AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00760_bsub_reg_100.orf -o00760_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 spoIIE 300 serine phosphatase #2 yabS 84 similar to hypothetical proteins #3 yabT 88 yabT #4 amhX 300 amidohydrolase #5 nadE 139 NH3-dependent NAD+ synthetase #6 yfkN 242 similar to 2',3'-cyclic-nucleotide 2'-phosphodiesterase #7 ptsG 238 phosphotransferase system (PTS) glucose-specific enzyme IIABC component #8 ptsH 97 histidine-containing phosphocarrier protein of the phosphotransferase system (PTS) (HPr protein) #9 splA 90 transcriptional regulator #10 splB 77 spore photoproduct lyase #11 deoD 300 purine nucleoside phosphorylase #12 drm 160 phosphodeoxyribomutase #13 nadB 102 L-aspartate oxidase #14 comQ 184 transcriptional regulator Motif number 1 AATGTTGTCTAAAAATGAAAAAAATCGGCTTC 1 137 0 AAAATGAAAA 0.828764 -164 ATTTTGTCAAAAGAAGGTAACAATACCAAAGA 1 219 0 AAAAGGTACA 0.684642 -82 AAATAAAGTAAAGAAGGTAAAAATTCATTCTG 4 257 1 AAAAGGTAAA 0.871848 -44 TGCTATATTTAATAGGGATACATAACAGTCAT 5 51 1 AAAGGGAACA 0.839573 -89 AATGATCAGTAATAAGGGAAAATGTACAGGAG 5 107 1 AAAAGGGAAA 0.91322 -33 TGATTATTGTAAAAGGGAGAAAAATGAGTATT 6 140 0 AAAGGGAAAA 0.942528 -103 AGTAACACGTTATAAGGATAAACTGAATTTAT 7 17 0 TAAAGGAAAA 0.973214 -222 GCATCAGTGATTGAGGGAAAAAAACGGGAAGT 7 60 1 TTAGGGAAAA 0.638203 -179 GGGTGCGCAAAAGAACGAGAATGAACTTCCCG 7 84 0 AAAACGAAAT 0.656528 -155 TTTTGTTGTGTAAAAGGGCAAATGTAAACGGT 7 132 1 TAAAGGGAAA 0.894537 -107 AGCTTTAAGTTAAAAGGAGAATGATAAAA 8 79 1 TAAAGGAAAT 0.829058 -19 AGTAAGGGTATAGAAGGACACAATAACATGGC 9 56 1 TAAAGGAACA 0.920619 -35 TATAAAGGAATATATCGAAAAAAGAAATGTTC 11 194 0 TAATCGAAAA 0.650745 -107 TGTATTTGGAAATAATGAGAAACTTCAATATT 12 50 0 AAAATGAAAA 0.828764 -111 CCTATATTTACACAAGGATAAAATAAACTCAA 13 46 0 CAAAGGAAAA 0.89464 -57 ATTGTATCGGTAGAACGAAAAAAAAGACTTGT 14 24 0 TAAACGAAAA 0.920286 -161 ACCGATACAATAAATGGATAAAGTATTATATG 14 45 1 TAATGGAAAA 0.854369 -140 ATGATTGTTAAAAAACGAAAAACCTGCTGTCC 14 74 1 AAAACGAAAA 0.93474 -111 TTCTGTCCGGATCAAGGAGAAA 14 173 1 ATAAGGAAAA 0.857492 -12 ** ***** *** Masking position 4 Map Score: 18.65 Number of sites scoring better than the average of aligned sites = 983 Number in coding regions = 796 Number in noncoding regions = 187 Number of orfs with sites within 600 bp upstream = 209 Fraction of orfs with sites within 600 bp upstream = 0.0335689 Motif number 2 TCCTCTCATCTCCCACCTGTTATATTCGT 1 282 0 TCTCCCCCTG 0.975133 -19 ATTCATTCCTCCTGGAGAATACGA 2 71 0 CATTCCCCTG 0.990525 -14 TAAGTGTTTCCATTCCACTTGCCTTTGATTG 3 28 0 CATTCCCTTG 0.929708 -61 TATTTCGATCCATCCCCTCTGTTTGAAAATA 4 161 1 CATCCCTCTG 0.927541 -140 TATATACAGCCTATCTTCCTGTTTCAATATA 4 227 1 CTATCTCCTG 0.649025 -74 CCCAATCATTCCTCCTGTACATTTTCC 5 123 0 CATTCCCCTG 0.990525 -17 GATTCATAACCTCCCGCTTTATATGTCTAC 6 10 1 CCTCCCCTTT 0.77406 -233 AACCAGACGGCCTCCGGCCTGTCTGGTTTTT 9 19 1 CCTCCGCCTG 0.973113 -72 ACTATCCCTCCTAGCCATGTTAT 9 78 0 TATCCCCCTA 0.791157 -13 AACTCATATCCTTTCCGCCTAGTGAGAAAAG 10 26 1 CTTTCCCCTA 0.909413 -52 ATGTCCCACCCCTCCTTCCTGCGGTTAGGTT 11 108 1 CCTCCTCCTG 0.977305 -193 ATGCCATCCTCCTGTTGTTTACAC 13 89 0 CCATCCCCTG 0.971468 -14 TCAATAACGACTTCCCCCCTCCCATTCCATT 14 127 0 CTTCCCCCTC 0.940074 -58 ****** **** Masking position 10 Map Score: 14.8333 Number of sites scoring better than the average of aligned sites = 486 Number in coding regions = 362 Number in noncoding regions = 124 Number of orfs with sites within 600 bp upstream = 100 Fraction of orfs with sites within 600 bp upstream = 0.0160617 Motif number 3 GTATTCTCCAGGAGGAATGAAT 2 73 1 GGAGGAATGA 0.890342 -12 TGAAGCGATTGCGCAAATGAAAGCAATCAT 4 51 1 GCGCAAATGA 0.920519 -250 CCCTAAATCAATGAAAATGAATCATGACTG 5 76 0 ATGAAAATGA 0.493693 -64 TCATTGATTTAGGGAAATGATCAGTAATAA 5 92 1 AGGGAAATGA 0.948695 -48 TCAGTAATAAGGGAAAATGTACAGGAGGAA 5 112 1 GGGAAAATGT 0.720813 -28 AAAATGTACAGGAGGAATGATTGGG 5 125 1 GGAGGAATGA 0.890342 -15 TGTAAAAGGGAGAAAAATGAGTATTATGTA 6 135 0 AGAAAAATGA 0.683083 -108 GCGCAAAAGAACGAGAATGAACTTCCCGTT 7 82 0 ACGAGAATGA 0.916685 -157 AAAATTGGGTGCGCAAAAGAACGAGAATGA 7 92 0 GCGCAAAAGA 0.702865 -147 TTGTGTAAAAGGGCAAATGTAAACGGTTAA 7 137 1 GGGCAAATGT 0.680469 -102 TTAAGTTAAAAGGAGAATGATAAAA 8 83 1 AGGAGAATGA 0.926106 -15 TTCTCACTAGGCGGAAAGGATATGAGTTGT 10 24 0 GCGGAAAGGA 0.923152 -54 ACGTTAGTAAAGGAAAAGGATGTGGCATC 10 59 1 AGGAAAAGGA 0.820698 -19 GAAGAAGCACACGGGAAAGAA 11 2 0 ACGGGAAAGA 0.80687 -299 AAACCTAACCGCAGGAAGGAGGGGTGGGAC 11 110 0 GCAGGAAGGA 0.766364 -191 TACATTGTCAACGGGAATGAAAACGGTTTA 12 78 1 ACGGGAATGA 0.953391 -83 ********** Masking position 6 Map Score: 13.5253 Number of sites scoring better than the average of aligned sites = 1086 Number in coding regions = 910 Number in noncoding regions = 176 Number of orfs with sites within 600 bp upstream = 205 Fraction of orfs with sites within 600 bp upstream = 0.0329264 Motif number 4 GAAAAGAATTTCCGGAATGTTGTCTAAAAATGAAA 1 149 0 TCCGTGTTGT 0.868416 -152 TCCTCTCATCTCCCACCTGTTATATTCGTTGCCTG 1 276 0 TCCATGTTAT 0.659566 -25 GACATAGGCGTCAGGCATTTTAAATGTCATACGTT 4 90 1 TCAGTTTTAT 0.947595 -211 ATTTTAAATGTCATACGTTTTTTCTTAGGCTGTGT 4 106 1 TCAATTTTTT 0.772884 -195 TGAAAATGAATCATGACTGTTATGTATCCCTATTA 5 60 0 TCAGTGTTAT 0.936913 -80 ATTCATAACCTCCCGCTTTATATGTCTACATAAAA 6 12 1 TCCGTTATAT 0.683837 -231 AGAATGAACTTCCCGTTTTTTTCCCTCAATCACTG 7 64 0 TCCGTTTTTC 0.83943 -175 CCAATTTTGCTCATGCCTTTTTGTTGTGTAAAAGG 7 114 1 TCAGTTTTTT 0.969422 -125 GAATTCGTTGTCATGATTTTTAGCTGTAAGGTCAG 7 187 1 TCAGTTTTAT 0.947595 -52 CTCCGGCCTGTCTGGTTTTTTTCATAAGTAAGGGT 9 30 1 TCTGTTTTTT 0.833272 -61 TTCTTTCCCGTGTGCTTCTTCAGCTGCAAT 11 6 1 TCCGTGCTTT 0.821948 -295 TAATCAATGCTGAAGTTTGTTTCATCATGACATTC 11 224 1 TGAGTGTTTT 0.812149 -77 CGCAGGTGGCTGCGGCTTTTTTGTTTAGAGCGACA 12 12 1 TGCGTTTTTT 0.864817 -149 TAAAATAAACTCAAGAGTTTTTTATGGAGAACGGA 13 25 0 TCAGTTTTTT 0.969422 -78 AGACTTGGAAACAAGTCTTTTTTTTCGTTCTACCG 14 14 1 ACAGTTTTTT 0.743739 -171 *** * ***** * Masking position 8 Map Score: 8.12835 Number of sites scoring better than the average of aligned sites = 641 Number in coding regions = 502 Number in noncoding regions = 139 Number of orfs with sites within 600 bp upstream = 144 Fraction of orfs with sites within 600 bp upstream = 0.0231288 Motif number 5 CCGCCCTTTCACGGCGGTAACACGGGTTCGAAT 1 66 1 AGGCGAACAC 0.88844 -235 AAAGGCAAGTGGAATGGAAACACTTATACATTG 3 33 1 GAATGAACAC 0.89737 -56 GAGTATGCCAGCAGCCGAAACACAGCCTAAGAA 4 127 0 GAGCGAACAC 0.995013 -174 TGAGTATTATGTAGCAGTATCAAACGACAAATA 6 115 0 GAGCGATCAA 0.918429 -128 TCTTACAATAGGAGCTGTAACACAAATTTCGTT 6 204 1 GAGCGAACAC 0.995013 -39 ATGCCTGATCGAATCAGTAACACGTTATAAGGA 7 31 0 GATCGAACAC 0.974511 -208 AAAAAACATCGTAACCGGATCACCGGCCAAAAA 11 71 0 GAACGATCAC 0.966997 -230 * *** * ***** Masking position 9 Map Score: 3.55031 Number of sites scoring better than the average of aligned sites = 116 Number in coding regions = 107 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 6 ATTCATTCCTCCTGGAGAATAC 2 73 0 TCATTCCTCC 0.811862 -12 CATTTAAAATGCCTGACGCCTATGTCCTCT 4 86 0 GCCTGACGCC 0.930576 -215 ATATGAGTATGCCAGCAGCCGAAACACAGC 4 134 0 GCCAGCAGCC 0.782833 -167 CCCAATCATTCCTCCTGTACATTTT 5 125 0 TCATTCCTCC 0.811862 -15 TAAACTGGAAGACTTACGCCTGTGAATTCG 7 164 1 GACTTACGCC 0.865044 -75 ACAAAAACCAGACGGCCTCCGGCCTGTCTG 9 14 1 GACGGCCTCC 0.933194 -77 CTTGAAAGCCTCCTTTTTTTCTA 12 148 0 GAAAGCCTCC 0.878253 -13 CCGGTCTTCCTCCATCCGTTCTC 13 4 1 GTCTTCCTCC 0.931845 -99 ATGCCATCCTCCTGTTGTTTAC 13 91 0 GCCATCCTCC 0.97889 -12 GCTCAATAACGACTTCCCCCCTCCCATTCC 14 130 0 GACTTCCCCC 0.932679 -55 ********** Masking position 9 Map Score: 3.70611 Number of sites scoring better than the average of aligned sites = 956 Number in coding regions = 845 Number in noncoding regions = 111 Number of orfs with sites within 600 bp upstream = 106 Fraction of orfs with sites within 600 bp upstream = 0.0170254 Motif number 7 TGACCAACGGGCCAAACAAATATGGTAGCG 1 23 0 GCCAAACAAA 0.973848 -278 GTACGGGTCATCCTAACAAATCGGTTTCTC 1 102 1 TCCTAACAAA 0.873628 -199 AGGTAACAATACCAAAGAAATCTTCGACGG 1 207 0 ACCAAAGAAA 0.828475 -94 CCGAAACACAGCCTAAGAAAAAACGTATGA 4 116 0 GCCTAAGAAA 0.967974 -185 CTCTACCCCAGCCACACTAAAATAAACATT 6 49 1 GCCACACTAA 0.828824 -194 CGGATCACCGGCCAAAAAAAGAACAATCAT 11 59 0 GCCAAAAAAA 0.877083 -242 GTTAGGCACTTCCTCAGAAAAACGGATAAT 11 156 0 TCCTCAGAAA 0.850796 -145 CTGAGGAAGTGCCTAACAGATCCTCGAACA 11 169 1 GCCTAACAGA 0.875959 -132 TTTGTTTAGAGCGACAGAAAATATTGAAGT 12 31 1 GCGACAGAAA 0.816946 -130 ********** Masking position 6 Map Score: 2.42166 Number of sites scoring better than the average of aligned sites = 381 Number in coding regions = 343 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 8 TGTCCTCTTATTTATGATTGCTTTCATTTG 4 64 0 TTTATGATTG 0.958376 -237 ATACTGGGCATTTATGCTTATCGTTTGTCA 6 88 0 TTTATGCTTA 0.934535 -155 TAGGTGTTTCTTTATGATTATTGTAAAAGG 6 156 0 TTTATGATTA 0.9 -87 ATAAATTCAGTTTATCCTTATAACGTGTTA 7 17 1 TTTATCCTTA 0.857625 -222 CTTTTTCAGGTATATGATTGTTCTTTTTTT 11 46 1 TATATGATTG 0.893944 -255 ATGAAAACGGTTTATACTTGAGTTGTCAGA 12 94 1 TTTATACTTG 0.849619 -67 TTGAGTTTATTTTATCCTTGTGTAAATATA 13 46 1 TTTATCCTTG 0.939063 -57 GATAAAGTATTATATGATTGTTAAAAAACG 14 61 1 TATATGATTG 0.893944 -124 ********** Masking position 4 Map Score: 5.55043 Number of sites scoring better than the average of aligned sites = 137 Number in coding regions = 115 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 9 TATCTGTGCTTTCGCTATAATGACAGGCAA 1 253 1 TTCGCTATAA 0.726585 -48 TCTTACAATAGGAGCTGTAACACAAATTTC 6 204 1 GGAGCTGTAA 0.796166 -39 TAACACAAATTTCGTTGAAAGGTGGAGAAC 6 221 1 TTCGTTGAAA 0.813116 -22 CGCCTGTGAATTCGTTGTCATGATTTTTAG 7 180 1 TTCGTTGTCA 0.932195 -59 GTCATGATTTTTAGCTGTAAGGTCAGACTA 7 196 1 TTAGCTGTAA 0.937494 -43 GGAAAGGATATGAGTTGTAATGATTTCCTT 10 12 0 TGAGTTGTAA 0.937502 -66 CATCATGACATTCGTTGTAAAATGGACGGG 11 246 1 TTCGTTGTAA 0.96044 -55 GGTTTATACTTGAGTTGTCAGACCTCTTAG 12 102 1 TGAGTTGTCA 0.894681 -59 ********** Masking position 10 Map Score: 2.084 Number of sites scoring better than the average of aligned sites = 119 Number in coding regions = 100 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 10 GGAAATTCTTTTCATAAACGAATATCAAGG 1 171 1 TTCATAAACG 0.787437 -130 GATTCTCAGATTCATATATTCCCATCTTCG 2 40 0 TTCATATATT 0.883589 -45 GCGCAATCGCTTCATATATTGTGCCGGCAG 4 35 0 TTCATATATT 0.883589 -266 GATTCATAACCTCCCGCTTTAT 6 3 1 TTCATAACCT 0.935644 -240 AATTTCATAAATTCAGTTTATCC 7 4 1 TTCATAAATT 0.85357 -235 ATCATTACAACTCATATCCTTTCCGCCTAG 10 18 1 CTCATATCCT 0.927213 -60 CTCATATCCTCCTGTAAATC 11 291 0 CTCATATCCT 0.927213 -10 ********** Masking position 6 Map Score: 1.41215 Number of sites scoring better than the average of aligned sites = 126 Number in coding regions = 93 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 11 TCGCTTCATATATTGTGCCGGCAGGTGAAT 4 29 0 TATTGTGCCG 0.977635 -272 GAAAAATGAGTATTATGTAGCAGTATCAAA 6 124 0 TATTATGTAG 0.76806 -119 TATGATATAATATTGTGAAGTAATAAAGCT 8 53 1 TATTGTGAAG 0.88584 -45 CTAGCCATGTTATTGTGTCCTTCTATACCC 9 61 0 TATTGTGTCC 0.910207 -30 TCTATACGTCTATTGTATCGCTAAGAGGTC 12 122 0 TATTGTATCG 0.934997 -39 TTTATCCATTTATTGTATCGGTAGAACGAA 14 37 0 TATTGTATCG 0.934997 -148 GGGAAGTCGTTATTGAGCAGATATGTTTAG 14 142 1 TATTGAGCAG 0.81461 -43 ********** Masking position 2 Map Score: 1.06754 Number of sites scoring better than the average of aligned sites = 152 Number in coding regions = 138 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 12 AACAAATATGGTAGCGGCGGAGGGGATC 1 9 0 GTAGCGGCGG 0.987418 -292 TTCATATATTGTGCCGGCAGGTGAATTTGA 4 25 0 GTGCCGGCAG 0.915095 -276 TTATTTTAGTGTGGCTGGGGTAGAGTGTTT 6 44 0 GTGGCTGGGG 0.986887 -199 CCGCAGGTGGCTGCGGCTTTTTTGTT 12 7 1 GTGGCTGCGG 0.995059 -154 ********** Masking position 2 Map Score: 0.390276 Number of sites scoring better than the average of aligned sites = 114 Number in coding regions = 103 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 13 CTGTTATATTCGTTGCCTGTCATTATAGCGA 1 264 0 CTTGCCTGTC 0.934451 -37 TTCCACTTGCCTTTGATTGTCGTACCCGGCT 3 16 0 CTTGATTGTC 0.929449 -73 TAACCTCCCGCTTTATATGTCTACATAAAAC 6 17 1 CTTATATGTC 0.853951 -226 CATAAATGCCCAGTATTTGTCGTTTGATACT 6 102 1 CGTATTTGTC 0.929449 -141 TGTTAGTACGCCGTGCTTGTCAGATGACAAG 8 14 1 CGTGCTTGTC 0.9745 -84 TATCATACAACCGTACTTGTCATCTGACAAG 8 29 0 CGTACTTGTC 0.974992 -69 CCTTTACTAACGTTACTTTTCTCACTAGGCG 10 41 0 CTTACTTTTC 0.816238 -37 ACCTGCTGTCCTTTAAATGTCCCATTTAGTA 14 95 1 CTTAAATGTC 0.853951 -90 * ********* Masking position 4 Map Score: 3.24125 Number of sites scoring better than the average of aligned sites = 241 Number in coding regions = 220 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 14 ********** No masking Map Score: -5.68902e-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 15 ********** No masking Map Score: -5.68902e-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