AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i131_bsub_mtub_300.orf -o131_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 glvA 300 6-phospho-alpha-glucosidase #2 yfiA 64 similar to hypothetical proteins #3 yfiB 105 similar to ABC transporter (ATP-binding protein) #4 yfiD 154 similar to hypothetical proteins #5 yfiF 93 similar to transcriptional regulator (AraC/XylS family) #6 yfiG 174 similar to metabolite transport protein #7 yfiH 26 yfiH #8 yfiJ 123 similar to two-component sensor histidine kinase [YfiK] #9 yfiL 143 similar to ABC transporter (ATP-binding protein) #10 yvfT 132 similar to two-component sensor histidine kinase [YvfU] #11 yvfR 283 similar to ABC transporter (ATP-binding protein) #12 Rv1458c 102 hypothetical protein Rv1458c #13 Rv1686c 71 hypothetical protein Rv1686c #14 Rv1687c 58 hypothetical protein Rv1687c Motif number 1 CCTTTTCATAAGAATTGGAAGGGCGTATATTCACTTA 1 72 1 AGATGGGCGA 0.925618 -229 TATAATAGAAAGAAAATGGGGGGATCTGAT 2 45 1 AGAAGGGATT 0.66731 -20 AAAACCCTCCCGAAAAGGAGGGCAGTCT 3 2 0 CGAAGGCAGC 0.942184 -104 TGTCTTCATATGATAAAGACGCGAGAAATCTCGTTGT 6 34 1 TGAAGGGAGA 0.966426 -141 ATTGTAGAAGAAAGAAAGGCGTGCGGCATGTAGCGGC 9 86 0 AAAAGGGCGC 0.931902 -58 GCAATGGATCAAAAAAAGGAGTGAGACGAC 9 124 1 AAAAGGGAGC 0.894851 -20 CTGGTGTATACGATTATGCCGTTCCTCTCTTTATTAA 10 71 1 CGAAGGTCCC 0.859189 -62 AGGATTGCCTAGACACCGGGGTGAGAAAAAAATGACA 11 170 1 AGACGGGAGA 0.954768 -114 TGGGGTGTCATGATGATGGAGTGACAAATGTCATTTT 11 198 0 TGAAGGGACA 0.849249 -86 AAAATGACGGAGAAGACGATGTTAGTATGGGGTGTCA 11 225 0 AGAAGGTAGA 0.894066 -59 TCAATGTAAACGATCAGGAGGTGCTCAT 11 266 1 CGAAGGGCTA 0.979792 -18 GCCGCGCCGACGACGATGCAGAGCGAAGCGATGAGGA 12 11 1 CGAAGGGCGA 0.996279 -92 CAGAGCGAAGCGATGAGGAGGAGCGGCGCTCGTGAAC 12 29 1 CGAAGGGCGC 0.996569 -74 ACCGCGCCGACGACGATGCAGAGCGAAGCGATGAGGA 12 64 1 CGAAGGGCGA 0.996279 -39 CAGAGCGAAGCGATGAGGAGGAGCGGCGCTC 12 82 1 CGAAGGGCGC 0.996569 -21 CGCGACACTGCGGTGATCAGCGGCAAGCT 13 53 0 CGACGGGATA 0.890159 -19 *** * * * *** * Masking position 3 Map Score: 23.7968 Number of sites scoring better than the average of aligned sites = 370 Number in coding regions = 341 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 2 AACGTTATCAAGGAGGTCGTCAT 1 288 1 AGGAGGTCAT 0.939307 -13 GAAAGAAAATGGGGGGATCTGAT 2 52 1 GGGGGGTGAT 0.862202 -13 CCTCCCGAAAAGGAGGGCAGTCT 3 1 0 AGGAGGGTCT 0.969001 -105 CCTCCTTTTCGGGAGGGTTTTCGTTTGCCGTCA 3 18 1 GGGAGGTTCG 0.879871 -88 ATCGAGTAAAAAGGGGTTTGGAGGCTTTTAC 3 85 1 AAGGGGGGAG 0.902202 -21 TTATTTCGGCAAGGGGATTGCAG 5 1 0 AAGGGGGCAG 0.869435 -93 AAATAACGGCAGGGGGATTTTTTATTTTTGTCC 5 28 1 AGGGGGTTTT 0.656733 -66 CCAACTTGTTAGGAGGCGTTTAC 5 81 1 AGGAGGTTAC 0.786297 -13 CGGTTACAACAAGGGGTATTGCTGAAGGAGGGA 6 91 1 AAGGGGTGCT 0.89133 -84 GTATTGCTGAAGGAGGGATGCATTGGCTTATGC 6 106 1 AGGAGGGCAT 0.972559 -69 CTGAGATACCAGGAGGAATCTATCA 7 12 1 AGGAGGCTAT 0.786296 -15 ATGAGGGAATGCGCCGCATATGA 8 1 1 ATGAGGTGCG 0.820358 -123 GTTTAAAAGAAAGAGGACATGGGAGATAGAAAA 11 110 1 AAGAGGTGGG 0.713195 -174 AAGATGCAGGAGGAGGATTGCCTAGACACCGGG 11 157 1 AGGAGGGCCT 0.98029 -127 GTAAACGATCAGGAGGTGCTCAT 11 271 1 AGGAGGTCAT 0.939307 -13 CGAAGCGATGAGGAGGAGCGGCGCTCGTGAACC 12 34 1 AGGAGGGGCG 0.988681 -69 CGAAGCGATGAGGAGGAGCGGCGCTC 12 87 1 AGGAGGGGCG 0.988681 -16 ****** **** Masking position 6 Map Score: 19.3393 Number of sites scoring better than the average of aligned sites = 584 Number in coding regions = 401 Number in noncoding regions = 183 Number of orfs with sites within 600 bp upstream = 186 Fraction of orfs with sites within 600 bp upstream = 0.0298747 Motif number 3 TGATTATAAATAATTCGGCATGTATCCGAA 1 29 1 TAATTCGGCA 0.716554 -272 ACCTTTGTCCTGCACAGAGGTCTT 4 5 1 TTGTCCTGCA 0.937931 -150 CCCCTGCCGTTATTTCGGCAAGGGGATTGC 5 13 0 TATTTCGGCA 0.716554 -81 AAATAAAAAATCCCCCTGCCGTTATTTCGG 5 25 0 TCCCCCTGCC 0.828709 -69 AATGCATCCCTCCTTCAGCAATACCCCTTG 6 100 0 TCCTTCAGCA 0.914411 -75 ACGCCTTTCTTTCTTCTACAATGGCAATGG 9 101 1 TTCTTCTACA 0.646126 -43 AAACCCGAATTCCTTCGGGAAAATAGATAT 10 26 0 TCCTTCGGGA 0.870606 -107 TAGGCAATCCTCCTCCTGCATCTTCCAATT 11 151 0 TCCTCCTGCA 0.983808 -133 TAACATCGTCTTCTCCGTCATTTTACAATC 11 238 1 TTCTCCGTCA 0.68307 -46 CCTCATCGCTTCGCTCTGCATCGTCGTCGG 12 17 0 TCGCTCTGCA 0.946069 -86 CCTCATCGCTTCGCTCTGCATCGTCGTCGG 12 70 0 TCGCTCTGCA 0.946069 -33 AGTGGCCGTGTAGTTCTGCAGCG 13 4 0 TAGTTCTGCA 0.919281 -68 ACGGCGCGGATTCTCCGGCAGCTTGCCGCT 13 34 1 TTCTCCGGCA 0.96778 -38 ********** Masking position 1 Map Score: 9.32109 Number of sites scoring better than the average of aligned sites = 1398 Number in coding regions = 1297 Number in noncoding regions = 101 Number of orfs with sites within 600 bp upstream = 107 Fraction of orfs with sites within 600 bp upstream = 0.017186 Motif number 4 TTATAAATAATTCGGCATGTATCCGAATCG 1 32 1 TTCGGCATGT 0.823872 -269 CTGCCGTTATTTCGGCAAGGGGATTGCAG 5 10 0 TTCGGCAAGG 0.906201 -84 TTATGTCATATGCGGCGCATTCCCTCAT 8 9 0 TGCGGCGCAT 0.91315 -115 AAGAAAGGCGTGCGGCATGTAGCGGCAGAT 9 82 0 TGCGGCATGT 0.901867 -62 CTGCATCGTCGTCGGCGCGGC 12 2 0 GTCGGCGCGG 0.985208 -101 GATGAGGAGGAGCGGCGCTCGTGAACCGCG 12 40 1 AGCGGCGCTC 0.947842 -63 CTGCATCGTCGTCGGCGCGGTTCACGAGCG 12 55 0 GTCGGCGCGG 0.985208 -48 GATGAGGAGGAGCGGCGCTC 12 93 1 AGCGGCGCTC 0.947842 -10 ACACGGCCACTACGGCGCGGATTCTCCGGC 13 23 1 TACGGCGCGG 0.967828 -49 TGCGGTGATCAGCGGCAAGCTGCCGGAGAA 13 44 0 AGCGGCAAGC 0.900081 -28 ********** Masking position 6 Map Score: 8.19817 Number of sites scoring better than the average of aligned sites = 862 Number in coding regions = 810 Number in noncoding regions = 52 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 5 ATTCTTATGAAAAGGTTCTTTTGTACGATTCGG 1 54 0 AAGGTTTTTG 0.836531 -247 TATGTCTGAGAGATTTGGTTTTTTTACCTTTTT 1 141 0 AATTGTTTTT 0.808711 -160 TGTCCTGCACAGAGGTCTTTTTTTGTTACAGTT 4 16 1 AAGGCTTTTT 0.986516 -139 TTACAGTTTTATAGTACTTTTATTTCATTTTCG 4 41 1 AAGTCTTTAT 0.697228 -114 CATAAAGTTCATATGCGGTTTTTATTTTCCAGA 8 34 1 AATGGTTTTT 0.944647 -90 GGCATTTTTGACAGGAGTTTCTGGAAAATAAAA 8 53 0 AAGGGTTCTG 0.792912 -71 CATACCTGCCTCAGGGCATTTTTGACAGGAGTT 8 67 0 TAGGCTTTTT 0.902881 -57 CATATGACGTTTTGCATATACGCT 9 2 1 AATGCTTTTG 0.96015 -142 AAGGCCTTTTACAGGCCTTTTTTTCATGCCCTA 9 43 1 AAGGCTTTTT 0.986516 -101 GGGAAAATAGATATTGCCTTTTTCATGTA 10 7 0 AATTCTTTTT 0.905022 -126 ATGGAGTGACAAATGTCATTTTTTTCTCACCCC 11 187 0 AATGCTTTTT 0.974647 -97 * *** * ***** Masking position 3 Map Score: 6.98509 Number of sites scoring better than the average of aligned sites = 581 Number in coding regions = 430 Number in noncoding regions = 151 Number of orfs with sites within 600 bp upstream = 150 Fraction of orfs with sites within 600 bp upstream = 0.0240925 Motif number 6 TTATGAAAAGGTTCTTTTGTACGATTCGGATA 1 51 0 GTTCTTTTGC 0.902392 -250 TGAGAGATTTGGTTTTTTTACCTTTTTTGTAA 1 136 0 GGTTTTTTTC 0.9709 -165 ATCAACTTTAGTGTTTTTTCCCATAGAGCGGG 1 191 0 GTGTTTTTTC 0.790477 -110 GGCGCACTTAGGTCATTTGATCAACTTTAGTG 1 210 0 GGTCATTTGC 0.761514 -91 TTACTATGGCGGTCTTTTTGACGGCAAACGAA 3 37 0 GGTCTTTTTC 0.984942 -69 CCTGCACAGAGGTCTTTTTTTGTTACAGTTTT 4 19 1 GGTCTTTTTG 0.884488 -136 GGCTTTCTTCCCCTTCTTTCAA 6 163 0 GGCTTTCTTC 0.882907 -12 TTCATATGCGGTTTTTATTTTCCAGAAACTCC 8 41 1 GTTTTTATTC 0.633064 -83 CCTGCCTCAGGGCATTTTTGACAGGAGTTTCT 8 64 0 GGCATTTTTC 0.950838 -60 GCCTTTTACAGGCCTTTTTTTCATGCCCTATG 9 46 1 GGCCTTTTTC 0.986118 -98 AGTGACAAATGTCATTTTTTTCTCACCCCGGT 11 184 0 GTCATTTTTC 0.876843 -100 ********* * Masking position 6 Map Score: 5.68461 Number of sites scoring better than the average of aligned sites = 626 Number in coding regions = 515 Number in noncoding regions = 111 Number of orfs with sites within 600 bp upstream = 97 Fraction of orfs with sites within 600 bp upstream = 0.0155798 Motif number 7 AAAAAGACCTCTGTGCAGGACAAAGGT 4 8 0 CTGTGCAGGA 0.920813 -147 ATGAATTGGAAGATGCAGGAGGAGGATTGC 11 148 1 AGATGCAGGA 0.94398 -136 GCGCCGACGACGATGCAGAGCGAAGCGATG 12 14 1 CGATGCAGAG 0.956726 -89 GTCGTCGGCGCGGTTCACGAGCGCCGCTCC 12 48 0 CGGTTCACGA 0.820683 -55 GCGCCGACGACGATGCAGAGCGAAGCGATG 12 67 1 CGATGCAGAG 0.956726 -36 CGCTGCAGAACTACACGGCC 13 1 1 CGCTGCAGAA 0.97368 -71 ATCAGCGGCAAGCTGCCGGAGAATCCGCGC 13 37 0 AGCTGCCGGA 0.828525 -35 TGTCAAGGGCCGGTGCACAATCGTCTCTG 14 10 0 CGGTGCACAA 0.959297 -49 ********** Masking position 4 Map Score: 4.01528 Number of sites scoring better than the average of aligned sites = 703 Number in coding regions = 660 Number in noncoding regions = 43 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 8 GGTTTTTTTACCTTTTTTGTAATCTTAAAGT 1 127 0 CCTTTTTGTA 0.89843 -174 TGAAATTCCCCCATTTTCGAATCTGTAATTG 2 12 1 CCATTTTGAA 0.97485 -53 TACTTTTATTTCATTTTCGTAAAATGTAACA 4 55 1 TCATTTTGTA 0.869519 -100 CTGCAATCCCCTTGCCGAAATAACGGCAG 5 9 1 CCCTTGCGAA 0.856598 -85 TGTCTTATAATCTTTTTAGAAAGCGGTTACA 6 68 1 TCTTTTTGAA 0.846779 -107 TCAGCAATACCCCTTGTTGTAACCGCTTTCT 6 85 0 CCCTTGTGTA 0.930609 -90 GGGTGCTCTGCCATTCTTGAAAGAAGGGGAA 6 147 1 CCATTCTGAA 0.934094 -28 TGATCCATTGCCATTGTAGAAGAAAGAAAGG 9 104 0 CCATTGTGAA 0.974355 -40 GTCTTCTCCGTCATTTTACAATCAATGTAAA 11 245 1 TCATTTTCAA 0.648611 -39 ******* *** Masking position 5 Map Score: 3.37738 Number of sites scoring better than the average of aligned sites = 449 Number in coding regions = 375 Number in noncoding regions = 74 Number of orfs with sites within 600 bp upstream = 63 Fraction of orfs with sites within 600 bp upstream = 0.0101189 Motif number 9 TTTTACTCGATTGTCTCTTTCTTTACTTTAC 3 65 0 TTTCTCTTTC 0.868792 -41 TTGATAAATGTTATCACTTACTTAATGTAAG 4 124 0 TTTCACTTAC 0.621631 -31 AACAAGTTGGTTCTCTCATCATAACAAGGCG 5 60 0 TTTCTCATCA 0.668189 -34 CCAATTCCCTTCTTATCATACCTGCCTCAGG 8 85 0 TCTATCATAC 0.513698 -39 GCTCATCACTCCCGATACCCAAT 8 111 0 TCTCACTCCC 0.949626 -13 ATGCCCTATGTTCTATCTGCCGCTACATGCC 9 68 1 TTTATCTGCC 0.641404 -76 GTCGTCTCACTCCTTTTTTTGA 9 132 0 TCTCTCACTC 0.919096 -12 GGTTTTTCCCTTATATCTTTCTGGTGTATAC 10 51 1 TTTATCTTTC 0.724611 -82 ATTATGCCGTTCCTCTCTTTATTAAAAGAAT 10 83 1 TCTCTCTTTA 0.593324 -50 AATATTTCTATCATAACACTCGGATGGTTTG 11 48 1 TCTAACACTC 0.720261 -236 CATCCATCTTTTCTATCTCCCATGTCCTCTT 11 120 0 TTTATCTCCC 0.915305 -164 AATGTCATTTTTTTCTCACCCCGGTGTCTAG 11 178 0 TTTCTCACCC 0.953812 -106 AAAATGACATTTGTCACTCCATCATCATGAC 11 198 1 TTTCACTCCA 0.737681 -86 CACTCCATCATCATGACACCCCATACTAACA 11 212 1 TCTGACACCC 0.675308 -72 ** ******** Masking position 4 Map Score: 4.04889 Number of sites scoring better than the average of aligned sites = 1339 Number in coding regions = 1039 Number in noncoding regions = 300 Number of orfs with sites within 600 bp upstream = 265 Fraction of orfs with sites within 600 bp upstream = 0.0425634 Motif number 10 ATGACGACCTCCTTGATAACGTTTACAA 1 283 0 CTCCTTGATA 0.907341 -18 ACTCGATTGTCTCTTTCTTTACTTTACTAT 3 62 0 CTCTTTCTTT 0.903924 -44 AGCCTCCAAACCCCTTTTTACTCGATTGTC 3 81 0 CCCCTTTTTA 0.906001 -25 TTTATCCTCCTTGATAAATGTTATCA 4 139 0 CTCCTTGATA 0.907341 -16 TATTTTTGTCCGCCTTGTTATGATGAGAGA 5 50 1 CGCCTTGTTA 0.937142 -44 TTGTTGTAACCGCTTTCTAAAAAGATTATA 6 73 0 CGCTTTCTAA 0.402535 -102 TTCAGCAATACCCCTTGTTGTAACCGCTTT 6 87 0 CCCCTTGTTG 0.883399 -88 GGCTTTCTTCCCCTTCTTTCAAGAATGGC 6 156 0 CCCCTTCTTT 0.968365 -19 GATACCCAATTCCCTTCTTATCATACCTGC 8 91 0 TCCCTTCTTA 0.73514 -33 GTCGTCTCACTCCTTTTTTTGATCCATTG 9 125 0 CTCCTTTTTT 0.882166 -19 TGCCGTTCCTCTCTTTATTAAAAGAATCAG 10 87 1 CTCTTTATTA 0.626869 -46 CTCCCATGTCCTCTTTCTTTTAAACTGCTG 11 105 0 CTCTTTCTTT 0.903924 -179 ACATCGTCTTCTCCGTCATTTTACAATCAA 11 240 1 CTCCGTCATT 0.623695 -44 ********** Masking position 6 Map Score: 6.73108 Number of sites scoring better than the average of aligned sites = 1132 Number in coding regions = 832 Number in noncoding regions = 300 Number of orfs with sites within 600 bp upstream = 350 Fraction of orfs with sites within 600 bp upstream = 0.0562159 Motif number 11 GAATTTTAAGTGAATATACGCCCTTCCAATT 1 84 0 TGATATACGC 0.991345 -217 AAACAAGTTATGTATATATACTAGCTTACAT 4 100 1 TGATATATAC 0.878877 -55 TATGACGTTTTGCATATACGCTTCTCTGAAA 9 13 1 TGATATACGC 0.991345 -131 GTGATGAATATCCGCCAGTCGTGCG 14 44 0 TGATATCCGC 0.985334 -15 ** ******** Masking position 6 Map Score: 0.078074 Number of sites scoring better than the average of aligned sites = 31 Number in coding regions = 16 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 12 ********** No masking Map Score: -5.32664e-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: -5.32664e-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: -5.32664e-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