 TCTGGTATCA 0.986806 -46 CAGATGATTGTCTAGTTTCAGCTTGGGCTC 3 36 1 TCTAGTTTCA 0.979394 -265 AACAATCCCTTCTGGTATAAATATTAGACT 3 90 0 TCTGGTATAA 0.934778 -211 AACGCTAATTTCTAATTTCAAGAAAAAAAC 6 87 0 TCTAATTTCA 0.900893 -214 AAAACCTCTATCTGGTTACACAAGCTTTTA 6 172 1 TCTGGTTACA 0.970191 -129 ********** Masking position 6 Map Score: 2.38227 Number of sites scoring better than the average of aligned sites = 28 Number in coding regions = 22 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 8 AGAAGGGATTGTTTATATAAATAAAAGTTT 3 107 1 GTTTATATAA 0.962543 -194 ATAAATAAAAGTTTATATAATGACGGGGGC 3 123 1 GTTTATATAA 0.962543 -178 ATCATTTGGCGTGTATATAACGATTTGCTT 3 252 1 GTGTATATAA 0.875502 -49 ATAACGATTTGCTTATATATTGATTTGGGA 3 268 1 GCTTATATAT 0.904431 -33 ATCAAAAAAATTTGATATAATACCTAAAAA 5 17 0 TTTGATATAA 0.942141 -44 TAATTCCCCCTCTTATATATTAATCAAAAA 5 39 0 TCTTATATAT 0.856398 -22 GCAACATCTCTTTGATATATGTCAAGGTAT 7 27 0 TTTGATATAT 0.911657 -75 TCGGCGCCATTTTGATATAAGTCAAACAAC 7 66 1 TTTGATATAA 0.942141 -36 ********** Masking position 5 Map Score: 7.54401 Number of sites scoring better than the average of aligned sites = 190 Number in coding regions = 141 Number in noncoding regions = 49 Number of orfs with sites within 600 bp upstream = 47 Fraction of orfs with sites within 600 bp upstream = 0.00754899 Motif number 9 AAGGTAGAAGAAATGAATAAACAAAGGCCCTT 2 87 0 AAATGATAAC 0.94809 -75 AAACTCTATAATAGGCAAAAACCAATTGGGTG 2 134 1 ATAGGAAAAC 0.917703 -28 AATCATCTGGATATTAAAAAACAGGTCTCTTT 3 13 0 ATATTAAAAC 0.905657 -288 ACGTAAAGGGGAATGTATAATCATTTGGCGTG 3 233 1 GAATGATAAC 0.828864 -68 ATTTTTGTGAATATGTAGAATCGATAATAATT 6 47 0 ATATGAGAAC 0.938836 -254 GAAATAATAAAAATGGAAAACCTCTATCTGGT 6 156 1 AAATGAAAAC 0.976735 -145 TATTTTGATTAATTGTAAAACCCGCTAAAAGC 6 195 0 AATTGAAAAC 0.938826 -106 TGCTTGCATTATTTTAAAAATCATGAGTATAA 6 239 1 ATTTTAAAAC 0.777908 -62 ***** **** * Masking position 7 Map Score: 2.37686 Number of sites scoring better than the average of aligned sites = 697 Number in coding regions = 591 Number in noncoding regions = 106 Number of orfs with sites within 600 bp upstream = 112 Fraction of orfs with sites within 600 bp upstream = 0.0179891 Motif number 10 TGGGAGTGGTCATAGAGCCCAAGCTGAAAC 3 50 0 CATAGAGCCC 0.741679 -251 GCTAAGGAAACGCGGGGAGCGACTCAGGTT 3 153 1 CGCGGGGAGC 0.97211 -148 CCTTAAGATATACGGAGCGCTACATATGGA 3 202 1 TACGGAGCGC 0.933906 -99 ATCAAAATGGCGCCGAACCCAGTGTGCAAC 7 52 0 CGCCGAACCC 0.939755 -50 GTCTCCAAGCCGCGGAGCCCACCCCGGGCC 8 34 1 CGCGGAGCCC 0.998097 -102 CCCCCTAACCCGCGTAGCGCCGTTCACCGC 8 72 1 CGCGTAGCGC 0.990903 -64 CGCCGTTCACCGCGTGGCCGCTTGCGGACC 8 89 1 CGCGTGGCCG 0.948721 -47 ********** Masking position 7 Map Score: 3.43124 Number of sites scoring better than the average of aligned sites = 337 Number in coding regions = 320 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 11 CTGCCTCCCGTTCACATCTATATCAAAGTT 2 16 1 TTCACATCTA 0.916426 -146 TTTTCAGCAATTGACCACAAGGTAGAAGAA 2 107 0 TTGACCACAA 0.834287 -55 ATTCTACATATTCACAAAAATTATTTAATG 6 58 1 TTCACAAAAA 0.876509 -243 GCCAGATACCTTGACATATATCAAAGAGAT 7 22 1 TTGACATATA 0.961979 -80 TCCCAGTTGTTTGACTTATATCAAAATGGC 7 71 0 TTGACTTATA 0.885027 -31 ACATCAATATTGACAAATATCGAATCAGG 8 117 0 TTGACAAATA 0.96203 -19 ********** Masking position 4 Map Score: 0.266268 Number of sites scoring better than the average of aligned sites = 144 Number in coding regions = 115 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 12 ********** No masking Map Score: 2.90145e-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 13 ********** No masking Map Score: 2.90145e-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: 2.90145e-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