AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i02060_bsub_reg_100.orf -o02060_bsub_100.ace -a/home/amcguire/genomes/ORF_bsub.txt -z/home/amcguire/genomes/bsub.fna -g0.44 -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 = 0.44 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 mtlA 172 phosphotransferase system (PTS) mannitol-specific enzyme IIABC component #2 ydhM 218 similar to cellobiose phosphotransferase system enzyme II #3 treP 192 phosphotransferase system (PTS) trehalose-specific enzyme IIBC component #4 ptsG 238 phosphotransferase system (PTS) glucose-specific enzyme IIABC component #5 ptsH 97 histidine-containing phosphocarrier protein of the phosphotransferase system (PTS) (HPr protein) #6 fruR 279 transcriptional regulator (DeoR family) #7 levD 189 phosphotransferase system (PTS) fructose-specific enzyme IIA component #8 licB 127 phosphotransferase system (PTS) lichenan-specific enzyme IIB component #9 bglP 300 phosphotransferase system (PTS) beta-glucoside-specific enzyme IIABC component Motif number 1 TGTATAGGGACTGTAAGCGTTTTAACATAGA 1 78 1 CTGTAAGCGT 0.935626 -95 ATAATAATCAATGTAAGCGTTTTAATAACAG 2 186 1 ATGTAAGCGT 0.985854 -33 CCAGACTAGGATGAAAGCGCTATAAAAAAGT 3 90 1 ATGAAAGCGT 0.991611 -103 TATACAAGTTATAAAAACGGATACGGAGGGG 3 167 1 ATAAAAACGA 0.734352 -26 AAAAGGGCAAATGTAAACGGTTAAACTGGAA 4 143 1 ATGTAAACGT 0.981108 -96 GCTAAAAATCATGACAACGAATTCACAGGCG 4 180 0 ATGACAACGA 0.868543 -59 TACAATTTCATTGTAAACGCTATTTTCGGTT 6 224 0 TTGTAAACGT 0.879626 -56 TCACCTCCTAATGAAAACGTATTCATTTTGA 6 256 0 ATGAAAACGA 0.972287 -24 TGAAATAACAATGAAAACGCTTAACACAACT 7 110 1 ATGAAAACGT 0.988774 -80 CTGAGTGTTTATGAAAGCGATTTCATAATAT 8 51 1 ATGAAAGCGT 0.991611 -77 AACACCAAAAATGAAAGCGTTGACATCTCAC 9 48 1 ATGAAAGCGT 0.991611 -253 ********* * Masking position 6 Map Score: 20.5107 Number of sites scoring better than the average of aligned sites = 213 Number in coding regions = 153 Number in noncoding regions = 60 Number of orfs with sites within 600 bp upstream = 83 Fraction of orfs with sites within 600 bp upstream = 0.0133312 Motif number 2 AACCAGGAGCCTTTTTATTTTTAAAAAAT 1 10 1 CCTTTTTATT 0.940721 -163 TAAACCCTCCCTGTTTTGTTTGTCGCTGTA 1 150 0 CTGTTTTGTT 0.881263 -23 TTCCGGTTCACCGTTTTATAAATTTTTCTA 2 101 0 CCGTTTTATA 0.878625 -118 GTAACCTTGTCTGTTTCATATATTCCAGAC 3 66 1 CTGTTTCATA 0.85122 -127 GTAGTCAACACTTTTTTATAGCGCTTTCAT 3 100 0 CTTTTTTATA 0.919912 -93 CCTCCGTATCCGTTTTTATAACTTGTATAT 3 166 0 CGTTTTTATA 0.840912 -27 AATGAACTTCCCGTTTTTTTCCCTCAATCA 4 67 0 CCGTTTTTTT 0.506246 -172 TTTGCTCATGCCTTTTTGTTGTGTAAAAGG 4 119 1 CCTTTTTGTT 0.90376 -120 ATGCATGAGGTTTTTTTATGTTTAGTGATT 6 22 1 TTTTTTTATG 0.656017 -258 TGAAAAAAGTCTTTTATATTCATAGTAGAA 6 51 0 CTTTTATATT 0.546614 -229 TATAAAAGACTTTTTTCATTAAAATAAGAA 6 63 1 TTTTTTCATT 0.809899 -217 AAAATGAATACGTTTTCATTAGGAGGTGAA 6 258 1 CGTTTTCATT 0.852331 -22 AAACAGTTTTTTCATATGAACCTGTA 7 7 1 TTTTTTCATA 0.73359 -183 ACAGGTTTATTTTTTTCGTTTTAAGTGTTT 7 59 1 TTTTTTCGTT 0.715995 -131 TTGTGTTAAGCGTTTTCATTGTTATTTCAG 7 109 0 CGTTTTCATT 0.852331 -81 TGCTCCTTTCCTGTTTTGTACATCCATATA 7 164 0 CTGTTTTGTA 0.827498 -26 TCCTGACGGGTCGTTTTATTTGTTTGTAGG 9 99 0 TCGTTTTATT 0.791856 -202 GTCATTTAGGTTTTTTTATTCTCTTTTAGG 9 194 1 TTTTTTTATT 0.857885 -107 TTTCACCAGCTTTTTTTGTATCAAATGCTG 9 232 0 TTTTTTTGTA 0.697772 -69 GTGTATACCTCCTTTTTATGGGGGGACTGC 9 281 0 CCTTTTTATG 0.83371 -20 ********** Masking position 5 Map Score: 17.026 Number of sites scoring better than the average of aligned sites = 2062 Number in coding regions = 1561 Number in noncoding regions = 501 Number of orfs with sites within 600 bp upstream = 490 Fraction of orfs with sites within 600 bp upstream = 0.0787022 Motif number 3 AGCTATTATCACTTGTATAACCTCAATAAT 2 16 0 ACTTGTATAA 0.957329 -203 AAATGTCTATACTTTTATAAAATAAATATA 2 142 0 ACTTTTATAA 0.744251 -77 AGTGTTGACTACCTGTATATACAGGAATAC 3 118 1 ACCTGTATAT 0.972667 -75 CGTTTTTATAACTTGTATATACAACTTATA 3 156 0 ACTTGTATAT 0.945145 -37 TTTCATATGAACCTGTATTAAATGGAACAC 7 20 1 ACCTGTATTA 0.952736 -170 AAAAAAATAAACCTGTATTAAAATGGTGTT 7 45 0 ACCTGTATTA 0.952736 -145 CAGCCTGTATATACCTTTTTTC 8 3 1 GCCTGTATAT 0.916316 -125 ********** Masking position 7 Map Score: 6.34407 Number of sites scoring better than the average of aligned sites = 88 Number in coding regions = 69 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 4 CTGTATATACAGGTAGTCAACACTTTTTTA 3 112 0 AGGTAGTCAA 0.776062 -81 TAGTAAAAAGAGGAGGTCAATTCTT 4 224 1 AGGAGGTCAA 0.983977 -15 CGTTTTCATTAGGAGGTGAAGC 6 268 1 AGGAGGTGAA 0.987755 -12 TGATAGCAACAGCAGGACATTACAAAATTG 8 84 1 AGCAGGACAT 0.857988 -44 GTGCAGGTGCAGGAGGAGACTCTCGCAATC 9 161 1 AGGAGGAGAC 0.940507 -140 ATTCTCTTTTAGGAGGTGATGCAGCATTTG 9 211 1 AGGAGGTGAT 0.977381 -90 ATACAAAAAAAGCTGGTGAAAGGCGGCCAC 9 241 1 AGCTGGTGAA 0.936741 -60 ********** Masking position 9 Map Score: 4.17059 Number of sites scoring better than the average of aligned sites = 226 Number in coding regions = 112 Number in noncoding regions = 114 Number of orfs with sites within 600 bp upstream = 110 Fraction of orfs with sites within 600 bp upstream = 0.0176678 Motif number 5 ACCATATTATTGAGGTTATACAAGTGA 2 7 1 TTTTGAGGTT 0.638775 -212 TTTAATTGATTCGTTTCCGTTGATGAGTGTA 2 47 1 TCTTTCCGTT 0.952127 -172 TAATCATATTTTTTTCCGGTTCACCGTTTTA 2 113 0 TTTTCCGGTT 0.927053 -106 GCCAACCCCTCCGTATCCGTTTTTATAACTT 3 172 0 CCTATCCGTT 0.693351 -21 AACGGGAAGTTCATTCTCGTTCTTTTGCGCA 4 82 1 TCTTCTCGTT 0.846827 -157 TGCATGAGGTTTTTTTATGTTTAGTGATTTC 6 23 1 TTTTTATGTT 0.598451 -257 ACTATCAAAATCTTTCACGTTTCTCCATATT 6 160 0 TCTTCACGTT 0.945932 -120 TTGTAAACGCTATTTTCGGTTTAGGCAACTA 6 214 0 TATTTCGGTT 0.86699 -66 GTGTTCCATTTAATACAGGTTCATATGAAAA 7 19 0 TATACAGGTT 0.606572 -171 AACACCATTTTAATACAGGTTTATTTTTTTC 7 45 1 TATACAGGTT 0.606572 -145 TACAGGTTTATTTTTTTCGTTTTAAGTGTTT 7 58 1 TTTTTTCGTT 0.673104 -132 ATCTATTGCTCCTTTCCTGTTTTGTACATCC 7 169 0 CCTTCCTGTT 0.700375 -21 TGTATATACCTTTTTTCCGTTGCTGCGGAAA 8 16 1 TTTTTCCGTT 0.900024 -112 TGCACCTGCACCATTTAGGTTTTGCCTGCTT 9 141 0 CCTTTAGGTT 0.876079 -160 GCAATCTGTGTCATTTAGGTTTTTTTATTCT 9 185 1 TCTTTAGGTT 0.943569 -116 ** ******** Masking position 4 Map Score: 8.55957 Number of sites scoring better than the average of aligned sites = 905 Number in coding regions = 783 Number in noncoding regions = 122 Number of orfs with sites within 600 bp upstream = 131 Fraction of orfs with sites within 600 bp upstream = 0.0210408 Motif number 6 ATTAAATAGCTATTATCACTTGTATAACCTC 2 22 0 TATATCACTT 0.709494 -197 ATAAAATAAATATAATCATATTTTTTTCCGG 2 125 0 TATATCATAT 0.939065 -94 TTTATAAAAGTATAGACATTTAAAATTAAAT 2 151 1 TATGACATTT 0.750576 -68 CATTGATTATTATAGTCATTTAATTTTAAAT 2 168 0 TATGTCATTT 0.923828 -51 CCCTGCTTTTTAATGTCATATTCAATAAGTG 3 20 1 TAAGTCATAT 0.851353 -173 ATATACAACTTATAATCATATTGTATTCCTG 3 139 0 TATATCATAT 0.939065 -54 CTTCACAATATTATATCATACAACCGTACTT 5 42 0 TTAATCATAC 0.58752 -56 TTTTATCATTCTCCTTTTAAC 5 87 0 TTTATCATTC 0.750579 -11 TTACAAACCCTATAGACATACGTTAATATGG 6 136 1 TATGACATAC 0.769812 -144 TTTAGGCAACTAAAATCATTCAAATTCATTC 6 195 0 TAAATCATTC 0.8285 -85 CTGCTGTTGCTATCATCATATTATGAAATCG 8 68 0 TATATCATAT 0.939065 -60 *** ******* Masking position 8 Map Score: 4.58567 Number of sites scoring better than the average of aligned sites = 180 Number in coding regions = 131 Number in noncoding regions = 49 Number of orfs with sites within 600 bp upstream = 59 Fraction of orfs with sites within 600 bp upstream = 0.00947639 Motif number 7 TTGACTCTATGTTAAAACGCTTACAGTCCC 1 84 0 GTTAAAACGC 0.917511 -89 AAACGAATCAATTAAATAGCTATTATCACT 2 33 0 ATTAAATAGC 0.851008 -186 CCCCCCTGTTATTAAAACGCTTACATTGAT 2 192 0 ATTAAAACGC 0.979426 -27 TGAATATGACATTAAAAAGCAGGGTGAGCC 3 14 0 ATTAAAAAGC 0.939768 -179 CCAGACTAGGATGAAAGCGCTATAAAAAAG 3 90 1 ATGAAAGCGC 0.96642 -103 TCACCTCCTAATGAAAACGTATTCATTTTG 6 257 0 ATGAAAACGT 0.901665 -23 ACAGGTTCATATGAAAAAACTGTTT 7 6 0 ATGAAAAAAC 0.750321 -184 TGAAATAACAATGAAAACGCTTAACACAAC 7 110 1 ATGAAAACGC 0.989421 -80 TCATCATATTATGAAATCGCTTTCATAAAC 8 57 0 ATGAAATCGC 0.971621 -71 ********** Masking position 5 Map Score: 11.8843 Number of sites scoring better than the average of aligned sites = 410 Number in coding regions = 341 Number in noncoding regions = 69 Number of orfs with sites within 600 bp upstream = 79 Fraction of orfs with sites within 600 bp upstream = 0.0126887 Motif number 8 TAAATTCAGTTTATCCTTATAACGTGTTAC 4 18 1 TTATCCTTAT 0.891586 -221 GAGAATGAACTTCCCGTTTTTTTCCCTCAA 4 70 0 TTCCCGTTTT 0.810024 -169 CCGTTTACATTTGCCCTTTTACACAACAAA 4 133 0 TTGCCCTTTT 0.920587 -106 TTTTATCATTCTCCTTTTAACTTAAAGC 5 80 0 TTCTCCTTTT 0.970553 -18 GTACGACATTTTCTTCTTATTTTAATGAAA 6 76 0 TTCTTCTTAT 0.847719 -204 TGTCGTACAATTGTCCTTATTTTTGTCGAA 6 98 1 TTGTCCTTAT 0.957323 -182 TCTTTCACGTTTCTCCATATTAACGTATGT 6 151 0 TTCTCCATAT 0.899091 -129 ********** Masking position 8 Map Score: 1.63892 Number of sites scoring better than the average of aligned sites = 371 Number in coding regions = 289 Number in noncoding regions = 82 Number of orfs with sites within 600 bp upstream = 104 Fraction of orfs with sites within 600 bp upstream = 0.0167041 Motif number 9 GCTCATGCCTTTTTGTTGTGTAAAAGGGCA 4 122 1 TTTTGTTGTG 0.714801 -117 TACGTTTTCATTAGGAGGTGAAGC 6 266 1 TTAGGAGGTG 0.957638 -14 CCAATAGCAATTTGTTGTTGAAACACTTAA 7 79 0 TTTGTTGTTG 0.810841 -111 CGCTTTCATTTTTGGTGTTGACTATCGTTT 9 37 0 TTTGGTGTTG 0.970629 -264 CCTGCACCATTTAGGTTTTGCCTGCTTTCG 9 138 0 TTAGGTTTTG 0.954202 -163 TCTGTGTCATTTAGGTTTTTTTATTCTCTT 9 189 1 TTAGGTTTTT 0.729912 -112 TTATTCTCTTTTAGGAGGTGATGCAGCATT 9 209 1 TTAGGAGGTG 0.957638 -92 ********** Masking position 2 Map Score: 0.863803 Number of sites scoring better than the average of aligned sites = 242 Number in coding regions = 199 Number in noncoding regions = 43 Number of orfs with sites within 600 bp upstream = 48 Fraction of orfs with sites within 600 bp upstream = 0.0077096 Motif number 10 AAAATTGTCACAGTCATGTGCCAAAGTCCT 1 35 1 CAGTCATGTG 0.906908 -138 CTGATTCGATCAGGCATCAGTGATTGAGGG 4 47 1 CAGGCATCAG 0.984185 -192 ACACAACAAAAAGGCATGAGCAAAATTGGG 4 113 0 AAGGCATGAG 0.969757 -126 AACGAATTCACAGGCGTAAGTCTTCCAGTT 4 166 0 CAGGCGTAAG 0.949692 -73 CCTCATGCAACATGCATGAGGTTTTTTTAT 6 11 1 CATGCATGAG 0.969755 -269 ********** Masking position 7 Map Score: 0.00789128 Number of sites scoring better than the average of aligned sites = 162 Number in coding regions = 141 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 11 ********** No masking Map Score: -4.59478e-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 12 ********** No masking Map Score: -4.59478e-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: -4.59478e-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